Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast Convolutional Sparse Coding ( FCSC )

Convolutional sparse coding remedies the shortcomings of the traditional (patch-based) sparse coding by modeling shift invariance directly. This yields more parsimonious coding schemes but increases complexity by coupling the coding problem for neighboring image patches where they overlap. Here we describe an optimization approach which exploits the separability of convolution across bands in the frequency domain in order to make dictionary learning efficient. Our presentation follows the notation in the paper of [Bristow et al. IEEE CVPR 2013] but includes additional implementation details and corrects some inaccuracies and typos. 1
Fluvial landscapes of the Harappan civilization

The collapse of the Bronze Age Harappan, one of the earliest urban civilizations, remains an enigma. Urbanism flourished in the western region of the Indo-Gangetic Plain for approximately 600 y, but since approximately 3,900 y ago, the total settled area and settlement sizes declined, many sites were abandoned, and a significant shift in site numbers and density towards the east is recorded. We report morphologic and chronologic evidence indicating that fluvial landscapes in Harappan territory became remarkably stable during the late Holocene as aridification intensified in the region after approximately 5,000 BP. Upstream on the alluvial plain, the large Himalayan rivers in Punjab stopped incising, while downstream, sedimentation slowed on the distinctive mega-fluvial ridge, which the Indus built in Sindh. This fluvial quiescence suggests a gradual decrease in flood intensity that probably stimulated intensive agriculture initially and encouraged urbanization around 4,500 BP. However, further decline in monsoon precipitation led to conditions adverse to both inundation- and rain-based farming. Contrary to earlier assumptions that a large glacier-fed Himalayan river, identified by some with the mythical Sarasvati, watered the Harappan heartland on the interfluve between the Indus and Ganges basins, we show that only monsoonal-fed rivers were active there during the Holocene. As the monsoon weakened, monsoonal rivers gradually dried or became seasonal, affecting habitability along their courses. Hydroclimatic stress increased the vulnerability of agricultural production supporting Harappan urbanism, leading to settlement downsizing, diversification of crops, and a drastic increase in settlements in the moister monsoon regions of the upper Punjab, Haryana, and Uttar Pradesh.
The Diseased Body and the Global Subject: The Circulation and Consumption of an Iconic AIDS Photograph in East Africa

This article focuses on a photographic image that has become iconic of the journey of AIDS patients in Kenya: the representation of a young man's emaciated body “before treatment” with antiretroviral therapy (ART), and another of the same man “after treatment” and the restoration of his health and life. Showing one of his patients in Haiti and taken by the medical anthropologist and activist Paul Farmer, the photograph traveled to Kenya where it was made into an AIDS-education poster and used as a key tool in ART programs. With its strong “conversion” narrative, the poster seeks to convert viewers to a biomedical way of seeing, and experiencing, disease and infection. I explore the production, circulation and reception of this image, its social history and its agency, as it entered into local moral economies concerning HIV, visibility and value, and drew globalized connections, discourses and practices into novel forms of self-fashioning. In being stretched across different scales, and in being displayed in public as well as domestic spaces, this photographic object creates new relationships between these spaces and the actors who inhabit them.
A XML-Based Approach to Integrating Heterogeneous Yeast Genome Data

While there are an increasing number of genomes (including the human genome) whose sequences have been fully or nearly completed, the budding yeast Saccharomyces cerevisiae was the first fully sequenced eukaryotic genome. Given its ease of genetic manipulation and the fact that many of its genes are strikingly similar to human genes, the yeast genome has been studied extensively through a wide range of biological experiments (e.g., microarray experiments). As a result, a large variety of types of yeast genome data have been generated and made accessible through many resources (e.g., SGD, MIPS, and YPD). While these resources serve many specific needs of individual researchers, we can reap more benefits by integrating these disparate datasets to facilitate larger-context data mining. However, such integrated analysis is hampered by the heterogeneous formats that are used for data distribution. With the increasing use of eXtensible Mark Language (XML) in the bioinformatics domain, we demonstrate how to use XML to standardize the exchange of a variety of types of yeast data between different resources. In particular, we propose a standard XML format called “Yeast Hub XML” (YHX). This format consists of: i) metadata and ii) data. While the former describes the resource and data structure, the latter is used to represent the data. In addition, we apply various XML-related technologies including XPath and XSLT to query, integrate, and transform multiple XML datasets. We have implemented a prototype yeast hub server that allows sharing, querying, and integration of different types and formats of yeast genome data that are located in disparate sources.
Aggregation of plant protoplasts by artificial lipid vesicles.

