Miracle-dz/UniFAR-FTUs huggingface dataset:
Higher-order Kerr effect including the uncertainties of their nonlinear coefficients

We numerically generalize the nonlinear propagation Schrödinger equation by introducing contribution (to the nonlinear refractive index variation) factor α , only for the numerical investigation of the higher-order Kerr effect (HOKE) with the higher-order Kerr nonlinear coefficients (n4, n6, n8). Our results confirm that the uncertainties of the higher-order Kerr nonlinear coefficients have a non-negligible effect on propagation of the intense femtosecond laser pulse in air, when the HOKE is considered. The smaller the α the larger the defocusing that is caused by HOKE, and the weaker the clamping intensity, and the remoter the position where the filamentation starts, and the longer the length of filament. Moreover, the higher-order Kerr terms play a role before the plasma defocusing, if the HOKE is considered.
Flame detection method based on improved YOLO-v3

This paper proposes a flame detection method based on the deep learning target detection algorithm YOLOv3 (You Only Look Once). The adaptive channel enhancement module (SE Module) proposed in SENet (Squeeze-and-Excitation Networks) is integrated into YOLOv3, so that the network can focus on learning more important feature information, and increase the detection accuracy and reliability of the network. Aiming at the characteristics of flames, this paper uses the characteristics of YOLOv3 multi-scale detection and adds a fourth detection scale to improve the network's detection of small flame areas. Experiments show that the improved YOLOv3 algorithm can effectively detect flames of different shapes in various backgrounds, and improve the accuracy and recall rate of the model without affecting the detection rate.
Research on suspended terahertz hollow Bragg waveguide

A THz hollow-core Bragg waveguide constructed by cascading waveguide units with supporting bridges on different air rings is proposed. The influence of the supporting bridges on the transmission loss of the waveguide is demonstrated numerically. Results show that the supporting bridges in the first air ring play the most important role on the transmission loss. By reasonably selecting the length ratio of the waveguide units, the waveguide transmission loss can be reduced to less than 0.5 dB/m in range from 0.572 to 0.62THz, and the loss of the proposed Bragg waveguide are close to those of the IHC Bragg waveguide.
Beam hardening artifact removal by the fusion of FBP and deep neural networks

Beam hardening caused cupping and light or dark streaks are one of the major problems in computer tomographic imaging. There are many possibilities to manage beam hardening artifacts. Deep learning is a set of techniques that proved to be useful in various fields, and it is more and more commonly used in computer tomography as well. Our goal in this paper was to reduce beam hardening artifact using deep convolutional neural networks and to develop a model, which can improve the quality of the beam hardening distorted image with the presence of high amount of electrical noise. Moreover, we investigated various ways of fusing deep neural networks with the process of computer tomographic imaging. For these purposes we produced a large heterogeneous simulated dataset. We tested the performance of four convolutional networks-based methods for correcting the distorted data at various stages of the tomographic imaging pipeline. The evaluations were based on three different error measures. The evaluations have shown that the best result can be achieved by the method which makes the reconstructions step as a part a neural network. This method was capable of removing a significant amount of distortion in case of high level of electrical noise.
Tomography imaging based on three-color digital holography

This paper discusses an approach for simultaneous tomography based on three-color digital holography and recording monochrome holograms. The numerical processing of the monochrome holograms to yield the multiple views is described. The process for 3D reconstruction from aberration-free view of the object are presented. Experimental results establish the proof of principle.
Deep learning for automated focus quality detection in wafer inspection

Scanning Electron Microscopes (SEM) and Dual Beam Focused Ion Beam Microscopes (FIB-SEM) are essential tools used in the semiconductor industry and in relation to this work, for wafer inspection in the production of hard drives at Seagate. These microscopes provide essential metrology during the build and help determine process bias and control. However, these microscopes will naturally drift out of focus over time, and if not immediately detected the consequences of this include: incorrect measurements, scrap, wasted resources, tool down time and ultimately delays in production. This paper presents an automated solution that uses deep learning to remove anomalous images and determine the degree of blurriness for SEM and FIB-SEM images. Since its first deployment, the first of its kind at Seagate, it has replaced the need for manual inspection on the covered processes and mitigated delays in production, realizing return on investment in the order of millions of US dollars annually in both cost savings and cost avoidance. The proposed solution can be broken into two deep learning steps. First, we train a deep convolutional neural network, a RetinaNet object detector, to detect and locate a Region Of Interest (ROI) containing the main feature of the image. For the second step, we train another deep convolutional neural network using the ROI, to determine the sharpness of the image. The second model identifies focus level based on a training dataset consisting of synthetically degraded infocus images, based on work by Google Research, achieving up to 99.3% test set accuracy.
Using Whole Genome Sequences to Investigate Adenovirus Outbreaks in a Hematopoietic Stem Cell Transplant Unit

