Transmission Pairs Research Articles

Development of a Test Bench for Transmission Efficiency of Small Modulus Worm Helical Gears

Worm helical gear transmission falls between lever transmission and inclined transmission in principle. There is large relative sliding speed between the conjugate tooth surfaces, and the transmission efficiency is low. To accurately grasp the changing law of worm helical gear transmission efficiency and propose an effective efficiency improvement method, this paper designed and built a transmission efficiency test bench for small modulus worm helical gear transmission pair.

SARS-CoV-2 Serial Interval Variation, Montana, USA, March 1–July 31, 2020

We report mean severe acute respiratory syndrome coronavirus 2 serial intervals for Montana, USA, from 583 transmission pairs; infectors’ symptom onset dates occurred during March 1–July 31, 2020. Our estimate was 5.68 (95% CI 5.27–6.08) days, SD 4.77 (95% CI 4.33–5.19) days. Subperiod estimates varied temporally by nonpharmaceutical intervention type and fluctuating incidence.

Estimation of the serial interval and proportion of pre-symptomatic transmission events of COVID\u2212\u200919 in Ireland using contact tracing data

BackgroundThe serial interval is the period of time between the onset of symptoms in an infector and an infectee and is an important parameter which can impact on the estimation of the reproduction number. Whilst several parameters influencing infection transmission are expected to be consistent across populations, the serial interval can vary across and within populations over time. Therefore, local estimates are preferable for use in epidemiological models developed at a regional level. We used data collected as part of the national contact tracing process in Ireland to estimate the serial interval of SARS-CoV-2 infection in the Irish population, and to estimate the proportion of transmission events that occurred prior to the onset of symptoms.ResultsAfter data cleaning, the final dataset consisted of 471 infected close contacts from 471 primary cases. The median serial interval was 4 days, mean serial interval was 4.0 (95% confidence intervals 3.7, 4.3) days, whilst the 25th and 75th percentiles were 2 and 6 days respectively. We found that intervals were lower when the primary or secondary case were in the older age cohort (greater than 64 years). Simulating from an incubation period distribution from international literature, we estimated that 67% of transmission events had greater than 50% probability of occurring prior to the onset of symptoms in the infector.ConclusionsWhilst our analysis was based on a large sample size, data were collected for the primary purpose of interrupting transmission chains. Similar to other studies estimating the serial interval, our analysis is restricted to transmission pairs where the infector is known with some degree of certainty. Such pairs may represent more intense contacts with infected individuals than might occur in the overall population. It is therefore possible that our analysis is biased towards shorter serial intervals than the overall population.

Unveiling local atomic bonding and packing of amorphous nanophases via independent component analysis facilitated pair distribution function

Amorphous nanophases play a significant role for the properties of a variety of nanoscale heterogeneous materials. Experimental characterization of the atomic arrangement of the amorphous structure, including nanoscale structural variations, is one of the main challenges limiting the rational design of the materials. Here, an approach to characterize local bonding and atomic packing in complex nanomaterials is introduced. Building on scanning transmission electron microscopy (STEM) and pair distribution function analysis (PDF) to record local diffraction information with nanometer spatial resolution, we show that independent component analysis for “blind source separation” of mixed information due to projection effects in STEM-PDF, enables full separation of these signals. The unprecedented information allows determining the structure of individual nanoscale phases and identifying the compounds inside. We analyzed a FeZr/ZrO2 multilayer as proof of principle, and discovered differently coordinated FeOx in the interfacial region. The approach was applied to Fe25Sc75 nanoglass and revealed Fe–Fe bonding concealed in the Sc-rich matrix. Finally, analysis of a shear band in a deformed Cu/CuZr nanolaminate confirmed Cu enrichment and reduced medium-range order in the shear band.

Smart Energy Harvesting for Internet of Things Networks.

