Single-molecule imaging of transcriptionally coupled and uncoupled splicing.

Introns are removed from pre-mRNAs during transcription while the pre-mRNA is still tethered to the gene locus via RNA polymerase. However, during alternative splicing, it is important that splicing be deferred until all of the exons and introns involved in the choice have been synthesized. We have developed an in situ RNA imaging method with single-molecule sensitivity to define the intracellular sites of splicing. Using this approach, we found that the normally tight coupling between transcription and splicing is broken in situations where the intron's polypyrimidine tract is sequestered within strong secondary structures. We also found that in two cases of alternative splicing, in which certain exons are skipped due to the activity of the RNA-binding proteins Sxl and PTB, splicing is uncoupled from transcription. This uncoupling occurs only on the perturbed introns, whereas the preceding and succeeding introns are removed cotranscriptionally. PAPERCLIP:

S309-CAR-NK cells bind the Omicron variants in vitro and reduce SARS-CoV-2 viral loads in humanized ACE2-NSG mice.

Recent progress on chimeric antigen receptor (CAR)-NK cells has shown promising results in treating CD19-positive lymphoid tumors with minimal toxicities [including graft versus host disease (GvHD) and cytokine release syndrome (CRS) in clinical trials. Nevertheless, the use of CAR-NK cells in combating viral infections has not yet been fully explored. Previous studies have shown that CAR-NK cells expressing S309 single-chain fragment variable (scFv), hereinafter S309-CAR-NK cells, can bind to SARS-CoV-2 wildtype pseudotyped virus (PV) and effectively kill cells expressing wild-type spike protein in vitro. In this study, we further demonstrate that the S309-CAR-NK cells can bind to different SARS-CoV-2 variants, including the B.1.617.2 (Delta), B.1.621 (Mu), and B.1.1.529 (Omicron) variants in vitro. We also show that S309-CAR-NK cells reduce virus loads in the NOD/SCID gamma (NSG) mice expressing the human angiotensin-converting enzyme 2 (hACE2) receptor challenged with SARS-CoV-2 wild-type (strain USA/WA1/2020). Our study demonstrates the potential use of S309-CAR-NK cells for inhibiting infection by SARS-CoV-2 and for the potential treatment of COVID-19 patients unresponsive to otherwise currently available therapeutics. IMPORTANCE: Chimeric antigen receptor (CAR)-NK cells can be "off-the-shelf" products that treat various diseases, including cancer, infections, and autoimmune diseases. In this study, we engineered natural killer (NK) cells to express S309 single-chain fragment variable (scFv), to target the Spike protein of SARS-CoV-2, hereinafter S309-CAR-NK cells. Our study shows that S309-CAR-NK cells are effective against different SARS-CoV-2 variants, including the B.1.617.2 (Delta), B.1.621 (Mu), and B.1.1.529 (Omicron) variants. The S309-CAR-NK cells can (i) directly bind to SARS-CoV-2 pseudotyped virus (PV), (ii) competitively bind to SARS-CoV-2 PV with 293T cells expressing the human angiotensin-converting enzyme 2 (hACE2) receptor (293T-hACE2 cells), (iii) specifically target and lyse A549 cells expressing the spike protein, and (iv) significantly reduce the viral loads of SARS-CoV-2 wild-type (strain USA/WA1/2020) in the lungs of NOD/SCID gamma (NSG) mice expressing hACE2 (hACE2-NSG mice). Altogether, the current study demonstrates the potential use of S309-CAR-NK immunotherapy as an alternative treatment for COVID-19 patients.

Albuminuria improves R2CHA2DS2-VASc score in predicting mortality in high cardiovascular risk population.

