Alignment-Free Viral Sequence Classification at Scale.

Background: The rapid increase in nucleotide sequence data generated by next-generation sequencing (NGS) technologies demands efficient computational tools for sequence comparison. Alignment-based methods, such as BLAST, are increasingly overwhelmed by the scale of contemporary datasets due to their high computational demands for classification. This study evaluates alignment-free (AF) methods as scalable and rapid alternatives for viral sequence classification, focusing on identifying techniques that maintain high accuracy and efficiency when applied to extremely large datasets.

A 10-year audit of pregnancies affected by diabetic ketoacidosis at the Pretoria Academic Complex.

Background: Diabetic ketoacidosis (DKA) during pregnancy is associated with increased rates of maternal and perinatal mortality and morbidity. DKA management guidelines are designed to ensure optimal management and minimize adverse outcomes.

Objective: To determine the level of adherence to DKA management guidelines at a tertiary center in Pretoria, South Africa and report on maternal and perinatal outcomes of the pregnancies complicated by DKA.

Risk Factors for Stroke in HIV-Positive and-Negative Patients in Pretoria, South Africa.

Objectives: Low- to middle-income countries experience a marked rise in cardiovascular diseases, and have the highest incidence of HIV infection. Stroke data in HIV-positive patients is still scarce. This study compares risk factors and types of stroke between HIV-positive and -negative patients in South Africa.

Inclusive HIV Prevention in South Africa: Reaching Foreign Migrant Adolescent Girls.

Within South Africa's HIV epidemic, foreign migrant adolescent girls and young women (AGYW) face unique challenges in an environment typified by xenophobia and structural inequity. The intersection of age, gender, and migrant-related factors creates threats that may exacerbate their HIV risk, including discrimination, limited social capital, and economic dependency. This paper explores HIV-related determinants of risk from the perspective of foreign migrant AGYW who participated in a Girls' Club project implemented by Community Media Trust.

Distinguishing reclamation, revegetation and phytoremediation, and the importance of geochemical processes in the reclamation of sulfidic mine tailings: A review.

The reclamation of tailings, especially acid-generating tailings resulting from the oxidation of sulfide minerals, has been an urgent but difficult task for a long period. Phytoremediation has been received great concerns in the area of metal (loid)s removal in recent two decades. However, in the reclamation of tailings, the term "revegetation" has been mentioned frequently.

Progress in EBV Vaccines.

The Epstein-Barr virus (EBV) is a ubiquitous pathogen that imparts a significant burden of disease on the human population. EBV is the primary cause of infectious mononucleosis and is etiologically linked to the development of numerous malignancies. In recent years, evidence has also been amassed that strongly implicate EBV in the development of several autoimmune diseases, including multiple sclerosis.

Immunogenic particles with a broad antigenic spectrum stimulate cytolytic T cells and offer increased protection against EBV infection ex vivo and in mice.

The ubiquitous Epstein-Barr virus (EBV) is the primary cause of infectious mononucleosis and is etiologically linked to the development of several malignancies and autoimmune diseases. EBV has a multifaceted life cycle that comprises virus lytic replication and latency programs. Considering EBV infection holistically, we rationalized that prophylactic EBV vaccines should ideally prime the immune system against lytic and latent proteins.

Titrating insulin in patients with type 2 diabetes using a structured self-monitoring blood glucose regimen.

Background: Self-monitoring of blood glucose (SMBG) can inform on the timing of hyperglycaemia, but there is currently no standardised approach to utilising these data to improve glycaemic control in patients with type 2 diabetes.

Objectives: To assess the improvement in glycaemic control when an insulin titration algorithm was used in combination with SMBG in patients with poorly controlled, insulin-treated type 2 diabetes.

Methods: This 6-month prospective study recruited 39 poorly controlled (glycated haemoglobin (HbA1c) ≥8.

Antibodies conjugated with viral antigens elicit a cytotoxic T cell response against primary CLL ex vivo.

Chronic lymphocytic leukemia (CLL) is the most frequent B cell malignancy in Caucasian adults. The therapeutic armamentarium against this incurable disease has recently seen a tremendous expansion with the introduction of specific pathway inhibitors and innovative immunotherapy. However, none of these approaches is curative and devoid of side effects.

