Miracle-dz/UniFAR-FTUs huggingface dataset:
Geocoding user queries

While human users refer to locations using toponyms and addresses, computers rely on latitude and longitude coordinates, or similar, numerical encoding of location information. Geocoding is the process of resolving such toponyms and addresses into machine-friendly numerical encoding. Thus, wherever human users need to specify a location to a computer, geocoding is involved. The process, thereby, is mainly dependent on two aspects. Firstly, the underlying address data needs to be complete, up-to-date, and accurate as otherwise, the geocoding result will not be precise. Secondly, the algorithms that process the user input query, browse candidates within the data and select the right result to the query need to be capable of handling queries of human users. In this thesis, the speci cs of human input addresses are tackled. Various kinds of modi cations occur to an address when humans are involved. For example, address formats are not adhered to, super uous tokens are speci ed, while required parts of an address are left out of the query. Also, humans abbreviate, escape, or misspell address element names often. The goal of this thesis is to investigate the algorithmic aspect of geocoding systems. Throughout the thesis, ways to process, organize, index, and rank address data are investigated independently of the underlying data. As a result, a method for creating a geocoding system with good precision and recall metrics even in the face of the human factor is developed. A sequence of experiments is executed that gradually build on top of each other. First, the use of a generic document search engine as the index of a geocoding system is validated. Next, a suitable address model for indexing and searching is selected. Then, using log data from a live geocoding system, a statistical model is created that can be used to generate user-like requests. A similar approach based on the log data is evaluated to create geocoding systems that perform measurably better than geocoding systems relying on common methods to handle user queries. Finally, a process is developed that continuously improves a geocoding system using user queries issued against it. The measurements prove that the path chosen in this thesis is a viable method to create geocoding systems that can handle user queries better than geocoding systems relying on common techniques.
The Cellular and Molecular Determinants of Naphthoquinone-Dependent Activation of the Aryl Hydrocarbon Receptor

1,2-naphthoquinone (1,2-NQ) and 1,4-naphthoquinone (1,4-NQ) are clinically promising biologically active chemicals that have been shown to stimulate the aryl hydrocarbon receptor (AhR) signaling pathway, but whether they are direct or indirect ligands or activate the AhR in a ligand-independent manner is unknown. Given the structural diversity of AhR ligands, multiple mechanisms of AhR activation of gene expression, and species differences in AhR ligand binding and response, we examined the ability of 1,2-NQ and 1,4-NQ to bind to and activate the mouse and human AhRs using a series of in vitro AhR-specific bioassays and in silico modeling techniques. Both NQs induced AhR-dependent gene expression in mouse and human hepatoma cells, but were more potent and efficacious in human cells. 1,2-NQ and 1,4-NQ stimulated AhR transformation and DNA binding in vitro and was inhibited by AhR antagonists. Ligand binding analysis confirmed the ability of 1,2-NQ and 1,4-NQ to competitively bind to the AhR ligand binding cavity and the molecular determinants for interactions were predicted by molecular modeling methods. NQs were shown to bind distinctly differently from that of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and differences were also observed between species. Mutation of amino acid residues (F289, M334, and M342) involved in critical NQ:AhR binding interactions, decreased NQ- and AhR-dependent gene expression, consistent with a role for these residues in binding and activation of the AhR by NQs. These studies provide insights into the molecular mechanism of action of NQs and contribute to the development of emerging NQ-based therapeutics.
Personal Risk and Protective Factors Involved in Aggressive Behavior

