Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Studies of Physiological Traits with Their Application to Sleep Apnea

Advances of modern sensing and sequencing technologies generate a deluge of high dimensional space-temporal physiological and next-generation sequencing (NGS) data. Physiological traits are observed either as continuous random functions, or on a dense grid and referred to as function-valued traits. Both physiological and NGS data are highly correlated data with their inherent order, spacing, and functional nature which are ignored by traditional summary-based univariate and multivariate regression methods designed for quantitative genetic analysis of scalar trait and common variants. To capture morphological and dynamic features of the data and utilize their dependent structure, we propose a functional linear model (FLM) in which a trait curve is modeled as a response function, the genetic variation in a genomic region or gene is modeled as a functional predictor, and the genetic effects are modeled as a function of both time and genomic position (FLMF) for genetic analysis of function-valued trait with both GWAS and NGS data. By extensive simulations, we demonstrate that the FLMF has the correct type 1 error rates and much higher power to detect association than the existing methods. The FLMF is applied to sleep data from Starr County health studies where oxygen saturation were measured in 22,670 seconds on average for 833 individuals. We found 65 genes that were significantly associated with oxygen saturation functional trait with P-values ranging from 2.40E-06 to 2.53E-21. The results clearly demonstrate that the FLMF substantially outperforms the traditional genetic models with scalar trait.
Angle sweeping and scheduling in downlink opportunistic beamforming systems

In the downlink wireless communication systems, opportunistic beamforming is a practical and widely used technique for user-scheduling. The critical element of the opportunistic beamforming is the beamforming. There are many studies focus on the channel fluctuations but put little eyes on the beam's angle. In this paper, we investigate system performance if the beam angle changes in a sweeping way. We consider the scheme under cellular network systems and put more eyes on the slow fading channel states. The base stations equipped with smart antennas which generate beams according to the defined algorithm. An angle sweeping scheme is proposed to change the beam angle from 0 to 2π and bring fluctuations to the channel which make the scheduling better. By combining memory function, the proposed scheme is more practical and suitable for the few user circumstance. We also demonstrate the performance of the proposed algorithm through MATLAB simulation.
Degradation of Nucleosome-associated Centromeric Histone H3-like Protein CENP-A Induced by Herpes Simplex Virus Type 1 Protein ICP0*

Cells infected by herpes simplex virus type 1 in the G2 phase of the cell cycle become stalled at an unusual stage of mitosis defined as pseudoprometaphase. This block correlates with the viral immediate-early protein ICP0-induced degradation of the centromere protein CENP-C. However, the observed pseudoprometaphase phenotype of infected mitotic cells suggests that the stability of other centromere proteins may also be affected. Here, we demonstrate that ICP0 also induces the proteasome-dependent degradation of the centromere protein CENP-A. By a series of Western blot and immunofluorescence experiments we show that the endogenous 17-kDa CENP-A and an exogenous tagged version of CENP-A are lost from centromeres and degraded in infected and transfected cells as a result of ICP0 expression. CENP-A is a histone H3-like protein associated with nucleosome structures in the inner plate of the kinetochore. Unlike fully transcribed lytic viral DNA, the transcriptionally repressed latent herpes simplex virus type 1 genome has been reported to have a nucleosomal structure similar to that of cellular chromatin. Because ICP0 plays an essential part in controlling the balance between the lytic and latent outcomes of infection, the ICP0-induced degradation of CENP-A is an intriguing feature connecting different aspects of viral and/or cellular genome regulation.
Genodroid: are privacy-preserving genomic tests ready for prime time?