A recent surge in human mastadenovirus (HAdV) cases, including five deaths, amongst a haematopoietic stem cell transplant population led us to use whole genome sequencing (WGS) to investigate. We compared sequences from 37 patients collected over a 20-month period with sequences from GenBank and our own database of HAdVs. Maximum likelihood trees and pairwise differences were used to evaluate genotypic relationships, paired with the epidemiological data from routine infection prevention and control (IPC) records and hospital activity data. During this time period, two formal outbreaks had been declared by IPC, while WGS detected nine monophyletic clusters, seven were corroborated by epidemiological evidence and by comparison of single-nucleotide polymorphisms. One of the formal outbreaks was confirmed, and the other was not. Of the five HAdV-associated deaths, three were unlinked and the remaining two considered the source of transmission. Mixed infection was frequent (10%), providing a sentinel source of recombination and superinfection. Immunosuppressed patients harboring a high rate of HAdV positivity require comprehensive surveillance. As a consequence of these findings, HAdV WGS is being incorporated routinely into clinical practice to influence IPC policy contemporaneously.
Pre-Treatment Neutrophil Count as a Predictor of Antituberculosis Therapy Outcomes: A Multicenter Prospective Cohort Study

Background Neutrophils have been associated with lung tissue damage in many diseases, including tuberculosis (TB). Whether neutrophil count can serve as a predictor of adverse treatment outcomes is unknown. Methods We prospectively assessed 936 patients (172 HIV-seropositive) with culture-confirmed pulmonary TB, enrolled in a multicenter prospective cohort study from different regions in Brazil, from June 2015 to June 2019, and were followed up to two years. TB patients had a baseline visit before treatment (month 0) and visits at month 2 and 6 (or at the end of TB treatment). Smear microscopy, and culture for Mycobacterium tuberculosis (MTB) were performed at TB diagnosis and during follow-up. Complete blood counts were measured at baseline. Treatment outcome was defined as either unfavorable (death, treatment failure or TB recurrence) or favorable (cure or treatment completion). We performed multivariable logistic regression, with propensity score regression adjustment, to estimate the association between neutrophil count with MTB culture result at month 2 and unfavorable treatment outcome. We used a propensity score adjustment instead of a fully adjusted regression model due to the relatively low number of outcomes. Results Among 682 patients who had MTB culture results at month 2, 40 (5.9%) had a positive result. After regression with propensity score adjustment, no significant association between baseline neutrophil count (103/mm3) and positive MTB culture at month 2 was found among either HIV-seronegative (OR = 1.06, 95% CI = [0.95;1.19] or HIV-seropositive patients (OR = 0.77, 95% CI = [0.51; 1.20]). Of 691 TB patients followed up for at least 18 months and up to 24 months, 635 (91.9%) were either cured or completed treatment, and 56 (8.1%) had an unfavorable treatment outcome. A multivariable regression with propensity score adjustment found an association between higher neutrophil count (103/mm3) at baseline and unfavorable outcome among HIV-seronegative patients [OR= 1.17 (95% CI= [1.06;1.30]). In addition, adjusted Cox regression found that higher baseline neutrophil count (103/mm3) was associated with unfavorable treatment outcomes overall and among HIV-seronegative patients (HR= 1.16 (95% CI = [1.05;1.27]). Conclusion Increased neutrophil count prior to anti-TB treatment initiation was associated with unfavorable treatment outcomes, particularly among HIV-seronegative patients. Further prospective studies evaluating neutrophil count in response to drug treatment and association with TB treatment outcomes are warranted.
Upregulation of Nogo‐B by hypoxia inducible factor‐1 and activator protein‐1 in hepatocellular carcinoma

Nogo‐B is an important regulator of tumor angiogenesis. Expression of Nogo‐B is remarkably upregulated in multiple tumor types, especially hepatocellular carcinoma (HCC). Here, we show the transcriptional regulation mechanisms of Nogo‐B in liver cancer. In response to hypoxia, expression of Nogo‐B significantly increased in HCC tissues and cells. The distal hypoxia‐responsive element in the promoter was essential for transcriptional activation of Nogo‐B under hypoxic conditions, which is the specific site for hypoxia inducible factor‐1α (HIF‐1α) binding. In addition, Nogo‐B expression was associated with c‐Fos expression in HCC tissues. Nogo‐B expression was induced by c‐Fos, yet inhibited by a dominant negative mutant A‐Fos. Deletion and mutation analysis of the predicted activator protein‐1 binding sites revealed that functional element mediated the induction of Nogo‐B promoter activity, which was confirmed by ChIP. These results indicate that HIF‐1α and c‐Fos induce the expression of Nogo‐B depending on tumor microenvironments, such as hypoxia and low levels of nutrients, and play a role in upregulation of Nogo‐B in tumor angiogenesis.
Interacting effects of cold snaps, rain, and agriculture on the fledging success of a declining aerial insectivore

