Miracle-dz/UniFAR-FTUs huggingface dataset:
A call to order

Scientific applications are infrequent users of commercial database management systems. We feel that a key reason is they do not offer good support for ordered data structures, such as multidimensional arrays, that are needed for natural representation of many scientific data types. In this papers, we lay out issues in database support of ordered structures, consider possible approaches along with their advantages and shortcomings, and direct the reader to the wide variety of prior work outside the data management field that might be successfully applied in this endeavor.
Assessing the Poverty Impact of an Assigned Program

Some public programs are assigned more-or-less exclusively to certain observational units. These may be people, households, villages or larger geographic areas. The key thing is that some units get the program and some do not. This chapter reviews tools that can help assess the impacts of such a program, judged against its agreed objectives. The following are examples of the types of programs that can be assessed with the tools discussed in this chapter: • A social fund asks for proposals from community organizations, with preference for proposals from poor areas. Some areas do not apply, and some do, but are rejected. • A workfare program entails extra earnings for participating workers, and gains to the residents of the areas in which the work is done. Others receive nothing. • Infrastructure projects (road or water connections, for example) are targeted to areas that are both poor and poorly endowed in that infrastructure. Other areas do not participate. Notice that in each of these examples, there may be some indirect (or " second-round ") impacts on non-participants. A workfare program may lead to higher earnings for non-participants. Or a road improvement project in one area might improve accessibility elsewhere. Depending on how important these indirect effects are thought to be in the specific application, the " program " may need to be redefined to embrace the spillover effects. Or one might need to combine the type of evaluation discussed here with other tools, such as a model of the labor market to pick up other benefits. The following discussion will assume that the program is already in place, which makes this a case of ex-post impact assessment. 1 That includes the evaluation of a pilot project, as an input to the ex-ante assessment of whether the project should be scaled up. However, doing ex-post evaluations does not mean that the evaluation should start after the program finishes, or even after it begins. Indeed, the best ex-post evaluations are designed ex-ante — often side-by-side with the program itself. This can 1 For an example of an ex-ante impact assessment of an anti-poverty program see Ravallion (1999).
Does indoxyl sulfate, a uraemic toxin, have direct effects on cardiac fibroblasts and myocytes?

AIMS Indoxyl sulfate (IS) is a uraemic toxin found at high concentration in patients with chronic kidney disease (CKD) co-morbid with chronic heart failure (CHF). The aim of this study was to determine direct effects of IS on cardiac cells as well as the pro-inflammatory effect of IS. METHODS AND RESULTS Indoxyl sulfate significantly increased neonatal rat cardiac fibroblast collagen synthesis (by 145.7% vs. control, P < 0.05) and myocyte hypertrophy (by 134.5% vs. control, P < 0.001) as determined by (3)H-proline or (3)H-leucine incorporation, respectively. Indoxyl sulfate stimulated tumour necrosis factor-alpha, interleukin-6 (IL-6), and IL-1beta mRNA expression in THP-1 cells as quantified by RT-PCR. Both p38 (RWJ-67657) and MEK1/2 (U0126) inhibitors suppressed all these effects by IS. Furthermore, western blot analysis showed that IS activated mitogen-activated protein kinase (MAPK) (p38, p42/44) and nuclear factor-kappa B (NFkappaB) pathways. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay showed that IS exerted its effects without affecting cell viability. CONCLUSION This study has, for the first time, demonstrated that IS has pro-fibrotic, pro-hypertrophic, and pro-inflammatory effects, indicating that IS might play an important role in adverse cardiac remodelling mediated via activation of the p38 MAPK, p42/44 MAPK, and NFkappaB pathways. Targeting reduction of IS and/or the pathways it activates may represent a novel therapeutic approach to the management of CHF with concomitant CKD.
Single trial BCI classification accuracy improvement for the novel virtual sound movement-based spatial auditory paradigm

