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Neutrophil-Lymphocyte-Ratio As Predictor Of Morbidity And Mortality In Adults With Gastrointestinal Obstruction, Agi S. Putranto, Bimo D. Pramesta

The New Ropanasuri Journal of Surgery

Introduction. Gastrointestinal (GI) obstruction is a condition that often requires surgery and can lead to severe complications. The neutrophil-to-lymphocyte ratio (NLR) has been used as an inflammation indicator in various medical conditions, but research on the relationship between NLR and GI obstruction is still limited. Therefore, this study aims to evaluate the role of NLR as a cost-effective and simple preoperative predictor of postoperative mortality and morbidity, mainly surgical site infection, in adult patients with GI obstruction.

Method. This cross-sectional study was conducted at Cipto Mangunkusumo General Hospital in Jakarta. The study sample consists of 150 adult patients with GI …

Preoperative Neutrophil–Lymphocyte Ratio And Serum Carcinoembryonic Antigen As Predictive Factors Of Colorectal Cancer Survival, Agi S. Putranto, Jackson Kamaruddin

The New Ropanasuri Journal of Surgery

Introduction. Colorectal cancer is the second leading cause of death worldwide, with a high mortality rate. This study investigates the predictive value of the neutrophil–lymphocyte ratio (NLR) and carcinoembryonic antigen (CEA) in predicting the survival rates of colorectal cancer patients in Indonesia.

Method. This retrospective cohort study enrolled the colorectal cancer stage I–IV patients treated at Cipto Mangunkusumo General Hospital (CMGH). The independent variables are NLR and CEA, while the dependent variable is the five–year survival of colorectal cancer. The log rank test proceeded to find a correlation between NLR and CEA with 5–year survival, and the Cox proportional hazard …

Factors Influencing Ulcer Healing In Chronic Limb Threatening Ischemia Patients After Endovascular Angioplasty At Cipto Mangunkusumo General Hospital, Raden Suhartono, Ghany H. Wijaya, Akhmadu Muradi

The New Ropanasuri Journal of Surgery

Introduction. Chronic limb–threatening ischemia (CLTI) can cause rest pain in the lower extremities and the formation of ulcers or gangrene. Revascularization, which can be done using open surgery or endovascular procedures, is the first line of treatment in CLTI management. CLTI patients at CMGH usually came with advanced conditions and high re–amputation rates even after revascularization. This study aimed to determine factors associated with the outcome of endovascular angioplasty, especially ulcer healing.

Method. A cross–sectional study was conducted at CMGH, enrolling CLTI patients with Rutherford grades 5 and 6 who underwent angioplasty. Age, gender, history of smoking, hypertension, atrial fibrillation, …

Act-Enhanced Behavior Therapy For A Hispanic Adult With Trichotillomania: A Case Report, Marissa L. Donahue, Michael P. Twohig

Psychology Faculty Publications

Trichotillomania, also known as Hair-Pulling Disorder, is characterized by recurrent pulling out of one’s hair over brief episodes or sustained periods of time and results in hair loss. ACT-enhanced behavior therapy (A-EBT) has been shown to be an effective approach in the treatment of trichotillomania by promoting psychological flexibility around hair pulling urges and teaching stimulus control and habit reversal training. However, there is limited support of A-EBT for clients with an ethnic minority identity. This case report focuses on an adult, Hispanic female client, Luna (pseudonym), who received eight sessions of A-EBT for the treatment of trichotillomania. At post-treatment, …

Social Determinants Of Health And Disparities In Hypertension And Cardiovascular Diseases, Abhishek Chaturvedi, Anqi Zhu, Naga Vaishnav Gadela, Dorairaj Prabhakaran, Tazeen Jafar

Department of Medicine

High blood pressure causes over 10 million preventable deaths annually globally. Populations in low- and middle-income countries suffer the most, experiencing increased uncontrolled blood pressure and cardiovascular disease (CVD) deaths. Despite improvements in high-income countries, disparities persist, notably in the United States, where Black individuals face up to 4× higher CVD mortality than White individuals. Social determinants of health encompass complex, multidimensional factors linked to an individual's birthplace, upbringing, activities, residence, workplaces, socioeconomic and environmental structures, and significantly affect health outcomes, including hypertension and CVD. This review explored how social determinants of health drive disparities in hypertension and related CVD …

Cover And Contents

Turkish Journal of Biology

No abstract provided.

