Miracle-dz/UniFAR-FTUs huggingface dataset:
Initial implementations of point-to-point Ethernet over SONET/SDH transport

There is considerable interest in using Ethernet over SONET/SDH (EoS) for Ethernet transport in a wide area network. EoS leverages the existing SONET/SDH infrastructure to provide efficient Ethernet transport with excellent OAM capabilities. In our initial evaluations and deployments of EoS, we have encountered some issues, as is common with any new technology. These issues include non-transparent transport of Ethernet information, lack of carrier-class performance monitoring and fault propagation, and non-standardized implementation of basic concepts. Vendors, service providers, and standards bodies should work together to resolve these remaining issues and thus bring forth the full potential of EoS.
Analyses of Tissue Culture Adaptation of Human Herpesvirus-6A by Whole Genome Deep Sequencing Redefines the Reference Sequence and Identifies Virus Entry Complex Changes

Tissue-culture adaptation of viruses can modulate infection. Laboratory passage and bacterial artificial chromosome (BAC)mid cloning of human cytomegalovirus, HCMV, resulted in genomic deletions and rearrangements altering genes encoding the virus entry complex, which affected cellular tropism, virulence, and vaccine development. Here, we analyse these effects on the reference genome for related betaherpesviruses, Roseolovirus, human herpesvirus 6A (HHV-6A) strain U1102. This virus is also naturally “cloned” by germline subtelomeric chromosomal-integration in approximately 1% of human populations, and accurate references are key to understanding pathological relationships between exogenous and endogenous virus. Using whole genome next-generation deep-sequencing Illumina-based methods, we compared the original isolate to tissue-culture passaged and the BACmid-cloned virus. This re-defined the reference genome showing 32 corrections and 5 polymorphisms. Furthermore, minor variant analyses of passaged and BACmid virus identified emerging populations of a further 32 single nucleotide polymorphisms (SNPs) in 10 loci, half non-synonymous indicating cell-culture selection. Analyses of the BAC-virus genome showed deletion of the BAC cassette via loxP recombination removing green fluorescent protein (GFP)-based selection. As shown for HCMV culture effects, select HHV-6A SNPs mapped to genes encoding mediators of virus cellular entry, including virus envelope glycoprotein genes gB and the gH/gL complex. Comparative models suggest stabilisation of the post-fusion conformation. These SNPs are essential to consider in vaccine-design, antimicrobial-resistance, and pathogenesis.
The components of shear stress affecting insect cells used with the baculovirus expression vector system

Abstract Insect-based expression platforms such as the baculovirus expression vector system (BEVS) are widely used for the laboratory- and industrial-scale production of recombinant proteins. Thereby, major drawbacks to gain high-quality proteins are the lytic infection cycle and the shear sensitivity of infected insect cells due to turbulence and aeration. Smaller bubbles were formerly assumed to be more harmful than larger ones, but we found that cell damage is also dependent on the concentration of protective agents such as Pluronic®. At the appropriate concentration, Pluronic forms a layer around air bubbles and hinders the attachment of cells, thus limiting the damage. In this context, we used microaeration to vary bubble sizes and confirmed that size is not the most important factor, but the total gas surface area in the reactor is. If the surface area exceeds a certain threshold, the concentration of Pluronic is no longer sufficient for cell protection. To investigate the significance of shear forces, a second study was carried out in which infected insect cells were cultivated in a hollow fiber module to protect them from shear forces. Both model studies revealed important aspects of the design and scale-up of BEVS processes for the production of recombinant proteins.
Lessons learned from the total evacuation of a hospital after the 2016 Kumamoto Earthquake.