Sonicated unilamellar lipid vesicles, consisting of egg lecithin, stearylamine, and cholesterol in 7:2:1 molar ratios, promoted the aggregation of tobacco (Nicotiana glutinosa) protoplasts with the aid of mono- or divalent cations.A reaction mixture containing liposomes (0.4 micromoles lipid per milliliter), 50 millimolar CaCl(2), 0.5 molar mannitol, and 5 x 10(5) protoplasts per milliliter resulted in approximately 25% protoplast aggregation. To achieve the maximum protoplast aggregation, 1.6 x 10(8) liposomes per protoplast per hour would be required.The kind of liposomes effective in protoplast aggregation were positively charged, small-size vesicles which were obtained either by 60-minute sonication or by membrane filtration in conjunction with sonication.
Intelligent control using generalizing case-based reasoning with neural networks

One model of human learning involves choosing an action based on past experiences in similar situations. The chosen action is typically modified to compensate for any discrepancies with the current situation. After sufficient experience has been obtained, at least in a particular regime, the experiences are conceptualized into a general response mechanism. This thesis presents an algorithm that formalizes this hybrid reasoning process and applies it to control of a nonlinear physical system. Experiences are stored as vectors of variables known as cases in a set called a casebase. Vector norms are used to select an appropriate case from the casebase which is then modified using an adaptation routine. Once the modified action is applied to the system and the resulting outcome is observed, the casebase is augmented to include the new experience for improved future performance. A gated expert neural network is eventually trained on subsets of the casebase to create local inverse model approximations for regions of the input space where sufficient data is available to support generalization. The gate network selects one of the experts if appropriate or otherwise defaults back to casebased reasoning. The applicability of the hybrid algorithm is demonstrated on a nonlinear control problem, setpoint regulation in a ball and beam system.
Dicer is required for the formation of white but not brown adipose tissue

Dicer, an enzyme involved in microRNA maturation, is required for proper embryo gastrulation and tissue morphogenesis during mammalian development. Using primary cultures of fibroblasts and pre‐adipocytes, we have previously shown that Dicer is essential for early stages of adipogenic cell differentiation. In this study, we have utilized Dicer‐conditional mice to explore a role for Dicer and microRNA biogenesis in the terminal differentiation of adipocytes in vivo and in the formation of white and brown adipose tissue. Deletion of Dicer in differentiated adipocytes in Dicer‐conditional, aP2‐Cre transgenic mice reduced the level of various adipogenic‐associated transcripts and inhibited lipogenesis in white adipocytes, resulting in a severe depletion of white adipose tissue in mice. In contrast, Dicer was not required in vivo for lipogenesis in brown adipose or for brown fat formation. However, Dicer deletion in brown adipose did decrease the expression of genes involved in thermoregulation. The results of our study provide genetic evidence of a role for microRNA molecules in regulating adipogenesis and reveal distinct requirements for Dicer in the formation of white and brown adipose tissue. J. Cell. Physiol. 226: 1399–1406, 2011. © 2010 Wiley‐Liss, Inc.
Teaching to enhance research

