An automated exact solution framework towards solving the logistic regression best subset selection problem

An automated logistic regression solution framework (ALRSF) is proposed to solve a mixed integer programming (MIP) formulation of the well known logistic regression best subset selection problem. The solution framework firstly determines the optimal number of independent variables that should be included in the model using an automated cardinality parameter selection procedure. The cardinality parameter dictates the size of the subset of variables and can be problem-specific. A novel regression parameter fixing heuristic that utilises a Benders decomposition algorithm is applied to prune the solution search space such that the optimal regression parameter values are found faster. An optimality gap is subsequently calculated to quantify the quality of the final regression model by considering the distance between the best possible log-likelihood value and a log-likelihood value that is calculated using the current parameter values. Attempts are then made to reduce the optimality gap by adjusting regression parameter values. The ALRSF serves as a holistic variable selection framework that enables the user to consider larger datasets when solving the best subset selection logistic regression problem by significantly reducing the memory requirements associated with its mixed integer programming formulation. Furthermore, the automated framework requires minimal user intervention during model training and hyperparameter tuning. Improvements in quality of the final model (when considering both the optimality gap and computing resources required to achieve a result) are observed when the ALRSF is applied to well-known real-world UCI machine learning datasets

Pantoea ananatis utilizes a type VI secretion system for pathogenesis and bacterial competition

Type VI secretion systems (T6SSs) are a class of macromolecular machines that are recognized as an important virulence mechanism in several Gram-negative bacteria. The genome of Pantoea ananatis LMG 2665T , a pathogen of pineapple fruit and onion plants, carries two gene clusters whose predicted products have homology with T6SS-associated gene products from other bacteria. Nothing is known regarding the role of these T6SS-1 and T6SS-3 gene clusters in the biology of P. ananatis. Here, we present evidence that T6SS-1 plays an important role in the pathogenicity of P. ananatis LMG 2665T in onion plants, while a strain lacking T6SS-3 remains as pathogenic as the wild-type strain. We also investigated the role of the T6SS-1 system in bacterial competition, the results of which indicated that several bacteria compete less efficiently against wild-type LMG 2665T than a strain lacking T6SS-1. Additionally, we demonstrated that these phenotypes of strain LMG 2665T were reliant on the core T6SS products TssA and TssD (Hcp), thus indicating that the T6SS-1 gene cluster encodes a functioning T6SS. Collectively, our data provides the first evidence demonstrating that the T6SS-1 system is a virulence determinant of P. ananatis LMG 2665T and plays a role in bacterial competition.The University of Pretoria, the National Research Foundation (NRF), the Forestry and Agricultural Biotechnology Institute (FABI), the Tree Protection Co- operative Programme (TPCP), the NRF/Department of Science and Technology Centre of Excellence in Tree Health Biotechnology (CTHB), and the THRIP support program of the Department of Trade and Industry, South Africa. IKT is supported by the Scottish Government Rural and Environment Research and Analysis Directorate (RERAD).http://apsjournals.apsnet.org/loi/mpmiam201

Phylogeny of imported and reestablished wild polioviruses in the Democratic Republic of the Congo from 2006 to 2011

BACKGROUND : The last case of polio associated with wild poliovirus (WPV) indigenous to the Democratic Republic of the Congo (DRC) was reported in 2001, marking a major milestone toward polio eradication in Africa. However, during 2006-2011, outbreaks associated with WPV type 1 (WPV1) were widespread in the DRC, with >250 reported cases. METHODS : WPV1 isolates obtained from patients with acute flaccid paralysis (AFP) were compared by nucleotide sequencing of the VP1 capsid region (906 nucleotides). VP1 sequence relationships among isolates from the DRC and other countries were visualized in phylogenetic trees, and isolates representing distinct lineage groups were mapped. RESULTS : Phylogenetic analysis indicated that WPV1 was imported twice in 2004-2005 and once in approximately 2006 from Uttar Pradesh, India (a major reservoir of endemicity for WPV1 and WPV3 until 2010-2011), into Angola. WPV1 from the first importation spread to the DRC in 2006, sparking a series of outbreaks that continued into 2011. WPV1 from the second importation was widely disseminated in the DRC and spread to the Congo in 2010-2011. VP1 sequence relationships revealed frequent transmission of WPV1 across the borders of Angola, the DRC, and the Congo. Long branches on the phylogenetic tree signaled prolonged gaps in AFP surveillance and a likely underreporting of polio cases. CONCLUSIONS : The reestablishment of widespread and protracted WPV1 transmission in the DRC and Angola following long-range importations highlights the continuing risks of WPV spread until global eradication is achieved, and it further underscores the need for all countries to maintain high levels of poliovirus vaccine coverage and sensitive surveillance to protect their polio-free status.Centers for Disease Control and Preventionhttp://jid.oxfordjournals.org2015-11-30hb201

