Immune classification of clear cell renal cell carcinoma

Since the outcome of treatments, particularly immunotherapeutic interventions, depends on the tumor immune micro-environment (TIM), several experimental and computational tools such as flow cytometry, immunohistochemistry, and digital cytometry have been developed and utilized to classify TIM variations. In this project, we identify immune pattern of clear cell renal cell carcinomas (ccRCC) by estimating the percentage of each immune cell type in 526 renal tumors using the new powerful technique of digital cytometry. The results, which are in agreement with the results of a large-scale mass cytometry analysis, show that the most frequent immune cell types in ccRCC tumors are CD8+ T-cells, macrophages, and CD4+ T-cells. Saliently, unsupervised clustering of ccRCC primary tumors based on their relative number of immune cells indicates the existence of four distinct groups of ccRCC tumors. Tumors in the first group consist of approximately the same numbers of macrophages and CD8+ T-cells and and a slightly smaller number of CD4+ T cells than CD8+ T cells, while tumors in the second group have a significantly high number of macrophages compared to any other immune cell type (P-value \u3c 0.01). The third group of ccRCC tumors have a significantly higher number of CD8+ T-cells than any other immune cell type (P-value \u3c 0.01), while tumors in the group 4 have approximately the same numbers of macrophages and CD4+ T-cells and a significantly smaller number of CD8+ T-cells than CD4+ T-cells (P-value \u3c 0.01). Moreover, there is a high positive correlation between the expression levels of IFNG and PDCD1 and the percentage of CD8+ T-cells, and higher stage and grade of tumors have a substantially higher percentage of CD8+ T-cells. Furthermore, the primary tumors of patients, who are tumor free at the last time of follow up, have a significantly higher percentage of mast cells (P-value \u3c 0.01) compared to the patients with tumors for all groups of tumors except group 3

SVNN:An efficient PacBio-specific pipeline for structural variations calling using neural networks

Abstract Background Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods are far from precise in low-coverage cases. To be accurate, they need to use high-coverage data, which in turn, results in an extremely time-consuming pipeline, especially in the alignment phase. Therefore, it is of utmost importance to have a structural variation calling pipeline which is both fast and precise for low-coverage data. Results In this paper, we present SVNN, a fast yet accurate, structural variation calling pipeline for PacBio long-reads that takes raw reads as the input and detects structural variants of size larger than 50 bp. Our pipeline utilizes state-of-the-art long-read aligners, namely NGMLR and Minimap2, and structural variation callers, videlicet Sniffle and SVIM. We found that by using a neural network, we can extract features from Minimap2 output to detect a subset of reads that provide useful information for structural variation detection. By only mapping this subset with NGMLR, which is far slower than Minimap2 but better serves downstream structural variation detection, we can increase the sensitivity in an efficient way. As a result of using multiple tools intelligently, SVNN achieves up to 20 percentage points of sensitivity improvement in comparison with state-of-the-art methods and is three times faster than a naive combination of state-of-the-art tools to achieve almost the same accuracy. Conclusion Since prohibitive costs of using high-coverage data have impeded long-read applications, with SVNN, we provide the users with a much faster structural variation detection platform for PacBio reads with high precision and sensitivity in low-coverage scenarios

Comparação da eficiência entre dois métodos de inseminação artificial utilizando sêmen fresco em gata doméstica (Felis Catus)

The objective of this study was to compare pregnancy rates in domestic cats using fresh semen for the bilateral intrauterine insemination (BIUI) method and the novel uterine body insemination (UBI) method. Queens received a single injection of equine chorionic gonadotropin (eCG) (200 IU; IM) to induce ovarian follicular development and, after 83 h, an injection of human chorionic gonadotropin (hCG) (100 IU; IM) for final oocyte maturation and ovulation induction. Thirty-four hours after hCG administration, 3 × 106 fresh spermatozoa were used for insemination by the BIUI (n = 8 queens) or by the UBI (n = 7 queens) techniques respectively. Pregnancy rates were 75.00% (6/8) by BIUI and 42.85% (3/7) by the UBI method. The mean litter size was 3.0 ± 0.86 for the BIUI, and 2.0 ± 1.0 for the UBI method. Spontaneous abortion occurred on day 35 of pregnancy in one queen following the UBI method. Our findings showed that the BIUI of queens with fresh semen resulted in higher pregnancy rates than the novel UBI method; also, acceptable pregnancy rates were achieved following BIUI with fresh semen in the domestic cat.O objetivo deste estudo foi comparar as taxas de prenhez em gatas domésticas usando sêmen fresco para o método de inseminação intrauterina bilateral (BIUI) e o novo método de inseminação do corpo uterino (UBI). As gatas receberam uma única injeção de gonadotrofina coriônica equina (eCG) (200 UI; IM) para induzir o desenvolvimento folicular ovariano e, após 83 h, uma injeção de gonadotrofina coriônica humana (hCG) (100 UI; IM) para maturação final do oócito e ovulação indução. Trinta e quatro horas após a administração de hCG, 3 × 106 espermatozoides frescos foram utilizados para inseminação pelas técnicas de BIUI (n = 8 gatas) ou UBI (n = 7 gatas), respectivamente. As taxas de gravidez foram de 75,00% (6/8) pela BIUI e 42,85% (3/7) pelo método UBI. O tamanho médio da ninhada foi de 3,0 ± 0,86 para o método BIUI e 2,0 ± 1,0 para o método UBI. Aborto espontâneo ocorreu no dia 35 de gestação em uma gata seguindo o método UBI. Nossos achados mostraram que a BIUI de gatas com sêmen fresco resultou em maiores taxas de prenhez do que o novo método UBI; também, taxas de prenhez aceitáveis ​​foram alcançadas após BIUI com sêmen fresco no gato doméstico