ABSTRACT In this paper, I present a conceptual argument for ‘teaching-led research’ in which university lecturers construct courses that directly and positively influence their research, while at the same time, safeguard and enhance the student experience. A research-pedagogy for higher education considers the link between teaching and research, but rather than the more usual conception of research-led teaching, in which teaching is enhanced by research, it becomes teaching-led research in which research is enhanced by teaching. I argue that this idea is foundational to the modern research university, but also difficult to realize unless teaching and learning are designed for these ends. A potential model is teaching undergraduates as researchers with students learning by doing research and I present a case study from a science degree programme. I conclude by anticipating the likely cultural and political barriers to teaching-led research and suggest how tensions can be managed.
Domain-Swapped Dimer of Pseudomonas aeruginosa Cytochrome c 551: Structural Insights into Domain Swapping of Cytochrome c Family Proteins

Cytochrome c (cyt c) family proteins, such as horse cyt c, Pseudomonas aeruginosa cytochrome c 551 (PA cyt c 551), and Hydrogenobacter thermophilus cytochrome c 552 (HT cyt c 552), have been used as model proteins to study the relationship between the protein structure and folding process. We have shown in the past that horse cyt c forms oligomers by domain swapping its C-terminal helix, perturbing the Met–heme coordination significantly compared to the monomer. HT cyt c 552 forms dimers by domain swapping the region containing the N-terminal α-helix and heme, where the heme axial His and Met ligands belong to different protomers. Herein, we show that PA cyt c 551 also forms domain-swapped dimers by swapping the region containing the N-terminal α-helix and heme. The secondary structures of the M61A mutant of PA cyt c 551 were perturbed slightly and its oligomer formation ability decreased compared to that of the wild-type protein, showing that the stability of the protein secondary structures is important for domain swapping. The hinge loop of domain swapping for cyt c family proteins corresponded to the unstable region specified by hydrogen exchange NMR measurements for the monomer, although the swapping region differed among proteins. These results show that the unstable loop region has a tendency to become a hinge loop in domain-swapped proteins.
A distance-based classifier built on class model

In this paper we propose a new type of distance-based classifier. Traditionally, these classifiers are instancebased: they classify a test instance by computation of a similarity measure between that instance and the instances in the training-set and assigning it the same class of the most similar k instances. This method is simple but has some disadvantages, among which there is the greater sensitivit y to the local presence of noise in the training-set, the need to compute many similarity measures and the difficulty to decide the value of k. In our approach the classifier is model-based: it first constructs a probabilistic model for each class based on a selection of the itemsets, weighted by their probability to appear in the training data instances of the given class. Then it uses these class models to predict the class of test instances by calculating the distance between the test instance and each of the class model. We have experimented with four different proximity measures and different metrics of itemsets selection on a large collection of datasets from UCI archive. We show that our methods has many benefits. It reduces the number of distance computations. It improves classification accuracy of state-of-the art cla ssifiers, like decision trees, SVM, k-nn, Naive Bayes, rulebased classifiers and association rule-based ones. Finally , it is less sensitive to overfitting and to noise. We perform also an automatic tuning of the algorithmic parameters like the itemsets frequency threshold and the itemsets selectio n.
An efficient approach to tune modern power system stabilizers using harmony search

A multiband power system stabilizer tuning method, in which objective is to enhance the damping of the rotor oscillations and system stability is proposed in this paper. This tuning approach is based on an efficient search algorithm known as harmony search algorithm. Robust design problem of PSS4B is considered as an optimization problem with nonlinear simulation based objective function. A single machine infinite bus (SMIB) system is evaluated under large range of loading conditions and disturbances for performance investigation of the proposed design. In order to demonstrate the effectiveness of designed PSS4B stabilizers, time domain simulations are carried out for SMIB system. Superiority of the proposed PSS4B design is proved by comparative study of transient responses with existing model of PSS4B.
A natural form of learning can increase and decrease the survival of new neurons in the dentate gyrus

