Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-Resolution 3D Convolutional Neural Networks for Automatic Coronary Centerline Extraction in Cardiac CT Angiography Scans

We propose a deep learning-based automatic coronary artery tree centerline tracker (AuCoTrack) extending the vessel work of [1]. A multi-resolution 3D Convolutional Neural Network (CNN) is employed to simultaneously predict movement directions and detect bifurcations. Moreover, an automated artery endpoint detector is used to prevent premature termination of the tracking process. On Coronary Computed Tomography Angiography (CCTA or coronary CTA) scans annotated by clinical experts, an average sensitivity of 87.1% and clinically relevant overlap of 89.1% could be obtained. In addition, the MICCAI 2008 Coronary Artery Tracking Challenge (CAT08) training and test datasets were used to benchmark the algorithm and to assess its generalization capabilities. On CAT08, an average overlap of 93.6% and a clinically relevant overlap of 96.4% were achieved.
On the linearity of large non-linear models: when and why the tangent kernel is constant

The goal of this work is to shed light on the remarkable phenomenon of transition to linearity of certain neural networks as their width approaches infinity. We show that the transition to linearity of the model and, equivalently, constancy of the (neural) tangent kernel (NTK) result from the scaling properties of the norm of the Hessian matrix of the network as a function of the network width. We present a general framework for understanding the constancy of the tangent kernel via Hessian scaling applicable to the standard classes of neural networks. Our analysis provides a new perspective on the phenomenon of constant tangent kernel, which is different from the widely accepted "lazy training". Furthermore, we show that the transition to linearity is not a general property of wide neural networks and does not hold when the last layer of the network is non-linear. It is also not necessary for successful optimization by gradient descent.
XDA: Accurate, Robust Disassembly with Transfer Learning

Accurate and robust disassembly of stripped binaries is challenging. The root of the difficulty is that high-level structures, such as instruction and function boundaries, are absent in stripped binaries and must be recovered based on incomplete information. Current disassembly approaches rely on heuristics or simple pattern matching to approximate the recovery, but these methods are often inaccurate and brittle, especially across different compiler optimizations. We present XDA, a transfer-learning-based disassembly framework that learns different contextual dependencies present in machine code and transfers this knowledge for accurate and robust disassembly. We design a self-supervised learning task motivated by masked Language Modeling to learn interactions among byte sequences in binaries. The outputs from this task are byte embeddings that encode sophisticated contextual dependencies between input binaries' byte tokens, which can then be finetuned for downstream disassembly tasks. We evaluate XDA's performance on two disassembly tasks, recovering function boundaries and assembly instructions, on a collection of 3,121 binaries taken from SPEC CPU2017, SPEC CPU2006, and the BAP corpus. The binaries are compiled by GCC, ICC, and MSVC on x86/x64 Windows and Linux platforms over 4 optimization levels. XDA achieves 99.0% and 99.7% F1 score at recovering function boundaries and instructions, respectively, surpassing the previous state-of-the-art on both tasks. It also maintains speed on par with the fastest ML-based approach and is up to 38x faster than hand-written disassemblers like IDA Pro.
The Cement Mechanical Activation Effective Application Field Determination

Of all the known methods for increasing the cement activity, mechanical grinding is distinguished in the work. For mechanical grinding, technological characteristics of grinding in an electromagnetic field are established (mill - linear induction rotator, LIV). The value of the increment of activity is determined depending on its initial (initial) value. To determine the estimated value of the cement consumption, the methods provided by the state standard of the Russian Federation were used. The experiments, as well as the measurement of the compressive strength (R), were carried out in accordance with the GOST requirements. The cement mechanical grinding effective application field in electromagnetic field is determined by comparing the costs and savings. The costs are calculated as the cost of electricity needed for grinding. The savings are the cost of the established difference between the cement consumption for the initial activity of cement and the actual value, which is able to provide the concrete with a given design strength. The results describing the field of the cement mechanical grinding effective application are presented in tabular form and graphically. When determining the area of the mechanical grinding effective use, the conclusion that it is necessary to adjust the technological grinding regimes depending on the initial activity of the cement, as well as on the chemical composition of the clinker (manufacturer) was confirmed. The prospects for the research on mechanical grinding technology are associated with obtaining grinding regimes depending on the initial size and composition of the clinker. The area of effective application of mechanical activation should be determined each time depending on the physical and mechanical cement properties.
Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox

Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
Evolutionary history of Mycobacterium leprae in the Pacific Islands

