Self-partitioning SlipChip for slip-induced droplet formation and human papillomavirus viral load quantification with digital LAMP

Human papillomavirus (HPV) is one of the most common sexually transmitted infections worldwide, and persistent HPV infection can cause warts and even cancer. Nucleic acid analysis of HPV viral DNA can be very informative for the diagnosis and monitoring of HPV. Digital nucleic acid analysis, such as digital PCR and digital isothermal amplification, can provide sensitive detection and precise quantification of target nucleic acids, and its utility has been demonstrated in many biological research and medical diagnostic applications. A variety of methods have been developed for the generation of a large number of individual reaction partitions, a key requirement for digital nucleic acid analysis. However, an easily assembled and operated device for robust droplet formation without preprocessing devices, auxiliary instrumentation or control systems is still highly desired. In this paper, we present a self-partitioning SlipChip (sp-SlipChip) microfluidic device for the slip-induced generation of droplets to perform digital loop-mediated isothermal amplification (LAMP) for the detection and quantification of HPV DNA. In contrast to traditional SlipChip methods, which require the precise alignment of microfeatures, this sp-SlipChip utilized a design of “chain-of-pearls” continuous microfluidic channel that is independent of the overlapping of microfeatures on different plates to establish the fluidic path for reagent loading. Initiated by a simple slipping step, the aqueous solution can robustly self-partition into individual droplets by capillary pressure-driven flow. This advantage makes the sp-SlipChip very appealing for the point-of-care quantitative analysis of viral load. As a proof of concept, we performed digital LAMP on an sp-SlipChip to quantify human papillomaviruses (HPVs) 16 and 18 and tested this method with fifteen anonymous clinical samples

A regulatory mutant on TRIM26 conferring the risk of nasopharyngeal carcinoma by inducing low immune response.

The major histocompatibility complex (MHC) is most closely associated with nasopharyngeal carcinoma (NPC), but the complexity of its genome structure has proven challenging for the discovery of causal MHC loci or genes. We conducted a targeted MHC sequencing in 40 Cantonese NPC patients followed by a two-stage replication in 1065 NPC cases and 2137 controls of Southern Chinese descendent. Quantitative RT-PCR analysis (qRT-PCR) was used to detect gene expression status in 108 NPC and 43 noncancerous nasopharyngeal (NP) samples. Luciferase reporter assay and chromatin immunoprecipitation (ChIP) were used to assess the transcription factor binding site. We discovered that a novel SNP rs117565607_A at TRIM26 displayed the strongest association (OR = 1.909, Pcombined = 2.750 × 10-19 ). We also observed that TRIM26 was significantly downregulated in NPC tissue samples with genotype AA/AT than TT. Immunohistochemistry (IHC) test also found the TRIM26 protein expression in NPC tissue samples with the genotype AA/AT was lower than TT. According to computational prediction, rs117565607 locus was a binding site for the transcription factor Yin Yang 1 (YY1). We observed that the luciferase activity of YY1 which is binding to the A allele of rs117565607 was suppressed. ChIP data showed that YY1 was binding with T not A allele. Significance analysis of microarray suggested that TRIM26 downregulation was related to low immune response in NPC. We have identified a novel gene TRIM26 and a novel SNP rs117565607_A associated with NPC risk by regulating transcriptional process and established a new functional link between TRIM26 downregulation and low immune response in NPC

Cross-Context Backdoor Attacks against Graph Prompt Learning

Graph Prompt Learning (GPL) bridges significant disparities between pretraining and downstream applications to alleviate the knowledge transfer bottleneck in real-world graph learning. While GPL offers superior effectiveness in graph knowledge transfer and computational efficiency, the security risks posed by backdoor poisoning effects embedded in pretrained models remain largely unexplored. Our study provides a comprehensive analysis of GPL's vulnerability to backdoor attacks. We introduce \textit{CrossBA}, the first cross-context backdoor attack against GPL, which manipulates only the pretraining phase without requiring knowledge of downstream applications. Our investigation reveals both theoretically and empirically that tuning trigger graphs, combined with prompt transformations, can seamlessly transfer the backdoor threat from pretrained encoders to downstream applications. Through extensive experiments involving 3 representative GPL methods across 5 distinct cross-context scenarios and 5 benchmark datasets of node and graph classification tasks, we demonstrate that \textit{CrossBA} consistently achieves high attack success rates while preserving the functionality of downstream applications over clean input. We also explore potential countermeasures against \textit{CrossBA} and conclude that current defenses are insufficient to mitigate \textit{CrossBA}. Our study highlights the persistent backdoor threats to GPL systems, raising trustworthiness concerns in the practices of GPL techniques.Comment: Accepted by KDD 202