Granule cells born in the adult dentate gyrus undergo a 4‐week developmental period characterized by high susceptibility to cell death. Two forms of hippocampus‐dependent learning have been shown to rescue many of the new neurons during this critical period. Here, we show that a natural form of associative learning, social transmission of food preference (STFP), can either increase or decrease the survival of young granule cells in adult rats. Increased numbers of pyknotic as well as phospho‐Akt‐expressing BrdU‐labeled cells were seen 1 day after STFP training, indicating that training rapidly induces both cell death and active suppression of cell death in different subsets. A single day of training for STFP increased the survival of 8‐day‐old BrdU‐labeled cells when examined 1 week later. In contrast, 2 days of training decreased the survival of BrdU‐labeled cells and the density of immature neurons, identified with crmp‐4. This change from increased to decreased survival could not be accounted for by the ages of the cells. Instead, we propose that training may initially increase young granule cell survival, then, if continued, cause them to die. This complex regulation of cell death could potentially serve to maintain granule cells that are actively involved in memory consolidation, while rapidly using and discarding young granule cells whose training is complete to make space for new naïve neurons. Published 2005 Wiley‐Liss, Inc.
Automatic speech summarization applied to English broadcast news speech

This paper reports an automatic speech summarization method and experimental results using English broadcast news speech. In our proposed method, a set of words maximizing a summarization score indicating an appropriateness of summarization is extracted from automatically transcribed speech. This extraction is performed using a Dynamic Programming (DP) technique according to a target compression ratio. We have previously tested the performance of our method using Japanese broadcast news speech. Since our method is based on a statistical approach, it could be applied to any language. In this paper, English broadcast news speech transcribed using a speech recognizer is automatically summarized. In order to apply our method to English, the model of estimating word concatenation probabilities based on a dependency structure in the original speech given by a Stochastic Dependency Context Free Grammar (SDCFG) is modified. A summarization method for multiple utterances using two-level DP technique is also proposed.
Phosphoinositide 3-Kinase Activation in Late G1 Is Required for c-Myc Stabilization and S Phase Entry

ABSTRACT Phosphoinositide 3-kinase (PI3K) is one of the early-signaling molecules induced by growth factor (GF) receptor stimulation that are necessary for cell growth and cell cycle entry. PI3K activation occurs at two distinct time points during G1 phase. The first peak is observed immediately following GF addition and the second in late G1, before S phase entry. This second activity peak is essential for transition from G1 to S phase; nonetheless, the mechanism by which this peak is induced and regulates S phase entry is poorly understood. Here, we show that activation of Ras and Tyr kinases is required for late-G1 PI3K activation. Inhibition of late-G1 PI3K activity results in low c-Myc and cyclin A expression, impaired Cdk2 activity, and reduced loading of MCM2 (minichromosome maintenance protein) onto chromatin. The primary consequence of inhibiting late-G1 PI3K was c-Myc destabilization, as conditional activation of c-Myc in advanced G1 as well as expression of a stable c-Myc mutant rescued all of these defects, restoring S phase entry. These results show that Tyr kinases and Ras cooperate to induce the second PI3K activity peak in G1, which mediates initiation of DNA synthesis by inducing c-Myc stabilization.
Comparative Experiments on Large Vocabulary Speech Recognition

We describe recent changes to the BYBLOS system's training and recognition algorithms and report on numerous experiments in large vocabulary speech recognition. In earlier work, we performed five key experiments that were designed to answer questions related to different training scenarios. We investigated (1) the effect of varying the number of training speakers if the total amount of training data remains constant, (2) data pooling versus model averaging for generating speaker-independent (SI) HMMs, (3) the benefit of doubling the acoustic training data, (4) SI versus SD performance when the SI training data is twelve times greater, (5) the effect of cross-domain training for both the acoustic and language models. Our recent work was focused on four specific problem areas sharing the common thread that the test condition exposes the recognizer to phenomena not observed in the training data. Here we investigated (1) words outside the vocabulary, (2) spoken language effects due to subject variability and spontaneous dictation, (3) non-native dialects of the language, and (4) new microphones not used in training. <<ETX>>
Versatile protein tag, SUMO: Its enzymology and biological function

