nils-herrmann/clean_scirepeval huggingface dataset:
Nutrition behavior of the middle aged and elderly: Compliance with dietary recommendations of the food pyramid.
Venue: Clinical nutrition

During the aging process, human physiology changes noticeably, mostly to the disadvantage of the individual. A healthy lifestyle that includes sufficient physical activity as well as a balanced and diverse diet contributes to healthy aging. One key factor that elderly people need to be aware of is compliance with nutritional recommendations. There is very little data concerning eating patterns, consumption behavior, and compliance with food guides (food pyramid) and nutritional recommendations among the Swiss, particularly for the middle aged and elderly. The objective of this study was to gather new and representative information about these issues, concentrating on people aged 50+ and living in Switzerland.  A questionnaire in online and written form was distributed to a representative sample of middle aged and elderly people living in Switzerland.  In total, 632 people returned the survey. Of those respondents, 71% knew the Swiss Food Pyramid but only 38% said they comply with it. Based on self reports, only a few participants met the recommendations for the different food groups listed in the food pyramid, whether in the pyramid comply or pyramid non comply group.  The survey shows that the middle aged and elderly living in Switzerland need more nutritional guidance to help them to meet dietary recommendations. As usage and understanding of food guides seem limited among this population group, new tools must be explored for transfer of recommendations to real applications.
Evaluation of Ketoconazole and Its Alternative Clinical CYP3A4/5 Inhibitors as Inhibitors of Drug Transporters: The In Vitro Effects of Ketoconazole, Ritonavir, Clarithromycin, and Itraconazole on 13 Clinically Relevant Drug Transporters
Venue: Drug Metabolism and Disposition

Ketoconazole is a potent CYP3A4/5 inhibitor and, until recently, recommended by the Food and Drug Administration (FDA) and the European Medicines Agency as a strong CYP3A4/5 inhibitor in clinical drug drug interaction (DDI) studies. Ketoconazole sporadically causes liver injury or adrenal insufficiency. Because of this, the FDA and European Medicines Agency recommended suspension of ketoconazole use in DDI studies in 2013. The FDA specifically recommended use of clarithromycin or itraconazole as alternative strong CYP3A4/5 inhibitors in clinical DDI studies, but many investigators have also used ritonavir as an alternative. Although the effects of these clinical CYP3A4/5 inhibitors on other CYPs are largely established, reports on the effects on the broad range of drug transporter activities are sparse. In this study, the inhibitory effects of ketoconazole, clarithromycin, ritonavir, and itraconazole (and its CYP3A4 inhibitory metabolites, hydroxy keto and N desalkyl itraconazole) toward 13 drug transporters (OATP1B1, OATP1B3, OAT1, OAT3, OCT1, OCT2, MATE1, MATE2 K, P gp, BCRP, MRP2, MRP3, and BSEP) were systematically assessed in transporter expressing HEK 293 cell lines or membrane vesicles. In vitro findings were translated into clinical context with the basic static model approaches outlined by the FDA in its 2012 draft guidance on DDIs. The results indicate that, like ketoconazole, the alternative clinical CYP3A4/5 inhibitors ritonavir, clarithromycin, and itraconazole each have unique transporter inhibition profiles. None of the alternatives to ketoconazole provided a clean inhibition profile toward the 13 drug transporters evaluated. The results provide guidance for the selection of clinical CYP3A4/5 inhibitors when transporters are potentially involved in a victim drug's pharmacokinetics.
Ibrutinib Dosing Strategies Based on Interaction Potential of CYP3A4 Perpetrators Using Physiologically Based Pharmacokinetic Modeling
Venue: Clinical pharmacology and therapeutics

