nils-herrmann/clean_scirepeval huggingface dataset:
Transcriptional reprogramming underpins enhanced plant growth promotion by the biocontrol fungus Trichoderma hamatum GD12 during antagonistic interactions with Sclerotinia sclerotiorum in soil
Venue: Molecular plant pathology

The free living soil fungus Trichoderma hamatum strain GD12 is notable amongst Trichoderma strains in both controlling plant diseases and stimulating plant growth, a property enhanced during its antagonistic interactions with pathogens in soil. These attributes, alongside its markedly expanded genome and proteome compared with other biocontrol and plant growth promoting Trichoderma strains, imply a rich potential for sustainable alternatives to synthetic pesticides and fertilizers for the control of plant disease and for increasing yields. The purpose of this study was to investigate the transcriptional responses of GD12 underpinning its biocontrol and plant growth promotion capabilities during antagonistic interactions with the pathogen Sclerotinia sclerotiorum in soil. Using an extensive mRNA seq study capturing different time points during the pathogen antagonist interaction in soil, we show that dynamic and biphasic signatures in the GD12 transcriptome underpin its biocontrol and plant (lettuce) growth promoting activities. Functional predictions of differentially expressed genes demonstrate the enrichment of transcripts encoding proteins involved in transportation and oxidation reduction reactions during both processes and an over representation of siderophores. We identify a biphasic response during biocontrol characterized by a significant induction of transcripts encoding small secreted cysteine rich proteins, secondary metabolite producing gene clusters and genes unique to GD12. These data support the hypothesis that Sclerotinia biocontrol is mediated by the synthesis and secretion of antifungal compounds and that GD12's unique reservoir of uncharacterized genes is actively recruited during the effective biological control of a plurivorous plant pathogen.
Attachment Capability of Antagonistic Yeast Rhodotorula glutinis to Botrytis cinerea Contributes to Biocontrol Efficacy
Venue: Front. Microbiol.

Rhodotorula glutinis as an antagonism show good biocontrol performance against various post harvest diseases in fruits. In the present study, strong attachment capability of R. glutinis to spores and hyphae of Botrytis cinerea was observed. Further analysis showed that certain protein components on the yeast cell surface played critical role during the interaction between R. glutinis and B. cinerea. The components mainly distributed at the poles of yeast cells and might contain glycosylation modification, as tunicamycin treated yeast cells lost attachment capability to B. cinerea. To investigate contributions of attachment capability of R. glutinis to its biocontrol efficacy, yeast cells were mutagenized with 3% methane sulfonic acid ethyl ester (EMS) and a mutant CE4 with stable non attaching phenotype was obtained. No significant difference was found on colony, cell morphology, reproductive ability, and capsule formation between the mutant and wild type. However, there was a distinct difference in India ink positive staining patterns between the two strains. Moreover, wild type strain of R. glutinis showed better performance on inhibiting spore germination and mycelial growth of B. cinerea than CE4 strain when yeast cells and B. cinerea were co cultured in vitro. In biocontrol assay, both wild type and CE4 strains showed significant biocontrol efficacy against gray mold caused by B. cinerea in apple fruit, whereas, control effect of CE4 strain was lower than that of wild type. Our findings provided new evidences that attachment capability of R. glutinis to B. cinerea contributed to its biocontrol efficacy.
Syndepositional diagenetic control of molybdenum isotope variations in carbonate sediments from the Bahamas

Molybdenum (Mo) isotope variations recorded in black shales provide important constraints on marine paleoredox conditions. However, suitable shales are not ubiquitous in the geologic record. Moreover, reliable reconstruction of Mo isotope records from shales requires deposition from a water column containing very high concentrations of sulfide a condition which is both rare and difficult to verify with certainty when examining preserved sediments. The utility of Mo isotopic records could be improved if reconstructions were possible using alternative lithologies, such as marine carbonates, which are more abundant in the geologic record. Here, we focus on the role of early diagenesis in determining the Mo isotopic composition preserved in shallow water carbonate sediments from four push cores collected in different shallow water depositional environments in the Bahamas. In contrast with carbonate primary precipitates, which generally contain 10 ppm Mo) The extent of this authigenic enrichment appears to be driven by high concentrations of hydrogen sulfide in the porewaters. In cores with the least authigenic Mo enrichment and lowest pore water sulfide, Mo isotopes are 1 1.2%0 lighter than seawater, while cores with greater Mo enrichments and higher pore water sulfide approach seawater Mo isotope values (2.2 2.5%0) even under oxic bottom water conditions. However, the sensitivity of bulk carbonate d 98 Mo to syndepositional diagenetic conditions potentially complicates interpretation of a carbonate Mo isotope paleoredox proxy. Robust reconstruction of seawater Mo isotopic composition from carbonates will thus require the ability to place constraints on early diagenetic conditions of pore waters at the time of deposition. We show that in order to record seawater Mo isotope values, carbonate pore waters must contain 50 100 mM H 2 S aq which is achieved only in organic and sulfide rich carbonate sediments.
DIAGNOSTIC CLASSIFICATION OF MENTAL HEALTH AND DEVELOPMENTAL DISORDERS OF INFANCY AND EARLY CHILDHOOD (DC:0 5) IMPLEMENTATION CONSIDERATIONS AND CLINICAL REMARKS.
Venue: Infant mental health journal

