Search

Colorectal carcinoma brain metastases (n = 60) were studied using next-generation sequencing and immunohistochemistry. RAS and BRAF mutations were detected in 58.2% and 7.3% of cases, respectively. Patients with RAS- and BRAF-mutant tumors could potentially benefit from the treatment with inhibitors. TP53 mutations were detected in 69.1% of metastases. Moreover, altered p53 expression was seen in 91.2% of cases. APC mutations were present in 41.8% of tumors. Diffuse nuclear accumulation of β-catenin was seen in 10.2% of metastases, although only 1 CTNNB1 mutant was identified. Nevertheless, targeting p53 and Wnt/β-catenin pathways may have potential therapeutic implications. Casein kinase 1α1 expression indicating susceptibility to protein kinase inhibitors, was seen in 95% metastases including 10 with strong immunoreactivity. The immune checkpoint marker CD276, a promising target for immunotherapy, was present on tumor cells in 50.8% of metastases and on stromal cells in almost all cases. PRAME, another immunotherapy target, was expressed in 21.7% of tumors. HER2 membrane immunostaining detected in 13.3% of cases implicated potential treatment with HER2 inhibitors. Expression of SLFN11, a predictor of response to DNA-damaging chemotherapies, and a biomarker of sensitivity to PARP inhibitors was seen in 8.3% of tumors. In 6.7% of metastases loss or partial loss of MTAP expression suggested sensitivity to PRMT5 inhibitors. CD44v5 expressed in 35% of cases indicated potential therapeutic utility of anti-CD44v5 monoclonal antibody treatment. Identification of predictive biomarkers through genomic profiling and proteomic analyses is a crucial step toward individually tailored therapeutic regimens for patients with colorectal carcinoma brain metastases., (Copyright © 2025 Elsevier Inc. All rights reserved.)

Central Eastern European countries (CEEc) are characterized both by huge diversity in income inequality and, on average, by lower levels of well-being than in the other European Union (EU) countries. Given that income inequality may affect well-being negatively, the present study aims to explore the links between income inequalities and different dimensions of well-being in the eight CEEc, i.e. Poland, Czech Republic, Slovakia, Slovenia, Hungary, Latvia, Lithuania, and Estonia. The analysis is conducted in the two groups of CEEc regarding low and high inequality in income distribution, namely CEE Continental group and CEE North group (corresponding to post-socialist corporatist and post-socialist liberal, respectively). The multidimensional concept of well-being is applied, enabling deep exploration of its links with income inequalities in the following dimensions: subjective well-being (happiness) and objective well-being (material, health, educational, and environmental dimensions). We estimate the vector autoregression (VAR) models based on annual data disaggregated into quarterly data covering 2004 to 2020. The empirical results of Granger causality testing, which was used to investigate the links between income inequality and multidimensional well-being, indicated that not only are there differences between the groups in the studied patterns of interconnectedness, but also the groups of CEE North and CEE Continental countries are not homogeneous in those links., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Geise, Szczepaniak. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Climate change and intense human activity are exacerbating changes in species' ranges. While the rapid spread of invasive alien species is well documented worldwide, the phenomenon of the spread of native species is poorly understood. To explain the problem of rapidly spreading species in the changing world, it is necessary to understand their ecology, genetic diversity and habitat limitation. The aim of our study was to analyze the ecological requirements and genetic diversity in the population of the macrophyte Trapa natans s. l., an invasive alien species in North America but native in Europe and Asia. We investigated the populations in its native range (Central and Northeastern Europe), where the species is defined as rare or extinct. We found the occurrence of T. natans in Northeastern Europe aquatic habitats where, up to now, it was described as an extinct species. The results of our environmental studies showed that the species has a wide range of tolerance to habitat conditions and lives in medium to highly nutrient-rich water with low and high salinity. Using Amplified Fragment Length Polymorphism (AFLP) analysis, we revealed high genetic variability within populations with relatively limited differentiation between populations. We showed that some populations are highly diverse (possibly refugia; Central Europe) and others are homogeneous (new sites, commercial reintroduction; Northeastern Europe). Conservation status of T. natans in its native range should be reconsidered, as the species has spread rapidly in recent decades and could be detrimental to aquatic habitats. The conclusion is that expansion/invasion can start from small populations, but under favorable conditions these populations spread rapidly. The introduction of species (even native) should be done carefully, if at all, as uncontrolled introduction to new locations, e.g. private ponds, could be the start of dispersal (native habitats) or invasion (non-native area)., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Despite the wealth of data available for mountain phylogeography, local-scale studies focused on narrow endemic species remain rare. Yet, knowledge of the genetic structure of such species biogeographically linked to a restricted area is of particular importance to understand the history of the local flora and its diversity patterns. Here, we aim to contribute to the phylogeographical overview of the Western Carpathians with a genetic study of Saxifragawahlenbergii , one of the most characteristic endemic species of this region. We sampled populations from all discrete parts of the species' distribution range to apply sequencing of selected non-coding cpDNA and nuclear ribosomal DNA (ITS) regions, as well as Amplified Fragment Length Polymorphism (AFLP) fingerprinting. First, while ITS sequences showed weak diversification, the genetic structure based on cpDNA sequences revealed two well-differentiated groups of haplotypes. One of them is restricted to the main center of the distribution range in the Tatra Mountains (Mts), while the second group included a series of closely related haplotypes, which in most cases were unique for particular isolated groups of populations in peripheral mountain ranges and in the south-eastern part of the Tatra Mts. AFLP fingerprinting also revealed a pattern of divergence among populations, while only partly corroborating the division observed in cpDNA. Taking into account all the data, the pattern of genetic structure, supported by the high levels of unique genetic markers in populations, may reflect the historical isolation of populations in several local refugia during the last glacial period. Not only the center of the range in the Tatra Mts, but also other, neighboring massifs (Malá Fatra, Nízke Tatry, Chočské vrchy, Muránska planina), where populations are characterized by separate plastid DNA haplotypes, could have acted as separate refugia., Competing Interests: The authors have declared that no competing interests exist., (Elżbieta Cieślak, Michał Ronikier, Magdalena Szczepaniak.)

Introduction: Corticotroph pituitary neuroendocrine tumors (PitNETs) develop from ACTH-producing cells. They commonly cause Cushing's disease (CD), however, some remain clinically silent. Recurrent USP8 , USP48 , BRAF and TP53 mutations occur in corticotroph PitNETs. The aim of our study was to determine frequency and relevance of these mutations in a possibly large series of corticotroph PitNETs., Methods: Study included 147 patients (100 CD and 47 silent tumors) that were screened for hot-spot mutations in USP8 , USP48 and BRAF with Sanger sequencing, while 128 of these patients were screened for TP53 mutations with next generation sequencing and immunohistochemistry., Results: USP8 mutations were found in 41% CD and 8,5% silent tumors, while USP48 mutations were found in 6% CD patients only. Both were more prevalent in women. They were related to higher rate of biochemical remission, non-invasive tumor growth, its smaller size and densely granulated histology, suggesting that these mutation may be favorable clinical features. Multivariate survival analyses did not confirm possible prognostic value of mutation in protein deubiquitinases. No BRAF mutations were found. Four TP53 mutations were identified (2 in CD, 2 in silent tumors) in tumors with size >10mm including 3 invasive ones. They were found in Crooke's cell and sparsely granulated tumors. Tumors with missense TP53 mutations had higher TP53 immunoreactivity score than wild-type tumors. Tumor with frameshift TP53 variant had low protein expression. TP53 mutation was a poor prognostic factor in CD according to uni- and multivariate survival analyses in spite of low mutations frequency., Conclusions: We confirmed high prevalence of USP8 mutations and low incidence of USP48 and TP53 mutations. Changes in protein deubiquitinases genes appear to be favorable prognostic factors in CD. TP53 mutations are rare, occur in both functioning and silent tumors and are related to poor clinical outcome in CD., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Pękul, Szczepaniak, Kober, Rusetska, Mossakowska, Baluszek, Kowalik, Maksymowicz, Zieliński, Kunicki, Witek and Bujko.)

