A one-step low-cost molecular test for SARS-CoV-2 detection suitable for community testing using minimally processed saliva.

The gold standard for coronavirus disease 2019 diagnostic testing relies on RNA extraction from naso/oropharyngeal swab followed by amplification through reverse transcription-polymerase chain reaction (RT-PCR) with fluorogenic probes. While the test is extremely sensitive and specific, its high cost and the potential discomfort associated with specimen collection made it suboptimal for public health screening purposes. In this study, we developed an equally reliable, but cheaper and less invasive alternative test based on a one-step RT-PCR with the DNA-intercalating dye SYBR Green, which enables the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly from saliva samples or RNA isolated from nasopharyngeal (NP) swabs. Importantly, we found that this type of testing can be fine-tuned to discriminate SARS-CoV-2 variants of concern. The saliva RT-PCR SYBR Green test was successfully used in a mass-screening initiative targeting nearly 4500 asymptomatic children under the age of 12. Testing was performed at a reasonable cost, and in some cases, the saliva test outperformed NP rapid antigen tests in identifying infected children. Whole genome sequencing revealed that the antigen testing failure could not be attributed to a specific lineage of SARS-CoV-2. Overall, this work strongly supports the view that RT-PCR saliva tests based on DNA-intercalating dyes represent a powerful strategy for community screening of SARS-CoV-2. The tests can be easily applied to other infectious agents and, therefore, constitute a powerful resource for an effective response to future pandemics.

Chronic gastric volvulus with diaphragmatic eventration: Case presentation.

INTRODUCTION AND IMPORTANCE: Gastric volvulus is a rare clinical entity which occurs due to the rotation of the stomach and can have life-threatening complications. This condition can have an acute or chronic presentation and its symptoms will vary according to the degree of obstruction and rapidity of onset. CASE PRESENTATION: We report a case of a 84-year-old male with history of frequent periods of constipation and lack of appetite who presented to the emergency room with left-sided abdominal pain and distension and persistent nausea, without the ability to vomit. Abdominal radiograph, computed tomography scan of the abdomen, contrast-enhanced examination and upper endoscopy were consistent with a gastric volvulus secondary to diaphragmatic eventration. The patient's symptoms resolved after nasogastric tube placement and fluid resuscitation. However, he was proposed to a laparoscopic anterior gastropexy to prevent symptom recurrence. He remains asymptomatic after 3 years of follow-up. CLINICAL DISCUSSION: The diagnosis of gastric volvulus is based mainly on clinical presentation and abdominal imaging. The main principles of surgical intervention include stomach decompression with volvulus reduction, followed by gastropexy and correction of any predisposing intra-abdominal factors. CONCLUSION: Definitive treatment of both acute and chronic gastric volvulus includes a surgical approach. Laparoscopic anterior gastropexy has been found to be a viable alternative in these patients.

Symptoms of anxiety and depression in patients with persistent asthma: a cross-sectional analysis of the INSPIRERS studies.

OBJECTIVES: Anxiety and depression are relevant comorbidities in asthma, but, in Portugal and Spain, data on this topic are scarce. We assessed, in patients with asthma, the frequency of anxiety and depression using the Hospital Anxiety and Depression Scale (HADS) and the European Quality of Life Five Dimension Questionnaire (EQ-5D); the level of agreement between these questionnaires, and the factors associated with these symptoms. METHODS: This is a secondary analysis of the INSPIRERS studies. A total of 614 adolescents and adults with persistent asthma (32.6±16.9 years, 64.7% female) were recruited from 30 primary care centres and 32 allergy, pulmonology and paediatric clinics. Demographic and clinical characteristics, HADS and EQ-5D were collected. A score ≥8 on Hospital Anxiety and Depression Scale-Anxiety/Hospital Anxiety and Depression Scale-Depression or a positive answer to EQ-5D item 5 indicated the presence of these symptoms. Agreement was determined by Cohen's kappa. Two multivariable logistic regressions were built. RESULTS: According to HADS, 36% of the participants had symptoms of anxiety and 12% of depression. According to EQ-5D, 36% of the participants had anxiety/depression. The agreement between questionnaires in identifying anxiety/depression was moderate (k=0.55, 95% CI 0.48 to 0.62). Late asthma diagnosis, comorbidities and female gender were predictors of anxiety/depression, while better asthma control, health-related quality of life and perception of health were associated with lower odds for anxiety/depression. CONCLUSION: At least 1/3 of the patients with persistent asthma experience symptoms of anxiety/depression, showing the relevance of screening these disorders in patients with asthma. EQ-5D and HADS questionnaires showed a moderate agreement in the identification of anxiety/depression symptoms. The identified associated factors need to be further investigated in long-term studies.