This paper presents a successful attempt to improve single trial P300 response classification results in a novel moving sound spatial auditory BCI paradigm. We present a novel paradigm, together with a linear support vector machine classifier application, which allows a boost in single trial based spelling accuracy in comparison with classic stepwise linear discriminant analysis methods. The results of the offline classification of the P300 responses of seven subjects support the proposed concept, with a classification improvement of up to 80%, leading, in the best case presented, to an information transfer rate boost of 28.8 bit/min.
Are the neurocognitive deficits associated with 3,4-methylenedioxymethamphetamine caused by statistical deficits in ecstasy research? A systematic review

There is growing concern that the majority of modern research may be comprised of false findings, which is partly attributed to unacceptable flexibility in data analyses. Here this issue is considered in the literature suggesting that MDMA (3,4-methylenedioxymethamphetamine) may be associated with neurocognitive deficits. Research suggests that increased exposure to ecstasy is associated with decreased performance on some neuropsychological tests. This claim is supported by the fact that “heavier” users often perform worse than “light” users on neurocognitive tests. However, most studies use different criteria for defining what is considered a “light” or “heavy” ecstasy user. Here the literature was systematically reviewed to compare the criteria used across studies which compare light and heavy ecstasy users. Out of the 19 studies reviewed nine unique points of dichotomization were found. In many cases, heavy users in one study would have been considered light users in another study and vice versa. Most studies (n = 11) did not explain how or justify why a particular criterion was chosen. Only eight studies provided justifications for why they chose a particular criterion and the reasons were often misleading. There are many methodological issues which bring into question the validity of research suggesting MDMA is the cause of neurocognitive deficits. Methodologists have demonstrated that it is unacceptably easy for researchers to report significant findings where no relationship exists, which may have been the case in some studies reporting on the neurocognitive deficits found in ecstasy users.
Investigating multidrug efflux pumps in relation to the antibiotic resistance pattern in Escherichia coli strains from patients in Iran

Objective: To investigate antibiotic resistance pattern of Escherichia coli strains isolated from patients admitted to the Shahid Mostafa Khomeini hospital in Behbahan city and survey its relationship with the presence of efflux pumps. Methods: In this study, 180 isolates of E. coli were collected from Shahid Mostafa Khomeini hospital. After confirmation of strains by standard culturing methods and biochemical tests, their antibiotic resistance was evaluated with agar diffusion test and CLSI standards guidelines. The genes encoding the AcrA-AcrB-TolC efflux pump were identified with PCR. Results: The percentages of resistance of the E. coli isolates to some antibiotics were as follow: novobiocin and rifampin, 68.9%; erythromycin, 52.8%; tetracycline, 52.2% and nalidixic acid, 51.7%. Isolates were sensitive to amikacin, 89.4%; tobramycin, 85.6%; meropenem, 81.7%; chloramphenicol, 77.8% and piperacillin, 65.6%, respectively. 110 (61.1%) strains from 180 taken isolates were found with multidrug- resistance (MDR) but no pandrug-resistance (PDR) was observed. 51.1%, 75.0% and 69.4% of isolates had genes acrA, acrB and tolC, respectively. Comparison of the results of antibiogram obtained from PCR with the two-way correlation test showed that there is a significant positive correlation between the presence of efflux pumps and resistance to antibiotics (excluding carbenicillin, meropenem, chloramphenicol, cefotaxime, rifampin and novobiocin). Conclusion: Due to differences in antibiotic resistance in different strains is required using antibiotic resistance pattern for experimental and specific treatment of patients.
Infrastructure-based MAC in wireless mobile ad-hoc networks