Despite the introduction of new molecular classifications, advanced colorectal cancer (CRC) is treated with chemotherapy supplemented with anti-EGFR and anti-VEGF targeted therapy. In this study, 552 CRC cases with different primary tumor locations (250 left side, 190 rectum, and 112 right side) were retrospectively analyzed by next generation sequencing for mutations in 50 genes. The most frequently mutated genes were TP53 in left-sided tumors compared to right-sided tumors and BRAF in right-sided tumors compared to left-sided tumors. Mutations in KRAS, NRAS, and BRAF were not detected in 45% of patients with left-sided tumors and in 28.6% of patients with right-sided tumors. Liver metastases were more common in patients with left-sided tumors. Tumors on the right side were larger at diagnosis and had a higher grade (G3) than tumors on the left. Rectal tumors exhibit distinctive biological characteristics when compared to left-sided tumors, including a higher absence rate of KRAS, NRAS, and BRAF mutations (47.4% in rectal versus 42.8% in left-sided tumors). These rectal tumors are also unique in their primary metastasis site, which is predominantly the lungs, and they have varying mutation rates, particularly in genes such as BRAF, FBXW7, and TP53, that distinguish them from tumors found in other locations. Primary tumor location has implications for the potential treatment of CRC with anti-EGFR therapy., (© 2024. The Author(s).)

Synovial sarcoma is a relatively common soft tissue tumor characterized by highly specific t(X;18)(p11;q11) translocation resulting in the fusion of SS18 with members of SSX gene family. Typically, detection of SS18 locus rearrangement by fluorescence in situ hybridization or SS18 :: SSX fusion transcripts confirms the diagnosis. More recently, immunohistochemistry (IHC) for SS18-SSX chimeric protein (E9X9V) and C-terminus of SSX (E5A2C) showed high specificity and sensitivity for synovial sarcoma. This study screened a cohort of >1000 soft tissue and melanocytic tumors using IHC and E9X9V and E5A2C antibodies. Three percent (6/212) of synovial sarcomas were either negative for SS18-SSX or had scattered positive tumor cells (n=1). In these cases, targeted RNA next-generation sequencing detected variants of SS18 :: SSX chimeric transcripts. DNA methylation profiles of 2 such tumors matched with synovial sarcoma. A few nonsynovial sarcoma tumors (n=6) revealed either focal SS18-SSX positivity (n=1) or scattered positive tumor cells. However, targeted RNA next-generation sequencing failed to detect SS18 :: SSX transcripts in these cases. The nature of this immunopositivity remains elusive and may require single cell sequencing studies. All synovial sarcomas showed positive SSX IHC. However, a mosaic staining pattern or focal loss of expression was noticed in a few cases. Strong and diffuse SSX immunoreactivity was also seen in epithelioid sclerosing osteosarcoma harboring EWSR1 :: SSX1 fusion, while several sarcomas and melanocytic tumors including cellular blue nevus (5/7, 71%) revealed focal to diffuse, mostly weak to intermediate SSX staining. The SS18-SSX and SSX IHC is a useful tool for synovial sarcoma differential diagnosis, but unusual immunophenotype should trigger molecular genetic testing., Competing Interests: Conflicts of Interest and Source of Funding: Supported as a part of NCI’s intramural research program. The authors have disclosed that they have no significant relationships with, or financial interest in, any commercial companies pertaining to this article., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)

Bladder cancer is a common malignancy associated with high recurrence rates and potential progression to invasive forms. Sorafenib, a multi-targeted tyrosine kinase inhibitor, has shown promise in anti-cancer therapy, but its cytotoxicity to normal cells and aggregation in solution limits its clinical application. To address these challenges, we investigated the formation of supramolecular aggregates of sorafenib with Congo red (CR), a bis-azo dye known for its supramolecular interaction. We analyzed different mole ratios of CR-sorafenib aggregates and evaluated their effects on bladder cancer cells of varying levels of malignancy. In addition, we also evaluated the effect of the test compounds on normal uroepithelial cells. Our results demonstrated that sorafenib inhibits the proliferation of bladder cancer cells and induces apoptosis in a dose-dependent manner. However, high concentrations of sorafenib also showed cytotoxicity to normal uroepithelial cells. In contrast, the CR-BAY aggregates exhibited reduced cytotoxicity to normal cells while maintaining anti-cancer activity. The aggregates inhibited cancer cell migration and invasion, suggesting their potential for metastasis prevention. Dynamic light scattering and UV-VIS measurements confirmed the formation of stable co-aggregates with distinctive spectral properties. These CR-sorafenib aggregates may provide a promising approach to targeted therapy with reduced cytotoxicity and improved stability for drug delivery in bladder cancer treatment. This work shows that the drug-excipient aggregates proposed and described so far, as Congo red-sorafenib, can be a real step forward in anti-cancer therapies.

Exosomes are secreted to the extracellular milieu when multivesicular endosomes (MVEs) dock and fuse with the plasma membrane. However, MVEs are also known to fuse with lysosomes for degradation. How MVEs are directed to the plasma membrane for exosome secretion rather than to lysosomes is unclear. Here we report that a conversion of phosphatidylinositol-3-phosphate (PI(3)P) to phosphatidylinositol-4-phosphate (PI(4)P) catalyzed sequentially by Myotubularin 1 (MTM1) and phosphatidylinositol 4-kinase type IIα (PI4KIIα) on the surface of MVEs mediates the recruitment of the exocyst complex. The exocyst then targets the MVEs to the plasma membrane for exosome secretion. We further demonstrate that disrupting PI(4)P generation or exocyst function blocked exosomal secretion of Programmed death-ligand 1 (PD-L1), a key immune checkpoint protein in tumor cells, and led to its accumulation in lysosomes. Together, our study suggests that the PI(3)P to PI(4)P conversion on MVEs and the recruitment of the exocyst direct the exocytic trafficking of MVEs for exosome secretion., (© 2023. The Author(s).)

Fluorescence nanoscopy has become increasingly powerful for biomedical research, but it has historically afforded a small field-of-view (FOV) of around 50 μm × 50 μm at once and more recently up to ∼200 μm × 200 μm. Efforts to further increase the FOV in fluorescence nanoscopy have thus far relied on the use of fabricated waveguide substrates, adding cost and sample constraints to the applications. Here we report PRism-Illumination and Microfluidics-Enhanced DNA-PAINT (PRIME-PAINT) for multiplexed fluorescence nanoscopy across millimeter-scale FOVs. Built upon the well-established prism-type total internal reflection microscopy, PRIME-PAINT achieves robust single-molecule localization with up to ∼520 μm × 520 μm single FOVs and 25-40 nm lateral resolutions. Through stitching, nanoscopic imaging over mm 2 sample areas can be completed in as little as 40 min per target. An on-stage microfluidics chamber facilitates probe exchange for multiplexing and enhances image quality, particularly for formalin-fixed paraffin-embedded (FFPE) tissue sections. We demonstrate the utility of PRIME-PAINT by analyzing ∼10 6 caveolae structures in ∼1,000 cells and imaging entire pancreatic cancer lesions from patient tissue biopsies. By imaging from nanometers to millimeters with multiplexity and broad sample compatibility, PRIME-PAINT will be useful for building multiscale, Google-Earth-like views of biological systems., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Co-published by Nanjing University and American Chemical Society.)

The United States Department of Agriculture's Gus Schumacher Nutrition Incentive Program (GusNIP) supports nutrition incentive (NI) and produce prescription programs (PPRs). PPRs allow healthcare providers to "prescribe" fruits and vegetables (FVs) to patients experiencing low income and/or chronic disease(s) and who screen positive for food insecurity. We developed a Theory of Change (TOC) that summarizes how and why PPRs work, identifies what the programs hope to achieve, and elucidates the causal pathways necessary to achieve their goals. We created the PPR TOC through an iterative, participatory process that adapted our previously developed GusNIP NI TOC. The participatory process involved food and nutrition security experts, healthcare providers, PPR implementors, and PPR evaluators reviewing the existing NI TOC and suggesting modifications to accurately reflect PPRs. The resulting TOC describes the mechanisms, assumptions, rationale, and underpinnings that lead to successful and equitable outcomes. Modifications of the NI TOC centered around equity and focused on inclusion of healthcare as an additional partner and the importance of health and healthcare utilization as outcomes. The TOC describes how the GusNIP PPR program reaches its goals. This understanding will be useful for PPR developers, implementers, funders, and evaluators for describing the pathways, assumptions, and foundations of successful PPRs.

