Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic analysis of transcription start sites in avian development

Cap Analysis of Gene Expression (CAGE) in combination with single-molecule sequencing technology allows precision mapping of transcription start sites (TSSs) and genome-wide capture of promoter activities in differentiated and steady state cell populations. Much less is known about whether TSS profiling can characterize diverse and non-steady state cell populations, such as the approximately 400 transitory and heterogeneous cell types that arise during ontogeny of vertebrate animals. To gain such insight, we used the chick model and performed CAGE-based TSS analysis on embryonic samples covering the full 3-week developmental period. In total, 31,863 robust TSS peaks (>1 tag per million [TPM]) were mapped to the latest chicken genome assembly, of which 34% to 46% were active in any given developmental stage. ZENBU, a web-based, open-source platform, was used for interactive data exploration. TSSs of genes critical for lineage differentiation could be precisely mapped and their activities tracked throughout development, suggesting that non-steady state and heterogeneous cell populations are amenable to CAGE-based transcriptional analysis. Our study also uncovered a large set of extremely stable housekeeping TSSs and many novel stage-specific ones. We furthermore demonstrated that TSS mapping could expedite motif-based promoter analysis for regulatory modules associated with stage-specific and housekeeping genes. Finally, using Brachyury as an example, we provide evidence that precise TSS mapping in combination with Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-on technology enables us, for the first time, to efficiently target endogenous avian genes for transcriptional activation. Taken together, our results represent the first report of genome-wide TSS mapping in birds and the first systematic developmental TSS analysis in any amniote species (birds and mammals). By facilitating promoter-based molecular analysis and genetic manipulation, our work also underscores the value of avian models in unravelling the complex regulatory mechanism of cell lineage specification during amniote development.
Model-driven Level 3 BLAS Performance Optimization on Loongson 3A Processor

Every mainstream processor vendor provides an optimized BLAS implementation for its CPU, as BLAS is a fundamental math library in scientific computing. The Loongson 3A CPU is a general-purpose 64-bit MIPS64 quad-core processor, developed by the Institute of Computing Technology, Chinese Academy of Sciences. To date, there has not been a sufficiently optimized BLAS on the Loongson 3A CPU. The purpose of this research is to optimize level 3 BLAS performance on the Loongson 3A CPU. We analyzed the Loongson 3A architecture and built a performance model to highlight the key point, L1 data cache misses, which is different from level 3 BLAS optimization on the mainstream x86 CPU. Therefore, we employed a variety of methods to avoid L1 cache misses in single thread optimization, including cache and register blocking, the Loongson 3A 128-bit memory accessing extension instructions, software prefetching, and single precision floating-point SIMD instructions. Furthermore, we improved parallel performance by reducing bank conflicts among multiple threads in the shared L2 cache. We created an open source BLAS project, OpenBLAS, to demonstrate the performance improvement on the Loongson 3A quad-core processor. Keywords-BLAS; Loongson 3A; MIPS64; Optimization; Multi-core
Towards a standard family of languages for matching patterns in source code

We make a case for the definition of a family of languages for expressing patterns over both the structure and semantics of source code. Our proposal is unique in that it attempts to provide a unified solution to the problem of searching for patterns in multiple programming languages, and in that it focuses on the semantics of the program rather than on its syntactic structure, all while striving to ensure simplicity and ease-of-use. We present the motivation and the unique difficulties involved in defining such languages, discuss strategies for dealing with these problems, and propose a prototype family of code pattern languages (CPLs).
The Bloomier filter: an efficient data structure for static support lookup tables

We introduce the Bloomier filter, a data structure for compactly encoding a function with static support in order to support approximate evaluation queries. Our construction generalizes the classical Bloom filter, an ingenious hashing scheme heavily used in networks and databases, whose main attribute---space efficiency---is achieved at the expense of a tiny false-positive rate. Whereas Bloom filters can handle only set membership queries, our Bloomier filters can deal with arbitrary functions. We give several designs varying in simplicity and optimality, and we provide lower bounds to prove the (near) optimality of our constructions.
Cross-classification of microalbuminuria and reduced glomerular filtration rate: associations between cardiovascular disease risk factors and clinical outcomes.

