Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysing blood from intraosseous access: a systematic review

Intraosseous (IO) access is used widely as an optional vascular route for critically ill patients. It is still unclear whether the IO access can be used as a source for emergency blood samples. The aim of this study was to systematically review the existing literature on the usability of IO blood samples for analysing the parameters relevant to emergency care. We performed a data search from the Medline and Embase databases, the Cochrane Library and the Clinical trials registry. Animal studies and studies with healthy and ill adults and children were included in the search. The data were collected and reported following the PRISMA guidelines. The PROSPERO database registration number of this review is CRD42017064194. We found 27 studies comparing the blood samples from the IO space with arterial or venous samples, but only three of them followed the recommended guidelines for method comparison studies. The study populations were heterogeneous, and the sample sizes were relatively small (14, 17 and 20 individuals) in the three studies. The results of specific laboratory parameters were scarce and discordant. The evidence on the agreement between IO and arterial and venous samples is still weak. Existing studies with healthy volunteers and animal models provide important insight into the analyses of IO samples, but more evidence, especially from haemodynamically unstable patients, is needed for wider implementation of IO blood sampling in critically ill patients.
Genetic Analysis of a Commercial Egg Laying Line Challenged With Newcastle Disease Virus

In low income countries, chickens play a vital role in daily life. They provide a critical source of protein through egg production and meat. Newcastle disease, caused by avian paramyxovirus type 1, has been ranked as the most devastating disease for scavenging chickens in Africa and Asia. High mortality among flocks infected with velogenic strains leads to a devastating loss of dietary protein and buying power for rural households. Improving the genetic resistance of chickens to Newcastle Disease virus (NDV), in addition to vaccination, is a practical target for improvement of poultry production in low income countries. Because response to NDV has a component of genetic control, it can be influenced through selective breeding. Adding genomic information to a breeding program can increase the amount of genetic progress per generation. In this study, we challenged a commercial egg-laying line with a lentogenic strain of NDV, measured phenotypic responses, collected genotypes, and associated genotypes with phenotypes. Collected phenotypes included viral load at 2 and 6 days post-infection (dpi), antibody levels pre-challenge and 10 dpi, and growth rates pre- and post-challenge. Six suggestive QTL associated with response to NDV and/or growth were identified, including novel and known QTL confirming previously reported associations with related traits. Additionally, previous RNA-seq analysis provided support for several of the genes located in or near the identified QTL. Considering the trend of negative genetic correlation between antibody and Newcastle Disease tolerance (growth under disease) and estimates of moderate to high heritability, we provide evidence that these NDV response traits can be influenced through selective breeding. Producing chickens that perform favorably in challenging environments will ultimately increase the supply of quality protein for human consumption.
Meta-analysis of genome-wide association studies for height and body mass index in ∼700,000 individuals of European ancestry

Genome-wide association studies (GWAS) stand as powerful experimental designs for identifying DNA variants associated with complex traits and diseases. In the past decade, both the number of such studies and their sample sizes have increased dramatically. Recent GWAS of height and body mass index (BMI) in ∼250,000 European participants have led to the discovery of ∼700 and ∼100 nearly independent SNPs associated with these traits, respectively. Here we combine summary statistics from those two studies with GWAS of height and BMI performed in ∼450,000 UK Biobank participants of European ancestry. Overall, our combined GWAS meta-analysis reaches N∼700,000 individuals and substantially increases the number of GWAS signals associated with these traits. We identified 3,290 and 716 near-independent SNPs associated with height and BMI, respectively (at a revised genome-wide significance threshold of p<1 × 10−8), including 1,185 height-associated SNPs and 554 BMI-associated SNPs located within loci not previously identified by these two GWAS. The genome-wide significant SNPs explain ∼24.6% of the variance of height and ∼5% of the variance of BMI in an independent sample from the Health and Retirement Study (HRS). Correlations between polygenic scores based upon these SNPs with actual height and BMI in HRS participants were 0.44 and 0.20, respectively. From analyses of integrating GWAS and eQTL data by Summary-data based Mendelian Randomization (SMR), we identified an enrichment of eQTLs amongst lead height and BMI signals, prioritisting 684 and 134 genes, respectively. Our study demonstrates that, as previously predicted, increasing GWAS sample sizes continues to deliver, by discovery of new loci, increasing prediction accuracy and providing additional data to achieve deeper insight into complex trait biology. All summary statistics are made available for follow up studies.
Syntree2Vec - An algorithm to augment syntactic hierarchy into word embeddings

Word embeddings aims to map sense of the words into a lower dimensional vector space in order to reason over them. Training embeddings on domain specific data helps express concepts more relevant to their use case but comes at a cost of accuracy when data is less. Our effort is to minimise this by infusing syntactic knowledge into the embeddings. We propose a graph based embedding algorithm inspired from node2vec. Experimental results have shown that our algorithm improves the syntactic strength and gives robust performance on meagre data.
IceBreaker: Solving Cold Start Problem for Video Recommendation Engines

