Miracle-dz/UniFAR-FTUs huggingface dataset:
Algorithmic Virtual Reality Reduces Parkinsonian Tremor

Parkinson's disease (PD) is one of the most prevalent neurodegenerative disorders, affecting approximately 6-7 million patients worldwide. Involuntary hand tremor (IHT), one of the cardinal motor symptoms of PD, is extremely debilitating to patients reducing their quality of life. In this study, we combined neuroscience together with the nascent field of medical virtual reality (VR). Our goals were to 1) generate technology to enable PD patients to leapfrog the real life difficulties of living with IHT by entering VR metaverse worlds in which they are tremor-free and can function at new heights, 2) to determine whether lack of tremors in VR modifies central biofeedback mechanisms to non-invasively reduce tremors in real life. We thus generated algorithms that adjusted the moving average centroid of digital hands to stabilize tremors in VR. We implemented these algorithms in the Oculus Rift VR system and enrolled nine subjects with PD in a trial that yielded several important observations. First, we established the Oculus Rift as a potent measurement device for IHT. Secondly, we determined parkinsonian tremors can be abolished in VR with algorithms that removed up to 99% of tremors from PD subjects' digital hands (76% average reduction). These data suggest PD subjects can enter VR and be asymptomatic of PD IHT. To test whether our algorithms have measurable practical utility, we created a VR painting application, FingerPaint, and tested it against TiltBrush the leading VR painting application. We empirically demonstrate that complex freeform art created in FingerPaint had up to 51% reduction in tremor-associated parkinsonian drawing irregularities (24% average reduction). Lastly, we generated a technical framework wherein movements in the real-world can be measured side-by-side with those in VR. With this framework, we observed real life parkinsonian tremors were significantly reduced by up to 87% in real life when our algorithms abolished digital hand tremors in VR (35% average reduction). This reduction was observed in 78% of subjects and was progressive as subjects had increasingly reduced real life tremors the longer they were in VR.
An improved α-decay energy formula for heavy and superheavy nuclei

Based on the liquid-drop model and using the first derivative of the normalized Gaussian function to consider the shell correction, a simple α-decay energy formula is proposed for heavy and superheavy nuclei. The values of corresponding adjustable parameters are obtained by fitting α-decay energies of 209 nuclei ranging from Z = 90 to Z = 118 with N ≥ 140. The calculated results are in good agreement with the experimental data. The average and standard deviations between the experimental data and theoretical results are 0.141 and 0.190 MeV, respectively. For comparison, the reliable formulae proposed by Dong T K et al (2010, Phys. Rev. C 82, 034 320), Dong J M et al (2010, Phys. Rev. C 81, 064 309) and the WS3+ nuclear mass model proposed by Wang N et al (2011, Phys. Rev. C 84, 051 303) are also used. The results indicate that our improved 7-parameter formula is superior to these empirical formulae and is largely consistent with the WS3+ nuclear mass model. In addition, we extend this formula to predict the α-decay energies for nuclei with Z = 117, 118, 119 and 120. The predicted results of these formulae are basically consistent.
A new spectral domain technique for the calculation of eigenvalues in curvilinear coordinates

We describe a new algorithm, used to decompose the system matrices of Finite Differences and Finite Integration into their high and low spectral parts. This is done by representing the matrix in terms of a new set of basis vectors in a sub space of the solution space excluding a priori large eigenvalues. The resulting mapping is symmetric and so contains orthogonal eigenvectors. The use of this method for the calculation of resonant frequencies yields a strong reduction of the algebraic condition and the solution time. >
Chemical composition of eclipsing binaries: a new approach to the helium-to-metal enrichment ratio

