Pre-Training and Ensembling of Deep Neural Networks for Target Gene Expression Prediction From Landmark Genes.

Gene expression profiling is used in many biological and biomedical studies. The L1000 assay is an efficient profiling method that measures the expression of a small number of "landmark" genes and predicts the expression of the remaining "target" genes. Extreme gradient boosting and deep neural networks (DNNs) have shown high accuracy in predicting target gene expression based on landmark genes.

Impact of ozone on kidney transplant outcomes.

Earlier work has shown adverse effects of air pollution on kidney disease outcomes, yet the specific impact of ozone (O) on kidney transplant (KT) recipients remains unclear. We investigated the effects of long-term O exposure on KT outcomes by employing a multipollutant model. This multicenter, longitudinal cohort study included 4796 adult KT recipients who survived ≥1 year after transplantation from 2002-2020 at 3 major hospitals in South Korea.

Transcriptomic profiling of PBMCs from mammary tumor dogs reveals two distinct immune states.

This study analyzed cancer-specific systemic immune responses in peripheral blood mononuclear cells (PBMCs) from dogs with benign tumors, malignant tumors, and normal conditions. By examining gene expression patterns - particularly immune checkpoint and TNFRSF genes - the study aimed to assess the immune state of cancer PBMCs. Surprisingly, half of the tumor PBMCs exhibited downregulation of both immunosuppressive genes (Pdcd1, Ctla4, Tigit) and immune activation molecules (CD27, CD357), suggesting immune inactivity rather than suppression.

CEBPD regulates CD47 and MAP4K4 via chromatin accessibility in canine mammary tumor monocytes.

Circulating immune cells that have interacted with tumor tissue exhibit distinct characteristics compared to those in healthy individuals, providing potential biomarkers for tumor presence and malignancy. However, the epigenetic mechanisms governing these immune cells, particularly chromatin accessibility, remain poorly understood in cancer. In this study, we investigated chromatin accessibility and transcription factor binding in peripheral blood mononuclear cells from dogs with mammary gland tumors using ATAC-seq.

Do COVID-19 responses associate with prior hazard experiences? An investigation among flood-vulnerable subsidized housing residents with digital vulnerability.

In light of the threat posed by the COVID-19 pandemic and the accompanying public health risks, understanding the mechanisms through which individuals discern accurate information about COVID-19 and adopt appropriate preventive behaviors has become an important research subject. However, few studies have directly examined the associations between the digital divide, previous experience of non-pandemic disasters, and preventive behaviors in response to COVID-19. This study focuses on two elements that may affect individuals' responses to COVID-19: (1) digital capabilities and (2) prior experience of and preparedness for flood risk.

Clinical Outcomes of Combined Phacoemulsification, Extended Depth-of-Focus Intraocular Lens Implantation, and Epiretinal Membrane Peeling Surgery.

: To evaluate the clinical efficacy and safety of combined phacoemulsification, extended depth-of-focus (EDOF) intraocular lens (IOL) implantation, and epiretinal membrane (ERM) peeling during vitrectomy surgery for treating patients with ERM, cataracts, and presbyopia. : Patients with preexisting low-grade ERM who underwent cataract surgery with the implantation of an EDOF IOL were included. Corrected distance visual acuity (CDVA), uncorrected distance visual acuity (UDVA), uncorrected intermediate visual acuity (UIVA), uncorrected near visual acuity (UNVA), autorefraction and keratometry, manifest refraction, and central foveal thickness (CFT) were measured before surgery and at postoperative months 3 and 6.

Efficacy and Safety of a Medical Robot for Non-Face-to-Face Nasopharyngeal Swab Specimen Collection: Nonclinical and Clinical Trial Findings for COVID-19 Testing.

ObjectivesTo meet the high demand for polymerase chain reaction (PCR) tests to diagnose COVID-19 and rapidly control the outbreak, an efficient and safe molecular diagnostic protocol is necessary. In this study, we evaluated the efficacy and safety of the medical robot developed for non-face-to-face nasopharyngeal swab specimen collection.MethodsIn a nonclinical study, an otorhinolaryngologist collected swab specimens manually and using a medical robot.