BACKGROUND Chronic kidney disease is defined by reduced estimated glomerular filtration rate (reduced eGFR) or by microalbuminuria (MA). Concordance between reduced eGFR and MA and associated cardiovascular disease (CVD) and all-cause mortality according to these definitions is uncertain. METHODS Participants (n = 2966 [52.6% were women], mean age, 59 years) were drawn from the Framingham Offspring Cohort. Participants were classified into 4 groups based on the presence or absence of reduced eGFR (eGFR < 59 mL/min/1.73 m(2) in women, < 64 mL/min/1.73 m(2) in men or MA (spot urinary albumin to creatinine ratio of at least 30 mg/g). Cox proportional hazard models were used to determine the combined risk of CVD events and all-cause mortality for each group. RESULTS Of the participants, 9.9% (n = 295) had reduced eGFR, and 12.2% (n = 362) had MA. Among those with reduced eGFR, 28% had MA. Those with reduced eGFR and with MA were at increased risk for combined CVD and all-cause mortality compared with those with neither condition (hazard ratio [HR] 1.7, 95% confidence interval [CI], 1.1-2.4; P = .009), whereas those with reduced eGFR and without MA and those without reduced eGFR and with MA had similar HRs (1.3 and 1.2, respectively). Those with reduced eGFR and with MA, as well as those with reduced eGFR and without MA, were at significantly increased risk of all-cause mortality (HR 2.2 [95% CI, 1.4-3.6] and HR 1.7 [95% CI, 1.1-2.6], respectively). CONCLUSIONS Reduced eGFR and MA are relatively common conditions with different risk factor profiles. The coexistence of reduced eGFR and MA was present in 2.8% of the study sample and conferred substantial increased risk for CVD and all-cause mortality, in part because of a heavy burden of CVD risk factors.
Composites formed by glass fibers and PS‐modified epoxy matrix. Influence of the glass fibers surface on the morphologies and mechanical properties of the interphases generated

In this work, the influence of the nature of the reinforcement surface on the interfacial morphologies developed in E-glass fibers/polystyrene (PS)-modified epoxy composites has been studied. Different surface modifications of the fibers were considered. In a complementary way, morphological analysis and nanoindentation measurements were carried out using atomic force microscopy to subsequently correlate the interfacial structure with the morphologies observed. In every composite, reaction-induced phase separation happened with a morphology composed of PS-rich domains immersed in an epoxy-rich phase. However, depending on the surface modification of the glass fibers, different distributions of PS-rich domains at the interfaces were obtained. The results were interpreted in terms of a gradual phase separation process because of stoichiometric gradients from the glass fibers surface to the matrix bulk caused by specific segregation of one of the components of the reactive epoxy mixture to the fibers occurs. It was concluded that specific and controlled reinforcement modification allows obtaining tailored interfaces formed by a polymer blend and a reinforcement in which the morphology can be previously selected. POLYM. COMPOS. , 2010. © 2009 Society of Plastics Engineers
Usefulness of a new immuno‐radiometric assay to detect hepatitis C core antigen in a community‐based population

Summary. A new immuno‐radiometric assay (IRMA) to detect hepatitis C virus (HCV) core antigen (HCVcAg) has been developed. The aim of the present study was to investigate the sensitivity and specificity of this IRMA to measure HCV antigenemia, based on the detection of HCV RNA as the gold standard, and to assess the utility of the IRMA in a community‐based population. Anti‐HCV positive residents in a hyperendemic area of HCV infection in Japan were studied. Serum levels of HCVcAg were measured using IRMA, and the presence of HCV RNA was determined by a qualitative reverse transcription‐polymerase chain reaction (RT‐PCR) assay. The sensitivity and the specificity of the IRMA were 96.4 and 100%, respectively. The sensitivity of the IRMA was similar between serological HCV group I (HCV genotypes 1a and 1b) (97.6%) and group II (HCV genotypes 2a and 2b) (94.0%). There was a strong correlation between serum HCVcAg level and HCV‐RNA measured by a quantitative RT‐PCR (r = 0.832, P < 0.0001). There also was a very strong correlation of HCVcAg level between IRMA measurements performed on serum and those performed on plasma (r = 0.984, P < 0.0001). In conclusion, this new IRMA is useful for the detection of HCV core antigen in a community‐based population.
Efficient trajectory bending with applications to loop closure