The chemical enrichment law Y(Z) is studied by using detached double-lined eclipsing binaries with accurate absolute dimensions and effective temperatures. A sample of 50 suitable systems was collected from the literature, and their effective temperatures were carefully re-determined. The chemical composition of each of the systems was obtained by comparison with stellar evolutionary models, under the assumption that they should fit an isochrone to the observed properties of the components. Evolutionary models covering a wide grid in Z and Y were adopted for our study. An algorithm was developed for searching the best-fitting chemical composition (and the age) for the systems, based on the minimization of a x 2 function. The errors (and biases) of these parameters were estimated by means of Monte Carlo simulations, with special care put on the correlations existing between the errors of both components. In order to check the physical consistency of the results, we compared our metallicity values with empirical determinations, obtaining excellent coherence. The independently derived Z and Y values yielded a determination of the chemical enrichment law via weighted linear least-squares fit. Our value of the slope, DY=DZ ˆ 2:2 ^ 0:8; is in good agreement with recent results, but it has a smaller formal error and it is free of systematic effects. Linear extrapolation of the enrichment law to zero metals leads to an estimation of the primordial helium abundance of Yp ˆ 0:225 ^ 0:013; possibly affected by systematics in the effective temperature determination.
Absolute electron impact emission cross section of the He+ 22P to 12S line at 304 AA produced by simultaneous ionisation-excitation

A simple and straightforward approach to an absolute emission cross section measurement of the He+ 22P to 12S line at 304 AA following the simultaneous ionisation-excitation of He by electron impact is presented. The undispersed He and He+ impact radiation in the extreme ultraviolet (XUV) region ( lambda <or=600 AA) is detected by a channel electron multiplier after passing through an XUV filter. A 304 AA emission cross section of (6.2+or-1.7)*10-19 cm2 at 200 eV impact energy is extracted utilising the known He cross sections, the measured He/He+ ratio and the wavelength-dependent transmission of the XUV filter and quantum yield of the photon detector. In the regime of high impact energies the emission cross section is found to be inversely proportional to the incident electron energy as expected for the optically forbidden two-electron simultaneous ionisation-excitation process.
Composition factors of monodromy groups

The authors prove the 1990 conjecture of Guralnick and Thompson on composition factors of monodromy groups. Using Riemann's existence theorem, the conjecture translates into a problem on primitive permutation groups. This group theoretic problem had been reduced to a question about actions of classical groups on subspaces of their natural modules. The key ingredients in the present proof are the authors' earlier fixed point ratio estimates for such actions and a result of Scott on the generation of linear groups.
Addressing a climate emergency amidst the COVID-19 pandemic: A mixed-methods study on a hospital evacuation during the 2021 European floods

Introduction: In July 2021, several European countries were affected by severe floods with water levels of the river Meuse reaching a record high. VieCuri Medical Center (Venlo, the Netherlands) is a hospital located directly adjacent to this river, and in response to the flood threat it was decided to completely evacuate the hospital. The aim of this study was to explore the decision-making process of this emergent evacuation. Methods: A mixed-method approach was used. Qualitative data were collected through semi-structured interviews with 11 key participants closely involved in the evacuation. Quantitative data on the patients that were admitted at the time of the evacuation decision were collected, and included 30-day mortality, 7-day readmission rates and Charlson Comorbidity Index. Results: Three themes were constructed from the interviews: risk-assessment, COVID-19 experience and collaboration. Participants highlighted the role of previous experiences from the COVID-19 pandemic. The use of a national patient coordination center enabled to rapidly assess capacity of potential destination hospitals. Furthermore, the hospital preparedness for evacuation could be improved by a thorough analysis of locoregional hazards and preparing for loss of regional healthcare capacity. Findings unrelated to decision-making included the inefficiency of large-scale ambulance dispatches and the expansion of business continuity plans. No patients died unanticipated during this hospital evacuation or within 30 days. Conclusion: Experiences of the COVID-19 pandemic and the availability of a national patient coordination center were found to be decisive in performing this evacuation. This allowed for the swift identification of available capacity in appropriate destination hospitals.
Pulp Therapy of Primary Dentition; its Relevance despite Insufficient Histological Evidence: A Review