Background: Student burnout during medical education is a prevalent and critical problem. Burnout has reaching consequences, including negative health outcomes for students, financial loss for schools, and worsened patient care as students transition to practice. Global Health Outreach Experiences (GHOEs), known to enhance cultural awareness and clinical knowledge among medical students, are offered in most programs. Prior studies document that GHOEs benefit physicians suffering from burnout, with effects demonstrating improvement over 6 months. No study, to our knowledge, has assessed the influence GHOEs may have on medical student burnout with a comparable control group. This study examines whether participation in a GHOE, compared to a standard break from school, has a positive effect on burnout., Methods: A case control study utilizing the Copenhagen Burnout Inventory was conducted on medical students. 41 students participated in a one-week, spring break GHOE and 252 were randomly selected as non-participating students in a control group. Assessments were gathered 1 week prior, 1 week after, and 10 weeks after spring break. Response across the surveys in chronological order included 22, 20, 19 GHOE and 70, 66, 50 control participants., Results: A significant reduction in personal burnout (PB) (P = 0.0161), studies related burnout (SRB) (P = 0.0056), and colleagues related burnout (CRB) (P = 0.0357) was found among GHOE attendees compared to control participants at 10-weeks after spring break. When modeled with potential confounders, CRB and SRB reductions remained significant., Conclusion: GHOEs may be a potential tool for institutions to combat burnout rates in their students. The benefits of GHOEs appear to enhance over time., (© 2023. The Author(s).)

Background: Although pregnancy is a physiological process it causes hormonal changes that can also affect the oral cavity. Pregnancy increases the risk of gum disease inflammation and tooth caries which could affect the health of the developing baby. Proper oral health is crucial both for mother and her babies and is related with mothers' awareness of this connection. The aim of this study was the self-assessment of women's both oral health and oral health literacy as well as mothers' awareness of the connection of oral health and pregnancy., Material and Methods: In the study anonymous questionnaire was prepared and provided to be filled in by 200 mothers at the age from 19 to 44 y.o. who gave birth in the gynecological clinic. The questionnaire included demographic, and concerning the areas of oral health before and during pregnancy and after the childbirth questions., Results: Only 20% of the investigated women underwent the oral examination before the pregnancy and the next 38.5% underwent it intentionally when the pregnancy had been confirmed. As much as 24% of women pointed out lack of awareness of the importance of proper oral hygiene during pregnancy. 41.5% of investigated women declared complaints during the pregnancy concerning teeth or gums and 30.5% underwent dental treatment; 68%, brushed their teeth properly-twice a day; 32% of women observed deterioration of oral health state during the pregnancy. The knowledge of the importance of oral health during pregnancy presented by the majority of mothers was relatively proper, which was strongly connected with higher education status and living in big cities. A significant correlation between higher birth weight and more frequent daily tooth brushing was observed. Both higher frequency of problems concerning the oral cavity and dental treatment during pregnancy were significantly related to the younger age of mothers., Conclusions: The knowledge of women concerning of oral health on the management of pregnancy and development of fetus is still insufficient. Gynecologists should inquire pregnant women if they have done dental examination, and provide wider education about importance of oral health in pregnancy., (© 2023. The Author(s).)

Background: A causal link between microbiota composition (dysbiosis) and oncogenesis has been demonstrated for several types of cancer. Neutrophils play a role in both immune protection against bacterial threats and carcinogenesis. This study aimed to characterise intratumoral bacteria in vulvar squamous cell carcinoma (VSCC) and their putative effect on neutrophil recruitment and cancer progression., Methods: Clinical material was obtained from 89 patients with VSCC. Next-generation sequencing (NGS) of 16S rRNA and quantitative polymerase chain reaction (qPCR) were used to detect bacterial species in VSCC. To verify neutrophil activation, CD66b expression in tumour specimens was analysed by immunohistochemistry (IHC). Subsequently, IHC was applied to detect the main neutrophil serine proteases (NSPs), cathepsin G (CTSG), neutrophil elastase (ELANE), and proteinase 3 (PRTN3) in VSCC., Results: Fusobacterium nucleatum and Pseudomonas aeruginosa were identified as tumour-promoting bacteria, and their presence was found to be associated with a shorter time to progression in VSCC patients. Furthermore, high abundance of CD66b, the neutrophil activation marker, in VSCC samples, was found to relate to poor survival of patients with VSCC. The selected NSPs were shown to be expressed in vulvar tumours, also within microabscess. The increased numbers of microabscesess were correlated with poor survival in VSCC patients., Conclusions: Our results show that neutrophilic inflammation seem to be permissive for tumour-promoting bacteria growth in VSCC. The findings provide new therapeutic opportunities, such as based on shifting the balance of neutrophil populations to those with antitumorigenic activity and on targeting NSPs produced by activated neutrophils at the inflammation sites., (© 2023. The Author(s).)

Objective: To explore the approaches applied by nutrition educators who work with the US Department of Agriculture Gus Schumacher Nutrition Incentive Program (GusNIP), Nutrition Incentive (NI), and Produce Prescription (PPR) programs., Methods: Multiple data collection methods, including descriptive survey (n = 41), individual interviews (n = 25), and 1 focus group (n = 5). Interviewees were educators who deliver nutrition education as a component of GusNIP NI/PPR programs. Descriptive statistics were calculated from survey responses. Transcripts were coded using thematic qualitative analysis methods., Results: Four overarching themes emerged. First, educators have many roles and responsibilities beyond providing curriculum-based nutrition education. Second, interviewees emphasized participant-centered nutrition education and support. Third, partnerships with collaborating cross-sector organizations are essential. Fourth, there are common challenges to providing nutrition education within GusNIP NI/PPR programs, and educators proposed solutions to mitigate these challenges., Conclusions: Nutrition educators promote multilevel solutions to improve dietary intake, and it is recommended they be included in conversations to improve GusNIP NI/PPR programs., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

The laser treatment of surfaces enables the alteration of their morphology and makes them suitable for various applications. This paper discusses the use of a laser beam to develop surface features that enhance pool boiling heat transfer. Two types of structures (in the 'macro' and 'micro' scale) were created on the samples: microfins (grooves) and surface roughness. The impact of the pulse duration and scanning velocity on the height of the microfins and surface roughness at the bottom of the grooves was analyzed with a high precision optical profilometer and microscope. The results indicated that the highest microfins and surface roughness were obtained with a pulse duration of 250 ns and scanning velocity of 200 mm/s. In addition, the influence of the 'macro' and 'micro' scale modifications on the boiling heat transfer of distilled water and ethyl alcohol was studied on horizontal samples heated with an electric heater. The largest enhancement was obtained for the highest microfins and roughest surfaces, especially at small superheats. Heat flux dissipated from the samples containing microfins of 0.4 mm height was, maximally, over three times (for water) and two times (for ethanol) higher than for the samples with smaller microfins (0.2 mm high). Thus, a modification of a selected model of boiling heat transfer was developed so that it would be applicable to laser-processed surfaces. The correlation proved to be quite successful, with almost all experimental data falling within the ±100% agreement bands.

