Miracle-dz/UniFAR-FTUs huggingface dataset:
Probabilistic analysis of gene expression measurements from heterogeneous tissues

Motivation: Tissue heterogeneity, arising from multiple cell types, is a major confounding factor in experiments that focus on studying cell types, e.g. their expression profiles, in isolation. Although sample heterogeneity can be addressed by manual microdissection, prior to conducting experiments, computational treatment on heterogeneous measurements have become a reliable alternative to perform this microdissection in silico. Favoring computation over manual purification has its advantages, such as time consumption, measuring responses of multiple cell types simultaneously, keeping samples intact of external perturbations and unaltered yield of molecular content. Results: We formalize a probabilistic model, DSection, and show with simulations as well as with real microarray data that DSection attains increased modeling accuracy in terms of (i) estimating cell-type proportions of heterogeneous tissue samples, (ii) estimating replication variance and (iii) identifying differential expression across cell types under various experimental conditions. As our reference we use the corresponding linear regression model, which mirrors the performance of the majority of current non-probabilistic modeling approaches. Availability and Software: All codes are written in Matlab, and are freely available upon request as well as at the project web page http://www.cs. tut.fi/∼erkkila2/. Furthermore, a web-application for DSection exists at http://informatics.systemsbiology. net/DSection. Contact: timo.p.erkkila@tut.fi; harri.lahdesmaki@tut.fi
The Persistence of Feedback-Induced Energy Savings

Advanced metering devices and new feedback programs and technologies are opening up a wide range of new opportunities to make energy consumption more visible to residential consumers and to engage individuals and households in more thoughtful energy use practices. Data from several recent studies suggest that feedback-induced energy savings can be significant (Darby 2006, EPRI 2009) ranging from 4 to 12 percent on average depending on the technologies employed, the characteristics of the program, and other relevant factors (Ehrhardt-Martinez et al. 2010). However few studies have considered the persistence of feedback-induced energy savings. This paper will assess the persistence of energy savings in three ways: 1) by assessing the relationship between study duration and energy savings across studies, 2) by assessing the persistence of energy savings as reported by a significant subset of the larger sample of primary studies, and 3) by assessing the persistence of energy savings associated with the seven longest feedback studies While the first approach suggests that feedback-related energy savings are smaller for longer studies, the second and third approaches suggests that savings are persistent over time. The paper discusses these seemingly paradoxical results and the insights gained by a further assessment of evidence.
Unemployment and Productivity in the Long Run: The Role of Macroeconomic Volatility

Abstract This paper presents a new empirical regularity between the volatility of productivity growth and long-run unemployment for a given level of long-run productivity growth. A theoretical framework based on asymmetric real wage rigidities is shown to have the potential to rationalize this finding. The model tends to fit U.S. long-run unemployment better than a specification based on long-run productivity growth only, especially during the Great Moderation and the Great Recession.
Somatic microsatellite variability as a predictive marker for colorectal cancer and liver cancer progression

Microsatellites (MSTs) are short tandem repeated genetic motifs that comprise ~3% of the genome. MST instability (MSI), defined as acquired/lost primary alleles at a small subset of microsatellite loci (e.g. Bethesda markers), is a clinically relevant marker for colorectal cancer. However, these markers are not applicable to other types of cancers, specifically, for liver cancer which has a high mortality rate. Here we show that somatic MST variability (SMV), defined as the presence of additional, non-primary (aka minor) alleles at MST loci, is a complementary measure of MSI, and a genetic marker for colorectal and liver cancer. Re-analysis of Illumina sequenced exomes from The Cancer Genome Atlas indicates that SMV may distinguish a subpopulation of African American patients with colorectal cancer, which represents ~33% of the population in this study. Further, for liver cancer, a higher rate of SMV may be indicative of an earlier age of onset. The work presented here suggests that classical MSI should be expanded to include SMV, going beyond alterations of the primary alleles at a small number of microsatellite loci. This measure of SMV may represent a potential new diagnostic for a variety of cancers and may provide new information for colorectal cancer patients.
Extracts of Feijoa Inhibit Toll-Like Receptor 2 Signaling and Activate Autophagy Implicating a Role in Dietary Control of IBD