BACKGROUND The 2016 Kumamoto Earthquakes were a series of earthquakes that included a foreshock earthquake (magnitude 6.2) on April 14 and a main shock (magnitude 7.0) on April 16, 2016. A number of hospitals in Kumamoto were severely damaged by the two major earthquakes and required total evacuation. METHODS The authors retrospectively analyzed the activity data of the Disaster Medical Assistance Teams using the Emergency Medical Information System records to investigate the cases in which the total evacuation of a hospital was attempted following the 2016 Kumamoto Earthquake. RESULTS Total evacuation was attempted at 17 hospitals. The evacuation of one of these hospitals was canceled. Most of the hospital buildings were more than 20 years old. The danger of collapse was the most frequent reason for evacuation. Various transportation methods were employed, some of which involved the Japan Ground Self-Defense Force; no preventable deaths occurred during transportation. CONCLUSIONS The hospitals must now be renovated to improve their earthquake resistance. The coordinated and combined use of military and civilian resources is beneficial and can significantly reduce human suffering in large-scale disasters.
Single-View Performance Monitoring of On-Line Applications Running on a Cloud

An important concern for current IaaS cloud providers is to be falsely accused by cloud users for the response delays of their applications running on the cloud. Since cloud computing brings an additional virtualization layer between guest-OS and hardware resources, the relationship between the performance of an application and its resource consumption becomes obscure. Only monitoring resource consumption (e.g., CPU, memory, disk I/O and so on) is often inadequate to detect the QoS degradation of a deployed application, not to mention resolving cloud users' QoS complaints. In this paper, we introduce a novel single-view performance visualization technique for a cloud platform to monitor the response delays of all the on-line applications running on it. Our technique sniffs network packets from a network switch in the platform and analyzes their flow to estimate the response time of each application. An important merit of this approach is the easy installation into a cloud platform. Concretely, our approach only requires changing the configuration of a network switch to enable port mirroring. To detect and visualize the response delay of each application in a single view, we convert the absolute response time of each application to a comparable value of delay degree ("delay ratio") which shows how serious the response delays compared to its baseline. The baseline is the service time of each application, which we estimate from the distribution of observed response times (service time + waiting time) by adopting an exponentially modified Gaussian (EMG) distribution fitting with an outlier elimination. We validate our approach through extensive experiments of a representative on-line application benchmark (RUBBoS). The results show high repeatability of the service time estimation (the standard deviation of 40 trials is 0.11). The results also show that our performance monitoring technique is able to accurately visualize response delays even when a training set of response times has a heavy-tailed distribution.
Translating the Social-Ecological Perspective Into Multilevel Interventions for Family Planning

Scholars and practitioners frequently make recommendations to develop family planning interventions that are “multilevel. ” Such interventions take explicit account of the role of environments by incorporating multilevel or social-ecological frameworks into their design and implementation. However, research on how interventions have translated these concepts into practice in the field of family planning—and generally in public health—remains scarce. This article seeks to review the current definitions of multilevel interventions and their operationalization in the field of family planning. First, we highlight the divergent definitions of multilevel interventions and show the persistent ambiguity around this term. We argue that interventions involving activities at several levels but lacking targets (i.e., objectives) to create change on more than one level have not incorporated a social-ecological framework and should therefore not be considered as “multilevel. ” In a second step, we assess the extent to which family planning interventions have successfully incorporated a social-ecological framework. To this end, the 63 studies featured in Mwaikambo et al.’s systematic review on family planning interventions were reexamined. This assessment indicates that the multilevel or social-ecological perspective has seldom been translated into interventions. Specifically, the majority of interventions involved some form of activity at the community and/or organizational level, yet targeted and measured intrapersonal change as opposed to explicitly targeting/measuring environmental modification.
Detecting the Sybil Attack Cooperatively in Wireless Sensor Networks

Sybil attack is a network threat introduced by one or more malicious nodes to declare numerous illegal identifies to confuse or even collapse the network applications. A new detection mechanism, called CRSD, is proposed for static wireless sensor networks, which takes use of the received signal strength (RSS) to infer the distance between two identities and further determines the positions relation of the interesting identities by use of the RSS information from multiple neighbor nodes, e.g., via node cooperation. A Sybil attack is detected when two or more different identities have almost the same position. The analysis and simulation results show that, first, Sybil attack deteriorates the system performance significantly and second, CRSD can detect such attack in most cases, thus protecting the overall performance effectively.
[POSTER] Decision Forest For Efficient and Robust Camera Relocalization

