Miracle-dz/UniFAR-FTUs huggingface dataset:
Traffic Patrolling Routing Problem with Drones in an Urban Road System

The remarkable development of various sensor equipment and communication technologies has stimulated many application platforms of automation. A drone is a sensing platform with strong environmental adaptability and expandability, which is widely used in aerial photography, transmission line inspection, remote sensing mapping, auxiliary communication, traffic patrolling, and other fields. A drone is an effective supplement to the current patrolling business in road traffic patrolling with complex urban buildings and road conditions and a limited ground perspective. However, the limited endurance of patrol drones can be directly solved by vehicles that cooperate with drones on patrolling missions. In this paper, we first proposed and studied the traffic patrolling routing problem with drones (TPRP-D) in an urban road system. Considering road network equations and the heterogeneity of patrolling tasks in the actual patrolling process, we modeled the problem as a double-layer arc routing problem (DL-ARP). Based on graph theory and related research work, we present the mixed integer linear programming formulations and two-stage heuristic solution approaches to solve practical-sized problems. Through analysis of numerical experiments, the solution method proposed in this paper can quickly provide an optimal path planning scheme for different test sets, which can save 9%–16% of time compared with traditional vehicle patrol. At the same time, we analyze several relevant parameters of the patrol process to determine the effect of coordinated traffic patrol. Finally, a case study was completed to verify the practicability of the algorithm.
Herpes Simplex Virus Latency Is Noisier the Closer We Look

During herpes simplex virus (HSV) latency, the viral genome is harbored in peripheral neurons in the absence of infectious virus but with the potential to restart infection. Advances in epigenetics have helped explain how viral gene expression is largely inhibited during latency. Paradoxically, at the same time, the view that latency is entirely silent has been eroding. This low-level noise has implications for our understanding of HSV latency and should not be ignored. ABSTRACT During herpes simplex virus (HSV) latency, the viral genome is harbored in peripheral neurons in the absence of infectious virus but with the potential to restart infection. Advances in epigenetics have helped explain how viral gene expression is largely inhibited during latency. Paradoxically, at the same time, the view that latency is entirely silent has been eroding. This low-level noise has implications for our understanding of HSV latency and should not be ignored.
Proliferation of Ly6C+ monocytes/macrophages contributes to their accumulation in mouse skin wounds

Monocytes and macrophages (Mo/MΦ) play critical roles in all phases of skin wound healing. The majority of these cells are thought to be recruited from blood Mo; however, the role local proliferation of Mo/MΦ in the wound has not been defined. Therefore, we tested the hypothesis that local proliferation of Mo and/or MΦ contributes to their accumulation during wound healing. Male C57Bl/6 mice (N = 4–9/group) were subjected to excisional skin wounding. Proliferating Mo/MΦ (F4/80+Ki67+) were observed in wound cryosections, peaking on day 5 post‐wounding. Cell cycle analysis on cells isolated from skin tissue revealed that wounding increased both the number and percentage of inflammatory Ly6C+F4/80lo/− Mo/MΦ in the S/G2/M phases, peaking on day 6 post‐wounding. In contrast, more mature Ly6C‐F4/80+ cells were found predominantly in the G0 phase with less than 1% cells in S/G2/M phase following injury. In peripheral blood, Mo were very rarely found in the S/G2/M phase, suggesting that the wound environment triggered the Ly6C+F4/80lo/− Mo proliferative response. Furthermore, injury induced several potential regulators of proliferation in wounds, including IL‐1β and IL‐6, and wound Mo/MΦ expressed surface receptors for these cytokines. However, wound Mo/MΦ proliferation was not altered in IL‐1R1 knockout (KO) or IL‐6 KO mice. In summary, our findings indicate that proliferation contributes to Mo/MΦ accumulation in wounds and, contrary to findings in other pathophysiologic conditions, Ly6C+/F4/80lo/− Mo/MΦ proliferate during skin wound healing whereas mature Ly6C−F4/80+ MΦ do not.
Selection of optimal reference genes for qRT-PCR analysis of shoot development and graviresponse in prostrate and erect chrysanthemums

The prostrate cultivars of ground-cover chrysanthemum have been used in landscape gardening due to their small stature, large crown width and strong branching ability. qRT-PCR is a rapid and powerful tool for gene expression analysis, while its accuracy highly depends on the stability of reference genes. The paucity of authentic reference genes presents a major hurdle in understanding the genetic regulators of prostrate architecture. Therefore, in order to reveal the regulatory mechanism of prostrate growth of chrysanthemum stems, here, stable reference genes were selected for expression analysis of key genes involved in shoot development and graviresponse. Based on transcriptome data, eleven reference genes with relatively stable expression were identified as the candidate reference genes. After the comprehensive analysis of the stability of these reference genes with four programs (geNorm, NormFinder, BestKeeper and RefFinder), we found that TIP41 was the most stable reference gene in all of the samples. SAND was determined as a superior reference gene in different genotypes and during the process of shoot development. The optimal reference gene for gravitropic response was PP2A-1. In addition, the expression patterns of LA1 and PIN1 further verified the reliability of the screened reference genes. These results can provide more accurate and reliable qRT-PCR normalization for future studies on the expression patterns of genes regulating plant architecture of chrysanthemums.
RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data

