Miracle-dz/UniFAR-FTUs huggingface dataset:
Distant metastases in squamous cell carcinoma of the pharynx and larynx: a population-based DAHANCA study

Abstract Background In head and neck cancer, distant metastases may be present at diagnosis (M1) or occur after treatment (DM). It is unknown whether M1 and DM follow the same clinical development and share prognosis, as population-based studies regarding outcomes are scarce. Therefore, we investigated the incidence, location of metastases and overall survival of patients with M1 and DM. Materials and methods Patients diagnosed with squamous cell carcinoma of the pharynx and larynx in Denmark 2008–2017 were identified in the Danish Head and Neck Cancer Group (DAHANCA) database. We identified 7300 patients, of whom 197 (3%) had M1 and 498 (8%) developed DM during follow-up. Results The 5-year cumulative incidence of DM was 8%. 1- and 2-year overall survival for DM (27% and 13%) vs. M1 (28% and 9%) were equally poor. There was no significant difference in location of metastases for M1 and DM and the most frequently involved organs were lungs, bone, lymph nodes and liver, in descending order. In oropharyngeal squamous cell carcinomas, the location of metastases did not differ by p16-status. For p16-positive patients, 21% of DM occurred later than three years of follow-up compared to 7% of p16-negative patients. Conclusion Incidence, location of metastases and prognosis of primary metastatic (M1) or post-treatment metastatic (DM) disease in pharyngeal and laryngeal squamous cell carcinoma are similar in this register-based study
Dignity and Predictors of Its Change Among Inpatients in Long-Term Care

The purpose of this study was to identify any differences in the dignity evaluation of geriatric inpatients after 1 month of hospitalization in a long-term care wards (LTC) and predictors of this change. This follow-up study included 125 geriatric inpatients who filled the Patient Dignity Inventory (PDI-CZ), Geriatric Depression Scale, Barthel Index, and Mini-Mental State Examination. In the initial measurement, the patients rated of PDI-CZ item “Not able to perform tasks of daily living” the worst. One month after, the items “Not able to perform tasks of daily living,” “Not able to attend to bodily functions,” and “Not feeling worthwhile or valued” were improved. Patients with higher education, for whom self-sufficiency improved and depression decreased, rated their dignity more positively 1 month after the hospitalization in LTC. Our findings suggest that these factors are important for the maintenance of the dignity of older adults hospitalized in LTC.
Heat and mass transfer model for a coffee roasting process

ii Abstract The roasting of coffee is a complex process and it takes years of experience to be able to produce a quality cup of coffee (as well as consistently reproducing the same quality coffee). Although there are various factors that can influence the final taste of coffee, from the green bean processing method to the roasting equipment used, the most crucial part in coffee flavour development is the roasting process. Even the highest quality green coffee beans can be spoiled with improper roasting procedures. No set rules exist to produce a specific roast of coffee and roasting techniques differ from roaster to roaster. It is the objective of this study to model the roasting process for the purpose of system optimisation and control. The usefulness of the model to be implemented to predict the quality of the final roasted coffee (in other words the degree of roast) was also considered. In order to model the roasting process, the heat and mass transfer that take place during roasting were investigated and further quantified by means of heat and mass transfer models. Three heat and mass transfer models were identified from literature to be able to adequately model the moisture content and temperature of the beans during roasting. From these models, the roasting process was modelled and the predicted roast profiles were obtained. For model validation, several experimental roasting procedures are conducted. A comparison between the experimental and modelled results (for the 9.09 wt% green beans) showed that all three proposed models could predict the roast profiles fairly well, with some deviations occurring with prolonged roasting times. However, all three moisture loss models consistently overestimated the moisture loss that occurs during roasting, which improved somewhat for the longer roasting times. Two of the proposed models were found to be very sensitive for the higher initial moisture contents, where the predicted roast profiles showed higher overestimations than with the normal green coffee beans. The third model performed fairly similar with all initial moisture contents and no adverse reactions (such as the significant levels of overestimation seen with the other two models) to the increased moisture content could be observed. All three moisture loss models still showed a degree of overestimation of the moisture content during a roast. The degree of roast of the roasted coffee beans was determined from the final moisture content, the roast loss percentage (which includes moisture loss, volatile release and dry matter) and the progression of the roast. It was found that some defining roasting characteristics of the coffee beans (referred to as the first and second crack) consistently occurred at the same temperatures, with the first crack occurring at about 175 to 180 °C, and the second crack occurring at temperatures above 200 °C. From this, it was concluded that a
Salivary Amylase in Cystic Fibrosis: A Marker of Disordered Autonomic Function