Svm-Do: Identification Of Tumor-Discriminating Mrna Signatures Via Support Vectormachines Supported By Disease Ontology, Mustafa Erhan Özer, Pemra Özbek Sarica, Kazim Yalçin Arğa

Turkish Journal of Biology

Background/aim: The complicated nature of tumor formation makes it difficult to identify discriminatory genes. Recently, transcriptome-based supervised classification methods using support vector machines (SVMs) have become popular in this field. However, the inclusion of less significant variables in the construction of classification models can lead to misclassification. To improve model performance, feature selection methods such as enrichment analysis can be used to extract useful variable sets. The detection of genes that can discriminate between normal and tumor samples in the association of cancer and disease remains an area of limited information. We therefore aimed to discover novel and practical sets …

Deep Learning In Bioinformatics, Malik Yousef, Jens Allmer

Turkish Journal of Biology

Deep learning is a powerful machine learning technique that can learn from large amounts of data using multiple layers of artificial neural networks. This paper reviews some applications of deep learning in bioinformatics, a field that deals with analyzing and interpreting biological data. We first introduce the basic concepts of deep learning and then survey the recent advances and challenges of applying deep learning to various bioinformatics problems, such as genome sequencing, gene expression analysis, protein structure prediction, drug discovery, and disease diagnosis. We also discuss future directions and opportunities for deep learning in bioinformatics. We aim to provide an …

Compcorona: A Web Application For Comparative Transcriptome Analyses Ofcoronaviruses Reveals Sars-Cov-2-Specific Host Response, Rana Sali̇hoğlu, Fati̇h Saraçoğlu, Mustafa Si̇bai̇, Tali̇p Zengi̇n, Başak Abak Masud, Onur Karasoy, Tuğba Önal Süzek

Turkish Journal of Biology

Background/aim: Understanding the mechanism of host transcriptomic response to infection by the SARS-CoV-2 virus is crucial, especially for patients suffering from long-term effects of COVID-19, such as long COVID or pericarditis inflammation, potentially linked to side effects of the SARS-CoV-2 spike proteins. We conducted comprehensive transcriptome and enrichment analyses on lung and peripheral blood mononuclear cells (PBMCs) infected with SARS-CoV-2, as well as on SARS-CoV and MERS-CoV, to uncover shared pathways and elucidate their common disease progression and viral replication mechanisms. Materials and methods: We developed CompCorona, the first interactive online tool for visualizing gene response variance among the family …

Stemnesscore: An R Package To Estimate The Stemness Of Glioma Cancer Cells At Single-Cell Resolution, Necla Koçhan, Yavuz Oktay, Gökhan Karakülah

Turkish Journal of Biology

Background/aim: Glioblastoma is the most heterogeneous and the most difficult-to-treat type of brain tumor and one of the deadliest among all cancers. The high plasticity of glioma cancer stem cells and the resistance they develop against multiple modalities of therapy, along with their high heterogeneity, are the main challenges faced during treatment of glioblastoma. Therefore, a better understanding of the stemness characteristics of glioblastoma cells is needed. With the development of various single-cell technologies and increasing applications of machine learning, indices based on transcriptomic and/or epigenomic data have been developed to quantitatively measure cellular states and stemness. In this study, …

Classification Of Colon Cancer Patients Into Consensus Molecular Subtypes Using Support Vector Machines, Necla Koçhan, Baris Emre Dayanc

Turkish Journal of Biology

Background/aim: The molecular heterogeneity of colon cancer has made classification of tumors a requirement for effective treatment. One of the approaches for molecular subtyping of colon cancer patients is the Consensus Molecular Subtypes (CMS) developed by the Colorectal Cancer Subtyping Consortium (CRCSC). CMS-specific RNA-Seq dependent classification approaches are recent with relatively low sensitivity and specificity. In this study, we aimed to classify patients into CMS groups using RNA-seq profiles. Materials and methods: We first identified subtype specific and survival associated genes using Fuzzy C-Means (FCM) algorithm and log-rank test. Then we classified patients using Support Vector Machines with Backward Elimination …