In this paper, an efficient and on-the fly infrastructure is created using our proposed mobile point coordinator (MPC) protocol. Based on this protocol, we also develop an efficient MAC protocol, namely MPC-MAC. Our MAC protocol extends the IEEE 802.11 standard for use in multihop wireless ad-hoc networks implementing both the DCF and PCF modes of operation. The goal, and also the challenge, is to achieve QoS delivery and priority access for real-time traffic in ad hoc wireless environments while maintaining backward compatibility with the IEEE 802.11 standard. The performance of MPC-MAC is compared to the IEEE 802.11 DCF-based MAC without MPC. Simulation experiments show that in all cases the use of PCF benefits real-time packets by decreasing the average delay and the discard ratio. However, this may come at the expense of increasing the average delay for non-real-time data. On the other hand, the discard ratio for both real-time and non-real-time packets improves with the use of PCF. Therefore, our MPC-MAC outperforms the standard DCF IEEE 802.11 MAC protocol in multi-hop ad-hoc environments.
A Novel Approach to Face Recognition using Image Segmentation based on SPCA-KNN Method

In this paper we propose a novel method for face recognition using hybrid SPCA-KNN (SIFT-PCAKNN) approach. The proposed method consists of three parts. The first part is based on preprocessing face images using Graph Based algorithm and SIFT (Scale Invariant Feature Transform) descriptor. Graph Based topology is used for matching two face images. In the second part eigen values and eigen vectors are extracted from each input face images. The goal is to extract the important information from the face data, to represent it as a set of new orthogonal variables called principal components. In the final part a nearest neighbor classifier is designed for classifying the face images based on the SPCA-KNN algorithm. The algorithm has been tested on 100 different subjects (15 images for each class). The experimental result shows that the proposed method has a positive effect on overall face recognition performance and outperforms other examined methods.
Estimating Energy Expenditure With Multiple Models Using Different Wearable Sensors

This paper presents an approach to designing a method for the estimation of human energy expenditure (EE). The approach first evaluates different sensors and their combinations. After that, multiple regression models are trained utilizing data from different sensors. The EE estimation method designed in this way was evaluated on a dataset containing a wide range of activities. It was compared against three competing state-of-the-art approaches, including the BodyMedia Fit armband, the leading consumer EE estimation device. The results show that the proposed method outperforms the competition by up to 10.2 percentage points.
Haptic teleoperation of multiple unmanned aerial vehicles over the internet

We propose a novel haptic teleoperation control framework for multiple unmanned aerial vehicles (UAVs) over the Internet, consisting of the three control layers: 1) UAV control layer, where each UAV is abstracted by, and is controlled to follow the trajectory of, its own kinematic virtual point (VP); 2) VP control layer, which modulates each VP's motion according to the teleoperation commands and local artificial potentials (for inter-VP/VP-obstacle collision avoidance and inter-VP connectivity preservation); and 3) teleoperation layer, through which a remote human user can command all (or some) of the VPs' velocity while haptically perceiving the state of all (or some) of the UAVs over the Internet. Master-passivity/slave-stability and some asymptotic performance measures are proved. Semi-experiment results are presented to validate the theory.
Optimal placement of monitoring equipment in transparent optical networks

The problem of optimal placement of monitoring equipment has been studied in other types of networks such as ad-hoc networks, sensors networks, etc., but to the best of our knowledge, it has been marginally studied for transparent optical networks, although transparent networks offer important advantages such as high capacity or the capability to transport information with different bit-rates, protocols and modulation formats. However, these networks have some limitations from the failure management point of view since failures may traverse longer distances and their effect are spread through the network, thereby increasing the number of alarms received by the network management and causing the degradation of more connections. The optimal placement of monitoring equipment gets even more interesting when considering the high cost of the monitoring equipment. This paper presents the problem definition and a possible solution for any topology of the transparent optical network independently of the lightpaths that are actually established.
The contributions of surface charge and geometry to protein-solvent interaction

