Miracle-dz/UniFAR-FTUs huggingface dataset:
A de novo splice donor mutation in the thrombopoietin gene causes hereditary thrombocythemia in a Polish family

Familial thrombocytosis may be associated with gain-of-function mutations in the thrombopoietin (THPO) gene, or an activating germline mutation of MPL, the gene encoding thrombopoietin receptor. This study of a large family with thrombocytosis associated with a germline THPO mutations illustrates the hematologic and clinical features of this rare condition. See related article on page 646. Background Hereditary thrombocythemia is an autosomal dominant disorder with clinical features resembling sporadic essential thrombocythemia. Germline mutations in families with hereditary thrombocythemia have been identified in the gene for thrombopoietin (TPHO) and its receptor, MPL. Design and Methods Here we characterized a THPO mutation in a hereditary thrombocythemia pedigree with 11 affected family members. Results Affected family members carry a G → C transversion in the splice donor of intron 3 of THPO that co-segregated with thrombocytosis within the pedigree. We previously described the identical mutation in a Dutch family with hereditary thrombocythemia. Haplotype analysis using single nucleotide polymorphisms surrounding the mutation indicated that the mutations arose independently in the two families. MPL protein levels, but not mRNA levels, were low in platelets from affected family members. Bone marrow histology showed features compatible with those of essential thrombocythemia, but the megakaryocytes were unusually compact, as assessed by planimetric analysis. Impaired microcirculation resulting in brief episodes of fainting and dizziness that responded well to aspirin were the predominant clinical features in a total of 23 affected family members studied. Disease onset is earlier in patients with hereditary thrombocythemia than in those with essential thrombocythemia, but the frequencies of thrombotic, vascular and hemorrhagic events are similar in the two groups. Conclusions A mutation in THPO occurred de novo in the same position as in a previously described family with hereditary thrombocythemia. Patients with this mutation have elevated serum levels of thrombopoietin and a phenotype that responds to aspirin and does not require cytoreductive treatment.
Predicting the Responses of Soil Nitrite-Oxidizers to Multi-Factorial Global Change: A Trait-Based Approach

Soil microbial diversity is huge and a few grams of soil contain more bacterial taxa than there are bird species on Earth. This high diversity often makes predicting the responses of soil bacteria to environmental change intractable and restricts our capacity to predict the responses of soil functions to global change. Here, using a long-term field experiment in a California grassland, we studied the main and interactive effects of three global change factors (increased atmospheric CO2 concentration, precipitation and nitrogen addition, and all their factorial combinations, based on global change scenarios for central California) on the potential activity, abundance and dominant taxa of soil nitrite-oxidizing bacteria (NOB). Using a trait-based model, we then tested whether categorizing NOB into a few functional groups unified by physiological traits enables understanding and predicting how soil NOB respond to global environmental change. Contrasted responses to global change treatments were observed between three main NOB functional types. In particular, putatively mixotrophic Nitrobacter, rare under most treatments, became dominant under the ‘High CO2+Nitrogen+Precipitation’ treatment. The mechanistic trait-based model, which simulated ecological niches of NOB types consistent with previous ecophysiological reports, helped predicting the observed effects of global change on NOB and elucidating the underlying biotic and abiotic controls. Our results are a starting point for representing the overwhelming diversity of soil bacteria by a few functional types that can be incorporated into models of terrestrial ecosystems and biogeochemical processes.
Total Recall: Blue Sky on Mars

There are presently plans to create permanent colonies on Mars so that humanity will have a second home. These colonists will need search, email, entertainment, and indeed most services provided on the modern web. The primary challenge is network latencies, since the two planets are anywhere from 4 to 24 light minutes apart. A recent article sketches out how we might develop search technologies for Mars based on physically transporting a cache of the web to Mars, to which updates are applied via predictive models. Within this general framework, we explore the problem of high-recall retrieval, such as conducting a scientific survey. We explore simple techniques for masking speed-of-light delays and find that "priming" the search process with a small Martian cache is sufficient to mask a moderate amount of network latency. Simulation experiments show that it is possible to engineer high-recall search from Mars to be quite similar to the experience on Earth.
Dynamical Sparse Recovery With Finite-Time Convergence

