Beyond Known Reality: Exploiting Counterfactual Explanations for Medical Research

This study employs counterfactual explanations to explore "what if?" scenarios in medical research, with the aim of expanding our understanding beyond existing boundaries. Specifically, we focus on utilizing MRI features for diagnosing pediatric posterior fossa brain tumors as a case study. The field of artificial intelligence and explainability has witnessed a growing number of studies and increasing scholarly interest. However, the lack of human-friendly interpretations in explaining the outcomes of machine learning algorithms has significantly hindered the acceptance of these methods by clinicians in their clinical practice. To address this, our approach incorporates counterfactual explanations, providing a novel way to examine alternative decision-making scenarios. These explanations offer personalized and context-specific insights, enabling the validation of predictions and clarification of variations under diverse circumstances. Importantly, our approach maintains both statistical and clinical fidelity, allowing for the examination of distinct tumor features through alternative realities. Additionally, we explore the potential use of counterfactuals for data augmentation and evaluate their feasibility as an alternative approach in medical research. The results demonstrate the promising potential of counterfactual explanations to enhance trust and acceptance of AI-driven methods in clinical settings

On some generalized q-difference sequence spaces

In this study, we construct the spaces of $q$-difference sequences of order $m$. We obtain some inclusion relations, topological properties, Schauder basis and alpha, beta and gamma duals of the newly defined spaces. We characterize certain matrix classes from the newly defined spaces to any one of the spaces $c_0, c, \ell_\infty$ and $\ell_p$

Paraoxonase 1 activity and survival in sepsis patients

Background: Sepsis is a state of augmented oxidative stress and diminished antioxidant capacity. High den- sity lipoprotein (HDL) particles were shown to possess antioxidant and anti-inflammatory properties, as well as Paraoxonase 1 (PON1), which is an enzyme that is also protective against HDL oxidation. Previous stud- ies suggested a possible role of decreased PON1 activ- ity or HDL levels in sepsis patients. Aims: The present study was designed to test a hypoth- esis that higher PON1 activity and HDL-cholesterol levels could predict a better survival in sepsis patients. Study Design: Observational study. Methods: Venous blood samples were collected from sepsis patients for HDL-cholesterol levels, PON1 ac- tivity and cytokine assays (TNF-α and IL-6) and Acute Physiologic and Chronic Health Evaluation II (APACHE II) scores were calculated in order to weight patients’ disease severity on the day of sepsis diagnosis. Patients were followed-up until the 28th day for any cause intra- hospital mortality. Data were statistically analyzed for effects of study parameters on patients’ survival. Results: In total, 85 patients with sepsis were included in the study. The mean age was 65.2±17.9 years and 48 were male; at the end of the 28-day follow-up pe- riod, 46 survived. TNF-α (86.9±10.5 vs 118.6±16.4) and IL-6 levels (906.7±82.7 vs 1323.1±54.3) were sig- nificantly higher in non-survivors, while PON1 activity (140.7±42.3 vs 66.7±46.6) and HDL-cholesterol lev- els (43.6±8.1 vs 34.5±8.9) were significantly higher in survivors (p<0.001 for all). TNF-α (r=-0.763) and IL-6 levels (r=-0.947) showed strong negative correlations, PON1 activity (r=0.644) and HDL-cholesterol levels (r=0.477) showed positive correlations with patient sur- vival (p<0.001 for all). Survival estimates significantly favored TNF-α (Log Rank 59.5, p<0.001) and IL-6 levels (Log Rank 53.2, p<0.001) according to PON1 activity (Log Rank 5.4, p<0.03) and HDL-cholesterol levels (Log Rank 8.3, p<0.005). Regression analyses for relative contributions of parameters to survival showed that higher IL-6 levels (t:-16.489, p<0.001) were the most significant negative factor for survival, and TNF-α levels (t:-4.417, p<0.001), whereas PON1 activity had a positive effect (t:3.210, p<0.003). Conclusion: The present study showed that although low PON1 activity and HDL-cholesterol levels were related to mortality, higher levels were not found to be as predictive as cytokine levels for survival

Prevalence of tick-borne haemoparasites in small ruminants in Turkey and diagnostic sensitivity of single-PCR and RLB

