Miracle-dz/UniFAR-FTUs huggingface dataset:
"Clustering Categorical Response" Application to Lung Cancer Problems in Living Scales

The study aims to estimate the ability of different grouping techniques on categorical response. We try to find out how well do they work? Do they really find clusters when clusters exist? We use Cancer Problems in Living Scales from the ACS as our categorical data variables and lung cancer survivors as our studying group. Five methods of cluster analysis are examined for their accuracy in clustering on both real CPILS dataset and simulated data. The methods include hierarchical cluster analysis (Ward's method), model-based clustering of raw data, model-based clustering of the factors scores from a maximum likelihood factor analysis, modelbased clustering of the predicted scores from independent factor analysis, and the method of latent class clustering. The results from each of the five methods are then compared to actual classifications. The performance of model-based clustering on raw data is poorer than that of the other methods and the latent class clustering method is most appropriate for the specific categorical data examined. These results are discussed and recommendations are made regarding future directions for cluster analysis research. INDEX WORDS: Cluster analysis, Categorical data, CPILS, ACS, Lung Cancer Survivors, Factor analysis, Latent class clustering. “CLUSTERING CATEGORICAL RESPONSE” APPLICATION TO LUNG CANCER PROBLEMS IN LIVING SCALES
Myelin basic protein-specific T lymphocyte repertoire in multiple sclerosis. Complexity of the response and dominance of nested epitopes due to recruitment of multiple T cell clones.

The human T cell response to the myelin basic protein (MBP) has been studied with respect to T cell receptor (TCR) usage, HLA class II restriction elements, and epitope specificity using a total of 215 long-term MBP-specific T cell lines (TCL) isolated from the peripheral blood of 13 patients with multiple sclerosis (MS) and 10 healthy donors. In most donors, the anti-MBP response was exceedingly heterogeneous. Using a panel of overlapping synthetic peptides spanning the entire length of human MBP, at least 26 epitopes recognized by human TCL could be distinguished. The MBP domain most commonly recognized was sequence 80-105 (31% of MS TCL, and 24% of control TCL). Sequence 29-48 was recognized more frequently by control-derived TCL (24%) than by TCL from MS patients (5%). The MBP epitopes were recognized in the context of DRB1 *0101, DRB5*0101, DRB1*1501, DRB1*0301, DRB1*0401, DRB1*1402, and DRB3*0102, as demonstrated using a panel of DR gene-transfected L cells. The TCR gene usage was also heterogeneous. V beta 5.2, a peptide of which is currently being used in a clinical trial for treatment of MS patients, was expressed by only one of our TCL. However, within this complex pattern of MBP-specific T cell responses, a minority of MS patients were found to exhibit a more restricted response with respect to their TCL epitope specificity. In these patients 75-87% of the TCL responded to a single, patient-specific cluster of immunodominant T cell epitopes located within a small (20-amino acid) domain of MBP. These nested clusters of immunodominant epitopes were noted within the amino acids 80-105, 108-131, and 131-153. The T cell response to the immunodominant epitopes was not monoclonal, but heterogeneous, with respect to fine specificity, TCR usage, and even HLA restriction. In one patient (H.K.), this restricted epitope profile remained stable for > 2 yr. The TCR beta chain sequences of TCL specific for the immunodominant region of HK are consistent with an oligoclonal response against the epitopes of this region (80-105). Further, two pairs of identical sequences were established from TCL generated from this patient at different times (June 1990 and June 1991), suggesting that some TCL specific for the immunodominant region persisted in the peripheral repertoire. The possible role of persistent immunodominant epitope clusters in the pathogenesis of MS remains to be established.
Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

The abundance of different SSU rRNA (“16S”) gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly – from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms. Despite this fact, many studies assume that the abundance of 16S gene sequences is a surrogate measure of the relative abundance of the organisms containing those sequences. Here we present a method that uses data on sequences and genomic copy number of 16S genes along with phylogenetic placement and ancestral state estimation to estimate organismal abundances from environmental DNA sequence data. We use theory and simulations to demonstrate that 16S genomic copy number can be accurately estimated from the short reads typically obtained from high-throughput environmental sequencing of the 16S gene, and that organismal abundances in microbial communities are more strongly correlated with estimated abundances obtained from our method than with gene abundances. We re-analyze several published empirical data sets and demonstrate that the use of gene abundance versus estimated organismal abundance can lead to different inferences about community diversity and structure and the identity of the dominant taxa in microbial communities. Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data.
Remote sensing of canopy chemistry

