Miracle-dz/UniFAR-FTUs huggingface dataset:
Ultrasonic histotripsy for cell therapy

Liver transplantation is the mainstay of the treatment for end stage liver diseases including metabolic and congenital liver diseases. The number of suitable donor organs is, however, limited. Intra-portal hepatocytes transplantation has been considered as a bridging therapy to liver transplantation but has shown a mixed clinical outcome with limited success including low level of engraftment of transplanted hepatocytes. To enhance the level of cell engraftment, this thesis introduces an alternative and novel approach to traditional intra-portal cell therapy mediated by High Intensity Focused Ultrasound (HIFU) histotripsy. The proposed novel strategy is to create damage to the recipient liver by producing a number of cavities inside the liver parenchyma through histotripsy and then delivering donor hepatocytes into the cavities. The aim of histotripsy is to mechanically fractionate soft tissue as an alternative to thermal ablation for therapeutic applications. While a number of studies have demonstrated the efficacy of histotripsy for fractionating solid tumours, the exact mechanisms underpinning this phenomenon are poorly understood. The main objectives of this thesis are to (a) investigate the major mechanisms involved in histotripsy and (b) demonstrate the feasibility of the proposed new cell therapy. A high-speed camera with a passive cavitation detection (PCD) system were used to observe the dynamics of bubbles produced in optically transparent tissue phantoms exposed to HIFU fields. Numerical studies on the bubble dynamics and both ex- and in vivo liver experiments were conducted with histological and serological analyses. Boiling bubbles were generated in a localised super-heated region and cavitation clouds were subsequently induced ahead of the expanding bubble. This process was repeated with HIFU pulses and eventually resulted in a tadpole shaped lesion. The in vivo experimental results together with histological observations showed that direct injection of cells inside the cavity facilitated successful uptake, proliferation and integration of the transplanted hepatocytes in the recipient liver. A week after the transplantation, the plasma albumin level was partially restored to 50% of the normal level in Nagase analbuminemic rats (serum albumin level was initially nil) by cell therapy after HIFU histotripsy. This novel method of intra-hepatic hepatocyte transplantation might be an invaluable tool for cell therapy in the future.
Current situation and perspectives regarding human Chagas disease in midwestern of the state of Minas Gerais, Brazil

Recognising the importance of Chagas disease in Brazil, Bambuí set up epidemiological surveillance for Chagas disease in 1974 and was the first municipality to do so. To ascertain the current epidemiology of Chagas disease in this municipality, 1.782 blood samples from the general population were analysed; 7.7% of samples were found to be seropositive for Chagas disease. A strong positive correlation between increasing age and Chagas disease was evident in both genders, with the highest prevalence in individuals aged over 60 years. Clinically, the cardiodigestive form of Chagas disease was the most common in these samples. These data confirm the interruption of Trypanosoma cruzi transmission, in parallel with a still important residual morbidity of Chagas disease in the county, thus supporting political decisions that will prioritise epidemiological surveillance and medical treatment of Chagas disease in the coming years.
An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population

Because of their high variability, microsatellites are still considered the marker of choice for studies on parentage and kinship in wild populations. Nevertheless, single nucleotide polymorphisms (SNPs) are becoming increasing popular in many areas of molecular ecology, owing to their high‐throughput, easy transferability between laboratories and low genotyping error. An ongoing discussion concerns the relative power of SNPs compared to microsatellites—that is, how many SNP loci are needed to replace a panel of microsatellites? Here, we evaluate the assignment power of 80 SNPs (HE = 0.30, 80 independent alleles) and 11 microsatellites (HE = 0.85, 192 independent alleles) in a wild population of about 400 sockeye salmon with two commonly used software packages (Cervus3, Colony2) and, for SNPs only, a newly developed software (SNPPIT). Assignment success was higher for SNPs than for microsatellites, especially for parent pairs, irrespective of the method used. Colony2 assigned a larger proportion of offspring to at least one parent than the other methods, although Cervus and SNPPIT detected more parent pairs. Identification of full‐sib groups without parental information from relatedness measures was possible using both marker systems, although explicit reconstruction of such groups in Colony2 was impossible for SNPs because of computation time. Our results confirm the applicability of SNPs for parentage analyses and refute the predictability of assignment success from the number of independent alleles.
Robust detection of comment spam using entropy rate

