Response to "Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" and "Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples".

Two correspondences raised concerns or comments about our analyses regarding exaggerated false positives found by differential expression (DE) methods. Here, we discuss the points they raise and explain why we agree or disagree with these points. We add new analysis to confirm that the Wilcoxon rank-sum test remains the most robust method compared to the other five DE methods (DESeq2, edgeR, limma-voom, dearseq, and NOISeq) in two-condition DE analyses after considering normalization and winsorization, the data preprocessing steps discussed in the two correspondences.

Congruent Long-Term Declines in Carbon and Biodiversity Are a Signature of Forest Degradation.

Recent global policy initiatives aimed at reducing forest degradation require practical definitions of degradation that are readily monitored. However, consistent approaches for monitoring forest degradation over the long term and at broad scales are lacking. We quantified the long-term effects of intensive wood harvest on above-ground carbon and biodiversity at fine resolutions (30 m) and broad scales (New Brunswick, Canada; 72,908 km).

Two-color fluorescence-guided surgery for head and neck cancer resections.

Significance: Head and neck squamous cell carcinoma (HNSCC) has the sixth highest incidence worldwide, with cases annually. Surgery is the primary treatment option for HNSCC, during which surgeons balance two main goals: (1) complete cancer resection and (2) preservation of normal tissues to ensure post-surgical quality of life. Unfortunately, these goals are not synergistic, where complete cancer resection is often limited by efforts to preserve normal tissues, particularly nerves, and reduce life-altering comorbidities.

Congenital pulmonary airway malformation in a cat.

Congenital structural anomalies of the lower airways of the respiratory tract are uncommon in cats. We describe here a case of cystic pulmonary lesions in a 6-wk-old domestic shorthair cat consistent with congenital pulmonary airway malformation (CPAM; formerly referred to as cystic adenomatoid malformation of the lung, or congenital pulmonary adenomatoid malformation; Stocker type II). CPAM is rarely reported in veterinary species and, to our knowledge, has not been reported in cats.

Experimental coral reef communities transform yet persist under mitigated future ocean warming and acidification.

Coral reefs are among the most sensitive ecosystems affected by ocean warming and acidification, and are predicted to collapse over the next few decades. Reefs are predicted to shift from net accreting calcifier-dominated systems with exceptionally high biodiversity to net eroding algal-dominated systems with dramatically reduced biodiversity. Here, we present a two-year experimental study examining the responses of entire mesocosm coral reef communities to warming (+2 °C), acidification (-0.

Canker and dieback of is caused by .

Understanding the ecology of pathogens is important for disease management. Recently a devastating canker disease was found on red alder () planted as landscape trees. Bacteria were isolated from two groups of symptomatic trees located approximately 1 kilometer apart and one strain from each group was used to complete Koch's postulates.

Digital Light Process 3D Printing of Magnetically Aligned Liquid Crystalline Elastomer Free-forms.

Liquid crystalline elastomers (LCEs) are anisotropic soft materials capable of large dimensional changes when subjected to a stimulus. The magnitude and directionality of the stimuli-induced thermomechanical response is associated with the alignment of the LCE. Recent reports detail the preparation of LCEs by additive manufacturing (AM) techniques, predominately using direct ink write printing.

Quantifying Parental Perceptions of Their Experiences With Their Young Children's Use of Power Mobility Devices.

Purpose: To quantify and explore parental perceptions of their experiences with their child's use of the Explorer Mini (EM) and a modified ride-on car (mROC) in young children with cerebral palsy.

Method: Data were gathered throughout a multisite, randomized, counterbalanced AB crossover 16-week clinical trial, wherein all participants used device A (EM) and device B (mROC) for 8-weeks each. Semistructured parent interviews were conducted at baseline (T0), post-intervention period 1 (T1), and post-intervention period 2 (T2).

Statistical optimization of cell-hydrogel interactions for green microbiology - a tutorial review.