BACKGROUND AND AIMS: The CHA2DS2-VASc score estimates the risk of cardioembolism in patients with atrial fibrillation (AF). It also predicts vascular events and death in different clinical settings, even in the absence of AF. The R2CHA2DS2-VASc score, obtained by adding the glomerular filtration rate to CHA2DS2-VASc, shows a higher prediction ability for new events and all-cause mortality. The present study aims to assess whether the addition of albuminuria to R2CHA2DS2-VASc score further improves its discrimination ability in predicting all-cause mortality in a sample of high cardiovascular risk population. METHODS AND RESULTS: Prospective, monocentric, observational study, evaluating a subset of 737 subjects consecutively undergoing to coronary angiography at Coronary Unit of Scientific Institute "Casa Sollievo della Sofferenza" from June 2016 to December 2018. The presence of albuminuria was significantly associated with all-cause mortality (p < 0.0001). Any one-point increase of Alb-R2CHA2DS2-VASc score increased mortality of about 1.5-fold (adjusted HR 1.49; 95%CI: 1.37-1.63; p < 0.0001). Considering tertiles of Alb-R2CHA2DS2-VASc, the third tertile showed a 9.5-fold increased risk of mortality (HR 9.52; 95% CI: 5.15-17.60, p < 0.001). Comparing the two scores, the Alb-R2CHA2DS2-VASc score (C-statistic = 0.751; 95%CI: 0.69-0.81) outperformed the R2-CHA2DS2-VASc score (C-statistic = 0.736; 95%CI: 0.68-0.961) in predicting mortality (delta C-statistic = 0.015; 95%CI: 0.001-0.029). The better prediction ability of the Alb-R2CHA2DS2-VASc score was also proven by an IDI of 0.024 (p < 0.0001) and a relative IDI of 24.11% (p < 0.0001), with an NRI = 0.608 (p < 0.00001). CONCLUSIONS: The addition of albuminuria to R2CHA2DS2-VASc significantly and independently predicts the risk of all-cause mortality in a sample of high CV risk patients. Moreover, Alb-R2CHA2DS2-VASc outperforms R2CHA2DS2-VASc.

12-year follow-up of the first endothelial keratoplasty without Descemet stripping in a 3-month newborn with Congenital Hereditary Endothelial Dystrophy (CHED).

BACKGROUND: Endothelial Keratoplasty (EK) is now considered as the standard treatment for Congenital Hereditary Endothelial Dystrophy (CHED) by many surgeons. We present the 12-year clinical outcome of the youngest operated patient with CHED in which we successfully performed a bilateral EK procedure without removing the recipient endothelium-Descemet complex. CASE PRESENTATION: In November 2010 we performed EK without Descemet Stripping in a 3-month female newborn, thinking that the lower manipulation obtained by leaving the recipient endothelium-Descemet complex could be the key factor for the success of our surgery. Such a particular technique was new in newborns. The surgery was a success, but the long-term visual result was not predictable at that time. We followed the patient at 4 months, and then yearly. At the latest visit in October 2022 the visual, cognitive, and motorial developments were normal, with Best-corrected Distance Visual Acuity of 0.4 LogMAR with - 0.75 D sf + 2.75 D cyl @ 105° in the right eye (RE) and 0.4 LogMAR with + 1.50 D sf + 2.50 D cyl @ 60° in the left eye (LE). The endothelial microscope showed an unexpected healthy endothelium, with a cell count of 2383 cells/mm2 in the RE and of 2547 cells/mm2 in the LE from a starting donor count of 2900 cells/mm2. No secondary procedures were performed during the 12-year follow-up. CONCLUSION: EK without Descemet stripping has proved to be a successful procedure over time in our newborn. The unexpected healthy endothelium suggests a role of the Descemet membrane in CHED.

Detection of Propionic Acids Trapped in Thin Zeolite Layer Using Thermal Desorption Analysis.

Volatile organic compounds (VOCs) have recently received considerable attention for the analysis and monitoring of different biochemical processes in biological systems such as humans, plants, and microorganisms. The advantage of using VOCs to gather information about a specific process is that they can be extracted using different types of samples, even at low concentrations. Therefore, VOC levels represent the fingerprints of specific biochemical processes. The aim of this work was to develop a sensor based on a photoionization detector (PID) and a zeolite layer, used as an alternative analytic separation technique for the analysis of VOCs. The identification of VOCs occurred through the evaluation of the emissive profile during the thermal desorption phase, using a stainless-steel chamber for analysis. Emission profiles were evaluated using a double exponential mathematical model, which fit well if compared with the physical system, describing both the evaporation and diffusion processes. The results showed that the zeolite layer was selective for propionic acid molecules if compared to succinic acid molecules, showing linear behavior even at low concentrations. The process to define the optimal adsorption time between the propionic acid molecules was performed in the range of 5 to 60 min, followed by a thermal desorption process at 100 °C. An investigation of the relationship between the evaporation and diffusion rates showed that the maximum concentration of detected propionic acid molecules occurred in 15 min. Other analyses were performed to study how the concentration of VOCs depended on the desorption temperature and the volume of the analysis chamber. For this purpose, tests were performed using three analysis chambers with volumes of 25 × 10-6, 50 × 10-6, and 150 × 10-6 m3 at three different desorption temperatures of 20 °C, 50 °C, and 100 °C, respectively. The results demonstrated that the evaporation rate of the VOCs increased rapidly with an increasing temperature, while the diffusion rate remained almost constant and was characterized by a slow decay time. The diffusion ratio increased when using a chamber with a larger volume. These results highlight the capabilities of this alternative technique for VOC analysis, even for samples with low concentrations. The coupling of a zeolite layer and a PID improves the detection selectivity in portable devices, demonstrating the feasibility of extending its use to a wide range of new applications.

