Miracle-dz/UniFAR-FTUs huggingface dataset:
Querying Uncertain Spatio-Temporal Data

The problem of modeling and managing uncertain data has received a great deal of interest, due to its manifold applications in spatial, temporal, multimedia and sensor databases. There exists a wide range of work covering spatial uncertainty in the static (snapshot) case, where only one point of time is considered. In contrast, the problem of modeling and querying uncertain spatio-temporal data has only been treated as a simple extension of the spatial case, disregarding time dependencies between consecutive timestamps. In this work, we present a framework for efficiently modeling and querying uncertain spatio-temporal data. The key idea of our approach is to model possible object trajectories by stochastic processes. This approach has three major advantages over previous work. First it allows answering queries in accordance with the possible worlds model. Second, dependencies between object locations at consecutive points in time are taken into account. And third it is possible to reduce all queries on this model to simple matrix multiplications. Based on these concepts we propose efficient solutions for different probabilistic spatio-temporal queries. In an experimental evaluation we show that our approaches are several order of magnitudes faster than state-of-the-art competitors.
RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition

Bias is a pervasive problem when characterizing microbial communities. An important source is the difference in lysis efficiencies of different populations, which vary depending on the extraction protocol used. To avoid such biases impacting comparisons between gene and transcript abundances in the environment, the use of one protocol that simultaneously extracts both types of nucleic acids from microbial community samples has gained popularity. However, knowledge regarding tradeoffs to combined nucleic acid extraction protocols is limited, particularly regarding yield and biases in the observed community composition. Here, we evaluated a commercially available protocol for simultaneous extraction of DNA and RNA, which we adapted for freshwater microbial community samples that were collected on filters. DNA and RNA yields were comparable to other commonly used, but independent DNA and RNA extraction protocols. RNA protection agents benefited RNA quality, but decreased DNA yields significantly. Choice of extraction protocol influenced the perceived bacterial community composition, with strong method-dependent biases observed for specific phyla such as the Verrucomicrobia. The combined DNA/RNA extraction protocol detected significantly higher levels of Verrucomicrobia than the other protocols, and those higher numbers were confirmed by microscopic analysis. Use of RNA protection agents as well as independent sequencing runs caused a significant shift in community composition as well, albeit smaller than the shift caused by using different extraction protocols. Despite methodological biases, sample origin was the strongest determinant of community composition. However, when the abundance of specific phylogenetic groups is of interest, researchers need to be aware of the biases their methods introduce. This is particularly relevant if different methods are used for DNA and RNA extraction, in addition to using RNA protection agents only for RNA samples.
Spatial orientations of visual word pairs to improve Bag-of-Visual-Words model

This paper presents a novel approach to incorporate spatial information in the bag-of-visual-words model for category level and scene classiﬁcation. In the traditional bag-of-visual-words model, feature vectors are histograms of visual words. This representation is appearance based and does not contain any information regarding the arrangement of the visual words in the 2D image space. In this framework, we present a simple and efﬁ- cient way to infuse spatial information. Particularly, we are interested in explicit global relationships among the spatial positions of visual words. Therefore, we take advantage of the orientation of the segments formed by Pairs of Identical visual Words (PIW). An evenly distributed normalized histogram of angles of PIW is computed. Histograms pro- duced by each word type constitute a powerful description of intra type visual words relationships. Experiments on challenging datasets demonstrate that our method is com- petitive with the concurrent ones. We also show that, our method provides important complementary information to the spatial pyramid matching and can improve the overall performance.
Differences in specificity of heparin‐dependent antibodies developed in heparin‐induced thrombocytopenia and consequences on cross‐reactivity with danaparoid sodium