Summary: Total serum amylase was determined in 83 patients with cystic fibrosis (CF) (14 of whom had no steatorrhea), 21 control patients, and 6 patients with Shwachman's syndrome. Patients with CF who had steatorrhea and therefore lacked pancreatic function had the same serum levels pre- and postprandially as the control subjects, whereas patients without steatorrhea and, therefore, with evidence of pancreatic function, had significantly higher levels. The patients with Shwachman's syndrome had significantly lower total serum amylase than the three other patient groups. Only the patients with Shwachman's syndrome demonstrated a significant postprandial rise in activity. Only the salivary isoenzyme was detected in patients with Shwachman's syndrome or CF and apparently absent pancreatic function, whereas CF patients without steatorrhea had both salivary and pancreatic isoenzymes. These results demonstrate that patients with CF have an increase in circulating salivary amylase isoenzyme whereas patients with Shwachman's syndrome do not. The increase probably reflects an autonomic hyperstimulation of salivary secretion which is primary to CF, and unrelated to the state of pancreatic activity.Speculation: We speculate that high serum salivary amylase isoenzyme levels are the result of a disordered secretory stimulus operating in CF which probably affects multiple organs and causes many of the manifestations of the disease.
Physicochemical and pasting properties of some local and improved maize varieties cultivated in Benin

Physicochemical and pasting properties of eighteen varieties of maize cultivated in Benin were investigated. Studied varieties were of various colors including red, yellow and white. Eleven varieties were more likely white, while all the white varieties had a yellowish saturation index. Moisture, fat and ash contents ranged from 6.09 to 11.57%, 2.87 to 12.54% and from 1.09 to 5.46% respectively. Varieties Gnonli and IWDC 2 SynF 2 showed respectively the lowest (22.58%) and the highest (26.86%) amylose contents. The pasting properties of the maize flours showed significant differences (p ≤ 0.05) between pasting parameters (peak, final viscosity, setback, pasting temperature and peak time) among the different varieties. The results of correlations between some physicochemical characteristics of maize and their pasting properties could be used to predict their behaviors and their potential for processing into different valuable products. © 2017 International Formulae Group. All rights reserved. Keywords: Zea mays , varieties, flour, proximate composition, viscosity
Development of thermodynamic databases in the system U–Zr–Ce–Cs–Fe–B–C–I–O–H for application to simulating phase equilibria in severe nuclear accidents

ABSTRACT In case of severe nuclear accidents involving melt down of nuclear fuels at high temperatures, it is of considerable importance to accurately evaluate the highly-volatizing behavior of fission products (FPs) over multicomponent debris. Particularly, cesium (Cs)- and iodine (I)- bearing chemical species are regarded as notable FPs. In the present work, the authors have generated original thermodynamic databases for the system U–Zr–Ce–Cs–Fe–B–C–I–O–H featuring Cs- as well as I-bearing subsystems, which are contained in oxide, iodide, and metal (including borides and carbides) sub-databases. It has been confirmed that the phase diagrams calculated by the present set of the databases reproduce the corresponding literature data well in various kinds of subsystems of the above multicomponent system. The present set of databases has subsequently been applied to simulate phase equilibria and volatizing behavior of Cs- and I-including species, respectively, in multicomponent debris under specific temperature and atmospheric conditions corresponding to severe nuclear accidents.
Lidocaine has antitumor effect on hepatocellular carcinoma via the circ_DYNC1H1/miR-520a-3p/USP14 axis

Abstract Lidocaine can inhibit the malignant development of various human cancers. Circular RNA (circRNA) dynein 1 heavy chain gene (circ_DYNC1H1) acted as a pro-cancer molecule in hepatocellular carcinoma (HCC). This study aimed to explore whether the function of lidocaine was related to the oncogenic circ_DYNC1H1 in HCC. Colony formation assay and 3-(4,5-dimethylthiazol-2-y1)-2, 5-diphenyl tetrazolium bromide (MTT) assay were used for proliferation detection. Cell apoptosis was assessed by flow cytometry, and migration or invasion was determined by the transwell assay. The levels of circ_DYNC1H1, microRNA-520a-3p (miR-520a-3p), and ubiquitin-specific protease 14 (USP14) were examined using the quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). Protein levels were measured using western blot. The binding between miR-520a-3p and circ_DYNC1H1 or USP14 was confirmed by the dual-luciferase reporter assay. In vivo assay was conducted by a xenograft model in mice. Lidocaine reduced proliferation, migration, and invasion but promoted apoptosis in HCC cells. The circ_DYNC1H1 expression was downregulated in lidocaine-treated HCC cells. The inhibitory effect of lidocaine on HCC progression was weakened after circ_DYNC1H1 overexpression. miR-520a-3p was a target of circ_DYNC1H1, and the function of lidocaine was related to the regulation of circ_DYNC1H1/miR-520a-3p axis. USP14 served as a target for miR-520a-3p, and circ_DYNC1H1 could sponge miR-520a-3p to regulate the USP14 expression. The lidocaine-induced suppression of HCC development was also achieved by mediating the miR-520a-3p/USP14 axis. In vivo assay revealed that lidocaine suppressed the tumor growth of HCC by reducing the expression of circ_DYNC1H1 to affect the levels of miR-520a-3p and USP14. Our results clarified that lidocaine impeded tumor progression via targeting the circ_DYNC1H1/miR-520a-3p/USP14 axis in HCC cells.
The ties that un-bind: decoupling IP from web services and sockets for robust addressing agility at CDN-scale

