pwc-archive/papers-with-abstracts huggingface dataset:
Robust Waveform Design for Integrated Sensing and Communication
Authors: Shixiong Wang, Wei Dai, Haowei Wang, Geoffrey Ye Li
Date: 2023-10-31 00:00:00
Tasks: Integrated sensing and communication, ISAC, Robust Design

Integrated sensing and communication (ISAC), which enables hardware, resources (e.g., spectra), and waveforms sharing, is becoming a key feature in future-generation communication systems. This paper investigates performance characterization and waveform design for ISAC systems when the underlying true communication channels are not accurately known. With uncertainty in a nominal communication channel, the nominal Pareto frontier of the sensing and communication performances cannot represent the true performance trade-off of a real-world operating ISAC system. Therefore, this paper portrays the robust (i.e., conservative) Pareto frontier considering the uncertainty in the communication channel. To be specific, the lower bound of the true (but unknown) Pareto frontier is investigated, technically by studying robust waveform design problems that find the best waveforms under the worst-case channels. The robust waveform design problems examined in this paper are shown to be non-convex and high-dimensional, which cannot be solved using existing optimization techniques. As such, we propose a computationally efficient solution framework to approximately solve them. Simulation results show that by solving the robust waveform design problems, the lower bound of the true but unknown Pareto frontier, which characterizes the sensing-communication performance trade-off under communication channel uncertainty, can be obtained.
Power law in Sandwiched Volterra Volatility model
Authors: Giulia Di Nunno, Anton Yurchenko-Tytarenko
Date: 2023-11-02 00:00:00
Tasks: model

In this paper, we present analytical proof demonstrating that the Sandwiched Volterra Volatility (SVV) model is able to reproduce the power-law behavior of the at-the-money implied volatility skew, provided the correct choice of the Volterra kernel. To obtain this result, we assess the second-order Malliavin differentiability of the volatility process and investigate the conditions that lead to explosive behavior in the Malliavin derivative. As a supplementary result, we also prove a general Malliavin product rule.
The molecular pathology of genioglossus in obstructive sleep apnea
Authors: Menghan Zhang, Yuehua Liu
Date: 2023-11-02 00:00:00

Obstructive sleep apnea (OSA) is a sleep respiratory disease characterized by sleep snoring accompanied by apnea and daytime sleeplessness. It is a complex disease, with the multifactorial etiology, and the pathology is incompletely understood. Genioglossus (GG), the largest dilator of upper airway, whose fatigue is strongly correlated to onset of OSA. This brief review was to investigate the pathogenesis of OSA targeting on GG from different risk factors as gender, obesity, and aging, and the molecular mechanism of GG injury in OSA pathogenesis. We hope to find the targeted molecular mechanism on GG in OSA treatment.
EMPOT: partial alignment of density maps and rigid body fitting using unbalanced Gromov-Wasserstein divergence
Authors: Aryan Tajmir Riahi, Chenwei Zhang, James Chen, Anne Condon, Khanh Dao Duc
Date: 2023-11-01 00:00:00
Tasks: Benchmarking, Cryogenic Electron Microscopy (cryo-EM)

Aligning EM density maps and fitting atomic models are essential steps in single particle cryogenic electron microscopy (cryo-EM), with recent methods leveraging various algorithms and machine learning tools. As aligning maps remains challenging in the presence of a map that only partially fits the other (e.g. one subunit), we here propose a new procedure, EMPOT (EM Partial alignment with Optimal Transport), for partial alignment of 3D maps. EMPOT first finds a coupling between 3D point-cloud representations, which is associated with their so-called unbalanced Gromov Wasserstein divergence, and second, uses this coupling to find an optimal rigid body transformation. Upon running and benchmarking our method with experimental maps and structures, we show that EMPOT outperforms standard methods for aligning subunits of a protein complex and fitting atomic models to a density map, suggesting potential applications of Partial Optimal Transport for improving Cryo-EM pipelines.
Generating site saturation mutagenesis libraries and transferring them to broad host range plasmids using type IIS restriction enzymes
Authors: Niels N. Oehlmann, Johannes G. Rebelein
Date: 2023-10-31 00:00:00