Pulp treatment in primary dentition is generally divided into vital and non-vital pulp therapies and assists in the preservation of pulpally involved primary teeth in the dental arch until the affected tooth naturally exfoliates. The success of pulp therapies depends on several factors; e.g. proper case selection, accurate diagnosis and good coronal seal. To date, studies on the success and failure rates of pulp treatments are based on clinical signs and symptoms, radiographic findings and histological analysis. However, the clinical and radiographic evidence may not completely portray the true status of the dental pulp. Histological evidence remains the gold standard in the assessment of pulp condition, whether it is in a healthy or adverse state. The aims of the current research were to summarise the treatment outcomes of pulp therapy in primary dentition based on clinical, radiographic and histological criteria, and to support its relevance in the presence of limited histological evidence to measure authentic treatment success. An electronic database search of dental literature from 1990 to 2022 was carried out using the MEDLINE, i.e. PubMed, database. Current dental literature showed that the success rates of primary tooth pulp therapy are high. The obtained results were based largely on clinical and radiographic studies with narrow histological investigations to assess the treatment outcome(s) of pulp therapy in primary dentition. Despite the scarcity of histological evidence, pulp therapies in primary teeth are still practical due to their statistically empirical success compared to their failure. Consequently, pulp therapy of primary dentition is still relevant, and should continue to be indicated as an important treatment option.
Idiopathic normal pressure hydrocephalus and frontotemporal dementia: an unexpected association

Abstract Idiopathic normal pressure hydrocephalus has a complex multifactorial pathogenesis and is associated with Alzheimer’s disease in many patients. To date, it is not well known if a similar association exists with behavioural variant of frontotemporal lobar degeneration. In a first step, we compare the prevalence of idiopathic normal pressure hydrocephalus in two groups of patients, one with behavioural variant of frontotemporal lobar degeneration (n = 69) and the other with Alzheimer’s disease (n = 178). In the second step, we describe more precisely the phenotype of patients with the association of idiopathic normal pressure hydrocephalus and behavioural variant of frontotemporal lobar degeneration. Firstly, we report that the prevalence of idiopathic normal pressure hydrocephalus was far higher in the group of patients with behavioural variant of frontotemporal lobar degeneration than in the group of patients with Alzheimer’s disease (7.25% and 1.1%, respectively, P = 0.02). Secondly, we show that patients with the double diagnosis share common clinical and para-clinical features of both idiopathic normal pressure hydrocephalus and behavioural variant of frontotemporal lobar degeneration patients, including CSF shunting efficacy in real-life experience. Overall, our results suggest a link between these two conditions and should encourage neurologists to look for idiopathic normal pressure hydrocephalus in their behavioural variant of frontotemporal lobar degeneration patients in the event of gait disturbances; the benefit/risk balance could indeed be in favour of shunt surgery for selected patients with this newly described entity.
The CASSINI Ka-band gravitational wave experiments

Cassini, a joint American/European interplanetary scientific mission to Saturn, will be continuously and coherently tracked for 40 days during its solar oppositions in the next three years, starting on 26 November 2001. Doppler tracking searches for gravitational waves in the millihertz frequency band will be performed by using newly implemented Ka-band (≈32 GHz) microwave capabilities on the ground and onboard the spacecraft. Use of the Ka-band coherent microwave link will suppress solar plasma scintillations to levels below those identified by remaining instrumental noise sources, making the Cassini Doppler tracking experiments the most sensitive searches for gravitational waves ever attempted in the millihertz frequency band. This paper provides a short review of the Doppler response to gravitational radiation, the noise sources and their transfer functions into the Doppler observable and estimates of the anticipated Cassini Doppler tracking sensitivities to gravitational radiation.
The Reflection of Guided Waves From Circumferential Notches in Pipes