The temporal effects of asymptomatic COVID-19 infection on peri-operative complications in patients receiving total joint arthroplasty.

INTRODUCTION: Recent coronavirus disease 2019 (COVID-19) infection may pose increased risk of post-operative complications after total joint arthroplasty (TJA). Current recommendations suggest waiting four-weeks before elective surgery in asymptomatic patients. The purpose of this study was to propensity-score-match patients who had positive COVID-19-test between (1) 0-2 weeks and (2) 2-4 weeks before TJA with a matching group without COVID-19 history to determine rates of complications at 90-days and 1-year post-operatively. MATERIALS AND METHODS: We queried a national-database for patients who tested positively for COVID-19 within 1-month (n = 1749) before TJA. A propensity-score-match analysis was conducted to limit influence of confounders. They were separated into mutually exclusive asymptomatic cohorts based on time of positive COVID-19-test before TJA: within 2-weeks (n = 1749) and between 2-to-4 weeks (n = 599). Asymptomatic patients were patients with positive test without symptoms of fever, shortness of breath, nausea, vomiting, diarrhea, loss of taste or smell, cough, bronchitis, pneumonia, lung infections, septic shock, and multiple-organ-dysfunction. Complications analyzed: 90-day and 1-year periprosthetic-joint infections (PJIs), surgical-site infections(SSIs), wound complications, cardiac complications, transfusions, and venous thromboembolisms. RESULTS: Asymptomatic patients who have COVID-19 demonstrated increased incidence of PJI in patients who had TJA performed within two weeks from positive test at 90-days compared to patients who did not test positive for COVID-19 (3.0 vs. 1.5%; p = 0.023). Upon totaling all 90-day post-operative complications, no significant difference was found amongst asymptomatic patients who tested positive for COVID-19 for total complications at 90-days (p = 0.936). CONCLUSIONS: Asymptomatic patients who test positive for COVID-19 don't have increased risk for post-operative complications after TJA. However, two-fold increased risk in PJI for patients who tested positive for COVID-19 in first 2-weeks cannot be ignored. These results should be taken into consideration when surgeons consider performing TJA. We recommend asymptomatic patients consider waiting two-weeks before TJA to mitigate risk of PJI. Nevertheless, there's reassurance these patients are not at increased total complication risk.

One-dioptre toric IOL versus spherical IOL in eyes with low preoperative corneal astigmatism.

PURPOSE: To investigate the advantages/disadvantages of a 1.0 D toric IOL vs spherical IOL after regular phacoemulsification in eyes with preoperative astigmatism ≤ 1 D. METHODS: Retrospective comparative series involving pseudophakic eyes with preoperative topographic astigmatism ≤ 1.0 D implanted either with monofocal 1.0 D Toric IOL (T-group), or with spherical IOL (S-group). The postoperative refractive astigmatism (PRA, i.e. surgically induced + corneal) was the main outcome; also considered in the analyses were the uncorrected and best-corrected distance visual acuity (VA). The data were referred to the last postoperative follow-up visit, 2 to 4 months after surgery. RESULTS: A total of 60 eyes were included: 30 in the T-group and 30 in the S-group, matched for patient's age, laterality, and axial length. Before surgery, the mean corneal astigmatism was 0.62 ± 0.39 D in the T-group and 0.54 ± 0.33 D in the S-group (p = 0.4). In the S-group, PRA was 0.73 ± 0.37 D, higher than the corresponding preoperative corneal astigmatism (p = 0.040). In the T-group, PRA was 0.58 ± 0.31 D; the variation was not statistically significant. Uncorrected VA was significantly better in the T-group vs the S-group (p = 0.007), and the best-corrected VA was comparable in the two groups. CONCLUSION: The present study indicated that in eyes with very low preoperative astigmatism, 1.0 D toric IOLs were able to limit the increase of the PRA instead of those observed with the spherical IOLs. This could support the better uncorrected VA recorded in the T-group.

CHA2DS2-VASc and R2CHA2DS2-VASc scores predict mortality in high cardiovascular risk population.