Suma: A Lightweight Machine Learning Model Powered Shared Nearest Neighbour Based Clustering Application Interface Of Scrna-Seq, Hamza Umut Karakurt, Pınar Pir

Turkish Journal of Biology

Background/aim: Single-cell transcriptomics (scRNA-Seq) explores cellular diversity at the gene expression level. Due to the inherent sparsity and noise in scRNA-Seq data and the uncertainty on the types of sequenced cells, effective clustering and cell type annotation are essential. The graph-based clustering of scRNA-Seq data is a simple yet powerful approach which presents data as a “shared nearest neighbour” graph and clusters the cells using graph clustering algorithms. These algorithms are dependent on several user-defined parameters. Here we present SUMA, a lightweight tool that uses a random forest model to predict the optimum number of neighbours to have the optimum …

Physicochemical Differences Between Camelid Single-Domain Antibodies And Mammalian Antibodies, Nazli Eda Eski̇er, Doğa Eski̇er, Esi̇n Fi̇ruzan, Si̇bel Kalyoncu

Turkish Journal of Biology

Background/aim: In recent years, single-domain antibodies, also known as nanobodies, have emerged as an alternative to full immunoglobulin Gs (IgGs), due to their various advantages including increased solubility, faster clearance, and cheaper production. Nanobodies are generally derived from the variable domain of the camelid heavy-chain-only immunoglobulin Gs (hcIgGs). Due to the high sequence homology between variable heavy chains of camelids (VHHs) and humans (VHs), hcIgGs are ideal candidates for nanobody development. However, further examination is needed to understand the structural differences between VHs and VHHs. This analysis is essential for nanobody engineering to mitigate potential immunogenicity while preserving stability, functionality, …

Oregon State Rank Assessment For Pit Roach (Hesperoleucus Mitrulus), Misty Nelson

Institute for Natural Resources Publications

Oregon state conservation status assessment for pit roach (Hesperoleucus mitrulus) using NatureServe methodology, 2023.

Glp1 Receptor Agonists-Effects Beyond Obesity And Diabetes, Sydney S Wilbon, Mikhail G Kolonin

Faculty, Staff and Student Publications

Glucagon-like peptide-1 receptor agonists (GLP1RA) have been transformative for patients and clinicians in treating type-2 diabetes and obesity. Drugs of this class, the bioavailability of which is continuously improving, enable weight loss and control blood glucose with minimal unwanted side effects. Since adopting GLP1RA for treating metabolic diseases, animal and clinical studies have revealed their beneficial effects on several other pathologies, including cardiovascular diseases, neurodegeneration, kidney disease, and cancer. A notable commonality between these diseases is their association with older age. Clinical trials and preclinical data suggest that GLP1RA may improve outcomes in these aging-related diseases. Some of the benefits …

Evolution Of Primate Vocal Repertoires: Vocal Systems As Embodied Capital For Mediating Within-Group Conflict, Eric Schniter, Mateo Peñaherrera-Aguirre

ESI Working Papers

Life history traits constrain investments in costly neural and somatic embodied capital, potentially shaping the evolution of primate vocal communication systems. This study integrates life history theory with the social complexity hypothesis to test a sequential pathway from longevity to social dynamics to vocal repertoire size, using updated vocal repertoire data for McComb & Semple’s (2005) set of 42 non-human primate species, alongside measures of group size and within-group conflict. We compiled data on vocal repertoire size, within-group conflict, group size, endocranial volume, and maximum longevity, analysing these via Phylogenetic Sequential Canonical Cascade Model and ancestral character reconstructions. …

Infernal Symbioses: Reading Dante’S Inferno In The Chthulucene, Rawitawan Sophonpanich