Data Driven Mathematical Model of Colon Cancer Progression

Every colon cancer has its own unique characteristics, and therefore may respond differently to identical treatments. Here, we develop a data driven mathematical model for the interaction network of key components of immune microenvironment in colon cancer. We estimate the relative abundance of each immune cell from gene expression profiles of tumors, and group patients based on their immune patterns. Then we compare the tumor sensitivity and progression in each of these groups of patients, and observe differences in the patterns of tumor growth between the groups. For instance, in tumors with a smaller density of naive macrophages than activated macrophages, a higher activation rate of macrophages leads to an increase in cancer cell density, demonstrating a negative effect of macrophages. Other tumors however, exhibit an opposite trend, showing a positive effect of macrophages in controlling tumor size. Although the results indicate that for all patients the size of the tumor is sensitive to the parameters related to macrophages, such as their activation and death rate, this research demonstrates that no single biomarker could predict the dynamics of tumor

Enhancing the deployment of solar energy in Norwegian high-sensitive built environments: challenges and barriers—a scoping review

Heritage and historical buildings often face climate vulnerabilities, decay of technical performance and energy inefficiency that threaten their use and consequently their long-term preservation. Due to urban densification and escalating energy consumption, addressing these vulnerabilities is crucial to protect, rehabilitate and keeping in use historical buildings in cities and utilizing renewable energy sources like solar energy should have a pivotal role towards sustainable cities and communities. However, integrating solar technology into historical buildings faces unique challenges mainly because of the significance, non-standard construction methods adopted, and the valuable original materials. Norway, with its Climate Action Plan and a substantial portion of cultural historic buildings in its building stock, aims to significantly reduce emissions and is seeking for novel solutions. This paper discusses challenges and barriers associated with adoption of solar energy in high-sensitive built environment in Norway, through a scoping review. The results outline conservation criteria as challenges, which include viability, feasibility, integration, reversibility, compatibility, reliability and safety, non-invasiveness, and acceptability. Additionally, the review identifies barriers such as economic, geographic, technical, conservative, legislative, and social factors. Initially, the frequency with which these challenges and barriers appear in academic papers is examined. Subsequently, the interconnections between these challenges and barriers are explored to assess their specific impacts within the Norwegian context. Recognizing these challenges and understanding their interconnection can represent the strength of the relationship between them and can allow to identify potential solutions and strategies to support stakeholders, experts, or public authorities for successfully implementation and integration of solar energy systems in high-sensitive built environments in the future

Effect of gelatin concentration, ribose and glycerol additions on the electrospinning process and physicochemical properties of gelatin nanofibers

Rheological properties of gelatin-based solutions containing different concentrations of ribose and/or glycerol were assessed before electrospun mats were manufactured and their properties investigated. Characterization included morphology, X-ray diffraction, Fourier transform infrared, solubility, swelling, the release of Maillard reaction (MR) products and their antioxidant activity. Gelatin concentrations >= 16 % w/v favoured the formation of smooth nanofibres in the electrospinning process due to their higher viscosity than for gelatin concentrations <= 14 % w/v. The diameters of the nanofibres were between 300 and 400 nm, irrespective of the concentration of gelatin and the additives. Heat treatments (80-110 degrees C) of the samples induced MR between gelatin and ribose, which provided the mats with water stability. Nevertheless, the fibrous morphology only remained for those mats heat-treated at 110 and 100 degrees C and containing 10 and 20 wt% ribose, respectively, after sample immersion in water. Heat treatment at 110 degrees C, along with glycerol addition, resulted in a decrease of solubility (from 100 to similar to 9 %) and provided a water absorption capacity (1,500-2,500 %), due to the crosslinking of ribose and glycerol with gelatin. Release of MR antioxidant compounds from the mats into water exhibited DPPH radical scavenging activity values up to 38 % (0.61 GAE mu g/mL).The authors would like to thank the Ministry of Business, Innovation and Employment of New Zealand (MBIE, Biocide Toolbox programme) and the Basque Government (IT1658-22) for funding. A.E. thanks the State Research Agency of Spain within the Juan de la Cierva-Incorporation action (IJC2019-039697I)