The study of aggression plays a prominent role in psychology and public health, because of the important adverse consequences of such behavior for victims, aggressors, and society in general. The General Aggression Model (GAM) provides a general conceptual framework for understanding the aggressive as a result of three stages: (a) inputs: personal and situational factors; (b) present internal states: affect, cognition, and arousal; and (c) outcomes: decision processes with a (non)aggressive result. The main objective of this research was to study the personal protective and risk factors most strongly associated with aggressive behavior acting at the first stage of the GAM model. A total of 282 young adult participants took part in this study. Participants were assessed for aggression levels and a set of the most relevant variables that have been associated with aggressive behavior in the previous literature. Stepwise multiple regression analysis revealed that levels of aggression were mainly associated (73.2% of the explained variance) with the following protective factors: the ability to manage emotions as a component of emotional intelligence (EI), and perspective-taking and personal distress as components of empathy, and with the following risk factors: negative and positive urgency as a component of impulsivity, fantasy as a component of empathy, negative affect, and expressive suppression of emotions. These findings provide a better understanding of the mechanisms underlying aggressive behavior and provide greater empirical value to the current theoretical models. In addition, this research can help to inform the design of more successful programs for the prevention, control, and treatment of aggressive behavior. Limitations and future lines of research are discussed.
Coding-Complete Genome Sequence of a Human Respirovirus 1 Strain from a Clinical Sample in Arizona

Human respirovirus 1 is a single-stranded, negative-sense RNA virus in the family Paramyxoviridae. Using a high-throughput metagenomic approach, we identified and sequenced the coding-complete genome of a human respirovirus 1 strain from a nasal pharyngeal swab sample from a local health clinic in Tempe, Arizona. ABSTRACT Human respirovirus 1 is a single-stranded, negative-sense RNA virus in the family Paramyxoviridae. Using a high-throughput metagenomic approach, we identified and sequenced the coding-complete genome of a human respirovirus 1 strain from a nasal pharyngeal swab sample from a local health clinic in Tempe, Arizona.
Impact of Endoplasmic Reticulum Stress in Otorhinolaryngologic Diseases

The endoplasmic reticulum (ER) is an important organelle for normal cellular function and homeostasis in most living things. ER stress, which impairs ER function, occurs when the ER is overwhelmed by newly introduced immature proteins or when calcium in the ER is depleted. A number of diseases are associated with ER stress, including otorhinolaryngological diseases. The relationship between ER stress and otorhinolaryngologic conditions has been the subject of investigation over the last decade. Among otologic diseases associated with ER stress are otitis media and hearing loss. In rhinologic diseases, chronic rhinosinusitis, allergic rhinitis, and obstructive sleep apnea are also significantly associated with ER stress. In this review, we provide a comprehensive overview of the relationship between ER stress and otorhinolaryngological diseases, focusing on the current state of knowledge and mechanisms that link ER stress and otorhinolaryngologic diseases.
Isolation and cDNA cloning of an Em‐like protein from mung bean (Vigna radiata) axes

Until now no ‘early-methionine-labelled’ (Em) proteins have been reported in the Fabaceae. To check whether a previously isolated low-molecular mass albumin from dry mung bean embryonic axes possibly corresponded to an Em-like protein, the protein was purified, sequenced and its cDNA clone isolated and characterized. N-terminal sequencing of cyanogen bromide cleavage products of the protein revealed homology with previously described Em-like proteins from other species. Analysis of cDNA clones encoding the mung bean Em protein revealed the presence of two classes of Em proteins and confirmed their homology to the previously characterized Em-like proteins. In vivo labelling and northern blot analysis further demonstrated that the mung bean protein is synthesized during early germination of the axes and that abscisic acid (ABA) extends its synthesis. It appears, therefore, that legumes also contain maturation-specific, ABA-responsive Em-like proteins.
Three Phase Transformerless Inverter for Grid Tied Renewable Application by Using Fuzzy Logic Based on P-Q Theory

his paper presents a three phase transformerless photovoltaic inverter for grid tied PV system. A three phase grid is connected to the photovoltaic system with maximum power point tracking (MPPT), along with fuzzy logic controller is used, the control strategy is applied based on p-q theory for better utilization of the photovoltaic system, according to this strategy during sunlight the system sends active power to the grid and at the same time compensates the reactive power of the load. In case there is no sunlight (during the night for instance), the inverter only compensates the reactive power of the load. The advantage of this strategy is the operation of the photovoltaic system the whole day.
Immediate Effects of Tibialis Anterior and Calf Muscle Taping on Center of Pressure Excursion in Chronic Stroke Patients: A Cross-Over Study

