Anatomy Commons^™

Cellbrf: A Feature Selection Method For Single-Cell Clustering Using Cell Balance And Random Forest, Yunpei Xu, Hong-Dong Li, Cui-Xiang Lin, Ruiqing Zheng, Yaohang Li, Jinhui Xu, Jianxin Wang

Computer Science Faculty Publications

Motivation

Single-cell RNA sequencing (scRNA-seq) offers a powerful tool to dissect the complexity of biological tissues through cell sub-population identification in combination with clustering approaches. Feature selection is a critical step for improving the accuracy and interpretability of single-cell clustering. Existing feature selection methods underutilize the discriminatory potential of genes across distinct cell types. We hypothesize that incorporating such information could further boost the performance of single cell clustering. Results

We develop CellBRF, a feature selection method that considers genes’ relevance to cell types for single-cell clustering. The key idea is to identify genes that are most important for discriminating …

Progenitor Cell Isolation From Mouse Epididymal Adipose Tissue And Sequencing Library Construction, Qianglin Liu, Chaoyang Li, Yuxia Li, Leshan Wang, Xujia Zhang, Buhao Deng, Peidong Gao, Mohammad Shiri, Fozi Alkaifi, Junxing Zhao, Jacqueline M. Stephens, Constantine A. Simintiras, Joseph Francis, Jiangwen Sun, Xing Fu

Computer Science Faculty Publications

Here, we present a protocol to isolate progenitor cells from mouse epididymal visceral adipose tissue and construct bulk RNA and assay for transposase-accessible chromatin with sequencing (ATAC-seq) libraries. We describe steps for adipose tissue collection, cell isolation, and cell staining and sorting. We then detail procedures for both ATAC-seq and RNA sequencing library construction. This protocol can also be applied to other tissues and cell types directly or with minor modifications.

For complete details on the use and execution of this protocol, please refer to Liu et al. (2023).¹

*¹ Liu, Q., Li, C., Deng, B., Gao, P., …

A Single-Cell Atlas Of Bovine Skeletal Muscle Reveals Mechanisms Regulating Intramuscular Adipogenesis And Fibrogenesis, Leshan Wang, Peidong Gao, Chaoyag Li, Qianglin Liu, Zeyang Yao, Yuxia Li, Xujia Zhang, Jiangwen Sun, Constantine Simintiras, Matthew Welborn, Kenneth Mcmillin, Stephanie Oprescu, Shihuan Kuang, Xing Fu

Computer Science Faculty Publications

Background: Intramuscular fat (IMF) and intramuscular connective tissue (IMC) are often seen in human myopathies and are central to beef quality. The mechanisms regulating their accumulation remain poorly understood. Here, we explored the possibility of using beef cattle as a novel model for mechanistic studies of intramuscular adipogenesis and fibrogenesis.

Methods: Skeletal muscle single-cell RNAseq was performed on three cattle breeds, including Wagyu (high IMF), Brahman (abundant IMC but scarce IMF), and Wagyu/Brahman cross. Sophisticated bioinformatics analyses, including clustering analysis, gene set enrichment analyses, gene regulatory network construction, RNA velocity, pseudotime analysis, and cell-cell communication analysis, were performed to elucidate …

Unttangling Irregular Actin Cytoskeleton Architectures In Tomograms Of The Cell With Struwwel Tracer, Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers

Computer Science Faculty Publications

In this work, we established, validated, and optimized a novel computational framework for tracing arbitrarily oriented actin filaments in cryo-electron tomography maps. Our approach was designed for highly complex intracellular architectures in which a long-range cytoskeleton network extends throughout the cell bodies and protrusions. The irregular organization of the actin network, as well as cryo-electron-tomography-specific noise, missing wedge artifacts, and map dimensions call for a specialized implementation that is both robust and efficient. Our proposed solution, Struwwel Tracer, accumulates densities along paths of a specific length in various directions, starting from locally determined seed points. The highest-density paths originating …

The Influence Of Decorin, A Potential Pro-Inflammatory Stimulant, On The Mechanical Properties Of The Annulus Fibrosus, Sabrina Sinopoli

Theses and Dissertations (Comprehensive)

Previous literature has investigated the biomechanical properties of various animal models, but few have studied an isolated and intact rat tail annulus fibrosus. Decorin, a class 1 small leucine-rich protein (SLRP) has the potential to trigger an inflammatory environment as previous research has shown that it may stimulate inflammation via the toll-like receptor (TLR) pathway. An increased inflammatory environment can have biomechanical implications for the disc, and so the ability of decorin to stimulate an environment that alters the mechanical properties of the disc was investigated.