The Diagnostic Classification of Mental Health and Developmental Disorders of Infancy and Early Childhood (DC: 0 3) gave infant mental health specialists a tool to describe behavioral symptoms during infancy, earlier often ignored as minor or transient baby problems. In a new form, called the DC: 0 5, the tool now aims to describe mental health problems during the first 6 years of life. In my commentary, I discuss some implications of the proposed changes. First, I address the never ending question regarding why a specific diagnostic classification system for young children is at all needed. The answer remains unchanged. Clinicians need to tell the world that mental health problems in young children do exist and that it is our responsibility to reduce their negative influence on early development. When DC: 0 3 was launched, it was described as a complement to other diagnostic systems; clinicians were encouraged to refer to the Diagnostic and Statistical Manual of Mental Disorders or the International Classification of Diseases (ICD) when possible. The DC: 0 3 focused on specific characteristics of infant problems that other systems had not described, and also acknowledged that some of these were early manifestations of problems also described among older children. The DC: 0 5 is meant to be the general single source for describing infant mental health problems in children under 6 years of age, including disorders also described in other systems. While attractive as an aim, the implementation of DC: 0 5 depends on how it is received by healthcare organizations around the world. In a society where healthcare is financed by governmental sources, as in Scandinavia, a classification system has to provide guidance on where resources are most effectively used. Today, the ICD 10 is used to register mental health disorders in all age groups, including infancy and early childhood, despite poor criteria for younger ages. In
Accommodative movements of the lens/capsule and the strand that extends between the posterior vitreous zonule insertion zone the lens equator, in relation to the vitreous face and aging
Venue: Ophthalmic physiological optics the journal of the British College of Ophthalmic Opticians

To elucidate the dynamic accommodative movements of the lens capsule, posterior lens and the strand that attaches to the posterior vitreous zonule insertion zone and posterior lens equator (PVZ INS LE) and their age related changes.
Miniscleral lens wear influences corneal curvature and optics
Venue: Ophthalmic physiological optics the journal of the British College of Ophthalmic Opticians

Transient changes in corneal topography associated with soft and conventional or reverse geometry rigid contact lens wear have been well documented; however, only a few studies have examined the influence of scleral contact lens wear upon the cornea. Therefore, in this study, we examined the influence of modern miniscleral contact lenses, which land entirely on the sclera and overlying tissues, upon anterior corneal curvature and optics.
Learning Deep Representation for Face Alignment with Auxiliary Attributes
Venue: IEEE Transactions on Pattern Analysis and Machine Intelligence

In this study, we show that landmark detection or face alignment task is not a single and independent problem. Instead, its robustness can be greatly improved with auxiliary information. Specifically, we jointly optimize landmark detection together with the recognition of heterogeneous but subtly correlated facial attributes, such as gender, expression, and appearance attributes. This is non trivial since different attribute inference tasks have different learning difficulties and convergence rates. To address this problem, we formulate a novel tasks constrained deep model, which not only learns the inter task correlation but also employs dynamic task coefficients to facilitate the optimization convergence when learning multiple complex tasks. Extensive evaluations show that the proposed task constrained learning (i) outperforms existing face alignment methods, especially in dealing with faces with severe occlusion and pose variation, and (ii) reduces model complexity drastically compared to the state of the art methods based on cascaded deep model.
Specifically neuropathic Gaucher's mutations accelerate cognitive decline in Parkinson's
Venue: Annals of neurology

We hypothesized that specific mutations in the b glucocerebrosidase gene (GBA) causing neuropathic Gaucher's disease (GD) in homozygotes lead to aggressive cognitive decline in heterozygous Parkinson's disease (PD) patients, whereas non neuropathic GD mutations confer intermediate progression rates.
Knowledge engineering for enterprise integration, interoperability and networking: Theory and applications
Venue: Data Knowl. Eng.

