Refined Edge Usage of Graph Neural Networks for Edge Prediction

Graph Neural Networks (GNNs), originally proposed for node classification, have also motivated many recent works on edge prediction (a.k.a., link prediction). However, existing methods lack elaborate design regarding the distinctions between two tasks that have been frequently overlooked: (i) edges only constitute the topology in the node classification task but can be used as both the topology and the supervisions (i.e., labels) in the edge prediction task; (ii) the node classification makes prediction over each individual node, while the edge prediction is determinated by each pair of nodes. To this end, we propose a novel edge prediction paradigm named Edge-aware Message PassIng neuRal nEtworks (EMPIRE). Concretely, we first introduce an edge splitting technique to specify use of each edge where each edge is solely used as either the topology or the supervision (named as topology edge or supervision edge). We then develop a new message passing mechanism that generates the messages to source nodes (through topology edges) being aware of target nodes (through supervision edges). In order to emphasize the differences between pairs connected by supervision edges and pairs unconnected, we further weight the messages to highlight the relative ones that can reflect the differences. In addition, we design a novel negative node-pair sampling trick that efficiently samples 'hard' negative instances in the supervision instances, and can significantly improve the performance. Experimental results verify that the proposed method can significantly outperform existing state-of-the-art models regarding the edge prediction task on multiple homogeneous and heterogeneous graph datasets.Comment: Pre-prin

Quality of reporting of systematic reviews published in “evidence-based” Chinese journals

BACKGROUND: The number of systematic reviews (SRs)/meta-analyses (MAs) has increased dramatically in China over the past decades. However, evaluation of quality of reporting of systematic reviews published has not been undertaken. The objective of this study is to evaluate the quality of reporting of SRs/MAs assessing efficacy and/or harms of clinical interventions published in “evidence-based” Chinese journals. METHODS: Web-based database searches were conducted for the Chinese Journal of Evidence-based Medicine, the Journal of Evidence-Based Medicine, the Chinese Journal of Evidence Based Pediatrics, and the Chinese Journal of Evidence-Based Cardiovascular Medicine. SRs/MAs assessing efficacy and/or harms of clinical interventions were included. The cut-off was December 31st 2011. The PRISMA statement was applied to assess the quality of reporting. Each item was assessed as follows: ‘Yes’ for total compliance, scored ‘1’; ‘partial’ for partial compliance, scored ‘0.5’; and ‘No’ for non-compliance, scored ‘0’. The review was considered to have major flaws if it received a total score of ≤15.0, minor flaws if it received a total score of 15.5 to 21.0, and minimal flaws if it received a total score 21.5 to 27.0. Odds ratios were used for binary variables, and the mean difference was used for continuous variables. Analyses were performed using RevMan 5.0 software. RESULTS: Overall, 487 SRs/MAs were identified and assessed. The included reviews had medium quality with minor flaws based on PRISMA total scores (range: 8.5–26.0; mean: 19.6 ± 3.3). The stratified analysis showed that SRs/MAs with more than 3 authors, from a university, hospital + university cooperation, multiple affiliations (≥2), and funding have significantly higher quality of reporting of SRs/MAs; 58% of the included reviews were considered to have minor flaws (total score of 15.6 to 21.0). Only 9.6% of reviews were considered to have major flaws. Specific areas needing improvement in reporting include the abstract, protocol and registration, and characteristics of the search. CONCLUSIONS: The reporting of SRs published in “evidence-based” Chinese journals is poor and needs to be improved in order for reviews to be useful. SR authors should use the PRISMA checklist to ensure complete and accurate accounts of their SRs

The 5'-end transitional CpGs between the CpG islands and retroelements are hypomethylated in association with loss of heterozygosity in gastric cancers

BACKGROUND: A loss of heterozygosity (LOH) represents a unilateral chromosomal loss that reduces the dose of highly repetitive Alu, L1, and LTR retroelements. The aim of this study was to determine if the LOH events can affect the spread of retroelement methylation in the 5'-end transitional area between the CpG islands and their nearest retroelements. METHODS: The 5'-transitional area of all human genes (22,297) was measured according to the nearest retroelements to the transcription start sites. For 50 gastric cancer specimens, the level of LOH events on eight cancer-associated chromosomes was estimated using the microsatellite markers, and the 5'-transitional CpGs of 20 selected genes were examined by methylation analysis using the bisulfite-modified DNA. RESULTS: The extent of the transitional area was significantly shorter with the nearest Alu elements than with the nearest L1 and LTR elements, as well as in the extragenic regions containing a higher density of retroelements than in the intragenic regions. The CpG islands neighbouring a high density of Alu elements were consistently hypomethylated in both normal and tumor tissues. The 5'-transitional methylated CpG sites bordered by a low density of Alu elements or the L1 and LTR elements were hypomethylated more frequently in the high-level LOH cases than in the low-level LOH cases. CONCLUSION: The 5'-transitional methylated CpG sites not completely protected by the Alu elements were hypomethylated in association with LOH events in gastric cancers. This suggests that an irreversible unbalanced decrease in the genomic dose reduces the spread of L1 methylation in the 5'-end regions of genes

