Miracle-dz/UniFAR-FTUs huggingface dataset:
Using novel MEMS EEG sensors in detecting drowsiness application

Electroencephalographic (EEG) analysis has been widely adopted for the monitoring of cognitive state changes and sleep stages because abundant information in EEG recording reflects changes in drowsiness, arousal, sleep, and attention, etc. In this study, micro-electro-mechanical systems (MEMS) based silicon spiked electrode array, namely dry electrodes, are fabricated and characterized to bring EEG monitoring to the operational workplaces without requiring conductive paste or scalp preparation. An isotropic/anisotropic reactive ion etching with inductive coupled plasma (RIE-ICP) micromachining fabrication process was developed to manufacture the needle-like micro probes to pierce the stratum corneum of skin and obtain superior electrically conducting characteristics. This article reports a series of prosperity testing and evaluations of continuous EEG recordings. Our results suggest that the dry electrodes have advantages in electrode-skin interface impedance, signal intensity and size over the conventional (wet) electrodes. In addition, we also developed an EEG-based drowsiness estimation system that consists of the dry-electrode array, power spectrum estimation, principal component analysis (PCA)-based EEG signal analysis, and multivariate linear regression to estimate driverpsilas drowsiness level in a virtual-reality-based dynamic driving simulator to demonstrate the potential applications of the MEMS electrodes in operational environments.
Identification of Novel Inhibitors for Tobacco Mosaic Virus Infection in Solanaceae Plants

Tobacco mosaic virus (TMV) infects several crops of economic importance (e.g., tomato) and remains as one of the major concerns to the farmers. TMV enters the host cell and produces the capping enzyme RNA polymerase. The viral genome replicates further to produce multiple mRNAs which encodes several proteins, including the coat protein and an RNA-dependent RNA polymerase (RdRp), as well as the movement protein. TMV replicase domain was chosen for the virtual screening studies against small molecules derived from ligand databases such as PubChem and ChemBank. Catalytic sites of the RdRp domain were identified and subjected to docking analysis with screened ligands derived from virtual screening LigandFit. Small molecules that interact with the target molecule at the catalytic domain region amino acids, GDD, were chosen as the best inhibitors for controlling the TMV replicase activity.
Ivermectin imposes selection pressure on P-glycoprotein from Onchocerca volvulus: linkage disequilibrium and genotype diversity

Widespread use of ivermectin (IVM) as part of the Onchocerciasis Control Program (OCP) in West Africa could influence the evolution of the human filarial parasite Onchocerca volvulus. Use of IVM, in some areas for 15 years, may have restricted genetic diversity of O. volvulus, resembling effects attributed to a population bottleneck. Large population-based chemotherapy programmes, such as the OCP, may impose strong selection pressure on parasites and an examination of possible genetic selection by IVM in O. volvulus is warranted. IVM is a substrate for P-glycoprotein; a homologue from O. volvulus (OvPGP) has been linked with IVM sensitivity. Linkage disequilibrium (LD) patterns of 28 genetic markers spanning the OvPGP locus were examined in 4 O. volvulus populations from the Volta Region of Ghana, West Africa. Reduced gene diversity, increased heterozygosity and an increase in the number of markers not in Hardy-Weinberg equilibrium were associated with increasing IVM treatment. The number of regions in LD decreased with treatment and with time. However, between 1999 and 2002, seven regions of OvPGP were always in complete LD, while surrounding areas showed a reduction in genetic variation. The use of IVM for onchocerciasis control has imposed strong selection on O. volvulus populations, reducing genetic variation and disrupting LD.
Are Unaligned Words Important for Machine Translation?

In this paper, we deal with the problem of a large number of unaligned words in automatically learned word alignments for machine translation (MT). These unaligned words are the reason for ambiguous phrase pairs extracted by a statistical phrase-based MT system. In translation, this phrase ambiguity causes deletion and insertion errors. We present hard and optional deletion approaches to remove the unaligned words in the source language sentences. Improvements in translation quality are achieved both on large and small vocabulary tasks with the presented methods.
Policy Enforcement Framework for Cloud Data Management

Cloud computing is a major emerging technology that is significantly changing industrial computing paradigms and business practices. However, security and privacy concerns have arisen as obstacles to widespread adoption of clouds by users. While much cloud security research focuses on enforcing standard access control policies typical of centralized systems, such policies often prove inadequate for the highly distributed, heterogeneous, data-diverse, and dynamic computing environment of clouds. To adequately pave the way for robust, secure cloud computing, future cloud infrastructures must consider richer, semantics-aware policies; more flexible, distributed enforcement strategies; and feedback mechanisms that provide evidence of enforcement to the users whose data integrity and confidentiality is at stake. In this paper, we propose a framework that supports such policies, including ruleand context-based access control and privacy preservation, through the use of in-lined reference monitors and a trusted application programming interface that affords enforceable policy management over heterogeneous cloud data.
Genetic Susceptibility to Type 2 Diabetes and Breast Cancer Risk in Women of European and African Ancestry