Today, enterprises can be characterized by various key facets: globalization, distributed manufacturing, data and knowledge management, advanced automation and robotics, virtual engineering, rapid response to market and more. In this competitive economy, enterprises must collaborate using Information Technology (IT) and other tools to succeed in this dynamic and heterogeneous business environment. Enterprise integration, interoperability and networking are some of the major disciplines that are enabling companies to improve collaboration and communication in the most effective way. Thriving enterprise information systems processes aim to develop information systems that respond to increasingly complex objectives, which align the information systems with business goals and processes of the company. Additionally, the enterprise must adapt and improve when facing new requirements or rapidly changing opportunities. As enterprise information systems models become more ubiquitous, the sharing of best in class models becomes more desirable. Interoperability between dissimilar systems in sharing information is important, but other aspects are also required in the sharing of enterprise systems knowledge. First, this process is based on the need for collaboration; sharing and mutual understanding of the needs of each stakeholder, i.e. each person involved or affected by the future information system, at each stage of its development. Second, this process follows principles, which highlight the need for formal semantic definition of these models, at various abstraction levels ranging from specification to implementation on site. There is a need to also couple new theoretical results with applied methods and tools supporting existing business reconfiguration and transformation both locally and globally.
Lesson Learned and Best Practice Management: A Tool to Support the Enterprise

This paper describes SKILLS Sharing Knowledge in Lesson Learned System, a solution composed by a web based tool and a business process that supports the enterprise in managing and sharing Lessons Learned and Best Practices. SKILLS follows a community based approach, increasing the percentage of explicit knowledge. The solution deals with real issues in Aerospace Company domain, following a methodology composed by three main phases: Analysis of operative contest; analysis of Processes and needs and Solution Development. Starting from a context analysis, conducted using interviews, we identify the company needs. Then, we propose a new Lesson Learned and Best Practice management process, and we explain the functionalities of SKILLS, a tool useful to solve the issues identified and satisfies the company needs. Several users can access to two types of services: the first one oriented to contents (discussion, lesson, lesson learned, best practice) creation and validation, the second one more oriented to horizontal functionality (advanced search, tagging and categorization, user profiling, user page, instant communication) SKILLS covers all activities of Lesson Learned and Best Practice management process, following a collaborative approach, where a community of knowledge workers share knowledge and know how and solve operative issue, enabling the externalization process of SECI model.
The biology, pathogenesis and clinical aspects of acute lymphoblastic leukemia in children with Down syndrome
Venue: Leukemia

Children with Down syndrome (DS) are at a 20 fold increased risk for acute lymphoblastic leukemia (DS ALL) Although the etiology of this higher risk of developing leukemia remains largely unclear, the recent identification of CRLF2 (cytokine receptor like factor 2) and JAK2 mutations and study of the effect of trisomy of Hmgn1 and Dyrk1a (dual specificity tyrosine phosphorylation regulated kinase 1A) on B cell development have shed significant new light on the disease process. Here we focus on the clinical features, biology and genetics of ALL in children with DS. We review the unique characteristics of DS ALL on both the clinical and molecular levels and discuss the differences in treatments and outcomes in ALL in children with DS compared with those without DS. The identification of new biological insights is expected to pave the way for novel targeted therapies.
TRANSLATION OF ENGLISH FEATURE FILM TITLES IN CROATIAN

This paper explores the challenges posed by English film titles and the translation strategies used to adapt them for the Croatian speaking audience. The corpus consisted of 190 feature length English language film titles and their corresponding Croatian translations. They were then grouped according to the source language challenges (puns and double meaning, character references, cultural references and idioms, ambiguity, wordplay by means of embedding the sequel number in the title, and intertextuality) and target language strategies (using keywords indicative of the film genre or plot, proverbs, expanding the original meaning or making it more explicit, introducing intertextuality, partially translating the titles, and retaining only part of the original meaning) The analysis shows that while a part of the target language titles in the corpus aim to familiarize the target language audience with source language structure and culture bound elements, extra linguistic factors affect the translation in over half of the instances. This points to the use of film titles as marketing devices.
Spatiotemporal prediction of fine particulate matter using high resolution satellite images in the Southeastern US 2003 2011
Venue: Journal of Exposure Science and Environmental Epidemiology

