Miracle-dz/UniFAR-FTUs huggingface dataset:
Agreement and reliability of lower limb muscle architecture measurements using a portable ultrasound device

High end ultrasonography devices lack in portability and are expensive. We investigated the agreement and reliability of a handheld and portable ultrasound system for human lower limb muscle architecture measurements. We captured ultrasound images of the rectus femoris (RF), vastus lateralis (VL) and gastrocnemius medialis (GM) in 36 active healthy participants (15 female, 21 male) at 50% of muscle length using the handheld Lumify (L12-4, linear-array 37 mm, Philips Healthcare, Amsterdam, Netherlands) and a high-end laboratory device (ACUSON Juniper, linear-array 54 mm, 12L3, SIEMENS Healthineers, Erlangen, Germany). We compared measurements of muscle fascicle length, pennation angle and thickness. To assess inter-session reliability of the Lumify system, participants were measured twice within 1 week. Comparing RF architecture measurements of both devices resulted in intra-class correlations (ICCs) ranging from 0.46–0.82 and standardized mean difference (SMDs) ranging from −0.45–0.05. For VL, ICCs ranged from 0.60–0.89 and SMDs ranged from −0.11–0.13. ICCs and SMDs for the GM ranged from 0.82–0.86 and −0.07–0.07. Calculating inter-session reliability for RF resulted in ICCs ranging from 0.44–0.76 and SMDs ranging from −0.38–0.15. For VL, ICCs and SMDs ranged from 0.57–0.75 and −0.13–0.02. ICCs for GM ranged from 0.75–0.92 and SMDs ranged from −0.15–0.16. Measurement of muscle thickness demonstrated the highest agreement (ICC ≥0.82) and reliability (ICC ≥0.75) across all muscles. The Lumify system was comparable to a high-end device and reliable for GM measurements. However, agreement and reliability were lower for the RF and VL. Of all evaluated architectural parameters, muscle thickness exhibited highest agreement and reliability.
An internet based virtual reality intervention for preventing posttraumatic stress disorder

Introduction: Research examining the prevention of Posttraumatic Stress Disorder (PTSD) has shown that selective treatments to those with high symptom levels, using trauma focused CBT are relatively successful in reducing symptoms and preventing chronic PTSD. However, uptake of these early treatments is often low. This study aimed to provide an internet based Virtual Reality treatment to overcome some of these barriers to early treatment. Method: The study received IRB approval from Hadassah Hospital (HMO 0056-013); its ClinicalTrials.gov identifier is NCT01760213. Recent survivors of motor vehicle accidents (N = 1,500) were assessed by telephone and online questionnaires. Patients meeting study criteria were randomly assigned to a Virtual Reality internet-based trauma-focused cognitive behavioral therapy (CBT) or waitlist control. Results: the majority of subjects recruited did not meet study criteria or were unwilling to participate. 14 subjects were randomly assigned to treatment or waitlist control. Results indicate that both groups show a decline in PTSD symptoms at follow up, with no significant differences between groups. Discussion: prevention of PTSD is a challenging goal, and internet-based interventions may play a role in this. The current study was not able to recruit sufficient participants to draw conclusions regarding the efficacy of the treatment. Proving services via the internet may not reduce barriers to care in this population. Clinical Trial Registration: https://clinicaltrials.gov/ct2/show/NCT01760213? term=Freedman&cond=PTSD&cntry=IL&draw=2&rank=2, identifier NCT01760213.
Characterization and comparison of novel adjuvants for a prefusion clamped MERS vaccine