As one of the oldest known human diseases, leprosy or Hansen's disease remains a public health concern around the world with over 200 000 new cases in 2018. Most human leprosy cases are caused by Mycobacterium leprae, but a small number of cases are now known to be caused by Mycobacterium lepromatosis, a sister taxon of M. leprae. The global pattern of genomic variation in M. leprae is not well defined. Particularly, in the Pacific Islands, the origins of leprosy are disputed. Historically, it has been argued that leprosy arrived on the islands during nineteenth century colonialism, but some oral traditions and palaeopathological evidence suggest an older introduction. To address this, as well as investigate patterns of pathogen exchange across the Pacific Islands, we extracted DNA from 39 formalin-fixed paraffin-embedded biopsy blocks dating to 1992–2016. Using whole-genome enrichment and next-generation sequencing, we produced nine M. leprae genomes dating to 1998–2015 and ranging from 4-63× depth of coverage. Phylogenetic analyses indicate that these strains belong to basal lineages within the M. leprae phylogeny, specifically falling in branches 0 and 5. The phylogeographical patterning and evolutionary dating analysis of these strains support a pre-modern introduction of M. leprae into the Pacific Islands. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
Unknown Road Profile Input Estimation with Two Levels of Complexity Models

Most advanced driver assistance systems (ADAS) are intended to improve ride comfort for vehicle suspension systems. A new road estimation method is proposed as a means of observing the road profile level. To achieve this, two complexity levels (quarter car and half car models) are presented and developed in Matlab to analyze the vertical vibration of a vehicle. The unknown input observers are then designed for observing unknown states and road profile level. The necessary measurements are the accelerations of the centers of the wheels. The results of simulations conducted with random road excitation show successfully simulated experimentations of the method using a realistic simulator as well as its robustness.
Insecticide Rotations for the Management of Lepidopteran Pests in Cabbage and Collards

Abstract Insecticide rotations for the management of the diamondback moth, Plutella xylostella (L), and other lepidopteran pests of cabbage and collard crops were evaluated in 2010, 2011, and 2012 at Tifton, GA, with the intent of identifying mode of action rotations equal in efficacy to single insecticide mode of action treatments. This was to demonstrate how insecticide rotations, which are purported to aid in the prevention of insecticide resistance, can be an economically-viable insect control option in Brassica crops. The insecticides and mode of actions tested included: chlorantraniliprole and flubendiamide (ryanodine receptor modulators), spinetoram (nicotinic acetylcholine receptor allosteric activator), indoxacarb (voltage-dependent sodium channel blocker), Bacillus thuringiensis subsp. aizawai (microbial disrupter of insect midgut membranes), novaluron (inhibitor of chitin biosynthesis) and zeta-cypermethrin (sodium channel modulator). The results demonstrated that all rotations were equally effective in the control lepidoteran pests in Brassica crops to the use of single insecticide treatments and that at least one rotation treatment provided the highest marketable yield each year.
Maternal hyperthyroidism during pregnancy and offspring risks of attention-deficit/hyperactivity disorder and autism spectrum disorder: A nationwide study

Objective: Thyroid hormones are crucial in normal brain development. Abnormal thyroid hormones in pregnancy may impair neurodevelopment in the offspring. In this study, we intended to determine whether prenatal hyperthyroidism can increase the offspring risk of autism spectrum disorders (ASD) or attention-deficit/hyperactivity disorder (ADHD). Methods: In our study, we identified 330 study pairs (mothers with hyperthyroidism and their children) and 1,320 matched control pairs (mothers without hyperthyroidism and their children) between 1998 and 2008 from the Taiwan Longitudinal Health Insurance. The offspring risk of major neurodevelopmental disorders, including ADHD and ASD, was analyzed in the follow-up period (from childbirth to the end of 2011). Results: The results of logistic regression analysis using adjustment for demographic data and maternal mental health disorders showed that prenatal hyperthyroidism significantly increased the offspring risk of ADHD (odd ratio = 2.23; 95% confidence interval [CI] = 1.19–4.18, p < 0.05) and nonsignificantly increased the risk of ASD (odds ratio = 6.62; 95% CI = 1.08–40.47) after having adjusted for children's demographical data and for maternal mental disorders. Conclusion: Those results suggest that prenatal hyperthyroidism increased the risk of ADHD and ASD in offspring, regardless of demographic conditions and maternal mental health disorders. We suggest that hyperthyroidism in pregnant women should be carefully managed and that additional studies are necessary to clarify the underlying mechanisms which maternal hyperthyroidism leads to neurodevelopmental risks.
Liproxstatin-1 is an effective inhibitor of oligodendrocyte ferroptosis induced by inhibition of glutathione peroxidase 4

