Neutron Energy Spectrum Measurements with a Compact Liquid Scintillation Detector on EAST

A neutron detector based on EJ301 liquid scintillator has been employed at EAST to measure the neutron energy spectrum for D-D fusion plasma. The detector was carefully characterized in different quasi-monoenergetic neutron fields generated by a 4.5 MV Van de Graaff accelerator. In recent experimental campaigns, due to the low neutron yield at EAST, a new shielding device was designed and located as close as possible to the tokamak to enhance the count rate of the spectrometer. The fluence of neutrons and gamma-rays was measured with the liquid neutron spectrometer and was consistent with 3He proportional counter and NaI (Tl) gamma-ray spectrometer measurements. Plasma ion temperature values were deduced from the neutron spectrum in discharges with lower hybrid wave injection and ion cyclotron resonance heating. Scattered neutron spectra were simulated by the Monte Carlo transport Code, and they were well verified by the pulse height measurements at low energies.Comment: 19 pages,10 figures, 1 tabl

Predicting nucleosome positioning using a duration Hidden Markov Model

<p>Abstract</p> <p>Background</p> <p>The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions. Increasing evidence has shown that genomic DNA sequence itself is highly predictive of nucleosome positioning genome-wide. Therefore a fast software tool for predicting nucleosome positioning can help understanding how a genome's nucleosome organization may facilitate genome function.</p> <p>Results</p> <p>We present a duration Hidden Markov model for nucleosome positioning prediction by explicitly modeling the linker DNA length. The nucleosome and linker models trained from yeast data are re-scaled when making predictions for other species to adjust for differences in base composition. A software tool named NuPoP is developed in three formats for free download.</p> <p>Conclusions</p> <p>Simulation studies show that modeling the linker length distribution and utilizing a base composition re-scaling method both improve the prediction of nucleosome positioning regarding sensitivity and false discovery rate. NuPoP provides a user-friendly software tool for predicting the nucleosome occupancy and the most probable nucleosome positioning map for genomic sequences of any size. When compared with two existing methods, NuPoP shows improved performance in sensitivity.</p

Archaeal Nucleosome Positioning In Vivo and In Vitro is Directed by Primary Sequence Motifs

Background: Histone wrapping of DNA into nucleosomes almost certainly evolved in the Archaea, and predates Eukaryotes. In Eukaryotes, nucleosome positioning plays a central role in regulating gene expression and is directed by primary sequence motifs that together form a nucleosome positioning code. The experiments reported were undertaken to determine if archaeal histone assembly conforms to the nucleosome positioning code. Results: Eukaryotic nucleosome positioning is favored and directed by phased helical repeats of AA/TT/AT/TA and CC/GG/CG/GC dinucleotides, and disfavored by longer AT-rich oligonucleotides. Deep sequencing of genomic DNA protected from micrococcal nuclease digestion by assembly into archaeal nucleosomes has established that archaeal nucleosome assembly is also directed and positioned by these sequence motifs, both in vivo in Methanothermobacter thermautotrophicus and Thermococcus kodakarensis and in vitro in reaction mixtures containing only one purified archaeal histone and genomic DNA. Archaeal nucleosomes assembled at the same locations in vivo and in vitro, with much reduced assembly immediately upstream of open reading frames and throughout the ribosomal rDNA operons. Providing further support for a common positioning code, archaeal histones assembled into nucleosomes on eukaryotic DNA and eukaryotic histones into nucleosomes on archaeal DNA at the same locations. T. kodakarensis has two histones, designated HTkA and HTkB, and strains with either but not both histones deleted grow normally but do exhibit transcriptome differences. Comparisons of the archaeal nucleosome profiles in the intergenic regions immediately upstream of genes that exhibited increased or decreased transcription in the absence of HTkA or HTkB revealed substantial differences but no consistent pattern of changes that would correlate directly with archaeal nucleosome positioning inhibiting or stimulating transcription. Conclusions: The results obtained establish that an archaeal histone and a genome sequence together are sufficient to determine where archaeal nucleosomes preferentially assemble and where they avoid assembly. We confirm that the same nucleosome positioning code operates in Archaea as in Eukaryotes and presumably therefore evolved with the histone-fold mechanism of DNA binding and compaction early in the archaeal lineage, before the divergence of Eukaryotes