In this article, we address the problem of prolonging the battery life of Internet of Things (IoT) nodes by introducing a smart energy harvesting framework for IoT networks supported by femtocell access points (FAPs) based on the principles of Contract Theory and Reinforcement Learning. Initially, the IoT nodes’ social and physical characteristics are identified and captured through the concept of IoT node types. Then, Contract Theory is adopted to capture the interactions among the FAPs, who provide personalized rewards, i.e., charging power, to the IoT nodes to incentivize them to invest their effort, i.e., transmission power, to report their data to the FAPs. The IoT nodes’ and FAPs’ contract-theoretic utility functions are formulated, following the network economic concept of the involved entities’ personalized profit. A contract-theoretic optimization problem is introduced to determine the optimal personalized contracts among each IoT node connected to a FAP, i.e., a pair of transmission and charging power, aiming to jointly guarantee the optimal satisfaction of all the involved entities in the examined IoT system. An artificial intelligent framework based on reinforcement learning is introduced to support the IoT nodes’ autonomous association to the most beneficial FAP in terms of long-term gained rewards. Finally, a detailed simulation and comparative results are presented to show the pure operation performance of the proposed framework, as well as its drawbacks and benefits, compared to other approaches. Our findings show that the personalized contracts offered to the IoT nodes outperform by a factor of four compared to an agnostic type approach in terms of the achieved IoT system’s social welfare.

HLA-associated preadaptation in HIV Vif is associated with higher set point viral load and faster CD4+ decline in Zambian transmission pairs.

We investigated the relationship between human leukocyte antigen (HLA)-associated preadaptation for the entire subtype C HIV-1 proteome of the transmitted founder virus and subsequent HIV-1 disease progression in a cohort of heterosexual linked transmission pairs in Zambia. An adaptation model was used to calculate an adaptation score for each virus-HLA combination in order to quantify the degree of preadaptation of the transmitted virus to the linked recipient's HLA alleles. These scores were then assessed for their relationship to viral load and longitudinal CD4+ decline in the recipient. Viral RNA was extracted from the plasma of the donor partner and the linked recipient near the time of transmission, as well as longitudinally from the linked recipient. Viral adaptation scores were calculated for each individual and each protein in the subtype C HIV-1 proteome. The majority of HLA-associated sites were located in Gag, Pol and Nef; however, proportional to protein length, the accessory and regulatory proteins contained a relatively high proportion of HLA-associated sites. Over the course of infection, HLA-mediated immune adaptation increased for all proteins except Vpu and gp120. Preadaptation was positively associated with higher early set point viral load and faster CD4+ decline. When examined by protein, preadaptation in Pol and Vif were statistically significantly associated with these markers of disease progression. Adaptation in Pol had the greatest impact on viral control. Despite containing a large proportion of HLA-associated sites, Vif was the only regulatory or accessory protein for which preadaptation significantly correlated with disease progression.

Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck.

The evolutionary mechanisms by which SARS-CoV-2 viruses adapt to mammalian hosts and, potentially, undergo antigenic evolution depend on the ways genetic variation is generated and selected within and between individual hosts. Using domestic cats as a model, we show that SARS-CoV-2 consensus sequences remain largely unchanged over time within hosts, while dynamic sub-consensus diversity reveals processes of genetic drift and weak purifying selection. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. This variant arises rapidly and persists at intermediate frequencies in index cats. It also becomes fixed following transmission in two of three pairs. These dynamics suggest this site may be under positive selection in this system and illustrate how a variant can quickly arise and become fixed in parallel across multiple transmission pairs. Transmission of SARS-CoV-2 in cats involved a narrow bottleneck, with new infections founded by fewer than ten viruses. In RNA virus evolution, stochastic processes like narrow transmission bottlenecks and genetic drift typically act to constrain the overall pace of adaptive evolution. Our data suggest that here, positive selection in index cats followed by a narrow transmission bottleneck may have instead accelerated the fixation of S H655Y, a potentially beneficial SARS-CoV-2 variant. Overall, our study suggests species- and context-specific adaptations are likely to continue to emerge. This underscores the importance of continued genomic surveillance for new SARS-CoV-2 variants as well as heightened scrutiny for signatures of SARS-CoV-2 positive selection in humans and mammalian model systems.

Molecular Transmission Dynamics of Primary HIV Infections in Lazio Region, Years 2013-2020.