Abstract Recently, newly developed ribosome profiling methods based on high-throughput sequencing of ribosome-protected mRNA footprints allow to study genome-wide translational changes in detail. However, computational analysis of the sequencing data still represents a bottleneck for many laboratories. Further, specific pipelines for quality control and statistical analysis of ribosome profiling data, providing high levels of both accuracy and confidence, are currently lacking. In this study, we describe automated bioinformatic and statistical diagnoses to perform robust quality control of ribosome profiling data (RiboQC), to efficiently visualize ribosome positions and to estimate ribosome speed (RiboMine) in an unbiased way. We present an R pipeline to setup and undertake the analyses that offers the user an HTML page to scan own data regarding the following aspects: periodicity, ligation and digestion of footprints; reproducibility and batch effects of replicates; drug-related artifacts; unbiased codon enrichment including variability between mRNAs, for A, P and E sites; mining of some causal or confounding factors. We expect our pipeline to allow an optimal use of the wealth of information provided by ribosome profiling experiments.
A Comprehensive Analysis of Runs of Homozygosity of Eleven Cattle Breeds Representing Different Production Types

Simple Summary Runs of homozygosity (ROH) regions are known to be common in the genomes of cattle and have become a subject of interest of various research in recent years. ROH can be used as a valuable tool to estimate inbreeding, which needs to be controlled in livestock populations. Moreover, analysis of ROH is considered to be an effective method of identifying genome regions that are a subject of selection pressure, which may help in understanding the genetic aspects of production traits under selection. In this study, we analyzed ROH characteristics of 11 cattle breeds, both commercial and native, maintained in Poland. We presented distinct differences in the length, quantity and frequency of ROH between the analyzed breeds as well as in the levels of genomic inbreeding. Higher levels of inbreeding were characteristic for commercial breeds, especially beef breeds. In addition, within ROH islands, we observed a number of genes with a confirmed influence on the level of production traits. The presented results and identified genes can be a basis for further research focused on the identification of genes and markers essential in the determination of the most important production traits in cattle. Abstract In the presented research, BovineSNP50 microarrays (Illumina) were applied to determine runs of homozygosity in the genomes of 11 cattle breeds maintained in Poland. These cattle breeds represent three basic utility types: milk, meat and dual purpose. Analysis of runs of homozygosity allowed the evaluation of the level of autozygosity within each breed in order to calculate the genomic inbreeding coefficient (FROH), as well as to identify regions of the genome with a high frequency of ROH occurrence, which may reflect traces of directional selectin left in their genomes. Visible differences in the length and distribution of runs of homozygosity in the genomes of the analyzed cattle breeds have been observed. The highest mean number and mean sums of lengths of runs of homozygosity were characteristic for Hereford cattle and intermediate for the Holstein-Friesian Black-and-White variety, Holstein-Friesian Red-and-White variety, Simmental, Limousin, Montbeliarde and Charolais breeds. However, lower values were observed for cattle of conserved breeds. Moreover, the selected livestock differed in the level of inbreeding estimated using the FROH coefficient. In regions of the genome with a high frequency of ROH occurrence, which may reflect the impact of directional selection, a number of genes were observed that can be potentially related to the production traits which are under selection pressure for specific production types. The most important detected genes were GHR, MSTN, DGAT1, FABP4, and TRH, with a known influence on the milk and meat traits of the studied cattle breeds.
Ostrich eggshell bead diameter in the Holocene: Regional variation with the spread of herding in eastern and southern Africa

Despite their ubiquity in Holocene African archaeological assemblages, ostrich eggshell (OES) beads are rarely studied in detail. An exception is in southern Africa, where there is a proposed relationship between OES bead diameter and the arrival of herding ~2000 years before present. In 1987, Leon Jacobson first observed that beads from forager sites in Namibia tended to be smaller than those associated with herder sites. Studies examining bead size around the Western Cape have generally confirmed Jacobson’s findings, though the driving forces of the diameter change remain unknown. Since this time, diameter has become an informal way of distinguishing forager and herder assemblages in southern Africa, but no large-scale studies of OES bead variation have been undertaken. Here we present an expanded analysis of Holocene OES bead diameters from southern, and for the first time, eastern Africa. Results reveal distinct patterns in OES bead size over time, reflecting different local dynamics associated with the spread of herding. In southern Africa, OES diameters display low variability and smaller absolute size through time. While larger beads begin to appear <2000 years ago, most beads in our study remained smaller. In contrast, eastern African OES bead diameters are consistently larger over the last 10,000 years and show no appreciable size change with the introduction of herding. Notably, larger beads thought to be associated with herders in southern Africa fall within the range of eastern African beads, indicating a potential connection between these regions in the Late Holocene consistent with genetic findings. Regional differences in bead size are subtle, on the order of millimeters, yet offer a potentially important line of evidence for investigating the spread of herding in sub-Saharan Africa. In order to understand the meaning of these changes, we encourage additional studies of OES bead assemblages and urge researchers to report individual bead diameters, rather than averages by level.
State of the Art of Underwater Active Optical 3D Scanners

