Miracle-dz/UniFAR-FTUs huggingface dataset:
Label-free chemical imaging flow cytometry by high-speed multicolor stimulated Raman scattering

Significance Imaging flow cytometry is a powerful tool for analyzing every single cell in a large heterogeneous population but relies on fluorescent labeling, which comes with cytotoxicity, nonspecific binding, and interference with natural cellular functions. This paper presents label-free multicolor chemical imaging flow cytometry based on stimulated Raman scattering (SRS), a highly sensitive method of molecular vibrational spectroscopy. With the help of deep learning, it demonstrates high-precision characterization and classification of microalgal cells and cancer cells without the need for fluorescent labeling. Combining the strength of flow cytometry with fluorescence imaging and digital image analysis, imaging flow cytometry is a powerful tool in diverse fields including cancer biology, immunology, drug discovery, microbiology, and metabolic engineering. It enables measurements and statistical analyses of chemical, structural, and morphological phenotypes of numerous living cells to provide systematic insights into biological processes. However, its utility is constrained by its requirement of fluorescent labeling for phenotyping. Here we present label-free chemical imaging flow cytometry to overcome the issue. It builds on a pulse pair-resolved wavelength-switchable Stokes laser for the fastest-to-date multicolor stimulated Raman scattering (SRS) microscopy of fast-flowing cells on a 3D acoustic focusing microfluidic chip, enabling an unprecedented throughput of up to ∼140 cells/s. To show its broad utility, we use the SRS imaging flow cytometry with the aid of deep learning to study the metabolic heterogeneity of microalgal cells and perform marker-free cancer detection in blood.
Opportunities and challenges using non-targeted methods for food fraud detection.

In recent years, non-targeted methods have been a popular "buzz" phrase in food fraud detection. Using analytical instrumentation techniques, non-targeted methods have been developed and applied in many food and agricultural situations. However, confusion and misstatements remain regarding how the methods are used. This perspective will discuss the definitions related to non-targeted testing, the procedure of developing and validating methods, the techniques and data analysis, and opportunities and challenges regarding the use of this class of analytical methods. The article seeks to provide readers with the latest information regarding recent advances in the use of non-targeted methods.
Knowledge engineering in adaptive interface and user modeling

This chapter presents the issues of user modeling and its role in adaptive humancomputer interface (HCI). Particularly, it focuses on knowledge acquisition and representation in user modeling. Several related problems in the traditional user modeling systems are also identified and discussed. ADAPTIVE INTERFACE AND USER MODELING The concept of an adaptive human-computer interface (HCI) has been recognized as a very promising and challenging area for both research and applications (Norcio and Stanley, 1989). The objective of an adaptive interface is to adapt system responses to the user effectively in a complex computer-based task. In the context of human computer interaction, the relationship between a human and a computer involves many factors such as the computing environment, the nature of the tasks to be performed, as well as various characteristics of the users. The effectiveness of a human-computer interface system is influenced greatly by its ability to adapt to these factors. As the functionality of computer systems becomes more complex and users’ tasks vary, users must adjust their behavior and problem solving strategies to the systems. This situation is often made worse because users lack the knowledge and experience to be effective. A well-designed interface can provide much more helpful information in a more appropriate manner during the interaction, especially for those users who have limited experiences. Therefore, an adaptive interface is not only beneficial for users but also for system resources management since the tasks and the related resources are better allocated between user and the computer. Generally, an adaptive interface should be able to offer an effective interaction and allocate tasks dynamically between the user and the computer system. It is not unusual that users are frequently confronted with an overwhelming amount of information in interacting with computers. Users must decide what information to request and use. In these situations, it has been found that users do not usually perform optimally (Card, Moran and Newell, 1983). In addition, users may not have the necessary information or expertise to adjust their
Positional effect of preoperative neuronavigational magnetic resonance image on accuracy of posterior fossa lesion localization.