Protein engineering is an established method for tailoring enzymatic reactivity. A commonly used method is directed evolution, where the mutagenesis and natural selection process is mimicked and accelerated in the laboratory. Here, we describe a reliable method for generating saturation mutagenesis libraries by golden gate cloning in a broad host range plasmid containing the pBBR1 replicon. The applicability is demonstrated by generating a mutant library of the iron nitrogenase gene cluster (anfHDGK) of Rhodobacter capsulatus, which is subsequently screened for the improved formation of molecular hydrogen.
scX: A user-friendly tool for scRNA-seq exploration
Authors: Tomás Vega Waichman, M. Luz Vercesi, Ariel A. Berardino, Maximiliano S. Beckel, Damiana Giacomini, Natalí B. Rasetto, Magalí Herrero, Daniela J. Di Bella, Paola Arlotta, Alejandro F. Schinder, Ariel Chernomoretz
Date: 2023-10-31 00:00:00

Single-cell RNA sequencing (scRNA-seq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. In this paper, we present scX, an R package built on the Shiny framework that streamlines the analysis, exploration, and visualization of single-cell experiments. With an interactive graphic interface, implemented as a web application, scX provides easy access to key scRNAseq analyses, including marker identification, gene expression profiling, and differential gene expression analysis. Additionally, scX seamlessly integrates with commonly used single-cell Seurat and SingleCellExperiment R objects, resulting in efficient processing and visualization of varied datasets. Overall, scX serves as a valuable and user-friendly tool for effortless exploration and sharing of single-cell data, simplifying some of the complexities inherent in scRNAseq analysis.
Shorter duration of slow wave sleep is related to symptoms of depression in patients with epilepsy
Authors: Stefanía Eyjolfsdóttir, Eugen Trinka, Yvonne Höller
Date: 2023-11-02 00:00:00
Tasks: EEG

Slow wave sleep duration and spectral abnormalities are related to both epilepsy and depression, but it is unclear how depressive symptoms in patients with epilepsy are affected by slow wave sleep duration and clinical factors, and how the spectral characteristics of slow wave sleep reflect a potential interaction of epilepsy and depression. Long-term video-EEG monitoring was conducted in 51 patients with focal epilepsy, 13 patients with generalized epilepsy, and 9 patients without epilepsy. Slow wave sleep segments were manually marked in the EEG and duration as well as EEG power spectra were extracted. Depressive symptoms were documented with the Beck Depression Inventory (BDI). At least mild depressive symptoms (BDI>9) were found among 23 patients with focal epilepsy, 5 patients with generalised epilepsy, and 6 patients who had no epilepsy diagnosis. Slow wave sleep duration was shorter for patients with at least mild depressive symptoms (p=.004), independently from epilepsy diagnosis, antiseizure medication, age, and sex. Psychoactive medication was associated with longer slow wave sleep duration (p=.008). Frontal sigma band power (13-15 Hz) during slow wave sleep was higher for patients without epilepsy and without depressive symptoms as compared to patients without depressive symptoms but with focal epilepsy (p=.005). Depressive symptoms affect slow wave sleep duration of patients with epilepsy similarly as in patients without epilepsy. Since reduced slow wave sleep can increase the likelihood of seizure occurrence, these results stress the importance of adequate treatment for patients with epilepsy who experience depressive symptoms.
Gray matter volume correlates of Comorbid Depression in Autism Spectrum Disorder
Authors: Dolcy Dhar, Manasi Chaturvedi, Saanvi Sehwag, Chehak Malhotra, Udit, Chetan Saraf, Mrinmoy Chakrabarty
Date: 2023-11-02 00:00:00