Preoperative education in hip and knee arthroplasty patients in Bloemfontein

Background: Total hip arthroplasty (THA) and total knee arthroplasty (TKA) are frequently performed surgeries worldwide. Preoperative education enhances patient physiotherapy management and satisfaction and should be tailored to patients’ educational needs. Limited research is available regarding the preoperative educational needs for these patients. Objectives: To determine the extent of preoperative education received and the preoperative educational needs of patients undergoing THA and TKA. Method: A structured interview utilising a self-developed questionnaire was used and included questions exploring preoperative education, educational needs, method of education and health care professional providing education. A total of 14 THA and 36 TKA patients, 2–4 days post-operatively at private hospitals in Bloemfontein, were conveniently sampled. Results: All participants had arthroplasties because of osteoarthritis. All participants with THA and 35 (98%) participants with TKA received preoperative education from orthopaedic surgeons, and 8 (57%) participants with THA and 9 (25%) participants with TKA received preoperative education from physiotherapists. Education was mostly given as pamphlets months before the surgery. Participants received the least amount of information regarding exercises, especially preoperative exercise, pain relief and activities of daily living. Conclusion: This study highlights the need for improvement in patient engagement and education, together with enhanced health care practitioner communication and collaboration. Patient centeredness and individualised THA and TKA preoperative education programmes are recognised as a necessary attribute of quality health care and can lead to improved THA and TKA outcomes. The importance of exercise as part of preoperative interprofessional education in the management of THA and TKA should be emphasised as exercise is the cornerstone for rehabilitation of THA and TKA. Clinical implications: This study aimed to emphasise the importance of tailored preoperative education for THA and TKA patients to improve patient outcomes

The African Network for Improved Diagnostics, Epidemiology and Management of common infectious Agents

In sub-Saharan Africa, acute respiratory infections (ARI), acute gastrointestinal infections (GI) and acute febrile disease of unknown cause (AFDUC) have a large disease burden, especially among children, while respective aetiologies often remain unresolved. The need for robust infectious disease surveillance to detect emerging pathogens along with common human pathogens has been highlighted by the ongoing novel coronavirus disease2019 (COVID-19) pandemic. The African Network for Improved Diagnostics, Epidemiology and Management of Common Infectious Agents (ANDEMIA) is a sentinel surveillance study on the aetiology and clinical characteristics of ARI, GI and AFDUC in sub-Saharan Africa.Peer Reviewe

Reflecting on research produced after more than 60 years of exclosures in the Kruger National Park

All data, in this case works of literature reviewed have been summarised in Online Appendix 2.Herbivores are a main driver of ecosystem patterns and processes in semi-arid savannas, with their effects clearly observed when they are excluded from landscapes. Starting in the 1960s, various herbivore exclosures have been erected in the Kruger National Park (KNP), for research and management purposes. These exclosures vary from very small (1 m2) to relatively large (almost 900 ha), from short-term (single growing season) to long-term (e.g. some of the exclosures were erected more than 60 years ago), and are located on different geologies and across a rainfall gradient. We provide a summary of the history and specifications of various exclosures. This is followed by a systematic overview of mostly peer-reviewed literature resulting from using KNP exclosures as research sites. These 75 articles cover research on soils, vegetation dynamics, herbivore exclusion on other faunal groups and disease. We provide general patterns and mechanisms in a synthesis section, and end with recommendations to increase research outputs and productivity for future exclosure experiments. CONSERVATION IMPLICATIONS : Herbivore exclosures in the KNP have become global research platforms, that have helped in the training of ecologists, veterinarians and field biologists, and have provided valuable insights into savanna dynamics that would otherwise have been hard to gain. In an age of dwindling conservation funding, we make the case for the value added by exclosures and make recommendations for their continued use as learning tools in complex African savannas.South African Environment Observation Network (SAEON).http://www.koedoe.co.zaam2023Paraclinical Science