In robotic applications the absolute pose is often obtained as the integral of successive relative rigid-body motions. As each relative rigid-body motion is typically the product of statistical inference, the integrated absolute pose will exhibit error build-up and the estimated trajectory will differ from the true trajectory undertaken by the system. Some application areas allow the system to receive additional information about its current absolute pose, for example from loop detection, which is more accurate than the integral of the relative rigid-body motions. The availability of this absolute information is usually less frequent than the information underlying the relative rigid-body motions. This contribution addresses an efficient closed form algorithm which minimally bends a trajectory such that the integrated pose is exactly equal to any particular desired pose. The manner in which the bending is distributed over the trajectory is controllable using weights. The proposed method will be compared against a maximum likelihood solution on simulated trajectories as well as on trajectories estimated from binocular and monocular data. The results indicate that the performance differences between the closed form approach and the maximum likelihood solution are negligible while the closed form approach is significantly more efficient.
Osteoarticular and intercalary allograft transplantation in the management of malignant tumors of bone

Since 1971, the Orthopaedic Service at the Massachusetts General Hospital has treated 106 patients with malignant or aggressive bone tumors by wide resection and replacement with frozen cadaveric allograft. Sixty‐one of these patients have been followed for over two years (mean, 4.5 years), allowing a comprehensive end‐results analysis. In 45 patients, mostly with giant‐cell tumors or chondrosarcomas, the resection involved the articular end of a long bone and the replacement not only included bone, but glycerolized (to prevent freezing injury) articular cartilage. Ten of the segments were intercalary (bone alone) and six involved a combination of bone and a metallic joint prosthesis. Patients were graded as excellent, good, fair, or failure, depending principally on functional capacity. End‐results analysis in this group showed that five of the 61 patients had either a local recurrence (2) and/or distant metastases (3); in five additional patients the limb was amputated or the implant removed, primarily because of infection (total failure rate, 16.5%). Forty‐five (73.8%) had successful transplants (graded excellent or good) and were able to live essentially normal lives. Six of the patients (10%) required a brace or cane but three of these patients were able to return to preoperative work activities. Although the operations were arduous and difficult, and despite a high infection rate (13%) and occasional pathologic fractures (10%), the results compare favorably with other techniques used to restore the skeleton following massive segmental resection. In long‐term follow‐up, the data suggest that if no complications ensue in the first two years, the results are generally quite good and the grafts show no evidence of progressive deterioration with time.
Integrated Information and State Differentiation

Integrated information (Φ) is a measure of the cause-effect power of a physical system. This paper investigates the relationship between Φ as defined in Integrated Information Theory and state differentiation (D), the number of, and difference between potential system states. Here we provide theoretical justification of the relationship between Φ and D, then validate the results using a simulation study. First, we show that a physical system in a state with high Φ necessarily has many elements and specifies many causal relationships. Furthermore, if the average value of integrated information across all states is high, the system must also have high differentiation. Next, we explore the use of D as a proxy for Φ using artificial networks, evolved to have integrated structures. The results show a positive linear relationship between Φ and D for multiple network sizes and connectivity patterns. Finally we investigate the differentiation evoked by sensory inputs and show that, under certain conditions, it is possible to estimate integrated information without a direct perturbation of its internal elements. In concluding, we discuss the need for further validation on larger networks and explore the potential applications of this work to the empirical study of consciousness, especially concerning the practical estimation of Φ from neuroimaging data.
Feature Selection and Feature Extraction for Text Categorization