Heparin‐induced thrombocytopenia (HIT) is frequently associated with antibodies (Abs) to heparin–PF4 complexes (H‐PF4). In order to investigate whether there are variations in specificity of Abs, we studied 63 samples from patients with suspected HIT. Two groups of samples were separated after comparing their reactivity against H‐PF4 or recombinant PF4 (r‐PF4) using ELISA. In group Ab1 (n = 46), Abs only or mainly bound to H‐PF4 complexes and thus most of the epitopes recognized probably involved both heparin and PF4. In group Ab2 (n = 17), Abs exhibited similar reactivity to r‐PF4 and H‐PF4, and the antigens recognized were possibly neoepitopes mainly expressed by modified PF4 and by H‐PF4 complexes. Platelet activation tests were positive with 56 samples containing high titres of Abs to H‐PF4. Most samples (n = 59) contained IgG antibodies, often associated with IgA antibodies which were more frequently found in group Ab2, and/or IgM. With unfractionated heparin treatment, HIT was associated with Ab1 or Ab2 antibodies, whereas only Ab1 antibodies were detected after low‐molecular‐weight heparin (LMWH). Furthermore, cross‐reactivity with danaparoid sodium was present only in group Ab1 and mainly involved LMWH‐treated patients.
Intracranial calcifications and hemorrhages: characterization with quantitative susceptibility mapping.

PURPOSE To compare gradient-echo (GRE) phase magnetic resonance (MR) imaging and quantitative susceptibility mapping (QSM) in the detection of intracranial calcifications and hemorrhages. MATERIALS AND METHODS This retrospective study was approved by the institutional review board. Thirty-eight patients (24 male, 14 female; mean age, 33 years ± 16 [standard deviation]) with intracranial calcifications and/or hemorrhages diagnosed on the basis of computed tomography (CT), MR imaging (interval between examinations, 1.78 days ± 1.31), and clinical information were selected. GRE and QSM images were reconstructed from the same GRE data. Two experienced neuroradiologists independently identified the calcifications and hemorrhages on the QSM and GRE phase images in two randomized sessions. Sensitivity, specificity, and interobserver agreement were computed and compared with the McNemar test and k coefficients. Calcification loads and volumes were measured to gauge intermodality correlations with CT. RESULTS A total of 156 lesions were detected: 62 hemorrhages, 89 calcifications, and five mixed lesions containing both hemorrhage and calcification. Most of these lesions (146 of 151 lesions, 96.7%) had a dominant sign on QSM images suggestive of a specific diagnosis of hemorrhage or calcium, whereas half of these lesions (76 of 151, 50.3%) were heterogeneous on GRE phase images and thus were difficult to characterize. Averaged over the two independent observers for detecting hemorrhages, QSM achieved a sensitivity of 89.5% and a specificity of 94.5%, which were significantly higher than those at GRE phase imaging (71% and 80%, respectively; P < .05 for both readers). In the identification of calcifications, QSM achieved a sensitivity of 80.5%, which was marginally higher than that with GRE phase imaging (71%; P = .08 and .10 for the two readers), and a specificity of 93.5%, which was significantly higher than that with GRE phase imaging (76.5%; P < .05 for both readers). QSM achieved significantly better interobserver agreements than GRE phase imaging in the differentiation of hemorrhage from calcification (κ: 0.91 vs 0.55, respectively; P < .05). CONCLUSION QSM is superior to GRE phase imaging in the differentiation of intracranial calcifications from hemorrhages and with regard to the sensitivity and specificity of detecting hemorrhages and the specificity of detecting calcifications.
Core executive functions are associated with success in young elite soccer players

Physical capacity and coordination cannot alone predict success in team sports such as soccer. Instead, more focus has been directed towards the importance of cognitive abilities, and it has been suggested that executive functions (EF) are fundamentally important for success in soccer. However, executive functions are going through a steep development from adolescence to adulthood. Moreover, more complex EF involving manipulation of information (higher level EF) develop later than simple executive functions such as those linked to simple working memory capacity (Core EF). The link between EF and success in young soccer players is therefore not obvious. In the present study we investigated whether EF are associated with success in soccer in young elite soccer players. We performed tests measuring core EF (a demanding working memory task involving a variable n-back task; dWM) and higher level EF (Design Fluency test; DF). Color-Word Interference Test and Trail Making Test were performed on an exploratory level as they contain a linguistic element. The lower level EF test (dWM) was taken from CogStateSport computerized concussion testing and the higher level EF test (DF) was from Delis-Kaplan Executive Function System test battery (D-KEFS). In a group of young elite soccer players (n = 30; aged 12–19 years) we show that they perform better than the norm in both the dWM (+0.49 SD) and DF (+0.86 SD). Moreover, we could show that both dWM and DF correlate with the number of goals the players perform during the season. The effect was more prominent for dWM (r = 0.437) than for DF (r = 0.349), but strongest for a combined measurement (r = 0.550). The effect was still present when we controlled for intelligence, length and age in a partial correlation analysis. Thus, our study suggests that both core and higher level EF may predict success in soccer also in young players.
Automated Tracking of Pallets in Warehouses: Beacon Layout and Asymmetric Ultrasound Observation Models