Our previous studies showed that ferroptosis plays an important role in the acute and subacute stages of spinal cord injury. High intracellular iron levels and low glutathione levels make oligodendrocytes vulnerable to cell death after central nervous system trauma. In this study, we established an oligodendrocyte (OLN-93 cell line) model of ferroptosis induced by RSL-3, an inhibitor of glutathione peroxidase 4 (GPX4). RSL-3 significantly increased intracellular concentrations of reactive oxygen species and malondialdehyde. RSL-3 also inhibited the main anti-ferroptosis pathway, i.e., SLC7A11/glutathione/glutathione peroxidase 4 (xCT/GSH/GPX4), and downregulated acyl-coenzyme A synthetase long chain family member 4. Furthermore, we evaluated the ability of several compounds to rescue oligodendrocytes from ferroptosis. Liproxstatin-1 was more potent than edaravone or deferoxamine. Liproxstatin-1 not only inhibited mitochondrial lipid peroxidation, but also restored the expression of GSH, GPX4 and ferroptosis suppressor protein 1. These findings suggest that GPX4 inhibition induces ferroptosis in oligodendrocytes, and that liproxstatin-1 is a potent inhibitor of ferroptosis. Therefore, liproxstatin-1 may be a promising drug for the treatment of central nervous system diseases.
Effect of lockdown on mental health during the COVID-19 pandemic among individuals attending services at a tertiary care center

Background: Lockdown is an emergency measure or condition in which people are temporarily prevented from entering or leaving a restricted area or building during a threat or danger. Since the start of COVID-19 till date, almost one-third of the world's population is under some degree of restriction and lockdown, and the mental health effect of which is something that is being discussed widely. Aim: The study aimed to assess the effect of lockdown on mental health among individuals (patients or accompanying person) seeking services at a tertiary care center. Materials and Methods: Kathmandu Medical College is a tertiary care center and a medical college in Kathmandu, Nepal. In this study, we enrolled every 4th individual coming to the hospital's outpatient department registration counter to seek service and giving consent, for the duration of 1 month during the ongoing lockdown period. A semi-structured questionnaire was developed and approved by the department and was used to collect sociodemographic details and to rate the stress level. The General Health Questionnaire (GHQ-12) Nepali version was used to assess psychological well-being of the participants and a score of ≥3 by binary method was taken as positive case. Results: The total number of cases enrolled in the study was 204, out of them 62.2% were male and 32.8% were female and the mean age was 32.03 years. Twenty-three percent (23.5%) had preexisting health conditions. Out of the 204 participants, 67.6% said they were stressed following the lockdown and the mean rated stress was 2.90 in a scale ranging from 1 to 7. The frequently identified stressors were fear of contamination, restricted movement, and for inadequate supplies. Twenty-seven percent said they had some psychological symptoms and the most common symptoms were palpitation and sleep disturbance. Seventy-three individuals (36.5%) were found to have psychiatric problem according to their scores in GHQ-12. Rated stress and GHQ-12 scores were found to be strongly correlated (P = 0.000). Similarly, those who stated “Yes” in psychological symptoms significantly scored higher on GHQ-12 and stress (both P = 0.000). Conclusion: The lockdown has caused stress in majority of cases, and a significant number of individuals have diagnosable mental health conditions. Mental health impact of the lockdown is something that needs to be addressed seriously.
Technical considerations for the generation of novel pseudotyped viruses

A pseudotyped virus (PV) is a virus particle with an envelope protein originating from a different virus. The ability to dictate which envelope proteins are expressed on the surface has made pseudotyping an important tool for basic virological studies such as determining the cellular targets of the envelope protein of the virus as well as identification of potential antiviral compounds and measuring specific antibody responses. In this review, we describe the common methodologies employed to generate PVs, with a focus on approaches to improve the efficacy of PV generation.
Postnatal therapeutic approaches in genetic neurodevelopmental disorders

Genetic neurodevelopmental disorders are characterized by abnormal neurophysiological and behavioral phenotypes, affecting individuals worldwide. While the subject has been heavily researched, current treatment options relate mostly to alleviating symptoms, rather than targeting the altered genome itself. In this review, we address the neurogenetic basis of neurodevelopmental disorders, genetic tools that are enabling precision research of these disorders in animal models, and postnatal gene-therapy approaches for neurodevelopmental disorders derived from preclinical studies in the laboratory.
The psychological impact of COVID-19 on the families of first-line rescuers

