PU-Flow: a Point Cloud Upsampling Network with Normalizing Flows

Point cloud upsampling aims to generate dense point clouds from given sparse ones, which is a challenging task due to the irregular and unordered nature of point sets. To address this issue, we present a novel deep learning-based model, called PU-Flow, which incorporates normalizing flows and weight prediction techniques to produce dense points uniformly distributed on the underlying surface. Specifically, we exploit the invertible characteristics of normalizing flows to transform points between Euclidean and latent spaces and formulate the upsampling process as ensemble of neighbouring points in a latent space, where the ensemble weights are adaptively learned from local geometric context. Extensive experiments show that our method is competitive and, in most test cases, it outperforms state-of-the-art methods in terms of reconstruction quality, proximity-to-surface accuracy, and computation efficiency. The source code will be publicly available at https://github.com/unknownue/pu-flow

TKwinFormer: Top k Window Attention in Vision Transformers for Feature Matching

Local feature matching remains a challenging task, primarily due to difficulties in matching sparse keypoints and low-texture regions. The key to solving this problem lies in effectively and accurately integrating global and local information. To achieve this goal, we introduce an innovative local feature matching method called TKwinFormer. Our approach employs a multi-stage matching strategy to optimize the efficiency of information interaction. Furthermore, we propose a novel attention mechanism called Top K Window Attention, which facilitates global information interaction through window tokens prior to patch-level matching, resulting in improved matching accuracy. Additionally, we design an attention block to enhance attention between channels. Experimental results demonstrate that TKwinFormer outperforms state-of-the-art methods on various benchmarks. Code is available at: https://github.com/LiaoYun0x0/TKwinFormer.Comment: 11 pages, 7 figure

Recombination Hotspots and Population Structure in Plasmodium falciparum

Understanding the influences of population structure, selection, and recombination on polymorphism and linkage disequilibrium (LD) is integral to mapping genes contributing to drug resistance or virulence in Plasmodium falciparum. The parasite's short generation time, coupled with a high cross-over rate, can cause rapid LD break-down. However, observations of low genetic variation have led to suggestions of effective clonality: selfing, population admixture, and selection may preserve LD in populations. Indeed, extensive LD surrounding drug-resistant genes has been observed, indicating that recombination and selection play important roles in shaping recent parasite genome evolution. These studies, however, provide only limited information about haplotype variation at local scales. Here we describe the first (to our knowledge) chromosome-wide SNP haplotype and population recombination maps for a global collection of malaria parasites, including the 3D7 isolate, whose genome has been sequenced previously. The parasites are clustered according to continental origin, but alternative groupings were obtained using SNPs at 37 putative transporter genes that are potentially under selection. Geographic isolation and highly variable multiple infection rates are the major factors affecting haplotype structure. Variation in effective recombination rates is high, both among populations and along the chromosome, with recombination hotspots conserved among populations at chromosome ends. This study supports the feasibility of genome-wide association studies in some parasite populations

Multiple Transporters Associated with Malaria Parasite Responses to Chloroquine and Quinine

Mutations and/or overexpression of various transporters are known to confer drug resistance in a variety of organisms. In the malaria parasite Plasmodium falciparum, a homologue of P-glycoprotein, PfMDR1, has been implicated in responses to chloroquine (CO), quinine (ON) and other drugs, and a putative transporter, PfCRT, was recently demonstrated to be the key molecule in CO resistance. However, other unknown molecules are probably involved, as different parasite clones carrying the same pfcrt and pfmdr1 alleles show a wide range of quantitative responses to CO and ON. Such molecules may contribute to increasing incidences of ON treatment failure, the molecular basis of which is not understood. To identify additional genes involved in parasite CO and ON responses, we assayed the in vitro susceptibilities of 97 culture-adapted cloned isolates to CO and ON and searched for single nucleotide polymorphisms (SNPs) in DNA encoding 49 putative transporters (total 113 kb) and in 39 housekeeping genes that acted as negative controls. SNPs in 11 of the putative transporter genes, including pfcrt and pfmdr1, showed significant associations with decreased sensitivity to CQ and/or ON in P. faliparum. Significant linkage disequilibria within and between these genes were also detected, suggesting interactions among the transporter genes. This study provides specific leads for better understanding of complex drug resistances in malaria parasite