Spatial beam self-cleaning in bi-tapered multimode fibers

We report the spatial beam self-cleaning in bi-tapered conventional multimode fibers (MMFs) with different tapered lengths. Through the introduction of the bi-tapered structure in MMFs, the input beam with poor beam quality from a high-power fiber laser can be converted to a centered, bell-shaped beam in a short length, due to the strengthened nonlinear modes coupling. It is found that the bi-tapered MMF with longer tapered length at the same waist diameter shows better beam self-cleaning effect and larger spectral broadening. The obtained results offer a new method to improve the beam quality of high-power laser at low cost. Besides, it may be interesting for manufacturing bi-tapered MMF-based devices to obtain the quasi-fundamental mode beam in spatiotemporal mode-locked fiber lasers

Identification of Chemical Components in Gannan Navel Orange Pulp by UPLC-QTOF-MS Coupled with HS-SPME-GC-MS

Using ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS), we separated and identified 148 non-volatile organic compounds including flavonoids, organic acids and amino acids in navel orange pulp in 37 min. The volatile organic compounds (VOCs) in the pulp of navel oranges from four major production regions in southern Jiangxi Province, Ruijin, Xinfeng, Anyuan and Nankang were detected by headspace solid phase microextraction combined with gas chromatography-mass spectrometry (HS-SPME-GC-MS). In total, 97 VOCs were identified including esters, alcohols, aldehydes and terpenes. The results of this study provide detailed data for further research on chemical substances in the pulp of Gannan navel oranges

Multiple-relaxation-time lattice Boltzmann model for compressible fluids

We present an energy-conserving multiple-relaxation-time finite difference lattice Boltzmann model for compressible flows. This model is based on a 16-discrete-velocity model. The collision step is first calculated in the moment space and then mapped back to the velocity space. The moment space and corresponding transformation matrix are constructed according to the group representation theory. Equilibria of the nonconserved moments are chosen according to the need of recovering compressible Navier-Stokes equations through the Chapman-Enskog expansion. Numerical experiments showed that compressible flows with strong shocks can be well simulated by the present model. The used benchmark tests include (i) shock tubes, such as the Sod, Lax, Sjogreen, Colella explosion wave and collision of two strong shocks, (ii) regular and Mach shock reflections, and (iii) shock wave reaction on cylindrical bubble problems. The new model works for both low and high speeds compressible flows. It contains more physical information and has better numerical stability and accuracy than its single-relaxation-time version.Comment: 11 figures, Revte

Two-point fixation enhanced the outcome of laparoscopy-assisted ventriculoperitoneal shunt in adult patients with hydrocephalus: a retrospective study

ObjectiveIn patients with hydrocephalus, laparoscopy significantly improved ventriculoperitoneal shunt (VPS) outcomes. However, abdominal complications still occur, which require revision surgeries. In this study, we aimed to examine whether laparoscopy-assisted VPS with two-point fixation (LAVPS-TPF) has better outcomes than those of VPS (open-VPS) and laparoscopy-assisted VPS with no fixation (LAVPS-NF).MethodsWe retrospectively reviewed clinical records of 105 open-VPS, 40 LAVPS-NF, and 49 LAVPS-TPF cases from 2015 to 2020. Data including body mass index, etiology, abdominal surgery history, Glasgow coma scale (GCS), operation time, in-hospital days, shunt failure, complications, and modified Rankin scores were analyzed, as well as subgroups of patients with history of abdominal surgery, GCS scores, and revision surgeries.ResultsThe LAVPS-TPF group demonstrated decreased shunt failure rates at 12 months (2.04%) compared to those of the open-VPS group (14.29%, P = 0.020) and reduced abdominal shunt-related complications (P = 0.004 vs. open-VPS and LAVPS-NF) and shunt revisions. In the LAVPS-TPF group with abdominal history (n = 51), 12-month shunt failure rates (P = 0.020 vs. open-VS), repair frequency (P = 0.020 vs. open-VS), and abdominal complications (P = 0.003 and 0.006 vs. open-VS and LAVPS-NF) were reduced. In the LAVPS-TPF group with GCS scores of 13–15 (n = 152), shunt failure rates at 12 months, abdominal complications, and revision frequency were decreased (P < 0.05 vs. other groups). Compared to the LAVPS-NF group, neurological complications were also reduced (P = 0.001). Among revision surgeries (n = 28), fixed shunts resulted in improved shunt survival rates at 12 months, reduced abdominal complications, and secondary revisions (P < 0.05). Moreover, a more optimal recovery without neurological sequelae was achieved by shunt fixation than that by LAVPS-NF (P < 0.01).ConclusionsLAVPS-TPF significantly improved shunt survival rates at 12 months and reduced the incidence of abdominal shunt-related complications compared to open-VPS and LAVPS-NF, especially in patients with history of abdominal surgery, higher GCS scores, and revision surgeries. However, further studies are required to confirm these benefits