The purpose of this study was to investigate the potential of decorin, a proteoglycan …

Material Characterization Of Thermoplastic Polyurethane (Tpu) And Thermoplastic Elastomers (Tpe) For Development Of 3d-Printed Surrogate Organs For Medical Training, Anastasia Elizabeth Lucci

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cadaveric specimens are a necessary, albeit limited, resource for training medical students on basic surgical skills. The availability of surrogate 3D-printed organs would readily allow access to resources that could reduce or potentially eliminate the need for cadaveric specimens or, at a minimum, provide students the opportunity to practice with 3D-printed surrogates before transitioning to those specimens. This research focuses on determining which thermoplastic material most closely mimics mechanical properties such as hardness and stiffness of human organs and allows 3D printing surrogate organs to be used as safe, educational tools. Relatively “soft” materials such as thermoplastic polyurethanes (TPU) and …

Expansion On The Use Of The Novel Compound, Elp-004, Using A Mycobacterium Tuberculosis Experimentation Model, Kendyl Marie Berry

Graduate Theses, Dissertations, and Problem Reports (ETD)

Osteoarticular tuberculosis (OAT) is a bone degenerative disease that results in bone erosion, joint effusion, joint swelling, and sometimes, nerve compression. OAT occurs from the hematogenous dissemination of Mycobacterium tuberculosis (Mtb) bacilli spreading from the primary site of infection to the bones and joints; the primary site of infection tends to be the lungs as pulmonary tuberculosis infections are the most common. OAT can occur as the result of an active or latent infection. Latent infections result in OAT when bacilli are able to escape granulomas. The incidence of OAT is not as high as pulmonary infections, making up about …

Haircare Practice And Dandruff Problems Among Indonesian Medical Students, Jessica Rosemary Wikanto, Lorettha Wijaya, Yunisa Astiarani, Regina Regina

Journal of General - Procedural Dermatology and Venereology Indonesia

Background: Dandruff is an understated hair and scalp problem that causes striking social and concentration issues among medical students. Haircare practice among them may or may not be related to the dandruff incident.

Methods: A cross-sectional study was conducted on 74 pre-clinical medical students at Atma Jaya Catholic University of Indonesia. Trained health staff assessed dandruff prevalence by physical examination, and the haircare practice was measured using a questionnaire. Bivariate analysis was utilized to assess the association between haircare practice and dandruff prevalence’s.

Result: Among respondents, 85.1% of them have dandruff. Respondents who shampooed less than five …

Clinicodemographic And Laboratory Characteristics Of Cutaneous Tuberculosis At Tertiary Referral Hospital In West Java, Indonesia, Anisa Sediadini, Hendra Gunawan, Risa Miliawati Nurul Hidayah

Journal of General - Procedural Dermatology and Venereology Indonesia

Background: Cutaneous tuberculosis (TB) is a chronic infectious disease affecting the skin caused by Mycobacterium tuberculosis (M. tuberculosis). It constitutes 1–1.5% of extrapulmonary TB, with Indonesia being the third-highest TB burden country worldwide. Cutaneous TB is difficult to diagnose due to its varied presentations. This study aimed to describe the clinicodemographic and laboratory characteristics of cutaneous TB in a tertiary referral hospital in West Java, Indonesia.

Methods: This was a descriptive retrospective cross-sectional study. Data were obtained from the medical record of patients with cutaneous TB in the Tropical Dermatology Clinic of Hasan Sadikin Hospital Bandung, West Java, …

The Difference In Transepidermal Water Loss (Tewl) Values Between Sun-Exposed And Non-Sun-Exposed Skin Among Male Medical Students, Ihsany Arafiasetyanto Prihadi, Endra Yustin Ellistasari, Arie Kusumawardani

Journal of General - Procedural Dermatology and Venereology Indonesia

Background: Transepidermal Water Loss (TEWL) is the amount of water released from the human body into the atmosphere through a diffusion process per unit of time. Changes in TEWL indicate impaired skin barrier function. Exposure to ultraviolet light for an extended period can cause photoaging, characterized by rough and dry skin (xerosis cutis). TEWL will increase significantly in the skin exposed to ultraviolet radiation. This study aims to determine the difference in the TEWL values among male medical students in the sun-exposed and non-sun-exposed skin areas.