As fast and accurate sequencing of human genomes becomes affordable, it is expected that individuals will soon be able to carry around copies of their sequenced DNA, using it for medical, identification, and social purposes. This will undoubtedly prompt a wide range of new and interesting genomic applications. However, the very same progress raises some worrisome privacy issues, since a genome represents a treasure trove of highly personal and sensitive information. Some recent research explored privacy-preserving personal genomic operations by applying (or customizing) cryptographic protocols based on techniques such as: conditional oblivious transfer, garbled circuits, and homomorphic encryption. In this paper, we take this line of work a step further by investigating real-world practicality and usability of (as well as interest in) some of these methods. Motivated by both medical and social applications, we aim to test viability of privacy-agile computational genomic tests in a portable and pervasive setting of modern smartphones. We design a personal genomic toolkit (called GenoDroid), implement it on the Android platform, assess its performance, and conduct a pilot usability study that yields some interesting results.
A new infantile acute febrile mucocutaneous lymph node syndrome (MLNS) prevailing in Japan.

What may be a new disease has been afflicting infants and young children in Japan since 1960. It is an acute, febrile, mucocutaneous condition accompanied by swelling of cervical lymph nodes (tentatively called mucocutaneous lymph node syndrome [MLNS]). It may be misdiagnosed as scarlet fever, the Stevens-Johnson syndrome, or infantile periarteritis nodosa. The disease is now known to be widely occurring all over Japan with an increasing incidence each year. More than 6,000 cases have been reported as of 1973. One to two percent of the patients reported have died suddenly of cardiac failure. All the autopsies showed infantile periarteritis nodosa-like arteritis accompanied by coronary thrombosis and aneurysm. Some of the surviving cases have been shown to have similar changes. These findings lead us to believe that this clinical picture is a new clinical entity. Recently, rickettsia-like bodies were found by electron microscopy in biopsy specimens from the skin and lymph nodes of the patients. The bodies were isolated by yolk sac culture and their pathogenicity is now under investigation.
Bounds on the Size of Sound Monotone Switching Networks Accepting Permutation Sets of Directed Trees

In this paper, we prove almost tight bounds on the size of sound monotone switching networks accepting permutations sets of directed trees. This roughly corresponds to proving almost tight bounds bounds on the monotone memory efficiency of the directed ST-connectivity problem for the special case in which the input graph is guaranteed to have no path from s to t or be isomorphic to a specific directed tree.
Overlapping structural and functional brain changes in patients with long-term exposure to fibromyalgia pain.

OBJECTIVE There is vast evidence to support the presence of brain aberrations in patients with fibromyalgia (FM), and it is possible that central plasticity is critical for the transition from acute to chronic pain. The aim of the present study was to investigate the relationship between brain structure and function in patients with FM. METHODS Functional connectivity of the brain during application of intermittent pressure-pain stimuli and measures of brain structure were compared between 26 patients with FM and 13 age- and sex-matched healthy controls. Magnetic resonance imaging (MRI) was performed to obtain high-resolution anatomic images and functional MRI scans of the brain, which were used for measurements of pain-evoked brain activity. RESULTS FM patients displayed a distinct overlap between decreased cortical thickness, decreased brain volumes, and decreased functional regional coherence in the rostral anterior cingulate cortex. The morphometric changes were more pronounced with longer exposure to FM pain. In addition, there was evidence of an association between structural and functional changes in the mesolimbic areas of the brain and the severity of comorbid depression symptoms in FM patients. CONCLUSION The combined integration of structural and functional measures allowed for a unique characterization of the impact of FM pain on the brain. These data may lead to the identification of early structural and functional brain alterations in response to pain, which could be used to develop markers for predicting the development of FM and other pain disorders.
Facial expression recognition on Android

In this paper we implemented an algorithm to detect facial expression in images provided by the camera in real time. The system is built on tree interesting stages: 1-Face detection using boosted cascade classifier based on haar-like features, to train the cascade a MIT-CBCL face database has been used ; 2-Tracking features points in the face; 3-Facial expression identification using facial Actions Units (AU) defined by P.Viola et al. in their Facial Action Coding System (FACS) [1]. The application can detect four facial expressions: joy, fear, sadness and anger.
Prenatal Insecticide Exposures and Birth Weight and Length among an Urban Minority Cohort

