bluuebunny/crossref_metadata_2025_split huggingface dataset:
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data
Authors: de Nies Laura , Lopes Sara , Busi Susheel Bhanu , Galata Valentina , Heintz-Buschart Anna , Laczny Cedric Christian , May Patrick , Wilmes Paul 
Published: February 2021

Abstract
Background
Pathogenic microorganisms cause disease by invading, colonizing, and damaging their host. Virulence factors including bacterial toxins contribute to pathogenicity. Additionally, antimicrobial resistance genes allow pathogens to evade otherwise curative treatments. To understand causal relationships between microbiome compositions, functioning, and disease, it is essential to identify virulence factors and antimicrobial resistance genes in situ. At present, there is a clear lack of computational approaches to simultaneously identify these factors in metagenomic datasets.

Results
Here, we present PathoFact, a tool for the contextualized prediction of virulence factors, bacterial toxins, and antimicrobial resistance genes with high accuracy (0.921, 0.832 and 0.979, respectively) and specificity (0.957, 0.989 and 0.994). We evaluate the performance of PathoFact on simulated metagenomic datasets and perform a comparison to two other general workflows for the analysis of metagenomic data. PathoFact outperforms all existing workflows in predicting virulence factors and toxin genes. It performs comparably to one pipeline regarding the prediction of antimicrobial resistance while outperforming the others. We further demonstrate the performance of PathoFact on three publicly available case-control metagenomic datasets representing an actual infection as well as chronic diseases in which either pathogenic potential or bacterial toxins are hypothesized to play a role. In each case, we identify virulence factors and AMR genes which differentiated between the case and control groups, thereby revealing novel gene associations with the studied diseases.

Conclusion
PathoFact is an easy-to-use, modular, and reproducible pipeline for the identification of virulence factors, bacterial toxins, and antimicrobial resistance genes in metagenomic data. Additionally, our tool combines the prediction of these pathogenicity factors with the identification of mobile genetic elements. This provides further depth to the analysis by considering the genomic context of the pertinent genes. Furthermore, PathoFact’s modules for virulence factors, toxins, and antimicrobial resistance genes can be applied independently, thereby making it a flexible and versatile tool. PathoFact, its models, and databases are freely available at https://pathofact.lcsb.uni.lu.
Just like fireworks in my brain – a Swedish interview study on experiences of emotions in female patients with eating disorders
Authors: Petersson Suzanne , Gullbing Lydia , Perseius Kent-Inge 
Published: February 2021

AbstractBackgroundPatients with eating disorders have reported poorer emotional awareness, more emotional suppression, less use of adaptive emotional regulation strategies, and more use of maladaptive emotional regulation strategies compared to people in healthy control groups.AimTo explore experiences of emotions by a transdiagnostic sample of patients with eating disorders.MethodNine patients with different eating disorder diagnoses at an eating disorder outpatient clinic in Sweden were interviewed for their thoughts on emotions. The interviews were analyzed with Thematic Analysis.ResultFour themes were constructed: “Not knowing what one feels”, “Switch off, run away, or hide behind a mask”, “Emotions in a lifelong perspective”, and “Using eating behaviours to regulate emotions”. The patients described uncertainty regarding whether they experienced emotions correctly. They described how they tried to avoid difficult emotions through suppressive strategies and eating disorder behaviour. All described strategies were inefficient and all emotions were experienced as problematic, even joy. Since joy was used as a mask, the real experience of happiness was lost and mourned.ConclusionAll kinds of emotions were considered problematic to experience, but shame, fear, and sadness were considered worst. It is difficult to know if the emotional difficulties preceded an eating disorder, however such difficulties may have increased as a result of the eating disorder.
Physiological, emotional and neural responses to visual stimuli in eating disorders: a review
Authors: Burmester Victoria , Graham Esme , Nicholls Dasha 
Published: February 2021

