Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the continuous transcriptional heterogeneity in Wilms’ tumors using unsupervised machine learning

Wilms’ tumors are pediatric malignancies that are thought to arise from faulty kidney development. To date, the course of treatment depends on manual histopathological classification which is difficult since the tumors differ between patients in a continuous manner. Here, we used three computational approaches to characterize the continuous heterogeneity of Wilms’ tumors. We first chose a published dataset of microarray gene expression measurements from high-risk blastemal-type Wilms’ tumors. Then, we used Pareto Task Inference to show that the tumors form a triangle-shaped continuum in latent space that is bounded by three tumor archetypes with “stromal”, “epithelial”, and “blastemal” characteristics, that resemble the un-induced mesenchyme, the Cap mesenchyme, and early epithelial structures of the fetal kidney. We confirmed this by fitting a generative probabilistic “grade of membership” model whereby each tumor is represented as a unique mixture of three hidden “topics” with blastemal, stromal, and epithelial characteristics. Finally, we used cellular deconvolution to show that each tumor is composed of a unique mixture of cell populations resembling the un-induced mesenchyme, the cap mesenchyme, and the early epithelial structures of the fetal kidney. We anticipate that these methodologies will pave the way for more quantitative strategies for tumor stratification and classification.
Contribution of ultra-slow fMRI fluctuations in the 4th ventricle to our understanding of sleep

Wakefulness levels modulate estimates of functional connectivity (FC), and, if unaccounted for, can become a substantial confound in resting-state fMRI. Unfortunately, wakefulness is rarely monitored due to the need for additional concurrent recordings (e.g., eye tracking, EEG). Recent work has shown that strong fluctuations around 0.05Hz, hypothesized to be CSF inflow, appear in the fourth ventricle (FV) when subjects fall asleep, and that they correlate significantly with the global signal. The analysis of these fluctuations could provide an easy way to evaluate wakefulness in fMRI-only data and improve our understanding of FC during sleep. Here we evaluate this possibility using the 7T resting-state sample from the Human Connectome Project (HCP). Our results replicate the observation that forth ventricle ultra-slow fluctuations (~0.05Hz) with inflow-like characteristics (decreasing in intensity for successive slices) are present in scans during which subjects did not comply with instructions to keep their eyes open (i.e., drowsy scans). This is true despite the HCP data not being optimized for the detection of inflow-like effects. In addition, time-locked BOLD fluctuations of the same frequency could be detected in large portions of grey matter with a wide range of temporal delays and contribute in significant ways to our understanding of how FC changes during sleep. First, these ultra-slow fluctuations explain half of the increase in global signal that occurs during descent into sleep. Similarly, global shifts in FC between awake and sleep states are driven by changes in this slow frequency band. Second, they can influence estimates of inter-regional FC. For example, disconnection between frontal and posterior components of the Defulat Mode Network (DMN) typically reported during sleep were only detectable after regression of these ultra-slow fluctuations. Finally, we report that the temporal evolution of the power spectrum of these ultra-slow FV fluctuations can help us reproduce sample-level sleep patterns (e.g., a substantial number of subjects descending into sleep 3 minutes following scanning onset), partially rank scans according to overall drowsiness levels, and predict individual segments of elevated drowsiness (at 60 seconds resolution) with 71% accuracy.
Compared with unstructured usual care , early goal-directed therapy does not decrease mortality in patients with severe sepsis or septic shock

TUDY SELECTION nly randomized controlled trials f adults, comparing early goalirected therapy with usual care or ther strategies, were included. he primary outcome was ortality among patients with evere sepsis or septic shock. econdary outcomes included ength of ICU and inhospital stay, echanical ventilation support, asopressor and inotropic agent upport, and fluid administration nd RBC transfusion in the first 6 ours.
The Effects of Courtyards on the Thermal Performance of a Vernacular House in a Hot-Summer and Cold-Winter Climate

Achieving comfort in hot summer and cold winter (HSCW) climate zones can be challenging, since the climate is characterized by high temperatures in the summer and relatively colder temperatures in the winter. Courtyards, along with other semi-open spaces such as verandas and overhangs, play an important role in mitigating outdoor climate fluctuations. In this research, the effects of courtyards on the thermal performance of vernacular houses in HSCW climate zones were studied via field measurements and computational fluid dynamics (CFD) models. The selected courtyard house was a representative vernacular timber dwelling situated in the southeast of Chongqing, China. The indoor and outdoor air temperature measurements revealed that the courtyard did play an active role as a climatic buffer and significantly reduced the temperature’s peak value in the summer, while during the winter, the courtyard prevented the surrounding rooms from receiving direct solar radiation, and thus to some extent acted as a heat barrier. The contributions of thermal mass are quite limited in this area, due to insufficient solar radiation in winter and general building operations. The natural ventilation mechanism of courtyard houses in HSCW zones was further studied through CFD simulations. The selected opened courtyard was compared to an enclosed structure with similar building configurations. The airflow patterns driven by wind and buoyancy effects were first simulated separately, and then together, to illustrate the ventilation mechanisms. The simulation results show that the courtyard’s natural ventilation behavior benefited from the proper openings on ground level.
Remote Sensing of Coral Reefs: Uncertainty in the Detection of Benthic Cover, Depth, and Water Constituents Imposed by Sensor Noise