Background: Epidemiologic studies have reported a positive association between type 2 diabetes (T2D) and breast cancer risk, independent of body weight. Methods: We investigated 40 genetic variants known to be associated with T2D in relation to breast cancer risk among 2,651 breast cancer cases and 2,520 controls of African or European ancestry that were pooled from seven studies. Results: We found that two T2D risk alleles in Caucasian women (rs5945326-G, rs12518099-C) and one in women of African ancestry (rs7578597-T) were positively associated with breast cancer risk at a nominal significance level of 0.05, whereas two T2D risk alleles were inversely associated with breast cancer risk in Caucasian women (rs1111875-C, rs10923931-T). The composite T2D susceptibility score (the number of risk allele) was not significantly associated with breast cancer risk. Conclusion: The association between established T2D genetic susceptibility variants and breast cancer risk in women of African or European ancestry is likely weak, if it does exist. Impact: The pleiotropic effects of known T2D risk alleles cannot explain the association between T2D and breast cancer risk. Cancer Epidemiol Biomarkers Prev; 21(3); 552–6. ©2012 AACR.
THE DIFFERENCES BETWEEN PERIMETER AND POST BASKETBALL PLAYERS IN SOME AEROBIC AND ANAEROBIC PARAMETERS

Original scientific paper The aim of this study was to find out the differences between perimeter and post basketball players in aerobic and anaerobic parameters. Thirty-four basketball players from four Bosnian teams were measured for body composition (body height and weight, fat%, fat free mass), aerobic power (VO2max prediction estimated using the multistage shuttle run test), anaerobic capacities (repeated anaerobic sprint test – RAST) and anaerobic power (peak and relative power output generated during the CMJ). The sample was divided in two sub-samples: the first was a group of perimeter basketball players (n = 17) and the second was a group of post players (n =17). The main finding of this research was the existence of differences between the perimeter and post basketball players in aerobic power and relative anaerobic parameters, but not in vertical jump height. The perimeter players had higher aerobic power and higher values of relative anaerobic power and capacities, while the post players have higher values of absolute anaerobic power. The findings confirm that the aerobic and anaerobic tests can be discriminative variables between perimeter and post basketball players. Additionally, the results emphasize the need for improvement of explosive power of the lower limbs in Bosnian players. Also, the coaches can use information obtained in the study to create more individualized strength and conditioning programs for different positional role in order to maximize players’ physiological potential which is very important for basketball to be successfully played.
The problem of workforce for the social world of Australian rural nurses: a collective action frame analysis.

AIM AND BACKGROUND Globally, nursing workforce shortages are a hot topic for discussion among politicians, academics and clinicians. This paper uses collective action framing to analyse the literature about the problem of workforce for Australian rural nurses. EVALUATION As part of a larger constructivist grounded theory study, we utilize collective action framing to bridge social world mapping and the literature. Data sources included journal databases, newspapers, newsletters and websites. We limited the years searched from 2000 to 2005. This analytical heuristic categorizes text into three main categories: diagnoses of a problem, postulations of solutions and actions to motivate change. KEY ISSUES Having mapped the social world of Australian rural nurses as comprising four groups of collective actors - community, advocates, academics and government - we trace the texts that they have produced with a focus on mentoring as a potential solution to the problem of workforce. CONCLUSIONS Mentoring entered the literature about the problem of workforce for Australian rural nurses because of a combination of political and academic will. These collective groups are now changing how they are framing the problem of workforce to focus instead on the globalization of nursing workforce shortages, which is resulting in diminished support for mentoring activities in clinical practice.
Blood Biomarkers Predict the Cognitive Effects of Aripiprazole in Patients with Acute Schizophrenia

Aripiprazole has been reported to exert variable effects on cognitive function in patients with schizophrenia. Therefore, in the present study, we evaluated biological markers, clinical data, and psychiatric symptoms in order to identify factors that influence cognitive function in patients with schizophrenia undergoing aripiprazole treatment. We evaluated cognitive function in 51 patients with schizophrenia using Brief Assessment of Cognition in Schizophrenia (BACS), as well as background information, psychiatric symptoms, plasma catecholamine metabolites—homovanillic acid (HVA), 3-methoxy-4-hydroxyphenylglycol (MHPG)—, and serum brain-derived neurotrophic factor (BDNF). Multivariate analyses were performed in order to identify factors independently associated with cognitive function. Brain-derived neurotrophic factor levels, number of hospitalizations, and MHPG levels were associated with verbal memory and learning. Total hospitalization period and MHPG levels were associated with working memory. Age at first hospitalization and education were associated with motor speed. The number of hospital admissions, Positive and Negative Syndrome Scale negative subscale scores (PANSS-N), MHPG levels, BDNF levels, and Drug-Induced Extrapyramidal Symptoms Scale (DIEPSS) scores were associated with verbal fluency. Homovanillic acid and MHPG levels, duration of illness, and PANSS-N scores were associated with attention and processing speed. Brain-derived neurotrophic factor and MHPG levels were associated with executive function. These results suggest that treatment of psychiatric symptoms and cognitive dysfunction may be improved in patients treated with aripiprazole by controlling for these contributing factors.
Landscape biology of western white pine: implications for conservation of a widely-distributed five-needle pine at its southern range limit