OBJECTIVE The aim of this study was to analyze the positional effect of MRI on the accuracy of neuronavigational localization for posterior fossa (PF) lesions when the operation is performed with the patient in the prone position. METHODS Ten patients with PF tumors requiring surgery in the prone position were prospectively enrolled in the study. All patients underwent preoperative navigational MRI in both the supine and prone positions in a single session. Using simultaneous intraoperative registration of the supine and prone navigational MR images, the authors investigated the images' accuracy, spatial deformity, and source of errors for PF lesions. Accuracy was determined in terms of differences in the ability of the supine and prone MR images to localize 64 test points in the PF by using a neuronavigation system. Spatial deformities were analyzed and visualized by in-house-developed software with a 3D reconstruction function and spatial calculation of the MRI data. To identify the source of differences, the authors investigated the accuracy of fiducial point localization in the supine and prone MR images after taking the surface anatomy and age factors into consideration. RESULTS Neuronavigational localization performed using prone MRI was more accurate for PF lesions than routine supine MRI prior to prone position surgery. Prone MRI more accurately localized 93.8% of the tested PF areas than supine MRI. The spatial deformities in the neuronavigation system calculated using the supine MRI tended to move in the posterior-superior direction from the actual anatomical landmarks. The average distance of the spatial differences between the prone and supine MR images was 6.3 mm. The spatial difference had a tendency to increase close to the midline. An older age (> 60 years) and fiducial markers adjacent to the cervical muscles were considered to contribute significantly to the source of differences in the positional effect of neuronavigation (p < 0.001 and p = 0.01, respectively). CONCLUSIONS This study demonstrated the superior accuracy of neuronavigational localization with prone-position MRI during prone-position surgery for PF lesions. The authors recommend that the scan position of the neuronavigational MRI be matched with the surgical position for more precise localization.
Type 2 diabetes causes skeletal muscle atrophy but does not impair resistance training‐mediated myonuclear accretion and muscle mass gain in rats

What is the central question of this study? Type 2 diabetes mellitus (T2DM) causes skeletal muscle atrophy; does it affect resistance training (RT)‐mediated molecular adaptations and subsequent muscle hypertrophy? What is the main finding and its importance? Although skeletal muscle mass and regulation were not preserved under conditions of T2DM, the response of RT‐induced skeletal muscle hypertrophy was not impaired in T2DM rat skeletal muscle. These findings suggest that the capacity of RT‐mediated muscle mass gain is not diminished in the T2DM condition.
Role of Ultrasound in Evaluation of Undifferentiated Shock in ICU Settings.

Objective To classify shock, using ultrasonography as the modality of choice for imaging and to assess the diagnostic accuracy of ultrasound as a tool to classify shock. Design Prospective study. Setting KEM Hospital, Pune in the ICU (Intensive care unit). Study Population 100 patients admitted to the ICU with undifferentiated shock. Methods Bedside ultrasound examination was performed within 1 hour of admission to the ICU. These patients were also evaluated clinically and biochemically to confirm the type of shock. All patients immediately received standard diagnostic emergent interventions including physical examination, intravenous access for whole blood assays, arterial gas analysis, electrocardiography, continuous cardiac monitoring, supplemental oxygen and chest radiograph. Clinical parameters, urine output, ECG and biochemical tests were performed within 12 hours of USG. Additional investigations were performed wherever required. The ultrasonographic diagnoses were compared with the respective final clinical diagnoses by employing the Cohen kappa inter-rater coefficient of agreement. In addition, various ultrasound parameters were also analyzed to assess the best predictors for each type of shock. Results The ultrasound diagnosis showed an overall good agreement (Cohen's kappa coefficient > or = 0.6) with the final clinical diagnosis, in identifying the type of shock, in the emergency setting, when ultrasound was done within 1 hour after admission to the ICU. In our study, ultrasound showed maximum sensitivity, specificity, negative and positive predictive values in the setting of obstructive shock. In addition, perfect agreement was seen between the ultrasound and clinical diagnosis, with a Cohen kappa coefficient of 1 in obstructive shock. The least sensitivity, specificity, negative and positive predictive values of ultrasound were seen in the setting of distributive shock. Least agreement between the ultrasound and clinical diagnosis was also seen in distributive shock, as most ultrasound findings were found to overlap with those in the other types of shock. (Cohen kappa coefficient of 0.6). Conclusion Ultrasonography carried out within 1 hour of admission to the ICU plays a major role in correct diagnosis of the type of shock and subsequent patient management. The best ultrasonographic predictors for diagnosis of each type of shock, can help the clinician to start timely specific interventions in critical care settings for each type of shock.
Characterization of acute TLR-7 agonist-induced hemorrhagic myocarditis in mice by multiparametric quantitative cardiac magnetic resonance imaging