Molecular investigation of primary HIV infections (PHI) is crucial to describe current dynamics of HIV transmission. Aim of the study was to investigate HIV transmission clusters (TC) in PHI referred during the years 2013–2020 to the National Institute for Infectious Diseases in Rome (INMI), that is the Lazio regional AIDS reference centre, and factors possibly associated with inclusion in TC. These were identified by phylogenetic analysis, based on population sequencing of pol; a more in depth analysis was performed on TC of B subtype, using ultra-deep sequencing (UDS) of env. Of 270 patients diagnosed with PHI during the study period, 229 were enrolled (median follow-up 168 (IQR 96–232) weeks). Median age: 39 (IQR 32–48) years; 94.8% males, 86.5% Italians, 83.4% MSM, 56.8% carrying HIV-1 subtype B. Of them, 92.6% started early treatment within a median of 4 (IQR 2–7) days after diagnosis; median time to sustained suppression was 20 (IQR 8–32) weeks. Twenty TC (median size 3, range 2–9 individuals), including 68 patients, were identified. A diagnosis prior to 2015 was the unique factor associated with inclusion in a TC. Added value of UDS was the identification of shared quasispecies components in transmission pairs within TC.

Antiretroviral Therapy Use and HIV Transmission Among Discordant Couples in Nonresearch Settings in Kigali, Rwanda.

Antiretroviral therapy (ART) efficacy for HIV prevention among discordant couples has been demonstrated in clinical trials. Effectiveness outside of research settings is less well understood. HIV-discordant couples were enrolled in couples' testing and follow-up at 20 government clinics in Kigali from 2010 to 2014. We performed viral linkage analysis on seroconverting couples to determine infection sources (intracouple vs. extracouple). Antiretroviral therapy use in index partners was collected at baseline and during follow-up by self-report with verification of government medical records. A total of 3777 HIV-discordant couples were identified and followed up at government health clinics. Fifty-four incident HIV infections were identified, of which 36 were confirmed linked to the index partner, 4 were unlinked, and 14 were unknown. Among the 50 linked or unknown transmission pairs, 38% occurred among couples in which the index partner was on ART (HIV incidence rate of 0.63/100 person-years), whereas 62% occurred among couples in which the index partner was not on ART (HIV incidence rate of 5.51/100 person-years; adjusted rate ratio, 6.9). HIV acquisition was higher in women than in men with non-ART using index partners (P < 0.001). Couples in a government clinic couples' HIV testing and follow-up program in Rwanda had an 89% reduction in HIV incidence when index partners were using ART, slightly lower than efficacy estimates from randomized trials. Antiretroviral therapy for prevention should be prioritized for key populations including discordant couples identified via couples' voluntary counseling and testing, with increased efforts to improve uptake, adherence, and viral load monitoring.

On the relationship between serial interval, infectiousness profile and generation time.

The timing of transmission plays a key role in the dynamics and controllability of an epidemic. However, observing generation times—the time interval between the infection of an infector and an infectee in a transmission pair—requires data on infection times, which are generally unknown. The timing of symptom onset is more easily observed; generation times are therefore often estimated based on serial intervals—the time interval between symptom onset of an infector and an infectee. This estimation follows one of two approaches: (i) approximating the generation time distribution by the serial interval distribution or (ii) deriving the generation time distribution from the serial interval and incubation period—the time interval between infection and symptom onset in a single individual—distributions. These two approaches make different—and not always explicitly stated—assumptions about the relationship between infectiousness and symptoms, resulting in different generation time distributions with the same mean but unequal variances. Here, we clarify the assumptions that each approach makes and show that neither set of assumptions is plausible for most pathogens. However, the variances of the generation time distribution derived under each assumption can reasonably be considered as upper (approximation with serial interval) and lower (derivation from serial interval) bounds. Thus, we suggest a pragmatic solution is to use both approaches and treat these as edge cases in downstream analysis. We discuss the impact of the variance of the generation time distribution on the controllability of an epidemic through strategies based on contact tracing, and we show that underestimating this variance is likely to overestimate controllability.