Objectives: In this first large-scale analysis of neurological emergency admissions in England, we determine the number and types of emergency admissions with neurological emergency diagnostic codes, how many are under the care of a neurologist or neurosurgeon and how such admissions vary by levels of deprivation., Design: Retrospective empirical research employing a derived list of neurological emergency diagnostic codes SETTING: This study used the Hospital Episode Statistics data set for the financial year 2019/2020 based on 17 million in-year inpatient admissions in England including 6.5 million (100%) emergency admissions with any diagnosis codes., Results: There were 1.4 million (21.2%) emergency inpatient admissions with a mention of any neurological code, approx. 248 455 (3.8%) with mention of a specific neurological emergency code from the derived list, and 72 485 (1.1%) included such a code as the primary reason for admission. The highest number of in-year admissions for adults was for epilepsy (145 995), with epilepsy as the primary diagnostic code in 15 945 (10.9%). Acute nerve root/spinal cord syndrome (41 215), head injury (29 235) and subarachnoid haemorrhage (18 505) accounted for the next three highest number of admissions. 3230 (1.4%) in-year emergency hospital admissions with mention of a neurological emergency code were under the care of a neurologist or neurosurgeon, with only 1315 (0.9%) admissions with mention of an epilepsy code under a neurologist. There was significant variation for epilepsy and functional neurological disorders (FNDs) in particular by Index of Multiple Deprivation decile. The association between deprivation and epilepsy and FND was significant with p-values of 2.5e-6 and 1.5e-8, respectively., Conclusions: This study has identified important findings in relation to the burden of neurological emergency admissions but further work is needed, with greater clinical engagement in diagnostic coding, to better understand the implications for workforce and changes to service delivery needing to be implemented., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY. Published by BMJ.)

Recent advances in super resolution microscopy have enabled imaging at the 10-20 nm scale on a light microscope, providing unprecedented details of native biological structures and processes in intact and hydrated samples. Of the existing strategies, DNA points accumulation in imaging nanoscale topography (DNA-PAINT) affords convenient multiplexing, an important feature in interrogating complex biological systems. A practical limitation of DNA-PAINT, however, has been the slow imaging speed. In its original form, DNA-PAINT imaging of each target takes tens of minutes to hours to complete. To address this challenge, several improved implementations have been introduced. These include DNA-PAINT-ERS (where E = ethylene carbonate; R = repeat sequence; S = spacer), a set of strategies that leads to both accelerated DNA-PAINT imaging speed and improved image quality. With DNA-PAINT-ERS, imaging of typical cellular targets such as microtubules takes only 5-10 min. Importantly, DNA-PAINT-ERS also facilitates multiplexing and can be easily integrated into current workflows for fluorescence staining of biological samples. Here, we provide a detailed, step-by-step guide for fast and multiplexed DNA-PAINT-ERS imaging of fixed and immunostained cells grown on glass substrates as adherent monolayers. The protocol should be readily extended to biological samples of a different format (for example tissue sections) or staining mechanisms (for example using nanobodies). © 2022 Wiley Periodicals LLC. Basic Protocol 1: Preparation of probes for DNA-PAINT-ERS Basic Protocol 2: Sample preparation for imaging membrane targets with DNA-PAINT-ERS in fixed cells Alternate Protocol: Immunostaining of extracted U2OS cells Basic Protocol 3: Super resolution image acquisition and analysis., (© 2022 Wiley Periodicals LLC.)

Sinonasal mucosal melanoma is a rare tumor arising within the nasal cavity, paranasal sinuses, or nasopharynx (sinonasal tract). This study evaluated 90 cases diagnosed in 29 males and 61 females with median age 68 years. Most tumors involved the nasal cavity and had an epithelioid morphology. Spectrum of research techniques used in this analysis includes targeted-DNA and -RNA next-generation sequencing, Sanger sequencing, fluorescence in situ hybridization and immunohistochemistry. Sinonasal melanomas were commonly driven by RAS (38/90, 42%), especially NRAS (n = 36) mutations and rarely (4/90, 4%) displayed BRAF pathogenic variants. BRAF/RAS mutants were more frequent among paranasal sinuses (10/14, 71%) than nasal (26/64, 41%) tumors. BRAF/RAS-wild type tumors occasionally harbored alterations of the key components and regulators of Ras-MAPK signaling pathway: NF1 mutations (1/17, 6%) or NF1 locus deletions (1/25, 4%), SPRED1 (3/25, 12%), PIK3CA (3/50, 6%), PTEN (4/50, 8%) and mTOR (1/50, 2%) mutations. These mutations often occurred in a mutually exclusive manner. In several tumors some of which were NRAS mutants, TP53 was deleted (6/48, 13%) and/or mutated (5/90, 6%). Variable nuclear accumulation of TP53, mirrored by elevated nuclear MDM2 expression was seen in >50% of cases. Furthermore, sinonasal melanomas (n = 7) including RAS/BRAF-wild type tumors (n = 5) harbored alterations of the key components and regulators of canonical WNT-pathway: APC (4/90, 4%), CTNNB1 (3/90, 3%) and AMER1 (1/90, 1%). Both, TERT promoter mutations (5/53, 9%) and fusions (2/40, 5%) were identified. The latter occurred in BRAF/RAS-wild type tumors. No oncogenic fusion gene transcripts previously reported in cutaneous melanomas were detected. Eight tumors including 7 BRAF/RAS-wild type cases expressed ADCK4::NUMBL cis-fusion transcripts. In summary, this study documented mutational activation of NRAS and other key components and regulators of Ras-MAPK signaling pathway such as SPRED1 in a majority of sinonasal melanomas., (© 2022. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Recent work suggests that Ras small GTPases interact with the anionic lipid phosphatidylserine (PS) in an isoform-specific manner, with direct implications for their biological functions. Studies on PS-Ras associations in cells, however, have relied on immuno-EM imaging of membrane sheets. To study their spatial relationships in intact cells, we have combined the use of Lact-C2-GFP, a biosensor for PS, with multicolor super resolution imaging based on DNA-PAINT. At ~20 nm spatial resolution, the resulting super resolution images clearly show the nonuniform molecular distribution of PS on the cell membrane and its co-enrichment with caveolae, as well as with unidentified membrane structures. Two-color imaging followed by spatial analysis shows that KRas-G12D and HRas-G12V both co-enrich with PS in model U2OS cells, confirming previous observations, yet exhibit clear differences in their association patterns. Whereas HRas-G12V is almost always co-enriched with PS, KRas-G12D is strongly co-enriched with PS in about half of the cells, with the other half exhibiting a more moderate association. In addition, perturbations to the actin cytoskeleton differentially impact PS association with the two Ras isoforms. These results suggest that PS-Ras association is context-dependent and demonstrate the utility of multiplexed super resolution imaging in defining the complex interplay between Ras and the membrane.

Introduction: In the following study we describe the diagnostic process and further case analysis of a 30-year-old woman admitted with typical COVID-19 symptoms, who subsequently developed additional symptoms suggesting cerebral autosomal dominant arteriopathy with sub-cortical infarcts and leukoencephalopathy (CADASIL)., Material and Methods: Other than the standard diagnostic procedures, whole genome sequencing (WGS) was used, which led to following findings. A new variant of the NOTCH3 gene, which led to CADASIL-like symptoms, was found, and it had been most likely activated by the SARS-CoV-2 infection. This novel variant in NOTCH3 has not been found in existing databases and has never been mentioned in research concerning CADASIL before., Results: Furthermore, after subjecting the patient's close relatives to WGS it was found that no other examined person demonstrated the same genetic mutation., Conclusions: It seems therefore that the new variant of NOTCH3 is of de novo origin in the patient's genome. Additionally, the relatively early onset of CADASIL and the unexpectedly severe COVID-19 infection suggest that the two occurred simultaneously: the infection with SARS-CoV-2 accelerated development of CADASIL symptoms and the unusual variant of the NOTCH3 gene contributed to the more severe course of COVID-19., Competing Interests: The authors declare no conflict of interest., (Copyright: © 2022 Termedia & Banach.)

A new nivicolous myxomycete is described as a result of a comprehensive study of Didymium nivicola collections from the entire range of its occurrence. Statistical analysis of 12 morphological characters, phylogenetic analyses of nuc 18S rDNA and elongation factor 1-alpha gene ( EF1A ), and a delimitation method (automatic barcode gap diversity) have been applied to corroborate the identity of the new species. A preliminary morphological analysis of D. nivicola revealed high variability of South American populations where four types of spore ornamentation were noted. However, results of molecular study and statistical analysis of morphological characters did not support recognition of these four forms but the distinction of two morphotypes. Consequently, two species have been recognized: D. nivicola and the newly proposed D. pseudonivicola . The new species can be distinguished from D. nivicola by distinctly larger and mostly plasmodiocarpic sporophores, which are scattered to gregarious, paler spores, and by the paler, more delicate and more elastic capillitium. Spore ornamentation of D. pseudonivicola is uniform and can be described as distinctly spiny (pilate under scanning electron microscope [SEM]), whereas those of D. nivicola is more variable, where spines (pilae under SEM) are delicate, distinct, or conspicuous. Additionally, whereas D. nivicola is a species distributed worldwide, D. pseudonivicola occurs only in the austral Andes of Argentina and Chile.