AbstractBackgroundOverconcern with food and shape/weight stimuli are central to eating disorder maintenance with attentional biases seen towards these images not present in healthy controls. These stimuli trigger changes in the physiological, emotional, and neural responses in people with eating disorders, and are regularly used in research and clinical practice. However, selection of stimuli for these treatments is frequently based on self-reported emotional ratings alone, and whether self-reports reflect objective responses is unknown.Main bodyThis review assessed the associations across emotional self-report, physiological, and neural responses to both food and body-shape/weight stimuli in people with anorexia nervosa (AN), bulimia nervosa (BN) and binge eating disorder (BED). For food stimuli, either an aversive or lack of physiological effect was generated in people with AN, together with a negative emotional response on neuroimaging, and high subjective anxiety ratings. People with BN showed a positive self-rating, an aversive physiological reaction, and a motivational neural response. In BED, an aversive physiological reaction was found in contrast to motivational/appetitive neural responses, with food images rated as pleasant. The results for shape/weight stimuli showed aversive responses in some physiological modalities, which was reflected in both the emotional and neural responses, but this aversive response was not consistent across physiological studies.ConclusionsShape/weight stimuli are more reliable for use in therapy or research than food stimuli as the impact of these images is more consistent across subjective and objective responses. Care should be taken when using food stimuli due to the disconnect reported in this review.
Overcoming limitations of self-report: an assessment of fear of weight gain in anorexia nervosa and healthy controls using implicit association tests
Authors: Borgers Tiana , Krüger Nathalie , Vocks Silja , Thomas Jennifer J. , Plessow Franziska , Hartmann Andrea S. 
Published: February 2021

Abstract
Background
Fear of weight gain is a characteristic feature of anorexia nervosa (AN), and reducing this fear is often a main target of treatment. However, research shows that 20% of individuals with AN do not report fear of weight gain. Studies are needed that evaluate the centrality of fear of weight gain for AN with a method less susceptible to deception than self-report.

Methods
We approximated implicit fear of weight gain by measuring implicit drive for thinness using implicit association tests (IATs). We asked 64 participants (35 AN, 29 healthy controls [HCs]) to categorize statements as pro-dieting vs. non-dieting and true vs. false in a questionnaire-based IAT, and pictures of underweight vs. normal-weight models and positive vs. negative words in a picture-based IAT using two response keys. We tested for associations between implicit drive for thinness and explicitly reported psychopathology within AN as well as group differences between AN and HC groups.

Results
Correlation analyses within the AN group showed that higher implicit drive for thinness was associated with more pronounced eating disorder-specific psychopathology. Furthermore, the AN group showed a stronger implicit drive for thinness than HCs in both IATs.

Conclusion
The results highlight the relevance of considering fear of weight gain as a continuous construct. Our implicit assessment captures various degrees of fear of weight gain in AN, which might allow for more individually tailored interventions in the future.
Understanding training needs in eating disorders of graduating and new graduate dietitians in Australia: an online survey
Authors: Denman Elyse , Parker Elizabeth Kumiko , Ashley Mellisa Anne , Harris Deanne Maree , Halaki Mark , Flood Victoria , Stefoska-Needham Anita 
Published: February 2021

Abstract
Background
Following recent reforms by the Australian Government to the Medicare Benefits Schedule, people living with a diagnosed eating disorder (ED) in Australia have greater access to dietetic services. However, new graduate dietitians anecdotally lack confidence to provide appropriate interventions to support patients with an ED. Therefore, this cross-sectional study aims to explore the perceived confidence, and educational and professional development needs of student dietitians and new graduate dietitians in the area of EDs.

Methods
An online survey with 17 questions was designed, consisting of a combination of discrete (yes/no) questions, free text, ordered scales and 5-point Likert scales. Student dietitians, and first- and second- year graduates (n = 1456) were approached via email as potential participants, from the professional organisation Dietitians Australia member list. Survey data was analysed using descriptive statistics and odds ratios.

Results
In total, 150 surveys were completed, with a response rate of 10.3%. Respondents reported a lack of confidence in managing patients with an ED and implementing ED treatment approaches (81 and 95%, respectively). However, participants previously exposed to patients with an ED, such as anorexia nervosa, were 4.7 times (95% CI 1.72, 12.97) more likely to be confident compared to those not exposed to patients with an ED. The majority of respondents (37%) stated they would seek assistance from other dietitians, and develop their skills via online webinars (27%) and workshops (25%).

Conclusions
This survey identified that final year dietetics students and new graduate dietitians perceive lower levels of confidence to practice in the area of EDs. The desire for further ED-specific training and education was reported.
Stress-free Everyday LiFe for Children and Adolescents REsearch (SELFCARE): a protocol for a cluster randomised trial testing a school teacher training programme to teach mindfulness (“.b”)
Authors: Juul Lise , Frydenberg Morten , Beck Michelle Sand , Fjorback Lone Overby 
Published: February 2021