Background: Tick-borne haemoparasitic diseases (TBHDs), caused by Theileria, Babesia, Anaplasma and Ehrlichia, are common in regions of the world where the distributions of host, pathogen and vector overlap. Many of these diseases threaten livestock production and some also represent a concern to human public health. The primary aim of this study was to determine the prevalence of the above-mentioned pathogens in a large number of blood samples (n = 1979) collected from sheep (n = 1727) and goats (n = 252) in Turkey. A secondary aim was to assess the diagnostic sensitivity of a number of species-specific polymerase chain reaction (PCR) tests and the reverse line blotting (RLB) assay. DNA samples were screened using species-specific PCR for the presence of Theileria ovis, Theileria sp. MK, T. lestoquardi, T. uilenbergi, T. luwenshuni, Babesia ovis, Anaplasma ovis and A. phagocytophilum while RLB was undertaken to test for the presence of all known Theileria, Babesia, Anaplasma and Ehrlichia species. The diagnostic sensitivity of these two approaches was then compared in terms of their ability to detect single species and mixed infections. Results: Overall, 84 and 74.43% of the small ruminants sampled were identified as hosting one or more pathogen(s) by species-specific PCR and RLB respectively. The presence of Theileria sp. OT1, T. luwenshuni and T. uilenbergi in Turkey was revealed for the first time while the presence of Babesia motasi, B. crassa and T. separata in Turkish small ruminants was confirmed using molecular methods. A high prevalence of mixed infection was evident, with PCR and RLB approaches indicating that 52.24 and 35.42% of animals were co-infected with multiple species, respectively. More than 80% of the mixed infections contained T. ovis and/or A. ovis. The RLB approach was found to be capable of detecting mixed infections with species such as Theileria sp. OT1, Theileria sp. OT3, T. separata, B. crassa and Babesia spp. Conclusion: The results indicated that pathogens causing TBHDs are highly prevalent in sheep and goats in Turkey. The diagnostic sensitivity of species-specific single PCR was generally higher than that of RLB. However, the latter approach was still capable of identifying a high proportion of individuals containing mixed-species infections. The use of species-specific single PCR is recommended to accurately estimate pathogen prevalence and to identify co-infected hosts

Loop mediated isothermal amplification (LAMP) of Theileria annulata DNA

In the past three decades, as an alternative to PCR (polymerase chain reaction) new diagnostic techniques like LAMP (loop mediated isothermal amplification) whereby target DNA can be amplified under isothermal conditions without using thermocycler have been developed. The LAMP method allows the synthesis of large amounts of DNA in a short time with high specificity and rapid and easy detection of generated products. In this study, specificity and sensitivity of LAMP method was evaluated for the detection of T. annulata in acute infected and/or carriers cattle using primer pair specifically designed to amplify merozoite surface antigen gene (Mero1), 30 kDa major merozoite surface antigen gene (Tams-1) and cytochrome b gene of T.annulata. Primer pairs with highest sensitivity were used to evaluate the applicability of LAMP to the field samples. Two LAMP primers (CYTOB1 and CYTOB341) targeting cytochrome b gene specifically amplified DNA of different T. annulata isolates successfully while no amplification was seen in other species DNAs and BL20. CYTOB1 primers detected T. annulata Ankara / D7 DNA up to 2 fg, however the detection limit of CYTOB341 was 10 fold lower. The sensitivity of CYTOB1 LAMP assay was same with F3/B3 PCR, however when compared with that of cytob1 PCR a 10 fold lower sensitivity was found. The LAMP product was confirmed by restriction digestion and sequencing. Results obtained from this study indicated that none of the designed primer pairs specific to target genes (Tams-1 and Mero1), except cytochrome b gene was able to specifically and sensitively detect different isolates of T. annulata. Consequently, it was shown that LAMP method using CYTOB1 primers is less effective than the cytob1 PCR in terms of detecting T. annulata in the field sample

The war in Ukraine: Why knowing the country of origin of tech components is vital

The war in Ukraine has highlighted the significance of knowing the Country of Origin (COO) of technology product components. A single Iranian drone was found to contain parts made by more than a dozen US and western companies, and digital products can contain hardware components, software elements, and embedded systems and data from a range of countries and computing environments. How can this conundrum best be addressed to support national security? How can the end-consumer be better informed about the origin of digital products he/she is buying? And what are the implications for sustainability and the recyclability of these products

Cybersecurity and Country of Origin: Towards a New Framework for Assessing Digital Product Domesticity