Stroke patients often have muscles spasticity, difficulty with posture control, and tend to fall. This study investigated the use of kinesiology tape for patients with spasticity of ankle muscles after stroke. This study had a randomized, repeated measures design, and evaluated the immediate effect of kinesiology tape on the center of pressure (COP) excursion when applied to the calf and tibialis anterior muscles in stroke survivors. We determined that the taping attachment direction affects the COP movement. Twenty subjects were randomly assigned to the tibialis anterior taping condition, calf taping condition, or nontaping condition. Condition excursion was assessed. The measured variables included the paretic side area, nonparetic side area, forward area, and backward area of COP. All evaluations were conducted immediately after taping. COP excursion for chronic stroke survivors improved after tibialis anterior and calf taping (p < 0.05). Calf taping conditions increased significantly in the forward area (p < 0.05), and tibialis anterior taping conditions increased significantly in the backward area (p < 0.05). Kinesiology tape immediately increased the forward and backward COP excursion for patients with stroke.
Cation-Exchange Capacity Pedotransfer Functions for Danish Soils

The soil cation-exchange capacity (CEC) has edaphological, pedological and environmental importance. CEC pedotransfer functions were developed for Danish soils by multiple linear regression analysis of 1643 samples from a nation-wide 7 km grid survey. By partitioning the data into four groups [podzolic B-horizons, organic soils (>10% soil organic matter), calcareous soils (>0.1% CaCO3), and a 'normal data set'], four separate functions were developed. Without further partitioning of the normal data, 90% of the variability in CEC values can be modelled by using clay and organic matter content as independent variables. This yields a standard error of the estimate of 1.99. The average soil organic matter-CEC is 284-291 cmolc kg
The effect of cyclosporin a on ischemia-reperfusion damage in a mouse model of ischemic stroke

ABSTRACT Objectives We aimed to investigate the protective effects of cyclosporin A (CsA) against ischemia-reperfusion (I/R) damage in a mouse ischemia model and the possible underlying mechanism. Methods Mice were divided equally into five groups: Sham, I/R, Vehicle, I/R plus CsA (10 mg/kg), and I/R plus CsA (20 mg/kg). Nerve function scores, infarct volume, brain water content, and Evans blue (EB) leakage were evaluated, and western blotting was performed to analyze the changes in CypA, p-Akt, NF-κB, MMP-9, and Claudin-5 expression. Results CsA can attenuate I/R damage in a mouse ischemic stroke model, as indicated by improved neurological function scores and decreased infarct volume, brain water content, and EB leakage. Additionally, high-dose CsA showed better protective effects than low-dose. The molecular mechanisms underlying the effects of CsA were explored, and it was found that CsA could inhibit the increase in CypA, p-Akt, NF-κB, and MMP-9 protein expression after middle cerebral artery occlusion, while Claudin-5 expression was decreased. Discussion CsA showed potential as a neuroprotective drug for the treatment of ischemic stroke patients; besides interfering with the typical NF-κB signaling pathway, the Akt pathway may also be involved in the effects of CsA.
Cytotoxin-producing Klebsiella oxytoca in the preterm gut and its association with necrotizing enterocolitis

ABSTRACT Necrotizing enterocolitis (NEC) is a devastating intestinal inflammatory disease of premature infants associated with gut bacterial dysbiosis. Using 16S rRNA-based methods, our laboratory identified an unclassified Enterobacteriaceae sequence (NEC_unk_OTU) with high abundance in NEC fecal samples. We aimed to identify this bacterium and determine its potential role in the disease. NCBI database searches for the 16S sequence, selective culture systems, biotyping and polymerase chain reaction were employed to refine classification of NEC_unk_OTU and identify toxin-encoding genes from the index NEC case. Bacterial cytotoxin production was confirmed by mass spectrometry and apoptosis assays. Additional fecal samples from 9 NEC and 5 non-NEC controls were analyzed using similar methods and multi-locus sequence typing (MLST) was performed to investigate clonal relationships and define sequence types of the isolates. NEC_unk_OTU was identified as Klebsiella oxytoca, a pathobiont known to cause antibiotic-associated hemorrhagic colitis, but not previously linked to NEC. Including the index case, cytotoxin-producing strains of K. oxytoca were isolated from 6 of 10 subjects with NEC; in these, the K. oxytoca 16S sequence predominated the fecal microbiota. Cytotoxin-producing strains of K. oxytoca also were isolated from 4 of 5 controls; in these, however, the abundance of the corresponding 16S sequence was very low. MLST analysis of the toxin-positive isolates demonstrated no clonal relationships and similar genetic clustering between cases and controls. These results suggest cytotoxin-producing strains of K. oxytoca colonize a substantial proportion of premature infants. Some, perhaps many, cases of NEC may be precipitated by outgrowth of this opportunistic pathogen.
Sonic Hedgehog-Gli1 Signaling and Cellular Retinoic Acid Binding Protein 1 Gene Regulation in Motor Neuron Differentiation and Diseases