Immunogenicity and protection of a triple repeat domain III mRNA vaccine against Zika virus.

Zika virus (ZIKV) infection is primarily transmitted by mosquitoes and often asymptomatic in most individuals. Infection during pregnancy can lead to severe birth defects such as congenital microcephaly, and currently, there is no approved vaccine for ZIKV. Several studies are investigating the development of ZIKV vaccine using DNA and RNA as well as recombinant protein technologies; however, the outcomes thus far have not been consistently noteworthy.

Attention and executive delays in early childhood: a meta-analysis of neurodevelopmental conditions.

The objective of this review was to evaluate attention and executive function performance in children with neurodevelopmental conditions across the first 5 years of life, compared to neurotypical peers. MEDLINE, EMBASE, and PsycINFO databases were searched until June 30, 2023, and studies comparing attention or executive function between children with (or at risk for) neurodevelopmental conditions and neurotypical (or low risk) peers, 0 to 5 years old, were included. Of the 4338 studies identified, 111 studies with 12292 participants were included in the meta-analysis.

Protective Effect of Memantine on Cisplatin-Induced Ototoxicity: An In Vitro Study.

Hypothesis: Memantine, an N -methyl- d -aspartate receptor antagonist, is widely used to treat Alzheimer's disease and has been found to have potential neuroprotective effects. In this study, we evaluated the protective effects of memantine against cisplatin-induced ototoxicity.

Background: Cisplatin is a widely used anticancer drug for various cancers; however, its use is limited by its side effects, including ototoxicity.

Seasonal patterns and bloom dynamics of phytoplankton based on satellite-derived chlorophyll-a in the eastern yellow sea.

Satellite-derived chlorophyll-a concentration (Chl-a) is essential for assessing environmental conditions, yet its application in the optically complex waters of the eastern Yellow Sea (EYS) is challenged. This study refines the Chl-a algorithm for the EYS employing a switching approach based on normalized water-leaving radiance at 555 nm wavelength according to turbidity conditions to investigate phytoplankton bloom patterns in the EYS. The refined Chl-a algorithm (EYS algorithm) outperforms prior algorithms, exhibiting a strong alignment with in situ Chl-a.

Deep learning model for differentiating nasal cavity masses based on nasal endoscopy images.

Background: Nasal polyps and inverted papillomas often look similar. Clinically, it is difficult to distinguish the masses by endoscopic examination. Therefore, in this study, we aimed to develop a deep learning algorithm for computer-aided diagnosis of nasal endoscopic images, which may provide a more accurate clinical diagnosis before pathologic confirmation of the nasal masses.

Exploring early life social and executive function development in infants and risk for autism: a prospective cohort study protocol of NICU graduates and infants at risk for cerebral palsy.

Background: Delays in early social and executive function are predictive of later developmental delays and eventual neurodevelopmental diagnoses. There is limited research examining such markers in the first year of life. High-risk infant groups commonly present with a range of neurodevelopmental challenges, including social and executive function delays, and show higher rates of autism diagnoses later in life.

Pectin Nanoporous Structures Prepared via Salt-Induced Phase Separation and Ambient Azeotropic Evaporation Processes.

Polysaccharide nanoporous structures are suitable for various applications, ranging from biomedical scaffolds to adsorption materials, owing to their biocompatibility and large surface areas. Pectin, in particular, can create 3D nanoporous structures in aqueous solutions by binding with calcium cations and creating nanopores by phase separation; this process involves forming hydrogen bonds between alcohols and pectin chains in water and alcohol mixtures and the resulting penetration of alcohols into calcium-bound pectin gels. However, owing to the dehydration and condensation of polysaccharide chains during drying, it has proven to be challenging to maintain the 3D nanoporous structure without using a freeze-drying process or supercritical fluid.

Ubiquitin ligase RNF20 coordinates sequential adipose thermogenesis with brown and beige fat-specific substrates.

In mammals, brown adipose tissue (BAT) and inguinal white adipose tissue (iWAT) execute sequential thermogenesis to maintain body temperature during cold stimuli. BAT rapidly generates heat through brown adipocyte activation, and further iWAT gradually stimulates beige fat cell differentiation upon prolonged cold challenges. However, fat depot-specific regulatory mechanisms for thermogenic activation of two fat depots are poorly understood.