To better understand protein-solvent interaction we have analyzed a variety of physical and geometrical properties of the solvent-excluded surfaces (SESs) over a large set of soluble proteins with crystal structures. We discover that all have net negative surface charges and permanent electric dipoles. Moreover both SES area and surface charge as well as several physical and geometrical properties defined by them change with protein size via well-fitted power laws. The relevance to protein-solvent interaction of these physical and geometrical properties is supported by strong correlations between them and known hydrophobicity scales and by their large changes upon protein unfolding. The universal existence of negative surface charge and dipole, the characteristic surface geometry and power laws reveal fundamental but distinct roles of surface charge and SES in protein-solvent interaction and make it possible to describe solvation and hydrophobic effect using theories on anion solute in protic solvent. In particular the great significance of surface charge for protein-solvent interaction suggests that a change of perception may be needed since from solvation perspective folding into a native state is to optimize surface negative charge rather than to minimize the hydrophobic surface area.
Testing an Alternative Method for Estimating the Length of Fungal Hyphae Using Photomicrography and Image Processing

This study aimed to develop and test an unbiased and rapid methodology to estimate the length of external arbuscular mycorrhizal fungal (AMF) hyphae in soil. The traditional visual gridline intersection (VGI) method, which consists in a direct visual examination of the intersections of hyphae with gridlines on a microscope eyepiece after aqueous extraction, membrane-filtration, and staining (e.g., with trypan blue), was refined. For this, (i) images of the stained hyphae were taken by using a digital photomicrography technique to avoid the use of the microscope and the method was referred to as “digital gridline intersection” (DGI) method; and (ii), the images taken in (i) were processed and the hyphal length was measured by using ImageJ software, referred to as the “photomicrography–ImageJ processing” (PIP) method. The DGI and PIP methods were tested using known grade lengths of possum fur. Then they were applied to measure the hyphal lengths in soils with contrasting phosphorus (P) fertility status. Linear regressions were obtained between the known lengths (Lknown) of possum fur and the values determined by using either the DGI (LDGI) (LDGI = 0.37 + 0.97 × Lknown, r2 = 0.86) or PIP (LPIP) methods (LPIP = 0.33 + 1.01 × Lknown, r2 = 0.98). There were no significant (P > 0.05) differences between the LDGI and LPIP values. While both methods provided accurate estimation (slope of regression being 1.0), the PIP method was more precise, as reflected by a higher value of r2 and lower coefficients of variation. The average hyphal lengths (6.5–19.4 m g–1) obtained by the use of these methods were in the range of those typically reported in the literature (3–30 m g–1). Roots growing in P-deficient soil developed 2.5 times as many hyphae as roots growing in P-rich soil (17.4 vs 7.2 m g–1). These tests confirmed that the use of digital photomicrography in conjunction with either the grid–line intersection principle or image processing is a suitable method for the measurement of AMF hyphal lengths in soils for comparative investigations.
Masjids and Maple Leafs: The Influence of Media Culture on Muslim Young Adults’ Ethnic Identities in a Canadian Context

MASJIDS AND MAPLE LEAFS: THE INFLUENCE OF MEDIA CULTURE ON MUSLIM YOUNG ADULTS’ ETHNIC IDENTITIES IN A CANADIAN CONTEXT Natasha Walji Advisory Committee: University of Guelph, June 2018 Dr. Andrea V. Breen Dr. Tricia van Rhijn Dr. Lynda Ashbourne The purpose of this qualitative study was to explore the influence of media stories on ethnic identity development in Muslim Young Adults. Twenty Muslim young adults aged 18-25 residing in Ontario participated in a qualitative interview which focused on the influence of media stories on their ethnic identity. Participant narratives were analyzed using thematic analysis (Braun & Clark, 2006). Findings suggest that master narratives about Muslims that are communicated through media stories tend to position Muslims as violent and scary. Participants described different perceptions and reactions in relation to these media stories, including prompting exploration and expression of ethnic identity, impacts on feelings of belonging and fear, the development of strategies for resistance and implications for current and possible life trajectories. Findings are discussed in relation to implications for future research.
Is the trophic diversity of marine benthic consumers decoupled from taxonomic and functional trait diversity? Isotopic niches of Arctic communities