BACKGROUND: The CHA2 DS2 -VASc score, widely used to estimate cardioembolic risk in patients with atrial fibrillation (AF), appears to be useful also in predicting vascular adverse events and death in different sets of patients without AF. The R2 CHA2 DS2 -VASc score, which includes renal impairment, allows a better prediction of death and thromboembolism in patients without AF. The aims of our study were to assess, in a large sample of patients at high cardiovascular (CV) risk, (i) the correlation between CHA2 DS2 -VASc and R2 CHA2 DS2 -VASc with all-cause mortality, and (ii) to compare the performances of CHA2 DS2 -VASc and R2 CHA2 DS2 -VASc in predicting all-cause mortality. METHODS: In this single-centre prospective observational study, conducted at the Research Hospital 'Casa Sollievo della Sofferenza' between June 2016 and December 2018, 1017 CV patients at high risk of undergoing coronary angiography were enrolled. RESULTS: CHA2DS2-VASc and R2 CHA2 DS2 -VASc scores significantly associated with all-cause mortality. For each one-point increase in CHA2 DS2 -VASc or R2 CHA2 DS2 -VASc scores, mortality increased by almost 1.5-fold. The R2 CHA2 DS2 -VASc score (C-statistic = 0.71; 95% CI = 0.65-76) outperformed the CHA2 DS2 -VASc score (C-statistic = 0.66; 95% CI = 0.61-0.71) in predicting 4-year mortality (delta C-statistic = 0.05; 95% CI = 0.02-0.07). The better predictive ability of the R-CHA2 DS2 -VASc score was also demonstrated by an IDI = 0.027 (95% CI = 0.021-0.034, p < .00001) and a relative IDI = 62.8% (95% CI = 47.9%-81.3%, p < .00001). The R2 CHA2 DS2 -VASc score correctly reclassified the patients with a NRI = 0.715 (95% = 0.544-0.940, p < .00001). CONCLUSIONS: The CHA2DS2-VASc and R2 CHA2 DS2 -VASc scores are useful predictors of all-cause mortality in subjects at high CV risk, with the R2 CHA2 DS2 -VASc score being the best performer.

The impact of surgical approach on short- and long-term outcomes after rectal cancer resection in elderly patients: a national cancer database propensity score matched comparison of robotic, laparoscopic, and open approaches.

BACKGROUND: Elderly patients are underrepresented in studies demonstrating the advantages of laparoscopy for the management of colorectal diseases. Moreover, few studies have examined the robotic approach in this population. In this retrospective analysis, we compare outcomes for open, laparoscopic, and robotic approaches in elderly patients with nonmetastatic rectal cancer. METHODS: The U.S. National Cancer Database was queried for patients aged ≥ 65 with nonmetastatic adenocarcinoma of the rectum who underwent surgical resection from 2010 to 2016. Groups were separated based on approach (open, laparoscopic, robotic). One-to-one nearest neighbor propensity score matching (PSM) ± 1% caliper was performed across surgical approach cohorts to balance potential confounding covariates. Kaplan-Meier estimation and Cox-proportional hazards regression were used to analyze the primary outcome of survival. Secondary outcomes were analyzed by way of logistic regression. RESULTS: Inclusion criteria and PSM identified 1891 patients per approach (n = 5673). PSM provided adequate discrimination between cohorts (0.6 < AUC < 0.8), and potential confounding covariates did not significantly differ (respective P > 0.05). After PSM, robotic and laparoscopic approaches were associated with decreased odds of 90 day mortality compared to the open approach (P < 0.05). Compared to laparoscopy, a robotic approach was associated with increased odds of ≥ 12 regional lymph nodes examined and negative circumferential resection margin (P < 0.05). No differences were seen in 30 day or 90 day mortality between robotic and laparoscopic approaches. Cox proportional hazards regression showed that both robotic and laparoscopic approaches were significantly associated with decreased mortality hazards relative to open. CONCLUSION: Our study demonstrates that in elderly patients, minimally invasive surgery for rectal adenocarcinoma was associated with equivalent or improved short- and long-term mortality over open surgery. Compared to laparoscopy, the robotic approach showed no survival disadvantage and greater odds of an appropriate oncological resection. Our study adds evidence to the conclusion that robotic rectal surgery can be safely performed in patients regardless of age.

Low GFR amplifies the association between coronary three-vessel disease and all-cause mortality.