Internet has brought about a tremendous increase in content of all forms and, in that, video content constitutes the major backbone of the total content being published as well as watched. Thus it becomes imperative for video recommendation engines to look for novel and innovative ways to recommend the newly added videos to their users. However, the problem with new videos is that they lack any sort of metadata and user interaction so as to be able to rate the videos for the consumers. To this effect, this paper introduces the several techniques we develop for the Content Based Video Relevance Prediction (CBVRP). We employ different architectures on the CBVRP dataset to make use of the provided frame and video level features and generate predictions of videos that are similar to the other videos. We also implement several ensemble strategies to explore complementarity between both the types of provided features. The obtained results are encouraging and will impel the boundaries of research for multimedia based video recommendation systems.
Randomized Least Squares Regression: Combining Model- and Algorithm-Induced Uncertainties

We analyze the uncertainties in the minimum norm solution of full-rank regression problems, arising from Gaussian linear models, computed by randomized (row-wise sampling and, more generally, sketching) algorithms. From a deterministic perspective, our structural perturbation bounds imply that least squares problems are less sensitive to multiplicative perturbations than to additive perturbations. From a probabilistic perspective, our expressions for the total expectation and variance with regard to both model- and algorithm-induced uncertainties, are exact, hold for general sketching matrices, and make no assumptions on the rank of the sketched matrix. The relative differences between the total bias and variance on the one hand, and the model bias and variance on the other hand, are governed by two factors: (i) the expected rank deficiency of the sketched matrix, and (ii) the expected difference between projectors associated with the original and the sketched problems. A simple example, based on uniform sampling with replacement, illustrates the statistical quantities.
Local risk perception enhances epidemic control

As infectious disease outbreaks emerge, public health agencies often enact vaccination and social distancing measures to slow transmission. Their success depends on not only strategies and resources, but also public adherence. Individual willingness to take precautions may be influenced by global factors, such as news media, or local factors, such as infected family members or friends. Here, we compare three modes of epidemiological decision-making in the midst of a growing outbreak using network-based mathematical models that capture plausible heterogeneity in human contact patterns. Individuals decide whether to adopt a recommended intervention based on overall disease prevalence, the proportion of social contacts infected, or the number of social contacts infected. While all strategies can substantially mitigate transmission, vaccinating (or self isolating) based on the number of infected acquaintances is expected to prevent the most infections while requiring the fewest intervention resources. Unlike the other strategies, it has a substantial herd effect, providing indirect protection to a large fraction of the population.
Distribution of Eg5 and TPX2 in mitosis: Insight from CRISPR tagged cells

The mitotic spindle is a dynamic bipolar structure that mediates chromosome segregation in mitosis. In most organisms, spindle formation requires the action of kinesin‐5 motor proteins that generate outward force on antiparallel microtubules to establish spindle bipolarity. Previous work has shown that Eg5 and TPX2, a spindle microtubule‐associated protein that suppresses Eg5 motor activity, are enriched on parallel microtubules near spindle poles. This distribution is inconsistent with the requirement for Eg5‐dependent force production during mitosis. To investigate this, we used CRISPR/Cas9 gene editing to tag Eg5 and TPX2 with EGFP and quantify protein distribution throughout mitosis. The results show that at metaphase both Eg5–EGFP and TPX2–EGFP are enriched toward spindle poles, but only TPX2–EGFP is enriched relative to microtubules. Eg5–EGFP and TPX2–EGFP show distinct localization patterns in anaphase, with Eg5–EGFP relocalizing to the midzone earlier than TPX2–EGFP. Analysis of spindles oriented at 90° to the coverslip confirmed that Eg5–EGFP was present on bridge microtubules in metaphase and anaphase; in contrast, TPX2 was not enriched, or enriched at later times, on these microtubules. Overall, TPX2 was present at 3.6X the level of Eg5 on the spindle and Eg5 was locally enriched at the prophase centrosome (~7×) compared to the whole cell. Our results show that using cells with fluorescent tags at the endogenous locus can provide novel insight into protein distribution during mitosis.
Systematizing Genome Privacy Research: A Privacy-Enhancing Technologies Perspective

Abstract Rapid advances in human genomics are enabling researchers to gain a better understanding of the role of the genome in our health and well-being, stimulating hope for more effective and cost efficient healthcare. However, this also prompts a number of security and privacy concerns stemming from the distinctive characteristics of genomic data. To address them, a new research community has emerged and produced a large number of publications and initiatives. In this paper, we rely on a structured methodology to contextualize and provide a critical analysis of the current knowledge on privacy-enhancing technologies used for testing, storing, and sharing genomic data, using a representative sample of the work published in the past decade. We identify and discuss limitations, technical challenges, and issues faced by the community, focusing in particular on those that are inherently tied to the nature of the problem and are harder for the community alone to address. Finally, we report on the importance and difficulty of the identified challenges based on an online survey of genome data privacy experts.
Masters of manipulation: Viral modulation of the immunological synapse

In order to thrive, viruses have evolved to manipulate host cell machinery for their own benefit. One major obstacle faced by pathogens is the immunological synapse. To enable efficient replication and latency in immune cells, viruses have developed a range of strategies to manipulate cellular processes involved in immunological synapse formation to evade immune detection and control T‐cell activation.
Prothrombotic markers in Thalassemia major patients: A paradigm shift.