We reported previously that insecticide exposures were widespread among minority women in New York City during pregnancy and that levels of the organophosphate chlorpyrifos in umbilical cord plasma were inversely associated with birth weight and length. Here we expand analyses to include additional insecticides (the organophosphate diazinon and the carbamate propoxur), a larger sample size (n = 314 mother–newborn pairs), and insecticide measurements in maternal personal air during pregnancy as well as in umbilical cord plasma at delivery. Controlling for potential confounders, we found no association between maternal personal air insecticide levels and birth weight, length, or head circumference. For each log unit increase in cord plasma chlorpyrifos levels, birth weight decreased by 42.6 g [95% confidence interval (CI), −81.8 to −3.8, p = 0.03] and birth length decreased by 0.24 cm (95% CI, −0.47 to −0.01, p = 0.04). Combined measures of (ln)cord plasma chlorpyrifos and diazinon (adjusted for relative potency) were also inversely associated with birth weight and length (p < 0.05). Birth weight averaged 186.3 g less (95% CI, −375.2 to −45.5) among newborns with the highest compared with lowest 26% of exposure levels (p = 0.01). Further, the associations between birth weight and length and cord plasma chlorpyrifos and diazinon were highly significant (p ≤ 0.007) among newborns born before the 2000–2001 U.S. Environmental Protection Agency’s regulatory actions to phase out residential use of these insecticides. Among newborns born after January 2001, exposure levels were substantially lower, and no association with fetal growth was apparent (p > 0.8). The propoxur metabolite 2-isopropoxyphenol in cord plasma was inversely associated with birth length, a finding of borderline significance (p = 0.05) after controlling for chlorpyrifos and diazinon. Results indicate that prenatal chlorpyrifos exposures have impaired fetal growth among this minority cohort and that diazinon exposures may have contributed to the effects. Findings support recent regulatory action to phase out residential uses of the insecticides.
Pharmacotherapy for alcohol dependence

Ms. Wortman, Ms. Rabinowitz, and Dr. Oslin are from the Center for the Study of Addictions, Department of Psychiatry, University of Pennsylvania; Dr. Oslin is also from the Section of Geriatric Psychiatry, Department of Psychiatry, University of Pennsylvania and the Mental Illness Research Education and Clinical Center at the University of Philadelphia VA Medical Center—All from Philadelphia, Pennsylvania.
nhaled Corticosteroids and the Risks of Diabetes Onset nd Progression

ACKGROUND: Systemic corticosteroids are known to increase diabetes risk, but the effects of high-dose nhaled corticosteroids are unknown. We assessed whether the use and dose of inhaled corticosteroids ncrease the risk of diabetes onset and progression. ETHODS: We formed a new-user cohort of patients treated for respiratory disease during 1990-2005, dentified using the Quebec health insurance databases and followed through 2007 or until diabetes onset. he subcohort treated with oral hypoglycemics was followed until diabetes progression. A nested caseontrol analysis was used to estimate the rate ratios of diabetes onset and progression associated with urrent inhaled corticosteroid use, adjusted for age, sex, respiratory disease severity, and co-morbidity. ESULTS: The cohort included 388,584 patients, of whom 30,167 had diabetes onset during 5.5 years of ollow-up (incidence rate 14.2/1000/year), and 2099 subsequently progressed from oral hypoglycemic reatment to insulin (incidence rate 19.8/1000/year). Current use of inhaled corticosteroids was associated ith a 34% increase in the rate of diabetes (rate ratio [RR] 1.34; 95% confidence interval [CI], 1.29-1.39) nd in the rate of diabetes progression (RR 1.34; 95% CI, 1.17-1.53). The risk increases were greatest with he highest inhaled corticosteroid doses, equivalent to fluticasone 1000 g per day or more (RR 1.64; 95% I, 1.52-1.76 and RR 1.54; 95% CI, 1.18-2.02; respectively). ONCLUSIONS: In patients with respiratory disease, inhaled corticosteroid use is associated with modest ncreases in the risks of diabetes onset and diabetes progression. The risks are more pronounced at the igher doses currently prescribed in the treatment of chronic obstructive pulmonary disease. 2010 Elsevier Inc. All rights reserved. • The American Journal of Medicine (2010) 123, 1001-1006
Influenza A Gradual and Epochal Evolution: Insights from Simple Models