Even though sparse recovery (SR) has been successfully applied in a wide range of research communities, there still exists a barrier to real applications because of the inefficiency of the state-of-the-art algorithms. In this paper, we propose a dynamical approach to SR, which is highly efficient and with finite-time convergence property. First, instead of solving the $\ell _1$ regularized optimization programs that requires exhausting iterations, which is computer-oriented, the solution to SR problem in this paper is resolved through the evolution of a continuous dynamical system which can be realized by analog circuits. Moreover, the proposed dynamical system is proved to have the finite-time convergence property, and thus more efficient than locally competitive algorithm (LCA) (the recently developed dynamical system to solve SR) with exponential convergence property. Consequently, our proposed dynamical system is more appropriate than LCA to deal with the time-varying situations. Simulations are carried out to demonstrate the superior properties of our proposed system.
Nonparametric Tree Graphical Models via Kernel Embeddings

We introduce a nonparametric representation for graphical model on trees which expresses marginals as Hilbert space embeddings and conditionals as embedding operators. This formulation allows us to dene a graphical model solely on the basis of the feature space representation of its variables. Thus, this nonparametric model can be applied to general domains where kernels are dened, handling challenging cases such as discrete variables with huge domains, or very complex, non-Gaussian continuous distributions. We also derive kernel belief propagation, a Hilbert-space algorithm for performing inference in our model. We show that our method outperforms state-of-the-art techniques in a cross-lingual document retrieval task and a camera rotation estimation problem.
J-shaped curves.

Antihypertensive treatment trials with more than 14,000 treated patients have indicated a J- or U-shaped relationship between achieved blood pressure (BP) and coronary heart disease (CHD) risk. However, similar studies involving more than 16,000 treated patients have not found such a relationship, only a rather flat response. Analysis bias may partly be responsible for the different results, but the findings of a non-linear relationship do appear to be significant in several of the studies. Pre-existing myocardial ischaemia (with or without symptoms) may explain some of the cases with increased CHD risk at low BP levels, but not others, However, myocardial ischaemia may still be a cause of the increased risk when BP is excessively lowered due to reduced myocardial autoregulatory reserve. In the long term it would appear reasonable to 'normalise' the BP as much as is possible. However, the question is whether a more gradual reduction would be advisable in some cases. As yet we do not know in which patients this would be so, hence at present no change of treatment practices are recommended.
Extracting refrained phrases from music signals using a frequent episode pattern mining algorithm

In this paper, we discuss a method for extracting refrained phrases from a music signal by a discrete knowledge discovery processing approach instead of a signal processing approach. The proposed method consists of two processes: translating a music signal into a sequence of events that represent pitch information, and then mining the frequent patterns from the event sequences. The former is performed by computing chroma vectors at every beat interval, and the latter is performed by enumerating the frequent episode patterns. We carried out a preliminary experiment on some pieces in the RWC music databases to examine if the extracted patterns represent the refrained phrases.
VS-ISA: A Video Specific Instruction Set Architecture for ASIP Design

This paper describes a novel video specific instruction set architecture for ASIP design. With SIMD (Single Instruction Multiple Data) instructions, and video specific instructions, an instruction set architecture is introduced to enhance the performance for video applications. Furthermore, we quantify the improvement on H.263 encoding. In this paper, we evaluate and compare the performance of VS ISA (Video Specific Instruction Set Architecture), other DSPs (digital signal processors) and conventional SIMD media extensions in the context of video coding. Our evaluation results show that VS ISA improves the processor¿s performance by approximate 5x on H.263 encoding, and VS ISA outperforms other architectures by 1.6x to 8.57x in computing IDCT.
Market-Based Resource Management for Cognitive Radios Using Machine Learning