Journal of Letters

This article explores the possibility of foregrounding Dante’s Inferno from the epic La Divina Commedia in this day and age of environmental crises. This catastrophic state has androgenic origins and has been labeled by climate scientists as the “Anthropocene” – a new geological era marked by the ways in which humanity has irrevocably altered the earth system. Nevertheless, Donna Haraway has voiced her opposition against this classification, postulating that it contains too much nihilistic and pessimistic connotations that function to discourage humans from doing the work necessary to alleviate the crises. Haraway therefore proposes “Chthulucene” to denote the temporally and …

Long-Term Variations In The Salinity Off The Egyptian Mediterranean Coast, Ebtessam E. Mohamed, Amna S. Dabbous, Hussein I. Maiyza, Tarek M. El-Geziry

Blue Economy

The variability in seawater salinity, an indicator of the global hydrological cycle, is crucial in basin-scale circulation and so many dynamical processes from basin to global scale. Salinity is significant for marine science because fluctuations in salinity can affect physical processes such as climate change, ocean current variations, and water mass formation. From a biological perspective, variations in salinity may pose a threat to marine animals and disrupt their normal functioning. In this study, the long-term variability of salinity in the photic zone (0-200 m) of the Egyptian Mediterranean Sea is examined using an extended data set from 1950 to …

Blue Economic Potency Of Marine Invertebrates For Bio-Drug Discovery, Hassan A.H. Ibrahim, Hanan M. Abdelnaby, Samia S. Abouelkheir, Hamdy A. Abo-Taleb, Nermeen A. El Sersy

Blue Economy

In terms of focus, promising results obtained from extensive investigations showed that the biodiversity of marine invertebrates has been documented. This poses the marine ecosystem as a hopeful resource in the discovery of novel compounds, with an ideal starting point in scaffolding additional screening of marine natural products (MNPs), especially to face the rise in the burden of diseases and treatment failure. A wide range of antimicrobial, antiviral, anticancer, anti-inflammatory, antiparasitic, neuroprotective, analgesic, antimalarial and other agents of marine origin have been pursued in the control and management of diseases. In the current review, we will focus on figuring out …

Ultradeformable Nanocarriers For Efficient Transdermal Drug Delivery, Hala N. Elshagea, Rana R. Makar, Alaa H. Salama, Nermeen A. Elkasabgy, Emad B. Basalious

Bulletin of Faculty of Pharmacy Cairo University

Ultradeformable nanovesicles (UDVs) have recently become one of the favorable tools used for the transdermal delivery of drugs into deep skin layers, leading to enhanced bioavailability and therapeutic effect. UDV are capable of carrying hydrophilic, lipophilic or amphiphilic drugs bypassing the skin barriers. This mini review presents examples of UDV, their advantages, different mechanisms for UDV skin penetration, and some of the recent studies that proved the liability of using such carriers for better skin penetration. The applicability of using UDV for transdermal drug delivery has expanded such that marketed drug products were recently approved and launched indicating its superiority …

Cost-Variation Analysis Of Antihemorrhagic Drugs In The Egyptian Market, Michael A. Kaldas, Aya M. Abdel Magid, Samar F. Farid

Bulletin of Faculty of Pharmacy Cairo University

Background: Cardiovascular diseases (CVDs) are considered the leading cause of death worldwide. An important category of the CVDs is the bleeding disorders. There is a significant variation in the drug products used in the treatment of hemorrhagic disorders in the Egyptian market. Therefore, our study aims to evaluate the cost variation of different brands of antihemorrhagic drugs in the Egyptian market. Methods: The study used an analytical method to obtain the different prices of the available antihemorrhagic drug products in the Egyptian market (in Egyptian Pound), from different drug categories considering all the concentrations available. Each generic name was checked …

Gc And Hptlc- Densitometric Methods For Simultaneous Determination Of Aspirin, Paracetamol, Caffeine Anhydrous, Dextromethorphan Hydrobromide And Chlorpheniramine Maleate: Method Validation And Application To Over The Counter Tablet, Lamia M. Abdel-Halim, Nesrin K. Ramadan, Mohamed K. Abd-El Rahman, Maha M. Galal