Throughout much of the range of western white pine, Pinus monticola Dougl. , timber harvesting, fire exclusion and the presence of Cronartium ribicola J. C. Fisch. , the white pine blister rust (WPBR) pathogen, have led to negative population and genetic consequences. To address these interactions, we examined population dynamics and genetic diversity in 10 populations of western white pine in upper montane forests of the Lake Tahoe Basin. We documented negative population trends for three of the 10 populations. These populations exhibited low estimated growth rates (λ), moderate to high incidences of WPBR and mountain pine beetle (MPB), and high levels of mortality. In contrast, seven populations appear to be stable (λ ≥ 1.0), with low to moderate disease and insect incidence, and evidence for genetic resistance to WPBR. Genetic diversity (HE) for a set of 160 single nucleotide polymorphisms was in the range of 0.245–0.272 across populations, and population-specific estimates of FST ranged from 0.0062 to 0.0244. Allele frequency of the Cr2 gene, which confers complete resistance to C. ribicola in western white pine, was low, averaging 0.009 for all populations sampled. However, a low frequency of pollen receptors (i.e., susceptible maternal parents pollinated by a local resistant parent) was found in nine of 10 populations. A moderate and negative relationship was found between the frequency of pollen receptors in a population and the incidence of WPBR (r2 = 0.32). In the context of an introduced pathogen, climate driven outbreaks of MPB, fire exclusion, and prolonged drought, conservation and management strategies are warranted for this species in the Lake Tahoe Basin and likely other locations in California. These strategies include gene conservation of western white pine, WPBR resistance screening, and forest restoration treatments.
Inability of CMIP5 Models to Simulate Recent Strengthening of the Walker Circulation: Implications for Projections

AbstractThis paper examines changes in the strength of the Walker circulation (WC) using the pressure difference between the western and eastern equatorial Pacific. Changes in observations and in 35 climate models from the Coupled Model Intercomparison Project (CMIP) phase 5 (CMIP5) are determined. On the one hand, 78% of the models show a weakening of the WC over the twentieth century, consistent with the observations and previous studies using CMIP phase 3 (CMIP3) models. However, the observations also exhibit a strengthening in the last three decades (i.e., from 1980 to 2012) that is statistically significant at the 95% level. The models, on the other hand, show no consensus on the sign of change, and none of the models shows a statistically significant strengthening over the same period. While the reasons for the inconsistency between models and observations is not fully understood, it is shown that the ability of the models to generate trends as large as the observed from internal variability is redu.
Shape Representations for Maya Codical Glyphs: Knowledge-driven or Deep?

This paper investigates two-types of shape representations for individual Maya codical glyphs: traditional bag-of-words built on knowledge-driven local shape descriptors (HOOSC), and Convolutional Neural Networks (CNN) based representations, learned from data. For CNN representations, first, we evaluate the activations of typical CNNs that are pretrained on large-scale image datasets; second, we train a CNN from scratch with all the available individual segments. One of the main challenges while training CNNs is the limited amount of available data (and handling data imbalance issue). Here, we attempt to solve this imbalance issue by introducing class-weights into the loss computation during training. Another possibility is oversampling the minority class samples during batch selection. We show that deep representations outperform the other, but CNN training requires special care for small-scale unbalanced data, that is usually the case in the cultural heritage domain.
Ultra low-cost optical biosensor based on guided mode resonance grating filter

Design and development of ultra low-cost, disposable devices for point-of-care diagnostics is the focus of scientific community in these days. In this work we propose a simple fabrication strategy, using non-conventional, low-cost, polycarbonate based micro-structured device which is supposed to be a low-cost, but highly sensitive sensing device for disposable bio-applications. The initial studies focused on the possibility of finding the concentration of sugar, the analyte, in honey being the sample using guided mode resonance grating filter (GMRGF) based biosensor, for both homogeneous as well as surface sensing. The sensitivity of 142nm/RIU and 23nm/RIU has been observed for homogeneous and surface sensing respectively.
Nanostructured self-assembling peptides as a defined extracellular matrix for long-term functional maintenance of primary hepatocytes in a bioartificial liver modular device