To robustly estimate the pose, classical methods assume some geometrical and temporal assumptions (SfM: Structure from Motion, SLAM: Simultaneous Localization and mapping). These approaches take a pair of images as input and establish correspondences based on global strategy (using the whole image information) or sparse strategy (using key-points features). These correspondences allow solving a set of linear equations related to the 3D information and camera pose in that environment. These past years, machine learning has been considered as an efficient way to tackle different problems in image processing and computer vision fields. To handle the task in hand, we propose to learn directly the mapping function between the acquired information from the camera and its pose using sparse decision forest. We achieved state-of the-art results on public and on our databases.
Resistance to HIV Integrase Inhibitors: About R263K and E157Q Mutations

The use of integrase inhibitors (INI) is increasing in antiretroviral therapies (ART) and INI are not all equal regarding genetic barrier to resistance. The aim of this manuscript was to review main in vivo and in vitro knowledge about two particular integrase resistance-associated mutations: R263K and E157Q. The R263K mutation was the first mutation rarely found selected at time of virological failure in patients failing a first-line dolutegravir-based treatment. Further in vitro studies on R263K mutants showed a moderate increase in phenotypic resistance level and a drastic reduction in viral replicative capacity. No compensatory mutations were evidenced. The E157Q mutation is polymorphic, found between 1.7% and 5.6% of viral sequences issued from ART-naïve patients depending on the viral subtype; as well as acquired resistance emerging at failure of a raltegravir-based regimen in two case reports. We reported data on phenotypic resistance level of E157Q mutants and virological response of patients harboring a E157Q virus initiating an INI-based regimen, showing that dolutegravir might be the most recommended INI in such patients. These findings show that there is still a need for a better understanding of resistance mechanisms to INI and emphasized the importance of genotypic background in viral evolution under drug pressure.
Transcriptomic and Metabolomic Reprogramming from Roots to Haustoria in the Parasitic Plant, Thesium chinense

Abstract Most plants show remarkable developmental plasticity in the generation of diverse types of new organs upon external stimuli, allowing them to adapt to their environment. Haustorial formation in parasitic plants is an example of such developmental reprogramming, but its molecular mechanism is largely unknown. In this study, we performed field-omics using transcriptomics and metabolomics to profile the molecular switch occurring in haustorial formation of the root parasitic plant, Thesium chinense, collected from its natural habitat. RNA-sequencing with de novo assembly revealed that the transcripts of very long chain fatty acid (VLCFA) biosynthesis genes, auxin biosynthesis/signaling-related genes and lateral root developmental genes are highly abundant in the haustoria. Gene co-expression network analysis identified a network module linking VLCFAs and the auxin-responsive lateral root development pathway. GC-TOF-MS analysis consistently revealed a unique metabolome profile with many types of fatty acids in the T. chinense root system, including the accumulation of a 25-carbon long chain saturated fatty acid in the haustoria. Our field-omics data provide evidence supporting the hypothesis that the molecular developmental machinery used for lateral root formation in non-parasitic plants has been co-opted into the developmental reprogramming of haustorial formation in the linage of parasitic plants.
Organized abuse in adulthood: Survivor and professional perspectives

ABSTRACT This paper reports on the preliminary findings of a qualitative study of Australian women disclosing organized abuse in adulthood and the mental health professionals who treat them. Drawing on interviews with survivors and mental health professionals, the paper analyses the fraught relationship between mental health and physical safety for adults subject to organized abuse. The therapeutic progress of adult organized abuse victims can be disrupted by ongoing threats, stalking, and group violence, which in turn reinforces the dissociative responses and pathological attachments that render them vulnerable to revictimization. The paper argues that breaking this cycle requires intervention from multiple agencies, and describes the responses of police, medical services, and child protection services to adult organized abuse from the perspective of survivors and mental health practitioners. Highlighting systemic failures but also opportunities, the paper calls for a coordinated response to organized abuse in adulthood, including inter-agency partnerships to support safety and bolster the efficacy of therapeutic interventions.
Hydroxylation of CYP11A1-Derived Products of Vitamin D3 Metabolism by Human and Mouse CYP27B1

