Miracle-dz/UniFAR-FTUs huggingface dataset:
Correcting Estimators of θ and Tajima's D for Ascertainment Biases Caused by the Single-Nucleotide Polymorphism Discovery Process

Most single-nucleotide polymorphism (SNP) data suffer from an ascertainment bias caused by the process of SNP discovery followed by SNP genotyping. The final genotyped data are biased toward an excess of common alleles compared to directly sequenced data, making standard genetic methods of analysis inapplicable to this type of data. We here derive corrected estimators of the fundamental population genetic parameter θ = 4Neμ (Ne, effective population size; μ, mutation rate) on the basis of the average number of pairwise differences and on the basis of the number of segregating sites. We also derive the variances and covariances of these estimators and provide a corrected version of Tajima's D statistic. We reanalyze a human genomewide SNP data set and find substantial differences in the results with or without ascertainment bias correction.
Alpha Promoter In Vivo Recruited to the Tumor Necrosis Factor CREB Binding Protein and p 300 Is Complex Involving Ets , Elk-1 , Sp 1 , and A Lipopolysaccharide-Specific Enhancer

10.1128/MCB.20. 16.6084-6094.2000. 2000, 20(16):6084. DOI: Mol. Cell. Biol. Goldfeld J. Fenton, David C. Gordon, Ian F. Dunn and Anne E. Barczak, Andreas M. Reimold, Laurie H. Glimcher, Matthew Eunice Y. Tsai, James V. Falvo, Alla V. Tsytsykova, Amy K. Alpha Promoter In Vivo Recruited to the Tumor Necrosis Factor CREB Binding Protein and p300 Is Complex Involving Ets, Elk-1, Sp1, and A Lipopolysaccharide-Specific Enhancer
A Comparative Analysis of Techniques for Predicting Student Performance

The problem of student final grade prediction in a particular course has recently been addressed using data mining techniques. In this paper, we present two different approaches solving this task. Both approaches are validated on 138 courses which were offered to students of the Faculty of Informatics of Masaryk University between the years of 2010 and 2013. The first approach is based on classification and regression algorithms that search for patterns in study-related data and also data about students' social behavior. We prove that students’ social behavior characteristics improve prediction for a quarter of courses. The second approach is based on collaborative filtering techniques. We predict the final grades based on previous achievements of similar students. The results show that both approaches reached similar average results and can be beneficially utilized for student final grade prediction. The first approach reaches significantly better results for courses with a small number of students. In contrary, the second approach achieves significantly better results for mathematical courses. We also identified groups of courses for which we are not able to predict the grades reliably. Finally, we are able to correctly identify half of all failures (that constitute less than a quarter of all grades) and predict the final grades only with the error of one degree in the grade scale.
Gradual Arbitrage

Capital often flows slowly from one market to another in response to buying opportunities. I provide an explanation for this phenomenon by considering arbitrage across two segmented markets when arbitrageurs face illiquidity frictions in the form of price impact costs. I show that illiquidity results in gradual arbitrage: mispricings are generally corrected slowly over time rather than instantaneously. The speed of arbitrage is decreasing in price impact costs and increasing in the level of competition among arbitrageurs. This means arbitrage is slower in more illiquid markets for two reasons: First, there is a direct effect, as illiquidity affects the equilibrium trading strategies for a given level of competition among arbitrageurs (strategic effect). Second, in equilibrium fewer arbitrageurs stand ready to trade between illiquid markets, further slowing down the speed of arbitrage (competition effect). Jointly, these two effects may help explain the observed cross-sectional variation of arbitrage speeds across different asset classes.
What Is the Iron Triangle, and How Has It Changed?

The Iron Triangle, also called the Triple Constraint, is a central concept to project management research and practice, representing the relationship between key performance criteria. However, there is disagreement about which criteria should be represented on the vertices of this triangle. The purpose of this paper is to explore which concepts are part of the Iron Triangle, and how these concepts have changed over time. ,This paper explores 45 years of project management research, drawing on a database of 109,804 records from 1970 to 2015. Three corpora were constructed, representing the project management and Time, Cost, and Quality Management literature. Time and Cost are consistently identified as part of the Iron Triangle. However, the status of quality is contested. Key concepts in the project management literature were explored using scientometric research techniques, to understand the relationship between these concepts. ,Significant links were found between Time, Cost, and Quality, verifying these concepts as the vertices on the Iron Triangle. These links were significantly stronger than links to alternatives, such as Scope, Performance, or Requirements. Other concepts that are core to the Iron Triangle were also identified, and how these have changed over time. ,This research develops the understanding of a key project management concept by clarifying which concepts are part of the Iron Triangle, based on evidence of how the concept is used in research. This paper also reveals the context in which this concept is used, and how this has changed over the last 45 years.
Hutchinson–Gilford progeria syndrome: Review of the phenotype