The recurrence of influenza A epidemics has originally been explained by a “continuous antigenic drift” scenario. Recently, it has been shown that if genetic drift is gradual, the evolution of influenza A main antigen, the haemagglutinin, is punctuated. As a consequence, it has been suggested that influenza A dynamics at the population level should be approximated by a serial model. Here, simple models are used to test whether a serial model requires gradual antigenic drift within groups of strains with the same antigenic properties (antigenic clusters). We compare the effect of status based and history based frameworks and the influence of reduced susceptibility and infectivity assumptions on the transient dynamics of antigenic clusters. Our results reveal that the replacement of a resident antigenic cluster by a mutant cluster, as observed in data, is reproduced only by the status based model integrating the reduced infectivity assumption. This combination of assumptions is useful to overcome the otherwise extremely high model dimensionality of models incorporating many strains, but relies on a biological hypothesis not obviously satisfied. Our findings finally suggest the dynamical importance of gradual antigenic drift even in the presence of punctuated immune escape. A more regular renewal of susceptible pool than the one implemented in a serial model should be part of a minimal theory for influenza at the population level.
Real-world engineering: a course for masters students headed for industry

This paper describes an experimental, project-oriented course whose technical content focuses on the interface between hardware and software. The underlying agenda for the course is to teach students - in one semester - as many skills as possible for succeeding in industrial engineering environments. In essence, we are functioning as part of a small company for one semester. The non-technical portion of the course focuses on communication in speaking and writing: within a project team, with rotating "project leaders ", among separate teams, and with the "CEO" (the first author). The students themselves are helping to create the project part of the course, and the Cornell Academic Technologies Center (via the second author) is supplying tools to enable and evaluate the communication portions of the course guest speakers from diverse branches of high-tech industry provide perspective and advice on career paths for graduates with engineering degrees.
Area coverage planning that accounts for pose uncertainty with an AUV seabed surveying application

This paper presents an overview of our research on accounting for robot pose uncertainty in area coverage applications. In the vast majority of existing literature on robotics area coverage, the location uncertainty of the robot is not considered. An uncertain robot pose results in an uncertain sensor swath, which in turn creates uncertainty about the achieved coverage. Here, we present a general framework where pose estimates are mapped through the coverage sensor model to obtain a probability of coverage over the discretized workspace. This probabilistic representation can then be used to adaptively plan paths for coverage based on an entropy reduction formulation. This framework is particularly well-suited to autonomous underwater vehicles (AUVs) performing seabed surveying operations. The AUV position estimate diverges from the actual AUV position while submerged due to the lack of a global position reference. This discrepancy can result in parts of the seabed being missed, which is unacceptable in safety-critical missions such as mine countermeasures. The proposed information-based path planning approach is able to guarantee area coverage even in the case of severe AUV position estimate drift. In-water experiments with an AUV show the effectiveness of the method.
Tension, what tension?: Website accessibility and visual design

There appears to be a widespread belief within the web design community -- and possibly amongst website commissioners - that accessible sites cannot be visually pleasing. We present the results of accessibility testing of 100 websites with 51 disabled users that should dispel this belief. While there are aspects of accessibility that do affect visual design, such as visual structure, colour contrast and text size, these are aspects of design that can affect all users, not only disabled users. These design concerns must be considered if both the users' experience and business objectives are to be met.
Is Vowel Normalization Independent of Lexical Processing?