ABSTRACT Hemorrhagic myocarditis is a potentially fatal complication of excessive levels of systemic inflammation. It has been reported in viral infection, but is also possible in systemic autoimmunity. Epicutaneous treatment of mice with the Toll-like receptor 7 (TLR-7) agonist Resiquimod induces auto-antibodies and systemic tissue damage, including in the heart, and is used as an inducible mouse model of systemic lupus erythematosus (SLE). Here, we show that overactivation of the TLR-7 pathway of viral recognition by Resiquimod treatment of CFN mice induces severe thrombocytopenia and internal bleeding, which manifests most prominently as hemorrhagic myocarditis. We optimized a cardiac magnetic resonance (CMR) tissue mapping approach for the in vivo detection of diffuse infiltration, fibrosis and hemorrhages using a combination of T1, T2 and T2* relaxation times, and compared results with ex vivo histopathology of cardiac sections corresponding to CMR tissue maps. This allowed detailed correlation between in vivo CMR parameters and ex vivo histopathology, and confirmed the need to include T2* measurements to detect tissue iron for accurate interpretation of pathology associated with CMR parameter changes. In summary, we provide detailed histological and in vivo imaging-based characterization of acute hemorrhagic myocarditis as an acute cardiac complication in the mouse model of Resiquimod-induced SLE, and a refined CMR protocol to allow non-invasive longitudinal in vivo studies of heart involvement in acute inflammation. We propose that adding T2* mapping to CMR protocols for myocarditis diagnosis improves diagnostic sensitivity and interpretation of disease mechanisms. This article has an associated First Person interview with the first author of the paper. Summary: The authors present a mouse model of acute hemorrhagic myocarditis and a refined technique of preclinical cardiac MR imaging to allow non-invasive detection of diffuse myocardial tissue damage accounting for iron deposition.
Inter- and Intra-Individual Differences in EMG and MMG during Maximal, Bilateral, Dynamic Leg Extensions

The purpose of this study was to compare the composite, inter-individual, and intra-individual differences in the patterns of responses for electromyographic (EMG) and mechanomyographic (MMG) amplitude (AMP) and mean power frequency (MPF) during fatiguing, maximal, bilateral, and isokinetic leg extension muscle actions. Thirteen recreationally active men (age = 21.7 ± 2.6 years; body mass = 79.8 ± 11.5 kg; height = 174.2 ± 12.7 cm) performed maximal, bilateral leg extensions at 180°·s−1 until the torque values dropped to 50% of peak torque for two consecutive repetitions. The EMG and MMG signals from the vastus lateralis (VL) muscles of both limbs were recorded. Four 2(Leg) × 19(time) repeated measures ANOVAs were conducted to examine mean differences for EMG AMP, EMG MPF, MMG AMP, and MMG MPF between limbs, and polynomial regression analyses were performed to identify the patterns of neuromuscular responses. The results indicated no significant differences between limbs for EMG AMP (p = 0.44), EMG MPF (p = 0.33), MMG AMP (p = 0.89), or MMG MPF (p = 0.52). Polynomial regression analyses demonstrated substantial inter-individual variability. Inferences made regarding the patterns of neuromuscular responses to fatiguing and bilateral muscle actions should be considered on a subject-by-subject basis.
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases

Abstract Community biological databases provide an important online resource for both public and private data, analysis tools and community engagement. These sites house genomic, transcriptomic, genetic, breeding and ancillary data for specific species, families or clades. Due to the complexity and increasing quantities of these data, construction of online resources is increasingly difficult especially with limited funding and access to technical expertise. Furthermore, online repositories are expected to promote FAIR data principles (findable, accessible, interoperable and reusable) that presents additional challenges. The open-source Tripal database toolkit seeks to mitigate these challenges by creating both the software and an interactive community of developers for construction of online community databases. Additionally, through coordinated, distributed co-development, Tripal sites encourage community-wide sustainability. Here, we report the release of Tripal version 3 that improves data accessibility and data sharing through systematic use of controlled vocabularies (CVs). Tripal uses the community-developed Chado database as a default data store, but now provides tools to support other data stores, while ensuring that CVs remain the central organizational structure for the data. A new site developer can use Tripal to develop a basic site with little to no programming, with the ability to integrate other data types using extension modules and the Tripal application programming interface. A thorough online User’s Guide and Developer’s Handbook are available at http://tripal.info, providing download, installation and step-by-step setup instructions.
Is Two Better Than One? The Impact of Doubling Training Volume in Severe COPD: A Randomized Controlled Study

Patients with severe chronic obstructive pulmonary disease (COPD) are unable to exercise at high intensities for sufficiently long periods of time to obtain true physiological training effects. It therefore appears sensible to increase training duration at sub-maximal exercise intensities to optimize the benefit of exercise training. We compared the effects on exercise tolerance of two endurance cycloergometer submaximal exercise protocols with different cumulative training loads (one (G1) versus two (G2) daily 40 min training sessions) both implemented over 20 consecutive days in 149 patients with COPD (forced expiratory volume at first second (FEV1): 39% predicted) admitted to an inpatient pulmonary rehabilitation program. Patients in G2 exhibited greater improvement (p = 0.011) in submaximal endurance time (from 258 (197) to 741 (662) sec) compared to G1 (from 303 (237) to 530 (555) sec). Clinically meaningful improvements in health-related quality of life, 6MWT, and chronic dyspnea were not different between groups. Doubling the volume of endurance training is feasible and can lead to an additional benefit on exercise tolerance. Future studies may investigate the applicability and benefits of this training strategy in the outpatient or community-based pulmonary rehabilitation settings to amplify the benefits of exercise interventions.
E/a′ ratio is closely related to pulmonary vein flow profile in patients with normal ejection fraction

Abstract Objectives. To compare the ability of the E/a′ ratio and the recommended diastolic parameters in the American Society of Echocardiography (ASE) and the European Association of Cardiovascular Imaging (EACVI), in predicting a dominant diastolic pulmonary vein flow in patients with normal ejection fraction. Design. We retrospectively evaluated the diastolic function according to the ASE/EACVI guidelines, the S/D ratio and the septal, lateral and average E/a′ ratio in 293 unselected in-hospital patients, aged 39–86 years, in sinus rhythm and with no or mild valve disease, having a normal systolic function (EF > 50%). Results. The S/D ratio had a positive association to septal, lateral and average E/a ratio (R2 = 0.25, 0.35 and 0.32). The association to average E/e′ ratio, LA vol index and TR velocity was weak (R2 = 0.037, 0.033 and 0.087) and for e′ velocity negatively. In patients with S/D ratio <1, septal, lateral, average E/a′ ratio, average E/e ratio, LA vol index (p<.001) and TR velocity (p<.05) were significantly higher compared to patients with S/D ratio ≥1. No significant difference was seen in e′ velocity. The septal, lateral and average E/a′ ratio were significantly higher in patients with S/D ratio <1 regardless a normal or impaired diastolic function according to the ASE/EACVI guidelines (p<.001). The ASE/EACVI algorithm detected 21 patients with S/D ratio <1 compared to 28 patients using average E/a′ ratio with cut-off >14. Conclusion: E/a′ ratio might be a useful new diastolic parameter in patients with a normal ejection fraction as it is more closely related to the S/D ratio than the established ASE/EACVI diastolic parameters.
Subclinical atrial fibrillation detection with a floating atrial sensing dipole in single lead implantable cardioverter‐defibrillator systems: Results of the SENSE trial