Hutchinson–Gilford progeria syndrome (HGPS) is a rare but well known entity characterized by extreme short stature, low body weight, early loss of hair, lipodystrophy, scleroderma, decreased joint mobility, osteolysis, and facial features that resemble aged persons. Cardiovascular compromise leads to early demise. Cognitive development is normal. Data on 10 of our own cases and 132 cases from literature are presented. The incidence in the last century in the Netherlands was 1:4,000,000. Sex ratio was 1.2:1. Main first symptoms were failure to thrive (55%), hair loss (40%), skin problems (28%), and lipodystrophy (20%). Mean age at diagnosis was 2.9 years. Growth in weight was more disturbed than growth in height, and growth delay started already prenatally. Mean height > 13 years was 109.0 cm, mean weight was 14.5 kg. Osteolysis was wide‐spread but not expressed, except in the viscerocranium, and remained limited to membranous formed bone. Lipodystrophy is generalized, only intra‐abdominal fat depositions remain present. Cardiovascular problems are extremely variable, both in age of onset and nature. Stroke and coronary dysfunctioning are most frequent. Pathologic findings in coronaries and aorta resemble sometimes the findings in elderly persons, but can also be much more limited. Loss of smooth muscle cells seems the most important finding. Mean age of demise was 12.6 years. Patients can be subdivided in patients with classical HGPS, which follows an autosomal dominant pattern of inheritance, (almost) all cases representing spontaneous mutations, and in non‐classical progeria, in whom growth can be less retarded, scalp hair remains present for a longer time, lipodystrophy is more slowly progressive, osteolysis is more expressed except in the face, and survival well into adulthood is not uncommon. Pattern of inheritance of non‐classical progeria is most probably autosomal recessive. The cause of HGPS is an abnormally formed Lamin A, either directly by a mutated LMNA gene, or through abnormal posttranslational processing (ZMPSTE24 gene mutations). Of 34 LMNA mutations found in progeria patients, there were 26 classical p.G608G mutations (76%). Pathogenesis is most likely to follow several different pathways. Potential therapeutic strategies are developed along these lines and include RNA interference techniques and inhibition of the dominant‐negative influence of abnormally formed Lamin A on polymerization with normally formed Lamin A. © 2006 Wiley‐Liss, Inc.
Variability of Black-Hole Binary Sources, and Lense-Thirring Orbital Precession

We discuss a possibility that observed radiation from active galactic nuclei (AGN) can be visibly modulated by collisions between stars (or secondary black holes) and an accretiondisc around a central black hole. It is proposed that materialswept out of the disc partly obscures the innermost region of the disc, while contributing by its own radiation. Under suitable circumstances, an individual orbiter can produce periodic modulation. If the central black hole is rotating and the companion star is at a low orbit, the Lense-Thirring orbital precession will show up in the signal and parameters of the central black hole can be thus determined.
Exhaled NO and assessment of anti-inflammatory effects of inhaled steroid: dose-response relationship

Exhaled nitric oxide (eNO) is an easily measured marker of airway inflammation. This study was undertaken to evaluate the usefulness of serial eNO in investigating the dose-response relationship for inhaled beclomethasone (BDP), and to compare eNO with other markers of airway inflammation. Following withdrawal of inhaled corticosteroid (ICS) therapy, 65 patients entered a double-blind, parallel-group, placebo-controlled trial of 50, 100, 200 or 500 µg·BDP·day−1 for eight weeks. eNO and spirometry were performed weekly and a hypertonic saline challenge with sputum induction was performed at the beginning and end of treatment. The relationship between the dose of ICS and changes in eNO and forced expiratory volume in one second (FEV1) was linear at 1 week and at the end of treatment. A linear dose-response relationship was also seen for sputum eosinophils. Changes in eNO correlated significantly with changes in sputum eosinophils. Changes in the provocative dose of saline causing a 15% fall in FEV1 saline did not differ across the treatment groups nor did they correlate with changes in other measurements. Exhaled nitric oxide may be used to assess the dose-response relationship for the anti-inflammatory effects of inhaled beclomethasone. The relationship found in this study was linear over the dose range 0–500 µg·day−1 soon after commencing therapy and continued over time.
Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway

The nonsense-mediated mRNA decay (NMD) pathway degrades mRNAs containing long 3'UTRs to perform dual roles in mRNA quality control and gene expression regulation. However, expansion of vertebrate 3'UTR functions has required a physical expansion of 3'UTR lengths, complicating the process of detecting nonsense mutations. We show that the polypyrimidine tract binding protein 1 (PTBP1) shields specific retroviral and cellular transcripts from NMD. When bound near a stop codon, PTBP1 blocks the NMD protein UPF1 from binding 3'UTRs. PTBP1 can thus mark specific stop codons as genuine, preserving both the ability of NMD to accurately detect aberrant mRNAs and the capacity of long 3'UTRs to regulate gene expression. Illustrating the wide scope of this mechanism, we use RNA-seq and transcriptome-wide analysis of PTBP1 binding sites to show that many human mRNAs are protected by PTBP1 and that PTBP1 enrichment near stop codons correlates with 3'UTR length and resistance to NMD. DOI: http://dx.doi. org/10.7554/eLife.11155. 001
On Numerical Error Propagation with Sensitivity