A Class of Evolutionary Algorithms for Determining Shortest Path Routing in 5G Ultra Dense Heterogeneous Networks

Ultra Dense Network (UDN), an important element of the upcoming 5G networks are characterised by extremely dynamic operations due to the presence and mobility of large number of users spread over small cells of varying sizes. It makes optimal path between the source/destination pairs for communication and data transmission be highly dynamic in nature and hence a challenging issue to deal with. Under such dynamic backdrops, routing procedures have to exhibit robustness, scalability and time efficiency in order to ensure seamless link reliability and Quality of Service (QOS) of the network. In the proposed work, the shortest optimal route of the source and destination pair is found using a combination of evolutionary optimization algorithms namely Genetic Algorithm (GA), Particle Swarm Optimization (PSO) Algorithm and our novel hybrid PSOGA approach which searches for an optimized solution by determining cost functions of individual fitness state and comparing states generated between individual solutions. Application of all the three above mentioned algorithms to the Shortest Path Routing Problem in UDNs and the results obtained have shown that the hybrid PSO-GA comparatively provided enhanced optimized solution.

Hepatitis C Virus Transmission Among Men Who Have Sex With Men in Amsterdam: External Introductions May Complicate Microelimination Efforts.

It is unclear whether unrestricted access and high uptake of direct-acting antivirals (DAAs) is sufficient to eliminate hepatitis C virus (HCV) in high-risk populations such as men who have sex with men (MSM). This study presents historic trends and current dynamics of HCV transmission among MSM in Amsterdam based on sequence data collected between 1994 and 2019. Hypervariable region 1 sequences of 232 primary HCV infections and 56 reinfections were obtained from 244 MSM in care in Amsterdam. Maximum-likelihood phylogenies were constructed for HCV genotypes separately, and time-scaled phylogenies were constructed using a Bayesian coalescent approach. Transmission clusters were determined by Phydelity and trends in the proportion of unclustered sequences over time were evaluated using logistic regression. Seventy-six percent (218/288) of sequences were part of 21 transmission clusters and 13 transmission pairs. Transmission cluster sizes ranged from 3 to 44 sequences. Most clusters were introduced between the late 1990s and early 2010s and no new clusters were introduced after 2012. The proportion of unclustered sequences of subtype 1a, the most prevalent subtype in this population, fluctuated between 0% and 20% in 2009-2012, after which an increase occurred from 0% in 2012 to 50% in 2018. The proportion of external introductions of HCV infections among MSM in Amsterdam has recently increased, coinciding with high DAA uptake. Frequent international transmission events will likely complicate local microelimination efforts. Therefore, international collaboration combined with international scale-up of prevention, testing, and treatment of HCV infections (including reinfections) is warranted, in particular for local microelimination efforts.

Epidemiological parameters of COVID-19 and its implication for infectivity among patients in China, 1 January to 11 February 2020.

BackgroundThe natural history of disease in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remained obscure during the early pandemic.AimOur objective was to estimate epidemiological parameters of coronavirus disease (COVID-19) and assess the relative infectivity of the incubation period.MethodsWe estimated the distributions of four epidemiological parameters of SARS-CoV-2 transmission using a large database of COVID-19 cases and potential transmission pairs of cases, and assessed their heterogeneity by demographics, epidemic phase and geographical region. We further calculated the time of peak infectivity and quantified the proportion of secondary infections during the incubation period.ResultsThe median incubation period was 7.2 (95% confidence interval (CI): 6.9‒7.5) days. The median serial and generation intervals were similar, 4.7 (95% CI: 4.2‒5.3) and 4.6 (95% CI: 4.2‒5.1) days, respectively. Paediatric cases < 18 years had a longer incubation period than adult age groups (p = 0.007). The median incubation period increased from 4.4 days before 25 January to 11.5 days after 31 January (p < 0.001), whereas the median serial (generation) interval contracted from 5.9 (4.8) days before 25 January to 3.4 (3.7) days after. The median time from symptom onset to discharge was also shortened from 18.3 before 22 January to 14.1 days after. Peak infectivity occurred 1 day before symptom onset on average, and the incubation period accounted for 70% of transmission.ConclusionThe high infectivity during the incubation period led to short generation and serial intervals, necessitating aggressive control measures such as early case finding and quarantine of close contacts.