This article examines the relationships between different dimensions of well-being and income inequalities across selected Central Eastern European countries after joining the European Union in 2004. Regarding the multivariety of well-being concept, it explores its 5 dimensions (material dimension, health dimension, education dimension, environmental dimension, happiness). Accounting for the interactions between dimensions of well-being matters for the inequalities, we conducted an in-depth analysis by adopting PMG estimation and panel ARDL model to assess the short-run and long-run links between variables. The results of conducted analysis allowed us to identify the canals through which income inequalities are linked directly or indirectly with the particular dimensions of well-being. In the long run, all the dimensions of well-being significantly affected income inequalities, and income inequality shaped material dimension, health, education, natural environment, and happiness. However, in the short run, the only dimension that shaped income inequalities was education. Income inequalities directly affected both health dimension and happiness., Competing Interests: The authors have declared that no competing interests exist.

Background: Borderline personality disorder (BPD) is characterized by instability in affective regulation that can result in a loss of cognitive control. Triggers may be neuronal responses to emotionally valenced context and/or stimuli. 'Neuronal priming' indexes the familiarity of stimuli, and may capture the obligatory effects of affective valence on the brain's processing system, and how such valence mediates responses to the repeated presentation of stimuli. We investigated the effects of affective valence of stimuli on neuronal priming (i.e. changes in activation to repeated presentation of stimuli), and if these effects distinguished BPD patients from controls., Methods: Forty BPD subjects and 25 control subjects (age range: 18-44) participated in an episodic memory task during fMRI. Stimuli were presented in alternating epochs of encoding (six images of positive, negative, and neutral valence) and recognition (six images for 'old' v. 'new' recognition). Analyses focused on inter-group differences in the change in activation to repeated stimuli (presented during Encoding and Recognition)., Results: Relative to controls, BPD showed greater priming (generally greater decrease from encoding to recognition) for negatively valenced stimuli. Conversely, BPD showed less priming for positively valenced stimuli (generally greater increase from encoding to recognition)., Conclusion: Plausibly, the relative familiarity of negative valence to patients with BPD exerts an influence on obligatory responses to repeated stimuli leading to repetition priming of neuronal profiles. The specific effects of valence on memory and/or attention, and consequently on priming can inform the understanding of mechanisms of altered salience for affective stimuli in BPD.

Background: Palmoplantar pustulosis (PPP) is a chronic inflammatory disease with poorly understood pathogenesis. The disease has a chronic course with improvements and exacerbations. Due to palmoplantar location, PPP has a severely negative impact on patients' quality of life., Objectives: To identify demographic and environmental factors, concomitant diseases, medications, and bacterial factors which may affect the course of PPP., Material and Methods: A total of 51 patients suffering from PPP took part in the study. They were classified according to the Palmoplantar Pustulosis Psoriasis Area and Severity Index (ppPASI) into 3 groups due to the severity of the disease. Pack-year of smoking score was established as a quotient of packets smoked every 24 h and the years of being addicted. Diagnosis of metabolic syndrome was based on the IDF criteria from 2009. Chlamydia trachomatis was detected using enzyme-linked immunosorbent assay (ELISA) technique, Staphylococcus aureus by the culture swabs. Contact hypersensitivity was examined with the T.R.U.E. test., Results: Significantly high severity of PPP was observed in patients addicted to smoking with a high pack-year score (p = 0.03). Significantly lower intensity of PPP lesions was observed in patients treated with ibuprofen (p < 0.01). There was no correlation between severity of PPP skin lesions and comorbidities., Conclusions: Addiction to cigarette smoking and a high pack-year score aggravates the course of PPP. Treatment with ibuprofen can improve the course of the disease.

The main objective of the present work is to determine the effects of laser processing on properties of WC-Co electro-spark deposited (ESD) coatings on steel substrates. Tungsten carbide coatings have been applied to steel substrates using a manual electrode feeder, model EIL-8A. The laser beam processing (LBP) of electro-spark coatings was performed using an Nd:YAG fiber laser. The microstructure and properties of laser treated/melted coatings were evaluated by means of scanning electron microscopy (SEM), X-ray diffraction (XRD), surface geometric structure (SGS) and roughness measurements and adhesion, microhardness, residual stresses, corrosion resistance and application tests. The obtained experimental data were subjected to statistical analysis and multidimensional numerical and visual exploratory techniques. It has been shown conclusively that the laser-treated ESD WC-Co coatings are characterized by lower microhardness, higher resistance to corrosion, increased roughness and better adhesion to the substrate. LBP homogenizes the chemical composition, refines the microstructure and heals microcracks and pores of ESD coatings. The laser treated ESD WC-Co coatings can be used in frictional sliding nodes (e.g., on the front seal rings used in pumps) and as protective layers.

Purpose: The aim of this work was to determine anaerobic performance in male amputee football players considering types and levels of limb impairment, playing position, anthropometric parameters, and comparing the findings to reference values. Relationship between parameters in the laboratory anaerobic test and the handgrip test was checked., Methods: The 30-second Wingate Anaerobic Test (peak power, mean power, relative peak power, relative mean power, time to achieve peak power, fatigue index) on the arm-crank ergometer (LODE ANGIO), the FUTREX 6100 (Futrex, Gaithersburg, USA) and the handgrip test were used in amputee football players (n = 23). Anthropometric measurements were collected., Results: There were no differences in anaerobic results between players considering types and levels of limb impairment. Forwards had significantly higher relative mean and peak power ( p = 0.049, d = 0.82; p = 0.049, d = 0.81), and lower amputation-adjusted body mass index ( p = 0.001, d = 1.50) than defenders. For peak power, 19 out 23 achieved, and for relative peak power, 22 out 23 achieved results from "average" to "elite". Peak power strongly correlated to handgrip strength results., Conclusions: Amputee football requires a high level of power from players. Maintaining appropriate body composition is important for amputee football players to have better anaerobic performance during the game. The 30-second Wingate Anaerobic Test can be used to assess anaerobic performance in AF players. Sport-specific anaerobic performance laboratory tests and field-based tests using in indirect upper limbs' peak power monitoring would be beneficial for coaches.

Background: Migration is a challenging life transition that may be a source of various problems related to well-being and mental health. However, the psychological adaptation of migrants may be potentially facilitated by social self-efficacy-the beliefs in one's ability to initiate and maintain interpersonal relationships. Previous research suggests that social self-efficacy is positively related to adjustment and negatively related to loneliness, depression, and psychological distress. Research also confirms that self-efficacy beliefs can be effectively enhanced using Internet-based interventions. These results served as a background for creating the New in Town, a self-help Internet-based intervention for internal migrants in Poland that aims at increasing social self-efficacy. Exercises in the intervention are based on the principles of Cognitive Behavioral Therapy and relate to sources of self-efficacy beliefs: mastery experiences, vicarious experiences, verbal persuasions, and emotional and physiological states. Users complete increasingly challenging tasks that encourage them to interact with their environment. The aim of this trial was to investigate the efficacy of the New in Town intervention., Methods: The efficacy of the New in Town intervention will be tested in a two-arm randomized controlled trial with a waitlist control group. Social self-efficacy will be the primary outcome. Secondary outcomes will include loneliness, perceived social support, and satisfaction with life. Additionally, we will measure user experience among participants allocated to the experimental group. We aim to recruit a total of N  = 280 participants aged at least 18 years who have changed their place of residence in the last 6 months and have an Internet connection. Participants will be assessed at baseline, 3-week post-test, and 8-week follow-up., Discussion: The trial will provide insights into the efficacy of Internet-based self-help interventions in increasing social self-efficacy. Given that the intervention works, New in Town could provide an easily accessible support option for internal migrants in Poland., Trial Registration: The trial was registered with ClinicalTrials.gov (identifier: NCT04088487) on 11th September 2019., Competing Interests: The authors declare that they have no competing interests., (© 2020 The Authors.)

