nils-herrmann/clean_scirepeval huggingface dataset:
A new integrated GIS based analysis to detect hotspots: A case study of the city of Sherbrooke.
Venue: Accident; analysis and prevention
Year: 2016

This paper proposes a two step integrated method for identifying traffic accident (TA) hotspots on a roadway network. The first step includes a spatial analysis method called network kernel density estimation (KDE) The second step is a network screening method using the critical crash rate, which it described in the Highway Safety Manual (HSM) The method was examined by using three years of TAs (2011 2013) in Sherbrooke, Canada. The network KDE uses TAs to graphically display sites with a high crash density. Two different crash patterns were used for identifying these locations: (1) a crash pattern that includes three year aggregated crash data, and (2) a crash pattern that involves three year merged crash data. The results of the two crash patterns were evaluated based on a prediction accuracy index (PAI) It was found that the results obtained from the merged crash data outperformed the other. On the other hand, crash clustering in a site does not imply a site is hotspot and it is better to tested by other factors. High crash density locations were then tested by the critical crash rate, which helps to create an accurate comparison of sites. The importance of the critical crash rate is that it takes several factors into account such as the amount of exposure, the type of intersection, variance in crash data, etc. We realized that the hotspots determined using the two methods reflect very problematic locations and filter out the locations that do not have a problem. This approach could help transportation authorities and safety specialists to identify and prioritize sites that require more safety attention.
A randomized controlled trial of the impact of a teacher classroom management program on the classroom behavior of children with and without behavior problems.
Venue: Journal of school psychology
Year: 2013

This randomized controlled trial (RCT) evaluated the efficacy of the Incredible Years (IY) Teacher Classroom Management (TCM; Webster Stratton Reid, 2002) program to assess whether training teachers in IY TCM principles improve teacher behavior, whether any observed improvements impact pupil behavior classroom wide, and whether these effects can be demonstrated with children at risk of developing conduct problems. Six intervention and six control classrooms comprising 12 teachers and 107 children (aged 3 to 7years) were recruited. Children were screened for high or low behavior problems using the cut off points of the teacher rated Strengths and Difficulties Questionnaire (Goodman, 1997) The primary outcome measure was independent classroom observations using the Teacher Pupil Observation Tool (Martin et al. 2010) Multilevel modeling analyses were conducted to examine the effect of the intervention on teacher, classroom, and child behavior. Results showed a significant reduction in classroom off task behavior (d=0.53) teacher negatives to target children (d=0.36) target child negatives towards the teacher (d=0.42) and target child off task behavior (d=0.48) These preliminary results demonstrate the potential impact of IY TCM on both teacher and child behavior.
Clinical Safety Incident Taxonomy Performance on C4.5 Decision Tree and Random Forest.
Venue: Studies in health technology and informatics
Year: 2019

The paper applies an artificial intelligence centered method to classify 12 clinical safety incident (CSI) classes. The paper aims to establish a taxonomy that classifies the CSI reports into their correct classes automatically and with high accuracy. The study investigates feasibility of applying the C4.5 decision tree (DT) classifier and the random forest (RF) classifier for this purpose. The classifiers were trained using randomly selected 3600 CSIs from an Incident Information Management System (IIMS) used by seven hospitals. The taxonomies investigated were the Generic Reference Model (GRM) and the World Health Organization (WHO) patient safety classification. The classifiers trained 13 GRM CSI classes and 9 WHO CSI classes using a bag of words approach. The overall taxonomies performance on the RF classifier was better than on the DT classifier. The performance achieved by the classifier applying the WHO taxonomy was better than the GRM taxonomy. Four of the five poorly performing classes in the GRM taxonomy significantly improved their performance on changing the taxonomy. To improve the WHO taxonomy performance the improved WHO (WHO I) taxonomy was built by adding a new class that did not exist in WHO but existed in GRM. The performance of the RF classifier applied to the WHO I taxonomy further improved.
OmniCells: Cross Device Cellular based Indoor Location Tracking Using Deep Neural Networks
Venue: 2020 IEEE International Conference on Pervasive Computing and Communications (PerCom)
Year: 2020