In this tutorial mini-review, we explore the application of Design of Experiments (DOE) as a powerful statistical tool in biotechnology. Specifically, we review the optimization of hydrogel materials for diverse microbial applications related to green microbiology, the use of microbes to promote sustainability. Hydrogels, three-dimensional polymers networks with high water retention capabilities, are pivotal in the immobilization of microorganisms and provide a customizable environment essential for directing microbial fate.

MicrobiomeKG: Bridging Microbiome Research and Host Health Through Knowledge Graphs.

The microbiome represents a complex community of trillions of microorganisms residing in various body parts, and plays critical roles in maintaining host health and well-being. Understanding the interactions between microbiota and host offers valuable insights into potential strategies to promote health, including microbiome-targeted interventions. We have created MicrobiomeKG, a Knowledge Graph for microbiome research, bridging various taxa and microbial pathways with host health.

Multiple resiliency metrics reveal complementary drivers of ecosystem persistence: An application to kelp forest systems.

Human-caused global change produces biotic and abiotic conditions that increase the uncertainty and risk of failure of restoration efforts. A focus of managing for resiliency, that is, the ability of the system to respond to disturbance, has the potential to reduce this uncertainty and risk. However, identifying what drives resiliency might depend on how one measures it.

ability to interact with the host mucosal cells plays an important role in pathogenesis of the infection.

Non-tuberculous mycobacteria (NTM) are opportunistic pathogens ubiquitous in the environment. is a relatively new pathogen associated with underlying lung chronic pathologies, accounting for most of the pulmonary infections linked to the rapidly growing mycobacteria group. This includes chronic obstructive pulmonary disease, bronchiectasis, or cystic fibrosis.

Navigating and Resisting Educational Systems: The Experiences of Latinx Families in Rural Oregon.

This study explores the experiences of Latinx parents in rural Oregon from the perspectives of Latinx parents, Latinx students, and community practitioners to understand the barriers Latinx families encounter and how they leverage their community cultural wealth to address these barriers within the context of initiatives implemented by the district. This qualitative study is guided by the following questions: What barriers do Latinx families encounter in rural schools, and how do parents leverage their community cultural wealth to address these barriers? Findings indicate that even when families were engaged in initiatives (e.g.

Health of Family Members of Road Transport Workers: Evaluation of Perceived Stress and Family Effectiveness.

The health of road transport workers is affected by working conditions and life. However, there is a lack of studies on the level of stress and health of the families of these workers. This study aimed to evaluate the perceived stress level and family effectiveness of family members of road transport workers.

(Ashwagandha) Improves Spatial Memory, Anxiety and Depressive-like Behavior in the 5xFAD Mouse Model of Alzheimer's Disease.

(WS), also known as ashwagandha, is a popular botanical supplement used to treat various conditions including memory loss, anxiety and depression. Previous studies from our group showed an aqueous extract of WS root (WSAq) enhances cognition and alleviates markers for depression in . Here, we sought to confirm these effects in the 5xFAD mouse model of β-amyloid (Aβ) accumulation.

The Promises and Potential Pitfalls of Highway Reclamation for Population Health: A Research Framework.

Highway reclamation (i.e., the removal of highways or placing existing highways underground to create mixed-use urban areas) is being implemented around the United States, often touting co-benefits for population health.

Distinct chemical structures inhibit the CEMIP hyaluronidase and promote oligodendrocyte progenitor cell maturation.

Growing evidence supports pathogenic roles for chronically elevated hyaluronidase activity in numerous conditions. Elevated expression of one such hyaluronidase, the Cell Migration Inducing and hyaluronan binding Protein (CEMIP), has been implicated in the pathogenesis and progression of several cancers as well as demyelinating diseases in the central nervous system (CNS). Developing effective and selective CEMIP inhibitors could therefore have efficacy in treating a variety of conditions where CEMIP is chronically elevated.

Developing a Screening Strategy to Identify Hepatotoxicity and Drug Interaction Potential of Botanicals.

Botanical supplements, herbal remedies, and plant-derived products are used globally. However, botanical dietary supplements are rarely subjected to robust safety testing unless there are adverse reports in post-market surveillance. Botanicals are complex and difficult to assess using current frameworks designed for single constituent substances (e.