Background Inflammatory bowel disease (IBD) is a heterogeneous chronic inflammatory disease affecting the gut with limited treatment success for its sufferers. This suggests the need for better understanding of the different subtypes of the disease as well as nutritional interventions to compliment current treatments. In this study we assess the ability of a hydrophilic feijoa fraction (F3) to modulate autophagy a process known to regulate inflammation, via TLR2 using IBD cell lines. Method Mouse embryonic fibroblasts (MEF) deleted for ATG5, and two intestinal epithelial cells HCT15 and HCT116, were used to test the anti-inflammatory effect of F3 after stimulating the cells with a TLR2 specific ligand PAM3CSK4. Results F3 was able to reduce TLR2 specific inflammation and stimulate autophagy in MEFs and HCT15 cells but not in HCT116 cells. The anti-inflammatory effect was reduced in the MEF cells deleted for ATG5. In addition, the activation of autophagy by F3 was enhanced by PAM3CSK4. Conclusion F3 of feijoa can interact with cells via a TLR2 specific mechanism and reduce Nuclear factor kappa B (NF-κB) activation in part due to stimulation of autophagy. These results suggest that there is potential benefit in using feijoa extracts as part of dietary interventions to manage IBD in patients.
Distant Field Blue Horizontal Branch Stars and the Mass of the Galaxy I: Classification of halo A-type stars

This is the first in a series of three papers presenting a new calculation of the mass of the Galaxy based on radial velocities and distances measured for a sample of some 100 faint 16 30 kpc with measured radial velocities by a factor of 5. Faint A-type stars in the Galactic halo have been identified from ubjr photometry in six UK Schmidt fields. These samples include field BHB stars as well as less luminous stars of main-sequence surface gravity, which are predominantly field blue stragglers. We obtain accurate charge-coupled device photometry and spectra to classify these stars. This paper describes our methods for separating out clean samples of BHB stars in a way that is efficient in terms of telescope time required. We use the high signal-to-noise (S/N) ratio spectra of A-type stars of Kinman, Suntzeff & Kraft (published in 1994), and their definitive spectrophotometric A classifications, to assess the reliability of two methods, and to quantify the S/N ratio requirements. First we revisit, refine and extend the hydrogen linewidth versus colour relation as a classifier (here called the D 0 . 1 5 -colour method). The second method is new and compares the shapes of the Balmer lines. With this method (here called the scale-width-shape method) there is no need for colours or spectrophotometry. Using the equivalent width of the Ca II K line as an additional filter we find we can reproduce Kinman, Suntzeff & Kraft's A classifications with both methods. In a sample of stars with strong Balmer lines, equivalent width Hy > 13 A [equivalent to the colour range 0 ≤ (B - V) 0 ≤ 0.2], halo BHB stars can be separated from halo blue stragglers reliably. For the spectroscopy (i.e. both classification methods) the minimum required continuum S/N ratio is 15 A - 1 . For the D 0 . 1 5 -colour method (B - V) 0 colours accurate to 0.03 mag are needed.
Symmetry as a Continuous Feature

Symmetry is treated as a continuous feature and a continuous measure of distance from symmetry in shapes is defined. The symmetry distance (SD) of a shape is defined to be the minimum mean squared distance required to move points of the original shape in order to obtain a symmetrical shape. This general definition of a symmetry measure enables a comparison of the "amount" of symmetry of different shapes and the "amount" of different symmetries of a single shape. This measure is applicable to any type of symmetry in any dimension. The symmetry distance gives rise to a method of reconstructing symmetry of occluded shapes. The authors extend the method to deal with symmetries of noisy and fuzzy data. Finally, the authors consider grayscale images as 3D shapes, and use the symmetry distance to find the orientation of symmetric objects from their images, and to find locally symmetric regions in images.
Learning, information and heterogeneity