We consider the use of wireless sensor networks to automatically track "perceptive pallets" of materials in warehouses for the purpose of monitoring volumetric and spatial constraints. A combination of radio frequency and ultrasound chirping produces position estimates that are noisy and prone to error. To address this, we measure and characterize the ultrasound response from standard "Cricket" wireless sensor motes and beacons. We develop a non-parametric particle filtering approach to estimate trajectories of moving motes and introduce two asymmetric observation models that incorporate measured cardioid-shaped response patterns of ultrasound. We use simulation to study the effects of mote placement: position error as a function of ceiling height and beacon density, and then perform physical experiments to evaluate the effectiveness of asymmetric vs. symmetric observation models for pallet tracking. Experiments suggest that asymmetric observation models can improve position estimates by as much as 11%.
A mechanism for the cortical computation of hierarchical linguistic structure

Biological systems often detect species-specific signals in the environment. In humans, speech and language are species-specific signals of fundamental biological importance. To detect the linguistic signal, human brains must form hierarchical representations from a sequence of perceptual inputs distributed in time. What mechanism underlies this ability? One hypothesis is that the brain repurposed an available neurobiological mechanism when hierarchical linguistic representation became an efficient solution to a computational problem posed to the organism. Under such an account, a single mechanism must have the capacity to perform multiple, functionally related computations, e.g., detect the linguistic signal and perform other cognitive functions, while, ideally, oscillating like the human brain. We show that a computational model of analogy, built for an entirely different purpose—learning relational reasoning—processes sentences, represents their meaning, and, crucially, exhibits oscillatory activation patterns resembling cortical signals elicited by the same stimuli. Such redundancy in the cortical and machine signals is indicative of formal and mechanistic alignment between representational structure building and “cortical” oscillations. By inductive inference, this synergy suggests that the cortical signal reflects structure generation, just as the machine signal does. A single mechanism—using time to encode information across a layered network—generates the kind of (de)compositional representational hierarchy that is crucial for human language and offers a mechanistic linking hypothesis between linguistic representation and cortical computation.
The effect of feeding level and physiological status on total flow and amino acid composition of endogenous protein at the distal ileum in swine.

An experiment was conducted to investigate the effects of BW, feed intake, and the physiological condition of the animal on the loss and amino acid composition of endogenous protein in swine. Ten growing barrows and five multiparous sows were equipped with a T-cannula in the distal ileum for digesta collection. A protein-free diet was fed to all animals. The barrows were given free access to the experimental diet. The sows also were allowed to consume the diet on an ad libitum basis, and digesta were collected during lactation and in the following gestation period. In addition, digesta from the gravid sows were collected after restricting the sows to 2 kg of feed per day. For each animal group, the endogenous losses of protein and amino acids were calculated in relation to DMI, and the amino acid composition of endogenous protein was calculated. The total endogenous gut protein loss at the distal ileum of growing pigs, lactating sows, and gestating sows, given free access to feed, was 12.4, 9.4, and 11.2 g/kg DMI, respectively. These values were not different (P > .10). However, when gestating sows were fed only 2 kg/d, 17.8 g of endogenous protein was lost per kilogram of DMI, which was higher (P < .05) than for any of the other groups. This difference was mainly caused by higher (P < .05) losses of glycine, proline, and serine. There were no differences (P > .05) in amino acid composition of endogenous protein between growing pigs, lactating sows, and gestating sows given free access to feed, but restricted-fed gestating sows had an amino acid composition of endogenous protein that was significantly different from that of the other groups. The results from the experiment showed that age, BW, and the physiological condition of the animal have little or no effect on the amount of endogenous protein and amino acids lost at the distal ileum of hogs if calculated in relation to DMI. Likewise, the amino acid composition was not affected by the BW or physiological condition of the animal. However, DMI had a significant effect on endogenous protein losses in sows as well as on amino acid composition of endogenous protein.
EFFECT OF SOIL STERILIZATION BY MERCURIC CHLORIDE ON HERBICIDE SORPTION BY SOIL

