The prognostic impact of non-driver gene mutations and variant allele frequency in primary myelofibrosis.

Prognostic impact of non-MPN driver gene mutations in primary myelofibrosis. MIPSS70: Mutation-Enhanced International Prognostic Score System.

Azoic sediments and benthic foraminifera: Environmental quality in a subtropical coastal lagoon in the gulf of California.

Marine transitional environments play an important role in human sustainability. Around these ecosystems, coastal lagoons are subject to high anthropogenic pressure from population growth. The increased demand for goods and services is associated with the elevated discharge of untreated and treated wastewater into lagoon systems. The absence of benthic organisms in lagoon environments has been linked to extreme natural conditions and severe anthropogenic impact at both spatial and temporal scales. However, the mechanisms that lead to the presence of azoic sediments in lagoon environments have yet to be studied. This study aimed to determine the vertical variability of textural groups, geochemistry, and benthic foraminiferal fauna to understand how natural and anthropogenic components generate a vertical sediment sequence with low or absent benthic foraminifera in a subtropical coastal lagoon in the southwestern end of the Gulf of California. A 41 cm-long sediment core was collected from La Paz Lagoon at a 1-m depth. The core was sectioned every centimeter, and sediment subsamples were dried and homogenized for grain size, calcium carbonate, elemental and isotopic carbon and nitrogen analyses, and benthic foraminifera quantification. Muds with fine sands towards the core's base characterized the sedimentary sequence. Organic carbon and total nitrogen increased from the base (1.4% and 0.06%, respectively) to the core-top (CT, 3.0% and 0.14%, respectively), significant from the 27 cm interval. Calcium carbonate content was very low (<0.8%). The relationship of δ13C vs. C:N ratio indicated that sedimentary organic carbon was derived from the marine and sewage source mixture. The δ15N of organic matter increased by 3.7‰, starting from the 27 cm interval towards the CT. The nitrogen sewage input source was relatively more significant than nitrogen fixation. The few individuals (<18 ind. in 10 g) and genera (Ammonia and Elphidium), as well as the absence of foraminifera in 19 of 41 intervals in the core, indicated that environmental conditions were unfavorable, even for colonization of environmentally stress-tolerant genera. The frequency of azoic sediments was higher from the 25 cm interval to the CT vs. from the base to the 25 cm interval. Moreover, the AEI revealed severe to moderate hypoxia in the study area. The limited presence of benthic foraminifera and calcium carbonate preservation corroborated that the quality of the lagoon's environment has deteriorated along with population growth, which requires strategic programs to sustain this transitional ecosystem.

Digital Microscopy Augmented by Artificial Intelligence to Interpret Bone Marrow Samples for Hematological Diseases.

Analysis of bone marrow aspirates (BMAs) is an essential step in the diagnosis of hematological disorders. This analysis is usually performed based on a visual examination of samples under a conventional optical microscope, which involves a labor-intensive process, limited by clinical experience and subject to high observer variability. In this work, we present a comprehensive digital microscopy system that enables BMA analysis for cell type counting and differentiation in an efficient and objective manner. This system not only provides an accessible and simple method to digitize, store, and analyze BMA samples remotely but is also supported by an Artificial Intelligence (AI) pipeline that accelerates the differential cell counting process and reduces interobserver variability. It has been designed to integrate AI algorithms with the daily clinical routine and can be used in any regular hospital workflow.

The Association of Genetic Markers Involved in Muscle Performance Responding to Lactate Levels during Physical Exercise Therapy by Nordic Walking in Patients with Long COVID Syndrome: A Nonrandomized Controlled Pilot Study.