Most DSGE models assume full information and model-consistent expectations. This paper relaxes both these assumptions in the context of the stochastic growth model with incomplete markets and heterogeneous agents. Households do not have direct knowledge of the structure of economy or the values of aggregate quanti? ties; instead they form expectations by learning from the prices in their market-consistent information sets. The economy converges quickly to an equilibrium which is similar to the equilibrium with model-consistent expectations and market-consistent information. Learning does not introduce strong dynamics at the aggre-gate level, though more interesting things happen at the household level. At least in the context of this model, assumptions about information seem important for aggregates; assumptions about the ability to form model-consistent expectations less so.
Practice of traditional Chinese medicine for psycho-behavioral intervention improves quality of life in cancer patients: A systematic review and meta-analysis

Background Cancer patients suffer from diverse symptoms, including depression, anxiety, pain, and fatigue and lower quality of life (QoL) during disease progression. This study aimed to evaluate the benefits of Traditional Chinese Medicine psycho-behavioral interventions (TCM PBIs) on improving QoL by meta-analysis. Methods Electronic literature databases (PubMed, CNKI, VIP, and Wanfang) were searched for randomized, controlled trials conducted in China. The primary intervention was TCM PBIs. The main outcome was health-related QoL (HR QoL) post-treatment. We applied standard meta analytic techniques to analyze data from papers that reached acceptable criteria. Results The six TCM PBIs analyzed were acupuncture, Chinese massage, Traditional Chinese Medicine five elements musical intervention (TCM FEMI), Traditional Chinese Medicine dietary supplement (TCM DS), Qigong and Tai Chi. Although both TCM PBIs and non-TCM PBIs reduced functional impairments in cancer patients and led to pain relief, depression remission, reduced time to flatulence following surgery and sleep improvement, TCM PBIs showed more beneficial effects as assessed by reducing both fatigue and gastrointestinal distress. In particular, acupuncture relieved fatigue, reduced diarrhea and decreased time to flatulence after surgery in cancer patients, while therapeutic Chinese massage reduced time to flatulence and time to peristaltic sound. Conclusion These findings demonstrate the efficacy of TCM PBIs in improving QoL in cancer patients and establish that TCM PBIs represent beneficial adjunctive therapies for cancer patients.
High-Fidelity Transmission Acquired via a Developmental Decrease in NMDA Receptor Expression at an Auditory Synapse

Central auditory relay synapses in mature animals follow high-frequency inputs for computation of sound localization. In immature mice, however, transmission at the calyx of Held synapse in auditory brainstem was inaccurate for high-frequency inputs because the summed slow synaptic potential components caused aberrant firings or blocked action potentials. As the mice matured, synaptic potentials became shorter, with smaller and faster NMDA receptor components, thereby establishing the precise one-to-one transmission for high-frequency inputs. Developmental acquisition of this high-fidelity transmission could be mimicked experimentally in immature mice by blocking NMDA receptors withd(−)2-amino-5-phosphonovaleric acid (d-APV). Furthermore, bilateral cochlear ablations at postnatal day 7 (P7) attenuated the developmental decrease of NMDA receptor expression and prevented the acquisition of high-fidelity transmission. We suggest that auditory activity, which begins at P10–P12 in mice, downregulates the expression of postsynaptic NMDA receptors, thereby contributing to the establishment of high-fidelity synaptic transmission.
MAPPING TROPICAL DRY FOREST SUCCESSION WITH CHRIS – PROBA HYPERSPECTRAL IMAGES USING NON – PARAMETRIC DECISSIONAL

Information on the distribution, level of fragmentation, extent and ecosystem health of tropical forests is key for sustainable landscape management. Therefore, information generated from different types of multispectral and hyperspectral sensors is key to monitoring programs that aimed to link ecosystems dynamics to ecosystem services such as carbon sequestration. This is especially significant for emerging tropical secondary forests which may play key roles on programs aimed to mitigate the effects of climate change. In this context, the aim of this presentation is to evaluate the accuracy of Chris/Proba and non – parametric classification as tools to monitor the ecological succession processes in tropical dry forests in Brazil (Parque Estadual da Mata Seca, Minas Gerais). Our results from the non parametric approach were separated into an age class map indicating the probably that a given pixel belongs to a forest succession class.
Output tracking control design of a helicopter model based on approximate linearization