Various chemical adjuvants are available to augment immune responses to non-replicative, subunit vaccines. Optimized adjuvant selection can ensure that vaccine-induced immune responses protect against the diversity of pathogen-associated infection routes, mechanisms of infectious spread, and pathways of immune evasion. In this study, we compare the immune response of mice to a subunit vaccine of Middle Eastern respiratory syndrome coronavirus (MERS-CoV) spike protein, stabilized in its prefusion conformation by a proprietary molecular clamp (MERS SClamp) alone or formulated with one of six adjuvants: either (i) aluminium hydroxide, (ii) SWE, a squalene-in-water emulsion, (iii) SQ, a squalene-in-water emulsion containing QS21 saponin, (iv) SMQ, a squalene-in-water emulsion containing QS21 and a synthetic toll-like receptor 4 (TLR4) agonist 3D-6-acyl Phosphorylated HexaAcyl Disaccharide (3D6AP); (v) LQ, neutral liposomes containing cholesterol, 1.2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and QS21, (vi) or LMQ, neutral liposomes containing cholesterol, DOPC, QS21, and 3D6AP. All adjuvanted formulations induced elevated antibody titers which where greatest for QS21-containing formulations. These had elevated neutralization capacity and induced higher frequencies of IFNƔ and IL-2-producing CD4+ and CD8+ T cells. Additionally, LMQ-containing formulations skewed the antibody response towards IgG2b/c isotypes, allowing for antibody-dependent cellular cytotoxicity. This study highlights the utility of side-by-side adjuvant comparisons in vaccine development.
Role of lipidomics in assessing the functional lipid composition in breast milk

Breast milk is the ideal source of nutrients for infants in early life. Lipids represent 2–5% of the total breast milk composition and are a major energy source providing 50% of an infant’s energy intake. Functional lipids are an emerging class of lipids in breast milk mediating several different biological functions, health, and developmental outcome. Lipidomics is an emerging field that studies the structure and function of lipidome. It provides the ability to identify new signaling molecules, mechanisms underlying physiological activities, and possible biomarkers for early diagnosis and prognosis of diseases, thus laying the foundation for individualized, targeted, and precise nutritional management strategies. This emerging technique can be useful to study the major role of functional lipids in breast milk in several dimensions. Functional lipids are consumed with daily food intake; however, they have physiological benefits reported to reduce the risk of disease. Functional lipids are a new area of interest in lipidomics, but very little is known of the functional lipidome in human breast milk. In this review, we focus on the role of lipidomics in assessing functional lipid composition in breast milk and how lipid bioinformatics, a newly emerging branch in this field, can help to determine the mechanisms by which breast milk affects newborn health.
Microbial community structure and shift pattern of industry brine after a long-term static storage in closed tank

Brine from Dingyuan Salt Mine (Anhui, China), an athalassohaline hypersaline environment formed in the early tertiary Oligocene, is used to produce table salt for hundreds of millions of people. However, halophiles preserved in this niche during deposition are still unknown. Here, we employed cultivation and high-throughput sequencing strategies to uncover the microbial community and its shift after a long-term storage in the brine collected from Dingyuan Salt Mine. High-throughput sequencing showed (1) in the fresh brine (2021), Cyanobium_stocktickerPCC-6307 spp. (8.46%), Aeromonas spp. (6.91%) and Pseudomonas spp. (4.71%) are the dominant species in bacteria while Natronomonas spp. (18.89%), Halapricum spp. (13.73%), and Halomicrobium spp. (12.35%) in archaea; (2) after a 3-year-storage, Salinibacter spp. (30.01%) and Alcanivorax spp. (14.96%) surpassed Cyanobium_stocktickerPCC-6307 spp. (8.46%) becoming the dominant species in bacteria; Natronomonas spp. are still the dominant species, while Halorientalis spp. (14.80%) outnumbered Halapricum spp. becoming the dominant species in archaea; (3) Alcanivorax spp. and Halorientalis spp. two hydrocarbons degrading microorganisms were enriched in the brine containing hydrocarbons. Cultivation using hypersaline nutrient medium (20% NaCl) combined with high-throughput 16S rRNA gene sequencing showed that (1) the biomass significantly increased while the species diversity sharply declined after a 3-year-storage; (2) Halorubrum spp. scarcely detected from the environment total stocktickerDNA were flourishing after cultivation using AS-168 or NOM medium; (3) twelve possible new species were revealed based on almost full-length 16S rRNA gene sequence similarity search. This study generally uncovered the microbial community and the dominant halophiles in this inland athalassohaline salt mine, and provided a new insight on the shift pattern of dominant halophiles during a long-term storage, which illustrated the shaping of microorganisms in the unique environment, and the adaptation of microbe to the specific environment.
Computational study on the binding of Mango-II RNA aptamer and fluorogen using the polarizable force field AMOEBA