Active Pharmacovigilance Study: A Follow-Up Model of Oral Anti-Cancer Drugs under Additional Monitoring.

Adverse drug reactions (ADRs) are responsible for almost 5% of hospital admissions, making it necessary to implement different pharmacovigilance strategies. The additional monitoring (AM) concept has been highlighted and intended to increase the number of suspected ADRs reported, namely in medicines with limited safety data. A prospective, descriptive study of active pharmacovigilance (AP) was conducted between 2019 and 2021 in the Local Health Unit of Matosinhos (LHUM) (Porto, Portugal). A model of AP for medicines under AM, namely oral antineoplastic agents, was designed. Follow-up consultations were performed, and adverse events (AEs) data were collected. The overall response to the treatment was evaluated through the Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 criteria. A total of 52 patients were included in the study, and 14 antineoplastic drugs under AM were analyzed. Of the total number of patients included, only 29 developed at least one type of toxicity. Hematological disorders were the most reported suspected ADR. However, only four patients interrupted their treatment due to toxicity. After 12 months of treatment, most patients had disease progression, which was the main reason for therapy discontinuation. This AP model played an important role in the early detection of AEs and, consequently, contributed to better management of them. Increasing the number of suspected ADR reports is crucial for drugs with limited safety data.

Spontaneous retroperitoneal biloma in a patient with choledocholithiasis: Presentation of case.

INTRODUCTION AND IMPORTANCE: Spontaneous perforation of the biliary tree, resulting in retroperitoneal biloma in adults is an extremely rare condition, and may unfold to a potentially fatal outcome, particularly when the diagnosis and definitive treatment are delayed. CASE PRESENTATION: We report a case of a 69-year-old male who presented to the emergency room with abdominal pain, localized to the right quadrants, associated with jaundice and dark-coloured urine. Abdominal imaging including CT scan, ultrasound and magnetic resonance cholangiopancreatography (MRCP) revealed a retroperitoneal fluid collection, a distended gallbladder with wall thickening and lithiasis, as well as a dilated common bile duct (CBD) with choledocholithiasis. The analysis of the retroperitoneal fluid obtained by CT-guided percutaneous drainage was consistent with biloma. A combined approach of biloma percutaneous drainage and endoscopic retrograde cholangiopancreatography (ERCP)-guided stent placement in the CBD with biliary stones removal was successful in the management of this patient, despite the fact that the perforation site could not be detected. CLINICAL DISCUSSION: The diagnosis of biloma is based mainly on clinical presentation and abdominal imaging. If urgent surgical intervention is not indicated, pressure necrosis and perforation of the biliary tree may be avoided by timely percutaneous aspiration of the biloma and ERCP to remove the impacted stones in the biliary tree. CONCLUSION: Biloma should be considered in the differential diagnosis of a patient presenting with right upper quadrant or epigastric pain and an intra-abdominal collection on imaging. Efforts should be made in order to offer a prompt diagnosis and treatment to the patient.

Measuring adherence to inhaled control medication in patients with asthma: Comparison among an asthma app, patient self-report and physician assessment.