BACKGROUND It is being increasingly recognised that thalassemia major patients, like intermedia, have increased propensity for thromboembolism. Deficiency of natural anticoagulants is more recently defined finding contributing to the hypercoagulable state. The aim this study is to determine natural anticoagulants levels and their correlation with maternal characteristics, haematological and biochemical markers. METHODS This is a prospective case-control study. We registered 80 patients and 60 healthy controls from Jan 2009 to Dec 2013. Complete blood counts, prothrombin time, activated partial thromboplastin time, protein C, protein S, antithrombin, serum ferritin, liver enzymes; HbsAg and Anti- HCV were evaluated. RESULT There were 42 males and 38 females with mean age of 12.30±5.50 years. The mean protein C, protein S and antithrombin in patients and control were 58.25±22.5 versus 110.67±22.60, 67.90±19.58 versus 98.70±21.54 and 89.73±18.09 versus 104.0±10.98 (p<0.001) respectively. Protein C was predominantly deficient in 65% followed by protein S and antithrombin in 35% and 20% respectively. Protein C deficiency divulged positive correlation with protein S deficiency (p = 0.035) and antithrombin deficiency with hemoglobin of ≤8gm% (p<0.0025). No significant correlation of prothrombotic markers was established with maternal characteristics, hepatic dysfunction, hepatitis and serum ferritin. CONCLUSION Substantial decrement in prothrombotic markers, primarily protein C, may be implicated in elevated thrombosis; however follow-up data is required to establish definitive thromboembolic events.
Nondegenerate multistationarity in small reaction networks

Much attention has been focused in recent years on the following algebraic problem arising from applications: which chemical reaction networks, when taken with mass-action kinetics, admit multiple positive steady states? The interest behind this question is in steady states that are stable. As a step toward this difficult question, here we address the question of multiple nondegenerate positive steady states. Mathematically, this asks whether certain families of parametrized, real, sparse polynomial systems ever admit multiple positive real roots that are simple. Our main results settle this problem for certain types of small networks, and our techniques point the way forward for larger networks.
Superior Capsular Release After Failed Combined Superior Labral Repair And Biceps Tenodesis For Slap Tear

Introduction: Optimal treatment of type II superior labrum anterior and posterior (SLAP) tears is controversial. There has been a recent trend towards biceps tenodesis over SLAP repair in older patients. Few surgeons have performed combined biceps tenodesis and SLAP repair with inferior results. Case Report: This case describes a 46-year-old patient who had persistent pain and stiffness after combined biceps tenodesis and SLAP repair for a type II SLAP tear. His pain and motion improved after arthroscopic superior capsular release. Conclusion: Failed SLAP repair is often multifactorial and a thorough workup is needed. Combined biceps tenodesis and SLAP repair can cause pain, stiffness, and dysfunction which can be successfully treated with arthroscopic superior capsular release.
You Do Not Mess with the Glia

Vertebrate neurons are enormously variable in morphology and distribution. While different glial cell types do exist, they are much less diverse than neurons. Over the last decade, we have conducted quantitative studies of the absolute numbers, densities, and proportions at which non-neuronal cells occur in relation to neurons. These studies have advanced the notion that glial cells are much more constrained than neurons in how much they can vary in both development and evolution. Recent evidence from studies on gene expression profiles that characterize glial cells—in the context of progressive epigenetic changes in chromatin during morphogenesis—supports the notion of constrained variation of glial cells in development and evolution, and points to the possibility that this constraint is related to the late differentiation of the various glial cell types. Whether restricted variation is a biological given (a simple consequence of late glial cell differentiation) or a physiological constraint (because, well, you do not mess with the glia without consequences that compromise brain function to the point of rendering those changes unviable), we predict that the restricted variation in size and distribution of glial cells has important consequences for neural tissue function that is aligned with their many fundamental roles being uncovered.
The GKR Protocol and Its Efficient Implementation