Effects of exogenous human insulin dose adjustment on body mass index in adult patients with type 1 diabetes mellitus at Kalafong Hospital, Pretoria, South Africa, 2009 - 2014.

Background: To maintain fasting blood glucose levels within near to the normal range in type 1 diabetes mellitus (DM), frequent insulin dose adjustments may be required with short-, intermediate- and long-acting insulin formulations. Patients on human insulin generally experience weight gain over time, regardless of the level of glycaemic control achieved.

Objectives: To determine the effects of human insulin, adjusted quarterly to achieve glycaemic control, on body mass index (BMI), and establish dose regimens that achieve optimal glycaemic control without increasing BMI in patients with type 1 DM at the Kalafong Diabetes Clinic in Pretoria, South Africa.

Impact of CYP2D6 genotype on amitriptyline efficacy for the treatment of diabetic peripheral neuropathy: a pilot study.

Aim: Therapy with low-dose amitriptyline is commonly used to treat painful diabetic peripheral neuropathy. There is a knowledge gap, however, regarding the role of variable CYP2D6-mediated drug metabolism and side effects (SEs). We aimed to generate pilot data to demonstrate that SEs are more frequent in patients with variant CYP2D6 alleles.

Cervical collars and immobilisation: A South African best practice recommendation.

Introduction: The consequences of spinal injury as a result of trauma can be devastating. Spinal immobilisation using hard trauma boards and rigid cervical collars has traditionally been the standard response to suspected spinal injury patients even though the risk may be extremely low. Recently, adverse events due to the method of immobilisation have challenged the need for motion restriction in all trauma patients.

The effect of acidic pH and presence of metals as parameters in establishing a sulfidogenic process in anaerobic reactor.

The successful use of anaerobic reactors for bioremediation of acid mine drainage has been shown in systems with neutral pH. However, the choice of an efficient and suitable process for such wastewater must consider the capability of operating at acidic pH and in the presence of metals. This work studies the performance of an anaerobic batch reactor, under conditions of varying initial pH for its efficiencies in sulfate removal and metal precipitation from synthetic acid mine drainage.

Diabetes care and complications in primary care in the Tshwane district of South Africa.

Aims: To describe the diabetic population receiving primary care from the Tshwane district public health services and to assess the quality of care of members of this population, their level of disease control and the extent of their complications.

Methods: A cluster-randomised trial was conducted in 12 primary care clinics in Tshwane district. A total of 599 diabetic patients attending these clinics for review were consecutively interviewed and clinically examined.

Parameters for sample size estimation from a group-randomized HIV prevention trial in HIV clinics in sub-Saharan Africa.

Sample size calculations for a group-randomized trial (GRT) require an estimate of the expected intraclass correlation coefficient (ICC). However, few ICC estimates from GRTs in HIV/AIDS research have been published, leaving investigators with little data on which to base expectations. We used data from a multi-country study to estimate ICCs for variables related to physical and mental health and HIV risk behaviors.

Fluid management in diabetic-acidosis--Ringer's lactate versus normal saline: a randomized controlled trial.

Objective: To determine if Ringer's lactate is superior to 0.9% sodium chloride solution for resolution of acidosis in the management of diabetic ketoacidosis (DKA).

Design: Parallel double blind randomized controlled trial.

Glycaemic control improves fibrin network characteristics in type 2 diabetes - a purified fibrinogen model.

Diabetic subjects have been shown to have altered fibrin network structures. One proposed mechanism for this is non-enzymatic glycation of fibrinogen due to high blood glucose. We investigated whether glycaemic control would result in altered fibrin network structures due to decreased fibrinogen glycation.

Glycation of fibrinogen in uncontrolled diabetic patients and the effects of glycaemic control on fibrinogen glycation.

Introduction: Evidence exists for a relationship between glycaemic control and macrovascular disease. Non-enzymatic glycation of proteins may explain this relationship in part. We investigated the effect of blood glucose control, under out-patient conditions, on fibrinogen glycation as well as the relationship between glycated fibrinogen and glycaemic control using a new sensitive method for the measurement of glycated fibrinogen.

The effect of glycaemic control on fibrin network structure of type 2 diabetic subjects.

Diabetic subjects have been shown to have altered fibrin network structures. One possible cause may be fibrinogen glycation resulting in altered structure/function properties. We investigated the effect of glucose control on fibrinogen glycation and fibrin network structure in type 2 diabetes.