BACKGROUND: Previous studies have demonstrated the feasibility of using an asthma app to support medication management and adherence but failed to compare with other measures currently used in clinical practice. However, in a clinical setting, any additional adherence measurement must be evaluated in the context of both the patient and physician perspectives so that it can also help improve the process of shared decision making. Thus, we aimed to compare different measures of adherence to asthma control inhalers in clinical practice, namely through an app, patient self-report and physician assessment. METHODS: This study is a secondary analysis of three prospective multicentre observational studies with patients (≥13 years old) with persistent asthma recruited from 61 primary and secondary care centres in Portugal. Patients were invited to use the InspirerMundi app and register their inhaled medication. Adherence was measured by the app as the number of doses taken divided by the number of doses scheduled each day and two time points were considered for analysis: 1-week and 1-month. At baseline, patients and physicians independently assessed adherence to asthma control inhalers during the previous week using a Visual Analogue Scale (VAS 0-100). RESULTS: A total of 193 patients (72% female; median [P25-P75] age 28 [19-41] years old) were included in the analysis. Adherence measured by the app was lower (1 week: 31 [0-71]%; 1 month: 18 [0-48]%) than patient self-report (80 [60-95]) and physician assessment (82 [51-94]) (p < 0.001). A negligible non-significant correlation was found between the app and subjective measurements (ρ 0.118-0.156, p > 0.05). There was a moderate correlation between patient self-report and physician assessment (ρ = 0.596, p < 0.001). CONCLUSIONS: Adherence measured by the app was lower than that reported by the patient or the physician. This was expected as objective measurements are commonly lower than subjective evaluations, which tend to overestimate adherence. Nevertheless, the low adherence measured by the app may also be influenced by the use of the app itself and this needs to be considered in future studies.

Prediction of Maize Phenotypic Traits With Genomic and Environmental Predictors Using Gradient Boosting Frameworks.

The development of crop varieties with stable performance in future environmental conditions represents a critical challenge in the context of climate change. Environmental data collected at the field level, such as soil and climatic information, can be relevant to improve predictive ability in genomic prediction models by describing more precisely genotype-by-environment interactions, which represent a key component of the phenotypic response for complex crop agronomic traits. Modern predictive modeling approaches can efficiently handle various data types and are able to capture complex nonlinear relationships in large datasets. In particular, machine learning techniques have gained substantial interest in recent years. Here we examined the predictive ability of machine learning-based models for two phenotypic traits in maize using data collected by the Maize Genomes to Fields (G2F) Initiative. The data we analyzed consisted of multi-environment trials (METs) dispersed across the United States and Canada from 2014 to 2017. An assortment of soil- and weather-related variables was derived and used in prediction models alongside genotypic data. Linear random effects models were compared to a linear regularized regression method (elastic net) and to two nonlinear gradient boosting methods based on decision tree algorithms (XGBoost, LightGBM). These models were evaluated under four prediction problems: (1) tested and new genotypes in a new year; (2) only unobserved genotypes in a new year; (3) tested and new genotypes in a new site; (4) only unobserved genotypes in a new site. Accuracy in forecasting grain yield performance of new genotypes in a new year was improved by up to 20% over the baseline model by including environmental predictors with gradient boosting methods. For plant height, an enhancement of predictive ability could neither be observed by using machine learning-based methods nor by using detailed environmental information. An investigation of key environmental factors using gradient boosting frameworks also revealed that temperature at flowering stage, frequency and amount of water received during the vegetative and grain filling stage, and soil organic matter content appeared as important predictors for grain yield in our panel of environments.

Determinants of the Use of Health and Fitness Mobile Apps by Patients With Asthma: Secondary Analysis of Observational Studies.

BACKGROUND: Health and fitness apps have potential benefits to improve self-management and disease control among patients with asthma. However, inconsistent use rates have been reported across studies, regions, and health systems. A better understanding of the characteristics of users and nonusers is critical to design solutions that are effectively integrated in patients' daily lives, and to ensure that these equitably reach out to different groups of patients, thus improving rather than entrenching health inequities. OBJECTIVE: This study aimed to evaluate the use of general health and fitness apps by patients with asthma and to identify determinants of usage. METHODS: A secondary analysis of the INSPIRERS observational studies was conducted using data from face-to-face visits. Patients with a diagnosis of asthma were included between November 2017 and August 2020. Individual-level data were collected, including age, gender, marital status, educational level, health status, presence of anxiety and depression, postcode, socioeconomic level, digital literacy, use of health services, and use of health and fitness apps. Multivariate logistic regression was used to model the probability of being a health and fitness app user. Statistical analysis was performed in R. RESULTS: A total of 526 patients attended a face-to-face visit in the 49 recruiting centers and 514 had complete data. Most participants were ≤40 years old (66.4%), had at least 10 years of education (57.4%), and were in the 3 higher quintiles of the socioeconomic deprivation index (70.1%). The majority reported an overall good health status (visual analogue scale [VAS] score>70 in 93.1%) and the prevalence of anxiety and depression was 34.3% and 11.9%, respectively. The proportion of participants who reported using health and fitness mobile apps was 41.1% (n=211). Multivariate models revealed that single individuals and those with more than 10 years of education are more likely to use health and fitness mobile apps (adjusted odds ratio [aOR] 2.22, 95%CI 1.05-4.75 and aOR 1.95, 95%CI 1.12-3.45, respectively). Higher digital literacy scores were also associated with higher odds of being a user of health and fitness apps, with participants in the second, third, and fourth quartiles reporting aORs of 6.74 (95%CI 2.90-17.40), 10.30 (95%CI 4.28-27.56), and 11.52 (95%CI 4.78-30.87), respectively. Participants with depression symptoms had lower odds of using health and fitness apps (aOR 0.32, 95%CI 0.12-0.83). CONCLUSIONS: A better understanding of the barriers and enhancers of app use among patients with lower education, lower digital literacy, or depressive symptoms is key to design tailored interventions to ensure a sustained and equitable use of these technologies. Future studies should also assess users' general health-seeking behavior and their interest and concerns specifically about digital tools. These factors may impact both initial engagement and sustained use.