Based on ibrutinib pharmacokinetics and potential sensitivity towards CYP3A4 mediated drug drug interactions (DDIs) a physiologically based pharmacokinetic approach was developed to mechanistically describe DDI with various CYP3A4 perpetrators in healthy men under fasting conditions. These models were verified using clinical data for ketoconazole (strong CYP3A4 inhibitor) and used to prospectively predict and confirm the inducing effect of rifampin (strong CYP3A4 inducer) DDIs with mild (fluvoxamine, azithromycin) and moderate inhibitors (diltiazem, voriconazole, clarithromycin, itraconazole, erythromycin) and moderate (efavirenz) and strong CYP3A4 inducers (carbamazepine) were also predicted. Ketoconazole increased ibrutinib area under the curve (AUC) by 24 fold, while rifampin decreased ibrutinib AUC by 10 fold; coadministration of ibrutinib with strong inhibitors or inducers should be avoided. The ibrutinib dose should be reduced to 140 mg (quarter of maximal prescribed dose) when coadministered with moderate CYP3A4 inhibitors so that exposures remain within observed ranges at therapeutic doses. Thus, dose recommendations for CYP3A4 perpetrator use during ibrutinib treatment were developed and approved for labeling.
Structure Based Inhibitor Design for Evaluation of a CYP3A4 Pharmacophore Model.
Venue: Journal of medicinal chemistry

Human cytochrome P450 3A4 (CYP3A4) is a key xenobiotic metabolizing enzyme that oxidizes and clears the majority of drugs. CYP3A4 inhibition may lead to drug drug interactions, toxicity, and other adverse effects but, in some cases, could be beneficial and enhance therapeutic efficiency of coadministered pharmaceuticals that are metabolized by CYP3A4. On the basis of our investigations of analogs of ritonavir, a potent CYP3A4 inactivator and pharmacoenhancer, we have built a pharmacophore model for a CYP3A4 specific inhibitor. This study is the first attempt to test this model using a set of rationally designed compounds. The functional and structural data presented here agree well with the proposed pharmacophore. In particular, we confirmed the importance of a flexible backbone, the H bond donor/acceptor moiety, and aromaticity of the side group analogous to Phe 2 of ritonavir and demonstrated the leading role of hydrophobic interactions at the sites adjacent to the heme and phenylalanine cluster in the ligand binding process. The X ray structures of CYP3A4 bound to the rationally designed inhibitors provide deeper insights into the mechanism of the CYP3A4 ligand interaction. Most importantly, two of our compounds (15a and 15b) that are less complex than ritonavir have comparable submicromolar affinity and inhibitory potency for CYP3A4 and, thus, could serve as templates for synthesis of second generation inhibitors for further evaluation and optimization of the pharmacophore model.
CYP3A4 intronic SNP rs35599367 (CYP3A4*22) alters RNA splicing.
Venue: Pharmacogenetics and genomics

Cytochrome P450 3A4 (CYP3A4) metabolizes 30 50% of clinically used drugs. Large interperson variability in CYP3A4 activity affects response to CYP3A4 substrate drugs. We had demonstrated that an intronic single nucleotide polymorphism rs35599367 (CYP3A4*22, located in intron 6) reduces mRNA/protein expression; however, the underlying mechanism remained unknown. Here we show that CYP3A4*22 is associated with a two fold or greater increase in formation of a nonfunctional CYP3A4 alternative splice variant with partial intron 6 retention in human liver (P=0.006) but not in small intestines. Consistent with this observation, in vitro transfection experiments with a CYP3A4 minigene (spanning from intron 5 to intron 7) demonstrated that plasmids carrying the rs35599367 minor T allele caused significantly greater intron 6 retention than the C allele in liver derived HepG2 cells, but not in intestine derived LS 174T cells. These results indicate that tissue specific increased formation of nonfunctional alternative splice variant causes reduced CYP3A4 mRNA/protein expression in CYP3A4*22 carriers.
Systematic and quantitative assessment of the effect of chronic kidney disease on CYP2D6 and CYP3A4/5
Venue: Clinical pharmacology and therapeutics