The reflection of the L(0, 2), axially symmetric guidea elastic wave from notches in pipes is examined, using laboratory experiments and finite element simulation The result show that the reflection coefficient of this mode is very close to a linear function of the circumferential extent of the notch, and is a stronger function of the through thickne depth of the notch. The motivation for the work was the development of a technique for inspecting chemical plant pipework, but the study addresses the nature of the reflection function and has general applicability.
Chronic viral coinfections differentially affect the likelihood of developing long COVID

BACKGROUND The presence and reactivation of chronic viral infections, such as EBV, CMV, and HIV, have been proposed as potential contributors to long COVID (LC), but studies in well-characterized postacute cohorts of individuals with COVID-19 over a longer time course consistent with current case definitions of LC are limited. METHODS In a cohort of 280 adults with prior SARS-CoV-2 infection, we assessed the presence and types of LC symptoms and prior medical history (including COVID-19 history and HIV status) and performed serological testing for EBV and CMV using a commercial laboratory. We used covariate-adjusted binary logistic regression models to identify independent associations between variables and LC symptoms. RESULTS We observed that LC symptoms, such as fatigue and neurocognitive dysfunction, at a median of 4 months following initial diagnosis were independently associated with serological evidence suggesting recent EBV reactivation (early antigen–diffuse IgG positivity) or high nuclear antigen (EBNA) IgG levels but not with ongoing EBV viremia. Serological evidence suggesting recent EBV reactivation (early antigen–diffuse IgG positivity) was most strongly associated with fatigue (OR = 2.12). Underlying HIV infection was also independently associated with neurocognitive LC (OR = 2.5). Interestingly, participants who had serologic evidence of prior CMV infection were less likely to develop neurocognitive LC (OR = 0.52). CONCLUSION Overall, these findings suggest differential effects of chronic viral coinfections on the likelihood of developing LC and association with distinct syndromic patterns. Further assessment during the acute phase of COVID-19 is warranted. TRIAL REGISTRATION Long-term Impact of Infection with Novel Coronavirus; ClinicalTrials.gov NCT04362150. FUNDING This work was supported by NIH/National Institute of Allergy and Infectious Diseases grants (3R01AI141003-03S1, R01AI158013, and K24AI145806); the Zuckerberg San Francisco General Hospital Department of Medicine and Division of HIV, Infectious Diseases, and Global Medicine; and the UCSF-Bay Area Center for AIDS Research (P30-AI027763).
Gene variant effects across sodium channelopathies predict function and guide precision therapy

Abstract Pathogenic variants in the voltage-gated sodium channel gene family lead to early onset epilepsies, neurodevelopmental disorders, skeletal muscle channelopathies, peripheral neuropathies and cardiac arrhythmias. Disease-associated variants have diverse functional effects ranging from complete loss-of-function to marked gain-of-function. Therapeutic strategy is likely to depend on functional effect. Experimental studies offer important insights into channel function but are resource intensive and only performed in a minority of cases. Given the evolutionarily conserved nature of the sodium channel genes, we investigated whether similarities in biophysical properties between different voltage-gated sodium channels can predict function and inform precision treatment across sodium channelopathies. We performed a systematic literature search identifying functionally assessed variants in any of the nine voltage-gated sodium channel genes until 28 April 2021. We included missense variants that had been electrophysiologically characterized in mammalian cells in whole-cell patch-clamp recordings. We performed an alignment of linear protein sequences of all sodium channel genes and correlated variants by their overall functional effect on biophysical properties. Of 951 identified records, 437 sodium channel-variants met our inclusion criteria and were reviewed for functional properties. Of these, 141 variants were epilepsy-associated (SCN1/2/3/8A), 79 had a neuromuscular phenotype (SCN4/9/10/11A), 149 were associated with a cardiac phenotype (SCN5/10A) and 68 (16%) were considered benign. We detected 38 missense variant pairs with an identical disease-associated variant in a different sodium channel gene. Thirty-five out of 38 of those pairs resulted in similar functional consequences, indicating up to 92% biophysical agreement between corresponding sodium channel variants (odds ratio = 11.3; 95% confidence interval = 2.8 to 66.9; P < 0.001). Pathogenic missense variants were clustered in specific functional domains, whereas population variants were significantly more frequent across non-conserved domains (odds ratio = 18.6; 95% confidence interval = 10.9–34.4; P < 0.001). Pore-loop regions were frequently associated with loss-of-function variants, whereas inactivation sites were associated with gain-of-function (odds ratio = 42.1, 95% confidence interval = 14.5–122.4; P < 0.001), whilst variants occurring in voltage-sensing regions comprised a range of gain- and loss-of-function effects. Our findings suggest that biophysical characterisation of variants in one SCN-gene can predict channel function across different SCN-genes where experimental data are not available. The collected data represent the first gain- versus loss-of-function topological map of SCN proteins indicating shared patterns of biophysical effects aiding variant analysis and guiding precision therapy. We integrated our findings into a free online webtool to facilitate functional sodium channel gene variant interpretation (http://SCN-viewer.broadinstitute.org).
Modelling of thrombus formation using smoothed particle hydrodynamics method