Bulletin of Faculty of Pharmacy Cairo University

This study presents two validated chromatographic methods for determining aspirin, paracetamol, caffeine anhydrous, dextromethorphan hydrobromide, and chlorpheniramine maleate in Vegaskin-D® tablets. Method I used high performance thin layer liquid chromatography densitometric method (HPTLC-densitometric), using a stationary phase of silica gel 60 F254, and UV detection at 254.0 nm resulting in well-resolved, symmetrical, and sharp peaks. Method II used gas chromatography (GC) with a flame ionization detector. The results showed that the proposed methods can effectively be implemented for routine analysis and quality control of drugs in fixed-dose combination tablets. The GC method has an advantage over HPTLC- densitometric method due …

Prolonged Antibiotic Use In A Preclinical Model Of Gulf War Chronic Multisymptom-Illness Causes Renal Fibrosis-Like Pathology Via Increased Micro-Rna 21-Induced Pten Inhibition That Is Correlated With Low Host, Ayushi Trivedi, Dipro Bose, Punnag Saha, Subhajit Roy, Madhura More, Jonathan Skupsky, Nancy G. Klimas, Saurabh Chatterjee

HPD Articles

Gulf War (GW) veterans show gastrointestinal disturbances and gut dysbiosis. Prolonged antibiotic treatments commonly employed in veterans, especially the use of fluoroquinolones and aminoglycosides, have also been associated with dysbiosis. This study investigates the effect of prolonged antibiotic exposure on risks of adverse renal pathology and its association with gut bacterial species abundance in underlying GWI and aims to uncover the molecular mechanisms leading to possible renal dysfunction with aging. Using a GWI mouse model, administration of a prolonged antibiotic regimen involving neomycin and enrofloxacin treatment for 5 months showed an exacerbated renal inflammation with increased NF-κB activation and pro-inflammatory …

Teaching Hispanic Culture, Diversity, And Tolerance Through Hispanic Dances And Music: Two Approaches For Flamenco & Caribbean Dances, Chita Espino-Bravo Ph.D., D. Nicole English

Modern Languages Faculty Publications

A Sociology Approach: Dance can be a useful tool for teaching students about culture and community. Through the language of Dance and Music (Caribbean Dance), context is given to social facts, which engages and informs students about such social issues as history, Colonialism,social class, gender, race/ethnicity, and social justice. The added bonus of using Dance as a lens is that it involves active, embodied learning (Dewey, English, Mead), making the material more memorable, meaningful, and relevant to the learner. A Communicative Approach (Task-based Learning Activity) & Language for Specific Purposes:Task-Based Language Teaching (TBLT) is a derivative of the Communicative Approach …

Case Report And Literature Review Of An Atypical Polymyalgia Rheumatica And Its Management, Saad Bilal Ahmed, Saara Ahmad, Hanmei Pan

Department of Biological & Biomedical Sciences

Polymyalgia rheumatica (PMR) is a systemic inflammatory disease of the elderly population that increases in incidence as age advances. It is characterised by the sudden or sub-acute onset of symptoms affecting the shoulder and pelvic girdles, often accompanied by constitutional symptoms. Due to the lack of consensual diagnostic criteria and specific laboratory or radiological investigations for PMR, its diagnosis can be very challenging, particularly because it can be mimicked or masked by other geriatric syndromes. PMR responds well to glucocorticoid treatment, but if left untreated, can lead to morbidity and poor quality of life. We present the case of an …

Structural Basis For Dna Proofreading, Gina Buchel, Ashok Nayak, Karl Herbine, Azadeh Sarfallah, Viktoriia Sokolova, Angelica Zamudio-Ochoa, Dmitry Temiakov

Department of Biochemistry and Molecular Biology Faculty Papers

DNA polymerase (DNAP) can correct errors in DNA during replication by proofreading, a process critical for cell viability. However, the mechanism by which an erroneously incorporated base translocates from the polymerase to the exonuclease site and the corrected DNA terminus returns has remained elusive. Here, we present an ensemble of nine high-resolution structures representing human mitochondrial DNA polymerase Gamma, Polγ, captured during consecutive proofreading steps. The structures reveal key events, including mismatched base recognition, its dissociation from the polymerase site, forward translocation of DNAP, alterations in DNA trajectory, repositioning and refolding of elements for primer separation, DNAP backtracking, and displacement …