Subclinical atrial fibrillation (AF), in the form of cardiac implantable device‐detected atrial high rate episodes (AHREs), has been associated with increased thromboembolism. An implantable cardioverter‐defibrillator (ICD) lead with a floating atrial dipole may permit a single lead (DX) ICD system to detect AHREs. We sought to assess the utility of the DX ICD system for subclinical AF detection in patients, with a prospective multicenter, cohort‐controlled trial.
The Role of Electrochemical Immunosensors in Clinical Analysis

An immunosensor is a kind of affinity biosensor based on interactions between an antigen and specific antigen immobilized on a transducer surface. Immunosensors possess high selectivity and sensitivity due to the specific binding between antibody and corresponding antigen, making them a suitable platform for several applications especially in the medical and bioanalysis fields. Electrochemical immunosensors rely on the measurements of an electrical signal recorded by an electrochemical transducer and can be classed as amperometric, potentiometric, conductometric, or impedimetric depending on the signal type. Among the immunosensors, electrochemical immunosensors have been more perfected due to their simplicity and, especially their ability to be portable, and for in situ or automated detection. This review addresses the potential of immunosensors destined for application in clinical analysis, especially cancer biomarker diagnosis. The emphasis is on the approaches used to fabricate electrochemical immunosensors. A general overview of recent applications of the developed electrochemical immunosensors in the clinical approach is described.
Magnetospheric Multiscale Observations of Electron Vortex Magnetic Hole in the Turbulent Magnetosheath Plasma

We report on the observations of an electron vortex magnetic hole corresponding to a new type of coherent structure in the turbulent magnetosheath plasma using the Magnetospheric Multiscale mission data. The magnetic hole is characterized by a magnetic depression, a density peak, a total electron temperature increase (with a parallel temperature decrease but a perpendicular temperature increase), and strong currents carried by the electrons. The current has a dip in the core region and a peak in the outer region of the magnetic hole. The estimated size of the magnetic hole is about 0.23 ρi (∼30 ρe) in the quasi-circular cross-section perpendicular to its axis, where ρi and ρe are respectively the proton and electron gyroradius. There are no clear enhancements seen in high-energy electron fluxes. However, there is an enhancement in the perpendicular electron fluxes at 90° pitch angle inside the magnetic hole, implying that the electrons are trapped within it. The variations of the electron velocity components Vem and Ven suggest that an electron vortex is formed by trapping electrons inside the magnetic hole in the cross-section in the M–N plane. These observations demonstrate the existence of a new type of coherent structures behaving as an electron vortex magnetic hole in turbulent space plasmas as predicted by recent kinetic simulations.
Development of a humanized murine model for the study of Oxalobacter formigenes intestinal colonization.

BACKGROUND Oxalobacter formigenes are bacteria that colonize the human gut and degrade oxalate, a component of most kidney stones. Clinical and epidemiological studies suggest that O. formigenes colonization reduces the risk for kidney stones. We sought to develop murine models to allow investigating O. formigenes in the context of its native human microbiome.For humanization, we transplanted pooled feces from healthy, non-colonized human donors supplemented with a human O. formigenes strain into recipient mice. We compared transplanting microbiota into mice that were either treated with broad-spectrum antibiotics to suppress their native microbiome, or were germ-free, or received humanization without pre-treatment or received a sham gavage (controls). RESULTS All humanized mice were stably colonized with O. formigenes through 8 weeks post-gavage, whereas mice receiving sham gavage remained uncolonized (p<0.001). Humanization significantly changed the murine intestinal microbial community structure (p<0.001) with humanized germ-free and antibiotic-treated groups overlapping in β-diversity. Both the germ-free and antibiotic-treated mice had significantly increased numbers of human species compared to sham-gavaged mice (p<0.001). CONCLUSIONS Transplanting mice with human feces and O. formigenes introduced new microbial populations resembling the human microbiome, with stable O. formigenes colonization; such models can define optimal O. formigenes strains to facilitate clinical trials.