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Weijia Chen

Publications and source records attributed to Weijia Chen.

6 recordsLinked to original sources
PubMed2026

A Practical Workflow for Spatial Transcriptomics Data Analysis: From Data Acquisition to Advanced Analyses.

Spatial transcriptomics (ST) profiles genome-wide gene expression while preserving the two-dimensional spatial context of mRNA molecules within tissue sections, enabling studies of tissue architecture and microenvironment-associated biology. However, ST analysis remains challenging because data import, quality control, integration, deconvolution, spatial statistics, and visualization often require multiple software environments and reproducible parameter choices. This protocol presents a practical computational workflow for public ST datasets in R, beginning with data acquisition and software setup and proceeding through Seurat-based data loading, quality control, normalization, multi-sample integration, clustering, and spatially variable gene analysis. The workflow then applies complementary deconvolution strategies, including reference-guided SPOTlight analysis and unsupervised STdeconvolve topic modeling, followed by Giotto-based spatial cell-cell communication analysis and interactive region-of-interest (ROI) selection using a custom Python Dash application. By emphasizing script-based execution, explicit parameter rationales, expected outputs, and troubleshooting checkpoints, the protocol provides an adaptable framework for standard array-based ST datasets and related platforms after dataset- and platform-specific parameter evaluation.

Spatial Transcriptomics↗
PubMed2026

Efficacy, tolerability, and threshold effect of atropine eye drops for myopia control: A systematic review and dose-response meta-analysis.

Atropine is an emerging therapy for myopia, yet the optimal concentration for prescription remains uncertain. We searched PubMed, Embase, Web of Science, Cochrane Library, World Health Organization International Clinical Trials, and ClinicalTrials.gov registry platforms. We included the randomized clinical trials (RCTs) that compared any dose of atropine against a placebo in myopic children. Among 3566 studies assessed, we identified 33 eligible RCTs involving 6301 children aged 4-18 years, with 10 different concentrations and a mean follow-up time of 19.5&#x202f;&#xb1;&#x202f;12.3 months. A nonlinear relationship was observed between atropine dosage and treatment efficacy (P&#x202f;<&#x202f;0.001). Compared to placebo groups, the mean differences in reducing annual spherical equivalent refraction progression for atropine concentrations of 0.01%, 0.02%, 0.03%, 0.04%, and 0.05% were 0.21 diopters (D) (95% CI, 0.13-0.28), 0.35 D (95% CI, 0.23-0.46), 0.42 D (95% CI, 0.28-0.56), 0.45 D (95% CI, 0.30-0.60), and 0.46 D (95% CI, 0.32-0.61) respectively For higher concentrations, the estimates were 0.49 D (95% CI, 0.34-0.63) for 0.1% and 0.99 D (95% CI, 0.66-1.31) for 1%, although these were based on fewer and smaller trials. Higher doses of atropine were associated with decreased amplitude of accommodation (P&#x202f;=&#x202f;0.02), increased pupil diameters (P&#x202f;=&#x202f;0.01) and a higher frequency of photophobia (P&#x202f;=&#x202f;0.02). Our findings suggest that the increase in treatment efficacy with higher concentrations may plateau beyond a certain range, and that the current practice of increasing atropine concentrations for children who show inadequate responses to lower doses should be confined to a specific concentration range. This analysis is limited by the number, design heterogeneity, and sample sizes of available trials for higher concentrations, and by the frequent lack of pre-intervention refractive history in included studies. Therefore, estimates-particularly for doses exceeding 0.1%-should be interpreted with caution.

Humans↗
PubMed2006

Proinflammatory cytokines gene expression in skin flaps with arterial and venous ischemia in rats.

Infiltration of inflammatory cells is the crucial element in ischemia-reperfusion injury of the microsurgical flap. Cytokines are a large functional group of polypeptide regulatory molecules that influence the activity of various cell types through autocrine and paracrine mechanisms. In this study, expression of selected proinflammatory cytokines was examined in skin flaps with arterial and venous ischemia in the rat model. Fifty-four Sprague-Dawley rats were used in the study. The ischemia of each flap was induced by clamping its vascular pedicle for 6 hr. The flap was then replaced and allowed to reperfuse. All flaps were biopsied immediately post-event, and at 3, 6 and 18 hr after reperfusion. Expression of tumor necrosis factor (TNF-alpha), interleukin (IL-1beta), and monocyte chemoattractant protein-1 (MCP-1) mRNA was determined by RT-PCR in each case. The same number of skin flaps without ischemia was used for baseline gene expression. Results showed that the TNF-alpha expression was significantly up-regulated in the flaps with arterial ischemia at 6 hr after reperfusion. In the flaps with venous ischemia, MCP-1 expression was increased with its peak expression at 3 hr after reperfusion. IL-1beta expression was increased threefold in the flaps subjected to venous ischemia and following reperfusion in 3 hr, but the peak expression in the flap with arterial ischemia was observed at 18 hr after reperfusion. This study delineated the changes in expression of these proinflammatory cytokines in flaps with arterial and venous ischemia reperfusion injury, and showed that cytokine expression was different in the arterial and venous injuries.

Animals↗
PubMed2006

Improvement of venous flap survival by application of vascular endothelial growth factor in a rat model.

Expression of vascular endothelial growth factor (VEGF) in the venous flap and the effect of exogenous VEGF on survival of the venous flap were studied in rats. A 4- x 4-cm groin type 2 venous skin flap was used in the study. In part 1, biopsies were taken from the flap at 0, 6, 12, 24, and 48 hours after the flaps were raised. VEGF gene expression was measured. In part 2, exogenous VEGF (1 microg/mL) was injected subdermally into the flaps in 10 rats before the flaps were replaced. Flaps that received a saline injection were used as the control. Skin paddle survival was measured on postoperative day 7. The results showed that VEGF expression was significantly increased at 24 and 48 hours after venous flap elevation (P < 0.05). Injection of exogenous VEGF to the flap significantly improved survival of the flap (73% of the flap) when compared with the control, which had a 39% mean percent survival (P < 0.05). We conclude that VEGF expression was increased in the venous flap. Administration of exogenous VEGF significantly improved survival of the venous flap.

Animals↗
PubMed2006

Treatment of painful neuroma of amputated phalanx with distal toe transfer: a case report.

A painful neuroma in the amputation stump of a finger can be psychologically and physically disabling. Numerous surgical procedures have been attempted to prevent and treat amputation neuromas of the finger, but the results are inconsistent. Microsurgical transfer of the distal second toe to the amputated stump of the finger can provide a pathway and target for the regenerating axons and avoid recurrence of neuromas. In this article, we present the experience of successful treatment of amputation neuromas of an index finger with microsurgical distal toe transfer.

Amputation, Traumatic↗