Measurement of proton electromagnetic form factors in e+e−→ppˉe^+e^- \to p\bar{p} in the energy region 2.00-3.08 GeV

The process of $e^+e^- \rightarrow p\bar{p}$ is studied at 22 center-of-mass energy points ($\sqrt{s}$) from 2.00 to 3.08 GeV, exploiting 688.5~pb$^{-1}$ of data collected with the BESIII detector operating at the BEPCII collider. The Born cross section~($\sigma_{p\bar{p}}$) of $e^+e^- \rightarrow p\bar{p}$ is measured with the energy-scan technique and it is found to be consistent with previously published data, but with much improved accuracy. In addition, the electromagnetic form-factor ratio ($|G_{E}/G_{M}|$) and the value of the effective ($|G_{\rm{eff}}|$), electric ($|G_E|$) and magnetic ($|G_M|$) form factors are measured by studying the helicity angle of the proton at 16 center-of-mass energy points. $|G_{E}/G_{M}|$ and $|G_M|$ are determined with high accuracy, providing uncertainties comparable to data in the space-like region, and $|G_E|$ is measured for the first time. We reach unprecedented accuracy, and precision results in the time-like region provide information to improve our understanding of the proton inner structure and to test theoretical models which depend on non-perturbative Quantum Chromodynamics

Observation of J/ψ→ppˉa0(980)J/\psi \rightarrow p\bar{p}a_{0}(980) at BESIII

Using $2.25\times10^{8}$ $J/\psi$ events collected with the BESIII detector at the BEPCII storage rings, we observe for the first time the process $J/\psi\rightarrow p\bar{p}a_{0}(980)$, $a_{0}(980)\rightarrow \pi^{0}\eta$ with a significance of $6.5\sigma$ ($3.2\sigma$ including systematic uncertainties). The product branching fraction of $J/\psi\rightarrow p\bar{p}a_{0}(980)\rightarrow p\bar{p}\pi^{0}\eta$ is measured to be $(6.8\pm1.2\pm1.3)\times 10^{-5}$, where the first error is statistical and the second is systematic. This measurement provides information on the $a_{0}$ production near threshold coupling to $p\bar{p}$ and improves the understanding of the dynamics of $J/\psi$ decays to four body processes.Comment: 8 pages, 7 figure

Precision measurement of the D∗0D^{*0} decay branching fractions

Using 482 pb$^{-1}$ of data taken at $\sqrt{s}=4.009$ GeV, we measure the branching fractions of the decays of $D^{*0}$ into $D^0\pi^0$ and $D^0\gamma$ to be \BR(D^{*0} \to D^0\pi^0)=(65.5\pm 0.8\pm 0.5)% and \BR(D^{*0} \to D^0\gamma)=(34.5\pm 0.8\pm 0.5)% respectively, by assuming that the $D^{*0}$ decays only into these two modes. The ratio of the two branching fractions is \BR(D^{*0} \to D^0\pi^0)/\BR(D^{*0} \to D^0\gamma) =1.90\pm 0.07\pm 0.05, which is independent of the assumption made above. The first uncertainties are statistical and the second ones systematic. The precision is improved by a factor of three compared to the present world average values

Search for C-parity violation in J/ψ→γγJ/ \psi \to \gamma\gamma and γϕ \gamma \phi

Using $1.06\times10^8$ $\psi(3686)$ events recorded in $e^{+}e^{-}$ collisions at $\sqrt{s}=$ 3.686 GeV with the BESIII at the BEPCII collider, we present searches for C-parity violation in $J/\psi \to \gamma\gamma$ and $\gamma \phi$ decays via $\psi(3686) \to J/\psi \pi^+\pi^-$. No significant signals are observed in either channel. Upper limits on the branching fractions are set to be $\mathcal{B}(J/\psi \to \gamma\gamma) < 2.7 \times 10^{-7}$ and $\mathcal{B}(J/\psi \to \gamma\phi) < 1.4 \times 10^{-6}$ at the 90\% confidence level. The former is one order of magnitude more stringent than the previous upper limit, and the latter represents the first limit on this decay channel.Comment: 7 pages, 2 figure