We have applied the CCSD(T)-F12a/cc-pVTZ-F12//CCSD(T)/cc-pVTZ level of theory to calculate energies for 22 reactions pertinent to the stability and reactivity of hardly isolable cyanoform (HC(CN) 3 ). A number of exothermic processes has been indicated, especially the hydration. In the predicted mechanism for the gas-phase hydration of cyanoform, the H 2 O addition to the C≡N bond corresponds to a rate-limiting step, which is aided by an extra molecule of water. Also, for the cyanoform dihydrate (H 2 NC(OH)C(CN)CONH 2 ) product, the experimentally identified compound, the more stable planar isomer exhibits intramolecular O-H···O═C (not N-H···O═C) H-bonding. Our calculated structures, binding energies, and NBO data for [HC(CN) 3 ] n ( n = 2,4) clusters suggest that the non-conventional C-H···N H-bonds contribute to their stability. Among the surveyed structures of the C≡N group incorporating products of reactions examined, the CCSD(T)/cc-pVTZ molecular parameters of cyanocarbons C 2 (CN) 4 , C 2 (CN) 6 , and C 6 (CN) 6 can be regarded as the most accurate gas-phase values up-to-date.

Palmoplantar pustulosis (PPP) is a chronic inflammatory disease, most often occurring in middle-aged women. In the course of the condition, painful skin lesions appear on the hands and feet, i.e., areas that are extremely important in everyday life. Therefore, the disease significantly reduces quality of life. The pathogenesis of this disease is poorly understood, although it is known that genetic, immunological and environmental factors play a role in its development. Clinical observations confirm the role of nicotine and contact allergens in the development of the lesions. The skin lesions can also occur as a side effect of certain medications. In some cases, PPP coexists with other diseases, i.e., seronegative arthropathies, as well as celiac and thyroid diseases. There is also a connection between the disease and infectious bacterial foci. Exacerbation of the skin lesions is triggered by stress. Therefore, patients require multidirectional tests, since finding the cause of the disease is essential to administering effective treatment.

Protein (un)folding rates depend on the free-energy barrier separating the native and unfolded states and a prefactor term, which sets the timescale for crossing such barrier or folding speed limit. Because extricating these two factors is usually unfeasible, it has been common to assume a constant prefactor and assign all rate variability to the barrier. However, theory and simulations postulate a protein-specific prefactor that contains key mechanistic information. Here, we exploit the special properties of fast-folding proteins to experimentally resolve the folding rate prefactor and investigate how much it varies among structural homologs. We measure the ultrafast (un)folding kinetics of five natural WW domains using nanosecond laser-induced temperature jumps. All five WW domains fold in microseconds, but with a 10-fold difference between fastest and slowest. Interestingly, they all produce biphasic kinetics in which the slower phase corresponds to reequilibration over the small barrier (<3 RT ) and the faster phase to the downhill relaxation of the minor population residing at the barrier top [transition state ensemble (TSE)]. The fast rate recapitulates the 10-fold range, demonstrating that the folding speed limit of even the simplest all-β fold strongly depends on the amino acid sequence. Given this fold's simplicity, the most plausible source for such prefactor differences is the presence of nonnative interactions that stabilize the TSE but need to break up before folding resumes. Our results confirm long-standing theoretical predictions and bring into focus the rate prefactor as an essential element for understanding the mechanisms of folding., Competing Interests: The authors declare no conflict of interest.

Compressed natural gas (CNG) is a widely used automotive fuel in a variety of countries. In case of a vehicle fire where the safety device also malfunctions, a failure of the CNG automotive cylinder could occur. Such a cylinder failure is associated with severe hazards for the surrounding environment. Firstly, a comprehensive analysis is given below, summarizing various accidents involving CNG automotive cylinders and their consequences. In an extensive experimental program, 21 CNG automotive cylinders with no safety device were tested. Of the 21, burst tests were carried out on 5 Type III and 5 Type IV cylinders. Furthermore, fire tests with 8 Type III and 3 Type IV cylinders were conducted. Apart from cylinder pressure, inner temperature and cylinder mantle temperature, the periphery consequences, such as nearfield blast pressure and fragmentation are documented. The maximum measured overpressure due to a Type III cylinder failure was p = 0.41 bar. Each traceable fragment was georeferenced. All-in-all, fragment throw distances of d > 300 m could be observed. As one key result, it can be stated that the tested Type IV CNG cylinders showed less critical failure behavior then the Type III cylinders under fire impingement., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Theory and experiments have shown that microsecond folding proteins exhibit characteristic thermodynamic properties that reflect the limited cooperativity of folding over marginal barriers (downhill folding). Those studies have mostly focused on proteins with large α-helical contents and small size, which tend to be the fastest folders. A key open question is whether such properties are also present in the fastest all-β proteins. We address this issue by investigating the unfolding thermodynamics of a collection of WW domains as representatives of the simplest β-sheet fold. WW domains are small microsecond folders, although they do not fold as fast as their α-helical counterparts. In previous work on the NEDD4-WW4 domain, we reported deviations from two-state thermodynamics that were less apparent and thus suggestive of an incipient downhill scenario. Here we investigate the unfolding thermodynamics of four other WW domains (NEDD4-WW3, YAP65-WW1(L30K), FBP11-WW1, and FBP11-WW2) by performing all of the thermodynamic tests for downhill folding that have been previously developed on α-helical proteins. This set of five WW domains shares low sequence identity and include examples from two specificity classes, thus providing a comprehensive survey. Thermodynamic analysis of the four new WW domains consistently reveals all of the properties of downhill folding equilibria, which are in all cases more marked than what we found before in NEDD4-WW4. Our results show that fast-folding all-β proteins do share limited cooperativity and gradual unfolding thermodynamics with fast α-helical proteins and suggest that the free energy barrier to folding of natural proteins is mostly determined by size and fold topology and much less by the specific amino acid sequence.

Detection of specific nucleic acid sequences is invaluable in biological studies such as genetic disease diagnostics and genome profiling. Here, we developed a highly sensitive and specific detection method that combines an advanced oligonucleotide ligation assay with multicolor single-molecule fluorescence. We demonstrated that under our experimental conditions, 7-nucleotide long DNA barcodes have the optimal short length to ascertain specificity while being long enough for sufficient ligation. Using four spectrally separated fluorophores to label DNA barcodes, we simultaneously distinguished four DNA target sequences differing by only a single nucleotide. Our single-molecule approach will allow for accurate identification of low-abundance molecules without the need for target DNA preamplification., (Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Proteomic analyses provide essential information on molecular pathways of cellular systems and the state of a living organism. Mass spectrometry is currently the first choice for proteomic analysis. However, the requirement for a large amount of sample renders a small-scale proteomics study challenging. Here, we demonstrate a proof of concept of single-molecule FRET-based protein fingerprinting. We harnessed the AAA+ protease ClpXP to scan peptides. By using donor fluorophore-labeled ClpP, we sequentially read out FRET signals from acceptor-labeled amino acids of peptides. The repurposed ClpXP exhibits unidirectional processing with high processivity and has the potential to detect low-abundance proteins. Our technique is a promising approach for sequencing protein substrates using a small amount of sample., Competing Interests: Conflict of interest statement: J.v.G., C.J., and A.S.M. hold a patent (“Single molecule protein sequencing”; WO2014014347).

