Miracle-dz/UniFAR-FTUs huggingface dataset:
Heart rate variability in mice with coronary heart disease

Heart rate variability (HRV), the beat-to-beat fluctuation of the heart rate, is a noninvasive test that measures the autonomic regulation of the heart. Assessment of HRV has been shown to predict the risk of mortality in patients after an acute myocardial infarction. Recently, the Krieger lab at MIT developed genetically engineered double knockout (dKO) mice that develop coronary artery disease accompanied by spontaneous myocardial infarctions and die at a very young age. This thesis investigated whether HRV could function as a prognostic indicator in the dKO mouse. A novel method for estimating physiological state of the mouse from the electrocardiogram using an innovative activity index was developed in order to compare HRV variables at different times while controlling for physiologic state. Traditional time and frequency domain variables were used to assess the prognostic power of HRV. Results have shown that none of the HRV variables were helpful in predicting mortality in the dKO mice. Mean heart rate showed some prognostic power, but it was not consistent in all the dKO mice. Finally, the activity index developed in this thesis provided a reliable metric for activity in mice as validated by a camera with motion detection. Thesis Supervisor: Roger G. Mark Title: Distinguished Professor of Health Science and Technology Professor of Electrical Engineering
Integrated Analysis of DNA Methylation and mRNA Expression Profiles to Identify Key Genes in Severe Oligozoospermia

Severe oligozoospermia (SO) is a complex disorder, whose etiology is the combined effect of genetic factors and epigenetic conditions. In this study, we examined DNA methylation and mRNA expression status in a set of testicular tissues of SO patients (n = 3), and compared methylated data with those derived from obstructive azoospermia (OA) patients (n = 3) with normal spermatogenesis phenotype. We identified 1,960 differentially methylated CpG sites showing significant alterations in SO vs. OA using the Illumina Infinium HumanMethylation450 bead array. By integrating above DNA methylation data and mRNA expression results, we totally identified 72 methylated CpG sites located in 65 genes with anti-correlation between DNA methylation and mRNA expression. Integrated pathways analysis indicates that these genes are involved in response to hormone stimulus, activation of protein kinase activity, and apoptotic process, among others. We also observed some genes with inversely correlated difference is novel in male infertility field, including PTPRN2, EPHX1, SERPINB9, SLIT3, etc. Our results lay a groundwork for further biological study of SO. Moreover, we generated a workflow for integrated analysis of DNA methylation and mRNA expression, which is expandable to other study types.
Ego depletion reduces proselfs' concern with the well-being of others

Previous research suggests that people predisposed toward a more cooperative orientation are stronger at self-control and, accordingly, are better able to ward off the adverse impact of ego depletion on self-regulation (Seeley & Gardner, 2003). Building on this research, we tested the hypothesis that ego depletion would lead to a reduction in concern with the well-being of others among proselfs, but not among prosocials. Study 1 supported the basic proposition that prosocials are higher than proselfs in trait self-control. In Study 2, participants originally classified as prosocials versus proselfs based on mathematical games engaged in an ego depletion task or a control task and later completed a similar measure of prosocial versus proself values. Supporting the primary hypothesis, ego depletion reduced proselfs concern with the well-being of others at time 2, but had no impact among prosocials. Theoretical and practical implications are discussed.
Peripheral blood progenitor uncontrolled‐rate freezing: a single pediatric center experience

BACKGROUND: Controlled‐rate freezing (CRF) followed by storage in liquid nitrogen is employed by most centers as the standard procedure for peripheral blood progenitor cell (PBPC) cryopreservation. Uncontrolled‐rate freezing (URF) at −80°C is more simple, time‐saving, less expensive, and, possibly, as effective as CRF. The aim of this retrospective analysis was to compare CRF and URF in childhood transplantation.
Activation processing of cathepsin H impairs recognition by its propeptide

Abstract Free propeptides are known to function as inhibitors of the parental mature cysteine cathepsins. This general rule, however, does not apply to the aminopeptidase cathepsin H. Screening of propeptide fragments for their inhibitory potency revealed no significant effect on the native mature cathepsin H. On the other hand, inhibitory interaction was established with recombinant cathepsin H that displays endopeptidase activity due to a lack of the mini-chain. This finding suggests that the propeptide-binding region is structurally rearranged during maturation processing and mini-chain formation, which impairs the effective recognition of mature cathepsin H by its own propeptide.
Forgotten connections: reviving the concept of upbringing in Scottish child welfare