The couplings between IP addresses, names of content or services, and socket interfaces, are too tight. This impedes system manageability, growth, and overall provisioning. In turn, large-scale content providers are forced to use staggering numbers of addresses, ultimately leading to address exhaustion (IPv4) and inefficiency (IPv6). In this paper, we revisit IP bindings, entirely. We attempt to evolve addressing conventions by decoupling IP in DNS and from network sockets. Alongside technologies such as SNI and ECMP, a new architecture emerges that ``unbinds'' IP from services and servers, thereby returning IP's role to merely that of reachability. The architecture is under evaluation at a major CDN in multiple datacenters. We show that addresses can be generated randomly \emph{per-query}, for 20M+ domains and services, from as few as ~4K addresses, 256 addresses, and even \emph{one} IP address. We explain why this approach is transparent to routing, L4/L7 load-balancers, distributed caching, and all surrounding systems -- and is \emph{highly desirable}. Our experience suggests that many network-oriented systems and services (e.g., route leak mitigation, denial of service, measurement) could be improved, and new ones designed, if built with addressing agility.
Extending the reach of Lagrangian analysis in turbulence

Abstract The hypothesis in the classical Kolmogorov picture of turbulence with perhaps the most far-reaching consequences is that of universality, the notion that small-scale turbulence dynamics are independent of the way the turbulence was generated. The assumption of universality can be evaluated by comparing measurements taken in many kinds of flows. However, up to now the range of flows that can be used to study universality from a Lagrangian viewpoint has been highly constrained, because large-scale Eulerian inhomogeneity manifests as Lagrangian non-stationarity. The recent work of Viggiano et al. (J. Fluid Mech., vol. 918, 2021, A25) significantly extends this range by showing how the dynamics along Lagrangian trajectories can be continuously renormalised using local Eulerian scales, at least in flows whose development is self-similar. They demonstrate their results on a turbulent jet, a classical flow that is well studied from the Eulerian perspective, though not in a Lagrangian sense. Their work provides an exciting roadmap for expanding the scope of Lagrangian analysis of turbulent flows.
CocoSketch: High-Performance Sketch-Based Measurement Over Arbitrary Partial Key Query

Sketch-based measurement has emerged as a promising solutions due to its high accuracy and resource efficiency. Prior sketches focus on measuring single flow keys and cannot support measurement on multiple keys. This work takes a significant step towards supporting arbitrary partial key queries, which aims to provide information for any key in the predefined range of possible flow keys. The designed system, CocoSketch, casts arbitrary partial key queries to the subset sum estimation problem and makes the theoretical tools for subset sum estimation practical. CocoSketch utilizes two techniques: (1) stochastic variance minimization to significantly reduce per-packet update delay, and (2) removing circular dependencies in the per-packet update logic to make the implementation hardware-friendly. This paper extends the conference version by discussing how CocoSketch adapts to new measurement requirements, including: (1) collecting the exact information of specified flow keys, and (2) distributed measurement. CocoSketch is implemented on five popular platforms (CPU, Open vSwitch, Redis, P4, and FPGA). Experiment results show that compared to baselines that use traditional single-key sketches, CocoSketch improves average packet processing throughput by $27.2\times $ and accuracy by $10.4\times $ when measuring six flow keys.
Quantitative analysis of tumour spheroid structure

Tumour spheroids are common in vitro experimental models of avascular tumour growth. Compared with traditional two-dimensional culture, tumour spheroids more closely mimic the avascular tumour microenvironment where spatial differences in nutrient availability strongly influence growth. We show that spheroids initiated using significantly different numbers of cells grow to similar limiting sizes, suggesting that avascular tumours have a limiting structure; in agreement with untested predictions of classical mathematical models of tumour spheroids. We develop a novel mathematical and statistical framework to study the structure of tumour spheroids seeded from cells transduced with fluorescent cell cycle indicators, enabling us to discriminate between arrested and cycling cells and identify an arrested region. Our analysis shows that transient spheroid structure is independent of initial spheroid size, and the limiting structure can be independent of seeding density. Standard experimental protocols compare spheroid size as a function of time; however, our analysis suggests that comparing spheroid structure as a function of overall size produces results that are relatively insensitive to variability in spheroid size. Our experimental observations are made using two melanoma cell lines, but our modelling framework applies across a wide range of spheroid culture conditions and cell lines.
Evidence Accumulates for Individual Attributes during Value-Based Decisions