Fluorescent light-up aptamers (FLAPs) are well-performed biosensors for cellular imaging and the detection of different targets of interest, including RNA, non-nucleic acid molecules, metal ions, and so on. They could be easily designed and emit a strong fluorescence signal once bound to specified fluorogens. Recently, one unique aptamer called Mango-II has been discovered to possess a strong affinity and excellent fluorescent properties with fluorogens TO1-Biotin and TO3-Biotin. To explore the binding mechanisms, computational simulations have been performed to obtain structural and thermodynamic information about FLAPs at atomic resolution. AMOEBA polarizable force field, with the capability of handling the highly charged and flexible RNA system, was utilized for the simulation of Mango-II with TO1-Biotin and TO3-Biotin in this work. The calculated binding free energy using published crystal structures is in excellent agreement with the experimental values. Given the challenges in modeling complex RNA dynamics, our work demonstrates that MD simulation with a polarizable force field is valuable for understanding aptamer-fluorogen binding and potentially designing new aptamers or fluorogens with better performance.
A versatile toolkit for overcoming AAV immunity

Recombinant adeno-associated virus (AAV) is a promising delivery vehicle for in vivo gene therapy and has been widely used in >200 clinical trials globally. There are already several approved gene therapy products, e.g., Luxturna and Zolgensma, highlighting the remarkable potential of AAV delivery. In the past, AAV has been seen as a relatively non-immunogenic vector associated with low risk of toxicity. However, an increasing number of recent studies indicate that immune responses against AAV and transgene products could be the bottleneck of AAV gene therapy. In clinical studies, pre-existing antibodies against AAV capsids exclude many patients from receiving the treatment as there is high prevalence of antibodies among humans. Moreover, immune response could lead to loss of efficacy over time and severe toxicity, manifested as liver enzyme elevations, kidney injury, and thrombocytopenia, resulting in deaths of non-human primates and patients. Therefore, extensive efforts have been attempted to address these issues, including capsid engineering, plasmapheresis, IgG proteases, CpG depletion, empty capsid decoy, exosome encapsulation, capsid variant switch, induction of regulatory T cells, and immunosuppressants. This review will discuss these methods in detail and highlight important milestones along the way.
How does political discussion frequency impact political moral opinions? The moral argument theory of opinion dynamics

Discussions of political issues may influence people's opinions. Is there any systematic difference in opinions between those who discuss frequently and those who do not? We measured the association between self-reported discussion frequency and the probability of holding the more liberal opinion on moral issues, using data from the General Social Survey (81 issues, n = 4,395) and the American National Election Studies (27 issues, n = 17,653). This association looked different among liberals and among conservatives. Having more frequent discussions is associated with a higher probability of holding more liberal opinions among liberals, while there is little association between discussion frequency and opinions among conservatives. These findings can be explained by the moral argument theory, which is an account of the long-term liberalization of public opinion on moral issues as an outcome of repeated discussions. The key assumption of this theory is that opinions that are justified by the kinds of arguments that only conservatives accept have a disadvantage compared to opinions that are justified by the kinds of arguments that everyone accepts. Consistent with this theory, we find that the effect of discussion frequency is stronger for moral opinions that have a bigger argument advantage.
Searching for Gravitational Waves from Compact Binary Coalescence Using LIGO and Virgo Data