The goal in the lecture on LFKN’s #SAT protocol was to develop an interactive proof for an intractable problem (such as #SAT [LFKN92] or TQBF [Sha92]), in which the verifier ran in polynomial time. The perspective taken in this lecture is different: it acknowledges that there are no “real world” entities that can act as the prover in the #SAT and TQBF protocols of earlier lectures, since real world entities cannot solve large instances of PSPACE-complete problems in the worst case. We would really like a “scaled down” version of the TQBF protocol of [LFKN92,Sha92], one that is useful for problems that can be solved in the real world, such as problems in the complexity classes P, or NC (capturing problems solvable by efficient parallel algorithms), or even L (capturing problems solvable in logarithmic space). But what is the point of developing verification protocols for such easy problems? Can’t the verifier just ignore the prover and solve the problem without help? The answer is that this lecture will describe protocols in which the verifier runs much faster than would be possible without a prover. Specifically, V will run linear time, doing little more than just reading the input. Meanwhile, we will require that the prover not do much more than solve the problem of interest. Ideally, if the problem is solvable by a Random Access Machine or Turing Machine in time T and space s, we want the prover to run in time O(T ) and space O(s), or as close to it as possible. At a minimum, P should run in polynomial time. Can the TQBF and #SAT protocols of prior lectures be scaled down to yield protocols where the verifier runs in (quasi-)linear time for a “low” complexity class like L? It turns out that it can, but the prover is not efficient. Recall that in the TQBF protocol, V ran in time O(S), and P ran in time O(S · 2N), when applied to a Boolean formula φ of size S over N variables. In principle, this yields an interactive proof for any problem solvable in space s: given an input x ∈ {0,1}n, V first transforms x to an instance φ of TQBF (see, e.g., [AB09, Chapter 4] for a lucid exposition of this transformation, which is reminiscent of Savitch’s Theorem), and then applies the interactive proof for TQBF to φ . However, the transformation yields a TQBF instance φ over N = O(s · logT ) variables when applied to a problem solvable in time T and space s. This results in a prover that runs in time in time 2O(s·logT ). This is superpolynomial (i.e., nΘ(logn)), even if s = O(logn) and t = poly(n). Until 2007, this was the state of the art in interactive proofs.
Fitness of Selected Indigenous Saccharomyces cerevisiae Strains for White Piceno DOC Wines Production

Verdicchio, Passerina and Pecorino are native grape cultivars of the Marche region, cultivated in winemaking area of Ascoli Piceno, in central Italy. In particular, Passerina and Pecorino varieties have been abandoned and forgotten for a long time and only in recent years are rediscovered and appreciated. Here, two indigenous yeasts, isolated from grapes of Verdicchio and Pecorino varieties and identified as Saccharomyces cerevisiae, were evaluated and compared with commercial starters cultures widely used for the vinification of Piceno DOC (Denominazione Origine Controllata) area at industrial scale. A polyphasic approach, including yeast genotyping, phenotypic traits evaluation and fermentative performance in natural grape juice, was applied to evaluate the fitness of strains. Using interdelta primers, the two selected cultures showed a unique profile while the results of microvinifications showed that both indigenous strains exhibited good enological parameters and fermentative aptitude comparable with that shown by commercial strains used as controls. The profile of volatile compounds of wines of indigenous strains was characterized by a significant high production of isoamyl acetate and ethyl esters at 22 °C and phenyl ethyl acetate at 16 °C. Overall results indicate that the two indigenous selected yeasts showed a genetic and phenotypic specificity and they could be profitably used to characterize the Piceno DOC area wines.
Management of Withdrawal Risk Through Optimal Life Cycle Asset Allocation

1 Retirees who do not have defined benefit pension plans typically must fund spending from 2 accumulated savings. This leads to the risk of depleting these savings, i.e. withdrawal risk. 3 We analyze this risk through full life cycle optimal dynamic asset allocation, including the 4 accumulation and decumulation phases. We pose the asset allocation strategy as a problem in 5 optimal stochastic control. Various possible objective functions are tested and compared using 6 metrics such as the probability of portfolio depletion, the median of the remaining portfolio 7 value, and conditional value at risk (CVAR). The control problem is solved using a Hamilton8 Jacobi-Bellman formulation, based on a parametric model of the underlying stochastic processes 9 and a variety of objective functions. Monte Carlo simulations which use the optimal controls 10 are presented to evaluate the performance metrics. These simulations are based on both the 11 parametric model and bootstrap resampling of 91 years of historical data. Based primarily on 12 the resampling tests, we conclude that target-based approaches which seek to establish a safety 13 buffer of wealth at the end of the decumulation period appear to be superior to strategies which 14 directly attempt to minimize risk measures such as the probability of portfolio depletion. 15
Why did chemical engineering emerge in America instead of Germany ?

As a scientific productive activity, engineering associates closely with natural science on the one hand and industry on the other. The America’s industrial structures and academic institutions influenced the emergence of chemical engineering. The science-oriented characteristic of chemical engineering in turn affected the development of industrial structures, especially the rapid rise of a competitive petrochemical industry.