Output tracking control of a helicopter model is investigated. The model is derived from Newton-Euler equations by assuming that the helicopter body is rigid. First, we show that for several choices of output variables exact input-output linearization fails to linearize the whole state space and results in having unstable zero dynamics. By neglecting the couplings between moments and forces, we show that the approximated system with dynamic decoupling is full state linearizable by choosing positions and heading as outputs. We prove that bounded tracking is achieved by applying the approximate control. Next, we derive a diffeomorphism showing that an approximation of the system is differentially flat, thus state trajectory and nominal inputs can be generated from a given output trajectory. Simulation results using both output tracking controllers based on exact and approximate input-output linearization are presented for comparison.
Feature selection for pose invariant lip biometrics

For the first time in this paper we present results showing the effect of out of plane speaker head pose variation on a lip biometric based speaker verification system. Using appearance DCT based features, we adopt a Mutual Information analysis technique to highlight the class discriminant DCT components most robust to changes in out of plane pose. Experiments are conducted using the initial phase of a new multi view AudioVisual database designed for research and development of poseinvariant speech and speaker recognition. We show that verification performance can be improved by substituting higher order horizontal DCT components for vertical, particularly in the case of a train/test pose angle mismatch. We show that the best performance can be achieved by combining this alternative feature selection with multi view training, reporting a relative 45% Equal Error Rate reduction over a common energy based selection.
Galaxy Number Counts from the Sloan Digital Sky Survey Commissioning Data

We present bright galaxy number counts in five broad bands (u′, g′, r′, i′, z′) from imaging data taken during the commissioning phase of the Sloan Digital Sky Survey (SDSS). The counts are derived from two independent stripes of imaging scans along the celestial equator, one each toward the northern and the southern Galactic cap, covering about 230 and 210 deg2, respectively. A careful study is made to verify the reliability of the photometric catalog. For galaxies brighter than r* = 16, the catalog produced by automated software is examined against eye inspection of all objects. Statistically meaningful results on the galaxy counts are obtained in the magnitude range 12 ≤ r* ≤ 21, using a sample of 900,000 galaxies. The counts from the two stripes differ by about 30% at magnitudes brighter than r* = 15.5, consistent with a local 2 σ fluctuation due to large-scale structure in the galaxy distribution. The shape of the number counts–magnitude relation brighter than r* = 16 is well characterized by N ∝ 100.6m, the relation expected for a homogeneous galaxy distribution in a "Euclidean" universe. In the magnitude range 16 < r* < 21, the galaxy counts from both stripes agree very well and follow the prediction of the no-evolution model, although the data do not exclude a small amount of evolution. We use empirically determined color transformations to derive the galaxy number counts in the B and I814 bands. We compute the luminosity density of the universe at zero redshift in the five SDSS bands and in the B band. We find ℛB = 2.4 ± 0.4 × 108 L⊙ h Mpc-3, for a reasonably wide range of parameters of the Schechter luminosity function in the B band.
Calpastatin Gene (CAST) Is Not Associated with Late Onset Sporadic Parkinson’s Disease in the Han Chinese Population

Recent studies point to an association between the late-onset sporadic Parkinson’s disease (PD) and single nucleotide polymorphisms (SNPs) rs1559085 and rs27852 in Ca2+-dependent protease calpain inhibitor calpastatin (CAST) gene. This finding is of interest since loss of CAST activity could result in over activated calpain, potentially leading to Ca2+ dysregulation and loss of substantia nigra neurons in PD. We explored the association between CAST SNPs and late-onset sporadic PD in the Han Chinese population. The study included 615 evaluable patients (363 male, 252 female) with PD and 636 neurologically healthy controls (380 male, 256 female) matched for age, gender, ethnicity, and area of residence. PD cases were identified from the PD cohort of the Chinese National Consortium on Neurodegenerative Diseases (www.chinapd.cn). A total of 24 tag-SNPs were genotyped capturing 95% of the genetic variation across the CAST gene. There was no association found between any of the polymorphisms and PD in all models tested (co-dominant, dominant-effect and recessive-effect). Similarly, none of the common haplotypes was associated with a risk for PD. Our data do not support a significant association between the CAST gene polymorphisms and late onset sporadic PD in the Han Chinese population.
A comparative assessment of handedness and its potential neuroanatomical correlates in chimpanzees (Pan troglodytes) and bonobos (Pan paniscus)