Autism Spectrum Disorder (ASD) involves diverse neurodevelopmental syndromes with significant deficits in communication, motor behaviours, emotional and social comprehension. Often, individuals with ASD exhibit comorbid conditions, one of the most prevalent being depression characterized by a persistent change in mood and diminished interest in previously enjoyable activities. Due to communicative challenges and lack of appropriate assessments in individuals with ASD, comorbid depression can often go undiagnosed during routine clinical examinations, which may aggravate their problems. The current literature on comorbid depression in adults with ASD is limited. Therefore, understanding the neural basis of the comorbid psychopathology of depression in ASD is crucial for identifying objective brain-based markers for its timely and effective management. Towards this end, using structural MRI and phenotypic data from the Autism Brain Imaging Data Exchange II (ABIDE II) repository, we specifically examined the pattern of relationship regional grey matter volume (rGMV) has with comorbid depression and autism severity within regions of a priori interest in adults with ASD (n = 44). The severity of comorbid depression correlated negatively with the rGMV of the right thalamus. Additionally, a significant interaction was evident between the severity of comorbid depression and core ASD symptoms towards explaining the rGMV in the left cerebellum crus II. The whole-brain regional rGMV differences between ASD and typically developed (TD, n = 39) adults remained inconclusive. The results further the understanding of the neurobiological underpinnings of comorbid depression in adults with ASD and are relevant in exploring structural neuroimaging-based biomarkers in the same cohort.
Statistics of C. elegans turning behavior reveals optimality under biasing constraints
Authors: W. Mathijs Rozemuller, Steffen Werner, Antonio Carlos Costa, Liam O'Shaughnessy, Greg J. Stephens, Thomas S. Shimizu
Date: 2023-11-01 00:00:00
Tasks: Anatomy

Animal locomotion is often subject to constraints arising from anatomical/physiological asymmetries. We use the nematode C.~elegans as a minimal model system to ask whether such constraints might shape locomotion patterns optimized during evolution. We focus on turning behaviours in two contrasting environmental contexts: (i) random exploration in the absence of strong stimuli and (ii) acute avoidance (escape) navigation upon encountering a strong aversive stimulus. We characterise the full repertoire of reorientation behaviours, including gradual reorientations and various posturally distinct sharp turns. During exploration, our measurements and theoretical modelling indicate that orientation fluctuations on short timescales are, on average, optimized to compensate the constraining gradual turn bias on long timescales. During escape, our data suggests that the reorientation is controlled not by an analog logic of continuous turn-amplitude modulations, but rather through the digital logic of selecting discrete turn types, leading to a symmetric escape performance despite strongly asymmetric turning biases.
Higher Mediterranean diet score is associated with longer time between relapses in Australian females with multiple sclerosis
Authors: Hajar Mazahery, Alison Daly, Ngoc Minh Pham, Madeleine Stephens, Eleanor Dunlop, Anne-Louise Ponsonby, Ausimmune/AusLong Investigator Group, Lucinda J Black
Date: 2023-11-02 00:00:00
Tasks: Survival Analysis, Time Series

A higher Mediterranean diet score has been associated with lower likelihood of multiple sclerosis. However, evidence regarding its association with disease activity and progression is limited. Using data from the AusLong Study, we tested longitudinal associations (over 10 years follow-up) between the alternate Mediterranean diet score (aMED) and aMED-Red (including moderate consumption of unprocessed red meat) and time between relapses and disability measured by Expanded Disability Status Scale (EDSS) (n=132; 27 males, 105 females). We used covariate-adjusted survival analysis for time between relapses, and time series mixed-effects negative binomial regression for EDSS. After adjusting for covariates, both higher aMED (aHR=0.94, 95%CI: 0.90, 0.99, p=0.009) and higher aMED-Red (aHR=0.93, 95%CI: 0.89, 0.97, p=0.001) were associated with significantly longer time between relapses in females. Whether specific dietary components of a Mediterranean diet are important in relation to relapses merits further study.
Next-generation MRD assays: do we have the tools to evaluate them properly?
Authors: Dan Stetson, Paul Labrousse, Hugh Russell, David Shera, Chris Abbosh, Brian Dougherty, J. Carl Barrett, Darren Hodgson, James Hadfield
Date: 2023-10-31 00:00:00
Tasks: Benchmarking, Sensitivity

