A mixed-methods study of patient and healthcare professional perceptions of care pathways for knee osteoarthritis.

Background: This study aimed to address research gap concerning the perception of the care pathway for knee osteoarthritis (KOA) patients, focusing on both the patient and health professional perspectives in countries with inefficient health systems, such as Slovenia, by examining patient satisfaction with conservative treatment, assessing the perceptions of both patients and health professionals regarding the latter's involvement, and justifying the chosen KOA treatment approaches.

Methods: A mixed-methods approach was employed, combining quantitative surveys and qualitative interviews with KOA patients (n = 82) and healthcare professionals (n = 68).

Results: The care pathway for conservative KOA treatment in Slovenia begins with general practitioners (GPs), who conduct initial examinations, prescribe analgesics, and refer patients to radiologists and orthopaedic surgeons.

Management Barriers to Inter-Organizational Collaboration in Preoperative Treatment of Patients with Hip or Knee Osteoarthritis.

Inter-organizational collaboration among healthcare institutions is widely recognized to improve healthcare services. Because there is a research gap in examining the management barriers to inter-organizational collaboration in countries with less efficient healthcare systems and the reasons for non-implementation of innovations, the aim of this study was to identify key management barriers to inter-organizational collaboration in the preoperative treatment of patients with hip or knee osteoarthritis in Slovenia using a mixed-methods approach with key stakeholders. A cross-sectional study was conducted using multiple methods.

Barriers to Inter-Organisational Collaboration in the Preoperative Management of Patients with Osteoarthritis of the Hip or Knee.

Introduction: Integrated clinical pathways should provide the best and most efficient treatment. As no study on barriers to inter-organisational collaboration has investigated the barriers to unimplemented integrated clinical care in a country with less efficiently organised health system, the study aimed to identify these barriers in the preoperative management of patients with hip or knee osteoarthritis in Slovenia.

Methods: A cross-sectional study was conducted using multiple methods, including a quantitative survey with participants involved in target patient groups, and in-depth interviews with involved key actors at micro, meso and macro levels in Slovenia.

Cancer Relevance of Human Genes.

Background: We hypothesize that genes that directly or indirectly interact with core cancer genes (CCGs) in a comprehensive gene-gene interaction network may have functional importance in cancer.

Methods: We categorized 12 767 human genes into CCGs (n = 468), 1 (n = 5467), 2 (n = 5573), 3 (n = 915), and more than 3 steps (n = 416) removed from the nearest CCG in the Search Tool for the Retrieval of Interacting Genes/Proteins network. We estimated cancer-relevant functional importance in these neighborhood categories using 1) gene dependency score, which reflects the effect of a gene on cell viability after knockdown; 2) somatic mutation frequency in The Cancer Genome Atlas; 3) effect size that estimates to what extent a mutation in a gene enhances cell survival; and 4) negative selection pressure of germline protein-truncating variants in healthy populations.

Network propagation-based prioritization of long tail genes in 17 cancer types.

Background: The diversity of genomic alterations in cancer poses challenges to fully understanding the etiologies of the disease. Recent interest in infrequent mutations, in genes that reside in the "long tail" of the mutational distribution, uncovered new genes with significant implications in cancer development. The study of cancer-relevant genes often requires integrative approaches pooling together multiple types of biological data.

Association Between Preventive Behaviour and Anxiety at the Start of the COVID-19 Pandemic in Slovenia.

Introduction: The first large outbreak of SARS-CoV-2 in Europe occurred in Northern Italy in February 2020. The relatively fast spread of the infection to Slovenia was expected, and preventive measures for its suppression were widely discussed.

Methods: An online questionnaire was designed to evaluate adherence to preventive measures and the extent to which the taking of preventive measures was associated with people's anxiety level, psychological burden, their perceived vulnerability to disease, germ aversion and a number of demographic characteristics in the early stage of Covid-19 spread.

Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden.

Cancers harbor many somatic mutations and germline variants, we hypothesized that the combined effect of germline variants that alter the structure, expression, or function of protein-coding regions of cancer-biology related genes (gHFI) determines which and how many somatic mutations (sM) must occur for malignant transformation. We show that gHFI and sM affect overlapping genes and the average number of gHFI in cancer hallmark genes is higher in patients who develop cancer at a younger age (r = -0.77, P = 0.

Race and Genetics: Somber History, Troubled Present.

Following the completion of the Human Genome Project (HGP) in 2003, advances in DNA sequencing technologies further popularized the field of genomics and brought its social ramifications to the fore. Scholars across disciplines recently voiced serious concerns about the re-emergence of genomic research that might be used to justify racism. In this piece, I trace the history of attempts to biologize the concept of race and its diffused presence in today's genomic research.

Exploring single-cell data with deep multitasking neural networks.

It is currently challenging to analyze single-cell data consisting of many cells and samples, and to address variations arising from batch effects and different sample preparations. For this purpose, we present SAUCIE, a deep neural network that combines parallelization and scalability offered by neural networks, with the deep representation of data that can be learned by them to perform many single-cell data analysis tasks. Our regularizations (penalties) render features learned in hidden layers of the neural network interpretable.

GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner.

There has been much effort to prioritize genomic variants with respect to their impact on "function". However, function is often not precisely defined: sometimes it is the disease association of a variant; on other occasions, it reflects a molecular effect on transcription or epigenetics. Here, we coupled multiple genomic predictors to build GRAM, a GeneRAlized Model, to predict a well-defined experimental target: the expression-modulating effect of a non-coding variant on its associated gene, in a transferable, cell-specific manner.

Histopathological expression of Yes-associated protein in neonatal cholestasis.

Background: Biliary atresia (BA) is a common cause of persistent neonatal cholestasis and liver transplantation in the pediatric population. Yes-associated protein (YAP) has also been shown to be necessary for development of bile ducts and adaptive responses within the gastrointestinal tract. We aimed to evaluate the YAP expression in liver tissues of infants with neonatal cholestasis as well as its diagnostic potential in the differential diagnosis of BA.

Genomics and data science: an application within an umbrella.

Data science allows the extraction of practical insights from large-scale data. Here, we contextualize it as an umbrella term, encompassing several disparate subdomains. We focus on how genomics fits as a specific application subdomain, in terms of well-known 3 V data and 4 M process frameworks (volume-velocity-variety and measurement-mining-modeling-manipulation, respectively).

Hepatic immunohistochemistry of bile transporters in progressive familial intrahepatic cholestasis.

Unlabelled:  Background. Diagnosis of progressive familial intrahepatic cholestasis (PFIC) is a challenging matter that involves the summation of clinical, laboratory, radiological, and liver histological parameters; in addition to specific investigations to exclude other causes of neonatal cholestasis. The aim of this study was to evaluate liver tissue immunohistochemistry of bile salt export pump (BSEP) and multidrug resistance 3 (MDR3) proteins in differentiating PFIC from other causes of neonatal cholestasis, particularly, when genotyping is unavailable.

Urinary urobilinogen in biliary atresia: A missed, simple and cheap diagnostic test.

Aim: Early diagnosis of biliary atresia (BA) is of utmost importance for good outcome; however, it is sometimes difficult due to the overlapping diagnostic test results with other causes of neonatal cholestasis. Moreover, many diagnostic tests are costly, invasive and not available in all centers, especially in developing countries. So, we aimed to investigate the diagnostic performance of urinary urobilinogen; an easy, cheap test that was not tested before in BA.

Monocyte-derived dendritic cells in children with chronic hepatitis C: correlation with interferon and ribavirin therapy.

Background: Hepatitis C virus (HCV) infection is a major health problem worldwide. Defective dendritic cell (DC) activation of T cells may underlie poor T-cell responsiveness in HCV infection.

Objective: To evaluate the DCs' functions in chronically infected HCV patients and its correlation with the response to therapy.

MRI evaluation of tibial tunnel wall cortical bone formation after platelet-rich plasma applied during anterior cruciate ligament reconstruction.

Background: After anterior cruciate ligament (ACL) reconstruction, formation of cortical sclerotic bone encircling the femoral and tibial tunnel is a part of intratunnel graft healing. During the physiological cascades of soft tissue healing and bone growth, cellular and hormonal factors play an important role. The purpose of this study was to non-invasively but quantitatively assess the effect of intraoperatively applied platelet-rich plasma (PRP) on the formation of cortical bone encircling the tibial tunnel.

Individualized anterior cruciate ligament surgery: a prospective study comparing anatomic single- and double-bundle reconstruction.

Background: Reconstruction of the anterior cruciate ligament (ACL) has become a commonly performed procedure. However, biomechanical studies have demonstrated that conventional single-bundle ACL reconstruction techniques are only successful in limiting anterior tibial translation but less effective for restoring rotatory laxity.

Purpose: This study aimed to compare the results of single- and double-bundle ACL reconstruction using an anatomic technique, individualized based on the patient's native ACL size.

Prospective randomized clinical evaluation of conventional single-bundle, anatomic single-bundle, and anatomic double-bundle anterior cruciate ligament reconstruction: 281 cases with 3- to 5-year follow-up.

Background: Three different techniques of anterior cruciate ligament (ACL) reconstruction--conventional (transtibial) single bundle (CSB), anatomic single bundle (ASB), and anatomic double bundle (ADB)--have been described.

Purpose: To determine if double-bundle reconstruction is needed to restore rotational stability or if anatomic placement of a single bundle can yield similar results.

Study Design: Randomized controlled trial; Level of evidence, 1.

Clinical Benefits of Biochemical Markers of Fibrosis in Egyptian Children With Chronic Liver Diseases.

Background: The need for repetition of liver biopsy, especially in assessing the degree of fibrosis and follow-up of treatment protocols, justifies an intensive search for non-invasive alternatives. We attempted to investigate the clinical usefulness of serum fibrogenesis markers in pediatric chronic liver diseases.

Methods: We measured serum levels of TGF-β1, collagen IV, laminin, MMP-2 and EGF-R, in 50 children with chronic liver disease (HBV, HCV and Bilharziasis) and 30 healthy controls, and determined their relationship to frequently used liver function tests and liver biopsy findings in patients.