Calibration and validation of predicted genomic breeding values in an advanced cycle maize population.

KEY MESSAGE: Model training on data from all selection cycles yielded the highest prediction accuracy by attenuating specific effects of individual cycles. Expected reliability was a robust predictor of accuracies obtained with different calibration sets. The transition from phenotypic to genome-based selection requires a profound understanding of factors that determine genomic prediction accuracy. We analysed experimental data from a commercial maize breeding programme to investigate if genomic measures can assist in identifying optimal calibration sets for model training. The data set consisted of six contiguous selection cycles comprising testcrosses of 5968 doubled haploid lines genotyped with a minimum of 12,000 SNP markers. We evaluated genomic prediction accuracies in two independent prediction sets in combination with calibration sets differing in sample size and genomic measures (effective sample size, average maximum kinship, expected reliability, number of common polymorphic SNPs and linkage phase similarity). Our results indicate that across selection cycles prediction accuracies were as high as 0.57 for grain dry matter yield and 0.76 for grain dry matter content. Including data from all selection cycles in model training yielded the best results because interactions between calibration and prediction sets as well as the effects of different testers and specific years were attenuated. Among genomic measures, the expected reliability of genomic breeding values was the best predictor of empirical accuracies obtained with different calibration sets. For grain yield, a large difference between expected and empirical reliability was observed in one prediction set. We propose to use this difference as guidance for determining the weight phenotypic data of a given selection cycle should receive in model retraining and for selection when both genomic breeding values and phenotypes are available.

Level of Medical Intervention in Geriatric Settings: Decision Factors and Correlation With Mortality.

OBJECTIVES: Level of medical intervention (LMI) has to be adapted to each patient in geriatric care. LMI scales intend to help nonintensive care (NIC) decisions, giving priority to patient choice and collegial discussion. In the present study, we aimed to assess the parameters associated with the NIC decision and whether these parameters differ from those associated with in-hospital mortality. DESIGN: Prospective observational study. SETTING AND PARTICIPANTS: All consecutive patients from a French 62-bed acute geriatric unit over 1 year. METHODS: Factors from the geriatric assessment associated with the decision of NIC were compared with those associated with in-hospital and 1-year mortality, in univariate and multivariate analyses. RESULTS: In total, 1654 consecutive patients (median age 87 years) were included. Collegial reflection led to NIC decision for 532 patients (32%). In-hospital and 1-year mortality were 22% and 54% in the NIC group vs 2% and 27% in the rest of the cohort (P < .001 for both). In multivariable analysis, high Charlson Comorbidity Index [odds ratio (OR) 1.15, 95% confidence interval (CI) 1.06-1.23, per point], severe neurocognitive disorders (OR 2.78, 95% CI 1.67-4.55), dependence (OR 1.92, 95% CI 1.45-2.59), and nursing home residence (OR 2.38, 95% CI 1.85-3.13) were highly associated with NIC decision but not with in-hospital mortality. Conversely, acute diseases had little impact on LMI despite their high short-term prognostic burden. CONCLUSIONS AND IMPLICATIONS: Neurocognitive disorders and dependence were strongly associated with NIC decision, even though they were not significantly associated with in-hospital mortality. The decision-making process of LMI therefore seems to go beyond the notion of short-term survival.

