Recovery of biological signals lost in single-cell batch integration with CellANOVA.

Data integration to align cells across batches has become a cornerstone of single-cell data analysis, critically affecting downstream results. Currently, there are no guidelines for when the biological differences between samples are separable from batch effects. Here we show that current paradigms for single-cell data integration remove biologically meaningful variation and introduce distortion.

Antifungal susceptibility, molecular epidemiology, and clinical risk factors of in intensive care unit in a Chinese Tertiary Hospital.

Background: The increasing incidence and high mortality rate of infection in ICU patients is an important issue. Therefore, it is imperative to investigate the antifungal susceptibility profiles and epidemiological characteristics in local regions.

Methods: Herein, antifungal susceptibility testing was conducted to determine the minimum inhibitory concentrations (MICs) of eight antifungal drugs.

Digital Mental Health Interventions for Alleviating Depression and Anxiety During Psychotherapy Waiting Lists: Systematic Review.

Background: Depression and anxiety have become increasingly prevalent across the globe. The rising need for treatment and the lack of clinicians has resulted in prolonged waiting times for patients to receive their first session. Responding to this gap, digital mental health interventions (DMHIs) have been found effective in treating depression and anxiety and are potentially promising pretreatments for patients who are awaiting face-to-face psychotherapy.

Integrated Framework to Model Microstructure Evolution and Decipher the Microstructure-Property Relationship in Polymeric Porous Materials.

Unraveling the microstructure-property relationship is crucial for improving material performance and advancing the design of next-generation structural and functional materials. However, this is inherently challenging because it requires both the comprehensive quantification of microstructural features and the accurate assessment of corresponding properties. To meet these requirements, we developed an efficient and comprehensive integrated modeling framework, using polymeric porous materials as a representative model system.

Distinct patterns of electrophysiologic-neuroimaging correlations between Parkinson's disease and multiple system atrophy.

Due to a high degree of symptom overlap in the early stages, with movement disorders predominating, Parkinson's disease (PD) and multiple system atrophy (MSA) may exhibit a similar decline in motor areas, yet they differ in their spread throughout the brain, ultimately resulting in two distinct diseases. Drawing upon neuroimaging analyses and altered motor cortex excitability, potential diffusion mechanisms were delved into, and comparisons of correlations across distinct disease groups were conducted in a bid to uncover significant pathological disparities. We recruited thirty-five PD, thirty-seven MSA, and twenty-eight matched controls to conduct clinical assessments, electromyographic recording, and magnetic resonance imaging scanning during the "on medication" state.

Molecular, biological characterization and drug sensitivity of chidamide-resistant MCF7 cells.

Background: Chidamide (CHI) is a subtype-selective histone deacetylase inhibitor (HDACI) developed in China and approved as a second-line treatment combined with the aromatase inhibitor for hormone receptor-positive (HR)/human epidermal growth factor receptor 2-negative (HER2) advanced breast cancer. However, drug resistance is commonly occurred after a long period of medication. This study aimed to investigate the characterization of induced resistance to CHI and explore the potential cross-resistance to chemotherapeutic agents.

A "What Matters Most" approach to investigating intersectional stigma toward HIV and cancer in Hanoi, Vietnam.

Background: Vietnam is experiencing a growing burden of cancer, including among people living with HIV. Stigma acts as a sociocultural barrier to the prevention and treatment of both conditions. This study investigates how cultural notions of "respected personhood" (or "what matters most") influence manifestations of HIV-related stigma and cancer stigma in Hanoi, Vietnam.

Wald χ Test for Differential Item Functioning Detection with Polytomous Items in Multilevel Data.

Identifying items with differential item functioning (DIF) in an assessment is a crucial step for achieving equitable measurement. One critical issue that has not been fully addressed with existing studies is how DIF items can be detected when data are multilevel. In the present study, we introduced a Lord's Wald test-based procedure for detecting both uniform and non-uniform DIF with polytomous items in the presence of the ubiquitous multilevel data structure.

Approaches to Item-Level Data with Cross-Classified Structure: An Illustration with Student Evaluation of Teaching.

Student evaluation of teaching (SET) questionnaires are ubiquitously applied in higher education institutions in North America for both formative and summative purposes. Data collected from SET questionnaires are usually item-level data with cross-classified structure, which are characterized by multivariate categorical outcomes (i.e.

Psychometric exploration of the RAADS-R with autistic adults: Implications for research and clinical practice.