One of the major uncertainties in predicting climate change comes from a full accounting of carbon-cycle feedbacks, which roughly double physical feedbacks (1, 2). Most of this uncertainty is a result of the many pathways and time scales at which ecosystems interact with the climate system and how these will respond to change (3). The relationship between leaf nitrogen and the carbon cycle is key to many ecosystem processes because photosynthesis provides the energy and carbon-cycle molecules for growth and reproduction (4⇓⇓–7) and decomposition for nutrient cycling (7, 8). Ecologists have long recognized that nitrogen was the most limited nutrient for plant growth (9, 10). Quantifying changes in canopy nitrogen content provides direct information about ecosystem functioning and a method to detect and monitor changes in response to climate forcing (9, 10); thus, it has been a long-term objective for airborne and spaceborne imaging spectroscopy (11⇓–13). Several papers have reported direct detection of canopy nitrogen from airborne imaging spectrometers (14⇓⇓–17). Ollinger (18) argues that selective pressure on plant competition for light, water, and nutrients should result in suites of biochemical and structural traits that integrate their functional strategies. Thus, structural traits affecting light scattering “over scales ranging from cells to canopies” (18) will be convergent with their biochemical traits. Knyazikhin et al. …
Distributed Certification Authority for Mobile Ad Hoc Networks - A Dynamic Approach

A Mobile Ad Hoc Network (MANET) is an infrastructureless network of wireless mobile nodes that cooperate among each other to maintain connectivity of the network. In comparison to wired networks, securing a MANET is more difficult and challenging. One of the effective ways of providing security in MANETs is by using Public Key Cryptography and Certificates. Certificates are issued by a trusted entity known as Certification Authority (CA). In order to provide certification service in MANETs, researchers have proposed the design of a distributed CA based on threshold cryptography. With a distributed CA, nodes obtain certification service from a coalition of threshold number of nodes in the network. In the design of distributed CA that we follow, nodes identify a coalition within their one-hop neighbors. With a distributed CA, when the number of nodes in the network reduces, number of neighbors for nodes also reduces resulting in substantial increase in the certification service delays. In this paper we propose the design of a distributed CA which follows dynamic approach to solve the above problem using a suite of network monitoring protocols. The proposed design is based on the observation that when the number of nodes in the network reduces, the delays involved in obtaining certificates can be reduced by dynamically varying the threshold value.
Effects of adiponectin polymorphisms on the risk of advanced age-related macular degeneration

Abstract Objective: To determine the relationships between variants in adiponectin gene (ADIPOQ) with advanced forms of age-related macular degeneration (AMD) susceptibility. Methods: A total of 189 advanced AMD patients and 168 controls were recruited. Seven tagging single-nucleotide polymorphisms in ADIPOQ were genotyped by the SNaPshot method. Results: Alleles or genotypes of rs822396 distributed significantly differently in advanced AMD patients and controls. The minor allele G at rs822396 was associated with an increased risk of advanced AMD in a dominant model. Furthermore, haplotype analysis revealed that haplotypes AGGACCT and TGACCCC were significantly increased the advanced AMD susceptibility, whereas haplotypes AGAACGC, TGAACGT and TGACAGC had protective effects. Conclusion: ADIPOQ genetic variant rs822396 might affect an individual’s susceptibility to AMD, making it efficient genetic biomarkers for early detection of AMD.
Control Improvisation

We formalize and analyze a new automata-theoretic problem termed control improvisation. Given an automaton, the problem is to produce an improviser, a probabilistic algorithm that randomly generates words in its language, subject to two additional constraints: the satisfaction of an admissibility predicate, and exhibition of a specified amount of randomness. This problem has proved useful, for example, in generating musical improvisations that satisfy rhythmic and melodic constraints, where admissibility was determined by some bounded divergence from a reference melody. We analyze the complexity of the control improvisation problem, giving cases where it is efficiently solvable and cases where it is #P-hard or undecidable. We also show how symbolic techniques based on SAT solvers can be used to approximately solve some of the intractable cases.
Metabolic syndrome and high-sensitivity C-reactive protein in Cubans.

OBJECTIVE We investigated metabolic syndrome and its association with high-sensitivity C-reactive protein (hs-CRP) levels in Cuban Americans. METHODS The study included 161 nondiabetic Cuban Americans (55 men and 106 women) aged > or = 30 years living in South Florida. Metabolic syndrome was defined by using Adult Treatment Panel III criteria. Elevated hs-CRP level was defined as > 3 mg/L. RESULTS Metabolic syndrome was present in 41% of participants, and no differences were seen by sex. The most common components of metabolic syndrome for women were abdominal obesity and elevated blood pressure, whereas for men they were elevated blood pressure and high triglyceride levels. A higher percentage of women had abdominal obesity and low high-density lipoprotein cholesterol levels, whereas a higher percentage of men had high triglyceride levels and abnormal glucose metabolism. The odds of having elevated hs-CRP levels were approximately 4 times higher in participants with metabolic syndrome than in those without it. Mean log hs-CRP increased as number of components of metabolic syndrome increased. Of the components of metabolic syndrome, only abdominal obesity was significantly associated with elevated hs-CRP. CONCLUSIONS Metabolic syndrome was highly prevalent in our population of Cuban Americans. Cuban Americans with metabolic syndrome had elevated hs-CRP levels that might be explained by their abdominal obesity, increasing the risk for type 2 diabetes and cardiovascular diseases.
SCaMC-1Like a Member of the Mitochondrial Carrier (MC) Family Preferentially Expressed in Testis and Localized in Mitochondria and Chromatoid Body