Functional Analysis of the Fusion and Attachment Glycoproteins of Mojiang Henipavirus.

Mojiang virus (MojV) is the first henipavirus identified in a rodent and known only by sequence data, whereas all other henipaviruses have been isolated from bats (Hendra virus, Nipah virus, Cedar virus) or discovered by sequence data from material of bat origin (Ghana virus). Ephrin-B2 and -B3 are entry receptors for Hendra and Nipah viruses, but Cedar virus can utilize human ephrin-B1, -B2, -A2 and -A5 and mouse ephrin-A1. However, the entry receptor for MojV remains unknown, and its species tropism is not well characterized. Here, we utilized recombinant full-length and soluble forms of the MojV fusion (F) and attachment (G) glycoproteins in membrane fusion and receptor tropism studies. MojV F and G were functionally competent and mediated cell-cell fusion in primate and rattine cells, albeit with low levels and slow fusion kinetics. Although a relative instability of the pre-fusion conformation of a soluble form of MojV F was observed, MojV F displayed significantly greater fusion activity when heterotypically paired with Ghana virus G. An exhaustive investigation of A- and B-class ephrins indicated that none serve as a primary receptor for MojV. The MojV cell fusion phenotype is therefore likely the result of receptor restriction rather than functional defects in recombinant MojV F and G glycoproteins.

Broadly neutralizing antibody cocktails targeting Nipah virus and Hendra virus fusion glycoproteins.

Hendra virus (HeV) and Nipah virus (NiV) are henipaviruses (HNVs) causing respiratory illness and severe encephalitis in humans, with fatality rates of 50-100%. There are no licensed therapeutics or vaccines to protect humans. HeV and NiV use a receptor-binding glycoprotein (G) and a fusion glycoprotein (F) to enter host cells. HNV F and G are the main targets of the humoral immune response, and the presence of neutralizing antibodies is a correlate of protection against NiV and HeV in experimentally infected animals. We describe here two cross-reactive F-specific antibodies, 1F5 and 12B2, that neutralize NiV and HeV through inhibition of membrane fusion. Cryo-electron microscopy structures reveal that 1F5 and 12B2 recognize distinct prefusion-specific, conserved quaternary epitopes and lock F in its prefusion conformation. We provide proof-of-concept for using antibody cocktails for neutralizing NiV and HeV and define a roadmap for developing effective countermeasures against these highly pathogenic viruses.

Impact of a Diagnosis-Centered Antibiotic Stewardship on Incident Clostridioides difficile Infections in Older Inpatients: An Observational Study.

In 2015, a major increase in incident hospital-onset Clostridioides difficile infections (HO-CDI) in a geriatric university hospital led to the implementation of a diagnosis-centered antibiotic stewardship program (ASP). We aimed to evaluate the impact of the ASP on antibiotic consumption and on HO-CDI incidence. The intervention was the arrival of a full-time infectiologist in the acute geriatric unit in May 2015, followed by the implementation of new diagnostic procedures for infections associated with an antibiotic withdrawal policy. Between 2015 and 2018, the ASP was associated with a major reduction in diagnoses for inpatients (23% to 13% for pneumonia, 24% to 13% for urinary tract infection), while median hospital stays and mortality rates remained stable. The reduction in diagnosed bacterial infections was associated with a 45% decrease in antibiotic consumption in the acute geriatric unit. HO-CDI incidence also decreased dramatically from 1.4‱ bed-days to 0.8‱ bed-days in the geriatric rehabilitation unit. The ASP focused on reducing the overdiagnosis of bacterial infections in the acute geriatric unit was successfully associated with both a reduction in antibiotic use and a clear reduction in the incidence of HO-CDI in the geriatric rehabilitation unit.

An antibody against the F glycoprotein inhibits Nipah and Hendra virus infections.