Methods: An analytical observational cross-sectional study was conducted at the Dermatology and …

Risk Factors For Hiv-Positive Status In Condyloma Acuminata, Izazi Hari Purwoko, Putri Laksmi Karim, Suroso Adi Nugroho, Theresia Toruan, Fitriani .

Journal of General - Procedural Dermatology and Venereology Indonesia

Background: Condyloma acuminata (CA) is a sexually transmitted infection (STI) caused by human papillomavirus (HPV), especially types 6 and 11. The number of HPV infections increases in immunosuppressed conditions, such as human immunodeficiency virus (HIV) infection. Risk factors in CA patients such as gender, sexual partner, sexual orientation, and sexual intercourse can increase HIV status.

Methods: This is a descriptive-analytic study with a cohort retrospective design. The subjects are all CA patients who visited the polyclinic STI Dr. Mohammad Hoesin, General Hospital, Palembang, Indonesia, between 2016-2020. The number of CA patients included in the study were 115 patients …

A Case Of Longitudinal Melanonychia In A Child: Benign Or Malignant?, Heffi Anindya Putri, Ennesta Asri, Qaira Anum

Journal of General - Procedural Dermatology and Venereology Indonesia

Background: Longitudinal melanonychia (LM) describes a longitudinal brown-to-black band of discoloration affecting a finger, thumb, or toenail. Discoloration of the nails can be a sign of benign or malignant nail disorders. Although nail melanoma rarely occurs in children, health practitioners should be aware of melanonychia. Dermoscopy and histopathology are helpful in the diagnosis.

Case Illustration: A case of LM in a thirteen-year-old girl was reported with a complaint of brownish-black discoloration, sometimes painful, on her right thumb since 1 year ago. She had no history of trauma, nail damage, or bleeding tendency. Dermatological examination found a homogeneous brownish-black …

Seborrheic Keratosis Profile At Dr. Hasan Sadikin Central General Hospital Bandung 2015-2019, Eva Krishna Sutedja, Resti Gradia, Tri Aswila Latifah

Journal of General - Procedural Dermatology and Venereology Indonesia

Background: Seborrheic keratosis (SK) is adults’ most prevalent benign skin tumor. SK originates from the proliferation of keratinocyte cells with varying morphology and degree of pigmentation. The lesions often resemble other types of malignancy. There are still many discrepancies in SK in Indonesia; hence, SK needs further understanding. This study aimed to describe the profile of seborrheic keratosis cases based on age, sex, location of lesions, and therapy at Dr. Hasan Sadikin Central General Hospital, Bandung, for five years

Methods: This was a retrospective descriptive study with total sampling. Secondary data were collected from medical records of SK …

Non-Pustular Annular Psoriasis With Signs Of High Disease Activity, Nevi Yasnova, Windy Keumala Budianti, Melody Febriana Andardewi

Journal of General - Procedural Dermatology and Venereology Indonesia

Background: Non-pustular annular psoriasis is a rare condition in which a type of plaque psoriasis appears with ring-like lesions and a clearer central appearance. The disease activities in psoriasis may be evaluated clinically. It is essential to provide a more meaningful approach to treatment management.

Case illustration: A 33-year-old woman complained of a one-year history of multiple erythematous, scaly, and annular plaques with central clearing. Some lesions were surrounded by discrete pinpoint papules on several parts of her body. The lesions worsened during seven weeks of topical and systemic therapy.

Discussion: Psoriasis is a chronic, multisystem inflammatory …

Pengaruh Diaphragmatic Breathing Dan Endurance Exercise Terhdap Peningkatan Kapasitas Kardiorespirasi Pada Pasien Hospital-Acquired Pneumonia, Alifia Azzahra, Annisya Puspitarani, Zahra Sativani, Riza Pahlawi

Jurnal Fisioterapi Terapan Indonesia

The purpose of this case study is to determine the effect of diaphragmatic breathing and endurance exercise in hospital-acquired pneumonia (HAP) cases. HAP is a nosocomial pneumonia that occurs 48 hours or more after the patient is admitted to the hospital, without any signs of pulmonary infection at the time of initial treatment. The existence of clinical manifestations that appear, patients with HAP tend to avoid physical activity which can decrease the functional capacity of the respiratory system and have an impact on decreasing endurance. Diaphragmatic breathing exercise is thought to be able to help reduce shortness of breath, reduce …