Mitochondrial carriers (MC) form a highly conserved family involved in solute transport across the inner mitochondrial membrane in eukaryotes. In mammals, ATP-Mg/Pi carriers, SCaMCs, form the most complex subgroup with four paralogs, SCaMC-1, -2, -3 and -3L, and several splicing variants. Here, we report the tissue distribution and subcellular localization of a mammalian-specific SCaMC paralog, 4930443G12Rik/SCaMC-1Like (SCaMC-1L), which displays unanticipated new features. SCaMC-1L proteins show higher amino acid substitution rates than its closest paralog SCaMC-1. In mouse, SCaMC-1L expression is restricted to male germ cells and regulated during spermatogenesis but unexpectedly its localization is not limited to mitochondrial structures. In mature spermatids SCaMC-1L is detected in the mitochondrial sheath but in previous differentiation stages appears associated to cytosolic granules which colocalize with specific markers of the chromatoid body (CB) in post-meiotic round spermatids and inter-mitochondrial cement (IMC) in spermatocytes. The origin of this atypical distribution was further investigated by transient expression in cell lines. Similarly to male germ cells, in addition to mitochondrial and cytosolic distribution, a fraction of SCaMC-1L-expressing COS-7 cells display cytosolic SCaMC-1L-aggregates which exhibit aggresomal-like features as the CB. Our results indicate that different regions of SCaMC-1L hinder its import into mitochondria and this apparently favours the formation of cytosolic aggregates in COS-7 cells. This mechanism could be also operational in male germ cells and explain the incorporation of SCaMC-1L into germinal granules.
SVD Feature Selection for Probabilistic Taxonomy Learning

In this paper, we propose a novel way to include unsupervised feature selection methods in probabilistic taxonomy learning models. We leverage on the computation of logistic regression to exploit unsupervised feature selection of singular value decomposition (SVD). Experiments show that this way of using SVD for feature selection positively affects performances.
A template privacy protection scheme for fingerprint minutiae descriptors

It is important in biometric person recognition systems to protect personal data and privacy of users. This paper introduces a new mechanism to revoke and protect fingerprint minutiae information, which can be used in today's security-aware society. The recently developed minutiae cylinder code (MCC), which provides rotation and translation invariant descriptors for accurate fingerprint recognition by describing minutiae neighborhoods with respect to each other, is used as baseline fingerprint descriptor. A hybrid scheme combining a transformation and a user key is designed to provide the MCC-based fingerprint representation with revocability and irreversibility properties for template privacy protection across multiple applications. Furthermore, using the publicly available FVC datasets, it is demonstrated that the designed scheme improves the baseline accuracy of fingerprint recognition using the MCC method.
Revisiting the empirical case against perceptual modularity

Some theorists hold that the human perceptual system has a component that receives input only from units lower in the perceptual hierarchy. This thesis, that we shall here refer to as the encapsulation thesis, has been at the center of a continuing debate for the past few decades. Those who deny the encapsulation thesis often rely on the large body of psychological findings that allegedly suggest that perception is influenced by factors such as the beliefs, desires, goals, and the expectations of the perceiver. Proponents of the encapsulation thesis, however, often argue that, when correctly interpreted, these psychological findings are compatible with the thesis. In our view, the debate over the significance and the correct interpretation of these psychological findings has reached an impasse. We hold that this impasse is due to the methodological limitations over psychophysical experiments, and it is very unlikely that such experiments, on their own, could yield results that would settle the debate. After defending this claim, we argue that integrating data from cognitive neuroscience resolves the debate in favor of those who deny the encapsulation thesis.
Simple and efficient leader election in the full information model