Underwater inspection, maintenance and repair (IMR) operations are being increasingly robotized in order to reduce safety issues and costs. These robotic systems rely on vision sensors to perform fundamental tasks, such as navigation and object recognition and manipulation. Especially, active optical 3D scanners are commonly used due to the domain-specific challenges of underwater imaging. This paper presents an exhaustive survey on the state of the art of optical 3D underwater scanners. A literature review on light projection and light-sensing technologies is presented. Moreover, quantitative performance comparisons of underwater 3D scanners present in the literature and commercial products are carried out.
Effects of vaginal birth versus caesarean section on hearing screening results in a large series from the Aegean region

Abstract Objective: To evaluate the effects of caesarian section (CS) versus vaginal birth (VB) delivery techniques on results from neonatal hearing screening tests (NHSTs). Design: Retrospective analysis. Study sample: A total of 10,767 neonates divided into two groups according to delivery technique underwent NHSTs. Those who failed TEOAE or AABR were sent for diagnostic ABR examination. Results: A total of 5620 of 6044 (92.9%) of the neonates in the CS group passed the TEOAE test bilaterally and 424 (7.1%) failed either unilaterally or bilaterally. In the VB group, 4496 of 4723 (95.1%) neonates passed the TEOAE test bilaterally, while the remaining 227 (4.9%) failed the test either unilaterally or bilaterally. Bilateral passing rate of TEOAE test results was significantly higher in the VB group than the CS group (p < 0.05). The AABR failure rate (unilaterally or bilaterally) was 1% in the CS group, which was significantly higher than that in the VB group (0.6%). Diagnostic ABR bilateral pass rate was not statistically different between the groups. Conclusions: Delivery method was shown to affect the results of NHSTs. We found that the rates of failing the TEOAE and screening AABR examinations were higher among neonates born by CS compared to VB.
Stratified exercise therapy compared with usual care by physical therapists in patients with knee osteoarthritis: A randomized controlled trial protocol (OCTOPuS study)

Abstract Objectives Knee osteoarthritis (OA) is characterized by its heterogeneity, with large differences in clinical characteristics between patients. Therefore, a stratified approach to exercise therapy, whereby patients are allocated to homogeneous subgroups and receive a stratified, subgroup‐specific intervention, can be expected to optimize current clinical effects. Recently, we developed and pilot tested a model of stratified exercise therapy based on clinically relevant subgroups of knee OA patients that we previously identified. Based on the promising results, it is timely to evaluate the (cost‐)effectiveness of stratified exercise therapy compared with usual, “nonstratified” exercise therapy. Methods A pragmatic cluster randomized controlled trial including economic and process evaluation, comparing stratified exercise therapy with usual care by physical therapists (PTs) in primary care, in a total of 408 patients with clinically diagnosed knee OA. Eligible physical therapy practices are randomized in a 1:2 ratio to provide the experimental (in 204 patients) or control intervention (in 204 patients), respectively. The experimental intervention is a model of stratified exercise therapy consisting of (a) a stratification algorithm that allocates patients to a “high muscle strength subgroup,” “low muscle strength subgroup,” or “obesity subgroup” and (b) subgroup‐specific, protocolized exercise therapy (with an additional dietary intervention from a dietician for the obesity subgroup only). The control intervention will be usual best practice by PTs (i.e., nonstratified exercise therapy). Our primary outcome measures are knee pain severity (Numeric Rating Scale) and physical functioning (Knee Injury and Osteoarthritis Outcome Score subscale daily living). Measurements will be performed at baseline, 3‐month (primary endpoint), 6‐month (questionnaires only), and 12‐month follow‐up, with an additional cost questionnaire at 9 months. Intention‐to‐treat, multilevel, regression analysis comparing stratified versus usual care will be performed. Conclusion This study will demonstrate whether stratified care provided by primary care PTs is effective and cost‐effective compared with usual best practice from PTs.
Exploring Target Genes Involved in the Effect of Quercetin on the Response to Oxidative Stress in Caenorhabditis elegans