Cellular retinoic acid-binding protein 1 (CRABP1) is highly expressed in motor neurons. Degenerated motor neuron-like MN1 cells are engineered by introducing SODG93A or AR-65Q to model degenerated amyotrophic lateral sclerosis (ALS) or spinal bulbar muscular atrophy neurons. Retinoic acid (RA)/sonic hedgehog (Shh)-induced embryonic stem cells differentiation into motor neurons are employed to study up-regulation of Crabp1 by Shh. In SODG93A or AR-65Q MN1 neurons, CRABP1 level is reduced, revealing a correlation of motor neuron degeneration with Crabp1 down-regulation. Up-regulation of Crabp1 by Shh is mediated by glioma-associated oncogene homolog 1 (Gli1) that binds the Gli target sequence in Crabp1′s neuron-specific regulatory region upstream of minimal promoter. Gli1 binding triggers chromatin juxtaposition with minimal promoter, activating transcription. Motor neuron differentiation and Crabp1 up-regulation are both inhibited by blunting Shh with Gli inhibitor GANT61. Expression data mining of ALS and spinal muscular atrophy (SMA) motor neurons shows reduced CRABP1, coincided with reduction in Shh-Gli1 signaling components. This study reports motor neuron degeneration correlated with down-regulation in Crabp1 and Shh-Gli signaling. Shh-Gli up-regulation of Crabp1 involves specific chromatin remodeling. The physiological and pathological implication of this regulatory pathway in motor neuron degeneration is supported by gene expression data of ALS and SMA patients.
Real-time monitoring of cellular oxidative stress during aerosol sampling: a proof of concept study

Abstract The Portable In Vitro Exposure Cassette (PIVEC) was developed for on-site air quality testing using lung cells. Here, we describe the incorporation of a sensor within the PIVEC for real time monitoring of cellular oxidative stress during exposure to contaminated air. An electrochemical, enzymatic biosensor based on cytochrome c (cyt c) was selected to measure reactive oxygen species (ROS), including hydrogen peroxide and super oxides, due to the stability of signal over time. Human A549 lung cells were grown at the air–liquid interface and exposed within the PIVEC to dry 40 nm copper nanoparticle aerosols for 10 minutes. The generation of ROS compounds was measured during exposure and post-exposure for one hour using the biosensor and compared to intracellular ROS determined using the 2′,7′-dichlorodihydrofluoroscein diacetate (DCFH-DA) assay. A similar increase in oxidative stress upon aerosol exposure was measured using both the cyt c biosensor and DCFH-DA assay. The incorporation of a biosensor within the PIVEC is a unique, first-of-its-kind system designed to monitor the real-time effect of aerosols.
Heaviness of Alcohol Use, Alcohol Problems, and Subjective Intoxication Predict Discrepant Drinking Reports in Daily Life.