Sustained proliferation in cancer: mechanisms and novel therapeutic targets

Proliferation is an important part of cancer development and progression. This is manifest by altered expression and/or activity of cell cycle related proteins. Constitutive activation of many signal transduction pathways also stimulates cell growth. Early steps in tumor development are associated with a fibrogenic response and the development of a hypoxic environment which favors the survival and proliferation of cancer stem cells. Part of the survival strategy of cancer stem cells may manifested by alterations in cell metabolism. Once tumors appear, growth and metastasis may be supported by overproduction of appropriate hormones (in hormonally dependent cancers), by promoting angiogenesis, by undergoing epithelial to mesenchymal transition, by triggering autophagy, and by taking cues from surrounding stromal cells. A number of natural compounds (e.g., curcumin, resveratrol, indole-3-carbinol, brassinin, sulforaphane, epigallocatechin-3-gallate, genistein, ellagitannins, lycopene and quercetin) have been found to inhibit one or more pathways that contribute to proliferation (e.g., hypoxia inducible factor 1, nuclear factor kappa B, phosphoinositide 3 kinase/Akt, insulin-like growth factor receptor 1, Wnt, cell cycle associated proteins, as well as androgen and estrogen receptor signaling). These data, in combination with bioinformatics analyses, will be very important for identifying signaling pathways and molecular targets that may provide early diagnostic markers and/or critical targets for the development of new drugs or drug combinations that block tumor formation and progression

Dietary Proteins as Determinants of Metabolic and Physiologic Functions of the Gastrointestinal Tract

Dietary proteins elicit a wide range of nutritional and biological functions. Beyond their nutritional role as the source of amino acids for protein synthesis, they are instrumental in the regulation of food intake, glucose and lipid metabolism, blood pressure, bone metabolism and immune function. The interaction of dietary proteins and their products of digestion with the regulatory functions of the gastrointestinal (GI) tract plays a dominant role in determining the physiological properties of proteins. The site of interaction is widespread, from the oral cavity to the colon. The characteristics of proteins that influence their interaction with the GI tract in a source-dependent manner include their physico-chemical properties, their amino acid composition and sequence, their bioactive peptides, their digestion kinetics and also the non-protein bioactive components conjugated with them. Within the GI tract, these products affect several regulatory functions by interacting with receptors releasing hormones, affecting stomach emptying and GI transport and absorption, transmitting neural signals to the brain, and modifying the microflora. This review discusses the interaction of dietary proteins during digestion and absorption with the physiological and metabolic functions of the GI tract, and illustrates the importance of this interaction in the regulation of amino acid, glucose, lipid metabolism, and food intake

Research needs in allergy: an EAACI position paper, in collaboration with EFA

Abstract In less than half a century, allergy, originally perceived as a rare disease, has become a major public health threat, today affecting the lives of more than 60 million people in Europe, and probably close to one billion worldwide, thereby heavily impacting the budgets of public health systems. More disturbingly, its prevalence and impact are on the rise, a development that has been associated with environmental and lifestyle changes accompanying the continuous process of urbanization and globalization. Therefore, there is an urgent need to prioritize and concert research efforts in the field of allergy, in order to achieve sustainable results on prevention, diagnosis and treatment of this most prevalent chronic disease of the 21 st century. The European Academy of Allergy and Clinical Immunology (EAACI) is the leading professional organization in the field of allergy, promoting excellence in clinical care, education, training and basic and translational research, all with the ultimate goal of improving the health of allergic patients. The European Federation of Allergy and Airways Diseases Patients' Associations (EFA) is a non-profit network of allergy, asthma and Chronic Obstructive Pulmonary Disorder (COPD) patients' organizations. In support of their missions, the present EAACI Position Paper, in collaboration with EFA, highlights the most important research needs in the field of allergy to serve as key recommendations for future research funding at the national and European levels. Although allergies may involve almost every organ of the body and an array of diverse external factors act as triggers, there are several common themes that need to be prioritized in research efforts. As in many other chronic diseases, effective prevention, curative treatment and accurate, rapid diagnosis represent major unmet needs. Detailed phenotyping/endotyping stands out as widely required in order to arrange or re-categorize clinical syndromes into more coherent, uniform and treatment-responsive groups. Research efforts to unveil the basic pathophysiologic pathways and mechanisms, thus leading to the comprehension and resolution of the pathophysiologic complexity of allergies will allow for the design of novel patient-oriented diagnostic and treatment protocols. Several allergic diseases require well-controlled epidemiological description and surveillance, using disease registries, pharmacoeconomic evaluation, as well as large biobanks. Additionally, there is a need for extensive studies to bring promising new biotechnological innovations, such as biological agents, vaccines of modified allergen molecules and engineered components for allergy diagnosis, closer to clinical practice. Finally, particular attention should be paid to the difficult-to-manage, precarious and costly severe disease forms and/or exacerbations. Nonetheless, currently arising treatments, mainly in the fields of immunotherapy and biologicals, hold great promise for targeted and causal management of allergic conditions. Active involvement of all stakeholders, including Patient Organizations and policy makers are necessary to achieve the aims emphasized herein