LFM-Pro: a tool for detecting significant local structural sites in proteins

Motivation: The rapidly growing protein structure repositories have opened up new opportunities for discovery and analysis of functional and evolutionary relationships among proteins. Detecting conserved structural sites that are unique to a protein family is of great value in identification of functionally important atoms and residues. Currently available methods are computationally expensive and fail to detect biologically significant local features

Rastall gravity extension of the standard Λ\LambdaCDM model: theoretical features and observational constraints

We present a detailed investigation of the Rastall gravity extension of the standard $\Lambda$CDM model. We review the model for two simultaneous modifications of different nature in the Friedmann equation due to the Rastall gravity: the new contributions of the material (actual) sources (considered as effective source) and the altered evolution of the material sources. We discuss the role/behavior of these modifications with regard to some low redshift tensions, including the so-called $H_0$ tension, prevailing within the standard $\Lambda$CDM. We constrain the model at the level of linear perturbations, and obtain the first constraints through a robust and accurate analysis using the latest full Planck CMB data, with and without including BAO data. We find that the Rastall parameter $\epsilon$ (null for general relativity) is consistent with zero at 68\% CL (with a tendency towards positive values, $-0.0001 < \epsilon < 0.0007$ (CMB+BAO) at 68\% CL), which in turn implies no significant statistical evidence for deviation from general relativity, and also a precision of $\mathcal{O}(10^{-4})$ for the coefficient $-1/2$ of the term $g_{\mu\nu}R$ in the Einstein field equations of general relativity (guaranteeing the local energy-momentum conservation). We explore the consequences led by the Rastall gravity on the cosmological parameters in the light of the observational analyses. It turns out that the effective source dynamically screens the usual vacuum energy at high redshifts, but this mechanism barely works due to the opposition by the altered evolution of CDM. Consequently, two simultaneous modifications of different nature in the Friedmann equation act against each other, and do not help to considerably relax the so-called low redshift tensions. Our results may offer a guide for the research community that studies the Rastall gravity in various aspects of gravitation and cosmology.Comment: 19 pages, 10 figures, 2 tables; matches the version published in EPJ

Multiple calculi in a single-system orthotopic ureterocele in a two-year-old boy presenting with hematuria: A case report

Ureterocele is the dilatation of the submucosal ureter as a result of a defect in the Chwalla membrane absorption. The many types and clinical presentations of ureters present a significant challenge to clinicians. Although stone formation in the ureterocele is common in adults, it is much less common in pediatric patients. Here, we present a case report of a two-year-old boy with single-system ureteroceles containing multiple small stones

A case of pulmonary aspergillosis in white storks

ΔΕΝ ΔΙΑΤΙΘΕΤΑΙ ΠΕΡΙΛΗΨΗAspergillosis is a fungal infection affecting respiratory system both in mammals and avian species. It is more commonly encountered in birds, in comparison with its mammalian counterpart. Mostly isolated strains are Aspergillus fumigatus (95%) and Aspergillus flavus (5%). Affected lungs and air sacs reveal miliary to gross lesions like gray-yellowish or white-grayish granulomatous foci surrounded by white halos indicative of inflammatory infiltration. Five storks found dead in the rural areas near Istanbul were submitted to our faculty between years 2008 and 2014. Two of them were thought to be younger than 1-year-old and the other three were older than one year of age. Necropsies were performed right after their submissions. Aspergillosis lesions were observed in the lungs and thoracic air sacs of the first four storks. In addition to these changes the lesions were detected at the aortic bifurcation and on the testicular and renal capsule of the fifth stork. Histopathology revealed encapsulated granulomas with foci of caseous necrosis at the center surrounded by numerous macrophages, heterophil leukocytes, lymphocytes and foreign body giant cells in all the storks. Following the gross, histopathological and mycological examinations the agents were detected as Aspergillus fumigatus. Although, the number of reported deaths due to Aspergillosis is not high in storks, we believe that these birds are quite susceptible to the disease and stress factors such as migration increases the risk of pathogenicity. This report was designed as a contribution to literature since there is only one reported case available with respect to aspergillosis associated death in storks and stress factors such as migration may also predispose storks to the disease

Glyphosate inhibition of ferric reductase activity in iron deficient sunflower roots

Iron (Fe) deficiency is increasingly being observed in cropping systems with frequent glyphosate applications. A likely reason for this is that glyphosate interferes with root uptake of Fe by inhibiting ferric reductase in roots required for Fe acquisition by dicot and nongrass species. This study investigated the role of drift rates of glyphosate (0.32, 0.95 or 1.89 mM glyphosate corresponding to 1, 3 and 6% of the recommended herbicidal dose, respectively) on ferric reductase activity of sunflower (Helianthus annuus) roots grown under Fe deficiency conditions. Application of 1.89 mM glyphosate resulted in almost 50% inhibition of ferric reductase within 6 h and complete inhibition 24 h after the treatment. Even at lower rates of glyphosate (e.g. 0.32 mM and 0.95 mM), ferric reductase was inhibited. Soluble sugar concentration and the NAD(P)H oxidizing capacity of apical roots were not decreased by the glyphosate applications. To our knowledge, this is the first study reporting the effects of glyphosate on ferric reductase activity. The nature of the inhibitory effect of glyphosate on ferric reductase could not be identified. Impaired ferric reductase could be a major reason for the increasingly observed Fe deficiency in cropping systems associated with widespread glyphosate usage