Several genetic markers have shown associations with muscle performance and physical abilities, but the response to exercise therapy is still unknown. The aim of this study was to test the response of patients with long COVID through an aerobic physical therapy strategy by the Nordic walking program and how several genetic polymorphisms involved in muscle performance influence physical capabilities. Using a nonrandomized controlled pilot study, 29 patients who previously suffered from COVID-19 (long COVID = 13, COVID-19 = 16) performed a Nordic walking exercise therapy program for 12 sessions. The influence of the ACE (rs4646994), ACTN3 (rs1815739), AMPD1 (rs17602729), CKM (rs8111989), and MLCK (rs2849757 and rs2700352) polymorphisms, genotyped by using single nucleotide primer extension (SNPE) in lactic acid concentration was established with a three-way ANOVA (group × genotype × sessions). For ACE polymorphism, the main effect was lactic acid (p = 0.019). In ACTN3 polymorphism, there were no main effects of lactic acid, group, or genotype. However, the posthoc analysis revealed that, in comparison with nonlong COVID, long COVID increased lactic acid concentrations in Nordic walking sessions in CT and TT genotypes (all p < 0.05). For AMPD1 polymorphism, there were main effects of lactic acid, group, or genotype and lactic acid × genotype or lactic acid × group × genotype interactions (all p < 0.05). The posthoc analysis revealed that, in comparison with nonlong COVID, long COVID increased lactic acid concentrations in Nordic walking sessions in CC and CT genotypes (all p < 0.05). Physical therapy strategy through Nordic walking enhanced physical capabilities during aerobic exercise in post-COVID19 patients with different genotypes in ACTN3 c.1729C>T and AMPD1 c.34C>T polymorphisms. These findings suggest that individuals who reported long COVID who presumably exercised less beforehand appeared to be less able to exercise, based on lactate levels, and the effect of aerobic physical exercise enhanced physical capabilities conditioned by several genetic markers in long COVID patients.

Recent advances in precision medicine for acute myeloid leukemia.

PURPOSE OF REVIEW: Acute myeloid leukemia (AML) is a heterogeneous disease, in which treatment response and patient survival are highly conditioned by the leukemia biology. The aim of this review is to summarize recent advances in AML classification, risk stratification models, measurable residual disease (MRD) and the increasing number of treatment options that are paving the way towards precision medicine in AML. RECENT FINDINGS: AML classification and risk stratification were recently updated by incorporating novel molecular markers that are important for diagnosis and outcome prediction. In addition, the impact of co-mutational patterns is under investigation and novel approaches using machine learning algorithms are starting to be used for individualized risk estimation. Molecular markers are also becoming useful in predicting response to non-intensive treatments. MRD informs of treatment response with high sensitivity, allowing dynamic patient risk assessment and early intervention. Finally, important advances were made in AML therapy, with an increasing number of targeted therapies becoming available and many novel treatment approaches being under development with promising early results. SUMMARY: A better understanding of AML biology is leading to improved risk stratification and important advances in treatments, which are allowing the development of precision medicine in AML at an unprecedented pace.

Intestinal-epithelial LSD1 controls goblet cell maturation and effector responses required for gut immunity to bacterial and helminth infection.

Infectious and inflammatory diseases in the intestine remain a serious threat for patients world-wide. Reprogramming of the intestinal epithelium towards a protective effector state is important to manage inflammation and immunity and can be therapeutically targeted. The role of epigenetic regulatory enzymes within these processes is not yet defined. Here, we use a mouse model that has an intestinal-epithelial specific deletion of the histone demethylase Lsd1 (cKO mice), which maintains the epithelium in a fixed reparative state. Challenge of cKO mice with bacteria-induced colitis or a helminth infection model both resulted in increased pathogenesis. Mechanistically, we discovered that LSD1 is important for goblet cell maturation and goblet-cell effector molecules such as RELMß. We propose that this may be in part mediated by directly controlling genes that facilitate cytoskeletal organization, which is important in goblet cell biology. This study therefore identifies intestinal-epithelial epigenetic regulation by LSD1 as a critical element in host protection from infection.

Philadelphia-negative chronic myeloproliferative neoplasm follow-up: when the phone rings. Changes during the COVID-19 pandemic and patient satisfaction. Experience in 30 health centers in Spain.