Climate change predicts the increased frequency, duration, and intensity of inclement weather periods, such as unseasonably low temperatures (i.e., cold snaps) and prolonged precipitation. Many migratory species have advanced the phenology of important life history stages, and as a result will likely be exposed to these periods of inclement spring weather more often, thus risking reduced fitness and population growth. For declining avian species, including aerial insectivores, anthropogenic landscape changes such as agricultural intensification are another driver of population declines. These landscape changes may affect the foraging ability of food provisioning parents, and reduce the survival of nestlings exposed to inclement weather, through for example pesticide exposure impairing thermoregulation and punctual anorexia. Breeding in agro-intensive landscapes may thus exacerbate the negative effects of inclement weather under climate change. We observed that a significant reduction in the availability of insect prey occurred when daily maximum temperatures fell below 18.3°C, and thereby defined any day where the maximum temperature fell below this value as a day witnessing a cold snap. We then combined daily information on the occurrence of cold snaps and measures of precipitation to assess their impact on the fledging success of Tree Swallows (Tachycineta bicolor) occupying a nest box system placed across a gradient of agricultural intensification. Estimated fledging success of this declining aerial insectivore was 36.2% lower for broods experiencing four cold snap days during the 12 days post hatching period versus broods experiencing none, and this relationship was worsened when facing more precipitation. We further found that the overall negative effects of a brood experiencing periods of inclement weather was exacerbated in more agro-intensive landscapes. Our results indicate that two of the primary hypothesized drivers of many avian population declines may interact to further increase the rate of declines in certain landscape contexts.
Delayed effects of climate on vital rates lead to demographic divergence in Amazonian forest fragments

Deforestation often results in landscapes where remaining forest habitat is highly fragmented, with remnants of different sizes embedded in an often highly contrasting matrix. Local extinction of species from individual fragments is common, but the demographic mechanisms underlying these extinctions are poorly understood. It is often hypothesized that altered environmental conditions in fragments drive declines in reproduction, recruitment, or survivorship. The Amazon basin, in addition to experiencing continuing fragmentation, is experiencing climate change related increases in the frequency and intensity of droughts and unusually wet periods. Whether plant populations in tropical forest fragments are particularly susceptible to extremes in precipitation remains unclear. Most studies of plants in fragments are relatively short (1–6 years), focus on a single life-history stage, and often do not compare to populations in continuous forest. Even fewer studies consider delayed effects of climate on demographic vital rates despite the importance of delayed effects in studies that consider them. Using a decade of demographic and climate data from an experimentally fragmented landscape in the Central Amazon, we assess the effects of climate on populations of an understory herb (Heliconia acuminata, Heliconiaceae). We used distributed lag non-linear models to understand the delayed effects of climate (measured as standardized precipitation evapotranspiration index, SPEI) on survival, growth, and flowering. We detected delayed effects of climate up to 36 months. Extremes in SPEI in the previous year reduced survival, drought in the wet season 8–11 months prior to the February census increased growth, and drought two dry seasons prior increased flowering probability. Effects of extremes in precipitation on survival and growth were more pronounced in forest fragments compared to continuous forest. The complex delayed effects of climate and habitat fragmentation in our study point to the importance of long-term demography experiments in understanding the effects of anthropogenic change on plant populations.
The P-selectin ligand PSGL-1 (CD162) is efficiently incorporated by primary HIV-1 isolates and can facilitate trans-infection

While P-selectin glycoprotein ligand-1 (PSGL-1/CD162) has been studied extensively for its role in mediating leukocyte rolling through interactions with its receptor, P-selectin, recently, it was identified as a novel HIV-1 host restriction factor. One key mechanism of HIV-1 restriction is the ability of PSGL-1 to be physically incorporated into the external viral envelope, which effectively reduces infectivity by blocking virus attachment through the steric hindrance caused by its large ectodomain. Importantly, a large portion of the literature demonstrating the antiviral activity of PSGL-1 has utilized viruses produced in transfected cells which express high levels of PSGL-1. However, herein we show that virion-incorporated PSGL-1 is far less abundant on the surface of viruses produced via infection of physiologically relevant models (T cell lines and primary cells) compared to transfection (overexpression) models. Unique to this study, we show that PSGL-1 is incorporated in a broad range of HIV-1 and SIV isolates, supporting the physiological relevance of this incorporation. We also report that high levels of virion-incorporated PSGL-1 are detectable in plasma from viremic HIV-1 infected individuals, further corroborating the clinical relevance of PSGL-1 in natural infection. Additionally, we show that PSGL-1 on viruses is functionally active and can bind its cognate receptor, P-selectin, and that virions captured via P-selectin can subsequently be transferred to HIV-permissive bystander cells in a model of trans-infection. Taken together, our data suggest that PSGL-1 may have diverse roles in the physiology of HIV-1 infection, not restricted to the current antiviral paradigm. IMPORTANCE PSGL-1 is an HIV-1 host restriction factor which reduces viral infectivity by physically incorporating into the envelope of virions. While the antiviral effects of PSGL-1 in viruses produced by transfection models is profound, HIV-1 continues to remain infectious when produced through natural infection, even when PSGL-1 is incorporated. To study this discordance, we compared the differences in infectivity and PSGL-1 abundance in viruses produced by transfection or infection. Viruses produced via transfection contained unnaturally high levels of incorporated PSGL-1 compared to viruses from primary cells, and were much less infectious. We also found PSGL-1 to be present on a broad range of HIV-1 isolates, including those found in plasma from HIV-infected patients. Remarkably, we show that virion-incorporated PSGL-1 facilitates virus capture and transfer to HIV-permissive host cells via binding to P-selectin. These findings suggest that PSGL-1 may also work to enhance infection in vivo.
Complex basis of hybrid female sterility and Haldane’s rule in Heliconius butterflies: Z-linkage and epistasis