Developing an Assessment Framework for Social Sustainability within Neighborhoods

dag har bærekraft oppnådd bred aksept i alle aspekter av samfunnet. Til tross for nyere trender i rammeverket for bærekraftsvurdering og verktøy som LEED og BREEAM for bygninger og nabolag for å adressere miljømessige og økonomiske faktorer, har sosial bærekraft fått mindre anerkjennelse siden den har blitt definert som et mål på menneskelig velferd som kan varieres etter kontekst. Et betydelig gap er beskrevet i litteraturen når det gjelder utvikling av et globalt verktøy for å evaluere sosial bærekraft. Denne studien foreslår et nytt Social Sustainability Assessment Tool (SSAT) for å kvantifisere og evaluere sosial bærekraft i nabolagene ved å bruke kvantitative og kvalitative data. Dette rammeverket benytter en flerkriteriebeslutningsmetode gjennom intervjuer med et ekspertpanel (fra Alna kommune og NTNU), nemlig AHP, for å veie de utvalgte sosiale bærekraftskategoriene og indikatorene og kombinere det med et spørreskjema utfylt av innbyggerne for å vurdere deres nivå av tilfredshet. Som en casestudie ble denne metoden brukt på tre soner i Furuset-området i Oslo (Gamble Furuset, Stjerneblokkveien og Furuset Sentrum) for å sammenligne deres sosiale bærekraft og nivå av innbyggertilfredshet i seks hovedkategorier. Resultatene indikerer at Furuset Sentrum har den høyeste totale sosiale bærekraften med en skår på 69 (en skala fra 0-100), etterfulgt av Stjerneblokkveien og Gamble Furuset med henholdsvis 67 og 61. I denne metodikken er ikke bare de samlede skårene sammenlignbare, men også hver kategori og indikator kan sammenlignes og diskuteres. Dette rammeverket kan være et verktøy for beslutningstakere med en omfattende forståelse av lokale levekår i ulike bysoner og tillate dem å prioritere sine prosjekter basert på deres begrensninger, utforme langsiktige planer, og evaluere deres fremtidige prosjekter gjennom linsen av sosiale bærekraft

Photophysical Diversity of Water-Soluble Fluorescent Conjugated Polymers Induced by Surfactant Stabilizers for Rapid and Highly Selective Determination of 2,4,6-Trinitrotoluene Traces

The increasing application of fluorescence spectroscopy in development of reliable sensing platforms has triggered a lot of research interest for the synthesis of advanced fluorescent materials. Herein, we report a simple, low-cost strategy for the synthesis of a series of water-soluble conjugated polymer nanoparticles with diverse emission range using cationic (hexadecyltrimethyl­ammonium bromide, CTAB), anionic (sodium dodecylbenzene­sulfonate, SDBS), and nonionic (TX114) surfactants as the stabilizing agents. The role of surfactant type on the photophisical and sensing properties of resultant polymers has been investigated using dynamic light scattering (DLS), FT-IR, UV–vis, fluorescence, and energy dispersive X-ray (EDS) spectroscopies. The results show that the surface polarity, size, and spectroscopic and sensing properties of conjugated polymers could be well controlled by the proper selection of the stabilizer type. The fluorescent conjugated polymers exhibited fluorescence quenching toward nitroaromatic compounds. Further studies on the fluorescence properties of conjugated polymers revealed that the emission of the SDBS stabilized polymer, <i>N</i>-methylpolypyrrole–SDBS (NMPPY–SDBS), is strongly quenched by 2,4,6-trinitrotoluene molecule with a large Stern −Volmer constant of 59 526 M^–1 and an excellent detection limit of 100 nM. UV–vis and cyclic voltammetry measurements unveiled that fluorescence quenching occurs through a charge transfer mechanism between electron rich NMPPY–SDBS and electron deficient 2,4,6-trinitrotoluene molecules. Finally, the as-prepared conjugated polymer and approach were successfully applied to the determination of 2,4,6-trinitrotoluene in real water samples