The SARS-CoV-2 pandemic has favored the expansion of telemedicine. Philadelphia-negative chronic myeloproliferative neoplasms (Ph-MPN) might be good candidates for virtual follow-up. In this study, we aimed to analyze the follow-up of patients with Ph-MPN in Spain during COVID-19, its effectiveness, and acceptance among patients. We present a multicenter retrospective study from 30 centers. Five hundred forty-one patients were included with a median age of 67 years (yr). With a median follow-up of 19 months, 4410 appointments were recorded. The median of visits per patient was 7 and median periodicity was 2.7 months; significantly more visits and a higher frequency of them were registered in myelofibrosis (MF) patients. 60.1% of visits were in-person, 39.5% were by telephone, and 0.3% were videocall visits, with a predominance of telephone visits for essential thrombocythemia (ET) and polycythemia vera (PV) patients over MF, as well as for younger patients (< 50 yr). The proportion of phone visits significantly decreased after the first semester of the pandemic. Pharmacological modifications were performed only in 25.7% of the visits, and, considering overall management, ET patients needed fewer global treatment changes. Telephone contact effectiveness reached 90% and only 5.4% required a complementary in-person appointment. Although 56.2% of the cohort preferred in-person visits, 90.5% of our patients claimed to be satisfied with follow-up during the pandemic, with an 83% of positive comments. In view of our results, telemedicine has proven effective and efficient, and might continue to play a complementary role in Ph-MPN patients' follow-up.

Predictive Factors and ACE-2 Gene Polymorphisms in Susceptibility to Long COVID-19 Syndrome.

Long COVID-19 syndrome is present in 5-10% of patients infected with SARS-CoV-2, and there is still little information on the predisposing factors that lead to its development. The purpose of the study was to evaluate the predictive factors in early symptoms, clinical features and the role of Angiotensin-Converting Enzyme-2 (ACE-2) c.513-1451G>A (rs2106806) and c.15643279T>C (rs6629110) polymorphisms in the susceptibility to developing Long COVID-19 syndrome subsequent to COVID-19 infectionA total of 29 patients who suffered COVID-19 were recruited in a descriptive longitudinal study of two groups: Long COVID-19 (n = 16) and non-Long COVID-19 (n = 13). Early symptoms and clinical features during COVID-19 were classified by a medical service. ACE-2 polymorphisms were genotyped by using a Single Nucleotide Primer Extension (SNPE). Of the early symptoms, fatigue, myalgia and headache showed a high risk of increasing Long COVID-19 susceptibility. Clinical features such as emergency care, SARS-CoV-2 reinfection, previous diseases, respiratory disease and brain fog also had a high risk of increasing Long COVID-19 susceptibility. The A allele in the rs2106806 variant was associated with an odds ratio (OR) of 4.214 (95% CI 2.521-8.853; p < 0.001), and the T allele in the rs6629110 variant was associated with an OR of 3.754 (95% CI 1.785-6.105; p = 0.002) of increasing Long COVID-19 susceptibility. This study shows the risk of ACE-2 polymorphisms, different early symptoms and clinical features during SARS-CoV-2 infection in susceptibility to Long COVID-19.

[Impact of the COVID-19 pandemic on thoracic surgery training in Spain]. / Impacto de la pandemia por COVID-19 en la formación de los cirujanos torácicos en España.

In the more than 2 years since its emergence, the SARS-CoV-2 pandemic has prompted important changes in healthcare systems and their organization. The aim of this study is to determine the implications in specialized thoracic surgery training as well as the repercussions on thoracic surgery residents. With this objective, the Spanish Society of Thoracic Surgery has conducted a survey among all its trainees and those who had finished their residency during the last 3 years. It consisted of 24 multiple-answer closed questions about the impact of the pandemic on their services, their training, and their personal experience. The response rate was 42% (52 out of a target population of 120). The effect of the pandemic on thoracic surgery services was high or extreme according to 78.8% of the participants. Academic activities were completely cancelled in 42.3% of the cases, and 57.7% of the respondents were required to treat hospitalized COVID patients (25% part-time, and 32.7% full-time). More than 80% of the survey participants believed that changes during the pandemic negatively affected their training, and 36.5% would prefer to extend their training period. In sum, we observe how the pandemic has had deep negative effects on specialized training in thoracic surgery in Spain.

Contribution of APOA5, APOC3, CETP, ABCA1 and SIK3 genetic variants to hypertriglyceridemia development in Mexican HIV-patients receiving antiretroviral therapy.