Coral reefs are biologically diverse and economically important ecosystems that are on the decline worldwide in response to direct human impacts and climate change. Ocean color remote sensing has proven to be an important tool in coral reef research and monitoring. Remote sensing data quality is driven by factors related to sensor design and environmental variability. This work explored the impact of sensor noise, defined as the signal to noise ratio (SNR), on the detection uncertainty of key coral reef ecological properties (bottom depth, benthic cover, and water quality) in the absence of environmental uncertainties. A radiative transfer model for a shallow reef environment was developed and Monte Carlo methods were employed to identify the range in environmental conditions that are spectrally indistinguishable from true conditions as a function of SNR. The spectrally averaged difference between remotely sensed radiance relative to sensor noise, ε, was used to quantify uncertainty in bottom depth, the fraction of benthic cover by coral, algae, and uncolonized sand, and the concentration of water constituents defined as chlorophyll, dissolved organic matter, and suspended calcite particles. Parameter uncertainty was found to increase with sensor noise (decreasing SNR) but the impact was non-linear. The rate of change in uncertainty per incremental change in SNR was greatest for SNR < 500 and increasing SNR further to 1000 resulted in only modest improvements. Parameter uncertainty was complicated by the bottom depth and benthic cover. Benthic cover uncertainty increased with bottom depth, but water constituent uncertainty changed inversely with bottom depth. Furthermore, water constituent uncertainty was impacted by the type of constituent material in relation to the type of benthic cover. Uncertainty associated with chlorophyll concentration and dissolved organic matter increased when the benthic cover was coral and/or benthic algae while uncertainty in the concentration of suspended calcite increased when the benthic cover was uncolonized sand. While the definition of an optimal SNR is subject to user needs, we propose that SNR of approximately 500 (relative to 5% Earth surface reflectance and a clear maritime atmosphere) is a reasonable engineering goal for a future satellite sensor to support research and management activities directed at coral reef ecology and, more generally, shallow aquatic ecosystems.
Satisfaction with childbirth care: Correlations between SERVICEQUAL dimensions

The model known as SERVICEQUAL (SQ) examines the correlation between service satisfaction and the gaps that occur between customers’ expectations prior to service and perceptions after being served. The gaps are tested over five dimensions: tangibles of the service, assurance, empathy, reliability, and responsiveness of the service provider. This paper aims to examine the satisfaction of women with childbirth care by exploring correlations between the gaps in the five SQ dimensions and testing the influence of each dimension on the others. Closed-ended questionnaires were used to evaluate satisfaction from SQ dimensions using 1-5 on Likert scale. This study adds to existing literature by offering an insight into the way mothers assess their birthing services by looking at their pre-procedure expectations compared to how they perceive performance post-delivery. The correlations between the gaps in the service’s dimensions were higher after birth than before birth. Significant correlations between the gaps themselves were seen in all five dimensions. The findings suggest that a successful child delivery reduces the mother's anxiety, such that if prior to birth, the five service dimensions exhibit no correlation, then after birth when the mother is less anxious, and her cognitive dissonance is reduced. Stronger correlations form between all five service dimensions. The significant correlations between all five dimensions suggest that receiving empathic treatment from the service provider causes the mother to be pleased with the tangibles, responsiveness, reliability, assurance of the medical staff.
Preventing identity theft

PurposeKnowledge-sharing (KS) for preventing identity theft has become a major challenge for organisations. The purpose of this paper is to fill a gap in the literature by investigating barriers to effective KS in preventing identity theft in online retail organisations.Design/methodology/approachA framework was proposed based on a reconceptualisation and extension of the KS enablers framework (Chong et al., 2011). A qualitative case study research method was used for the data collection. In total, 34 semi-structured interviews were conducted in three online retail organisations in the UK.FindingsThe findings suggest that the major barriers to effective KS for preventing identify theft in online retail organisations are: lack of leadership support; lack of employee willingness to share knowledge; lack of employee awareness of KS; inadequate learning opportunities; lack of trust in colleagues; insufficient information-sourcing opportunities and information and communications technology infrastructure; a weak KS culture; lack of feedback on performance; and lack of job rotation.Practical implicationsThe research provides solutions for removing existing barriers to KS in preventing identity theft. This is important to reduce the number of cases of identity theft in the UK.Originality/valueThis research extends knowledge of KS in a new context: preventing identity theft in online retail organisations. The proposed framework extends the KS enablers framework by identifying major barriers to KS in the context of preventing identity theft.
SHORT REPORT Impact of vanB vancomycin-resistant enterococcal bacteraemia analysed as a time-varying covariate on length of hospital stay