Numerous studies have demonstrated that fine particulate matter (PM2.5, particles smaller than 2.5 mm in aerodynamic diameter) is associated with adverse health outcomes. The use of ground monitoring stations of PM2.5 to assess personal exposure, however, induces measurement error. Land use regression provides spatially resolved predictions but land use terms do not vary temporally. Meanwhile, the advent of satellite retrieved aerosol optical depth (AOD) products have made possible to predict the spatial and temporal patterns of PM2.5 exposures. In this paper, we used AOD data with other PM2.5 variables, such as meteorological variables, land use regression, and spatial smoothing to predict daily concentrations of PM2.5 at a 1 km2 resolution of the Southeastern United States including the seven states of Georgia, North Carolina, South Carolina, Alabama, Tennessee, Mississippi, and Florida for the years from 2003 to 2011. We divided the study area into three regions and applied separate mixed effect models to calibrate AOD using ground PM2.5 measurements and other spatiotemporal predictors. Using 10 fold cross validation, we obtained out of sample R2 values of 0.77, 0.81, and 0.70 with the square root of the mean squared prediction errors of 2.89, 2.51, and 2.82 mg/m3 for regions 1, 2, and 3, respectively. The slopes of the relationships between predicted PM2.5 and held out measurements were approximately 1 indicating no bias between the observed and modeled PM2.5 concentrations. Predictions can be used in epidemiological studies investigating the effects of both acute and chronic exposures to PM2.5. Our model results will also extend the existing studies on PM2.5 which have mostly focused on urban areas because of the paucity of monitors in rural areas.
A Review on Predicting Ground PM2.5 Concentration Using Satellite Aerosol Optical Depth

This study reviewed the prediction of fine particulate matter (PM2.5) from satellite aerosol optical depth (AOD) and summarized the advantages and limitations of these predicting models. A total of 116 articles were included from 1436 records retrieved. The number of such studies has been increasing since 2003. Among these studies, four predicting models were widely used: Multiple Linear Regression (MLR) (25 articles) Mixed Effect Model (MEM) (23 articles) Chemical Transport Model (CTM) (16 articles) and Geographically Weighted Regression (GWR) (10 articles) We found that there is no so called best model among them and each has both advantages and limitations. Regarding the prediction accuracy, MEM performs the best, while MLR performs worst. CTM predicts PM2.5 better on a global scale, while GWR tends to perform well on a regional level. Moreover, prediction performance can be significantly improved by combining meteorological variables with land use factors of each region, instead of only considering meteorological variables. In addition, MEM has advantages in dealing with the AOD data with missing values. We recommend that with the help of higher resolution AOD data, future works could be focused on developing satellite based predicting models for the prediction of historical PM2.5 and other air pollutants.
High Resolution Satellite Mapping of Fine Particulates Based on Geographically Weighted Regression
Venue: IEEE Geoscience and Remote Sensing Letters

Satellite retrieved aerosol optical depth (AOD) has been increasingly utilized for the mapping of fine particulate matter (PM2.5) concentrations. An accurate estimation and mapping of PM2.5 concentrations depends on the high resolution AOD data and a robust mathematical model that takes into account the spatial nonstationary relationship between PM2.5 and AOD. Take the core portion of the Beijing Hebei Tianjin (Jing Jin Ji) urban agglomeration as case study (the most seriously polluted region in China) Land use, population, meteorological variables, and simplified aerosol retrieval algorithm retrieved AOD at 1 km resolution are employed as the predictors for the geographically weighted regression (GWR) and the ordinary least squares (OLS) model to map the spatial distribution of PM2.5 concentrations. The GWR model shows significant spatial variations in PM2.5 concentrations over the region than the traditional OLS model, which reveals relative homogeneous variations. Validation with ground level PM2.5 concentrations demonstrates that PM2.5 concentrations predicted by the GWR model (R2 0.75, RMSE 10 mg/m3) correlate better than those by the OLS model (R2 0.53, RMSE 16 mg/m3) These results suggest that the GWR model offered a more reliable way for the prediction of spatial distribution of PM2.5 concentrations over urban areas.
The survival of direct composite restorations in the management of severe tooth wear including attrition and erosion: A prospective 8 year study.
Venue: Journal of dentistry

Survival of directly placed composite to restore worn teeth has been reported in studies with small sample sizes, short observation periods and different materials. This study aimed to estimate survival for a hybrid composite placed by one clinician up to 8 years follow up.  All patients were referred and recruited for a prospective observational cohort study. One composite was used: Spectrum((r) (DentsplyDeTrey) Most restorations were placed on the maxillary anterior teeth using a Dahl approach.  A total of 1010 direct composites were placed in 164 patients. Mean follow up time was 33.8 months (s.d. 27.7) 71 of 1010 restorations failed during follow up. The estimated failure rate in the first year was 5.4% (95% CI 3.7 7.0% Time to failure was significantly greater in older subjects (p=0.005) and when a lack of posterior support was present (p=0.003) Bruxism and an increase in the occlusal vertical dimension were not associated with failure. The proportion of failures was greater in patients with a Class 3 or edge to edge incisal relationship than in Class 1 and Class 2 cases but this was not statistically significant. More failures occurred in the lower arch (9.6% compared to the upper arch (6% with the largest number of composites having been placed on the maxillary incisors (n=519)  The worn dentition presents a restorative challenge but composite is an appropriate restorative material.  This study shows that posterior occlusal support is necessary to optimise survival.