Microbial inhibitors such as mercuric chloride are frequently used to sterilize soil or soil–water slurries in experimental studies on the fate of xenobiotics in the environment. This study examined the influence of mercuric chloride additions to soil–water slurries on the sorptive behaviour of a phenoxy herbicide (2,4-D) in soil. The results demonstrated that mercuric chloride strongly decreased the capacity of the soil to retain herbicides, and that the interference of mercuric chloride with herbicide sorption increased with increasing soil organic carbon contents. Because of the competitive sorption between mercuric chloride and the phenoxy herbicide, we conclude that mercuric chloride may not be a good soil sterilization procedure for use in xenobiotic fate studies.
Resolving journaling of journal anomaly in android I/O: multi-version B-tree with lazy split

Misaligned interaction between SQLite and EXT4 of the Android I/O stack yields excessive random writes. In this work, we developed multi-version B-tree with lazy split (LS-MVBT) to effectively address the Journaling of Journal anomaly in Android I/O. LS-MVBT is carefully crafted to minimize the write traffic caused by fsync() call of SQLite. The contribution of LS-MVBT consists of two key elements: (i) Multi-version B-tree effectively reduces "the number of fsync() calls" via weaving the crash recovery information within the database itself instead of maintaining a separate file, and (ii) it significantly reduces "the number of dirty pages to be synchronized in a single fsync() call" via optimizing the multi-version B-tree for Android I/O. The optimization of multi-version B-tree consists of three elements: lazy split, metadata embedding, and disabling sibling redistribution. We implemented LS-MVBT in Samsung Galaxy S4 with Android 4.3 Jelly Bean. The results are impressive. For SQLite, the LS-MVBT exhibits 70% (704 insertions/sec vs. 416 insertions/sec), and 1,220% performance improvement against WAL mode and TRUNCATE mode (704 insertions/sec vs. 55 insertions/sec), respectively.
Food-addiction scale measurement in 2 cohorts of middle-aged and older women.

BACKGROUND Excess weight is a major threat to public health. An addiction-like tendency toward certain foods may contribute to overeating. OBJECTIVE We aimed to describe the prevalence and associated characteristics in relation to a food-addiction scale in middle-aged and older women. DESIGN We examined the prevalence and associated characteristics of a food-addiction scale measure in a cross-sectional analysis of 134,175 women participating in 2 ongoing prospective cohort studies of US nurses. RESULTS Overall, 7839 (5.8%) of the women surveyed met the criteria for food addiction measured by using the modified Yale Food Addiction Scale. The prevalence of food addiction was 8.4% in the younger cohort of women aged 45-64 y and 2.7% in the older cohort of women aged 62-88 y. In the multivariate model, body mass index (BMI; in kg/m²) ≥ 35.0 (compared with 18.5-22.9) was associated with food addiction, a prevalence ratio (PR) of 15.83 (95% CI: 12.58, 19.91) in the younger cohort of women, and a PR of 18.41 (95% CI: 11.63, 29.14) in the older cohort of women. Several other demographic characteristics and other factors were associated with the food-addiction measure in both cohorts of women. CONCLUSIONS To our knowledge, for the first time in a large, US-based population of women, we documented the prevalence of food addiction by using a novel measurement scale in middle-aged and older women. The results may provide insight into the strong association between behavioral attributes of food consumption and the development of obesity.
Highly Polarized Optically Selected BL Lacertae Objects

