A statistical approach for systematic identification of transition cells from scRNA-seq data.

Decoding cellular state transitions is crucial for understanding complex biological processes in development and disease. While recent advancements in single-cell RNA sequencing (scRNA-seq) offer insights into cellular trajectories, existing tools primarily study expressional rather than regulatory state shifts. We present CellTran, a statistical approach utilizing paired-gene expression correlations to detect transition cells from scRNA-seq data without explicitly resolving gene regulatory networks.

Conjugation of visual enhancers in lateral flow immunoassay for rapid forensic analysis: A critical review.

During crime scene investigations, numerous traces are secured and may be used as evidence for the evaluation of source and/or activity level propositions. The rapid chemical analysis of a biological trace enables the identification of body fluids and can provide significant donor profiling information, including age, sex, drug abuse, and lifestyle. Such information can be used to provide new leads, exclude from, or restrict the list of possible suspects during the investigative phase.

BATF is a major driver of NK cell epigenetic reprogramming and dysfunction in AML.

Myelodysplastic syndrome and acute myeloid leukemia (AML) belong to a continuous disease spectrum of myeloid malignancies with poor prognosis in the relapsed/refractory setting necessitating novel therapies. Natural killer (NK) cells from patients with myeloid malignancies display global dysfunction with impaired killing capacity, altered metabolism, and an exhausted phenotype at the single-cell transcriptomic and proteomic levels. In this study, we identified that this dysfunction was mediated through a cross-talk between NK cells and myeloid blasts necessitating cell-cell contact.

Interleukin-21 engineering enhances NK cell activity against glioblastoma via CEBPD.

Glioblastoma (GBM) is an aggressive brain cancer with limited therapeutic options. Natural killer (NK) cells are innate immune cells with strong anti-tumor activity and may offer a promising treatment strategy for GBM. We compared the anti-GBM activity of NK cells engineered to express interleukin (IL)-15 or IL-21.

Dynamics of Land use and Land cover in the Belitung Island, Indonesia.

Belitung Island, situated in the Southeast Asian tin belt, experiences substantial transformations in land use and land cover (LULC) driven by mining activities, impacting both local economic growth and the ecosystem. This study aims to elucidate the dynamic LULC changes on Belitung Island and evaluate deforestation trends. LULC data spanning from 1990 to 2020 were acquired from The Indonesian Ministry of Environment and Forestry (KLHK), employing supervised classification of satellite imageries.

Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles.

Recent developments in immunotherapy, including immune checkpoint blockade (ICB) and adoptive cell therapy (ACT), have encountered challenges such as immune-related adverse events and resistance, especially in solid tumors. To advance the field, a deeper understanding of the molecular mechanisms behind treatment responses and resistance is essential. However, the lack of functionally characterized immune-related gene sets has limited data-driven immunological research.

Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles.

Recent developments in immunotherapy, including immune checkpoint blockade (ICB) and adoptive cell therapy, have encountered challenges such as immune-related adverse events and resistance, especially in solid tumors. To advance the field, a deeper understanding of the molecular mechanisms behind treatment responses and resistance is essential. However, the lack of functionally characterized immune-related gene sets has limited data-driven immunological research.

Forecasting acute kidney injury and resource utilization in ICU patients using longitudinal, multimodal models.

Background: Advances in artificial intelligence (AI) have realized the potential of revolutionizing healthcare, such as predicting disease progression via longitudinal inspection of Electronic Health Records (EHRs) and lab tests from patients admitted to Intensive Care Units (ICU). Although substantial literature exists addressing broad subjects, including the prediction of mortality, length-of-stay, and readmission, studies focusing on forecasting Acute Kidney Injury (AKI), specifically dialysis anticipation like Continuous Renal Replacement Therapy (CRRT) are scarce. The technicality of how to implement AI remains elusive.

Forecasting Acute Kidney Injury and Resource Utilization in ICU patients using longitudinal, multimodal models.