The demand for a ubiquitous and accurate indoor localization service is continuously growing. Cellular based systems are a good candidate to provide such ubiquitous service due to their wide availability worldwide. One of the main barriers for accuracy is the large number of models of cell phones, which results in variations of the measured received signal strength (RSS) even at the same location and time. In this paper, we propose OmniCells, a deep learning based system that leverages cellular measurements from one or more training devices to provide a consistent performance across unseen tracking phones. Specifically, OmniCells uses a novel approach to multi task learning based on autoencoders that allows it to learn a rich and device invariant RSS representation without any assumptions about the source or target devices. OmniCells also incorporates different modules to boost the system's accuracy with RSS relative difference based features and to improve the deep model's generalization and robustness. Evaluation of OmniCells in two realistic testbeds using different Android phones with different form factors and cellular radio hardware shows that OmniCells can achieve a consistent median localization accuracy when tested on different phones. This is better than the state of the art indoor cellular based systems by at least 101%
The failure of zero tolerance
Year: 2014

There is no doubt that the safety of children in schools and in communities is paramount. Incidents of school violence in the United States have motivated researchers and practitioners to explore and employ effective methodologies and strategies to promote safety in classrooms and schools. Still, issues of disruptive behavior top the list of concerns about education among teachers and parents. The message of zero tolerance is intuitively appealing. When disruption and disorder threaten schools and communities, it becomes increasingly easy to accept the notion that greater authority and force are necessary in order to keep schools secure. This article suggests that exclusionary, zero tolerance approaches to school discipline are not the best way to create a safe climate for learning. Increasingly, there are sound alternatives available to schools that can promote a safe school climate conducive to learning without removing large numbers of students from the opportunity to learn or creating a more negative school climate through increased punishment. The preeminent researcher on zero tolerance reviews the evidence about these practices and proposes a preventive model to insure school safety without discarding our most marginalized youth.
Diferencias en las actitudes hacia el ejercicio, la habilidad atletica percibida, el atractivo fisico percibido y la participacion en actividades fisicas de ninos y adolescentes entre 10 y 18 anos
Year: 2011

Antecedentes: Varios autores han estudiado la influencia del ejercicio sobre el sistema nervioso y el funcionamiento cognitivo en sujetos desentrenados y ante diferentes estimulos de ejercicio desde ejercicios anaerobicos intensos hasta el agotamiento a ejercicios de resistencia submaximos mediante los Umbrales Flicker Fusion (UFF) Aunque el efecto en el sistema nervioso central (SNC) de estimulos maximos aerobicos no esta muy estudiado.  El presente trabajo de investigacion pretende estudiar los cambios en los UFF antes y despues de realizar una prueba incremental maxima en cicloergometro, como medio para valorar la fatiga del SNC.  La muestra la componen 7 sujetos varones (62.6+ 4.11 kg, 172.8+ 7.94 cm, 14.7+ 0.8 anos, 13.4+ 3.53 grasa, 21.0+ 1.83 kg/m2; VO2max [ml/ kg/min] 63.2+ 5.13, VO2max [l] 4.1+ 0.5) Metodo: Se realizo un test incremental maximo en cicloergometro, comenzando en 50w con incrementos de 50w cada 5 minutos hasta la fatiga completa. Previo al test y al finalizar este, se realizaron las mediciones de los UFF ascendente, descendente y clasico, el criterio subjetivo y la sensibilidad sensorial. Cada sujeto realizo el test de UFF en tres ocasiones obteniendose un valor promedio.  Los resultados muestran un aumento de los UFF, por lo que no se produce fatiga en el SNC despues de una prueba incremental maxima en cicloergometro.
Analysis of Kernel Mean Matching under Covariate Shift
Venue: ICML
Year: 2012