This thesis describes current efforts to search for gravitational waves from compact binary coalescences (CBCs) by the LIGO Scientific Collaboration (LSC) and the Virgo Collaboration. We briefly review the physics of gravitational-wave emission and detection, describing how gravitational waves are emitted from “inspiraling” compact stellar mass objects and how the LSC and Virgo try to detect them using interferometers. Next we review the data-analysis principles used to search for potential signals in the detectors’ noise. These principles are employed by “ihope,” which is the dataanalysis pipeline used to search for CBCs. We describe each step in this pipeline and discuss how interferometer data is stored and examined. Next we present the results from a six-month long search which occurred in early 2007, during LIGO’s fifth science run. This is followed by details of tuning studies carried out on LIGO’s sixth-, and Virgo’s secondand third-, science runs (S6, VSR2, and VSR3), which ran from July 2009 to October 2010. No gravitational waves were detected in these searches. A “blind injection” was performed during S6/VSR3 and detected by our pipeline, however. We detail studies into assigning a statistical significance to this injection. Next we use these studies to show that we can expect to detect gravitational waves with high significance using two detectors in the advanced detector era. Finally, we review some future developments for the CBC pipeline currently being undertaken. SEARCHING FOR GRAVITATIONAL WAVES FROM COMPACT BINARY COALESCENCE USING LIGO AND VIRGO DATA
Pediatric eosinophilic esophagitis outcomes vary with co-morbid eczema and pollen food syndrome

Background Eosinophilic esophagitis (EoE) is a chronic immune-mediated inflammatory disease characterized by eosinophil inflammation of the esophagus. It has been described as a component of the Allergic March and is often seen with other atopic diseases. Some atopic diseases, including asthma, are known to be heterogenous with endotypes that guide treatment. Similarly, we propose that EoE is a heterogenous disease with varying phenotypes and endotypes that might impact response to therapy. Methods A single-center retrospective review of pediatric patients ≤18 years of age diagnosed with EoE was conducted. All gastrointestinal clinic visits and esophagogastroduodenoscopies (EGD) from disease presentation through the first three years after diagnosis were reviewed. Histologic remission rate and therapies utilized [proton pump inhibitor (PPI), topical steroid, dietary elimination] were assessed. Results One hundred and thirty-seven patients were included, 80% of whom had at least one concurrent atopic condition at diagnosis, with food allergies being the most common (57%) followed by eczema (34%), and asthma (29%). The remission rate of the overall cohort was 65%, and by concurrent allergy, comorbid pollen food syndrome and eczema had the highest remission rates at 100% and 81%, respectively followed by asthma (62%), food allergies (62%), seasonal allergic rhinitis (60%), and history of anaphylaxis (56%). Kaplan-Meier curves for each atopic condition show that patients with eczema and pollen food syndrome achieve histologic remission faster than those without. All treatment modalities were more successful in patients with eczema than those without, and PPI was most effective treatment at inducing remission. Conclusions In a real-world pediatric cohort, 80% of patients with EoE had an underlying atopic condition. Patients with eczema and pollen food syndrome had a swifter response and were more likely to achieve histologic remission than patients with other atopic conditions. This study suggests that EoE, like other allergic diseases, may have heterogenous phenotypes that could affect response to treatment. There is currently a knowledge gap in classifying EoE based on endotypes and phenotypes at diagnosis and correlating responses to various treatment modalities.
Video fingerprinting: Past, present, and future

The last decades have seen video production and consumption rise significantly: TV/cinematography, social networking, digital marketing, and video surveillance incrementally and cumulatively turned video content into the predilection type of data to be exchanged, stored, and processed. Belonging to video processing realm, video fingerprinting (also referred to as content-based copy detection or near duplicate detection) regroups research efforts devoted to identifying duplicated and/or replicated versions of a given video sequence (query) in a reference video dataset. The present paper reports on a state-of-the-art study on the past and present of video fingerprinting, while attempting to identify trends for its development. First, the conceptual basis and evaluation frameworks are set. This way, the methodological approaches (situated at the cross-roads of image processing, machine learning, and neural networks) can be structured and discussed. Finally, fingerprinting is confronted to the challenges raised by the emerging video applications (e.g., unmanned vehicles or fake news) and to the constraints they set in terms of content traceability and computational complexity. The relationship with other technologies for content tracking (e.g., DLT - Distributed Ledger Technologies) are also presented and discussed.
CASP6 predicts poor prognosis in glioma and correlates with tumor immune microenvironment