OBJECTIVE: To investigate the impact of single nucleotide polymorphisms (SNPs) from APOA5, APOC3, CETP, ATP binding cassette transporter A1 and SIK3 genes in the development of hypertriglyceridemia in HIV patients under antiretroviral therapy. MATERIAL AND METHODS: A case-control study was developed. Leukocytic genomic DNA was extracted and genotyping for SNPs rs662799, rs964184, rs5128, rs2854116, rs2854117, rs3764261, rs4149310, rs4149267 and rs139961185 was performed by real time-PCR using TaqMan allelic discrimination assays, in Mexican mestizo patients with HIV infection, with hypertriglyceridemia (>1.7 mmol/L) under antiretroviral therapy. Genetic variants were also investigated in a control group of normolipidemic HIV patients (≤ 1.7 mmol/L). Haplotypes and gene interactions were analyzed. RESULTS: A total of 602 HIV patients were genotyped (316 cases and 286 controls). Age and antiretroviral regimen based on protease inhibitors were associated with hypertriglyceridemia (P = 0.0001 and P = 0.0002. respectively). SNP rs964184 GG genotype in APOA5 gene exhibited the highest association with hypertriglyceridemia risk (OR, 3.2, 95% CI, 1.7-5.8, P = 0.0001); followed by SNP rs139961185 in SIK3 gene (OR = 2.3; (95% CI, 1.1-4.8; P = 0.03 for AA vs. AG genotype; and APOC3 rs5128 GG genotype, (OR, 2.2; 95% CI, 1.1-4.9; P = 0.04) under codominant models. These associations were maintained in the adjusted analysis by age and protease inhibitors based antiretroviral regimens. CONCLUSIONS: This study reveals an association between rs964184 in APOA5; rs5128 in APOC3 and rs139961185 in SIK3 and high triglyceride concentrations in Mexican HIV-patients receiving protease inhibitors. These genetic factors may influence the adverse effects related to antiretroviral therapy.

Nuclear transport and subcellular localization of the dystrophin Dp71 and Dp40 isoforms in the PC12 cell line.

The shortest dystrophins, Dp71 and Dp40, are transcribed from the DMD gene through an internal promoter located in intron 62. These proteins are the main product of the DMD gene in the nervous system and have been involved in various functions related to cellular differentiation and proliferation as well as other cellular processes. Dp71 mRNA undergoes alternative splicing that results in different Dp71 protein isoforms. The subcellular localization of some of these isoforms in the PC12 cell line has been previously reported, and a differential subcellular distribution was observed, which suggests a particular role for each isoform. With the aim of obtaining information on their function, this study identified factors involved in the nuclear transport of Dp71 and Dp40 isoforms in the PC12 cell line. Cell cultures were treated with specific nuclear import/export inhibitors to determine the Dp71 isoform transport routes. The results showed that all isoforms of Dp71 and Dp40 included in the analysis have the ability to enter the cell nucleus through α/ß importin, and the main route of nuclear export for Dp71 isoforms is through the exportin CRM1, which is not the case for Dp40.

Universal Feature of Charged Entanglement Entropy.

Rényi entropies, S_{n}, admit a natural generalization in the presence of global symmetries. These "charged Rényi entropies" are functions of the chemical potential µ conjugate to the charge contained in the entangling region and reduce to the usual notions as µâ†’0. For n=1, this provides a notion of charged entanglement entropy. In this Letter, we prove that for a general d(≥3)-dimensional conformal field theory, the leading correction to the uncharged entanglement entropy across a spherical entangling surface is quadratic in the chemical potential, positive definite, and universally controlled (up to fixed d-dependent constants) by the coefficients C_{J} and a_{2}. These fully characterize, for a given theory, the current correlators ⟨JJ⟩ and ⟨TJJ⟩, as well as the energy flux measured at infinity produced by the insertion of the current operator. Our result is motivated by analytic holographic calculations for a special class of higher-curvature gravities coupled to a (d-2) form in general dimensions as well as for free fields in d=4. A proof for general theories and dimensions follows from previously known universal identities involving the magnetic response of twist operators introduced in A. Belin et al. [J. High Energy Phys. 12 (2013) 059.JHEPFG1029-847910.1007/JHEP12(2013)059] and basic thermodynamic relations.

Interobserver variability of ultrasound measurements for the differential diagnosis of uterine prolapse and cervical elongation without uterine prolapse.