Observations of candidate BL Lacertae objects spectroscopically selected from the Sloan Digital Sky Survey (SDSS) reveal a large fraction of objects with high polarizations (P > 3%). This result confirms that synchrotron radiation makes an important contribution to the observed optical continuum for most objects in the sample. The SDSS sample can be divided into separate categories, with objects of undetermined redshift generally having the highest optical polarization. Polarization as high as 23% and the lack of spectral features suggests that the synchrotron continuum completely dominates the spectra of these sources. The mean polarization levels observed for objects that have measured redshifts is much lower, with the maximum observed polarization for this group being ~10%. The lower polarizations of these objects are reminiscent of the less spectacular polarization levels shown by BL Lac objects discovered in X-ray surveys. We find no SDSS BL Lac candidates at z ≳ 1 with P > 3%, which calls their classification as BL Lac objects into question. In addition, the existence of radio-quiet BL Lac objects is not verified, since none of the 10 potentially radio-weak BL Lac candidates observed are highly polarized. Regardless of whether the high-redshift and radio-weak objects are included in this optical sample, the overall levels of polarization observed are intermediate between those seen for X-ray- and radio-selected BL Lac objects.
Lactobacillus reuteri Surface Mucus Adhesins Upregulate Inflammatory Responses Through Interactions With Innate C-Type Lectin Receptors

The vertebrate gut symbiont Lactobacillus reuteri exhibits strain-specific adhesion and health-promoting properties. Here, we investigated the role of the mucus adhesins, CmbA and MUB, upon interaction of L. reuteri ATCC PTA 6475 and ATCC 53608 strains with human monocyte-derived dendritic cells (moDCs). We showed that mucus adhesins increased the capacity of L. reuteri strains to interact with moDCs and promoted phagocytosis. Our data also indicated that mucus adhesins mediate anti- and pro-inflammatory effects by the induction of interleukin-10 (IL-10), tumor necrosis factor alpha (TNF-α), IL-1β, IL-6, and IL-12 cytokines. L. reuteri ATCC PTA 6475 and ATCC 53608 were exclusively able to induce moDC-mediated Th1 and Th17 immune responses. We further showed that purified MUB activates moDCs and induces Th1 polarized immune responses associated with increased IFNγ production. MUB appeared to mediate these effects via binding to C-type lectin receptors (CLRs), as shown using cell reporter assays. Blocking moDCs with antibodies against DC-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) or Dectin-2 did not affect the uptake of the MUB-expressing strain, but reduced the production of TNF-α and IL-6 by moDCs significantly, in line with the Th1 polarizing capacity of moDCs. The direct interaction between MUB and CLRs was further confirmed by atomic force spectroscopy. Taken together these data suggest that mucus adhesins expressed at the cell surface of L. reuteri strains may exert immunoregulatory effects in the gut through modulating the Th1-promoting capacity of DCs upon interaction with C-type lectins.
Polymorphism of Fecundity Genes (FecB, FecX, and FecG) in the Indian Bonpala Sheep

The present study was designed for screening polymorphism of known fecundity genes in prolific Indian Bonpala sheep. Employing tetra-primer amplification refractory mutation system PCR, 11-point mutations of BMP1B, BMP15, and GDF9 genes of 97 Bonpala ewes were genotyped. The FecB locus of the BMPR1B gene and two loci (G1 and G4) of GDF9 gene were found to be polymorphic. In FecB locus, three genotypes, namely, wild type (Fec++, 0.02), heterozygous (FecB+, 0.23), and mutant (FecBB, 0.75) were detected. At G1 locus of GDF9 gene, three genotypes, namely, wild type (GG, 0.89), heterozygous (GA, 0.10), and mutant (AA, 0.01) were detected. At G4 locus of GDF9 gene, three genotypes, namely, wild type (AA, 0.01), heterozygous (AG, 0.14), and mutant (GG, 0.85) were detected. Statistically no significant correlation of polymorphism of FecB, G1, and G4 loci and litter size was found in this breed. All five loci of BMP15 and three loci of GDF 9 genes were monomorphic. This study reports Bonpala sheep as the first sheep breed where concurrent polymorphism at three important loci (FecB, G1, and G4) of two different fecundity genes (BMPR1B and GDF9) has been found.