In real supervised learning scenarios, it is not uncommon that the training and test sample follow different probability distributions, thus rendering the necessity to correct the sampling bias. Focusing on a particular covariate shift problem, we derive high probability confidence bounds for the kernel mean matching (KMM) estimator, whose convergence rate turns out to depend on some regularity measure of the regression function and also on some capacity measure of the kernel. By comparing KMM with the natural plug in estimator, we establish the superiority of the former hence provide concrete evidence/ understanding to the effectiveness of KMM under covariate shift.
Two Tabersonine 6,7 Epoxidases Initiate Lochnericine Derived Alkaloid Biosynthesis in Catharanthus roseus1
Venue: Plant Physiology
Year: 2018

Two cytochrome P450s with high substrate specificity catalyze the synthesis of the alkaloid lochnericine in Catharanthus roseus, representing valuable tools for metabolic engineering in yeast. Lochnericine is a major monoterpene indole alkaloid (MIA) in the roots of Madagascar periwinkle (Catharanthus roseus) Lochnericine is derived from the stereoselective C6,C7 epoxidation of tabersonine and can be metabolized further to generate other complex MIAs. While the enzymes responsible for its downstream modifications have been characterized, those involved in lochnericine biosynthesis remain unknown. By combining gene correlation studies, functional assays, and transient gene inactivation, we identified two highly conserved P450s that efficiently catalyze the epoxidation of tabersonine: tabersonine 6,7 epoxidase isoforms 1 and 2 (TEX1 and TEX2) Both proteins are quite divergent from the previously characterized tabersonine 2,3 epoxidase and are more closely related to tabersonine 16 hydroxylase, involved in vindoline biosynthesis in leaves. Biochemical characterization of TEX1/2 revealed their strict substrate specificity for tabersonine and their inability to epoxidize 19 hydroxytabersonine, indicating that they catalyze the first step in the pathway leading to horhammericine production. TEX1 and TEX2 displayed complementary expression profiles, with TEX1 expressed mainly in roots and TEX2 in aerial organs. Our results suggest that TEX1 and TEX2 originated from a gene duplication event and later acquired divergent, organ specific regulatory elements for lochnericine biosynthesis throughout the plant, as supported by the presence of lochnericine in flowers. Finally, through the sequential expression of TEX1 and up to four other MIA biosynthetic genes in yeast, we reconstituted the 19 acetylhorhammericine biosynthetic pathway and produced tailor made MIAs by mixing enzymatic modules that are naturally spatially separated in the plant. These results lay the groundwork for the metabolic engineering of tabersonine/lochnericine derivatives of pharmaceutical interest.
Conservation genetics of the threatened catfish Conorhynchos conirostris (Siluriformes: incertae sedis) an evolutionary relict endemic to the Sao Francisco River Basin, Brazil
Venue: Conservation Genetics
Year: 2018

Analysis of genetic datasets can be particularly useful in providing guidelines for conservation management of understudied species targeted by commercial activities. Here we used population genetic approaches to inform on the conservation status of the Neotropical long nose pira catfish, Conorhynchos conirostris. Pira is a large migratory fish endemic to the Sao Francisco River Basin (SFRB) It is an evolutionarily divergent and relict species, being the sole representative of an incertae sedis family. The species is considered locally extinct in the upper and lower SFRB, listed as vulnerable on the IUCN Red List and as endangered on the Brazilian Red List (ICMBIO) Fishing prohibition has received severe criticism from middle SFRB fisheries that claim that this understudied species is relatively abundant in that region. We used information from 13 microsatellite markers and COI mitochondrial sequences to clarify the genetic diversity of this enigmatic species in the middle SFRB, to estimate contemporary effective population size (Ne) and to assess its conservation status. Results from bottleneck analyses indicated that the species has experienced recent reductions in population size, which is consistent with small estimates of contemporary Ne. The predicted amount of heterozygosity loss (Ht) in t generations ranged from 0.1152 (for an estimated Ne of 26.4; t 100) to 0.7573 (for an estimated Ne of 169.9; t 10) Our study supports the conservation status proposed by the ICMBIO to the remaining pira population. Moreover, we highlight the need for demographic data and the re assessment of the current IUCN classification for this evolutionary relict lineage.
Realismo estructural ontico en H.P. Lovecraft
Year: 2020