The impact of vanB vancomycin-resistant enterococci (VRE) bacteraemia on length of stay (LOS) in hospital, after adjusting for the time-varying nature of enterococcal bacteraemia (variable onset of bacteraemia post-admission), is unknown. Survival analyses (time-varying Cox and competing risks regression) were performed on vanB VRE bacteraemia patients, matched 1:1 with vancomycin-susceptible enterococci bacteraemia patients to determine the factors associated with LOS in these patients. In Cox regression analysis, vanB VRE bacteraemia, intensive-care-unit admission, Charlson co-morbidity index score 5 4, and an increase in the time to receive appropriate antibiotics were associated with prolonged LOS. Competing risks regression which accounts for the in ﬂ uence of in-patient mortality on the ability to observe the event discharge alive from hospital suggests that, vanB VRE bacteraemia was not signi ﬁ cantly associated with prolonged LOS. For the ﬁ rst time, the rate of discharge from hospital in patients with vanB VRE bacteraemia has been quanti ﬁ ed.
Baer sums and fibered aspects of Mal'cev operations

Le sens geometrique des axiomes des lois de Mal'cev est ici reaffirme de sorte que, dans le cas associatif, la classique action de groupe associee en decoule naturellement dans le cadre general des categories exactes au sens de Barr, lorsque le support est global. Cette action est definie par l'intermediaire d'un foncteur direction d que l'on montre etre une cofibration preservant les produits et l'objet final. On est alors dans la plaisante situation ou toute structure de groupe sur un objet X de la base determine canoniquement une structure monoidale fermee sur la fibre au-dessus de X. On retrouve ainsi de maniere conceptuelle la construction de Baer de la somme de deux extensions du groupe Q a noyaux abeliens determinant la meme structure de Q-module. Par ailleurs cette meme cofibration d permet de preciser le lien entre categories Naturellement Mal'cev et categories essentiellement affines. On precise enfin la structure de la direction lorsque le support n'est pas global.
Novel Design for Photonic Crystal Ring Resonators Based Optical Channel Drop Filter

(Received 21 Jun. 2018; Revised 17 Jul. 2018; Accepted 20 Aug. 2018; Published 15 Sep. 2018) Abstract: Photonic crystal ring resonators (PCRRs) are traditional structures for designing optical channel drop filters. In this paper, Photonic crystal channel drop filter (CDFs) with a new configuration of ring resonator is presented. The structure is made of a square lattice of silicon rods with the refractive index nsi=3. 4 which are perforated in air with refractive index nair=1. Calculations of band structure and propagation of electromagnetic field through devices are done by plane wave expansion (PWE) and finite difference time domain (FDTD) methods, respectively. The simulation shows, 100% dropping efficiency and suitable quality factor at 1592. 6 nm wavelength achieved for this filter. Also, in this paper, we investigate parameters which have an effect on resonant wavelength and transmission spectrum in this CDF, such as refractive index of inner rods and whole of dielectric rods of the structure. The proposed structure is small which is more suitable for used in the future photonic integrated circuits, wavelength division multiplexing (WDM) systems and optical communication network applications. Also, we suggested a heterostructure wavelength demultiplexer is composed of four ring resonators. These ring resonators are located in four different regions (heterostructure) which each region has specific dielectric constant.
The chain graph Markov property

A new class of graphs, chain graphs, suitable for modelling conditional independencies are introduced and their Markov properties investigated. This class of graphs, which includes the undirected and directed acyclic graphs, enables modelling recursive models with multivariate response variables. Results concerning the equivalence of different definitions of their Markov properties including a factorization of the density are shown. We give a necessary and sufficient condition for two chain graphs to have the same Markov properties
Learning with metric losses

We propose a practical algorithm for learning mappings between two metric spaces, X and Y . Our procedure is strongly Bayes-consistent whenever X and Y are topologically separable and Y is “bounded in expectation” (our term; the separability assumption can be somewhat weakened). At this level of generality, ours is the ﬁrst such learnability result for unbounded loss in the agnostic setting. Our technique is based on metric medoids (a variant of Fréchet means) and presents a signiﬁcant departure from existing methods, which, as we demonstrate, fail to achieve Bayes-consistency on general instance-and label-space metrics. Our proofs introduce the technique of semi-stable compression , which may be of independent interest.
Using field data–based large eddy simulation to understand role of atmospheric stability on energy production of wind turbines