With the growth in wireless network technologies and the emergence of cognitive radios, the need arises for mechanisms to effectively manage the resources involved in such environments. In this paper, we propose a market-based resource management approach for cognitive radios using machine learning, consisting of a negotiation phase where nodes are allocated resources in order to meet their requested bit rate, and a learning phase where nodes adjust their pricing of the resources in order to steer the cognitive radio environment towards the greater network good. We are interested in improving the utilization of the resources through price adjustments as compared to the case where the prices are kept fixed. We perform extensive simulations to study the performance of the proposed resource management mechanism in the cognitive radio environment.
An object based motion method for video coding

In order to improve efficiency of video coding, temporal redundancy between neighboring frames can be reduced. In MPEG-2, some frames, named interframes, are predicted using a motion estimation based on the conservation of intensity over time. In the new standard MPEG-4, frames are separated into several objects that are transmitted separately. Therefore, the prediction has to be performed on objects instead of frames. So, interframe-objects have to be predicted in order to improve video coding efficiency. The goal of this paper is to propose a new method for object-based prediction using the level sets. First, we propose an efficient object-based motion estimation. The motion of the objects is estimated by assuming the conservation of the level sets function over time, instead of the conservation of the intensity. Secondly, the estimation of the object motion between two frames is used to predict interframe-objects using both forward and backward motion estimations. The method is evaluated on real sequences, illustrating the potential of our approach for an object-based prediction of interframes.
Circulating Plasma Extracellular Microvesicle MicroRNA Cargo and Endothelial Dysfunction in Children with Obstructive Sleep Apnea.

RATIONALE Obese children are at increased risk for developing obstructive sleep apnea (OSA), and both of these conditions are associated with an increased risk for endothelial dysfunction (ED) in children, an early risk factor for atherosclerosis and cardiovascular disease. Although weight loss and treatment of OSA by adenotonsillectomy improve endothelial function, not every obese child or child with OSA develops ED. Exosomes are circulating extracellular vesicles containing functional mRNA and microRNA (miRNA) that can be delivered to other cells, such as endothelial cells. OBJECTIVES To investigate whether circulating exosomal miRNAs of children with OSA differentiate based on endothelial functional status. METHODS Obese children (body mass index z score >1.65) and nonobese children were recruited and underwent polysomnographic testing (PSG), and fasting endothelial function measurements and blood draws in the morning after PSG. Plasma exosomes were isolated from all subjects. Isolated exosomes were then incubated with confluent endothelial cell monolayer cultures. Electric cell-substrate impedance sensing systems were used to determine the ability of exosomes to disrupt the intercellular barrier formed by confluent endothelial cells. In addition, immunofluorescent assessments of zonula occludens-1 tight junction protein cellular distribution were conducted to examine endothelial barrier dysfunction. miRNA and mRNA arrays were also applied to exosomes and endothelial cells, and miRNA inhibitors and mimics were transfected for mechanistic assays. MEASUREMENTS AND MAIN RESULTS Plasma exosomes isolated from either obese children or nonobese children with OSA were primarily derived from endothelial cell sources and recapitulated ED, or its absence, in naive human endothelial cells and also in vivo when injected into mice. Microarrays identified a restricted signature of exosomal miRNAs that readily distinguished ED from normal endothelial function. Among the miRNAs, expression of exosomal miRNA-630 was reduced in children with ED and normalized after therapy along with restoration of endothelial function. Conversely, transfection of exosomes from subjects without ED with an miRNA-630 inhibitor induces the ED functional phenotype. Gene target discovery experiments further revealed that miRNA-630 regulates 416 gene targets in endothelial cells that include the Nrf2, AMP kinase, and tight junction pathways. CONCLUSIONS These observations elucidate a novel role of exosomal miRNA-360 as a putative key mediator of vascular function and cardiovascular disease risk in children with underlying OSA and/or obesity, and identify therapeutic targets.
Immuno-Positron Emission Tomography with Zirconium-89-Labeled Monoclonal Antibodies in Oncology: What Can We Learn from Initial Clinical Trials?