The effect of selecting varying numbers and kinds of features for use in predicting category membership was investigated on the Reuters and MUC-3 text categorization data sets. Good categorization performance was achieved using a statistical classifier and a proportional assignment strategy. The optimal feature set size for word-based indexing was found to be surprisingly low (10 to 15 features) despite the large training sets. The extraction of new text features by syntactic analysis and feature clustering was investigated on the Reuters data set. Syntactic indexing phrases, clusters of these phrases, and clusters of words were all found to provide less effective representations than individual words.
Is there a dichotomy in the radio loudness distribution of quasars

We present a new approach to tackling the issue of radio loudness in quasars. We constrain a (simple) prescription for the intrinsic distribution of radio-to-optical ratios by comparing properties of Monte Carlo simulatedsamples with those of observed optically selected quasars. We find strong evidence for a dependence of the radio luminosity on the optical one, even though with a large scatter. The dependence of the fraction of radio-loud quasars on apparent and absolute optical magnitudes results in a selection effect related to the radio and optical limits of current surveys. The intrinsic distribution of the radio-to-optical ratios shows a peak at R* 1 . 4 ∼ 0.3, with only ≤5 per cent of objects being included in a high-R* 1 . 4 tail, which identifies the radio-loud regime. No lack or deficit of sources - but only a steep transition region - is present between the radio-loud and radio-quiet populations at any R* 1 . 4 . Briefly, we discuss possible origins for this behaviour (e.g. an absence of jets in radio-quiet sources, a large range of radiative radio efficiency, different lifetimes for the accretion and jet ejection phenomena, etc.).
User evaluation of a task for shortlisting papers from researcher's reading list for citing in manuscripts

Although many interventional approaches have been proposed to address the apparent gap between novices and experts for literature review (LR) search tasks, there have been very few approaches proposed for manuscript preparation (MP) related tasks. The purpose of this paper is to describe a task and an incumbent technique for shortlisting important and unique papers from the reading list (RL) of researchers, meant for citation in a manuscript. ,A user evaluation study was conducted on the prototype system which was built for supporting the shortlisting papers (SP) task along with two other LR search tasks. A total of 119 researchers who had experience in authoring research papers participated in this study. An online questionnaire was provided to the participants for evaluating the task. Both quantitative and qualitative analyses were performed on the collected evaluation data. ,Graduate research students prefer this task more than research and academic staff. The evaluation measures relevance, usefulness and certainty were identified as predictors for the output quality measure “good list”. The shortlisting feature and information cues were the preferred aspects while limited data set and rote steps in the study were ascertained as critical aspects from the qualitative feedback of the participants. ,Findings point out that researchers are clearly interested in this novel task of SP from the final RL prepared during LR. This has implications for digital library, academic databases and reference management software where this task can be included to benefit researchers at the manuscript preparatory stage of the research lifecycle.
A 50mW-TX 65mW-RX 60GHz 4-element phased-array transceiver with integrated antennas in 65nm CMOS

The 60GHz band has gained great interest as an enabler for multi-Gb/s wireless links. Recent efforts [1-4] have focused on reducing transceiver power to drive adoption of 60GHz in mobile devices. To further accelerate this adoption, the cost of current mm-Wave solutions should also be reduced. Especially for short range designs (<;1m), overall cost may be dominated by packaging and testing. This paper therefore presents a low-power 60GHz CMOS 4-element phased-array QPSK transceiver with integrated slot-loop antennas. Utilizing such antennas as well as circuit stacking techniques, the transceiver achieves 10.4Gb/s with a range of >40cm in all directions while consuming only 115mW (TX+RX).
Grand challenge: the bluebay soccer monitoring engine