WellFactor: Patient Profiling using Integrative Embedding of Healthcare Data

In the rapidly evolving healthcare industry, platforms now have access to not only traditional medical records, but also diverse data sets encompassing various patient interactions, such as those from healthcare web portals. To address this rich diversity of data, we introduce WellFactor: a method that derives patient profiles by integrating information from these sources. Central to our approach is the utilization of constrained low-rank approximation. WellFactor is optimized to handle the sparsity that is often inherent in healthcare data. Moreover, by incorporating task-specific label information, our method refines the embedding results, offering a more informed perspective on patients. One important feature of WellFactor is its ability to compute embeddings for new, previously unobserved patient data instantaneously, eliminating the need to revisit the entire data set or recomputing the embedding. Comprehensive evaluations on real-world healthcare data demonstrate WellFactor's effectiveness. It produces better results compared to other existing methods in classification performance, yields meaningful clustering of patients, and delivers consistent results in patient similarity searches and predictions.Comment: 2023 IEEE International Conference on Big Data (IEEE BigData 2023

The interrelations of radiologic findings and mechanical ventilation in community acquired pneumonia patients admitted to the intensive care unit: a multicentre retrospective study

BACKGROUND: We evaluated patients admitted to the intensive care units with the diagnosis of community acquired pneumonia (CAP) regarding initial radiographic findings. METHODS: A multicenter retrospective study was held. Chest x ray (CXR) and computerized tomography (CT) findings and also their associations with the need of ventilator support were evaluated. RESULTS: A total of 388 patients were enrolled. Consolidation was the main finding on CXR (89%) and CT (80%) examinations. Of all, 45% had multi-lobar involvement. Bilateral involvement was found in 40% and 44% on CXR and CT respectively. Abscesses and cavitations were rarely found. The highest correlation between CT and CXR findings was observed for interstitial involvement. More than 80% of patients needed ventilator support. Noninvasive mechanical ventilation (NIV) requirement was seen to be more common in those with multi-lobar involvement on CXR as 2.4-fold and consolidation on CT as 47-fold compared with those who do not have these findings. Invasive mechanical ventilation (IMV) need increased 8-fold in patients with multi-lobar involvement on CT. CONCLUSION: CXR and CT findings correlate up to a limit in terms of interstitial involvement but not in high percentages in other findings. CAP patients who are admitted to the ICU are severe cases frequently requiring ventilator support. Initial CT and CXR findings may indicate the need for ventilator support, but the assumed ongoing real practice is important and the value of radiologic evaluation beyond clinical findings to predict the mechanical ventilation need is subject for further evaluation with large patient series

Whole shaft visibility and mechanical performance for active MR catheters using copper-nitinol braided polymer tubes

<p>Abstract</p> <p>Background</p> <p>Catheter visualization and tracking remains a challenge in interventional MR.</p> <p>Active guidewires can be made conspicuous in "profile" along their whole shaft exploiting metallic core wire and hypotube components that are intrinsic to their mechanical performance. Polymer-based catheters, on the other hand, offer no conductive medium to carry radio frequency waves. We developed a new "active" catheter design for interventional MR with mechanical performance resembling braided X-ray devices. Our 75 cm long hybrid catheter shaft incorporates a wire lattice in a polymer matrix, and contains three distal loop coils in a flexible and torquable 7Fr device. We explored the impact of braid material designs on radiofrequency and mechanical performance.</p> <p>Results</p> <p>The incorporation of copper wire into in a superelastic nitinol braided loopless antenna allowed good visualization of the whole shaft (70 cm) <it>in vitro </it>and <it>in vivo </it>in swine during real-time MR with 1.5 T scanner. Additional distal tip coils enhanced tip visibility. Increasing the copper:nitinol ratio in braiding configurations improved flexibility at the expense of torquability. We found a 16-wire braid of 1:1 copper:nitinol to have the optimum balance of mechanical (trackability, flexibility, torquability) and antenna (signal attenuation) properties. With this configuration, the temperature increase remained less than 2°C during real-time MR within 10 cm horizontal from the isocenter. The design was conspicuous <it>in vitro </it>and <it>in vivo</it>.</p> <p>Conclusion</p> <p>We have engineered a new loopless antenna configuration that imparts interventional MR catheters with satisfactory mechanical and imaging characteristics. This compact loopless antenna design can be generalized to visualize the whole shaft of any general-purpose polymer catheter to perform safe interventional procedures.</p