OBJECTIVES: Our study aims to determine the interobserver variability of different ultrasound measurements (pubis-cervix distance, pubis-uterine fundus distance, and pubis-Douglascul-de-sac distance) previously analyzed for the ultrasound differential diagnosis of uterine prolapse (UP) and cervical elongation CE without UP. MATERIALS AND METHODS: We conducted a prospective observational study with 40 patients scheduled to undergo surgical correction of UP and CE without UP. All patients underwent pelvic floor ultrasound examination by an examiner (E1) who acquired ultrasound images. Using these images, E1 measured the distances for the ultrasound differential diagnosis of UP and CE without UP, and these distances were compared with those measured by the other examiner (E2). Values were analyzed by calculating ICCs with 95% CIs. RESULTS: For UP, excellent reliability was obtained for all measurements except the pubis-Douglascul-de-sac measurement at rest, which was moderate (ICC 0.596; p = 0.028) and for the difference between the pubis-Douglascul-de-sac measurement at rest and during the Valsalva maneuver, which was good (ICC 0.691; p < 0.0005). For CE without UP, interobserver reliability was excellent for all measurements analyzed except the pubis-cervix measurement during the Valsalva maneuver, which was moderate (ICC 0.535; p = 0.052) and for the pubis-Douglascul-de-sac measurement at rest, which was good (ICC 0.768; p < 0.0005). CONCLUSIONS: There is excellent interobserver reliability in measurements of the difference in the distance from the pubic symphysis to the uterine fundus at rest and during the Valsalva maneuver for both UP and CE without UP, which are used for the ultrasound differential diagnosis of UP and CE without UP.

Differential diagnosis of middle compartment pelvic organ prolapse with transperineal ultrasound.

INTRODUCTION AND HYPOTHESIS: The objective was to identify the best parameter (pubis-cervix measurement, pubis-uterine fundus measurement or pubis-pouch of Douglas measurement) on transperineal ultrasound, based on the difference between measurements taken at rest and with the Valsalva maneuver, for presurgical differential diagnosis between uterine prolapse (UP) and cervical elongation (CE) without UP. METHODS: A prospective observational study of 60 consecutively recruited patients who underwent corrective surgery of the middle compartment (UP or CE without UP). A transperineal ultrasound was performed, and the descent of the pelvic organ was measured in relation to the posteroinferior margin of the pubis in the midsagittal plane, referencing the uterine fundus, pouch of Douglas and the cervix at rest and with the Valsalva test. RESULTS: Receiver operating characteristic (ROC) curves were constructed for the three evaluated measures, based on the difference between rest and Valsalva, for the diagnosis of UP. For the pubis-cervix distance, an area under the curve (AUC) of 0.59 was obtained; for the pubis-uterine fundus distance, the AUC was 0.81; and for the pubis-pouch of Douglas distance, the AUC was 0.69. Based on the best AUC (the difference in the pubis-uterine fundus distance at rest and with the Valsalva maneuver), a cut-off point of 15 mm was established for the diagnosis of UP (sensitivity: 75%; specificity: 95%; positive predictive value: 86%; and negative predictive value: 89%). CONCLUSION: A difference of ≥15 mm in the pubis-uterine fundus distance at rest and with the Valsalva maneuver is useful for differentiating UP from CE without UP by ultrasound.

Visually guided classification trees for analyzing chronic patients.

BACKGROUND: Chronic diseases are becoming more widespread each year in developed countries, mainly due to increasing life expectancy. Among them, diabetes mellitus (DM) and essential hypertension (EH) are two of the most prevalent ones. Furthermore, they can be the onset of other chronic conditions such as kidney or obstructive pulmonary diseases. The need to comprehend the factors related to such complex diseases motivates the development of interpretative and visual analysis methods, such as classification trees, which not only provide predictive models for diagnosing patients, but can also help to discover new clinical insights. RESULTS: In this paper, we analyzed healthy and chronic (diabetic, hypertensive) patients associated with the University Hospital of Fuenlabrada in Spain. Each patient was classified into a single health status according to clinical risk groups (CRGs). The CRGs characterize a patient through features such as age, gender, diagnosis codes, and drug codes. Based on these features and the CRGs, we have designed classification trees to determine the most discriminative decision features among different health statuses. In particular, we propose to make use of statistical data visualizations to guide the selection of features in each node when constructing a tree. We created several classification trees to distinguish among patients with different health statuses. We analyzed their performance in terms of classification accuracy, and drew clinical conclusions regarding the decision features considered in each tree. As expected, healthy patients and patients with a single chronic condition were better classified than patients with comorbidities. The constructed classification trees also show that the use of antipsychotics and the diagnosis of chronic airway obstruction are relevant for classifying patients with more than one chronic condition, in conjunction with the usual DM and/or EH diagnoses. CONCLUSIONS: We propose a methodology for constructing classification trees in a visually guided manner. The approach allows clinicians to progressively select the decision features at each of the tree nodes. The process is guided by exploratory data analysis visualizations, which may provide new insights and unexpected clinical information.