Background: Advances in artificial intelligence (AI) have realized the potential of revolutionizing healthcare, such as predicting disease progression via longitudinal inspection of Electronic Health Records (EHRs) and lab tests from patients admitted to Intensive Care Units (ICU). Although substantial literature exists addressing broad subjects, including the prediction of mortality, length-of-stay, and readmission, studies focusing on forecasting Acute Kidney Injury (AKI), specifically dialysis anticipation like Continuous Renal Replacement Therapy (CRRT) are scarce. The technicality of how to implement AI remains elusive.

Safety, efficacy and determinants of response of allogeneic CD19-specific CAR-NK cells in CD19 B cell tumors: a phase 1/2 trial.

There is a pressing need for allogeneic chimeric antigen receptor (CAR)-immune cell therapies that are safe, effective and affordable. We conducted a phase 1/2 trial of cord blood-derived natural killer (NK) cells expressing anti-CD19 chimeric antigen receptor and interleukin-15 (CAR19/IL-15) in 37 patients with CD19 B cell malignancies. The primary objectives were safety and efficacy, defined as day 30 overall response (OR).

The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status.

Eukaryotes have historically been studied as parasites, but recent evidence suggests they may be indicators of a healthy gut ecosystem. Here, we describe the eukaryome along the gastrointestinal tract of children aged 2-5 years and test for associations with clinical factors such as anaemia, intestinal inflammation, chronic undernutrition, and age. Children were enrolled from December 2016 to May 2018 in Bangui, Central African Republic and Antananarivo, Madagascar.

Characterizing cancer metabolism from bulk and single-cell RNA-seq data using METAFlux.

Cells often alter metabolic strategies under nutrient-deprived conditions to support their survival and growth. Characterizing metabolic reprogramming in the tumor microenvironment (TME) is of emerging importance in cancer research and patient care. However, recent technologies only measure a subset of metabolites and cannot provide in situ measurements.

Efficacy of Endodontic Disinfection Protocols in an Biofilm Model-Using DAPI Staining and SEM.

The aim of this study was to investigate the antimicrobial efficacy of different disinfection protocols in a novel biofilm model based on a visualization method and to evaluate the potential alteration of dentinal surface. A total of 120 extracted human premolars were allocated to 6 groups with different irrigation protocols. The assessment of the effectiveness of each protocol and the alteration of dentinal surface were visualized by using SEM and fluorescence microscopy (DAPI).

Perspectives of Emergency Physicians, Primary Care Physicians, and Otolaryngologists on the Diagnosis and Treatment of Acute Vertigo.

Purpose: This study aimed to explore the differences in diagnosis (Dix-Hallpike test; the head impulse, nystagmus, and the test of skew [HINTS] procedures; imaging modalities; and audiological battery) and treatment (pharmacological treatments and the Epley maneuver) of acute vertigo (AV) by examining the perspectives of otolaryngologists, emergency physicians (EPs), and primary care physicians (PCPs).

Method: A total of 123 physicians (otolaryngologists [ = 40], EPs [ = 41], PCPs [ = 42]) were included in this study. This study was conducted using an online questionnaire created in Google Forms.

Recovering false negatives in CRISPR fitness screens with JLOE.

It is widely accepted that pooled library CRISPR knockout screens offer greater sensitivity and specificity than prior technologies in detecting genes whose disruption leads to fitness defects, a critical step in identifying candidate cancer targets. However, the assumption that CRISPR screens are saturating has been largely untested. Through integrated analysis of screen data in cancer cell lines generated by the Cancer Dependency Map, we show that a typical CRISPR screen has a ∼20% false negative rate, in addition to library-specific false negatives.

Utilizing library repository for sexual harassment study in Indonesia: A systematic literature review.

Sexual harassment is a social problem that needs urgent attention to reduce its frequent occurrence. This paper is a systematic literature review (SLR) that summarizes the previous studies of sexual harassment from Islamic state universities (UIN) in Indonesia. Data were collected from the final year bachelor's theses available in the online library repository of UIN Syarif Hidayatullah Jakarta, UIN Walisongo Semarang, UIN Sunan Ampel Surabaya, UIN Ar-Raniry Aceh, UIN Alauddin Makassar and UIN Raden Fatah Palembang with open-access facilities.