The evolutionary origins of human right-handedness remain poorly understood. Some have hypothesized that tool use served as an important preadaptation for the eventual evolution of population-level right-handedness. In contrast, others have suggested that complex gestural and vocal communication served as prerequisite for the evolution of human right-handedness. In this study, we tested these competing hypotheses by comparing the handedness of bonobos and chimpanzees, two closely related species of Pan, on three different measures of hand use including simple reaching, manual gestures and coordinated bimanual actions. Chimpanzees are well known for their tool using abilities whereas bonobos rarely use tools in the wild. In contrast, many have suggested that bonobos have a more flexible gestural and vocal communication system than chimpanzees. The overall results showed that chimpanzees were significantly more right-handed than bonobos for all three measures suggesting that adaptations for tool use rather than communication may have led to the emergence of human right-handedness. We further show that species differences in handedness may be linked to variation in the size and asymmetry of the motor-hand area of the precentral gyrus. The results are discussed within the context of evolutionary theories of handedness, as well as some limitations in the approach to handedness measurement in nonhuman primates.
A comparative study on shape retrieval using Fourier descriptiors with different shape signatures

Shape is one of the most important features in Content Based Image Retrieval (CBIR). Many shape representations and retrieval methods exists. However, most of those methods either do not well represent shape or are difficult to do normalization (making matching hard). Among them, methods based Fourier descriptors (FD) achieve both well representation and well normalization. Different shape signatures have been exploited to derive FDs, however, FDs derived from different signatures can have significant different effect on the result of retrieval. In this paper, we build a Java retrieval framework to compare shape retrieval using FDs derived from different signatures. Common issues and techniques for shape representation and normalization are also analyzed in the paper. Data is given to show the retrieval result.
Estimating Influenza Disease Burden from Population-Based Surveillance Data in the United States

Annual estimates of the influenza disease burden provide information to evaluate programs and allocate resources. We used a multiplier method with routine population-based surveillance data on influenza hospitalization in the United States to correct for under-reporting and estimate the burden of influenza for seasons after the 2009 pandemic. Five sites of the Influenza Hospitalization Surveillance Network (FluSurv-NET) collected data on the frequency and sensitivity of influenza testing during two seasons to estimate under-detection. Population-based rates of influenza-associated hospitalization and Intensive Care Unit admission from 2010–2013 were extrapolated to the U.S. population from FluSurv-NET and corrected for under-detection. Influenza deaths were calculated using a ratio of deaths to hospitalizations. We estimated that influenza-related hospitalizations were under-detected during 2010-11 by a factor of 2.1 (95%CI 1.7–2.9) for age < 18 years, 3.1 (2.4–4.5) for ages 18-64 years, and 5.2 (95%CI 3.8–8.3) for age 65+. Results were similar in 2011-12. Extrapolated estimates for 3 seasons from 2010–2013 included: 114,192–624,435 hospitalizations, 18,491–95,390 ICU admissions, and 4,915–27,174 deaths per year; 54–70% of hospitalizations and 71–85% of deaths occurred among adults aged 65+. Influenza causes a substantial disease burden in the U.S. that varies by age and season. Periodic estimation of multipliers across multiple sites and age groups improves our understanding of influenza detection in sentinel surveillance systems. Adjusting surveillance data using a multiplier method is a relatively simple means to estimate the impact of influenza and the subsequent value of interventions to prevent influenza.