Neuroglial transmitophagy and Parkinson's disease.

Mitophagy is essential for the health of dopaminergic neurons because mitochondrial damage is a keystone of Parkinson's disease. The aim of the present work was to study the degradation of mitochondria in the degenerating dopaminergic synapse. Adult Sprague-Dawley rats and YFP-Mito-DAn mice with fluorescent mitochondria in dopaminergic neurons were injected in the lateral ventricles with 6-hydroxydopamine, a toxic that inhibits the mitochondrial chain of dopaminergic neurons and blockades the axonal transport. Dopaminergic terminals closest to the lateral ventricle showed an axonal fragmentation and an accumulation of damaged mitochondria in 2-9 µ saccular structures (spheroids). Damaged mitochondria accumulated in spheroids initiated (showing high Pink1, parkin, ubiquitin, p-S65-Ubi, AMBRA1, and BCL2L13 immunoreactivity and developing autophagosomes) but did not complete (mitochondria were not polyubiquitinated, autophagosomes had no STX17, and no lysosomes were found in spheroids) the mitophagy process. Then, spheroids were penetrated by astrocytic processes and DAergic mitochondria were transferred to astrocytes where they were polyubiquitinated (UbiK63+) and linked to mature autophagosomes (STX17+) which became autophagolysosomes (Lamp1/Lamp2 which co-localized with LC3). Present data provide evidence that the mitophagy of degenerating dopaminergic terminals starts in the dopaminergic spheroids and finishes in the surrounding astrocytes (spheroid-mediated transmitophagy). The neuron-astrocyte transmitophagy could be critical for preventing the release of damaged mitochondria to the extracellular medium and the neuro-inflammatory activity which characterizes Parkinson's disease.

A decrease in hepatitis C virus RNA to undetectable levels in chronic hepatitis C patients after PegIFNα + RVB or sofosbuvir + NS5A inhibitor treatment is associated with decreased insulin resistance and persistent oxidative stress.

Oxidative stress (OS) and insulin resistance (IR) induced by hepatitis C virus (HCV) infection, are involved in the development of chronic hepatitis C (CHC) complications and progression to hepatocellular carcinoma. The aim of this study was to investigate the effect of pegylated interferon alpha (IFNα) + ribavirin (PegIFNα+RVB) or sofosbuvir + NS5A inhibitor (SOF+InNS5A) on IR and the components of OS. HCV was genotyped in 20 CHC patients grouped by treatment with either PegIFNα+RVB (n = 10) or SOF+InNS5A (n = 10). The treatment's effect on OS-induced damage to lipids (HNE-HDL), proteins (advanced glycation end products [AGEs]), and DNA (8-OHdG) as well as the concentrations of proinflammatory cytokines (IL-2, TNFα, IFNγ), ALT, AST, GSH and platelets was determined. Superoxide dismutase (SOD) and catalase activity as well as IR, determined by the HOMA1-IR index, was evaluated. The HCV genotypes (GT) found were GT1b (45%), GT1a (30%), GT2b (20%), and GT2a (5%). Viral RNA became undetectable by week 12 with SOF+InNS5A in 100% of the cases and with PegIFNα+RVB in 70% of the cases. After viral RNA became undetectable, regardless of treatment and GT, a significant increase in the platelet concentration and SOD activity was observed, whereas ALT, insulin, and IR decreased (p < 0.05). However, only for the SOF+InNS5A treated group was there an increase in oxidative damage to lipids (p < 0.017) and proteins (p < 0.05). None of the other parameters demonstrated any differences. These data confirm that OS persisted after treatment with either SOF+InNS5A or PegIFNα+RVB. IR could be considered a response biomarker to treatment with direct-acting antivirals.