Background Glioma is an aggressive tumor of the central nervous system. Caspase-6 (CASP6) plays a crucial role in cell pyroptosis and is a central protein involved in many cellular signaling pathways. However, the association between CASP6 and prognosis of glioma patients remains unclear. Methods Four bioinformatic databases were analyzed to identify differentially expressed genes (DEGs) between glioma and healthy tissues. Eighty-one protein-coding pyroptosis-related genes (PRGs) were obtained from the GeneCards database. The pyroptosis-related DEGs (PRDEGs) were extracted from each dataset, and CASP6 was found to be aberrantly expressed in glioma. We then investigated the biological functions of CASP6 and the relationship between CASP6 expression and the tumor microenvironment and immunocyte infiltration. The half maximal inhibitory concentration of temozolomide and the response to immune checkpoint blockade in the high- and low-CASP6 expression groups were estimated using relevant bioinformatic algorithms. Quantitative real-time reverse transcription PCR and western blotting were carried out to confirm the different expression levels of CASP6 between human astrocytes and glioma cell lines (U251 and T98G). We determined the role of CASP6 in the tumorigenesis of glioma by knocking down CASP6 in U251 and T98G cell lines. Results We found that CASP6 was overexpressed in glioma samples and in glioma cell lines. CASP6 expression in patients with glioma correlated negatively with overall survival. In addition, CASP6 expression correlated positively with the degree of glioma progression. Functional analysis indicated that CASP6 was primarily involved in the immune response and antigen processing and presentation. Patients with high CASP6 levels responded more favorably to temozolomide, while patients with low expression of CASP6 had a better response to immunotherapy. Finally, in vitro experiments showed that CASP6 knockdown inhibited glioma proliferation. Conclusions The pyroptosis-related gene CASP6 might represent a sensitive prognostic marker for patients with glioma and might predict their response of immunotherapy and temozolomide therapy. Our results might lead to more precise immunotherapeutic strategies for patients with glioma.
The Newborn's Reaction to Light as the Determinant of the Brain's Activation at Human Birth

Developmental neuroscience research has not yet fully unveiled the dynamics involved in human birth. The trigger of the first breath, often assumed to be the marker of human life, has not been characterized nor has the process entailing brain modification and activation at birth been clarified yet. To date, few researchers only have investigated the impact of the extrauterine environment, with its strong stimuli, on birth. This ‘hypothesis and theory' article assumes the role of a specific stimulus activating the central nervous system (CNS) at human birth. This stimulus must have specific features though, such as novelty, efficacy, ubiquity, and immediacy. We propose light as a robust candidate for the CNS activation via the retina. Available data on fetal and neonatal neurodevelopment, in particular with reference to retinal light-responsive pathways, will be examined together with the GABA functional switch, and the subplate disappearance, which, at an experimental level, differentiate the neonatal brain from the fetal brain. In this study, we assume how a very rapid activation of retinal photoreceptors at birth initiates a sudden brain shift from the prenatal pattern of functions to the neonatal setup. Our assumption implies the presence of a photoreceptor capable of capturing and transducing light/photon stimulus, transforming it into an effective signal for the activation of new brain functions at birth. Opsin photoreception or, more specifically, melanopsin-dependent photoreception, which is provided by intrinsically photosensitive retinal ganglion cells (ipRGCs), is considered as a valid candidate. Although what is assumed herein cannot be verified in humans based on knowledge available so far, proposing an important and novel function can trigger a broad range of diversified research in different domains, from neurophysiology to neurology and psychiatry.