Nipah virus (NiV) and Hendra virus (HeV) are zoonotic henipaviruses (HNVs) responsible for outbreaks of encephalitis and respiratory illness with fatality rates of 50-100%. No vaccines or licensed therapeutics currently exist to protect humans against NiV or HeV. HNVs enter host cells by fusing the viral and cellular membranes via the concerted action of the attachment (G) and fusion (F) glycoproteins, the main targets of the humoral immune response. Here, we describe the isolation and humanization of a potent monoclonal antibody cross-neutralizing NiV and HeV. Cryo-electron microscopy, triggering and fusion studies show the antibody binds to a prefusion-specific quaternary epitope, conserved in NiV F and HeV F glycoproteins, and prevents membrane fusion and viral entry. This work supports the importance of the HNV prefusion F conformation for eliciting a robust immune response and paves the way for using this antibody for prophylaxis and post-exposure therapy with NiV- and HeV-infected individuals.

Structural and functional analyses reveal promiscuous and species specific use of ephrin receptors by Cedar virus.

Cedar virus (CedV) is a bat-borne henipavirus related to Nipah virus (NiV) and Hendra virus (HeV), zoonotic agents of fatal human disease. CedV receptor-binding protein (G) shares only ∼30% sequence identity with those of NiV and HeV, although they can all use ephrin-B2 as an entry receptor. We demonstrate that CedV also enters cells through additional B- and A-class ephrins (ephrin-B1, ephrin-A2, and ephrin-A5) and report the crystal structure of the CedV G ectodomain alone and in complex with ephrin-B1 or ephrin-B2. The CedV G receptor-binding site is structurally distinct from other henipaviruses, underlying its capability to accommodate additional ephrin receptors. We also show that CedV can enter cells through mouse ephrin-A1 but not human ephrin-A1, which differ by 1 residue in the key contact region. This is evidence of species specific ephrin receptor usage by a henipavirus, and implicates additional ephrin receptors in potential zoonotic transmission.

Yeast AP-1 like transcription factors (Yap) and stress response: a current overview.

Yeast adaptation to stress has been extensively studied. It involves large reprogramming of genome expression operated by many, more or less specific, transcription factors. Here, we review our current knowledge on the function of the eight Yap transcription factors (Yap1 to Yap8) in Saccharomyces cerevisiae, which were shown to be involved in various stress responses. More precisely, Yap1 is activated under oxidative stress, Yap2/Cad1 under cadmium, Yap4/Cin5 and Yap6 under osmotic shock, Yap5 under iron overload and Yap8/Arr1 by arsenic compounds. Yap3 and Yap7 seem to be involved in hydroquinone and nitrosative stresses, respectively. The data presented in this article illustrate how much knowledge on the function of these Yap transcription factors is advanced. The evolution of the Yap family and its roles in various pathogenic and non-pathogenic fungal species is discussed in the last section.

[Quality and determinants of anticoagulation therapy by AVK in elderly subjects: study of a continuous series of 155 patients hospitalized in geriatric medicine]. / Qualité et déterminants de l'équilibre de l'anticoagulation par AVK des sujets âgés : étude d'une série continue de 155 patients hospitalisés en gériatrie aiguë.

AVK could be prescribed in elderly patients over 75 years for the prevention of thromboembolic complications of atrial fibrillation (AF). The objective of this study was to study the quality of the anticoagulation balance by AVK and its determinants. Inclusion of all patients ≥ 75 years of age treated with AVK for an AF hospitalized in the acute geriatric department of the University hospital of Dijon. The balance of the AVK treatment was determined by the input INR and the calculation of the TTR. The last four INRs prior to admission were retrospectively collected for its calculation. Each patient had a standardized geriatric evaluation (EGS): lifestyle, MMSE, nutritional status (albumin), polypathology (Charlson), level of dependence (ADL-IADL). Bleeding complication were collected. 155 patients aged over 75 years (87±5.6 years, 88 women and 67 men) were included. The mean TTR was 55.4±31.2%. Only 46% of patients had a correct TTR (≥ 75%). The balance was significantly worse in women than in men (49.3±29.5 vs 60.1±31.8%; p=0.0326), and in case of haematological pathology (41.7±27.1 vs 57.2± 9.8; p=0.047) but better with high BMI (r=0.416, p=0.001). No EGS parameters were associated with the quality of anticoagulation. The control of AVK therapy is insufficient in geriatric elderly subjects. No modifiable explicative geriatric factor has been identified. If AVK remains a therapeutic option, direct oral anticoaulants should be considered as the first choice.