Systematic Analysis of Actively Transcribed Core Matrisome Genes Across Tissues and Cell Phenotypes.

The extracellular matrix (ECM) is a highly dynamic, well-organized acellular network of tissue-specific biomolecules, that can be divided into structural or core ECM proteins and ECM-associated proteins. The ECM serves as a blueprint for organ development and function and, when structurally altered through mutation, altered expression, or degradation, can lead to debilitating syndromes that often affect one tissue more than another. Cross-referencing the FANTOM5 SSTAR (Semantic catalog of Samples, Transcription initiation And Regulators) and the defined catalog of core matrisome ECM (glyco)proteins, we conducted a comprehensive analysis of 511 different human samples to annotate the context-specific transcription of the individual components of the defined matrisome.

Spatial differentiation and determinants of COVID-19 in Indonesia.

Background: The spread of the coronavirus disease 2019 (COVID-19) has increasingly agonized daily lives worldwide. As an archipelagic country, Indonesia has various physical and social environments, which implies that each region has a different response to the pandemic. This study aims to analyze the spatial differentiation of COVID-19 in Indonesia and its interactions with socioenvironmental factors.

Genome-wide CRISPR screens using isogenic cells reveal vulnerabilities conferred by loss of tumor suppressors.

Exploiting cancer vulnerabilities is critical for the discovery of anticancer drugs. However, tumor suppressors cannot be directly targeted because of their loss of function. To uncover specific vulnerabilities for cells with deficiency in any given tumor suppressor(s), we performed genome-scale CRISPR loss-of-function screens using a panel of isogenic knockout cells we generated for 12 common tumor suppressors.

Comparison of health-related quality of life of women undergoing robotic surgery, laparoscopic surgery or laparotomy for gynecologic conditions: A cross-sectional study.

Objective: To assess and compare the health-related quality of life of women undergoing robotic gynecologic surgery, laparoscopic gynecologic surgery or laparotomy for benign and cancerous conditions.

Methods: Cross-sectional study design was used. The present study was carried out with 240 women, who underwent gynecologic surgery (robotic 48, laparoscopic 96, and laparotomy 96) in a tertiary care hospital.

Site suitability-based spatial-weighted multicriteria analysis for nuclear power plants in Indonesia.

Nuclear energy is a choice to meet the electricity needs of West Kalimantan, Indonesia to support new industrial areas. Nuclear Power Plants (NPPs) require an appropriate location in terms of biogeophysical, socio-economic, and disaster considerations. This study aims to determine potential sites for NPPs using spatial-weighted multicriteria analysis.

Electrosurgical bipolar vessel sealing versus conventional clamping and suturing for total abdominal hysterectomy.

Objectives: To compare the use of Electrosurgical bipolar vessel sealing LigaSure™ small jaw instrument (LSJI) with conventional suture ligation in total abdominal hysterectomy (TAH).

Methods: In this retrospective study 80 patients who underwent hysterectomy in the Gynecology and Obstetrics Department of Gulhane Education and Research Hospital between April 2017 and August 2018 were included. Two different groups that underwent Electrosurgical bipolar vessel sealing LigaSure™ small jaw instrument (LSJI) and conventional suture ligation in hysterectomy operation were analyzed retrospectively.

Discovery of putative tumor suppressors from CRISPR screens reveals rewired lipid metabolism in acute myeloid leukemia cells.

CRISPR knockout fitness screens in cancer cell lines reveal many genes whose loss of function causes cell death or loss of fitness or, more rarely, the opposite phenotype of faster proliferation. Here we demonstrate a systematic approach to identify these proliferation suppressors, which are highly enriched for tumor suppressor genes, and define a network of 145 such genes in 22 modules. One module contains several elements of the glycerolipid biosynthesis pathway and operates exclusively in a subset of acute myeloid leukemia cell lines.