Este articulo pretende mostrar que, a traves de la obra de Lovecraft, es posible ilustrar una forma de realismo estructural ontico (REO) Se postula que la literatura de Lovecraft permite ejemplificar una ontologia orientada hacia las relaciones (entre entidades) y no a las entidades mismas. Ademas, puesto que en esta forma de REO las entidades se definirian por sus relaciones, se concluye que estas deberian ser abstractas, habilitadas para contar con todas las caracteristicas que extrinsecamente les sean asignadas en una actualizacion determinada de la estructura que las alberga.
Gestion des toxicites cutanees severes induites par l'immunotherapie la place du dupilumab
Year: 2020

La peau est une des principales cibles des toxicites induites par l'immunotherapie (IT) antitumorale. Il s'agit souvent d'une toxicite precoce, variable en termes de presentation clinique et de severite mais qui peut parfois persister longtemps apres l'arret du traitement et impacter considerablement la qualite de vie des patients. Nous rapportons l'efficacite spectaculaire du dupilumab dans la prise en charge d'une toxicite cutanee tardive severe induite par l'IT.  Il s'agissait d'une patiente jeune, aux antecedents d'eczema dans l'enfance, suivie pour melanome metastatique. Le genotypage individualisait une mutation BRAFV600E motivant un traitement par dabrafenib et trametinib. Devant une evolution metastatique dissociee a 1 an, un traitement par pembrolizumab etait introduit. Apres 6 mois de traitement, la patiente developpait une eruption cutanee de grade 3, prurigineuse, d'aspect eczematiforme. Une hypereosinophilie avec elevation significative des IgE totales etaient associees. L'histologie trouvait un aspect de dermoepidermite vesiculobulleuse eczematiforme avec de rares necroses keratinocytaires. L'association des dermocorticoides et du methotrexate (25 mg/semaine) ne permettait pas de controler les lesions et l'IT etait interrompue apres 24 mois du fait d'une gene fonctionnelle majeure et de l'obtention d'une reponse tumorale complete et durable. Le taux d'IL4 serique etait normal, l'IL6 moderement elevee. Devant la persistance de la toxicite cutanee a 6 mois de l'arret de l'IT, le dupilumab etait introduit a posologie habituelle, permettant une amelioration spectaculaire des lesions apres seulement deux injections.  La grande majorite des toxicites cutanees induites par l'IT peut etre controlee par des traitements locaux adaptes. Cependant, certaines formes particulieres restent refractaires et peuvent necessiter l'introduction d'immunosuppresseurs ou de traitements cibles plus specifiques, notamment en cas d'elevation des taux seriques d'IL6, IL10, des eosinophiles ou des IgE totales. L'utilisation de ces nouvelles therapies pour la gestion des toxicites dermatologiques severes ou persistantes, integrant la physiopathologie variable de ces toxicites, est interessante mais ne fait l'objet d'aucun consensus. Le dupilumab, anticorps monoclonal inhibant la voie de signalisation de l'interleukine 4 et de l'interleukine 13, apparait interessant chez des patients predisposes presentant des formes avec prurit refractaire associees a des biomarqueurs de type 2.
Addressing Instructional Gaps in K to 12 Science Teaching through Learning Action Cell (LAC)
Year: 2020

The predominant effect in the shift of curriculum to the K to 12 programs challenged the pedagogy, content, and knowledge of science teachers as well as the learning outcomes of students. In order to address the issue, the Department of Education (DepEd) through DepEd Order No. 35, s. 2016 tasked every public school to conduct Learning Action Cell (LAC) sessions. With the aid of collaboration guided by principal or assigned LAC leaders, teachers are grouped to give solutions to the prevailing problems of the school. Thus, the study generally aimed to evaluate the conduct of LAC sessions in selected public junior high schools in the City of Sta. Rosa, Laguna to address instructional gaps in K to 12 science teaching. A phenomenological research design was used in the study. Eleven science teachers were interviewed. The results yielded that needs assessment is being administered to the teachers, however, there are concerns with regards to the actual topics covered by LAC sessions. Science teachers unanimously appealed that content is the major problem due to the spiral progression of the K to 12 science curriculum. Science teachers recommended that LAC sessions should be according to the field of teaching load or specialization, not just the typical general session, in order to address individual group concerns of teachers.
Prostaglandin E2 secreted from feline adipose tissue derived mesenchymal stem cells alleviate DSS induced colitis by increasing regulatory T cells in mice
Venue: BMC Veterinary Research
Year: 2018