In this paper, we study the leader election problem in the full information model. We show two results in this context. First, we exhibit a constructive O(logN) round protocol that is resilient against linear size coalitions. That is, our protocol is resilient against any coalition of size less then N for some constant (but small) value of . Second, we provide an easy, non-constructive probabilistic argument that shows the existence of O(logN) round protocol in which can be made as large as 1 2 for any positive . Our protocols are extremely simple. Preliminary version appeared in STOC y Work done while at Computer Science Division, University of California at Berkeley, and International Computer Science Institute, Berkeley, CA 94720. Email: rafail@bellcore.com. Supported by an NSF Postdoctoral Fellowship and ICSI. z IBM, Almaden. Work done while at Computer Science Division, University of California at Berkeley, CA 94720. Email: sridhar@cs.Berkeley. EDU. Supported by NSF grant IRI 91-20074 and CCR-9310214. x Computer Science Division, University of California at Berkeley, CA 94720. Email: vazirani@cs.Berkeley. EDU. Supported by NSF grant IRI 91-20074 and CCR-9310214.
Focused crawling with ontology using semi-automatic tagging for relevancy

World Wide Web (WWW) is considered to be the most important source of information now a days but it's difficult to decide which resources are useful and which are more important. Thus to make a specific part of web leading to only the required resources is searched for. The focused crawler crawl a specific part of the web to retrieve the relevant resources. Here in this paper the focused crawler is applied on social network having ontology dependent tags. The ontology here is also used in preprocessing step of focused crawlers to make the search more specific by expanding the search topic semantically. Further the relevancy of manually tagged and semi-automatically tagged resource is compared. Then finally the harvest rate is evaluated for focused crawlers with ontology and using semi-automatic tagging to check for the relevance.
Design dimensions of ambient information systems to facilitate the development of AAL environments

AAL (Ambient Assisted Living) aims to extend the time elderly can live in their home environment by assisting them in carrying out activities of daily living (ADLs). Designers of AAL must not only consider the needs and problems that elders face when carrying out their ADLs, but that elders are characterized by presenting a natural cognitive decline, their attention levels are diminished and that they may consider that new technologies are complex to use. Considering these characteristics of elders, we propose Ambient Information Systems (AIS) as the appropriate technology to assist elders, since they are aesthetically pleasing applications which provide users with abstract representations of valued information. The aim of this work was to identify the design issues that should be addressed for developing AIS that effectively assist elderly with their ADLs. To reach this end, we designed mobile and embedded AIS that help elderly to manage their medication, since it is one of the critical ADLs for enabling "ageing in place". As a result of designing AIS, we identified a set of design attributes that were validated and extended through inspection evaluations with Computer Science and Health professionals.
Multicenter Quality Assessment of PCR Methods for Detection of Enteroviruses

ABSTRACT We conducted a multicenter evaluation of commercial and in-house PCR methods for the detection of enteroviruses. Three coded panels of test and control RNA samples, artificial clinical specimens, and representative enterovirus serotypes were used to assess amplification methods, RNA extraction methods, and reactivities with different enterovirus serotypes. Despite several differences between PCR methods, there was good agreement, although some variation in sensitivity was observed. Most PCR methods were able to detect enterovirus RNA derived from 0.01 50% tissue culture infective dose (TCID50) and were able to detect at least 1 TCID50 of enterovirus in cerebrospinal fluid, stool, or throat swab specimens. Most were also able to detect a wide range of enterovirus serotypes, although serotypic identification was not possible. Some laboratories experienced false-positive results due to PCR contamination, which appeared to result mainly from cross-contamination of specimens during RNA extraction. Provided that this problem is overcome, these PCR methods will prove to be a sensitive and rapid alternative to cell culture for the diagnosis of enterovirus infection.
Parallel Compressed Sensing Reconstruction

In this letter, a parallel reconstruction architecture for compressed sensing is proposed. In this architecture, a measurement matrix is constructed from a block-diagonal sensing matrix and the sparsifying basis of the target signal. In this way, the projection of the signal onto the sparsifying basis can be divided into several segments and all segments can be reconstructed in parallel. Thus, the computational complexity and the time for reconstruction can be reduced significantly. Furthermore, to reduce the number of measurements needed to achieve the desired reconstruction error performance, permutation is introduced for the projection of the signal. To implement permutation in the parallel reconstruction architecture, only a modification is needed for the measurem ent matrix at the encoder side, while decoding can be achieved in parallel.
A Five-Stage Model of the Mental Activities Involved in Directed Skill Acquisition

Abstract : In acquiring a skill by means of instruction and experience, the student normally passes through five developmental stages which we designate novice, competence, proficiency, expertise and mastery. We argue, based on analysis of careful descriptions of skill acquisition, that as the student becomes skilled, he depends less on abstract principles and more on concrete experience. We systematize and illustrate the progressive changes in a performer's ways of seeing his task environment. We conclude that any skill- training procedure must be based on some model of skill acquisition, so that it can address, at each stage of training, the appropriate issues involved in facilitating advancement.