CYP11A1 can hydroxylate vitamin D3 at carbons 17, 20, 22, and 23, producing a range of secosteroids which are biologically active with respect to their ability to inhibit proliferation and stimulate differentiation of various cell types, including cancer cells. As 1α-hydroxylation of the primary metabolite of CYP11A1 action, 20S-hydroxyvitamin D3 [20(OH)D3], greatly influences its properties, we examined the ability of both human and mouse CYP27B1 to 1α-hydroxylate six secosteroids generated by CYP11A1. Based on their kcat/Km values, all CYP11A1-derived metabolites are poor substrates for CYP27B1 from both species compared with 25-hydroxyvitamin D3. No hydroxylation of metabolites with a 17α-hydroxyl group was observed. 17α,20-Dihydroxyvitamin D3 acted as an inhibitor on human CYP27B1 but not the mouse enzyme. We also tested CYP27B1 activity on 20,24-, 20,25-, and 20,26-dihydroxyvitamin D3, which are products of CYP24A1 or CYP27A1 activity on 20(OH)D3. All three compounds were metabolized with higher catalytic efficiency (kcat/Km) by both mouse and human CYP27B1 than 25-hydroxyvitamin D3. CYP27B1 action on these new dihydroxy derivatives was confirmed to be 1α-hydroxylation by mass spectrometry and nuclear magnetic resonance analyses. Both 1,20,25- and 1,20,26- trihydroxyvitamin D3 were tested for their ability to inhibit melanoma (SKMEL-188) colony formation, and were significantly more active than 20(OH)D3. This study shows that CYP11A1-derived secosteroids are 1α-hydroxylated by both human and mouse CYP27B1 with low catalytic efficiency, and that the presence of a 17α-hydroxyl group completely blocks 1α-hydroxylation. In contrast, the secondary metabolites produced by subsequent hydroxylation of 20(OH)D3 at C24, C25, or C26 are very good substrates for CYP27B1.
An efficient inverse BEM algorithm to characterize space dependent thermal conductivity with an evolutionary-genetic approach

A Genetic Algorithm approach is used as an optimization tool combined with the generalized BEM formulation for heat conduction in heterogeneous media to estimate space varying thermal conductivities. A least-squares functional measuring the difference between over-imposed observed temperatures and current temperatures generated by the BEM under current thermal conductivity is minimized using a Genetic Algorithm.
Addiction of Hypertransformable Pneumococcal Isolates to Natural Transformation for In Vivo Fitness and Virulence

ABSTRACT Natural genetic transformation of Streptococcus pneumoniae, an important human pathogen, mediates horizontal gene transfer for the development of drug resistance, modulation of carriage and virulence traits, and evasion of host immunity. Transformation frequency differs greatly among pneumococcal clinical isolates, but the molecular basis and biological importance of this interstrain variability remain unclear. In this study, we characterized the transformation frequency and other associated phenotypes of 208 S. pneumoniae clinical isolates representing at least 30 serotypes. While the vast majority of these isolates (94.7%) were transformable, the transformation frequency differed by up to 5 orders of magnitude between the least and most transformable isolates. The strain-to-strain differences in transformation frequency were observed among many isolates producing the same capsule types, indicating no general association between transformation frequency and serotype. However, a statistically significant association was observed between the levels of transformation and colonization fitness/virulence in the hypertransformable isolates. Although nontransformable mutants of all the selected hypertransformable isolates were significantly attenuated in colonization fitness and virulence in mouse infection models, such mutants of the strains with relatively low transformability had no or marginal fitness phenotypes under the same experimental settings. This finding strongly suggests that the pneumococci with high transformation capability are “addicted” to a “hypertransformable” state for optimal fitness in the human host. This work has thus provided an intriguing hint for further investigation into how the competence system impacts the fitness, virulence, and other transformation-associated traits of this important human pathogen.
Recombinant Human Peptidoglycan Recognition Proteins Reveal Antichlamydial Activity