Background: Low bone mineral density is a common finding in children with systemic connective tissue diseases, including juvenile idiopathic arthritis (JIA). The influence of the ongoing process of bone remodeling on the disease course merits further investigation. The aim of this study was to assess the clinical relevance of markers of bone turnover and their potential role as predictors of higher fracture risk and, by extension, risk of osteoporosis., Materials and Methods: Blood samples were collected from 59 patients diagnosed with JIA in order to determine serum levels of the following markers of bone turnover: Beta-Crosslaps, osteocalcin, bone alkaline phosphatase, osteoprotegerin and receptor activator for nuclear factor kappa-B ligand. The values were analyzed with laboratory parameters and results of dual X-ray absorptiometry (DXA)., Results: Osteoprotegerin and bone alkaline phosphatase levels were age-dependent. Beta-Crosslaps values were significantly higher in patients with positive JADAS27 score (p=0.0410). Osteoprotegerin levels were higher in patients treated with biological agents than only with disease-modifying anti-rheumatic drugs (p=0.0273). There was no relation between markers of bone turnover and sex, DXA results, dosage of glucocorticosteroids and disease duration., Conclusions: The authors postulate performing DXA measurements every 6 months in patients with higher disease activity. The potential lower fracture risk in children with JIA within biological treatment needs further assessment. Age- and sex-adjusted reference rates of bone turnover markers need to be developed for Central European patients in order to assess individual values properly.

Several prokaryotic Argonaute proteins (pAgos) utilize small DNA guides to mediate host defense by targeting invading DNA complementary to the DNA guide. It is unknown how these DNA guides are being generated and loaded onto pAgo. Here, we demonstrate that guide-free Argonaute from Thermus thermophilus (TtAgo) can degrade double-stranded DNA (dsDNA), thereby generating small dsDNA fragments that subsequently are loaded onto TtAgo. Combining single-molecule fluorescence, molecular dynamic simulations, and structural studies, we show that TtAgo loads dsDNA molecules with a preference toward a deoxyguanosine on the passenger strand at the position opposite to the 5' end of the guide strand. This explains why in vivo TtAgo is preferentially loaded with guides with a 5' end deoxycytidine. Our data demonstrate that TtAgo can independently generate and selectively load functional DNA guides., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Although an isolation of elusive tricyanomethane HC(CN) 3 was recently reported, the existence of other HC 4 N 3 species has yet to be confirmed. In this work, the relative stabilities, spectroscopic features, and rearrangements of tricyanomethane and its four isomers are examined using single- (CCSD(T), CCSD(T)-F12) and multireference (MCSCF, MRPT2) methods. Tricyanomethane and dicyanoketenimine (NC) 2 CCNH, which are found to be the two most stable HC 4 N 3 isomers lying within 9 kcal/mol, can be discriminated by their spectroscopic parameters. The predicted stepwise interconversion path relating HC(CN) 3 and (NC) 2 CCNH features the HC 4 N 3 species comprising the C-C-N ring moiety, with the largest barrier being associated with the initial H migration to one of the CN carbons. Adding a water molecule reduces the H migration barrier strongly and makes it possible to interconvert tricyanomethane to dicyanoketenimine in a "concerted" way.

We present a comprehensive benchmark computational study which has explored a complete path of the anomerization reaction of bare d-erythrose involving a pair of the low-energy α- and β-furanose anomers, the former of which was observed spectroscopically (Cabezas et al., Chem. Commun. 2013, 49, 10826). We find that the ring opening of the α-anomer yields the most stable open-chain tautomer which step is followed by the rotational interconversion of the open-chain rotamers and final ring closing to form the β-anomer. Our results indicate the flatness of the reaction's potential energy surface (PES) corresponding to the rotational interconversion path and its sensitivity to the computational level. By using the explicitly correlated coupled cluster CCSD(T)-F12/cc-pVTZ-F12 energies, we determine the free energy barrier for the α-furanose ring-opening (rate-determining) step as 170.3 kJ/mol. The question of the number of water molecules (n) needed for optimal stabilization of the erythrose anomerization reaction rate-determining transition state is addressed by a systematic exploration of the PES of the ring opening in the α-anomer-(H 2 O) n and various β-anomer-(H 2 O) n (n = 1-3) clusters using density functional and CCSD(T)-F12 computations. These computations suggest the lowest free energy barrier of the ring opening for doubly hydrated α-anomer, achieved by a mechanism that involves water-mediated multiple proton transfer coupled with the furanose CO bond breakage. Among the methods used, the G4 performed best against the CCSD(T)-F12 reference at estimating the ring-opening barrier heights for both the hydrated and bare erythrose conformers. Our results for the hydrated species are most relevant to an experimental study of the anomerization reaction of d-erythrose to be carried out in microsolvation environment. © 2016 Wiley Periodicals, Inc., (© 2016 Wiley Periodicals, Inc.)

The genome and transcriptome are constantly modified by proteins in the cell. Recent advances in single-molecule techniques allow for high spatial and temporal observations of these interactions between proteins and nucleic acids. However, due to the difficulty of obtaining functional protein complexes, it remains challenging to study the interactions between macromolecular protein complexes and nucleic acids. Here, we combined single-molecule fluorescence with various protein complex pull-down techniques to determine the function and stoichiometry of ribonucleoprotein complexes. Through the use of three examples of protein complexes from eukaryotic cells (Drosha, Dicer, and TUT4 protein complexes), we provide step-by-step guidance for using novel single-molecule techniques. Our single-molecule methods provide sub-second and nanometer resolution and can be applied to other nucleoprotein complexes that are essential for cellular processes., (Copyright © 2016 Elsevier Inc. All rights reserved.)

D-Erythrose is a C4 monosaccharide with a biological and potential astrobiological relevance. We have investigated low-energy structures of d-erythrose and their interconversion in the gas phase with the highest-level calculations up-to-date. We have identified a number of structurally distinct furanose and open-chain isomers and predicted α ↔ α and β ↔ β furanose interconversion pathways involving the O-H rotamers. We have estimated relative Gibbs free energies of the erythrose species based on the CCSD(T)/aug-cc-pVTZ electronic energies and MP2/aug-cc-pVTZ vibrational frequencies. By using natural bond orbital theory we have also quantified a stabilization of erythrose conformers and interconversion transition states by intramolecular H-bonds.

Argonaute proteins play a central role in mediating post-transcriptional gene regulation by microRNAs (miRNAs). Argonautes use the nucleotide sequences in miRNAs as guides for identifying target messenger RNAs for repression. Here, we used single-molecule FRET to directly visualize how human Argonaute-2 (Ago2) searches for and identifies target sites in RNAs complementary to its miRNA guide. Our results suggest that Ago2 initially scans for target sites with complementarity to nucleotides 2-4 of the miRNA. This initial transient interaction propagates into a stable association when target complementarity extends to nucleotides 2-8. This stepwise recognition process is coupled to lateral diffusion of Ago2 along the target RNA, which promotes the target search by enhancing the retention of Ago2 on the RNA. The combined results reveal the mechanisms that Argonaute likely uses to efficiently identify miRNA target sites within the vast and dynamic agglomeration of RNA molecules in the living cell., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Introduction: Toll-like receptors (TLRs) are an important component of a innate immune system. Stimulation of TLRs, through action with helper T cells, could change Th1/Th2 balance and thus affect adaptive immune response. Receptors TLR2 and TLR4 play important role in immune response to measles virus. The aim of this work was stimulation of the peripheral blood mononuclear cells (PBMC) and determination of Toll-like gene expression in these cells., Methods: PBMCs from 20 healthy donors were stimulated with measles viruses and ligands for TLR2 and TLR4. For examinations the real time RT-PCR (QuantiFast® Assay, Qiagen) was used. The expression of Toll-like receptors was determined on muRNA level, using real-time one step RT-PCR (QuantiFast® Assay, Qiagen) with simultaneous detection of TLR2 and TLR4 genes and housekeeping gene (GAPDH)., Results: Virus-specific influence of wild measles virus strains activity on PBMC derived from vaccinated seronegative individuals manifested in higher level of expression of TLR2 and TLR4 genes in compare to the expression of these genes in PBMC of seropositive individuals., Conclusions: Toll-like receptors participate in the development of immune response to measles virus.