In this work, we design a method for blog comment spam detection using the assumption that spam is any kind of uninformative content. To measure the "informativeness" of a set of blog comments, we construct a language and tokenization independent metric which we call content complexity, providing a normalized answer to the informal question "how much information does this text contain? " We leverage this metric to create a small set of features well-adjusted to comment spam detection by computing the content complexity over groupings of messages sharing the same author, the same sender IP, the same included links, etc. We evaluate our method against an exact set of tens of millions of comments collected over a four months period and containing a variety of websites, including blogs and news sites. The data was provided to us with an initial spam labeling from an industry competitive source. Nevertheless the initial spam labeling had unknown performance characteristics. To train a logistic regression on this dataset using our features, we derive a simple mislabeling tolerant logistic regression algorithm based on expectation-maximization, which we show generally outperforms the plain version in precision-recall space. By using a parsimonious hand-labeling strategy, we show that our method can operate at an arbitrary high precision level, and that it significantly dominates, both in terms of precision and recall, the original labeling, despite being trained on it alone. The content complexity metric, the use of a noise-tolerant logistic regression and the evaluation methodology are thus the three central contributions with this work.
Cortical Lead Fields of Electroencephalographic and Magnetoencephalographic Sensors

The spatial relationship of electroencephalography (EEG) and magnetoencephalography (MEG) to brain activation is quantified as their cortical lead fields: the sensitivity of each sensor to activation of each cortical location. Here we map the lead fields of EEG and MEG across the cortical surface using a realistic boundary element model with four compartments. These calculations demonstrate that inclusion of CSF is essential for accurate calculation of EEG lead fields. The typical referential EEG derivation is affected by activity in all lobes of both hemispheres, while the typical MEG planar gradiometer is sensitive to part of one lobe. The proportion of cortical dipoles that have an effect on the average sensor that is ≥25% of the most effective dipole, is ~40% for referential EEG and <2% for MEG gradiometers. Gradiometers are substantially more focal than magnetometers and both are typically more focal than EEG. These findings indicate that gradiometer signals usually arise from the underlying cortex and that their coherence can often be inferred to reflect neural interaction rather than overlapping lead fields; such inferences are unwarranted for referential EEG. Quantitative differences between EEG and MEG lead fields may give rise to qualitative differences in the neural systems that they record.
Viewpoint: Paradoxical excess mortality in the PLATO trial should be independently verified

Summary The PLATO trial revealed excess all-cause (4.5%) and vascular (4.0%) mortality after experimental pyrimidine, ticagrelor, and even higher death rates (5.9% and 5.1%, respectively) after clopidogrel, which have never been seen in any previous acute coronary syndrome (ACS) trial. The Food and Drug Administration (FDA) conducted, and recently released the ticagrelor review outlining some paradoxical mortality patterns in PLATO, including the existence of alive patient, who initially was reported dead. The drug was recently approved in Europe, but repeatedly delayed in the USA. The objective of this viewpoint article was to evaluate extremely high death rates in PLATO by scrutinising FDA-released evidence, and comparing mortality patterns in recent ACS trials. These data were first presented as the analytical report submitted to the FDA on October 26, 2010. The available evidence suggest that mortality rates in PLATO, so as death benefit of ticagrelor over clopidogrel are extreme, despite incomplete follow-up, short duration of the trial, frequent preloading with clopidogrel, and gross mismatch between conventional average myocardial infarction rates but disproportionally frequent vascular fatalities, and heavily imbalanced sepsis-related deaths. In contrast to the overall PLATO results, the deaths rates in the USA were much lower (3.2% vs. 3.8%) not only favouring clopidogrel, but more importanly matching very well with identical rates in TRITON (3.2%), and one-year ACUITY (3.6%-3.9%) fatalities. Since the «play of chance» cannot explain these discrepancies due to excess death rates in both PLATO arms, and considering that study sponsor self-monitored sites in most countries, but not in the USA, the mortality data are questionable, and should be independently virified. It was concluded that excess mortality rates and delayed timing of the benefit onset in PLATO do not match with any recent ACS trial, and do not look natural. Reevaluation of the survival, especially driven from the several high-volume sponsor monitored sites in Eastern Europe may reveal discrepancies between those reported in PLATO and actual vital records. Future practice of self monitoring in pivotal indication-seeking clinical trials should be completely banned.
Factors and measurement of mental illness stigma: a psychometric examination of the Attribution Questionnaire.