This paper presents the design and implementation of a custom-built event processing engine called BlueBay developed for live monitoring of soccer games. We experimentally evaluated our system using a real workload and report on its performance. Our results indicate that BlueBay achieves a throughput of up to 790k events per second, therefore processing the game's input sensor stream about 60 times faster than real-time. In addition to our custom implementation, we also investigated the applicability of off-the-shelf general-purpose event processing engines to address the soccer monitoring problem. This effort resulted in two additional and fully functional implementations based on Esper and Storm.
The Integrin Antagonist Cilengitide Activates αVβ3, Disrupts VE-Cadherin Localization at Cell Junctions and Enhances Permeability in Endothelial Cells

Cilengitide is a high-affinity cyclic pentapeptdic αV integrin antagonist previously reported to suppress angiogenesis by inducing anoikis of endothelial cells adhering through αVβ3/αVβ5 integrins. Angiogenic endothelial cells express multiple integrins, in particular those of the β1 family, and little is known on the effect of cilengitide on endothelial cells expressing αVβ3 but adhering through β1 integrins. Through morphological, biochemical, pharmacological and functional approaches we investigated the effect of cilengitide on αVβ3-expressing human umbilical vein endothelial cells (HUVEC) cultured on the β1 ligands fibronectin and collagen I. We show that cilengitide activated cell surface αVβ3, stimulated phosphorylation of FAK (Y397 and Y576/577), Src (S418) and VE-cadherin (Y658 and Y731), redistributed αVβ3 at the cell periphery, caused disappearance of VE-cadherin from cellular junctions, increased the permeability of HUVEC monolayers and detached HUVEC adhering on low-density β1 integrin ligands. Pharmacological inhibition of Src kinase activity fully prevented cilengitide-induced phosphorylation of Src, FAK and VE-cadherin, and redistribution of αVβ3 and VE-cadherin and partially prevented increased permeability, but did not prevent HUVEC detachment from low-density matrices. Taken together, these observations reveal a previously unreported effect of cilengitide on endothelial cells namely its ability to elicit signaling events disrupting VE-cadherin localization at cellular contacts and to increase endothelial monolayer permeability. These effects are potentially relevant to the clinical use of cilengitide as anticancer agent.
Frequency Tunable Antenna Using a Magneto-Dielectric Material for DVB-H Application

This paper presents an ultracompact antenna design suited for digital video broadcasting-handheld (DVB-H) reception devices. The DVB-H frequency band is ranging from 4 70 to 862 MHz and divided in 49 channels of 8 MHz. Designed to be integrated in a tablet, it is not only heavily miniaturized (λ0 /49 × λ0/71 ×λ0/160 at 470 MHz), but also able to cover each channel thanks to the use of a magneto-dielectric material. The advantage of using such a material is studied and described in this paper. Moreover, the operating frequency is continuously tuned over the whole DVB-H band by the integration of a varactor diode. This varactor diode has been characterized and modeled to properly cosimulate its behavior within the antenna. Limitations in terms of accepted power by the diode are emphasizing. Finally, the antenna design, including both magneto-dielectric material and varactor diode is integrated in the DVB-H receiver device. Measurement performances are presented and discussed.
Genes Encoding Antigenic Surface Glycoproteins in Pneumocystis from Humans

Pneumocystis is a eukaryotic microbe that causes pneumocystosis, an AIDS‐associated pneumonia. Pneumocystosis also occurs in many other mammalian species, and animal‐derived organisms have been extensively utilized in Pneumocystis research. Pneumocystis from diverse hosts contain a large glycoprotein (gpA/MSG) on the surface. Antibodies elicited against gpA/MSG of Pneumocystis from humans sometimes cross‐react with epitopes on proteins of similar size from Pneumocystis from other host species. Here we report the isolation and partial sequence of two presumptive gpA/MSG genes from human‐derived Pneumocystis. The cloned human‐derived Pneumocystis gpA/MSG genes and predicted peptides were different from those previously isolated from Pneumocystis from rats and ferrets. The genome of human‐derived Pneumocystis contained multiple copies of sequences related to the two cloned gpA/MSG genes.