Whole-Genome Long-Read Sequencing Downsampling And Its Effect On Variant-Calling Precision And Recall., William T Harvey, Peter Ebert, Jana Ebler, Peter A Audano, Katherine M Munson, Kendra Hoekzema, David Porubsky, Christine R Beck, Tobias Marschall, Kiran Garimella, Evan E Eichler

Faculty Research 2024

Advances in long-read sequencing (LRS) technologies continue to make whole-genome sequencing more complete, affordable, and accurate. LRS provides significant advantages over short-read sequencing approaches, including phased de novo genome assembly, access to previously excluded genomic regions, and discovery of more complex structural variants (SVs) associated with disease. Limitations remain with respect to cost, scalability, and platform-dependent read accuracy and the tradeoffs between sequence coverage and sensitivity of variant discovery are important experimental considerations for the application of LRS. We compare the genetic variant-calling precision and recall of Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) HiFi platforms over a range …

Impact Of Homoeopathy Along With Yoga As An Integrated Pilot Project With The National Programme For Prevention And Control Of Cancer, Diabetes, Cardiovascular Diseases And Stroke: A Cross-Sectional Study, Roja Varanasi, Shashi Giri, Jyotika Bhatti, Khushboo Garg, Gurudev Choubey, Ramesh Supadu Bawaskar, Umakanta Prusty, Raveender Chinta, Manjula Narang, Praveen Oberai, Anil Khurana, Leimapokhpam Swasticharan, Raj K. Manchanda, Npcdcs-Ayush (Homoeopathy) Integration Project Study Group

Indian Journal of Research in Homoeopathy

Background: There is a growing concern about the increasing burden of non-communicable diseases (NCDs) and their risk factors globally.

Objectives: This study assesses the impact of the integration of Ayush (homoeopathy along with yoga) in the National Programme for Prevention and Control of Cancer, Diabetes, Cardiovascular Diseases, and Stroke at the level of patients and conventional physicians.

Methods: This cross-sectional study was carried out on the participants already enrolled for the treatment of NCDs at 22 Ayush-Lifestyle Disorders clinics in four districts across India. Participants of any gender, aged 30 years or older, were included. A structured …

Review On Therapeutic Potential Of Phytochemicals From Medicinal Plants, Iqra Afzal, Ume Habiba, Humaira Yasmeen

Journal of Bioresource Management

Nature has provided plants with a vast range of phytochemicals. These phytochemicals are enriched with different pharmacological activities. These pharmacological activities have a potential to be wisely used for therapeutic purpose. It can be utilized in so many ways for the expansion of therapeutic strategies. With the advancement in the field of medicine and due to increasing side effects of synthetic medicines there emerges a need to discover novel therapeutic remedies. Medicinal plants serve as the best source for the manufacture of new remedies for many diseases. Medicinal plants bear a potential towards treating incurable chronic diseases. The aim of …

Description Of Sivalhippus (Equidae: Perissodactyla) From The Late Miocene Siwalik Sub-Group Of Pakistan, Muhammad Tahir Waseem, Ayesha Iqbal, Sania Zubaid, Abdul Majid Khan, Muhammad Ammar

Journal of Bioresource Management

New fossil mandible as well as isolated upper and lower dentitions of the late Miocene Hipparionine species, have been discovered from a locality of Chakwal, Punjab, Pakistan. By using morphometric and morphologic analysis, we have deduced that these specimens belong to Sivalhippus theobaldi. The body size of this species was intermediate between Sivalhippus perimensis and Hipparion antilopinum while its hypsodonty indicates that this species was a grazer to a larger extent which existed in mosaic of woodland and grassland in the Latest Miocene. However, the comparison with the recent horse (Equus caballus) mandible indicates some differences in …