We performed large-scale second-order perturbation theory gas-phase calculations to study about five hundred structures of D-fructose. The two lowest energy fructose structures identified are β-pyranoses possessing (2)C5 chair, with ΔG(298 K) of 6 kJ/mol, differing in orientation of the equatorially positioned hydroxymethyl group, gt and g'g, where the gt rotamer is the global minimum, consistent with the recent microwave spectroscopy study. We have found that interconversions from the fructose global minimum to the second and third most stable β-pyranose rotamers involve the energy barriers of ca. 30 kJ/mol. Among numerous fructofuranose conformers discovered (about 250), a pair of the ((3)T2) α- and (E3) β-anomers are energetically most preferred and lie at least 12 kJ/mol above the global minimum. We also found that the fructose open-chain structures lie significantly higher in energy than the most stable cyclic species. The commonly used M06-2X density functional performs well compared to MP2 and G4 theory at identifying the low-energy fructose minima, including the global one, and at reproducing their intramolecular H-bond geometric parameters. The lowest-energy gas-phase pyranose and furanose structures of fructose benefit from stabilization due to the cooperative or quasi-linear H-bonding and both endo and exo anomeric effects.

Background: Neurofibromatosis type I (NF1, Recklinghausen's disease) is an autosomal dominant disorder characterized by the following clinical features: café au lait spots, neurofibromas, Lisch nodules, freckling of the axillary and inguinal regions, optic nerve gliomas, bone dysplasia and increased risk of certain tumors. NF1 is diagnosed on the basis of clinical criteria, while identifying the genetic background of the disease is important mainly for genetic counseling. NF1 genetic analysis is based on searching for NF1 exon deletions/duplications using Multiplex ligation-dependent probe amplification (MLPA), searching for microdeletions of the critical region using fluorescence in situ hybridization (FISH), searching for point mutations by gene sequencing (in most cases) and analyzing mRNA., Objectives: The aim of this study was to estimate the frequency of single and multi-exon deletions/duplications in the NF1 gene in Polish patients, and to evaluate the usefulness of MLPA as a cheap and easy method for NF1 molecular diagnosis, despite the fact that such changes may be found in only a small group of NF1 patients., Material and Methods: The study included 65 patients suspected of NF1 or with recognized NF1 on the basis of clinical criteria. Cytogenetic analysis were carried out for all the patients, and for one patient with a translocation [46,XY,t(17;22)(q11.2;q11.2)], a FISH analysis was performed. All patients were tested for deletions/duplications in the NF1 gene using two MLPA kits for neurofibromatosis I., Results: The MLPA analysis showed deletions in the NF1 gene in 7.7% of the cases (5/65)., Conclusions: The results indicate that an MLPA analysis may be performed in patients with a clinical diagnosis of NF1 or patients with suspected NF1 as an easy and inexpensive first molecular test, enabling the exclusion of about 7% of NF1 patients from expensive and time-consuming molecular diagnosis by DNA sequencing.

Background: The aim of the study was to assess idiopathic nephrotic syndrome (INS) relapse rate, co-morbidities, and social status of adults diagnosed with INS in childhood., Material and Methods: A written questionnaire was sent to 118 adults treated for INS in childhood. In 61 (51.7%) responders (aged 26.0 ± 6.2 years, range 18 - 51.5 years), we used available medical records to evaluate age at the onset of INS, number of INS relapses below 18 years of age, response to corticosteroids (CS), renal biopsy findings, and immunosuppressive treatment as well as questionnaire to evaluate the number and treatment of INS relapses above 18 years of age, co-morbidities, age at menarche, marital status, offspring, educational status, and occupation., Results: In the group of 61 responders, median age at the onset of INS was 3 (range 1.3 - 14.0) years, median number of INS relapses at < 18 years of age was 5 (1 - 20). Steroid-sensitive nephrotic syndrome (SSNS) was diagnosed in 37 (60.7%) patients, steroid-dependent nephrotic syndrome SDNS in 18 (29.5%) patients, and steroid-resistant nephrotic syndrome (SRNS) in 6 (9.8%) patients. Mesangial proliferation was the most common pattern in renal biopsy (35.7%). All patients received CS, 15 were treated with methylprednisolone pulses, 13 with cyclophosphamide, 11 with chlorambucil, 2 with cyclosporine, and 21 with levamisole. All patients achieved remission and had normal renal function at the age of 18. In adulthood, INS relapsed in 10 (16.4%) patients, including 5 (13.5%) patients with SSNS, 4 (22.2%) with SDNS, and 1 (16.7%) with SRNS (p = 0.72). Median number of relapses was 2 (range 1 - 11). Patients with relapses at > 18 years of age had more (p < 0.005) relapses at < 18 years of age. Hypertension was diagnosed in 8 (16.1%), overweight in 14 (23.0%), obesity in 3 (4.9%), and bone fractures in 12 (19.7%) patients. Five patients had height < 3rd percentile, including 4 with INS onset at < 3 years of age. One patient had growth retardation before the treatment. No myocardial infarctions, strokes, severe infections, or malignancies were reported. Mean age at menarche was 12.9 ± 1.4 years, 37 (60.7%) patients were in a steady relationship/ married, 1/18 (5.6%) patients treated with cytostatic agents and 12/43 (24/7%) patients not treated with cytostatic agents had offspring (p < 0.05). Elementary education was reported by 4 (6.6%), secondary education by 32 (52.5%), and higher education by 25 (40.9%) patients, and 34 (55.7%) patients were professionally active. None of the 6 patients with SRNS developed end-stage renal disease., Conclusions: 1. High number of INS relapses in childhood is a risk factor for recurrences in adulthood. 2. INS relapses in childhood do not preclude active professional life in adulthood.

We present an extensive computational study of a complex conformational isomerism of two gas phase pentoses of biological and potential astrobiological importance, d-ribose and 2-deoxy-d-ribose. Both cyclic (α- and β-pyranoses, α- and β-furanoses) and open-chain isomers have been probed using second order Møller-Plesset perturbation theory (MP2), M06-2X density functional, and multi-level G4 methods. This study revealed a multitude of existing minima structures. Numerous furanose conformers found are described with the Altona and Sundaralingam pseudorotation parameters. In agreement with the recent gas-phase microwave (MW) investigation of Cocinero et al., the calculated free ribose isomers of lowest energy are the two β-pyranoses with the (1)C4 and (4)C1 ring chair conformations. Both β-pyranoses lie within 0.9kJ/mol in terms of ΔG(298K) (G4), thus challenge the computational methods used to predict the ribose global minimum. The calculated most favoured ribofuranose is the α-anomer having the twist (2)T1 ring conformation, put 10.4kJ/mol higher in ΔG than the global minimum. By contrast with d-ribose, the lowest energy 2-deoxy-d-ribose is the α-pyranose, with the most stable 2-deoxy-d-furanose (the α-anomer) being only 6.2kJ/mol higher in free energy. For both pentoses, the most favoured open-chain isomers are significantly higher in energy than the low-lying cyclic forms. A good overall agreement is observed between the M06-2X and MP2 results in terms of both the existing low-energy minima structures and intramolecular H-bonding geometrical parameters. The natural orbital analysis confirms the occuring of the endo- and exo-anomeric effects and maximization of intramolecular H-bonding in the lowest-lying pyranoses and furanoses of both sugars., (Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.)

Introduction: Toll-like receptors (TLRs) are an important component of a innate immune system. Stimulation of TLRs, through action with helper T cells, could change Th1/Th2 balance and thus affect adaptive immune response. The aim of this work was to optimize the stimulation of the peripheral blood mononuclear cells (PBMC) and the validation of real-time RT-PCR method for determination of Toll-like gene expression in these cells., Methods: PBMCs from healthy donors were stimulated with measles viruses and ligands for TLR2 and TLR4. For examinations the real time RT-PCR (QuantiFast Assay, Qiagen) was used. Fold change of TLRs expression was normalized to GAPDH and estimated by 2(-deltadeltaCt) method. Validation of real-time RT-PCR method was performed for repeatability and efficiency., Results: The level of gene expression varies between individuals and was dose and time of incubation dependent. The efficiency ofreal-time RT-PCR was 90.4% +/- 10.2 for GAPDH, 87.0% +/- 8.2 for TLR2 and 44.5% +/- 9.2 for TLR4. Repeatability, expressed as relative standard deviation (RSD) for Ct values was less than 0.70% for GAPDH, < 3.2% for TLR2 and < 2.84% for TLR4., Conclusions: Based on obtained results, the optimal conditions for stimulation were: 10 microg/ml/24h for LPS, 1 microg/ml/6h for Pam3CSK4 and 1250 MeV infectious particles/24h.