Selection of the right drug for the right patient is a promising approach to increase clinical benefit of targeted therapy with monoclonal antibodies (mAbs). Assessment of in vivo biodistribution and tumor targeting of mAbs to predict toxicity and efficacy is expected to guide individualized treatment and drug development. Molecular imaging with positron emission tomography (PET) using zirconium-89 (89Zr)-labeled monoclonal antibodies also known as 89Zr-immuno-PET, visualizes and quantifies uptake of radiolabeled mAbs. This technique provides a potential imaging biomarker to assess target expression, as well as tumor targeting of mAbs. In this review we summarize results from initial clinical trials with 89Zr-immuno-PET in oncology and discuss technical aspects of trial design. In clinical trials with 89Zr-immuno-PET two requirements should be met for each 89Zr-labeled mAb to realize its full potential. One requirement is that the biodistribution of the 89Zr-labeled mAb (imaging dose) reflects the biodistribution of the drug during treatment (therapeutic dose). Another requirement is that tumor uptake of 89Zr-mAb on PET is primarily driven by specific, antigen-mediated, tumor targeting. Initial trials have contributed toward the development of 89Zr-immuno-PET as an imaging biomarker by showing correlation between uptake of 89Zr-labeled mAbs on PET and target expression levels in biopsies. These results indicate that 89Zr-immuno-PET reflects specific, antigen-mediated binding. 89Zr-immuno-PET was shown to predict toxicity of RIT, but thus far results indicating that toxicity of mAbs or mAb-drug conjugate treatment can be predicted are lacking. So far, one study has shown that molecular imaging combined with early response assessment is able to predict response to treatment with the antibody-drug conjugate trastuzumab-emtansine, in patients with human epithelial growth factor-2 (HER2)-positive breast cancer. Future studies would benefit from a standardized criterion to define positive tumor uptake, possibly supported by quantitative analysis, and validated by linking imaging data with corresponding clinical outcome. Taken together, these results encourage further studies to develop 89Zr-immuno-PET as a predictive imaging biomarker to guide individualized treatment, as well as for potential application in drug development.
Developmental aspects of the spacing effect

The are spa spacing effect ced apart are r refers to the emembe red bet t fact er th that repetitions en those which ar which e adjacent or massed. Recently there has been a growing interest in this phenomenon in young children. The results of this small body of research, however, have been equivocal. For example, Cornell (1980) suggested that the spacing effect is the result of innate mechanisms, while Toppino and DiGeorge (1984) claimed that the spacing effect emerges with development. The present study was implemented in order to address issues raised by the above researchers and attempted to determine both the developmental course of the spacing effect, as well as some of the factors that may underly it. Experiment 1 was a modified replication of Toppino and DiGeorge's study. Ninety-six children (24 each from 4 age groups; preschool, kindergarten, 1st and 3rd grade) served as subjects. Each child was presented with 4 lists ( 2 of words and 2 of pictures) and received a 2 minute free recall test at the end of each list. Mode of presentation was audio-visual. Items were presented either once ( 1 ~ ) or repeated twice at spacings (or lags) of 0, 1 or 3 intervening items. The results showed that the spacing effect was obtained for all age groups with both words and pictures, suggesting that the spacing effect does not emerge with development, but rather, may be the result of more fundamental mechanisms. Experiment 2 focused on the role that very brief spacings, with no intervening items between repetitions, has on later retention. Ninety-six children served as subjects (24 each from preschool, kindergarten, 1st and 3rd grade). Each child was presented with 4 lists ( 2 of words and 2 of pictures) and received a 2 minute free recall at the end of each list. In addition to once presented items (1P) four different levels of spacing were included ( 0 , 1 . 1 , 2.5, and 5 secs.). The results of Experiment 2 demonstrated that the spacing effect was obtained using very brief blank intervals, for all age groups with both words and pictures. The results of Experiments 1 and 2 are discussed in terms of the role of retrieval operations in producing the spacing effect. Further discussion focuses on implications of these findings for various theories of the spacing effect as well as directions for future research and possible practical applications.
How do we count? The Problem of Tagging Phrasal Verbs in Parts