ABSTRACT Peptidoglycan recognition proteins (PGLYRPs) are innate immune components that recognize the peptidoglycan and lipopolysaccharides of bacteria and exhibit antibacterial activity. Recently, the obligate intracellular parasite Chlamydia trachomatis was shown to have peptidoglycan. However, the antichlamydial activity of PGLYRPs has not yet been demonstrated. The aim of our study was to test whether PGLYRPs exhibit antibacterial activity against C. trachomatis. Thus, we cloned the regions containing the human Pglyrp1, Pglyrp2, Pglyrp3, and Pglyrp4 genes for subsequent expression in human cell lines. We obtained stable HeLa cell lines that secrete recombinant human PGLYRPs into culture medium. We also generated purified recombinant PGLYRP1, -2, and -4 and confirmed their activities against Gram-positive (Bacillus subtilis) and Gram-negative (Escherichia coli) bacteria. Furthermore, we examined the activities of recombinant PGLYRPs against C. trachomatis and determined their MICs. We also observed a decrease in the infectious ability of chlamydial elementary bodies in the next generation after a single exposure to PGLYRPs. Finally, we demonstrated that PGLYRPs attach to C. trachomatis elementary bodies and activate the expression of the chlamydial two-component stress response system. Thus, PGLYRPs inhibit the development of chlamydial infection.
Unlicensed Taxis Detection Service Based on Large-Scale Vehicles Mobility Data

Unlicensed taxis are widely considered as major obstacles to city traffic regulation and public safety. Thus, many governments have issued restrictions for car-hailing services and alleged that the use of unlicensed vehicles was illegal. However, it is very challenging that traffic administrative enforcements face limited manpower to prohibit unlicensed taxis, due to costly and time-consuming procedure of on-site evidence collection. In this paper, we propose an effective service to incorporate human mobility mechanism into unlicensed taxis detection from massive city-wide vehicles. We first extract 276 spatio-temporal features, which are grouped into two categories, including daily behaviors and sustainable behaviors to capture the mobility characteristics of unlicensed taxis. Second, we investigate the detection accuracy of three machine learning techniques, viz. support vector machines, decision tree, and logical regression. We illustrate our approach using real-world vehicle license plate recognition dataset in Xiamen, China, which contains 336 million passing records for 6.2 million vehicles filmed by 439 devices in August 2016. Experimental results reveal that LR outperforms SVM and DT in prediction accuracy and F-score measurement, while SVM is capable of identifying the largest number of unlicensed taxis.
Iterative Variance Stabilizing Transformation Denoising of Spectral Domain Optical Coherence Tomography Images Applied to Retinoblastoma

Background: Due to the presence of speckle Poisson noise, the interpretation of spectral domain-optical coherence tomography (SD-OCT) images frequently requires the use of data averaging to improve the signal-to-noise ratio. This implies long acquisition times and requires patient sedation in some cases. Iterative variance stabilizing transformation (VST) is a possible approach by which to remove speckle Poisson noise on single images. Methods: We used SD-OCT images of human and murine (LH Beta-Tag mouse model) retinas with and without retinoblastoma acquired with 2 different imaging devices (Bioptigen and Micron IV). These images were processed using a denoising workflow implemented in Matlab. Results: We demonstrated the presence of speckle Poisson noise, which can be removed by a VST-based approach. This approach is robust as it works in all used imaging devices and in both human and mouse retinas, independently of the tumor status. The implemented algorithm is freely available from the authors on demand. Conclusions: On a single denoised image, the proposed method provides results similar to those expected from the SD-OCT averaging. Because of the friendly user interface, it can be easily used by clinicians and researchers in ophthalmology.