Recent reviews suggest that chronic kidney disease (CKD) can affect the pharmacokinetics of nonrenally eliminated drugs, but the impact of CKD on individual elimination pathways has not been systematically evaluated. In this study we developed a comprehensive dataset of the effect of CKD on the pharmacokinetics of CYP2D6 and CYP3A4/5 metabolized drugs. Drugs for evaluation were selected based on clinical drug drug interaction (CYP3A4/5 and CYP2D6) and pharmacogenetic (CYP2D6) studies. Information from dedicated CKD studies was available for 13 and 18 of the CYP2D6 and CYP3A4/5 model drugs, respectively. Analysis of these data suggested that CYP2D6 mediated clearance is generally decreased in parallel with the severity of CKD. There was no apparent relationship between the severity of CKD and CYP3A4/5 mediated clearance. The observed elimination route dependency in CKD effects between CYP2D6 and CYP3A4/5 may inform the need to conduct clinical CKD studies with nonrenally eliminated drugs for optimal use of drugs in patients with CKD.
The EpiDerm(tm) 3D human reconstructed skin micronucleus (RSMN) assay: Historical control data and proof of principle studies for mechanistic assay adaptations.
Venue: Mutation research. Genetic toxicology and environmental mutagenesis

The in vitro human reconstructed skin micronucleus (RSMN) assay in EpiDerm(tm) is a promising novel animal alternative for evaluating genotoxicity of topically applied chemicals. It is particularly useful for assessing cosmetic ingredients that can no longer be tested using in vivo assays. To advance the use of this test especially for regulatory decision making, we have established the RSMN assay in our laboratory according to Good Laboratory Practice and following the principles of the OECD test guideline 487 in vitro mammalian cell micronucleus test. Proficiency with the assay was established by correctly identifying direct acting genotoxins and genotoxins requiring metabolism, as well as non genotoxic/non carcinogenic chemicals. We also report the analysis of our historical control data that demonstrate vehicle control and positive control values for %micronuclei in binucleated cells are in the ranges reported previously. Technical issues including evaluating various solvents with both 48h and 72h treatment regimens were investigated. For the first time, mechanistic studies using CREST analysis revealed that the RSMN assay is suitable for distinguishing aneugens and clastogens. Moreover, the assay is also suitable for measuring cytokines as markers for proliferative and toxic effects of chemicals.
Prevalence of hypertension among adolescents: systematic review and meta analysis
Venue: Revista de saude publica

To estimate the prevalence of hypertension among adolescent Brazilian students.  A systematic review of school based cross sectional studies was conducted. The articles were searched in the databases MEDLINE, Embase, Scopus, LILACS, SciELO, Web of Science, CAPES thesis database and Trip Database. In addition, we examined the lists of references of relevant studies to identify potentially eligible articles. No restrictions regarding publication date, language, or status applied. The studies were selected by two independent evaluators, who also extracted the data and assessed the methodological quality following eight criteria related to sampling, measuring blood pressure, and presenting results. The meta analysis was calculated using a random effects model and analyses were performed to investigate heterogeneity.  We retrieved 1,577 articles from the search and included 22 in the review. The included articles corresponded to 14,115 adolescents, 51.2% (n 7,230) female. We observed a variety of techniques, equipment, and references used. The prevalence of hypertension was 8.0% (95%CI 5.0 11.0; I2 97.6% 9.3% (95%CI 5.6 13.6; I2 96.4% in males and 6.5% (95%CI 4.2 9.1; I2 94.2% in females. The meta regression failed to identify the causes of the heterogeneity among studies.  Despite the differences found in the methodologies of the included studies, the results of this systematic review indicate that hypertension is prevalent in the Brazilian adolescent school population. For future investigations, we suggest the standardization of techniques, equipment, and references, aiming at improving the methodological quality of the studies.
Executive function of Spanish speaking language minority preschoolers: Structure and relations with early literacy skills and behavioral outcomes.
Venue: Journal of experimental child psychology