OBJECTIVE A number of scales are employed to measure mental illness stigma, but many fail to have documented or adequate psychometric properties. The purpose of this study was to further evaluate the psychometric properties of one such measure, the Attribution Questionnaire (AQ). METHODS Based on responses from 774 college students, exploratory factor analyses were conducted followed by an examination of the reliability and validity of the newly formed factor scales. RESULTS A six-factor structure emerged and four of these factor scales (Fear/Dangerousness, Help/Interact, Forcing Treatment, and Negative Emotions) had acceptable internal consistency, test-retest reliability, and convergent validity with other stigma measures. CONCLUSIONS Twenty items from the AQ provide reliable and valid measurement of four important aspects of stigmatizing attitudes/beliefs towards the mentally ill. Accurate measurement of these attitudes/beliefs will be critical to more fully understanding the stigma process and developing effective strategies to address stigma.
High dimensional feature reduction via projection pursuit

The recent development of more sophisticated remote sensing systems enables the measurement of radiation in many more spectral intervals than previously possible. An example of that technology is the AVIRIS system, which collects image data in 220 bands. As a result of this, new algorithms must be developed in order to analyze the more complex data effectively. Data in a high dimensional space presents a substantial challenge, since intuitive concepts valid in a 2-3 dimensional space do not necessarily apply in higher dimensional spaces. For example, high dimensional space is mostly empty. This results from the concentration of data in the corners of hypercubes. Other examples may be cited. Such observations suggest the need to project data to a subspace of a much lower dimension on a problem specific basis in such a manner that information is not lost. Projection pursuit is a technique that will accomplish such a goal. Since it processes data in lower dimensions, it should avoid many of the difficulties of high dimensional spaces. The authors investigate some of the properties of projection pursuit. <<ETX>>
Severe skeletal Class II Division 1 malocclusion in postpubertal girl treated using Forsus with miniplate anchorage

This case report outlines the treatment of a 17-year-old female with Class II Division 1 malocclusion with mandibular retrusion, deep bite, and convex facial profile. The Forsus fatigue resistance device with miniplate was used for this patient and it was very affecting tool in correcting both skeletal and dental parameters. The total active treatment time was 19 months. This method can serve as an alternate choice of treatment, especially those who refuse orthognathic surgery. Hence, Forsus with miniplate might be useful in both growing and postpubertal patients.
Towards Linkset Quality for ComplementingSKOS Thesauri

Linked Data is largely adopted to share and make data more accessible on the web. A quite impressive number of datasets has been exposed and interlinked according to the Linked Data paradigm but the quality of these datasets is still a big challenge in the consuming process. Measures for quality of linked data datasets have been proposed, mainly by adapting concepts defined in the research field of information systems. However, very limited attention has been dedicated to the quality of linksets, the result of which might be important as dataset’s quality in consuming data coming from distinct sources. In this paper, we address linkset quality proposing the linkset importing, a novel measure which estimates the completeness of dataset obtained by complementing SKOS thesauri with their skos:exactMatch-related information. We validate the proposed measure with an in-house developed synthetic benchmark: experiments demonstrate that our measure may be adopted as a predictor of the gain that is obtained when complementing thesauri.
Predictive Score Model for Delayed Graft Function Based on Easily Available Variables before Kidney Donation after Cardiac Death

Background: How to evaluate the quality of donation after cardiac death (DCD) kidneys has become a critical problem in kidney transplantation in China. Hence, the aim of this study was to develop a simple donor risk score model to evaluate the quality of DCD kidneys before DCD. Methods: A total of 543 qualified kidneys were randomized in a 2:1 manner to create the development and validation cohorts. The donor variables in the development cohort were considered as candidate univariate predictors of delayed graft function (DGF). Multivariate logistic regression was then used to identify independent predictors of DGF with P < 0.05. Date from validation cohort were used to validate the donor scoring model. Results: Based on the odds ratios, eight identified variables were assigned a weighted integer; the sum of the integer was the total risk score for each kidney. The donor risk score, ranging from 0 to 28, demonstrated good discriminative power with a C-statistic of 0.790. Similar results were obtained from validation cohort with C-statistic of 0.783. Based on the obtained frequencies of DGF in relation to different risk scores, we formed four risk categories of increasing severity (scores 0–4, 5–9, 10–14, and 15–28). Conclusions: The scoring model might be a good noninvasive tool for assessing the quality of DCD kidneys before donation and potentially useful for physicians to make optimal decisions about donor organ offers.
Heisenbugs and Bohrbugs: Why Are They Different?

Jim Gray proposed a classification of bugs based on the type of failures they induce. Bohrbugs are bugs which always cause a failure when a particular operation is performed. Heisenbugs are bugs which may or may not cause a fault for a given operation. It has often been questioned as to whether these two bug categories are the same or different. The main reason for the argument is that if everything is the same, a bug should resurface and then by definition a Heisen-bug should be the same as a Bohrbug. We take the position that Heisenbugs and Bohrbugs are different types of bugs. As argument , we try to clarify the definition of Heisen-bugs and Bohrbugs and explain what an " operation " really means in context of the definitions. Although Heisenbugs could resurface if the conditions which lead to the failure reappear, we show that it is very difficult to recreate the conditions which existed when the fault first happened. After giving evidence in our favor, we explain how to debug software systems in the presence of Heisenbugs.
MODOMICS: a database of RNA modification pathways. 2017 update