Lack of allele-specific efficacy of a bivalent AMA1 malaria vaccine

<p>Abstract</p> <p>Background</p> <p>Extensive genetic diversity in vaccine antigens may contribute to the lack of efficacy of blood stage malaria vaccines. Apical membrane antigen-1 (AMA1) is a leading blood stage malaria vaccine candidate with extreme diversity, potentially limiting its efficacy against infection and disease caused by <it>Plasmodium falciparum </it>parasites with diverse forms of AMA1.</p> <p>Methods</p> <p>Three hundred Malian children participated in a Phase 2 clinical trial of a bivalent malaria vaccine that found no protective efficacy. The vaccine consists of recombinant AMA1 based on the 3D7 and FVO strains of <it>P. falciparum </it>adjuvanted with aluminum hydroxide (AMA1-C1). The gene encoding AMA1 was sequenced from <it>P. falciparum </it>infections experienced before and after immunization with the study vaccine or a control vaccine. Sequences of <it>ama1 </it>from infections in the malaria vaccine and control groups were compared with regard to similarity to the vaccine antigens using several measures of genetic diversity. Time to infection with parasites carrying AMA1 haplotypes similar to the vaccine strains with respect to immunologically important polymorphisms and the risk of infection with vaccine strain haplotypes were compared.</p> <p>Results</p> <p>Based on 62 polymorphic AMA1 residues, 186 unique <it>ama1 </it>haplotypes were identified among 315 <it>ama1 </it>sequences that were included in the analysis. Eight infections had <it>ama1 </it>sequences identical to 3D7 while none were identical to FVO. Several measures of genetic diversity showed that <it>ama1 </it>sequences in the malaria vaccine and control groups were comparable both at baseline and during follow up period. Pre- and post-immunization <it>ama1 </it>sequences in both groups all had a similar degree of genetic distance from FVO and 3D7 <it>ama1</it>. No differences were found in the time of first clinical episode or risk of infection with an AMA1 haplotype similar to 3D7 or FVO with respect to a limited set of immunologically important polymorphisms found in the cluster 1 loop of domain I of AMA1.</p> <p>Conclusion</p> <p>This Phase 2 trial of a bivalent AMA1 malaria vaccine found no evidence of vaccine selection or strain-specific efficacy, suggesting that the extreme genetic diversity of AMA1 did not account for failure of the vaccine to provide protection.</p

Long-term exposure to air pollution and lung function among children in China: Association and effect modification

BackgroundChildren are vulnerable to the respiratory effects of air pollution, and their lung function has been associated with long-term exposure to low air pollution level in developed countries. However, the impact of contemporary air pollution level in developing countries as a result of recent efforts to improve air quality on children's lung function is less understood.MethodsWe obtained a cross-sectional sample of 617 schoolchildren living in three differently polluted areas in Anhui province, China. 2-year average concentrations of air pollutants at the year of spirometry and the previous year (2017–2018) obtained from district-level air monitoring stations were used to characterize long-term exposure. Forced vital capacity (FVC), forced expiratory volume in 1 second (FEV1), and forced expiratory flow between 25 and 75% of FVC (FEF25−75) were determined under strict quality control. Multivariable regression was employed to evaluate the associations between air pollution level and lung function parameters, overall and by demographic characteristics, lifestyle, and vitamin D that was determined by liquid chromatography tandem mass spectrometry.ResultsMean concentration of fine particulate matter was 44.7 μg/m3, which is slightly above the interim target 1 standard of the World Health Organization. After adjusting for confounders, FVC, FEV1, and FEF25−75 showed inverse trends with increasing air pollution levels, with children in high exposure group exhibiting 87.9 [95% confidence interval (CI): 9.5, 166.4] mL decrement in FEV1 and 195.3 (95% CI: 30.5, 360.1) mL/s decrement in FEF25−75 compared with those in low exposure group. Additionally, the above negative associations were more pronounced among those who were younger, girls, not exposed to secondhand smoke, non-overweight, physically inactive, or vitamin D deficient.ConclusionsOur study suggests that long-term exposure to relatively high air pollution was associated with impaired lung function in children. More stringent pollution control measures and intervention strategies accounting for effect modification are needed for vulnerable populations in China and other developing countries