Direct Anonymous Attestation with Optimal TPM Signing Efficiency

Direct Anonymous Attestation (DAA) is an anonymous signature scheme, which allows the Trusted Platform Module (TPM), a small chip embedded in a host computer, to attest to the state of the host system, while preserving the privacy of the user. DAA provides two signature modes: fully anonymous signatures and pseudonymous signatures. One main goal of designing DAA schemes is to reduce the TPM signing workload as much as possible, as the TPM has only limited resources. In an optimal DAA scheme, the signing workload on the TPM will be no more than that required for a normal signature like ECSchnorr. To date, no scheme has achieved the optimal signing efficiency for both signature modes. In this paper, we propose the first DAA scheme which achieves the optimal TPM signing efficiency for both signature modes. In this scheme, the TPM takes only a single exponentiation to generate a signature, and this single exponentiation can be pre-computed. Our scheme can be implemented using the existing TPM 2.0 commands, and thus is compatible with the TPM 2.0 specification. We benchmarked the TPM 2.0 commands needed for three DAA use cases on an Infineon TPM 2.0 chip, and also implemented the host signing and verification algorithm for our scheme on a laptop with 1.80GHz Intel Core i7-8550U CPU. Our experimental results show that our DAA scheme obtains a total signing time of about 144 ms for either of two signature modes (compared to an online signing time of about 65 ms). Based on our benchmark results for the pseudonymous signature mode, our scheme is roughly 2x (resp., 5x) faster than the existing DAA schemes supported by TPM 2.0 in terms of total (resp., online) signing efficiency. In addition, our DAA scheme supports selective attribute disclosure, which can satisfy more application require- ments. We also extend our DAA scheme to support signature-based revocation and to guarantee privacy against subverted TPMs. The two extended DAA schemes keep the TPM signing efficiency optimal for both of two signa- ture modes, and outperform existing related schemes in terms of signing performance

A Machine Learning Model for Identifying Sexual Health Influencers to Promote the Secondary Distribution of HIV Self-Testing Among Gay, Bisexual, and Other Men Who Have Sex With Men in China: Quasi-Experimental Study

BACKGROUND: Sexual health influencers (SHIs) are individuals actively sharing sexual health information with their peers, and they play an important role in promoting HIV care services, including the secondary distribution of HIV self-testing (SD-HIVST). Previous studies used a 6-item empirical leadership scale to identify SHIs. However, this approach may be biased as it does not consider individuals' social networks. OBJECTIVE: This study used a quasi-experimental study design to evaluate how well a newly developed machine learning (ML) model identifies SHIs in promoting SD-HIVST compared to SHIs identified by a scale whose validity had been tested before. METHODS: We recruited participants from BlueD, the largest social networking app for gay men in China. Based on their responses to the baseline survey, the ML model and scale were used to identify SHIs, respectively. This study consisted of 2 rounds, differing in the upper limit of the number of HIVST kits and peer-referral links that SHIs could order and distribute (first round ≤5 and second round ≤10). Consented SHIs could order multiple HIV self-testing (HIVST) kits and generate personalized peer-referral links through a web-based platform managed by a partnered gay-friendly community-based organization. SHIs were encouraged to share additional kits and peer-referral links with their social contacts (defined as "alters"). SHIs would receive US $3 incentives when their corresponding alters uploaded valid photographic testing results to the same platform. Our primary outcomes included (1) the number of alters who conducted HIVST in each group and (2) the number of newly tested alters who conducted HIVST in each. We used negative binomial regression to examine group differences during the first round (February-June 2021), the second round (June-November 2021), and the combined first and second rounds, respectively. RESULTS: In January 2021, a total of 1828 men who have sex with men (MSM) completed the survey. Overall, 393 SHIs (scale=195 and ML model=198) agreed to participate in SD-HIVST. Among them, 229 SHIs (scale=116 and ML model=113) ordered HIVST on the web. Compared with the scale group, SHIs in the ML model group motivated more alters to conduct HIVST (mean difference [MD] 0.88, 95% CI 0.02-2.22; adjusted incidence risk ratio [aIRR] 1.77, 95% CI 1.07-2.95) when we combined the first and second rounds. Although the mean number of newly tested alters was slightly higher in the ML model group than in the scale group, the group difference was insignificant (MD 0.35, 95% CI -0.17 to -0.99; aIRR 1.49, 95% CI 0.74-3.02). CONCLUSIONS: Among Chinese MSM, SHIs identified by the ML model can motivate more individuals to conduct HIVST than those identified by the scale. Future research can focus on how to adapt the ML model to encourage newly tested individuals to conduct HIVST. TRIAL REGISTRATION: Chinese Clinical Trials Registry ChiCTR2000039632; https://www.chictr.org.cn/showprojEN.html?proj=63068. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.1186/s12889-021-11817-2

Effectiveness of sexual health influencers identified by an ensemble machine learning model in promoting secondary distribution of HIV self-testing among men who have sex with men in China: study protocol for a quasi-experimental trial