BACKGROUND Self-reported consumption is pervasive in alcohol research, though retrospective recall bias is a concern. Fine-grained methods are designed to limit retrospection; yet, discrepancies can arise when comparing responses on fine-grained surveys with responses to retrospective surveys across weeks or months. Many fine-grained studies use both repeated daily surveys (RDS) and end-of-day (EOD) summaries, but little research has examined whether these survey types are consistent. The purpose of this study was to quantify the magnitude and directionality of discrepancy between EOD summaries and RDS and identify alcohol-related predictors of discrepancy. METHODS As a part of a larger study, college student alcohol and cannabis users (N = 341; 53% women; Mage = 19.79 years) were recruited to complete 56 days of data collection, including 5 daily assessments of their substance use and related constructs, one of which included an EOD summary of the previous day. Generalized linear mixed-effects models were used to examine between- and within-person predictors of a 5-category, discrepancy outcome: no discrepancy, low discrepancy where RDS < EOD, low discrepancy where EOD < RDS, high discrepancy where RDS < EOD, and high discrepancy where EOD < RDS. RESULTS Discrepancies between EOD and RDS were observed in both directions. Alcohol problems predicted more alcohol consumption reported on the EOD survey than across RDS. Within-person alcohol quantity and hourly rate of consumption were most strongly related to less alcohol consumption reported on the EOD survey. Between- and within-person peak subjective intoxication and within-person liquor consumption were associated with discrepancies in both directions. CONCLUSIONS Surveys requiring more retrospection may overestimate alcohol consumption in problematic drinkers and underestimate consumption on days where more alcohol is consumed than typical. Evidence also suggests that greater day-to-day instability in alcohol behavior is linked to less consistent reporting overall. More research is needed to discern factors contributing to inconsistent reporting on fine-grained surveys to maximize the validity of reports.
Plant growth stages in the interspecific oviposition preference of the european corn borer and relations with chemicals present on the leaf surfaces

The oviposition preference of the European Corn Borer Ostrinia nubilalis Hbn. Lepidoptera pyralidae was studied in relation to phenological stages of different plant species (Zea mays L., Helianthus annuus L., Phaseolus vulgaris L.). The experiments were done in greenhouses in binary choices. The results show that the plant phenological stages were more important than the plant species in the insect oviposition preference. When the choice was given between two plant species throughout their growth, the preference varied in relation to the development of each species. The relative differences in fructose amounts found on the leaf surfaces (phylloplane) were highly correlated with the insect oviposition preference. Amounts of proline, glucose and sucrose may accentuate this previous effect.
A Signature of Circulating miRNAs Associated With Fibrous Dysplasia of Bone: the mirDys Study

Fibrous dysplasia (FD) is a rare bone disease caused by activating mutations of GNAS encoding the Gsα protein, enhancing cyclic adenosine monophosphate (cAMP) production by overstimulation of adenylyl cyclase and impairing osteoblastic differentiation. The clinical presentation ranges from asymptomatic to polyostotic forms with severe disability, explained by the mosaic distribution of the GNAS mutation. Physicians have to deal with the gap of knowledge in FD pathogenesis, the absence of prognostic markers and the lack of specific treatment. The identification of specific biomarkers for FD is an important step to improve the clinical and therapeutic approaches. An epigenetic regulation driven by microRNAs (miRNAs), known as promising biomarkers in bone disease, could be involved in FD. We have sought circulating miRNAs that are differentially expressed in FD patients compared to controls and would reflect dysregulations of osteogenesis‐related genes and bone disorder. The global miRNA profiling was performed using Next Generation Sequencing in patient serum collected from a discovery cohort of 20 patients (10 polyostotic and 10 monostotic) and 10 controls. From these, we selected 19 miRNAs for a miRNA validation phase from serum of 82 patients and 82 controls, using real‐time qPCR. Discovery screening identified 111 miRNAs differentially expressed in patient serum, after adjusting for the false discovery rate (FDR). Among the 82 patients, 55% were polyostotic, and 73% were women with a mean age of 42 years. Six miRNAs (miR‐25‐3p, miR‐93‐5p, miR‐182‐5p, miR‐324‐5p, miR‐363‐3p, and miR‐451a) were significantly overexpressed in serum, with FDR <0.05. The expression level of these six miRNAs was not associated with the FD severity. In conclusion, we identified a signature of circulating miRNAs associated with FD. These miRNAs are potential negative regulators of gene expression in bone cell progenitors, suggesting their activity in FD by interfering with osteoblastic and osteoclastic differentiation to impair bone mineralization and remodeling processes. © 2020 American Society for Bone and Mineral Research.