BACKGROUND AND AIM: Three vessels disease (3VD) has been associated with worse prognosis and higher mortality. Chronic kidney disease (CKD) is an independent risk factor for premature death, mostly due to coronary artery disease (CAD). We aim to examine the prognostic impact of 3VD on all-cause mortality in a cohort of high cardiovascular risk subjects undergoing coronary angiography (CA) and to explore whether low eGFR (<60 ml/min/1.73 m2) modulates the risk of all-cause mortality associated to 3VD. METHODS AND RESULTS: One-thousand-seventeen subjects (759 M, mean age 68.4 ± 11 years) consecutive subjects undergoing CA from 2016 to 2018 were evaluated. Subjects were classified according to the severity of CAD as follows: group "three vessels disease" (3VD), and "no three vessels disease" (No 3VD). Serum creatinine was measured to estimate glomerular filtration rate (eGFR). The whole population was divided into 4 groups (A, B, C, D), according to the presence/absence of low eGFR and/or 3VD. One-hundred-fourteen deaths occurred (median follow-up:44 months). The risk of death in subjects with 3VD was almost 2-time higher than subject without 3VD (adjusted HR = 1.61; 95% CI 1.094-2.373, p = 0.0157). Among 4 subgroups, subjects with low eGFR and 3VD (Group D) had the highest risk of death (adjusted HR = 3.881; 95% CI 2.256-6.676, p < 0.0001). CONCLUSIONS: Low eGFR significantly amplifies the risk of all-cause mortality associated to 3VD. Our results strengthen the role of kidney disease as a risk multiplier for cardiovascular and all-cause mortality and highlight the need to prevent its onset and progression.

High-fidelity amplified FISH for the detection and allelic discrimination of single mRNA molecules.

Amplification of signals by the hybridization chain reaction (HCR) is a powerful approach for increasing signal strength in single-molecule fluorescence in situ hybridization, but probes tagged with an HCR initiator sequence are prone to producing false signals. Here we describe a system of interacting hairpin binary probes in which the HCR initiator sequence is conditionally sequestered. The binding of these probes to a perfectly complementary target unmasks the initiator, enabling the generation of an amplified signal. This probe system can distinguish single-nucleotide variations within single mRNA molecules and produces amplified signals in situ for both mutant and wild-type variants, each in a distinguishable color. This technology will augment studies of imbalanced allelic expression and will be useful for the detection of somatic mutations in cancer biopsies. By tiling these probes along the length of an mRNA target, enhanced signals can be obtained, thereby enabling the scanning of tissue sections for gene expression utilizing lower magnification microscopy, overcoming tissue autofluorescence, and allowing the detection of low-abundance biomarkers in flow cytometry.

Ultrasensitive Detection of Multidrug-Resistant Mycobacterium tuberculosis Using SuperSelective Primer-Based Real-Time PCR Assays.

The emergence of drug-resistant tuberculosis is a significant global health issue. The presence of heteroresistant Mycobacterium tuberculosis is critical to developing fully drug-resistant tuberculosis cases. The currently available molecular techniques may detect one copy of mutant bacterial genomic DNA in the presence of about 1-1000 copies of wild-type M. tuberculosis DNA. To improve the limit of heteroresistance detection, we developed SuperSelective primer-based real-time PCR assays, which, by their unique assay design, enable selective and exponential amplification of selected point mutations in the presence of abundant wild-type DNA. We designed SuperSelective primers to detect genetic mutations associated with M. tuberculosis resistance to the anti-tuberculosis drugs isoniazid and rifampin. We evaluated the efficiency of our assay in detecting heteroresistant M. tuberculosis strains using genomic DNA isolated from laboratory strains and clinical isolates from the sputum of tuberculosis patients. Results show that our assays detected heteroresistant mutations with a specificity of 100% in a background of up to 104 copies of wild-type M. tuberculosis genomic DNA, corresponding to a detection limit of 0.01%. Therefore, the SuperSelective primer-based RT-PCR assay is an ultrasensitive tool that can efficiently diagnose heteroresistant tuberculosis in clinical specimens and contributes to understanding the drug resistance mechanisms. This approach can improve the management of antimicrobial resistance in tuberculosis and other infectious diseases.

Clinical impact of COVID-19 on patients with cancer (CCC19): a cohort study.