Under the COVID-19 epidemic, the families of front-line rescue workers are under unusual pressure. We aim to understand the extent of their psychological distress in this epidemic and whether they have received sufficient support. Thus targeted to provide support for them and indirectly reduce the concerns of the rescue workers. From February 27 to March 1, 2020, we used the scales of Perceived Stress Scale, 10-items Connor-Davidson Resilience Scale, Generalized Anxiety Disorder-7, Patient Health Questionnaire-2, and primary care-posttraumatic stress disorder (PTSD) to evaluate the mental health level of the family members of front-line rescue workers online. Six hundred and seventy one family members voluntarily filled out the questionnaire after reading the purpose of the study. A total of 671 family members of front-line rescue workers participated in the survey, including 194 husbands/wives, 52 parents, 49 children, 76 brothers and sisters, and 300 other relationships. Among them, 55% of the family members reported sleep problems, 49.0% of the family members had mild, and above anxiety symptoms, 12.2% of the family members reported clinically significant depression symptoms, and 10.4% of the family members may have PTSD, 8.3% of family members had thoughts of self-injury or suicide. The feeling of stress was positively correlated with anxiety and depression, but there was no significant correlation between psychological elasticity and various symptoms. Family members who are more worried about the safety, physical condition and living security of front-line rescue workers are more likely to report symptoms such as sleep disorders, anxiety, and depression. Family members' first-line rescue has a significant impact on their daily life, raising children and supporting the elderly, which is also related to the occurrence of mental and psychological symptoms. During the period of front-line support, they received support from the units or organizations of the first-line workers, mainly including telephone greetings and daily necessities. The top three concerns about the information of the epidemic were the time of the end of the epidemic, the time of the return of the family and the progress of COVID-19's treatment. After the end of the epidemic, what they most want to do is to pay more attention to and accompany their families, family gatherings, and do more exercise. The psychological impact of this epidemic on the families of front-line rescue workers is mainly sleep problems and anxiety. The psychological intervention of family members should mainly start from the relief of stress and increase of material and spiritual support.
33 Herpes Simplex Virus

The herpesviridae are a large family of double-strand DNA viruses responsible for many human and veterinary diseases (Appendix, Table VI). Although members of this family differ in tissue tropism and many aspects of their interactions with their hosts, the mechanisms by which they replicate their DNA during lytic infection are for the most part conserved. The molecular mechanisms involved in herpesvirus DNA replication and its regulation are of interest for several reasons. Herpesviruses provide important models for the study of eukaryotic DNA replication. Many of the replication proteins encoded by herpesviruses represent functional analogs of the eukaryotic DNA replication machinery. In addition, viral enzymes involved in DNA replication have provided a rich store of useful targets for antiviral therapy against herpesviruses. Herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are the most extensively studied of all the herpesviruses, in part because they are most amenable to genetic and biochemical approaches. DNA replication by the other herpesviruses resembles that of HSV, although there are also many interesting differences. Because there is not enough space to discuss other herpesviruses, this chapter focuses primarily on DNA replication of HSV-1. Because this chapter is intended to augment the chapter on herpesvirus DNA replication written for the previous edition of DNA Replication in Eukaryotic Cells , material draws primarily from work published in the last 9 years. Topics covered in detail in the previous chapter will reference the previous chapter and other review articles. HSV GENOME AND ORIGINS OF DNA REPLICATION The HSV genome is.
A Longitudinal Study of Aphasia Due to Pure Sub-Cortical Strokes

Introduction: Contemporary neuro-imaging techniques have significantly advanced our understanding of the brain organization of language and the involvement of subcortical areas in aphasia. However, articles on sub-cortical aphasia, particularly in non-western languages, remain to be few and far between. We set out to explore aphasia typology in sub-cortical strokes among Bengali-speaking population with a focus towards providing a longitudinal view over a period of 3 months post-stroke. Methods: Bengali version of Western Aphasia Battery (BWAB) was used to assess and classify language dysfunction in our study participants. Conventional brain imaging techniques (CT scan & MRI) were used to detect and localize strokes. Uni-variate analysis for categorical variable (location versus aphasia typology) was performed using Chi square and Fischer's exact test (as applicable). Directional measures were calculated using lambda and Goodman-Kruskal tau (Range of -1 to + 1). Boot strapping was applied while calculating the directional measures because of inadequate numbers in some sub-sections the sample. Results: Frequency of sub-cortical aphasia was observed to be 29.80% (62/208) in the index study. Four location of strokes were associated with language dysfunction, of which putamen (53.23%) was the commonest followed by striato-capsular region (33.87%). Thalamus and peri-ventricular white matter (PVWM) strokes (6.45% each) were infrequent in our sample of sub-cortical aphasia. Global aphasia (30/62, 48.38%) was the most frequent type observed in acute phase while Broca's aphasia (23/53, 43.39%) dominated among the follow up cases. Aphasia recovery (with follow up AQ of 90.0 or more) was observed in 12 (22.64%) patients of whom majority (8/12) had striato-capsular strokes. Conclusion: The present paper illustrates the epidemiological aspects as well as longitudinal course aphasia following pure sub-cortical strokes.