Reduced Simulations for High-Energy Physics, a Middle Ground for Data-Driven Physics Research

Subatomic particle track reconstruction (tracking) is a vital task in High-Energy Physics experiments. Tracking is exceptionally computationally challenging and fielded solutions, relying on traditional algorithms, do not scale linearly. Machine Learning (ML) assisted solutions are a promising answer. We argue that a complexity-reduced problem description and the data representing it, will facilitate the solution exploration workflow. We provide the REDuced VIrtual Detector (REDVID) as a complexity-reduced detector model and particle collision event simulator combo. REDVID is intended as a simulation-in-the-loop, to both generate synthetic data efficiently and to simplify the challenge of ML model design. The fully parametric nature of our tool, with regards to system-level configuration, while in contrast to physics-accurate simulations, allows for the generation of simplified data for research and education, at different levels. Resulting from the reduced complexity, we showcase the computational efficiency of REDVID by providing the computational cost figures for a multitude of simulation benchmarks. As a simulation and a generative tool for ML-assisted solution design, REDVID is highly flexible, reusable and open-source. Reference data sets generated with REDVID are publicly available. Data generated using REDVID has enabled rapid development of multiple novel ML model designs, which is currently ongoing

Accès à l’expertise en ressources informationnelles : enjeux et pistes de réflexion : rapport final

Cette recherche s’inscrit dans un effort pour mieux comprendre la dynamique qui entoure l’accès à l’expertise en ressources informationnelles. Le but est de pouvoir mieux comprendre les enjeux, les contraintes pour les organisations dans leur démarche d’accès à ce type d’expertise et enfin tenter de proposer des pistes de solutions

Myofascial urinary frequency syndrome is a novel syndrome of bothersome lower urinary tract symptoms associated with myofascial pelvic floor dysfunction

This study describes a novel, distinct phenotype of urinary symptoms named myofascial urinary frequency syndrome (MUFS) present in one-third of individuals presenting with urinary frequency. In addition to a characteristic symptom constellation suggestive of myofascial dysfunction, MUFS subjects exhibit persistency : a persistent feeling of needing to urinate regardless of urine volume. On examination, 97% of MUFS patients demonstrated pelvic floor hypertonicity with either global tenderness or myofascial trigger points, and 92% displayed evidence of impaired muscular relaxation, hallmarks of myofascial dysfunction. To confirm this symptom pattern was attributable to the pelvic floor musculature, we confirmed the presence of persistency in 68 patients with pelvic floor myofascial dysfunction established through comprehensive examination and electromyography and corroborated by improvement with pelvic floor myofascial release. These symptoms distinguish subjects with myofascial dysfunction from subjects with OAB, IC/BPS, and asymptomatic controls, confirming MUFS is a distinct LUTS symptom complex

Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs

This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited

Limitations of dual-sgRNA CRISPR strategies for the treatment of CNS genetic disorders

International audienc

The Persistency Index: A novel screening tool for identifying myofascial pelvic floor dysfunction in patients seeking care for lower urinary tract symptoms

BACKGROUND: Patients with myofascial pelvic floor dysfunction often present with lower urinary tract symptoms, such as urinary frequency, urgency, and bladder pressure. Often confused with other lower urinary tract disorders, this constellation of symptoms, recently termed myofascial urinary frequency syndrome, is distinct from other lower urinary tract symptoms and optimally responds to pelvic floor physical therapy. A detailed pelvic floor myofascial examination performed by a skilled provider is currently the only method to identify myofascial urinary frequency syndrome. Despite a high influence on quality of life, low awareness of this condition combined with no objective diagnostic testing leads to the frequent misdiagnosis or underdiagnosis of myofascial urinary frequency syndrome. OBJECTIVE: This study aimed to develop a screening measure to identify patients with myofascial urinary frequency syndrome (bothersome lower urinary tract symptoms secondary to myofascial pelvic floor dysfunction) from patient-reported symptoms. STUDY DESIGN: A population of patients with isolated myofascial urinary frequency syndrome was identified by provider diagnosis from a tertiary urology practice and verified by standardized pelvic floor myofascial examination and perineal surface pelvic floor electromyography. Least Angle Shrinkage and Selection Operator was used to identify candidate features from the Overactive Bladder Questionnaire, Female Genitourinary Pain Index, and Pelvic Floor Distress Index predictive of myofascial urinary frequency syndrome in a pooled population also containing subjects with overactive bladder (n=42), interstitial cystitis/bladder pain syndrome (n=51), and asymptomatic controls (n=54) (derivation cohort). A simple, summated score of the most discriminatory questions using the original scaling of the Pelvic Floor Distress Index 5 (0-4) and Genitourinary Pain Index 5 (0-5) and modified scaling of Female Genitourinary Pain Index 2b (0-3) had an area under the curve of 0.75. As myofascial urinary frequency syndrome was more prevalent in younger subjects, the inclusion of an age penalty (3 points added if under the age of 50 years) improved the area under the curve to 0.8. This score was defined as the Persistency Index (possible score of 0-15). The Youden Index was used to identify the optimal cut point Persistency Index score for maximizing sensitivity and specificity. RESULTS: Using a development cohort of 215 subjects, the severity (Pelvic Floor Distress Index 5) and persistent nature (Female Genitourinary Pain Index 5) of the sensation of incomplete bladder emptying and dyspareunia (Female Genitourinary Pain Index 2b) were the most discriminatory characteristics of the myofascial urinary frequency syndrome group, which were combined with age to create the Persistency Index. The Persistency Index performed well in a validation cohort of 719 patients with various lower urinary tract symptoms, including overactive bladder (n=285), interstitial cystitis/bladder pain syndrome (n=53), myofascial urinary frequency syndrome (n=111), controls (n=209), and unknown diagnoses (n=61), exhibiting an area under the curve of 0.74. A Persistency Index score ≥7 accurately identified patients with myofascial urinary frequency syndrome from an unselected population of individuals with lower urinary tract symptoms with 80% sensitivity and 61% specificity. A combination of the Persistency Index with the previously defined Bladder Pain Composite Index and Urge Incontinence Composite Index separated a population of women seeking care for lower urinary tract symptoms into groups consistent with overactive bladder, interstitial cystitis/bladder pain syndrome, and myofascial urinary frequency syndrome phenotypes with an overall diagnostic accuracy of 82%. CONCLUSION: Our study recommends a novel screening method for patients presenting with lower urinary tract symptoms to identify patients with myofascial urinary frequency syndrome. As telemedicine becomes more common, this index provides a way of screening for myofascial urinary frequency syndrome and initiating pelvic floor physical therapy even before a confirmatory pelvic examination