In this paper a novel model, based on the smoothed particle hydrodynamics (SPH) method, is proposed to simulate thrombus formation. This describes the main phases of the coagulative cascade through the balance of four biochemical species and three type of platelets. SPH particles can switch from fluid to solid phase when specific biochemical and physical conditions are satisfied. The interaction between blood and the forming blood clot is easily handled by an innovative monolithic FSI approach. Fluid-solid coupling is modelled by introducing elastic binds between solid particles, without requiring detention and management of the interface between the two media. The proposed model is able to realistically reproduce the thromboembolic process, as confirmed by the comparison of numerical results with experimental data available in the literature.
Graph Generation with Destination-Driven Diffusion Mixture

Generation of graphs is a major challenge for real-world tasks that require understanding the complex nature of their non-Euclidean structures. Although diffusion models have achieved notable success in graph generation recently, they are ill-suited for modeling the structural information of graphs since learning to denoise the noisy samples does not explicitly capture the graph topology. To tackle this limitation, we propose a novel generative process that models the topology of graphs by predicting the destination of the process. Speciﬁcally, we design the generative process as a mixture of diffusion processes conditioned on the endpoint in the data distribution, which drives the process toward the probable destination. Further, we introduce new training objectives for learning to predict the destination, and discuss the advantages of our generative framework that can explicitly model the graph topology and exploit the inductive bias of the data. Through extensive experimental validation on general graph and 2D/3D molecular graph generation tasks, we show that our method outperforms previous generative models, generating graphs with correct topology with both continuous and discrete features.
IB-UQ: Information bottleneck based uncertainty quantification for neural function regression and neural operator learning

We propose a novel framework for uncertainty quantification via information bottleneck (IB-UQ) for scientific machine learning tasks, including deep neural network (DNN) regression and neural operator learning (DeepONet). Specifically, we incorporate the bottleneck by a confidence-aware encoder, which encodes inputs into latent representations according to the confidence of the input data belonging to the region where training data is located, and utilize a Gaussian decoder to predict means and variances of outputs conditional on representation variables. Furthermore, we propose a data augmentation based information bottleneck objective which can enhance the quantification quality of the extrapolation uncertainty, and the encoder and decoder can be both trained by minimizing a tractable variational bound of the objective. In comparison to uncertainty quantification (UQ) methods for scientific learning tasks that rely on Bayesian neural networks with Hamiltonian Monte Carlo posterior estimators, the model we propose is computationally efficient, particularly when dealing with large-scale data sets. The effectiveness of the IB-UQ model has been demonstrated through several representative examples, such as regression for discontinuous functions, real-world data set regression, learning nonlinear operators for partial differential equations, and a large-scale climate model. The experimental results indicate that the IB-UQ model can handle noisy data, generate robust predictions, and provide confident uncertainty evaluation for out-of-distribution data.