Different Evolutionary Pathways of HIV-1 between Fetus and Mother Perinatal Transmission Pairs Indicate Unique Immune Selection Pressure in Fetuses

Study of evolution and selection pressure on HIV-1 in fetuses will lead to a better understanding of the role of immune responses in shaping virus evolution and vertical transmission. Detailed genetic analyses of HIV-1 env gene from 12 in utero transmission pairs show that most infections (67%) occur within two months from childbirth. In addition, env sequences from long-term infected fetuses were highly divergent and formed separate phylogenetic lineages from their cognate maternal viruses. Host selection sites unique to infant viruses were identified in regions frequently targeted by broadly neutralizing antibodies and T cell immune responses. The identification of unique selection sites in the env gene of fetal viruses indicates that the immune system in fetuses is capable of exerting selection pressure on viral evolution. Studying selection and evolution of HIV-1 or other viruses in fetuses can be an alternative approach to investigate adaptive immunity in fetuses.

Livestock-associated methicillin-resistant Staphylococcus aureus: Establishing links between animals and humans on livestock holdings.

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) represents a concern in both human and veterinary medicine. The aim of this study was to investigate potential LA-MRSA transmission between animals and humans in rural settings. To this aim, a study was designed to include 14 farms in Slovenia, which were selected on the basis of a farmer (initial patient) with confirmed LA-MRSA infection and regular animal contacts. On all farms, the initial patients, their household members, animals and barn environment were analysed for the presence of LA-MRSA. In addition, the epidemiologically linked hospital-related LA-MRSA isolates were included to investigate possible nosocomial transmissions. On five farms, LA-MRSA was discovered both in animals and in humans. In total, 49 LA-MRSA isolates of different origins underwent whole-genome sequencing, antimicrobial susceptibility testing and spa typing. All 49 isolates belonged to the sequence type 398 (ST398), spa types t011 and t034, and harboured staphylococcal chromosomal cassette mec Vc. High levels of concordance between resistance phenotypes and genotypes were observed. No transmission pairs between animals and initial patients were discovered. However, several isolates originating from farm animals and other household members formed clusters with pairwise distances of ≤14 single nucleotide polymorphisms (SNPs), indicating recent transmission events. In addition, three closely related isolates (0 SNP) form hospitalized patients were observed, indicating a possible nosocomial transmission. Two hospital-related isolates harboured the immune evasion cluster genes, which are associated with adaptation to the human host; however, these two isolates differed in >30 SNPs from the remaining isolates. Characteristics of LA-MRSA from Slovenia reflect those observed previously in other European studies. Immune evasion cluster-positive LA-MRSA ST398 suggests its re-adaptation to the human host and calls for a closer monitoring of such emerging LA-MRSA lineages, in addition to monitoring and preventing the introduction of LA-MRSA from farms to hospitals where transmission is highly plausible.

From cough to splutter

Coronavirus In epidemiology, serial intervals are measured from when one infected person starts to show symptoms to when the next person infected becomes symptomatic. For any specific infection, the serial interval is assumed to be a fixed characteristic. Using valuable transmission pair data for coronavirus disease (COVID-19) in mainland China, Ali et al. noticed that the average serial interval changed as nonpharmaceutical interventions were introduced. In mid-January 2020, serial intervals were on average 7.8 days, whereas in early February 2020, they decreased to an average of 2.2 days. The more quickly infected persons were identified and isolated, the shorter the serial interval became and the fewer the opportunities for virus transmission. The change in serial interval may not only measure the effectiveness of infection control interventions but may also indicate rising population immunity. Science , this issue p. [1106][1] [1]: /lookup/doi/10.1126/science.abc9004

Power Flow and Efficiency Analysis of High-Speed Heavy Load Herringbone Planetary Transmission Using a Hypergraph-Based Method

The existing research problem is that the hypergraph-based method does not comprehensively consider the power loss factors of the mechanical transmission system, especially the existing windage power loss. In the power flow diagram, it is difficult to express and calculate the power loss separately, based on the power loss mechanism. Furthermore, the hypergraph-based methods purposed by some researches are not suitable for high-speed and heavy-load conditions. This paper presents a new hypergraph-based method for analyzing the transmission efficiency of complex planetary gear trains. In addition, a formula for calculating transmission efficiency is derived. The power loss model is established for a high-speed heavy-load herringbone planetary transmission pair considering several sources of power losses such as gear meshing friction, windage, and bearing friction. Then, the efficiency of a two-stage herringbone planetary transmission system is calculated using the proposed method. Furthermore, the influence of input speed, input power, and lubrication state on transmission efficiency is investigated. Finally, the proposed method is verified by comparing calculated values with values published in the literature.