Dermal Lymphatic Capillaries Do Not Obey Murray's Law

Lymphatic vessels serve as a major conduit for the transport of interstitial fluid, immune cells, lipids and drugs. Therefore, increased knowledge about their development and function is relevant to clinical issues ranging from chronic inflammation and edema, to cancer metastasis to targeted drug delivery. Murray's Law is a widely-applied branching rule upheld in diverse circulatory systems including leaf venation, sponge canals, and various human organs for optimal fluid transport. Considering the unique and diverse functions of lymphatic fluid transport, we specifically address the branching of developing lymphatic capillaries, and the flow of lymph through these vessels. Using an empirically-generated dataset from wild type and genetic lymphatic insufficiency mouse models we confirmed that branching blood capillaries consistently follow Murray's Law. However surprisingly, we found that the optimization law for lymphatic vessels follows a different pattern, namely a Murray's Law exponent of ~1.45. In this case, the daughter vessels are smaller relative to the parent than would be predicted by the hypothesized radius-cubed law for impermeable vessels. By implementing a computational fluid dynamics model, we further examined the extent to which the assumptions of Murray's Law were violated. We found that the flow profiles were predominantly parabolic and reasonably followed the assumptions of Murray's Law. These data suggest an alternate hypothesis for optimization of the branching structure of the lymphatic system, which may have bearing on the unique physiological functions of lymphatics compared to the blood vascular system. Thus, it may be the case that the lymphatic branching structure is optimized to enhance lymph mixing, particle exchange, or immune cell transport, which are particularly germane to the use of lymphatics as drug delivery routes

Opportunities for organoids as new models of aging.

The biology of aging is challenging to study, particularly in humans. As a result, model organisms are used to approximate the physiological context of aging in humans. However, the best model organisms remain expensive and time-consuming to use. More importantly, they may not reflect directly on the process of aging in people. Human cell culture provides an alternative, but many functional signs of aging occur at the level of tissues rather than cells and are therefore not readily apparent in traditional cell culture models. Organoids have the potential to effectively balance between the strengths and weaknesses of traditional models of aging. They have sufficient complexity to capture relevant signs of aging at the molecular, cellular, and tissue levels, while presenting an experimentally tractable alternative to animal studies. Organoid systems have been developed to model many human tissues and diseases. Here we provide a perspective on the potential for organoids to serve as models for aging and describe how current organoid techniques could be applied to aging research

Development of Diaminoquinazoline Histone Lysine Methyltransferase Inhibitors as Potent Blood-Stage Antimalarial Compounds

Modulating epigenetic mechanisms in malarial parasites is an emerging avenue for the discovery of novel antimalarial drugs. Previously we demonstrated the potent in vitro and in vivo antimalarial activity of BIX01294 (1), a known human G9a inhibitor, together with its dose-dependent effects on histone methylation in the malarial parasite. This work describes our initial medicinal chemistry efforts to optimize the diaminoquinazoline chemotype for antimalarial activity. A variety of analogues were designed by substituting the 2 and 4 positions of the quinazoline core and these molecules were tested against Plasmodium falciparum (3D7 strain). Several analogues with IC50 values as low as 18.5 nM and with low mammalian cell toxicity (HepG2) were identified. Certain pharmacophoric features required for the antimalarial activity were found to be analogous to the previously published SAR of these analogues for G9a inhibition, thereby suggesting potential similarities between the malarial and the human HKMT targets of this chemotype. Physiochemical, in vitro activity, and in vitro metabolism studies were also performed for a select set of potent analogues to evaluate their potential as anti-malarial leads