Surveys used to screen for autism are being used much more by adults. Adults and clinicians want to be confident that the results from their surveys are accurate. If scores are not accurate, it is not possible to compare the scores of different groups of individuals.

Regulatory role of Mss11 in virulence: adhesion and biofilm formation.

Introduction: has emerged as a fungal pathogen with high infection and mortality rates, and its primary virulence factors are related to adhesion and biofilm formation. These virulence factors in are primarily mediated by epithelial adhesins (Epas), most of which are encoded in subtelomeric regions and regulated by subtelomeric silencing mechanisms. The transcription factor Mss11, known for its regulatory role in adhesion, biofilm formation, and filamentous growth in and , has also been implicated in the expression of , suggesting its potential influence on virulence.

An Explanatory Multidimensional Random Item Effects Rating Scale Model.

Random item effects item response theory (IRT) models, which treat both person and item effects as random, have received much attention for more than a decade. The random item effects approach has several advantages in many practical settings. The present study introduced an explanatory multidimensional random item effects rating scale model.

A random item effects generalized partial credit model with a multiple imputation-based scoring procedure.

Purpose: Random item effects item response theory (IRT) models have received much attention for more than a decade. However, more research is needed on random item effects IRT models for polytomous data. Additionally, to improve the utility of this new class of IRT models, the scoring issue must be addressed.

Integration of spatial and single-cell data across modalities with weakly linked features.

Although single-cell and spatial sequencing methods enable simultaneous measurement of more than one biological modality, no technology can capture all modalities within the same cell. For current data integration methods, the feasibility of cross-modal integration relies on the existence of highly correlated, a priori 'linked' features. We describe matching X-modality via fuzzy smoothed embedding (MaxFuse), a cross-modal data integration method that, through iterative coembedding, data smoothing and cell matching, uses all information in each modality to obtain high-quality integration even when features are weakly linked.

Single-cell transcriptomes reveal a molecular link between diabetic kidney and retinal lesions.

The occurrence of diabetic nephropathy (DN) and diabetic retinopathy (DR) are closely associated in patients with diabetes. However, the cellular and molecular linkage of DN and DR has not been elucidated, and further revelations are needed to improve mutual prognostic decisions and management. Here, we generate and integrate single-cell RNA sequencing profiles of kidney and retina to explore the cellular and molecular association of kidney and retina in both physiological and pathological conditions.

Mettl3-catalyzed mA regulates histone modifier and modification expression in self-renewing somatic tissue.

-methyladenosine (mA) is the most abundant modification on messenger RNAs (mRNAs) and is catalyzed by methyltransferase-like protein 3 (Mettl3). To understand the role of mA in a self-renewing somatic tissue, we deleted in epidermal progenitors in vivo. Mice lacking demonstrate marked features of dysfunctional development and self-renewal, including a loss of hair follicle morphogenesis and impaired cell adhesion and polarity associated with oral ulcerations.

Construction and validation of a prognostic model based on autophagy-related genes for hepatocellular carcinoma in the Asian population.

Background And Objective: Hepatocellular carcinoma (HCC), which has a complex pathogenesis and poor prognosis, is one of the most common malignancies worldwide. Hepatitis virus B infection is the most common cause of HCC in Asian patients. Autophagy is the process of digestion and degradation, and studies have shown that autophagy-associated effects are closely related to the development of HCC.

Simple Bioparticle Filtration Device Based on an Ultralow-Fouling Zwitterionic Polyurethane Membrane for Rapid Large-Volume Separation of Plasma and Viruses from Whole Blood.

Plasma separation from whole blood is oftent required as an essential first step when performing blood tests with a viral assay. However, developing a point-of-care plasma extraction device with a large output and high virus recovery remains a significant obstacle to the success of on-site viral load tests. Here, we report a portable, easy-to-use, cost-efficient, membrane-filtration-based plasma separation device that enables rapid large-volume plasma extraction from whole blood, designed for point-of-care virus assays.

Signal recovery in single cell batch integration.

Data integration to align cells across batches has become a cornerstone of single cell data analysis, critically affecting downstream results. Yet, how much biological signal is erased during integration? Currently, there are no guidelines for when the biological differences between samples are separable from batch effects, and thus, data integration usually involve a lot of guesswork: Cells across batches should be aligned to be "appropriately" mixed, while preserving "main cell type clusters". We show evidence that current paradigms for single cell data integration are unnecessarily aggressive, removing biologically meaningful variation.