BACKGROUND: Data on patients with COVID-19 who have cancer are lacking. Here we characterise the outcomes of a cohort of patients with cancer and COVID-19 and identify potential prognostic factors for mortality and severe illness. METHODS: In this cohort study, we collected de-identified data on patients with active or previous malignancy, aged 18 years and older, with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection from the USA, Canada, and Spain from the COVID-19 and Cancer Consortium (CCC19) database for whom baseline data were added between March 17 and April 16, 2020. We collected data on baseline clinical conditions, medications, cancer diagnosis and treatment, and COVID-19 disease course. The primary endpoint was all-cause mortality within 30 days of diagnosis of COVID-19. We assessed the association between the outcome and potential prognostic variables using logistic regression analyses, partially adjusted for age, sex, smoking status, and obesity. This study is registered with ClinicalTrials.gov, NCT04354701, and is ongoing. FINDINGS: Of 1035 records entered into the CCC19 database during the study period, 928 patients met inclusion criteria for our analysis. Median age was 66 years (IQR 57-76), 279 (30%) were aged 75 years or older, and 468 (50%) patients were male. The most prevalent malignancies were breast (191 [21%]) and prostate (152 [16%]). 366 (39%) patients were on active anticancer treatment, and 396 (43%) had active (measurable) cancer. At analysis (May 7, 2020), 121 (13%) patients had died. In logistic regression analysis, independent factors associated with increased 30-day mortality, after partial adjustment, were: increased age (per 10 years; partially adjusted odds ratio 1·84, 95% CI 1·53-2·21), male sex (1·63, 1·07-2·48), smoking status (former smoker vs never smoked: 1·60, 1·03-2·47), number of comorbidities (two vs none: 4·50, 1·33-15·28), Eastern Cooperative Oncology Group performance status of 2 or higher (status of 2 vs 0 or 1: 3·89, 2·11-7·18), active cancer (progressing vs remission: 5·20, 2·77-9·77), and receipt of azithromycin plus hydroxychloroquine (vs treatment with neither: 2·93, 1·79-4·79; confounding by indication cannot be excluded). Compared with residence in the US-Northeast, residence in Canada (0·24, 0·07-0·84) or the US-Midwest (0·50, 0·28-0·90) were associated with decreased 30-day all-cause mortality. Race and ethnicity, obesity status, cancer type, type of anticancer therapy, and recent surgery were not associated with mortality. INTERPRETATION: Among patients with cancer and COVID-19, 30-day all-cause mortality was high and associated with general risk factors and risk factors unique to patients with cancer. Longer follow-up is needed to better understand the effect of COVID-19 on outcomes in patients with cancer, including the ability to continue specific cancer treatments. FUNDING: American Cancer Society, National Institutes of Health, and Hope Foundation for Cancer Research.

A Molecular-Beacon-Based Multiplex Real-Time PCR Assay To Distinguish Mycobacterium abscessus Subspecies and Determine Macrolide Susceptibility.

Mycobacterium abscessus is a rapidly growing nontuberculous mycobacterial species that comprises three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii. These predominantly environmental microorganisms have emerged as life-threatening chronic pulmonary pathogens in both immunocompetent and immunocompromised patients, and their acquisition of macrolide resistance due to the erm(41) gene and mutations in the 23S rrl gene has dramatically impacted patient outcome. However, standard microbiology laboratories typically have limited diagnostic tools to distinguish M. abscessus subspecies, and the testing for macrolide resistance is often not done. Here, we describe the development of a real-time multiplex assay using molecular beacons to establish a robust, rapid, and highly accurate method to both distinguish M. abscessus subspecies and to determine which strains are susceptible to macrolides. We report a bioinformatic approach to identify robust subspecies sequence targets, the design and optimization of six molecular beacons to identify all genotypes, and the development and application of a 2-tube 3-color multiplex assay that can provide clinically significant treatment information in less than 3 h.

The robotic colorectal experience: an outcomes and learning curve analysis of 502 patients.

AIM: This study aimed to present our experience with robotic colorectal surgery since its establishment at our institution in 2009. By examining the outcomes of over 500 patients, our experience provides a basis for assessing the introduction of a robotic platform in a colorectal practice. Specific measures investigated include intraoperative data and postoperative outcomes for all operations using the robotic platform. In addition, for our most commonly performed operations we wished to analyse the learning curve to improve operative proficiency. This is the largest single-surgeon robotic database analysed to date. METHOD: A prospectively maintained database of patients who underwent robotic colorectal surgery by a single surgeon at the George Washington University Hospital was retrospectively reviewed. Demographic data and perioperative outcomes were assessed. Additionally, an operating time learning curve analysis was performed. RESULTS: Inclusion criteria identified 502 patients who underwent robotic colorectal surgery between October 2009 and December 2018. The most common indications for surgery were diverticulitis (22.9%), colon adenocarcinoma (22.1%) and rectal adenocarcinoma (19.5%). The most common operations were anterior/low anterior resection (33.9%), right hemicolectomy/ileocaecectomy (24.9%) and left hemicolectomy/sigmoidectomy (21.9%). The rate of conversion to open surgery was 4.8%. The most common postoperative complications were wound infection (5.0%), anastomotic leakage (4.0%) and abscess formation (2.8%). The operating time learning curve plateaued at 55-65 cases for anterior and low anterior resection and 35-45 cases for left hemicolectomy and sigmoidectomy. A clear learning curve was not seen in right hemicolectomy. CONCLUSION: Robotic-assisted surgery can be performed in a diverse colorectal practice with low rates of conversion and postoperative complications. Plateau performance was achieved after 65 anterior/low anterior resections and 45 left and sigmoid colectomies.