Three-Dimensional Evaluation Of The Mandibular Lingula On Cone-Beam Computed Tomographic Images In The Turkish Population, Zerrin Unal Erzurumlu, Damla Torul

Journal of Dentistry Indonesia

Objective: The purpose of this study was to provide morphometric and anatomical data for mandibular lingula (Li) in The Turkish population using three dimensional-cone beam computed tomography (3D-CBCT) images. Methods: CBCT images of the patients taken between July 2020 and March 2021, were retrieved from the archival records. A total of 100 Li’s of 50 patients who met the criteria of this study were evaluated. The distances between the tip of the Li and ramal landmarks/occlusal plane were measured and the shape of the Li was evaluated on 3D-CBCT images. Results: CBCT images of the 50 patients (19 males and …

Clinicodemographic Characteristics Of Cutaneous Larva Migrans: A 10-Year Study In Tertiary Referral Hospital-West Java, Indonesia, Tuesi Fredella Avissa, Hendra Gunawan, Risa Miliawati Nurul Hidayah

Journal of General - Procedural Dermatology and Venereology Indonesia

Background: Cutaneous larva migrans (CLM) is the most common helminthic dermatosis caused by animal hookworm, commonly reported in tropical and subtropical regions. Most studies are on travellers returning from endemic areas, paradoxically very few reports in endemic countries, including Indonesia, where they mostly take place. This study aimed to describe the demographic and clinical characteristics of CLM patients for 10 years in a tertiary referral hospital in West Java, Indonesia.

Methods: This was a descriptive retrospective cross-sectional study. The data were obtained from the medical record of patients who was diagnosed as CLM in Tropical Dermatology Clinic Hasan …

Correlation Between Serum 25 Hydroxy-Vitamin D Levels And The Worst Pain Intensity In Postherpetic Neuralgia, Wizar Putri Mellaratna, Nelva K. Jusuf, Ariyati Yosi

Journal of General - Procedural Dermatology and Venereology Indonesia

Background: Postherpetic neuralgia (PHN) is persistent pain in the affected dermatome that occurs more than three months after the eruption of the herpes zoster has disappeared. Vitamin D has a role in Schwann cell regeneration and stimulates the release of nerve growth factors.

Methods: Blood sampling was performed to test serum 25(OH)D levels. Patients filled out their worst pain intensity using the Zoster Brief Pain Inventory questionnaire. The score was reported in Likert score (0-10), 0 indicating no pain and 10 indicating the most severe pain. Spearman correlation test was used, and p 0.05) and PHN durations (p …

Torch Re-Activation Concomitant With Drug-Induced Hypersensitivity Syndrome Shows Erythema Multiforme-Like And Vasculitis Clinical Features, Windy Keumala Budianti, Rahadi Rihatmadja, Izzah Aulia, Isaak Effendy

Journal of General - Procedural Dermatology and Venereology Indonesia

Background: Drug-induced hypersensitivity syndrome (DIHS) can be associated with cytomegalovirus (CMV) infection, besides induced by drugs. We report a case of DIHS with prolonged atypical clinical features and vasculitis precipitated by drug allergy, CMV, and other viral infections.

Case illustration: A 54-year-old female presented with generalized follicular erythematous papules and waxy palmoplantar keratoderma since one month before admission. The symptoms started as a purpuric lesion on the upper extremities, spreading as erythematous papules on the trunk with facial edema, accompanied by fever and chronic cough. She had been previously treated with ambroxol and cephalosporin. Cutaneous drug allergy reaction …

Role Of Adenylyl Cyclase Type 7 In Functions Of Bv-2 Microglia, Yawen Hu, Rebecca A. Hill, Masami Yoshimura

School of Medicine Faculty Publications

To assess the role of adenylyl cyclase type 7 (AC7) in microglia’s immune function, we generated AC7 gene knockout (AC7 KO) clones from a mouse microglial cell line, BV-2, using the CRISPR-Cas9 gene editing system. The ability of BV-2 cells to generate cAMP and their innate immune functions were examined in the presence or absence of ethanol. The parental BV-2 cells showed robust cAMP production when stimulated with prostaglandin-E1 (PGE1) and ethanol increased cAMP production in a dose-dependent manner. AC7 KO clones of BV-2 cells showed diminished and ethanol-insensitive cAMP production. The phagocytic activity of the parental BV-2 cells was …