Circulating tumour DNA (ctDNA) detection of molecular residual disease (MRD) in solid tumours correlates strongly with patient outcomes and is being adopted as a new clinical standard. ctDNA levels are known to correlate with tumor volume, and although the absolute levels vary across indication and histology, its analysis is driving the adoption of MRD. MRD assays must detect tumor when imaging cannot and, as such, require very high sensitivity to detect the low levels of ctDNA found after curative intent therapy. The minimum threshold is 0.01% Tumour Fraction but current methods like Archer and Signatera are limited by detection sensitivity resulting in some patients receiving a false negative call thereby missing out on earlier therapeutic intervention. Multiple vendors are increasing the number of somatic variants tracked in tumour-informed and personalized NGS assays, from tens to thousands of variants. Most recently, assays using other biological features of ctDNA, e.g methylation or fragmentome, have been developed at the LOD required for clinical utility. These uniformed, or tumour-naive and non-personalised assays may be more easily, and therefore more rapidly, adopted in the clinic. However, this rapid development in MRD assay technology results in significant challenges in benchmarking these new technologies for use in clinical trials. This is further complicated by the fact that previous reference materials have focused on somatic variants, and do not retain all of the epigenomic features assessed by newer technologies. In this Comments and Controversy paper, we detail what is known and what remains to be determined for optimal reference materials of MRD methods and provide opinions generated during three-years of MRD technology benchmarking in AstraZeneca Translational Medicine to help guide the community conversation.
Stochastic viability in an island model with partial dispersal : Approximation by a diffusion process in the limit of a large number of islands
Authors: Dhaker Kroumi, Sabin Lessard
Date: 2023-11-01 00:00:00

In this paper, we study a finite population undergoing discrete, nonoverlapping generations, that is structured into $D$ demes, each containing $N$ individuals of two possible types, $A$ and $B$, whose viability coefficients, $s_A$ and $s_B$, respectively, vary randomly from one generation to the next. We assume that the means, variances and covariance of the viability coefficients are inversely proportional to the number of demes $D$, while higher-order moments are negligible in comparison to $1/D$. We use a discrete-time Markov chain with two time scales to model the evolutionary process, and we demonstrate that as the number of demes $D$ approaches infinity, the accelerated Markov chain converges to a diffusion process for any deme size $N\geq 2$. This diffusion process allows us to evaluate the fixation probability of type $A$ following its introduction as a single mutant in a population that was fixed for type $B$. We explore the impact of increasing the variability in the viability coefficients on this fixation probability. At least when $N$ is large enough, it is shown that increasing this variability for type $B$ or decreasing it for type $A$ leads to an increase in the fixation probability of a single $A$. The effect of the population-scaled variances, $\sigma^2_A$ and $\sigma^2_B$, can even cancel the effects of the population-scaled means, $\mu_A$ and $\mu_B$. We also show that the fixation probability of a single $A$ increases as the deme-scaled migration rate increases. Moreover, this probability is higher for type $A$ than for type $B$ if the population-scaled geometric mean is higher for type $A$ than for type $B$, which means that $\mu_A-\sigma_A^2/2>\mu_B-\sigma_B^2/2$.
Evolutionary game with stochastic payoffs in a finite island model
Authors: Dhaker Kroumi, Sabin Lessard
Date: 2023-11-01 00:00:00