Abstract Vowel normalization in speech perception was investigated in three experiments.The range of the second formant in a carrier phrase was manipulated and thisaffected the perception of a target vowel in a compensatory fashion: A low F2 rangein the carrier phrase made it more likely that the target vowel was perceived as afront vowel, that is, with a high F2. Recent experiments indicated that this effectmight be moderated by the lexical status of the constituents of the carrier phrase.Manipulation of the lexical status in the present experiments, however, did notaffect vowel normalization. In contrast, the range of vowels in the carrier phrase didinfluence vowel normalization. If the carrier phrase consisted of mid-to-high frontvowels only, vowel categories shifted only for mid-to-high front vowels. It is arguedthat these results are a challenge for episodic models of word recognition.
Mechanism of water-stress induced cavitation in conifers: bordered pit structure and function support the hypothesis of seal capillary-seeding

Resistance to water-stress induced cavitation is an important indicator of drought tolerance in woody species and is known to be intimately linked to the anatomy of the xylem. However, the actual mechanical properties of the pit membrane are not well known and the exact mode of air-seeding by which cavitation occurs is still uncertain. We examined the relationship between cavitation resistance and bordered pit structure and function in 40 coniferous species. Xylem pressure inducing 50% loss of hydraulic conductance (P50, a proxy for cavitation resistance) varied widely among species, from −2.9 to −11.3 MPa. The valve effect of the pit membrane, measured as a function of margo flexibility and torus overlap, explained more variation in cavitation-resistance than simple anatomical traits such as pit membrane, pit aperture or torus size. Highly cavitation resistant species exhibited both a high flexibility of the margo and a large overlap between the torus and the pit aperture, allowing the torus to tightly seal the pit aperture. Our results support the hypothesis of seal capillary-seeding as the most likely mode of air-seeding, and suggest that the adhesion of the torus to the pit border may be the main determinant of cavitation resistance in conifers.
A process-based approach to knowledge management

U ovom radu analizira se veza između modeliranja poslovnih procesa, upravljanja znanjem i razvoja informacijskih sustava. Cilj rada je opisati pristup prikazivanju znanja o poslovnoj praksi u obliku poslovnih pravila. Objasnjava se postupak pohranjivanja znanja u obliku meta-modela kao sastavnog dijela repozitorija poslovnih procesa koji omogucuje prikaz, pohranjivanje i pracenje znanja, od trenutka njegovog nastanka u poslovnom okruženju, do njegove primjene u razvoju informacijskih sustava. U radu je prikazana studija slucaja Ministarstva financija Republike Hrvatske i opisana je integracija organizacijskog znanja u repozitoriju poslovnih procesa koji je koristen kao osnova za razvoj informacijskog sustava.
Design and Implementation of Decimal Reciprocal Unit

This paper presents the efficient design and implementation of a decimal reciprocal unit according to the Standard for Floating-Point Arithmetic (IEEE-754R), in which the initial approximation of the reciprocal is obtained by using a look-up table and a multiplication. An efficient look-up table creation is described in detail, and the error analysis for the ROMs of different sizes is carefully done in this paper. The presented design utilizes a 210times10 bits ROM followed by three Newton-Raphson iterations. It takes 119 clock cycles to achieve the 16-digit (Decimal-64) accuracy approximation of the reciprocal of a decimal floating-point number. The proposed implementation of decimal reciprocal unit is verified with a Xilinx Virtex-II Pro P70 FPGA device and synthesized by using TMSC 0.18 mum standard cell library.
Designing a Standards-Based Master’s Program in Educational Leadership: Trends, Contexts, and Adaptations, 8(9)

We present a dialogue about the current context for educational leadership preparation that draws upon worldwide thought and discussion. We examine some of the significant developments and a new conceptualization of educational leadership, and we link these developments to implications for preparation of school leaders for the future. These developments may be categorized as shifts in epistemology and values, concerns about the integration of theory with practice, the rise of the standards movement in education for leadership preparation, the contested role of the academy in addressing these issues, new ideas about program design, and specific features of the Alberta context that inform the orientation of an educational leadership program. Upon reflection of these trends and contexts, we conclude with a structure and content proposal for a Master of Education cohort focus group specializing in educational leadership at The University of Lethbridge, Alberta. Appendix A features a description of topics that each of our courses tackle; Appendix B includes some of the Internet sources we used to scan what others say about educational leadership programming.