A novel and a robust high-fidelity numerical methodology has been developed to realistically estimate the net energy production of full-scale horizontal axis wind turbines in a convective atmospheric boundary layer, for both isolated and multiple wind turbine arrays by accounting for the wake effects between them. Large eddy simulation has been used to understand the role of atmospheric stability in net energy production (annual energy production) of full-scale horizontal axis wind turbines placed in the convective atmospheric boundary layer. The simulations are performed during the convective conditions corresponding to the National Renewable Energy Laboratory field campaign of July 2015. A mathematical framework was developed to incorporate the field-based measurements as boundary conditions for the large eddy simulation by averaging the surface flux over multiple diurnal cycles. The objective of the study is to quantify the role of surface flux in the calculation of energy production for an isolated, two and three wind turbine configuration. The study compares the mean value, +1 standard deviation, and −1 standard deviation from the measured surface flux to demonstrate the role of surface heat flux. The uniqueness of the study is that power deficits from large eddy simulation were used to determine wake losses and obtain a net energy production that accounts for the wake losses. The frequency of stability events, from field measurements, is input into the calculation of an ensemble energy production prediction with wake losses for different wind turbine arrays. The increased surface heat flux increases the atmospheric turbulence into the wind turbines. Higher turbulence results in faster wake recovery by a factor of two. The faster wake recovery rates result in lowering the power deficits from 46% to 28% for the two-turbine array. The difference in net energy production between the +1 and −1 standard deviation (with respect to surface heat flux) simulations was 10% for the two-turbine array and 8% for the three-turbine array. An ensemble net energy production by accounting for the wake losses indicated the overestimation of annual energy production from current practices could be corrected by accounting for variation of surface flux from the mean value.
Detecting Baseline Platelet Hyperreactivity ( Prothrombotic Status ) and Cardiac Risk

This review is a critical evaluation of publications in the past decade on the usefulness of platelet function tests (PFTs) in clinical cardiology, in aiding diagnosis, predicting risk, and monitoring therapy. The ideal PFT should: 1) detect baseline platelet hyperreactivity; 2) allow individualization of antiplatelet medication; 3) predict thrombotic risk; and 4) predict bleeding risk. The practicalities of clinical cardiology demand rapid, accurate, and reliable tests that are simple to operate at the bedside and available 24 h a day, 7 days a week. Point-of-care PFTs most widely evaluated clinically include PFA-100 and VerifyNow. None of these tests can reliably detect platelet hyperreactivity and thus identify a prothrombotic state. Identification of antiplatelet nonresponsiveness or hyporesponsiveness is highly test specific, and does not allow individualization of therapy. The power of PFTs in predicting thrombotic events for a given individual is variable and often modest, and alteration of antithrombotic treatment on the basis of the results of PFTs has not been shown to alter clinical outcome. PFTs in current mainstream use cannot reliably assess bleeding risk. These tests have been in use for over a decade, but the hopes raised by PFTs in clinical practice remain unfulfilled. Although physiologically relevant measurement of platelet function now is more important than ever, a critical reappraisal of available techniques in light of clinical requirements is needed. The use of native blood, global stimulus instead of individual agonists, contribution of thrombin generation by activated platelets to the test results, and establishment of a PFT therapeutic range for each antiplatelet drug should be considered and is discussed. (J Am Coll Cardiol 2013;61:2115–29) © 2013 by the American College of Cardiology Foundation Published by Elsevier Inc. http://dx.doi. org/10.1016/j.jacc. 2012.11. 080
Theories of modified gravity and reconstruction schemes of cosmological models

ADVERTIMENT. La consulta d’aquesta tesi queda condicionada a l’acceptació de les següents condicions d'ús: La difusió d’aquesta tesi per mitjà del servei TDX (www.tdx.cat) i a través del Dipòsit Digital de la UB (diposit.ub.edu) ha estat autoritzada pels titulars dels drets de propietat intel·lectual únicament per a usos privats emmarcats en activitats d’investigació i docència. No s’autoritza la seva reproducció amb finalitats de lucre ni la seva difusió i posada a disposició des d’un lloc aliè al servei TDX ni al Dipòsit Digital de la UB. No s’autoritza la presentació del seu contingut en una finestra o marc aliè a TDX o al Dipòsit Digital de la UB (framing). Aquesta reserva de drets afecta tant al resum de presentació de la tesi com als seus continguts. En la utilització o cita de parts de la tesi és obligat indicar el nom de la persona autora.