The concept of upbringing is a central one in social pedagogy. It is also apparent in a Scottish social welfare tradition, most evidently in the 1964 Kilbrandon Report. Kilbrandon’s broad understanding of upbringing or social education was, however, subsequently subsumed beneath increasingly compartmentalised and instrumental approaches to child care and education. These fail to adequately understand and, arguably, impede and distort adult responsibility for bringing up children. This article draws on European literature, and particularly the writing of the German social pedagogue Klaus Mollenhauer, to begin to articulate the concept of upbringing, locating it as the central task of child care and education. Bringing up children is identified as, fundamentally, a moral and cultural endeavour, brought about through caring, inter-generational relationships. The article concludes by suggesting that elements within a Scottish tradition and within current policy might be drawn on to support a broad understanding of upbringing.
A firewall approach to personal knowledge system

All of the computers on the world, the need for automated to protecting customer data files and personal information stored on the computer and network file server became evident. This is especially the case for a patient file shared system, such as a medical system, and the need is even more acute for systems that can be accessed over a public telephone or data network. The problem of how to protect patient data on a computer files system is an important topic. A personal knowledge system system is a personal knowledge system that applies a set of rules to each incoming access client and then forwards or discards the access right. It is the main component of a firewall approach to personal knowledge system. In this paper, we proposed a firewall approach system and implement it on Windows NT operating system by using the security mechanism to protect patient data files. We consider is the personal knowledge system. The patient data file server systems can be privacy of protecting a local patient data system or network of medical systems from network-based security treats. Even when at the urgent call for hospital time affording access to the outside world via wide area networks and the Internet. Our system can protect hospital data and keep privacy for patient. Further more, a group of doctors can collabe together dynamically from a secure virtual subnet within a firewall approach to personal knowledge system which to conduct their join e-health industry.
Molecular design and computer simulations of novel mesophases

The simulation of systems of simple particles interacting through a suitable model potential allows the identification of the essential physical features (anisotropy and biaxiality, electrostatic moments etc.) responsible for a certain collective behaviour. Here attractive–repulsive models of the so called Gay–Berne type, that have proved capable of generating nematic, smectic and columnar liquid crystals are described. In particular we discuss the generalization of this simple potential needed to handle biaxial and non-centrosymmetric molecules and we show that by suitable tuning of attractive and repulsive interactions biaxial and polar ferroelectric nematic phases can be obtained in simulations. This could hopefully offer a guide for the design of new mesogenic molecules that are reasonable candidates for the synthesis of these novel mesophases.
Foreign Accent, Comprehensibility, and Intelligibility in the Speech of Second Language Learners

One of the chief goals of most second language learners is to be understood in their second language by a wide range of interlocutors in a variety of contexts. Although a nonnative accent can sometimes interfere with this goal, prior to the publication of this study, second language researchers and teachers alike were aware that an accent itself does not necessarily act as a communicative barrier. Nonetheless, there had been very little empirical investigation of how the presence of a nonnative accent affects intelligibility, and the notions of “heavy accent” and “low intelligibility” had often been confounded. Some of the key findings of the study—that even heavily accented speech is sometimes perfectly intelligible and that prosodic errors appear to be a more potent force in the loss of intelligibility than phonetic errors—added support to some common, but weakly substantiated beliefs. The study also provided a framework for a program of research to evaluate the ways in which such factors as intelligibility and comprehensibility are related to a number of other dimensions. The authors have extended and replicated the work begun in this study to include learners representing other L1 backgrounds (Cantonese, Japanese, Polish, Spanish) and different levels of learner proficiency, as well as other discourse types (Derwing & Munro, 1997; Munro & Derwing, 1995). Further support for the notion that accent itself should be regarded as a secondary concern was obtained in a study of processing difficulty (Munro & Derwing, 1995), which revealed that nonnative utterances tend to require more time to process than native-produced speech, but failed to indicate a relationship between strength of accent and processing time. The approach to L2 speech evaluation used in this study has also proved useful in investigations of the benefits of different methods of teaching of pronunciation to ESL learners. In particular, it is now clear that learner assessments are best carried out with attention to the multidimensional nature of L2 speech, rather than with a simple focus on global accentedness. It has been shown, for instance, that some pedagogical methods may be effective in improving intelligibility while others may have an effect only on accentedness (Derwing, Munro, & Wiebe,1998).
Probing Lipid Mobility of Raft-exhibiting Model Membranes by Fluorescence Correlation Spectroscopy*

Confocal fluorescence microscopy and fluorescence correlation spectroscopy (FCS) have been employed to investigate the lipid spatial and dynamic organization in giant unilamellar vesicles (GUVs) prepared from ternary mixtures of dioleoyl-phosphatidylcholine/sphingomyelin/cholesterol. For a certain range of cholesterol concentration, formation of domains with raft-like properties was observed. Strikingly, the lipophilic probe 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate (DiI-C18) was excluded from sphingomyelin-enriched regions, where the raft marker ganglioside GM1 was localized. Cholesterol was shown to promote lipid segregation in dioleoyl-phosphatidylcholine-enriched, liquid-disordered, and sphingomyelin-enriched, liquid-ordered phases. Most importantly, the lipid mobility in sphingomyelin-enriched regions significantly increased by increasing the cholesterol concentration. These results pinpoint the key role, played by cholesterol in tuning lipid dynamics in membranes. At cholesterol concentrations >50 mol%, domains vanished and the lipid diffusion slowed down upon further addition of cholesterol. By taking the molecular diffusion coefficients as a fingerprint of membrane phase compositions, FCS is proven to evaluate domain lipid compositions. Moreover, FCS data from ternary and binary mixtures have been used to build a ternary phase diagram, which shows areas of phase coexistence, transition points, and, importantly, how lipid dynamics varies between and within phase regions.
A new approach for higher data reduction capacity based on spike detection technique in wireless multichannel neural recordings