An emerging area of research is to automatically compute reasonably accurate upper bounds on numerical errors, including roundoffs due to the use of a finite-precision representation for real numbers such as floating point or fixed-point arithmetic. Previous approaches for this task are limited in their accuracy and scalability, especially in the presence of nonlinear arithmetic. Our main idea is to decouple the computation of newly introduced roundoff errors from the amplification of existing errors. To characterize the amplification of existing errors, we use the derivatives of functions corresponding to program fragments. We implemented this technique in an analysis for programs containing nonlinear computation, conditionals, and a certain class of loops. We evaluate our system on a number of benchmarks from embedded systems and scientific computation, showing substantial improvements in accuracy and scalability over the state of the art.
Neurologic Outcome of Laminoplasty for Acute Traumatic Spinal Cord Injury without Instability

Objective The purpose of this study is to evaluate the efficacy of laminoplasty in the treatment of spinal cord injury (SCI) without instability. Methods 79 patients with SCI without instability who underwent surgical treatment in our institute between January 2005 and September 2012 were retrospectively reviewed. Twenty nine patients fulfilled the inclusion criteria as follows: SCI without instability, spinal cord contusion in MRI, cervical stenosis more than 20%, follow up at least 6 months. Preoperative neurological state, clinical outcome and neurological function was measured using the American Spinal Injury Association (ASIA) impairment scale, modified Japanese Orthopedic Association (mJOA) grading scale and Hirabayashi recovering rate. Results Seventeen patients showed improvement in ASIA grade and twenty six patients showed improvement in mJOA scale at 6 month follow up. However, all patients with ASIA grade B and C have shown improvement of one or more ASIA grade. Mean Hirabayashi recovery rate was 47.4±23.7%. There was better neurologic recovery in those who had cervical spondylosis without ossification of posterior longitudinal ligament (OPLL) (p<0.05, χ2 test). Conclusions It is different in B, C, D with ASIA A that there are debates going on about the application of surgical treatment in ASIA A, and surgical treatment is helpful in B, C, D since it contributes to neurologic improvement. We concluded that laminoplasty provided good neurologic recovery in SCI without instability that cervical canal stenosis, especially spondylosis without OPLL and neurologic deterioration in ASIA B, C and D.
Multi-video summary and skim generation of sensor-rich videos in geo-space

User-generated videos have become increasingly popular in recent years. Due to advances in camera technology it is now very easy and convenient to record videos with mobile devices, such as smartphones. Here we consider an application where users collect and share a large set of videos that are related to a geographic area, say a city. Such a repository can be a great source of information for prospective tourists when they plan to visit a city and would like to get a preview of its main areas. The challenge that we address is how to automatically create a preview video summary from a large set of source videos. The main features of our technique are that it is fully automatic and leverages meta-data sensor information which is acquired in conjunction with videos. The meta-data is collected from GPS and compass sensors and is used to describe the viewable scenes of the videos. Our method then proceeds in three steps through the analysis of the sensor data. First, we generate a single video summary. Shot boundaries are detected based on different motion types of camera movements and key frames are extracted related to motion patterns. Second, we build video skims for popular places (i.e., hotspots) aiming to provide maximal coverage of hotspot areas with minimal redundancy (per-spot multi-video summary). Finally, the individual hotspot skims are linked together to generate a pleasant video tour that visits all the popular places (multi-spot multi-video summary).
Resource Aware Routing and Intelligent Wavelength Assignment for Cooperative Clustered OBS networks

Burst loss is a critical issue in Optical Burst Switching (OBS) networks which restrains its deployment. This article presents a novel routing and wavelength assignment strategy for the Cooperative Clustered OBS (C20BS) network architecture, to proactively avoid contention. In C20BS, the network topology is divided into several manageable overlapping zones/clusters, with a Zone Head (ZH) node keeping an information base of zone resources. The ZH pre-computes a list of alternate k-shortest disjoint paths for every ingress-egress node pair within the zone. The ZH utilizes both the inferred knowledge about wavelength usage at the zone intermediate nodes and a novel poles apart heuristic for assigning wavelengths to incoming bursts. A route is selected among the pre-computed paths where the selected wavelength is available. As a result, traffic is balanced among the set of pre-computed routes, thus proactively reducing probability of contention. This strategy is called Resource Aware Routing (RAR) and Intelligent Wavelength Assignment (IWA).
A single stage high power factor supply for HB-LEDs