When choosing between different options, we tend to consider specific attribute qualities rather than deliberating over some general sense of the options’ overall values. The importance of each attribute together with its quality will determine our preference rankings over the available alternatives. Here, we test the hypothesis that the most prominent class of model for simple decisions – sequential sampling or evidence accumulation to bound – can be bolstered by explicitly incorporating variables related to individual attributes in addition to the standard usage of overall value estimates. We examine six datasets in which participants evaluated snack foods both in terms of overall value and individual attributes, then chose between pairs of the same snacks, and show that only models that explicitly incorporate information about the individual attributes are able to reproduce fundamental patterns in the choice data, such as the influence of attribute disparity on decisions, and such models provide quantitatively better fits to the choice outcomes, response times, and confidence ratings compared to models based on overall value alone. Our results provide important evidence that incorporating attribute-level information into computational models helps us to better understand the cognitive processes involved in value-based decision- making.
Quantitation of human enteric viruses as alternative indicators of fecal pollution to evaluate wastewater treatment processes

We investigated the potential use and quantitation of human enteric viruses in municipal wastewater samples of Winnipeg (Manitoba, Canada) as alternative indicators of contamination and evaluated the processing stages of the wastewater treatment plant. During the fall 2019 and winter 2020 seasons, samples of raw sewage, activated sludge, effluents, and biosolids (sludge cake) were collected from the North End Sewage Treatment Plant (NESTP), which is the largest wastewater treatment plant in the City of Winnipeg. DNA and RNA enteric viruses, as well as the uidA gene found in Escherichia coli were targeted in the samples collected from the NESTP. Total nucleic acids from each wastewater treatment sample were extracted using a commercial spin-column kit. Enteric viruses were quantitated in the extracted samples via quantitative PCR using TaqMan assays. The average gene copies assessed in the raw sewage were not significantly different (p-values ranged between 0.0547 and 0.7986) than the average gene copies assessed in the effluents for Adenovirus and crAssphage (DNA viruses), Pepper Mild Mottle Virus (RNA virus), and uidA in terms of both volume and biomass. A significant reduction of these enteric viruses was observed consistently in activated sludge samples compared with those for raw sewage. Corresponding reductions in gene copies per volume and gene copies per biomass were also seen for uidA but were not statistically significant (p-value = 0.8769 and p-value = 0.6353, respectively). The higher gene copy numbers of enteric viruses and E. coli observed in the effluents may be associated with the 12-hour hydraulic retention time in the facility. Enteric viruses found in gene copy numbers were at least one order of magnitude higher than the E. coli marker uidA. This indicate that enteric viruses may survive the wastewater treatment process and viral-like particles are being released into the aquatic environment. Our results suggest that Adenovirus, crAssphage, and Pepper mild mottle virus can be used as complementary viral indicators of human fecal pollution.
Functionalized Biomimetic Hydrogels Enhance Salivary Stem/Progenitor Cell Organization

Complex branched salivary structures remain challenging to replicate within implant ready hydrogels. We showed previously that hyaluronic acid (HA)-based hydrogels enable growth and organization of primary salivary-derived human stem/progenitor cells (hS/PCs) into multicellular spheroids. Here, we systematically functionalized three components of migration-permissive hydrogels to foster salivary tissue morphogenesis. We separately analyzed contributions of an enzymatically degradable crosslinker, a pendant integrin-binding site, and hydrogel porosity to best support high viability, integrin-dependent cell adhesion and migration. Structure size, frequency, and morphology were all affected by hydrogel crosslink density and integration of biofunctional peptides. Viability and proliferation data suggested that integration of integrin binding sites had the greatest effect on hS/PCs behavior. A larger internal matrix space, created by increasing both crosslinker length and PEG content, was needed to form large multicellular hS/PC structures. Peptide-modified hydrogels with more internal space shifted hS/PC organization from spheroidal, surrounded by thick basement membrane, to an asymmetric arrangement with punctate matrix proteins defining a “wrinkled” perimeter. Integrin-binding peptides activated integrin β1, with highest activation observed in hydrogels having both cleavable peptide and integrin ligand. The design parameters we prescribe allowed us to encapsulate hS/PCs in a humanized biomimetic hydrogel matrix able to support morphogenesis needed for salivary restoration.