We present, in this paper, a simple approach for increasing data reduction capacity based on spike detection techniques in wireless multichannel neural recordings. The impact of the number of bits per sample and the sampling rate used by each data acquisition channel are analysed and quantified. The approach consists of minimizing the sampling frequency and the number of bits per sample of the extracellular neural recordings. The proposed approach allows increasing the number of channels that may be monitored simultaneously without additional computation, by a factor up to 5.
Selection of Feature Genes and Construction of Regulatory Network on Colon Carcinoma

Research of gene regulatory network is critically important for diagnosis and therapy of tumor. We propose a method on construction of gene regulatory network and selection of feature genes on cancer. Firstly we selected 277 genes whose expressions differ greatly between tumor tissues and normal tissues ,then collected multiple group feature genes using Peano Count Tree; Secondly we picked the gene which had been validated contributing to the process of tumor forming as the kernel of pathway where it participates , then selected the genes involved in the same pathway to the kernel gene by Pearson correlation coefficients; Finally the regulatory relationships of selected genes were predicted on Bayesian Network. Consulting relating experiment articles, the network structure we predicted obtained biological supports.
First demonstration of silicon-based parallel-fed travelling-wave photodetector array (TWPDA)

We demonstrate the first silicon-based parallel-fed travelling-wave photodetector array (TWPDA). Impedance-matched travelling-wave electrode is designed considering periodic loading effect. The demonstrated up to 4-channel TWPDAs show >10GHz 3-dB bandwidths and ~0.75A/W responsivity using 30μm-length PDs.
Termination of Derivations in a Fragment of Transitive Distributed Knowledge Logic

A transitive distributed knowledge logic is considered. The considered logic S4 nD is obtained from multi-modal logic S4 n by adding transitive distributed knowledge operator. For a fragment of this logic loop-check-free sequent calculus is proposed. The considered fragment is such that it can be applied for specification and verification of safety properties of knowledge-based distributed systems. By relying on the constructed loop-check-free sequent calculus a PSPACE procedure to determine a termination of backward derivation in considered fragment of the logic S4 nD is presented.
An improved algorithm for mining frequent Inter-transaction patterns

Mining Inter-transaction patterns (ITPs) from large databases is a common data mining task, which discovers the patterns across several transactions in a transaction database. Although, several algorithms have been proposed for this task, they remain computationally expensive. To resolve this issue, this paper presents an efficient method called DITP-Miner to mine ITPs. In our proposed algorithm, there are four phases. First, we scan the database once to find frequent 1-patterns with their tidsets. Second, we generate inter-transaction 1-pattern candidates with the given span values and sort all the frequent 1-patterns in an ascending order according to their supports. Third, based on frequent items found in phases 1 and 2, we find frequent 2-patterns with their diffsets. In the fourth phase, we use diffsets and DFS (Depth-First-Search) technique to get all frequent ITPs. In addition, three propositions are also offered to early prune infrequent patterns in the processing. Proposition 1 is used to early prune infrequent inter-transaction 1-pattrens, Proposition 2 is used to quickly compute the support of patterns, and Proposition 3 (subsume concept) is used to quickly compute the support of patterns and to early prune infrequent patterns, which reduce the search space. Through experimental results, we find out our proposed approach is more efficient than ITP-miner in both the mining time and the memory usage.
Differential effects of citalopram and reboxetine on cortical Glx measured with proton MR spectroscopy

The pharmacological effects of monoamine potentiating antidepressants are likely to be expressed ultimately on cortical pyramidal neurones that use glutamate as a neurotransmitter. However, there are few data on the effects of antidepressant treatment on cortical glutamate levels in humans. The aim of the present study was to use proton magnetic resonance spectroscopy (MRS) to assess the effects of short-term administration of the selective serotonin re-uptake inhibitor, citalopram and the selective noradrenaline re-uptake inhibitor, reboxetine, on a composite measure of glutamate and glutamine (Glx) in occipital cortex in healthy volunteers using a parallel group, placebo-controlled design. We found that relative both to placebo and reboxetine, seven days treatment with citalopram significantly increased cortical Glx. Our data suggest that short-term treatment with citalopram, but not reboxetine, increases occipital Glx in healthy subjects. Further studies are needed to find out if similar effects occur in anterior brain regions and whether they reflect changes in glutamate or glutamine or both.
Tissue Doppler Assessment of Longitudinal Right and Left Ventricular Strain and Strain Rate in Pulmonary Artery Hypertension