In recent years, high brightness light emitting diodes are widely used in many applications. This paper presents an integrated converter topology for driving HB LEDs. The integrated buck flyback converter is a single stage, low cost, high power factor AC-DC converter with fast output regulation. The converter is used to provide power factor correction in streetlight application. To obtain high power factor, the buck stage and flyback stage are operated in discontinuous mode. Dimming operation of HB LED is also described. A closed loop is used for enabling the PWM dimming. The simulation studies using MATLAB/Simulink is also presented.
Synthetic Aperture Radar Processing with GPGPU

This article focuses on methodologies with recurrent use to code examples that try to couple with the flow of the main steps of the SAR processing. The possibility to be comprehensive was prevented by the wide scenario of variations of the focusing algorithm as well as the spread of applications. The reader should look at this work as a sample of possibilities offered by this new technology and a collection of suggestions and considerations that may guide to new applications and horizons.
Identification of a regulatory motif in Hsp70 that affects ATPase activity, substrate binding and interaction with HDJ‐1.

The Hsp70 family of molecular chaperones has an essential role in the synthesis, folding and translocation of the nascent peptide chain. While the general features of these activities are well documented, less is understood about the regulation of these activities. The ATPase rate is stimulated by non‐native proteins, furthermore, interaction with ATP leads to the release of protein substrate concurrent with a conformational change in Hsp70. One interpretation of these data is that the two domains of Hsp70 interact. In the process of mapping the carboxyl‐terminal boundary of the substrate binding domain for human Hsp70, we identified a regulatory motif, EEVD, which is conserved at the extreme carboxyl terminus among nearly all cloned cytosolic eukaryotic Hsp70s. Deletion or mutation of EEVD affects the ATPase activity, the ability to interact with substrates, and interferes with the ability of the mutant Hsp70 to interact with HDJ‐1 in the refolding of denatured firefly luciferase. Examination of the biophysical properties of the mutant Hsp70s reveals a change in the overall shape and conformation of the protein consistent with reduced interactions between the two domains. These data suggest that the EEVD motif is involved in the intramolecular regulation of Hsp70 function and intermolecular interactions with HDJ‐1.
Inside insights: A phenomenology of interoception

This chapter undertakes a phenomenology of inner-body experience, starting with a focus on visceral interoception. While highly personal, such experience also reveals a level of the lived body that is pre-personal, beyond our understanding and control. In contrast to exteroception, elements of the visceral field can be inaccessible, or surface only indistinctly and intermittently to conscious awareness. Nonetheless, interoception is more than just a series of such sensations. This chapter argues for the “exterior interior”—that is, we interpret inner body experiences through models drawn from the outer world, and interoception itself is bound up with emotion, purpose, and projects. In the West, we tend to valorize the interiority of rational thought; by contrast, experience of the inner body is a kind of “inferior interior,” often overlooked or overridden, yet inside insights—gained from attending to messages from the inner body—may preserve our health and wellbeing.
Diversity performance of interleaved spread spectrum OFDM signals over frequency selective multipath fading channels

In this paper we propose an interleaved spread spectrum orthogonal frequency division multiplexing (ISS-OFDM) system for achieving both frequency diversity and time diversity and investigate the system performance over frequency selective fading channels. The purpose is to exploit the diversity capability of OFDM systems, develop efficient spectrum spreading technique and improve the system performance against frequency selective channel fading. At the transmitter, the ISS-OFDM signal is generated by employing spread spectrum modulation and interleaving techniques. At the receiver, the received signals are combined by using maximum ratio combining (MRC) technique. The simulation indicates that the ISS-OFDM system has improved performance in multipath fading channels. Another unique characteristic is that the spectrum spreading factor and diversity order provided by the system are reconfigurable to achieve cognitive communications.
The Impact of Brand Equity on Customer Acquisition, Retention, and Profit Margin

The authors investigate the relationships between brand equity and customer acquisition, retention, and profit margin, the key components of customer lifetime value (CLV). They examine a unique database from the U.S. automobile market that combines ten years of acquisition rate, retention rate, and customer profitability data with measures of brand equity from Young & Rubicam's Brand Asset Valuator (BAV) over the same period. They hypothesize and find that BAV brand equity is significantly associated with the components of CLV in expected and meaningful ways. For example, customer knowledge of a brand has an especially strong positive relationship with all three components of CLV. Notably, however, differentiation is a double-edged sword. While it is associated with higher customer profitability, it is also associated with lower acquisition and retention rates. The authors also find that marketing efforts exert indirect impacts on CLV through brand equity. Simulations show that changes in marketing, or exogenous changes in brand equity, can exert important effects on CLV. Overall, the findings suggest that the “soft” and “hard” sides of marketing need to be managed in a coordinated way. The authors conclude with a discussion of these and other implications for researchers and practitioners.