Hybrids between diverging populations are often sterile or inviable. Hybrid unfitness usually evolves first in the heterogametic sex – a pattern known as Haldane’s rule. The genetics of Haldane’s Rule have been extensively studied in species where the male is the heterogametic (XX/XY) sex, but its basis in taxa where the female is heterogametic (ZW/ZZ), such as Lepidoptera and birds, is largely unknown. Here, we analyse a new case of female hybrid sterility between geographic subspecies of Heliconius pardalinus. The two subspecies mate freely in captivity, but female F1 hybrids in both directions of cross are sterile. Sterility is due to arrested development of oocytes after they become differentiated from nurse cells, but before yolk deposition. We backcrossed fertile male F1 hybrids to parental females, and mapped quantitative trait loci (QTLs) for female sterility. We also identified genes differentially expressed in the ovary, and as a function of oocyte development. The Z chromosome has a major effect, similar to the “large X effect” in Drosophila, with strong epistatic interactions between loci at either end of the Z chromosome, and between the Z chromosome and autosomal loci on chromosomes 8 and 20. Among loci differentially expressed between females with arrested vs. non-arrested ovary development, we identified six candidate genes known also from Drosophila melanogaster and Parage aegeria oogenesis. This study is the first to characterize hybrid sterility using genome mapping in the Lepidoptera. We demonstrate that sterility is produced by multiple complex epistastic interactions often involving the sex chromosome, as predicted by the dominance theory of Haldane’s Rule.
The convergent CTCF loop formed by DNA extrusion is the basis of promoter enhancer interactions

The connections between HiC data and DNA extrusion have not been fully understood. In this study, we proposed a new method to reconstruct the DNA extrusion scenarios through modeling the aggregated HiC pattern. We examined several DNA extrusion scenarios which specify how promoters, enhancers, and CTCF binding sites interact with other regions. In particular, we showed that about half of all promoters tend to search enhancers in a specific direction. The underlying DNA extrusion scenario is characterized by a divergent CTCF pair and the imbalanced DNA extrusion activities which pull the promoters to a specific direction. Our findings proposed that most promoters do not contact enhancers directly. In contrast, promoters and enhancers are brought in proximity by the convergent CTCF loops.
Comprehensive analysis of full-length transcripts reveal aberrations of splicing variants in liver cancer

Genes generate various transcripts by alternative splicing, and these transcripts can have diverse functions. However, in most transcriptome studies, short-reads sequencing technologies (next-generation sequencers) have been used and full-length transcripts have not been observed directly. Although long-reads sequencing technologies would enable us to sequence full-length transcripts, analysis of the data is a difficult task. In the present study, we developed an analysis pipeline named SPLICE to analyze full-length cDNA sequences. Using this method, we analyzed cDNA sequences from 42 pairs of hepatocellular carcinoma (HCC) and matched non-cancerous liver with Oxford Nanopore technology. Our analysis detected 46,663 transcripts from the protein-coding genes in the HCCs and the matched non-cancerous livers, of which 5,366 (11.5 %) were novel. Comparison of expression levels identified 9,933 differentially expressed transcripts (DETs) in 4,744 genes. Importantly, 746 genes with DET were not found by the gene-level analysis. We also identified novel exons derived from transposable elements (TEs). In the analysis of transcripts from hepatitis B virus (HBV), HBx-human TE fusions were found to be overexpressed in the HCCs. Furthermore, fusion gene detection showed novel recurrent fusion events. These results suggest that long-reads sequencing technologies allow us to analyze full-length transcripts, and show the importance of splicing variants in carcinogenesis.