Comparison of direct sequencing of the NS5B region with the Versant HCV genotype 2.0 assay for genotyping of viral isolates in Mexico.

Hepatitis C virus (HCV) infection affects an estimated 71 million people worldwide. HCV is classified into eight genotypes and >70 subtypes. Determination of HCV genotype is important for selection of type and duration of antiviral therapy, and genotype is also a predictor of treatment response. The most commonly used HCV genotyping method in clinical laboratories is a hybridization-based line probe assay (LiPA; Versant HCV Genotype 2.0). However, these methods have a lack of specificity in genotype identification and subtype assignment. Here, we compared the performance of Versant HCV Genotype 2.0 with the gold standard direct sequencing of the NS5B region, in 97 samples from Mexican patients. We found a genotypic concordance of 63.9% between these methods. While 68 samples (70%) were classified into HCV genotype 1 (GT1) by NS5B sequencing, it was not true for 17 samples (17.5%), which were not match HCV subtype by LiPA. Furthermore, nine of the 33 samples classified by NS5B sequencing as GT1a were not identified by LiPA. Use of direct sequencing could improve selection of the optimal therapy, avoid possible failures of therapy and avoid high costs resulting from incorrect genotyping tests in settings without broad access to pangenotypic regimens.

Portable Ultrasound-Based Device for Detecting Older Adults' Sit-to-Stand Transitions in Unsupervised 30-Second Chair-Stand Tests.

Lower-limb strength is a marker of functional decline in elders. This work studies the feasibility of using the quasi-periodic nature of the distance between a subjects' back and the chair backrest during a 30-s chair-stand test (CST) to carry out unsupervised measurements based on readings from a low-cost ultrasound sensor. The device comprises an ultrasound sensor, an Arduino UNO board, and a Bluetooth module. Sit-to-stand transitions are identified by filtering the signal with a moving minimum filter and comparing the output to an adaptive threshold. An inter-rater reliability (IRR) study was carried out to validate the device ability to count the same number of valid transitions as the gold-standard manual count. A group of elders (age: mean (m) = 80.79 years old, SD = 5.38; gender: 21 female and seven male) were asked to perform a 30-s CST using the device while a trained nurse manually counted valid transitions. Ultimately, a moving minimum filter was necessary to cancel the effect of outliers, likely produced because older people tend to produce more motion artefacts and, thus, noisier signals. While the intra-class correlation coefficient (ICC) for this study was good (ICC = 0.86, 95% confidence interval (CI) = 0.73, 0.93), it is not yet clear whether the results are sufficient to support clinical decision-making.

Tox_(R)CNN: Deep learning-based nuclei profiling tool for drug toxicity screening.

Toxicity is an important factor in failed drug development, and its efficient identification and prediction is a major challenge in drug discovery. We have explored the potential of microscopy images of fluorescently labeled nuclei for the prediction of toxicity based on nucleus pattern recognition. Deep learning algorithms obtain abstract representations of images through an automated process, allowing them to efficiently classify complex patterns, and have become the state-of-the art in machine learning for computer vision. Here, deep convolutional neural networks (CNN) were trained to predict toxicity from images of DAPI-stained cells pre-treated with a set of drugs with differing toxicity mechanisms. Different cropping strategies were used for training CNN models, the nuclei-cropping-based Tox_CNN model outperformed other models classifying cells according to health status. Tox_CNN allowed automated extraction of feature maps that clustered compounds according to mechanism of action. Moreover, fully automated region-based CNNs (RCNN) were implemented to detect and classify nuclei, providing per-cell toxicity prediction from raw screening images. We validated both Tox_(R)CNN models for detection of pre-lethal toxicity from nuclei images, which proved to be more sensitive and have broader specificity than established toxicity readouts. These models predicted toxicity of drugs with mechanisms of action other than those they had been trained for and were successfully transferred to other cell assays. The Tox_(R)CNN models thus provide robust, sensitive, and cost-effective tools for in vitro screening of drug-induced toxicity. These models can be adopted for compound prioritization in drug screening campaigns, and could thereby increase the efficiency of drug discovery.