Tissue Doppler imaging (TDI) in 38 adult patients with pulmonary artery hypertension of varied etiology and normal left ventricular systolic function by two‐dimensional transthoracic echocardiography showed significantly reduced peak systolic strain (SS) in all three segments of left ventricular free wall and ventricular septum and two of three segments of right ventricular free wall when compared to 29 adults with no clinical or echocardiographic evidence of heart disease and normal left and right ventricular systolic function. A similar reduction in peak diastolic strain (DS) was also noted in all three segments of left ventricular free wall and ventricular septum and one of three segments of right ventricular free wall. This reduction in strain indices in patients with pulmonary hypertension was noted irrespective of whether right ventricular systolic function was normal or reduced as assessed by two‐dimensional transthoracic echocardiography. SS and DS rates also showed reductions in patients with pulmonary artery hypertension. Our study shows the potential value of TDI indices in identifying reduced regional left ventricular systolic and diastolic longitudinal function in patients with pulmonary artery hypertension and normal left ventricular systolic function by two‐dimensional transthoracic echocardiography. This reduction in left ventricular function was noted in patients with both normal and reduced right ventricular systolic functions by two‐dimensional echocardiography.
Optical manipulation of plasmonic nanoparticles, bubble formation and patterning of SERS aggregates

We present an optical method for patterning SERS (surface-enhanced Raman spectroscopy)—enhancing aggregates of gold nanoparticles, using a focused laser beam to optically trap the nanoparticles in suspension. At high laser powers, heat generated from the plasmonic excitation causes boiling of the aqueous suspension and the formation of gaseous bubbles of water vapor. By measuring the Raman peak of the hydroxyl bond of water, the temperature in the laser spot during the aggregation can be determined in situ. The hydrophilic nanoparticles are found to aggregate at the liquid–vapor interface. By allowing the suspension to dry, a ring of gold nanoparticles is deposited on the substrate, producing a highly SERS-active region. These aggregates are studied using optical microscopy, scanning electron microscopy and micro-Raman spectroscopy.
Homography-based trajectory tracking of industrial manipulator with iterative learning control

In this paper, a repetitive assembling task is considered for industrial manipulator, where vision-based precise trajectory tracking is necessary. Conventional visual servoing methods suffer from their poor dynamic performance, while the proposed open-plus-closed loop framework solved this problem by iterative learning. System error is defined by the directly measurable homography matrix and feature points, without any homography decomposition. Besides, in the proposed controller, image Jacobean is not used so that no singularity problem exists. System convergence is analyzed and simulation results are given to demonstrate the effectiveness, i.e. fairly accurate trajectory tracking is achieved.
SUPPLEMENTAL METHODS AND EXTENDED DERIVATIONS

1.1. MAIT single-cell sequencing data processing. Adaptor sequences from the FastQ files were trimmed by fastqtrimmer (Blankenberg et al., 2010). Sequences were aligned to the UCSC Human genome assembly version 19 and gene expression levels quantified using RSEM (Li and Dewey, 2011), and TPM values were loaded into R (Gentleman et al., 2004) for analyses. Libraries were deemed to be of good quality if they met the following conditions: exonic rate greater than 30%, percent of reads mapped to human greater than 60%, and number of genes with non-zero TPM values greater than 4000. Transcripts were annotated using the BioConductor (Gentleman et al., 2004) transcript annotation database TxDB.Hsapiens. UCSC.hg19. knownGene.
Marvel Universe looks almost like a real social network

We investigate the structure of the Marvel Universe collaboration network, where two Marvel characters are considered linked if they jointly appear in the same Marvel comic book. We show that this network is clearly not a random network, and that it has most, but not all, characteristics of “real-life” collaboration networks, such as movie actors or scientific collaboration networks. The study of this artificial universe that tries to look like a real one, helps to understand that there are underlying principles that make real-life networks have definite characteristics.
A Solution to the Effect of Sample Size on Outlier Elimination

Results from a Monte Carlo study demonstrate how a non-recursive, a simple recursive, a modified recursive, and a hybrid outlier elimination procedure are influenced by population skew and sample size. All the procedures are based on computing a mean and a standard deviation from a sample in order to determine whether an observation is an outlier. Miller (1991) showed that the estimated mean produced by the simple non-recursive procedure can be affected by sample size and that this effect can produce a bias in certain kinds of experiments. We extended this result to the other three procedures. We also create two new procedures in which the criterion used to identify outliers is adjusted as a function of sample size so as to produce results that are unaffected by sample size.