It is predicted that a diverse array of functional traits in species‐rich assemblages can lead to strong resource partitioning among coexisting species and moderate a wider spectrum of resource use. We compared two benthic communities in an Arctic fjord: a species‐rich community (in an outer basin) and an impoverished community (in a glacially impacted bay) and explored (1) if high species richness was translated into high functional trait richness and (2) if high taxonomic and functional diversity promoted high trophic diversity in terms of resource use (indicated by isotopic niche measures). We documented higher functional trait richness in the outer basin (computed based on traits describing feeding mode, mobility, food source, body size and life habit), but the area occupied by consumers in the δ15N vs. δ13C iso‐space (a proxy for total trophic resource use) did not differ between the two sites. A wide array of functional traits used to acquire food may extend the benthic community trophic niche spatially (where and how animals forage) without impacting the isotopic niche breadth (in this system, mostly reflecting “what animals feed on”) due to the relatively homogenous distribution of isotopic characteristics of detritus pool across vertical scales in marine sediments. Moreover, this trend could indicate that a species‐poor community tends to exploit all the available food items, possibly due to the low food availability for primary consumers in a glacially impacted environment. Communities in glacial bays could therefore be particularly sensitive to future changes in glacial inputs and associated organic matter fluxes.
Sparse and Locally Constant Gaussian Graphical Models

Locality information is crucial in datasets where each variable corresponds to a measurement in a manifold (silhouettes, motion trajectories, 2D and 3D images). Although these datasets are typically under-sampled and high-dimensional, they often need to be represented with low-complexity statistical models, which are comprised of only the important probabilistic dependencies in the datasets. Most methods attempt to reduce model complexity by enforcing structure sparseness. However, sparseness cannot describe inherent regularities in the structure. Hence, in this paper we first propose a new class of Gaussian graphical models which, together with sparseness, imposes local constancy through l1-norm penalization. Second, we propose an efficient algorithm which decomposes the strictly convex maximum likelihood estimation into a sequence of problems with closed form solutions. Through synthetic experiments, we evaluate the closeness of the recovered models to the ground truth. We also test the generalization performance of our method in a wide range of complex real-world datasets and demonstrate that it captures useful structures such as the rotation and shrinking of a beating heart, motion correlations between body parts during walking and functional interactions of brain regions. Our method outperforms the state-of-the-art structure learning techniques for Gaussian graphical models both for small and large datasets.
Defining adolescent common mental disorders using electronic primary care data: a comparison with outcomes measured using the CIS-R

Objective To compare the prevalence of common mental disorders (CMDs) derived from data held in primary care records with that measured using the revised Clinical Interview Schedule (CIS-R) in order to assess the potential robustness of findings based only on routinely collected data. Design and setting Comparison study using linkage between the Avon Longitudinal Study of Parents and Children (ALSPAC) and electronic primary care records. Participants We studied 1562 adolescents who had completed the CIS-R in ALSPAC at age 17–18 years and had linkage established to their primary care records. Outcome measures Outcome measures from ALSPAC were whether or not an individual met International Classification of Diseases-10 criteria for a diagnosis of (1) a CMD or, specifically, (2) depression. Lists of Read codes corresponding to diagnoses, symptoms and treatments were used to create 12 definitions of CMD and depression alone using the primary care data. We calculated sensitivities and specificities of these, using CIS-R definitions as the reference standard. Results Sensitivities ranged from 5.2% to 24.3% for depression and from 3.8% to 19.2% for CMD. The specificities of all definitions were above 98% for depression and above 96% for CMD. For both outcomes, the definition that included current diagnosis, treatment or symptoms identified the highest proportion of CIS-R cases. Conclusions Most individuals meeting case definitions for CMD based on primary care data also met CIS-R case definitions. Conversely many individuals identified as cases using the CIS-R had no evidence of CMD in their clinical records. This suggests that clinical databases are likely to yield underestimates of the burden of CMD in the population. However, clinical records appear to yield valid diagnoses which may be useful for studying risk factors and consequences of CMD. The greatest epidemiological value may be obtained when information is available from survey and clinical records.