Periodontitis of maxillary teeth screened by community periodontal index is associated with chronic rhinosinusitis defined by EPOS 2020 guideline.

We aimed to evaluate the association between periodontitis in the upper jaw and chronic rhinosinusitis (CRS) using the nationwide Korean National Health and Nutrition Examination Survey (KNHANES) data. In this cross-sectional study, data of KNHANES participants enrolled between 2008 and 2012 were reviewed. Periodontitis of the upper teeth was diagnosed by dentists according to the community periodontal index with standardized methods.

Primary Production in the Kara, Laptev, and East Siberian Seas.

Understanding of the primary production of phytoplankton in the Kara Sea (KS), the Laptev Sea (LS), and the East Siberian Sea (ESS) remains limited, despite the recognized importance of phytoplankton in the Arctic Ocean. To address this knowledge gap, we conducted three NABOS (Nansen and Amundsen Basins Observational System) expeditions in 2013, 2015, and 2018 to measure in situ primary production rates using a C-N dual-tracer method and examine their major controlling factors. The main goals in this study were to investigate regional heterogeneity in primary production and derive its contemporary ranges in the KS, LS, and ESS.

Gene-specific machine learning for pathogenicity prediction of rare BRCA1 and BRCA2 missense variants.

Machine learning-based pathogenicity prediction helps interpret rare missense variants of BRCA1 and BRCA2, which are associated with hereditary cancers. Recent studies have shown that classifiers trained using variants of a specific gene or a set of genes related to a particular disease perform better than those trained using all variants, due to their higher specificity, despite the smaller training dataset size. In this study, we further investigated the advantages of "gene-specific" machine learning compared to "disease-specific" machine learning.

Multi-targeted therapy resistance via drug-induced secretome fucosylation.

Cancer secretome is a reservoir for aberrant glycosylation. How therapies alter this post- translational cancer hallmark and the consequences thereof remain elusive. Here, we show that an elevated secretome fucosylation is a pan-cancer signature of both response and resistance to multiple targeted therapies.

CXCL5 inhibits excessive oxidative stress by regulating white adipocyte differentiation.

Chemokines have been well-documented as a major factor in immune cell migration and the regulation of immune responses. However, recent studies have reported that chemokines have diverse roles, both in immune cells and other cell types, including adipocytes. This study investigated the molecular functions of C-X-C motif chemokine ligand 5 (CXCL5) in white adipose cells using Cxcl5 knock-out (KO) mice fed a high-fat diet (HFD).

Different Methods and Formulations of Drugs and Vaccines for Nasal Administration.

Nasal drug delivery is advantageous when compared with other routes of drug delivery as it avoids the hepatic first-pass effect, blood-brain barrier penetration, and compliance issues with parenteral administration. However, nasal administration also has some limitations, such as its low bioavailability due to metabolism on the mucosal surface, and irreversible damage to the nasal mucosa due to the ingredients added into the formula. Moreover, the method of nasal administration is not applicable to all drugs.

Selective CO adsorption and bathochromic shift in a phosphocholine-based lipid and conjugated polymer assembly.

We assemble a film of a phosphocholine-based lipid and a crystalline conjugated polymer using hydrophobic interactions between the alkyl tails of the lipid and alkyl side chains of the polymer, and demonstrated its selective gas adsorption properties and the polymer's improved light absorption properties. We show that a strong attractive interaction between the polar lipid heads and CO was responsible for 6 times more CO being adsorbed onto the assembly than N, and that with repeated CO adsorption and vacuuming procedures, the assembly structures of the lipid-polymer assembly were irreversibly changed, as demonstrated by grazing-incidence X-ray diffraction during the gas adsorption and desorption. Despite the disruption of the lipid structure caused by adsorbed polar gas molecules on polar head groups, gas adsorption could promote orderly alkyl chain packing by inducing compressive strain, resulting in enhanced electron delocalization of conjugated backbones and bathochromic light absorption.