Recent events concerning the Kaspersky anti-virus software in the UK and the Android operating system in the US have highlighted the significance of the domesticity of digital products for national cybersecurity, and the importance of establishing the origin of digital products has been further brought into focus by the war in Ukraine and China’s military activities around Taiwan. Digital products can contain hardware components, software elements, embedded systems, and data, and determining the country of origin (COO) in these circumstances is problematic. The aim of this research, and its main contribution, is to provide an operational framework for the application of the COO concept to address this problem. Using an inductive research methodology based on semi-structured interviews and an online survey, a 19-parameter framework for assessing the COO of digital products is developed and then applied to the case example of a mobile phone import in Turkey. This article concludes that new processes and policies are urgently required to enhance the cyber and information security for digital products, aid domestic digital technology production, and support the transition to recyclable technologies. Such developments are of significance not only for western nations concerned with data and security issues, but also for developing world countries trying to develop their own domestic digital product manufacturing capabilities. This is also of relevance to the computer end-user, who would benefit from greater clarity on the origin of digital products ahead of a purchase decision

Arthroscopic release of the subscapularis for shoulder contracture of obstetric palsy

Objective Retrospective study of one surgeon’s experience with arthroscopic release in obstetrical brachial plexus palsy. Methods Over a four-year period, 6 patients who presented with a shoulder contracture secondary to obstetric palsy before the age of 8 years were treated arthroscopically. Small arthroscopy instruments, small shaver blades, including a 2.7-mm, 30° angled scope, and 90° radiofrequency probe, were used for this surgery. Patient selection for this approach was based on the lack of bone deformity and targeted soft tissue release. Postoperative brace immobilization for 6 weeks was used in all patients. Functional status of the patients was evaluated pre- and postoperatively with the assessment of external rotation. Results The case series consisted of 2 girls and 4 boys with a mean age of 5.1 years (range, 3–8 years). No patient was lost to follow-up, and all patients completed a minimum 1 year of clinical and radiographic follow-up. Increases in external rotation were observed in all patients. There was no intra- or postoperative complications. Conclusion Arthroscopic treatment of the shoulder contracture in obstetric palsy was found to be a safe and eVective procedure in patients who are likely to undergo future tendon transfer or bone surgery

Proximal aortic arch cannulation for proximal ascending aortic aneurysms

Introduction: Different arterial inflow sites have been reported to date for particularly challenging cardiac operations. The ascending aorta, femoral artery, and subclavian artery are the most commonly used sites. Although its use has been reported, the aortic arch has not gained popularity in the performance of cannulation. According to a search performed in the PubMed database, aortic arch cannulation for ascending aorta replacement has not been examined in a separate study before. In the present study, we report the treatment outcomes of patients with ascending aortic aneurysms in whom the aortic arch was cannulated for arterial inflow. Material and methods: Twenty-seven patients with aneurysmal dilatation of the ascending aorta underwent ascending aorta replacement from April 2010 to March 2013. The mean age of the patients was 64 years. All operations were carried out by cannulating the aortic arch distally from the origin of the innominate artery. Results: There was no mortality or cannulation-related morbidity. In 23 patients, only the supracoronary ascending aorta was replaced, whereas in 4 patients, the button modification of the Bentall procedure was performed to replace the root and the ascending aorta. Conclusions: The technique of aortic arch cannulation distal to the origin of the innominate artery is worthy of consideration in the treatment of aneurysms limited to the ascending aorta due to its safety, simplicity, and low morbidity

Prognostic markers of mortality in patients with methanol poisoning

Aim: Methanol is a kind of alcohol, which is used in industry in numerous different products. Methanol intoxication entails high mortality and morbidity rates. In this study, we aimed to investigate the effectiveness of laboratory parameters in determining the severity of exposure in patients presenting with methanol intoxication. Material and Methods: The study was performed in the university hospital between January 1, 2015, and January 1, 2020. All data were obtained retrospectively from the hospital automation system. Receiver Operating Characteristic (ROC) curve was used to determine ideal cut-off values. A logistic regression model was used to perform univariate and multivariate analyses. Results: The study included 49 patients and 3 of them were women. Thirty (61%) received both hemodialysis and intravenous ethanol for treatment. Univariate analysis revealed increased mortality in patients with pH below 7.00, HCO3 below 8.40 (mmol/L), lactate 4.35 (mmol/L), glucose 183 (mg/dl) and above, PCO2 42.7 (mmHg), high osmolarity, and a high anion gap. The results of multivariate logistic regression analysis for model 1 is (pH, bicarbonate, lactate, glucose, PCO2, osmolarity, and anion gap); pH = 4.35 (OR:31.66, 95% CI 3.25-308.5, p=0.003) and PCO2 >= 42.7 (OR: 7.01, 95% CI 1.12-43.96, p=0.038). Discussion: Laboratory parameters would predict mortality. PH emerged as a predictive mortality marker, while blood lactate and high partial carbon dioxide pressure were capable of predicting mortality if pH was excluded. Starting on the treatment with clinical diagnoses decreases mortality in methanol intoxication