Young children's executive function (EF) is increasingly recognized as an important construct associated with development in cognitive and socioemotional domains. To date, however, few studies have examined EF in populations of language minority children. In this study, 241 Spanish speaking language minority preschoolers who ranged in age from 38 to 69 months (M=54.23 months, SD=6.17) completed three tasks designed to measure inhibitory control (IC) and four tasks designed to measure working memory (WM) Children completed assessments of their vocabulary skills, early literacy skills, and behavioral self regulation in both English and Spanish, and their classroom teachers completed three behavior rating measures. Children were classified as more proficient in English or Spanish based on their scores on the vocabulary measures, and all IC and WM measures were administered in the children's more proficient language. Results of confirmatory factor analyses supported a two factor model of EF for both groups of children as well as strong measurement and structural invariance across groups. Children's EF was substantially related to the language, early literacy, and behavioral self regulation measures as well as teacher ratings of inattention and hyperactivity/impulsivity. For children with more proficient English, EF was associated with skills in both English and Spanish; however, for children with more proficient Spanish, EF was associated primarily with skills in Spanish. These results provide evidence of strong correspondence for EF measured in Spanish speaking language minority preschoolers and monolingual preschoolers, and they identify a potential key factor that can enhance understanding of development in this population of children.
Interlocutor differential effects on the expressive language skills of Spanish speaking English learners
Venue: International journal of speech language pathology

The primary objective of this study was to investigate the relationship between language use with different interlocutors, maternal education level and the expressive language skills of US English learners (ELs) in Spanish and English.  Two hundred and twenty four Spanish speaking ELs in kindergarten provided narrative language samples in Spanish and English. Parents completed a questionnaire of maternal education level and language use with parents, older siblings and peers.  Multiple linear regression analyses demonstrated that language used with different interlocutors and maternal education level had unique effects on participants' expressive language skills. ELs' expressive language skills in English were predicted by interactions with older siblings, peers and maternal education level; Spanish expressive language skills were predicted by interactions with older siblings.  The findings from this study suggest that the determination of language experience of school age bilingual children should examine differential language use with multiple interlocutors, particularly interactions with older siblings and peers.
The NTNU YZU System in the AESW Shared Task: Automated Evaluation of Scientific Writing Using a Convolutional Neural Network
Venue: BEA@NAACL HLT

This study describes the design of the NTNU YZU system for the automated evaluation of scientific writing shared task. We employ a convolutional neural network with the Word2Vec/GloVe embedding representation to predict whether a sentence needs language editing. For the Boolean prediction track, our best F score of 0.6108 ranked second among the ten submissions. Our system also achieved an F score of 0.7419 for the probabilistic estimation track, ranking fourth among the nine submissions.
Introducing automated hand hygiene surveillance to an Australian hospital: Mirroring the HOW2 Benchmark Study.
Venue: American journal of infection control

Human auditing and collating hand hygiene compliance data take hundreds of hours. We report on 24/7 overt observations to establish adjusted average daily hand hygiene opportunities (HHOs) used as the denominator in an automated surveillance that reports daily compliance rates.  Overt 24/7 automated surveillance collected HHOs in medical and surgical wards. Accredited auditors observed health care workers' interaction between patient and patient zones to collect the total number of HHOs, indications, and compliance and noncompliance. Automated surveillance captured compliance (ie, events) via low power radio connected to alcohol based handrub (ABHR) dispensers. Events were divided by HHOs, adjusted for daily patient to nurse ratio, to establish daily rates.  Human auditors collected 21,450 HHOs during 24/7 with 1,532 average unadjusted HHOs per day. This was 4.4 times larger than the minimum ward sample required for accreditation. The average adjusted HHOs for ABHR alone on the medical ward was 63 HHOs per patient day and 40 HHOs per patient day on the surgical ward. From July 1, 2014 July 31, 2015 the automated surveillance system collected 889,968 events.  Automated surveillance collects 4 times the amount of data on each ward per day than a human auditor usually collects for a quarterly compliance report.
Unsupervised Multilayer Feature Learning for Satellite Image Scene Classification
Venue: IEEE Geoscience and Remote Sensing Letters