Small ubiquitin‐related modifier (SUMO) is a member of a ubiquitin‐like protein family that regulates cellular function of a variety of target proteins. SUMO and ubiquitin are synthesized as precursors that need to be processed prior to conjugation to target proteins, and their mature forms have a similar tertiary structure. The mechanism for SUMO conjugation is also analogous to that of the ubiquitin system, such as the utilization of E1, E2, and E3 cascade enzymes. However, the biological consequence of SUMO modification is quite different from that of the ubiquitin system. Whereas ubiquitination of most proteins is for the degradative pathway, SUMO modification of target proteins is involved in nuclear protein targeting, formation of subnuclear structures, regulation of transcriptional activities or DNA binding abilities of transcription factors, and control of protein stability. This review will summarize the recent progress made in the enzymology of SUMO and its biological significance. © 2002 Wiley‐Liss, Inc.
An Analysis Tool to Evaluate Effect of Retransmissions on SIP Server Overloading

As the number of mobile application traffic keeps increasing, the operators face the scalability challenges of VoIP protocols. We introduce an analysis tool to evaluate the effect of SIP retransmission mechanism on the SIP server overloading. Our tool is capable of creating various arrival and departure processes using Markov Modulated Poisson Process (MMPP). Extensive numerical experiments are performed by varying mode durations of MMPP and buffer sizes of SIP server. Numerical results indicate that the number of total retransmissions significantly decreases if an incoming request is dropped instead of buffered when the queuing delay of the server has an approximate value of the first retransmission timer. The results provide valuable insights for designing an efficient overload control mechanism for SIP servers.
A population‐based case‐control study of EBV and other viral antibodies among persons with Hodgkin's disease and their siblings

The Epstein‐Barr virus (EBV) has been consistently found to be associated with Hodgkin's disease (HD) in two ways: cases generally have elevated titer distributions of antibodies against the viral capsid antigen, and the occurrence of HD among persons with a history of EBV infectious mononucleosis is two or three times higher than expected. We evaluated this association by measuring the prevalence and level of antibodies against EBV and related viruses among 304 cases of HD interviewed in a population‐based study in comparison to 285 of their siblings. The most significant finding was that antibody titers to the viral capsid antigen of EBV were elevated (± 1:320) in 39% of the cases and in only 14% of the sibling‐controls; the relative risk adjusted for age and sex was 4.1. The geometric mean titer was three‐fold higher among cases (175.6vs. 58.1) Subjects who reported a history of IM had a higher distribution of titers than those who did not. Cases also had elevated titers against the early antigen of EBV ‐ the D Component being most prominent. A significantly higher proportion of cases has elevated titers against CMV, relative risk = 3.4, but the prevalence of CMV antibody was relatively low and not consistently higher among cases. The findings support the hypothesis that EBV may play a role in the pathogenesis of HD among persons with elevated titers. The findings neither confirm nor deny a possible role of CMV.
High efficiency test system for envelope tracking Power amplifier

Design houses are facing business challenges as improving chip performance and integrating latest technologies now. Particularly in PA design area, envelop tracking (ET) and digital distortion (DPD) are main approaches used in improving the performance of PA. The system is discussed in this paper, which is not only including the regular PA test, but also the additional details for ET, such as the synchronization between Radio Frequency (RF) signal and envelope reference signal, and the extraction of shaping table. This paper discusses a method to improve the performance of Power Modulator, which is used to amplify the reference signal as the power amplifier's DC signal. Normally, ATE is used in production line test, but in lab test, traditional test instruments are used. So this approach consumes a lot of time from engineers in data correlation. This paper promotes a high efficiency test system for ETPA, which is based on an open, modular-based platform, compatible for both lab test and production line test.