Quercetin is one the most abundant flavonoids in the human diet. Although it is well known that quercetin exhibits a range of biological activities, the mechanisms behind these activities remain unresolved. The aim of this work is to progress in the knowledge of the molecular mechanisms involved in the biological effects of quercetin using Caenorhabditis elegans as a model organism. With this aim, the nematode has been used to explore the ability of this flavonoid to modulate the insulin/insulin-like growth factor 1(IGF-1) signaling pathway (IIS) and the expression of some genes related to stress response. Different methodological approaches have been used, i.e., assays in knockout mutant worms, gene expression assessment by RT-qPCR, and C. elegans transgenic strains expressing green fluorescent protein (GFP) reporters. The results showed that the improvement of the oxidative stress resistance of C. elegans induced by quercetin could be explained, at least in part, by the modulation of the insulin signaling pathway, involving genes age-1, akt-1, akt-2, daf-18, sgk-1, daf-2, and skn-1. However, this effect could be independent of the transcription factors DAF-16 and HSF-1 that regulate this pathway. Moreover, quercetin was also able to increase expression of hsp-16.2 in aged worms. This observation could be of particular interest to explain the effects of enhanced lifespan and greater resistance to stress induced by quercetin in C. elegans, since the expression of many heat shock proteins diminishes in aging worms.
Co-infection of Dirofilaria immitis and Japanese encephalitis virus in a spotted seal (Phoca largha) in the Republic of Korea

A 10-year-old male spotted seal presented with loss of appetite and decreased activity. Grossly, the internal organs revealed several filarial nematodes in the right ventricle of the heart and the pulmonary vessels. Histopathological examination of the brain revealed moderate nonsuppurative meningoencephalitis with glial nodules and neuronophagia. Japanese encephalitis virus (JEV) of genotype I was isolated from the brain. All nematodes were identified as Dirofilaria immitis. This is the first clinical case of co-infection with D. immitis and JEV in a seal, suggesting that the seal, may be a dead-end host, like the human and horse, for JEV.
A quantitative single-cell assay for retrograde membrane traffic enables rapid detection of defects in cellular organization

Retrograde membrane trafficking from plasma membrane to Golgi and endoplasmic reticulum typifies one of the key sorting steps emerging from the early endosome that affects cell surface and intracellular protein dynamics underlying cell function. While some cell surface proteins and lipids are known to sort retrograde, there are few effective methods to quantitatively measure the extent or kinetics of these events. Here we took advantage of the well-known retrograde trafficking of cholera toxin and newly defined split fluorescent protein technology to develop a quantitative, sensitive, and effectively real-time single-cell flow cytometry assay for retrograde membrane transport. The approach can be applied in high throughput to elucidate the underlying biology of membrane traffic and how endosomes adapt to the physiologic needs of different cell types and cell states.
Workplace Bullying as Experienced by Managers and How They Cope: A Qualitative Study of Swedish Managers

Background: The aim of the study was to describe factors that contribute to the occurrence of workplace bullying, that enable it to continue and the coping strategies managers use when they are bullied. Methods: A qualitative study design was applied. Twenty-two managers from the private and public sectors were interviewed. Data were analyzed by means of content analysis. Results: Several factors could be linked to the bullying: being new in the managerial position; lack of clarity about roles and expectations; taking over a work group with ongoing conflicts; reorganizations. The bullying usually lasted for quite some time. Factors that allowed the bullying to continue were passive bystanders and the bullies receiving support from higher management. The managers in this study adopted a variety of problem-focused and emotion-focused coping strategies. However, in the end most chose to leave the organization. Only four remained in their managerial position at the time of the interview. Conclusions: The study concludes that bullying can occur in all types of organization. To prevent it we need to look primarily at organizational factors. Social support is also crucial for managers’ ability to cope successfully with bullying.
Selenocysteine Substitution into a Class I Ribonucleotide Reductase.

Ribonucleotide reductases (RNRs) employ a complex radical-based mechanism during nucleotide reduction involving multiple active site cysteines that both activate the substrate and reduce it. Using an engineered allo-tRNA, we substituted two active site cysteines with distinct function in the class Ia RNR of Escherichia coli for selenocysteine (U) via amber codon suppression, with efficiency and selectivity enabling biochemical and biophysical studies. Examination of the C439U α2 mutant protein interactions with nucleotide substrates and the cognate β2 subunit demonstrates that the endogenous Y122● of β2 is reduced under turnover conditions, presumably through radical transfer >35 Å to form a transient U439• species. This putative U439● species is formed in a kinetically competent fashion, but is incapable of initiating nucleotide reduction via 3´-H abstraction. An analogous C225U α2 protein is also capable of radical transfer from Y122●, but the radical-based substrate chemistry partitions between turnover and stalled reduction akin to the reactivity of mechanism-based inhibitors of RNR. The results collectively demonstrate the essential role of cysteine redox chemistry in the class I RNRs and establish a new tool for investigating thiyl radical reactivity in biology.