BackgroundInflammatory bowel disease (IBD) is an intractable autoimmune disease, relatively common in cats, with chronic vomiting and diarrhea. Previous studies have reported that mesenchymal stem cells (MSCs) alleviate inflammation by modulating immune cells. However, there is a lack of research on cross talk mechanism between feline adipose tissue derived mesenchymal stem cells (fAT MSCs) and immune cells in IBD model. Hence, this study aimed to evaluate the therapeutic effects of fAT MSC on mice model of colitis and to clarify the therapeutic mechanism of fAT MSCs.ResultsIntraperitoneal infusion of fAT MSC ameliorated the clinical and histopathologic severity of colitis, including body weight loss, diarrhea, and inflammation in the colon of Dextran sulfate sodium (DSS) treated mice (C57BL/6) Since regulatory T cells (Tregs) are pivotal in modulating immune responses and maintaining tolerance in colitis, the relation of Tregs with fAT MSC secreted factor was investigated in vitro. PGE2 secreted from fAT MSC was demonstrated to induce elevation of FOXP3 mRNA expression and adjust inflammatory cytokines in Con A induced feline peripheral blood mononuclear cells (PBMCs) Furthermore, in vivo, FOXP3+ cells of the fAT MSC group were significantly increased in the inflamed colon, relative to that in the PBS group.ConclusionOur results suggest that PGE2 secreted from fAT MSC can reduce inflammation by increasing FOXP3+ Tregs in mice model of colitis. Consequently, these results propose the possibility of administration of fAT MSC to cats with not only IBD but also other immune mediated inflammatory diseases.
Estimation Variability, Heritability and Genetic Advance of Mutant Black Rice (M6)
Venue: Caraka Tani: Journal of Sustainable Agriculture
Year: 2019

A better understanding of variability in plant populations is crucial for crop improvement which plant breeders can use through selection. This study aimed to determine selection criteria for the sixth generation of black rice through genetic variability, heritability value and genetic advance. This research was conducted from March to July 2018 at Pakahan Village, Jogonalan Sub district, Klaten Regency, Central Java, using a Randomized Complete Block Design (RCBD) The variables observed were plant height, total number of tillers and productive tillers, panicle length, number of seeds per panicle, panicle intensity index, weight per panicle, 1,000 seed weight, seed weight per plant, flowering age, harvest age, plot yield, yield per hectare, rice color and total anthocyanin content. Variance analysis showed that there was a very significant difference (p <0.01) among the genotypes tested for all observed characters indicating variability. In this study, the phenotypic coefficient of variance (PCV) values was relatively higher than the genotypic coefficient of variance (GCV) for all traits. However, GCV values were close to PCV values in some characters such as plant height, flowering age, harvest age, rice color and anthocyanin content which showed a high contribution of genotypic effects to the phenotypic expression of these characters. The high heritability and high average value of genetic advance were indicated in the parameters of plant height, flowering age, harvest age, rice color and anthocyanin content. The characters of plant height, flowering age, harvest age, rice color and anthocyanin content can be used as sixth generation black rice selection criteria.
The Ceratodon purpureus genome uncovers structurally complex, gene rich sex chromosomes
Year: 2020

Non recombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration1,2. The correlation between suppressed recombination and degeneration is clear in animal XY systems1,2, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions3,4. Here we test for degeneration in the bryophyte UV sex chromosome system through genomic comparisons with new female and male chromosome scale reference genomes of the moss Ceratodon purpureus. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes show signs of weaker purifying selection than autosomes, we find suppressed recombination alone is insufficient to drive gene loss on sex specific chromosomes. Instead, the U and V sex chromosomes harbor thousands of broadly expressed genes, including numerous key regulators of sexual development across land plants.