Much effort has been directed towards the optimization of the capture of in vivo hepatocytes from their microenvironment. Some methods of capture include an ex vivo cellular model in a bioreactor based liver module, a micropatterned module, a microfluidic 3D chip, coated plates, and other innovative approaches for the functional maintenance of primary hepatocytes. However, none of the above methods meet US Food and Drug Administration (FDA) guidelines, which recommend and encourage that the duration of a toxicity assay of a drug should be a minimum of 14 days, to a maximum of 90 days for a general toxicity assay. Existing innovative reports have used undefined extracellular matrices like matrigel, rigid collagen, or serum supplementations, which are often problematic, unacceptable in preclinical and clinical applications, and can even interfere with experimental outcomes. We have overcome these challenges by using integrated nanostructured self-assembling peptides and a special combination of growth factors and cytokines to establish a proof of concept to mimic the in vivo hepatocyte microenvironment pattern in vitro for predicting the in vivo drug hepatotoxicity in a scalable bioartificial liver module. Hepatocyte functionality (albumin, urea) was measured at days 10, 30, 60, and 90 and we observed stable albumin secretion and urea function throughout the culture period. In parallel, drug metabolizing enzyme biomarkers such as ethoxyresorufin-O-deethylase, the methylthiazol tetrazolium test, and the lactate dehydrogenase test were carried out at days 10, 30, 60, and 90. We noticed excellent mitochondrial status and membrane stability at 90 days of culture. Since alpha glutathione S-transferase (GST) is highly sensitive and a specific marker of hepatocyte injury, we observed significantly low alpha GST levels on all measured days (10, 30, 60, and 90). Finally, we performed the image analysis of mitochondria-cultured hepatocytes at day 90 in different biophysical parameters using confocal microscopy. We applied an automatic algorithm-based method for 3D visualization to show the classic representation of the mitochondrial distribution in double hepatocytes. An automated morphological measurement was conducted on the mitochondrial distribution in the cultured hepatocytes. Our proof of concept of a scalable bioartificial liver modular device meets FDA guidelines and may function as an alternative model of animal experimentation for pharmacological and toxicological studies involving drug metabolism, enzyme induction, transplantation, viral hepatitis, hepatocyte regeneration, and can also be used in other existing bioreactor modules for long-term culture for up to 90 days or more.
Generalized Uno and Yagiura ’ s Algorithm for Alignment Decomposition

We generalize Uno and Yagiura’s algorithm for finding all common intervals of two permutations to the setting of two sequences with many-to-many alignment links across the two sides. Common intervals in such a setting can be interpreted as translationally equivalent phrases between two sentences. We show how to decompose an alignment into hierarchical phrase pairs in linear time.
Mineralogical–geochemical constraints on intrusives in central Anatolia, Turkey: tectono-magmatic evolution and characteristics of mantle source

Collision-related rocks intrude metamorphic rocks overthrust by ophiolitic units to make up the Central Anatolian Crystalline Complex. A wide variety of rock types were produced by the latest Cretaceous magmatism in the complex. These rocks can be divided into three distinct units: (1) calc-alkaline (Ağaçören, Behrekdağ, Cefalıkdağ, Çelebi, Ekecikdağ, Halaçlı, Karamadazı, Kösefakılı, Terlemez, Üçkapılı, Yozgat); (2) sub-alkaline (Baranadağ); and (3) alkaline (Atdere, Davulalan, Eğrialan, Hamit, İdişdağı, Karaçayır). The calc-alkaline rocks are metaluminous/peraluminous I- to S-type plutons ranging from monzodiorite to granite. The sub-alkaline rocks are metaluminous I-type plutons ranging from monzonite to granite. The alkaline rocks are metaluminous to peralkaline plutons, predominantly A-type, ranging from foid-bearing monzosyenite to granite. These plutons crystallized under varying pressures (5.3–2.6 kbar) and a wide range of temperatures (858–698 °C) from highly oxidized magmas (log fO2 −17 to −12). All intrusive rocks display enrichment in LILE and LREE compare to HFSE and have high 87Sr/86Sr and low 143Nd/144Nd ratios. These characteristics indicate that these rocks are derived from a mantle source containing large subduction components, and have experienced assimilation coupled with fractional crystallization (AFC) during uprise through crust. The coexistence of calc-alkaline and alkaline magmatism in the complex may be ascribed to mantle source heterogeneity before collision. Either thermal perturbation of the metasomatized lithosphere by delamination of the thermal boundary layer or removal of a subducted plate (slab breakoff) are the likely mechanisms for the initiation of the collision-related magmatism in the complex.