ERK5 MAP Kinase Regulates Neurogenin1 during Cortical Neurogenesis

The commitment of multi-potent cortical progenitors to a neuronal fate depends on the transient induction of the basic-helix-loop-helix (bHLH) family of transcription factors including Neurogenin 1 (Neurog1). Previous studies have focused on mechanisms that control the expression of these proteins while little is known about whether their pro-neural activities can be regulated by kinase signaling pathways. Using primary cultures and ex vivo slice cultures, here we report that both the transcriptional and pro-neural activities of Neurog1 are regulated by extracellular signal-regulated kinase (ERK) 5 signaling in cortical progenitors. Activation of ERK5 potentiated, while blocking ERK5 inhibited Neurog1-induced neurogenesis. Furthermore, endogenous ERK5 activity was required for Neurog1-initiated transcription. Interestingly, ERK5 activation was sufficient to induce Neurog1 phosphorylation and ERK5 directly phosphorylated Neurog1 in vitro. We identified S179/S208 as putative ERK5 phosphorylation sites in Neurog1. Mutations of S179/S208 to alanines inhibited the transcriptional and pro-neural activities of Neurog1. Our data identify ERK5 phosphorylation of Neurog1 as a novel mechanism regulating neuronal fate commitment of cortical progenitors

Flow Channel Influence of a Collision-Based Piezoelectric Jetting Dispenser on Jet Performance

To improve the jet performance of a bi-piezoelectric jet dispenser, mathematical and simulation models were established according to the operating principle. In order to improve the accuracy and reliability of the simulation calculation, a viscosity model of the fluid was fitted to a fifth-order function with shear rate based on rheological test data, and the needle displacement model was fitted to a nine-order function with time based on real-time displacement test data. The results show that jet performance is related to the diameter of the nozzle outlet and the cone angle of the nozzle, and the impacts of the flow channel structure were confirmed. The approach of numerical simulation is confirmed by the testing results of droplet volume. It will provide a reliable simulation platform for mechanical collision-based jet dispensing and a theoretical basis for micro jet valve design and improvement

An Investigation of Effects and Safety of Pipelines due to Twin Tunneling

To efficiently and accurately predict the effects of twin tunneling on adjacent buried pipelines, the effects of upward and downward relative pipeline-soil interactions were considered. A series of numerical parametric studies encompassing 8640 conditions were performed to investigate the responses of a pipeline to twin tunneling. Based on the dimensionless analysis and normalized calculation results, the concept of equivalent relative pipeline-soil stiffness was proposed. Additionally, expressions for the relative pipeline-soil stiffness and relative pipeline curvature and for the relative pipeline-soil stiffness and relative pipeline settlement were established, along with the related calculation plots. Relying on a comparison of prediction results, centrifuge model test results, and field measured results, the accuracy and reliability of the obtained expressions for predicting the bending strain and settlement of adjacent buried pipelines caused by twin tunneling were validated. Based on the calculation method, the maximum bending strain and maximum settlement of pipelines can be calculated precisely when the pipeline parameters, burial depth, soil parameters, and curve parameters of ground settlement due to tunneling are provided. The proposed expressions can be used not only to predict the maximum bending strain and maximum settlement of pipelines caused by single and twin tunneling but also to evaluate the effects of single and twin tunneling on the safety of existing buried pipelines. The relevant conclusions of this article can also provide a theoretical basis for the normal service of buried pipelines adjacent to subway tunnels