Background HIV self-testing (HIVST), especially the secondary distribution of HIVST (SD-HIVST) initiated by sexual health influencers (SHIs), has been recognized as an effective strategy in promoting HIV testing, especially among men who have sex with men (MSM). This quasi-experimental study aimed to evaluate whether SHIs identified through the ensemble machine learning approach can distribute more HIVST than those who identified by the empiricalscale. Methods We will recruit eligible adults (≥18 years old) who were assigned male gender at birth, and willing to participate in potential SD-HIVST online. Participants will be assigned randomly to two groups (scale group or machine learning group), followed by a separate process of SHI identification based on the group assignment. After identification, all index participants (defined as identified SHIs who are verbally consented to participate in SD-HIVST or who directly order HIVST kits) will follow the same procedure for SD-HIVST acquisition and distribution. Index participants can order HIVST online and distribute them to members within their social networks (defined as alters) in-person or virtually through a personalized peer referral link. Once a unique alter uploads a photographed test result to the platform, both the alter and the corresponding index participant will receive a fixed incentive of 3 USD. The index MSM can order up to five HIVST in the first three months and ten HIVST in the following three months. Each index participant will need to complete a baseline survey at the first-time ordering and one to two follow-upbased on the times of ordering,, three months after ordering. This trial will be comparing 1) the mean number of alters motivated by each index participant in each group and 2) the mean number of newly-tested alters motivated by each index participant in each group. Discussion In promoting the efficacy of identifying SHIs for SD-HIVST, our study has the potential to enhance testing coverage, particularly among marginalized individuals and those who are reluctant to for HIV and other sexually transmitted infections. Trial registration We registered the study on the Chinese Clinical Trial Registry website on 4th November 2021, with registration number ChiCTR2000039632

Monetary incentives and peer referral in promoting digital network-based secondary distribution of HIV self-testing among men who have sex with men in China: study protocol for a three-arm randomized controlled trial.

BACKGROUND: Human immunodeficiency virus (HIV) testing is a crucial strategy for HIV prevention. HIV testing rates remain low among men who have sex with men (MSM) in China. Digital network-based secondary distribution is considered as an effective model to enhance HIV self-testing (HIVST) among key populations. Digital platforms provide opportunities for testers to apply for HIVST kits by themselves, and secondary distribution allows them to apply for multiple kits to deliver to their sexual partners or members within their social network. We describe a three-arm randomized controlled trial to examine the effect of monetary incentives and peer referral in promoting digital network-based secondary distribution of HIVST among MSM in China. METHODS: Three hundred MSM in China will be enrolled through a digital platform for data collection. The eligibility criteria include being biological male, 18 years of age or over, ever having had sex with another man, being able to apply for kits via the online platform, and being willing to provide personal telephone number for follow-up. Eligible participants will be randomly allocated into one of the three arms: standard secondary distribution arm, secondary distribution with monetary incentives arm, and secondary distribution with monetary incentives plus peer referral arm. Participants (defined as "index") will distribute actual HIV self-test kits to members within their social network (defined as "alter") or share referral links to encourage alters to apply HIV self-test kits by themselves. All index participants will be requested to complete a baseline survey and a 3-month follow-up survey. Both indexes and alters will complete a survey upon returning the results by taking a photo of the used kits with the unique identification number. DISCUSSION: HIV testing rates remain suboptimal among MSM in China. Innovative interventions are needed to further expand the uptake of HIV testing among key populations. The findings of the trial can provide scientific evidence and experience on promoting secondary distribution of HIVST to reach key populations who have not yet been covered by existing testing services. TRIAL REGISTRATION: The study was registered in the Chinese Clinical Trial Registry (ChiCTR1900025433) on 26, August 2019, http://www.chictr.org.cn/showproj.aspx?proj=42001. Prospectively registered

Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae

The exact lengths of linker DNAs connecting adjacent nucleosomes specify the intrinsic three-dimensional structures of eukaryotic chromatin fibers. Some studies suggest that linker DNA lengths preferentially occur at certain quantized values, differing one from another by integral multiples of the DNA helical repeat, ∼10 bp; however, studies in the literature are inconsistent. Here, we investigate linker DNA length distributions in the yeast Saccharomyces cerevisiae genome, using two novel methods: a Fourier analysis of genomic dinucleotide periodicities adjacent to experimentally mapped nucleosomes and a duration hidden Markov model applied to experimentally defined dinucleosomes. Both methods reveal that linker DNA lengths in yeast are preferentially periodic at the DNA helical repeat (∼10 bp), obeying the forms 10n+5 bp (integer n). This 10 bp periodicity implies an ordered superhelical intrinsic structure for the average chromatin fiber in yeast