Abstract MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. In the current database version, we included the following new features and data: extended mass spectrometry and liquid chromatography data for modified nucleosides; links between human tRNA sequences and MINTbase - a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments; new, machine-friendly system of unified abbreviations for modified nucleoside names; sets of modified tRNA sequences for two bacterial species, updated collection of mammalian tRNA modifications, 19 newly identified modified ribonucleosides and 66 functionally characterized proteins involved in RNA modification. Data from MODOMICS have been linked to the RNAcentral database of RNA sequences. MODOMICS is available at http://modomics.genesilico. pl.
Nonresonant and Resonant Frequency-Selectable Induction-Heating Targets

This paper examines a scheme for developing frequency-selectable induction-heating targets for stimulating temperature-sensitive polymer gels. The phrase “frequency selectable” implies that each target has a frequency at which it heats preferentially in the presence of other targets. Targets using both nonresonant and resonant designs are discussed. In the case of nonresonant targets, single-turn conductors whose critical dimensions are small compared to their associated skin depth (over the frequency range of interest) are examined. One way to achieve frequency selectivity with these nonresonant targets is by designing each to have the same self-inductance while forcing the resistance of each target to differ from the previous one by a specified factor (α). In this way, a target driven at its R/L break-point frequency will heat by at least a factor of (α2 + 1)/(2 α) more than the remaining targets. In the resonant-target case, RLC circuits that are inductively coupled to a primary induction coil are examined. Frequency selectivity in resonant targets is achieved by designing each target to have a different resonant frequency. When such a target is driven at its resonant frequency, it will heat preferentially compared to the remaining targets.
H2S removal from biogas using bioreactors: a review

This review aims to provide an overview of the bioprocesses used for the removal of H2S from biogas. The ability of aerobic and anoxic bioreactors (biotrickling filters, bioscrubbers, and a combination of chemical scrubbers and bioreactors) to perform the degradation of H2S is considered. For each operating mode (aerobic and anoxic), the bioprocesses are presented, the operating conditions affecting performance are summarized, the state of the art of research studies is described and commercial applications are given. At laboratory-scale, whatever their operating mode, biological processes are effective for biogas cleaning and provide the same performance. The clogging of the packed bed due to the deposit of elemental sulfur S and biomass accumulation clearly represents the main drawback of bioprocesses. Although elimination capacities (EC) determined at laboratory-scale can be very high, EC should not be higher than 90 g m h at industrial-scale in order to limit clogging effects. For aerobic processes, the need to control the oxygen mass transfer accurately remains a key issue for their development at full-scale. As a result, the aerobic processes alone are probably not the most suitable bioprocesses for the treatment of biogas highly loaded with H2S. For anaerobic bioprocesses using nitrate as an electron acceptor, the scale-up of the laboratory process to a full-size plant remains a challenge. However, the use of wastewater from treatment plants, which constitutes a cheap source of nitrates, represents an interesting opportunity for the development of innovative bioprocesses enabling the simultaneous removal of H2S and nitrates. Copyright © 2015 International Energy and Environment Foundation All rights reserved.
'More of an Art than a Science': Supporting the Creation of Playlists and Mixes

This paper presents an analysis of how people construct playlists and mixes. Interviews with practitioners and postings made to a web site are analyzed using a grounded theory approach to extract themes and categorizations. The information sought is often encapsulated as music information retrieval tasks, albeit not as the traditional “known item search” paradigm. The collated data is analyzed and trends identified and discussed in relation to music information retrieval algorithms that could help support such activity.
Steroidogenic Factor 1 in the Ventromedial Nucleus of the Hypothalamus Regulates Age-Dependent Obesity

The ventromedial nucleus of the hypothalamus (VMH) is important for the regulation of whole body energy homeostasis and lesions in the VMH are reported to result in massive weight gain. The nuclear receptor steroidogenic factor 1 (SF-1) is a known VMH marker as it is exclusively expressed in the VMH region of the brain. SF-1 plays a critical role not only in the development of VMH but also in its physiological functions. In this study, we generated prenatal VMH-specific SF-1 KO mice and investigated age-dependent energy homeostasis regulation by SF-1. Deletion of SF-1 in the VMH resulted in dysregulated insulin and leptin homeostasis and late onset obesity due to increased food intake under normal chow and high fat diet conditions. In addition, SF-1 ablation was accompanied by a marked reduction in energy expenditure and physical activity and this effect was significantly pronounced in the aged mice. Taken together, our data indicates that SF-1 is a key component in the VMH-mediated regulation of energy homeostasis and implies that SF-1 plays a protective role against metabolic stressors including aging and high fat diet.