In this paper, we consider a two-player two-strategy game with random payoffs in a population subdivided into $d$ demes, each containing $N$ individuals at the beginning of any given generation and experiencing local extinction and recolonization with some fixed probability $m$ after reproduction and selection among offspring. Within each deme, offspring engage in random pairwise interactions, and the payoffs are assumed to have means and variances proportional to the inverse of the population size. By verifying the conditions given in Ethier and Nagylaki (1980) to approximate Markov chains with two time scales, we establish that the discrete-time evolutionary dynamics with $Nd$ generations as unit of time converges to a continuous-time diffusion as $d\rightarrow\infty$. The infinitesimal mean and variance of this diffusion are expressed in terms of the population-scaled means and variances of the payoffs besides identity-by-descent measures between offspring in the same deme in a neutral population. We show that the probability for a strategy to fix in the population starting from an initial frequency $(Nd)^{-1}$ generally increases as the payoffs to that strategy exhibit less variability or the payoffs to the other strategy more variability. As a result, differences in variability can make this fixation probability for cooperation larger than the corresponding one for defection. As the deme-scaled extinction rate $\nu=mN$ decreases for $N$ large enough and $m$ small enough, creating a higher level of identity among offspring within demes, the differences between the population-scaled variances of the payoffs for interacting offspring of different types increases this effect to a greater extent than the differences for interacting offspring of the same type.
Development and application of SEM/EDS in biological, biomedical & nanotechnological research
Authors: Aniruddha Acharya
Date: 2023-11-01 00:00:00

This comprehensive review discusses the development of scanning electron microscopy and the application of this technology in different fields such as biology, nanobiotechnology and biomedical science. Besides being a tool for high resolution imaging of surface or topography, the technology is coupled with analytical techniques such as energy dispersive spectroscopy for elemental mapping. Since the commercialization of the technology, it has developed manifold and currently very high-resolution nano scale imaging is possible by this technology. The development of FIB-SEM has allowed three-dimensional imaging of materials while the development of cryostage allows imaging of hydrated biological samples. Though variable pressure or environmental SEM can be used for imaging hydrated samples, they cannot capture a high-resolution image. SBEM and ATUM-SEM has automated the sampling process while improved and more powerful software along with user-friendly computer interface has made image analysis faster and more reliable. This review presents one of the most widely used analytical techniques used across the globe for scientific investigation. The power and potential of SEM is expanding with the development of accessory technology.
Comparative analysis of taper models for Pinus nigra: A study across parametric, semi-parametric, and non-parametric models using terrestrial laser scanner acquired data
Authors: Issam Boukhris, Nicola Puletti, Christian Vonderach, Matteo Guasti, Said Lahssini, Monia Santini, Riccardo Valentini
Date: 2023-10-31 00:00:00

Taper equations are indispensable tools for characterizing the stem profile of trees, providing valuable insights for forest management, timber inventory, and optimal assortments allocation. The recent progress in Terrestrial Laser Scanning (TLS) has revolutionized forest inventory practices by enabling non-destructive data collection. In this study, four taper models from three different model categories were established based on point cloud data of 219 Pinus nigra trees. The taper equations fitted with TLS data were used to predict the diameter at specific stem heights and the total stem volume. The results show that among fitted models, the Max and Burkhart segmented model calibrated by the means of a mixed-effects approach provided the best estimate of the diameter at different heights and the total stem volume evaluated for different diameter at breast height (DBH) classes. In numerical terms, this model estimated the diameter and the volume with a respective overall error of 0.781 cm and 0.021 m3. The predicted profile also shows that above a relative height of 0.7, the diameter error tends to increase due to the low reliability of data collected beyond the base of the crown primarily caused by interference from branches and leaves. Nevertheless, this study shows that TLS technology presents a compelling opportunity and a promising non-destructive alternative for generating taper profiles and estimating tree volume.
The management of obstructive sleep apnea accompanied with mandibular retrognathia across the lifespan from orthodontic perspective
Authors: Menghan Zhang, Yuehua Liu
Date: 2023-11-02 00:00:00
Tasks: Management

Obstructive sleep apnea (OSA) is a complex disease with complex etiology, which requires multidisciplinary cooperation in diagnosis and treatment. Mandibular retrognathia is strongly associated with OSA. Orthodontists can either correct the mandibular retrognathia of pediatric OSA via various kinds of orthodontic appliances, following adenoidectomy and tonsillectomy, or enlarge upper airway by mandibular advancement device (MAD) through repositioning the mandible and tongue of adult OSA patients. This mini review was to investigate the therapy of MAD to adult OSA as well as orthodontic treatment to pediatric OSA.