This paper examines the current performance of the stochastic tagger PARTS (Church 88) in handling phrasal verbs, describes a problem that arises from the statistical model used, and suggests a way to improve the tagger's performance. The solution involves a change in the definition of what counts as a word for the purpose of tagging phrasal verbs.
An efficient optimized method for isolation of villous trophoblast cells from human early pregnancy placenta suitable for functional and molecular studies.

PROBLEM The uniqueness of the human placenta cannot be replaced by animal models. In vitro studies are compulsory to elucidate the biology of human placenta and require isolation and purification of villous trophoblasts, which can be used in molecular and functional studies. Constant improvement in the isolation technique is required to obtain a high yield of pure trophoblast cells with high viability and well preserved morphology. METHOD OF STUDY Optimized isolation procedure for human villous trophoblasts based on mild enzymatic treatment, Percoll gradient centrifugation and additional purification step involving positive or negative immunoselection on magnetic beads is described. RESULTS A simple and effective isolation protocol gave a reasonably high yield of villous trophoblast cells with high purity and viability, and excellent morphology as assessed by flow cytometry and electron microscopy. CONCLUSION This protocol provides an efficient, optimized method for isolation and enrichment of villous trophoblast cells, suitable for phenotypic, ultrastructural, molecular and functional analyses and for establishment of primary cultures.
Animal Sounds-Toward Management and Retrieval Challenges

For decades, biologists around the world have recorded animal sounds. As the number of records grows, so does the difficulty to manage them, presenting challenges to save, retrieve, share and manage the sounds. These challenges are complicated by the fact that animal sound recordings have peculiarities, such as frequencies that cannot be heard by humans, or background environmental noise. This paper presents our efforts to manage and retrieve large volumes of animal sound data. We provide an overview of our prototype, an online portal focused on management of this data. The paper also discusses our case study, concerning more than 1 terabyte of animal recordings from Fonoteca Neotropical ”Jacques Vielliard”, at UNICAMP, Brazil. We introduce our preliminary research towards using semantics in order to overcome challenges faced by animal sound retrieval. Part of this text was published in the V eScience Workshop [Cugler et al. 2011].
1-out-of-n Proxy Oblivious Signature Schemes and its E-voting Application

—In a proxy signature scheme, an original signer delegates his signing authority to one or more proxy signers, which helps the proxy signers to sign messages on behalf of the original signer. In an oblivious signature scheme, a signee is allowed to choose one of the predetermined messages to get signed while not revealing any information about the selected message to the signer. Since the protocol provides ambiguity of the signee's selection, it is very suitable for electronic voting applications. In this paper, we first propose a proxy oblivious signature scheme based on discrete logarithm problem (DLP), which combines the advantages of proxy signature and oblivious signature and satisfies the security properties of both signatures. Performance comparisons are also given which shows that our scheme is not only capable but also efficient.
Effect of ultraviolet radiation on the infectivity of icterogenic plasma.

The danger of homologous serum hepatitis from blood and blood products is now well recognized. The literature with respect to its occurrence and incidence has been well summarized by Allen 1 and by Paine and Janeway. 2 Early encouraging reports 3 on the effectiveness of ultraviolet radiation as a method of eliminating or reducing this hazard, at least in the case of serum, led to the introduction of the process as a means of freeing plasma of the virus of serum hepatitis. 4 A special feature of this method was that the plasma proteins appeared to be unaffected by the amount of ultraviolet energy used. 5 A number of reports 6 now indicate that cases of hepatitis are being encountered after administration even of materials that it was believed had been rendered safe by ultraviolet irradiation. One recent study indicates a rate as high as 11.9% 7 in patients who