Trends in utilization, conversion rates, and outcomes for minimally invasive approaches to non-metastatic rectal cancer: a national cancer database analysis.

BACKGROUND: This study examined utilization and conversion rates for robotic and laparoscopic approaches to non-metastatic rectal cancer. Secondary aims were to examine short- and long-term outcomes of patients who underwent conversion to laparotomy from each approach. METHODS: The National Cancer Database (NCDB) was reviewed for all cases of non-metastatic adenocarcinoma of the rectum or rectosigmoid junction who underwent surgical resection from 2010 to 2016. Utilization rates of robotic, laparoscopic, and open approaches were examined. Patients were split into cohorts by approach. Subgroup analyses were performed by primary tumor site and surgical procedure. Multivariable analysis was performed by multivariable logistic regression for binary outcomes and multivariable general linear models for continuous outcomes. Survival analysis was performed by Kaplan-Meier and multivariable cox-proportional hazards regression. RESULTS: From 2010 to 2016, there was a statistically significant increase in utilization of the robotic and laparoscopic approaches over the study period and a statistically significant decrease in utilization of the open approach. The conversion rates for robotic and laparoscopic cohorts were 7.0% and 15.7%, p < 0.0001. Subgroup analysis revealed statistically lower conversion rates between robotic and laparoscopic approaches for rectosigmoid and rectal tumors and for LAR and APR. Converted cohorts had statistically significant higher odds of short term mortality than the non-converted cohorts (p < 0.05).Laparoscopic conversion had statistically higher odds of positive margins (p < 0.0001) and 30-day unplanned readmission (p < 0.0001) than the laparoscopic non-conversion. Increased adjusted mortality hazard was seen for converted laparoscopy relative to non-converted laparoscopy (p = 0.0019). CONCLUSION: From 2010 to 2016, there was a significant increase in utilization of minimally invasive approaches to surgical management of non-metastatic rectal cancer. A robotic approach demonstrated decreased conversion rates than a laparoscopic approach at the rectosigmoid junction and rectum and for LAR and APR. Improved outcomes were seen in the minimally invasive cohorts compared to those that converted to laparotomy.

Parsplana vitrectomy alone versus parsplana vitrectomy combined with phacoemulsification for the treatment of rhegmatogenous retinal detachment: a randomized study.

BACKGROUND: To compare parsplana vitrectomy (PPV) with and without phacoemulsification to treat rhegmatogenous retinal detachment (RRD). METHODS: Subjects aged 48-65 years with RRD in a phakic eye due to superior retinal tears with an overall extension of retinal breaks < 90° underwent to PPV alone (group A); or PPV plus phacoemulsification (phacovitrectomy, PCV, group B). Post-operative follow-up visits occurred at 1 week, 1 month (m1), 3 months (m3), and 6 months (m6) after surgery. The main outcome was the rate of retinal reattachment. Secondary outcomes included best-corrected visual acuity (BCVA), intraocular pressure (IOP), central macular thickness (CMT), and cataract progression (in the lens-sparing [PPV-alone] group). RESULTS: In this initial phase of the study a total of 59 patients (mean age: 55 years, 59 eyes) were enrolled: 29 eyes in group A and 30 eyes in group B. Both groups had similar gas tamponade. During the follow-up there were three cases of RRD recurrence in group A and one in group B. The relative risk of recurrence in group A was 3.22 times higher but the difference was not significant (p = 0.3). The two groups were also similar in terms of BCVA and IOP variation. At m3, CMT was significantly higher in group B (p = 0.014). In group A, cataract progression was significant at m6 (p = 0.003). CONCLUSIONS: In a cohort of RRD patients selected according to their preoperative clinical characteristics, PPV was comparable to PCV in terms of the rate of retinal reattachment after 6 months. TRIAL REGISTRATION: ISRCTN15940019 . Date registered: 15/01/2021 (retrospectively registered).

Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.).

BACKGROUND: The investigation of transcriptome profiles using short reads in non-model organisms, which lack of well-annotated genomes, is limited by partial gene reconstruction and isoform detection. In contrast, long-reads sequencing techniques revealed their potential to generate complete transcript assemblies even when a reference genome is lacking. Cynara cardunculus var. altilis (DC) (cultivated cardoon) is a perennial hardy crop adapted to dry environments with many industrial and nutraceutical applications due to the richness of secondary metabolites mostly produced in flower heads. The investigation of this species benefited from the recent release of a draft genome, but the transcriptome profile during the capitula formation still remains unexplored. In the present study we show a transcriptome analysis of vegetative and inflorescence organs of cultivated cardoon through a novel hybrid RNA-seq assembly approach utilizing both long and short RNA-seq reads. RESULTS: The inclusion of a single Nanopore flow-cell output in a hybrid sequencing approach determined an increase of 15% complete assembled genes and 18% transcript isoforms respect to short reads alone. Among 25,463 assembled unigenes, we identified 578 new genes and updated 13,039 gene models, 11,169 of which were alternatively spliced isoforms. During capitulum development, 3424 genes were differentially expressed and approximately two-thirds were identified as transcription factors including bHLH, MYB, NAC, C2H2 and MADS-box which were highly expressed especially after capitulum opening. We also show the expression dynamics of key genes involved in the production of valuable secondary metabolites of which capitulum is rich such as phenylpropanoids, flavonoids and sesquiterpene lactones. Most of their biosynthetic genes were strongly transcribed in the flower heads with alternative isoforms exhibiting differentially expression levels across the tissues. CONCLUSIONS: This novel hybrid sequencing approach allowed to improve the transcriptome assembly, to update more than half of annotated genes and to identify many novel genes and different alternatively spliced isoforms. This study provides new insights on the flowering cycle in an Asteraceae plant, a valuable resource for plant biology and breeding in Cynara and an effective method for improving gene annotation.

A Recursive Algorithm for Indoor Positioning Using Pulse-Echo Ultrasonic Signals.

Low frequency ultrasounds in air are widely used for real-time applications in short-range communication systems and environmental monitoring, in both structured and unstructured environments. One of the parameters widely evaluated in pulse-echo ultrasonic measurements is the time of flight (TOF), which can be evaluated with an increased accuracy and complexity by using different techniques. Hereafter, a nonstandard cross-correlation method is investigated for TOF estimations. The procedure, based on the use of template signals, was implemented to improve the accuracy of recursive TOF evaluations. Tests have been carried out through a couple of 60 kHz custom-designed polyvinylidene fluoride (PVDF) hemicylindrical ultrasonic transducers. The experimental results were then compared with the standard threshold and cross-correlation techniques for method validation and characterization. An average improvement of 30% and 19%, in terms of standard error (SE), was observed. Moreover, the experimental results evidenced an enhancement in repeatability of about 10% in the use of a recursive positioning system.

High-Resolution Respirometry Reveals MPP+ Mitochondrial Toxicity Mechanism in a Cellular Model of Parkinson's Disease.

MPP+ is the active metabolite of MPTP, a molecule structurally similar to the herbicide Paraquat, known to injure the dopaminergic neurons of the nigrostriatal system in Parkinson's disease models. Within the cells, MPP+ accumulates in mitochondria where it inhibits complex I of the electron transport chain, resulting in ATP depletion and neuronal impairment/death. So far, MPP+ is recognized as a valuable tool to mimic dopaminergic degeneration in various cell lines. However, despite a large number of studies, a detailed characterization of mitochondrial respiration in neuronal cells upon MPP+ treatment is still missing. By using high-resolution respirometry, we deeply investigated oxygen consumption related to each respiratory state in differentiated neuroblastoma cells exposed to the neurotoxin. Our results indicated the presence of extended mitochondrial damage at the inner membrane level, supported by increased LEAK respiration, and a drastic drop in oxygen flow devoted to ADP phosphorylation in respirometry measurements. Furthermore, prior to complex I inhibition, an enhancement of complex II activity was observed, suggesting the occurrence of some compensatory effect. Overall our findings provide a mechanistic insight on the mitochondrial toxicity mediated by MPP+, relevant for the standardization of studies that employ this neurotoxin as a disease model.