This letter proposes a simple but effective approach to automatically learn a multilayer image feature for satellite image scene classification. Different from the hand crafted features which are empirically designed but lack high generalization ability, the proposed approach can autonomously extract the data dependent feature. The presented feature extraction algorithm is composed of two layers, and the bases of these two layers are uniformly learned by a plain $K$ means clustering algorithm. Coincidentally, the feature extraction performance of the aforementioned two layers is consistent with visual processing of human visual cortex. More specifically, the first layer can generate edgelike bases, which are analogous to the neuron responses of primary visual cortex (V1) and the second layer can produce cornerlike bases, which resemble the neuron responses of visual extrastriate cortical area two (V2) The proposed feature extraction approach can automatically extract not only simple structure features (e.g. edges) but also complex structure features (e.g. corners and junctions) The learned feature is further discriminated by the linear support vector machine classifier for scene classification. In order to fairly demonstrate the validity of the proposed feature extraction approach, its satellite image scene classification performance is evaluated on the public UCM 21 data set. Experimental results show that the proposed approach can outperform several recent state of the art approaches.
The collection 6 MODIS active fire detection algorithm and fire products
Venue: Remote sensing of environment

The two Moderate Resolution Imaging Spectroradiometer (MODIS) instruments, on board NASA's Terra and Aqua satellites, have provided more than a decade of global fire data. Here we describe improvements made to the fire detection algorithm and swath level product that were implemented as part of the Collection 6 land product reprocessing, which commenced in May 2015. The updated algorithm is intended to address limitations observed with the previous Collection 5 fire product, notably the occurrence of false alarms caused by small forest clearings, and the omission of large fires obscured by thick smoke. Processing was also expanded to oceans and other large water bodies to facilitate monitoring of offshore gas flaring. Additionally, fire radiative power (FRP) is now retrieved using a radiance based approach, generally decreasing FRP for all but the comparatively small fraction of high intensity fire pixels. We performed a Stage 3 validation of the Collection 5 and Collection 6 Terra MODIS fire products using reference fire maps derived from more than 2500 high resolution Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) images. Our results indicated targeted improvements in the performance of the Collection 6 active fire detection algorithm compared to Collection 5, with reduced omission errors over large fires, and reduced false alarm rates in tropical ecosystems. Overall, the MOD14 Collection 6 daytime global commission error was 1.2% compared to 2.4% in Collection 5. Regionally, the probability of detection for Collection 6 exhibited a ~3% absolute increase in Boreal North America and Boreal Asia compared to Collection 5, a ~1% absolute increase in Equatorial Asia and Central Asia, a ~1% absolute decrease in South America above the Equator, and little or no change in the remaining regions considered. Not unexpectedly, the observed variability in the probability of detection was strongly driven by regional differences in fire size. Overall, there was a net improvement in Collection 6 algorithm performance globally.
Detection of Poly and Perfluoroalkyl Substances (PFASs) in U.S. Drinking Water Linked to Industrial Sites, Military Fire Training Areas, and Wastewater Treatment Plants
Venue: Environmental science technology letters

Drinking water contamination with poly and perfluoroalkyl substances (PFASs) poses risks to the developmental, immune, metabolic, and endocrine health of consumers. We present a spatial analysis of 2013 2015 national drinking water PFAS concentrations from the U.S. Environmental Protection Agency's (US EPA) third Unregulated Contaminant Monitoring Rule (UCMR3) program. The number of industrial sites that manufacture or use these compounds, the number of military fire training areas, and the number of wastewater treatment plants are all significant predictors of PFAS detection frequencies and concentrations in public water supplies. Among samples with detectable PFAS levels, each additional military site within a watershed's eight digit hydrologic unit is associated with a 20% increase in PFHxS, a 10% increase in both PFHpA and PFOA, and a 35% increase in PFOS. The number of civilian airports with personnel trained in the use of aqueous film forming foams is significantly associated with the detection of PFASs above the minimal reporting level. We find drinking water supplies for 6 million U.S. residents exceed US EPA's lifetime health advisory (70 ng/L) for PFOS and PFOA. Lower analytical reporting limits and additional sampling of smaller utilities serving <10000 individuals and private wells would greatly assist in further identifying PFAS contamination sources.