Serial interval of SARS-CoV-2 was shortened over time by nonpharmaceutical interventions.

Studies of novel coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have reported varying estimates of epidemiological parameters, including serial interval distributions-i.e., the time between illness onset in successive cases in a transmission chain-and reproduction numbers. By compiling a line-list database of transmission pairs in mainland China, we show that mean serial intervals of COVID-19 shortened substantially from 7.8 to 2.6 days within a month (9 January to 13 February 2020). This change was driven by enhanced nonpharmaceutical interventions, particularly case isolation. We also show that using real-time estimation of serial intervals allowing for variation over time provides more accurate estimates of reproduction numbers than using conventionally fixed serial interval distributions. These findings could improve our ability to assess transmission dynamics, forecast future incidence, and estimate the impact of control measures.

Reconstruction of Transmission Pairs for Novel Coronavirus Disease 2019 (COVID-19) in Mainland China: Estimation of Superspreading Events, Serial Interval, and Hazard of Infection.

BackgroundKnowledge on the epidemiological features and transmission patterns of novel coronavirus disease (COVID-19) is accumulating. Detailed line-list data with household settings can advance the understanding of COVID-19 transmission dynamics.MethodsA unique database with detailed demographic characteristics, travel history, social relationships, and epidemiological timelines for 1407 transmission pairs that formed 643 transmission clusters in mainland China was reconstructed from 9120 COVID-19 confirmed cases reported during 15 January–29 February 2020. Statistical model fittings were used to identify the superspreading events and estimate serial interval distributions. Age- and sex-stratified hazards of infection were estimated for household vs nonhousehold transmissions.ResultsThere were 34 primary cases identified as superspreaders, with 5 superspreading events occurred within households. Mean and standard deviation of serial intervals were estimated as 5.0 (95% credible interval [CrI], 4.4–5.5) days and 5.2 (95% CrI, 4.9–5.7) days for household transmissions and 5.2 (95% CrI, 4.6–5.8) and 5.3 (95% CrI, 4.9–5.7) days for nonhousehold transmissions, respectively. The hazard of being infected outside of households is higher for people aged 18–64 years, whereas hazard of being infected within households is higher for young and old people.ConclusionsNonnegligible frequency of superspreading events, short serial intervals, and a higher risk of being infected outside of households for male people of working age indicate a significant barrier to the identification and management of COVID-19 cases, which requires enhanced nonpharmaceutical interventions to mitigate this pandemic.

Low-Resolution Limited-Feedback NOMA for mmWave Communications

The spectrum-efficient millimeter-wave (mmWave) communications has recently attracted much attention as a viable solution to spectrum crunch problem. In this work, we propose a novel non-orthogonal multiple access (NOMA) framework, which makes use of the directional propagation characteristics of mmWave communications so as to improve the spectral efficiency through non-orthogonal signaling. In particular, we consider one-bit quantized angle information as a limited yet effective feedback scheme describing the channel quality of user equipment (UE) in mmWave bands. The UE pairs for NOMA transmission are then established using not only the one-bit distance feedback as a classical approach, but also the one-bit angle feedback. The proposed strategy is therefore referred to as two-bit NOMA. We also propose a novel hybrid strategy, called combined NOMA, for the circumstances with no UE pair through two-bit NOMA. Whenever no UE pair is available through any NOMA strategy, we resort to single user transmission (SUT) with proper UE selection schemes. The hybrid sum-rate performance is also analyzed thoroughly with the respective outage and rate expressions. The numerical results verify that the proposed strategy outperforms one-bit NOMA schemes with either angle- or distance-only feedback.