AbstractBackgroundThere is a call for sustainable, evidence-based interventions in schools to promote mental health in schoolchildren. Our primary aim of this trial is to evaluate the effectiveness in vulnerable pupils of a school teacher training programme to teach mindfulness (“.b” programme) as a part of compulsory class room teaching in Danish schools on the pupils’ self-reported mental health at 6-month follow-up. Our secondary aim is to evaluate the effectiveness of the school teacher training programme to teach the “.b”-programme as a part of compulsory class room teaching among the total pupil population on the pupils’ self-reported mental health at 3 and 6 months after baseline.MethodsThe pragmatic cluster two-armed randomised controlled trial includes 110 municipal or private schools from all five regions in Denmark; 191 school teachers and approximately 2000 pupils at 11–15 years of age. Exclusion criteria; for schools: < 100 pupils; for pupils: parental opt out. Our intervention consists of (A) a school teacher training programme and (B) the “.b”-programme delivered as part of compulsory class room teaching in schools to pupils at the age of 11–15 years. The pupils in the control schools receive education as usual. Our primary study population is the vulnerable subgroup with a Strengths and Difficulties Questionnaire (SDQ) total difficulties score > 80% percentile at baseline (approximately 400 pupils). The primary outcome is change in the SDQ total score by the pupils. We also evaluate the effectiveness among the total pupil study population and in girls and boys, respectively and use other measures on mental health. Data will be analysed with repeated measurement models taken clusters into account.DiscussionThis large-scale trial will estimate the effectiveness of a population-based strategy on mental health in Danish schoolchildren. The trial evaluates the effect of a school teacher training programme, where teachers are trained in teaching the “.b” programme. The “.b” programme will be taught as a part of compulsory class room teaching. The intervention takes implementation issues into account. Effectiveness will be evaluated both in a vulnerable subgroup and among the total population.Trial registration numberClinicalTrials.gov Identifier: NCT04208113, registered December 23 2019,https://clinicaltrials.gov/ct2/show/NCT04208113.
A transparent dialogue between iconography and chemical characterisation: a set of foreign stained glasses in Portugal
Authors: Rodrigues Alexandra , Coutinho Mathilda , Machado Andreia , Martinho Bruno A. , Cerqueira Alves Luís , Macedo Maria Filomena , Vilarigues Márcia 
Published: February 2021

Abstract
This work presents the first results of the iconographic study and analytical characterisation of a set of four stained-glass panels that are part of the collection of National Palace of Pena (Sintra, Portugal). These panels were collected by the King Ferdinand II in the mid-nineteenth century, for his main residence the Palace of Necessidades (Lisbon, Portugal), and only first presented to the general public in 2011. This study contributes with the knowledge of Technical Art History and Heritage Science to a better and deeper understanding of their history, materials and techniques used in the production, where an art-historical and a scientific approach are applied to attribute their origins. Based on the analysis of the formal and stylistic characteristic of the panels, it is proposed that the drawings used for the production of three of these panels may be based on the design and painting being carried out in the same workshop, and that the four panels have the same provenance (Germany). The composition of the glass and grisaille was determined and colourising elements were identified. Through this approach, conclusive correlation between the analysed glasses was possible: all are calcium rich or calcium–potassium rich types, and the results also suggest that the same source of silica was used for their production. A typical mixture of glass and lead oxide was found in the grisaille applied on the painted panels. However, less usual was the use of a copper oxide pigment for the black grisaille. All these findings support the proposals made regarding provenance and production period (fifteenth century).
The microstructure of multicolor hare’s fur glaze: the correlation between morphological and compositional characteristics and glaze color
Authors: Guan Ming , Kang Baoqiang , Wei Xiangjun , Li Gen , Jia Cui , Li He , Ding Yinzhong , Lei Yong 
Published: February 2021

Abstract
The hare’s fur glazed Jian wares characterized by radial fur-like strips, as one of the typical representatives of Chinese ceramics in the 10th-13th century (A.D.), were famous for the aesthetic values in highlighting the color sparkling effects of tea soup, which were one of the indispensable tea wares in tea culture. The firing technology of hare’s fur glaze of Jian wares not only played a crucial role in the development of Chinese ceramic history, but also enlightened the modern imitation technology. The hare’s fur glaze of Jian wares can be further grouped according to the color of strips, of which the yellowish-brown hare’s fur glaze (yellowish-brown matte strips), gold hare’s fur glaze (golden shiny strips) and silver hare’s fur glaze (bright silvery strips) were the most representative types. Epsilon-Fe2O3, a specific metastable crystal phase, has become a research hotspot as the chromogenic crystals of hare’s fur glaze, however, the comparative analysis focused on the correlation between ε-Fe2O3 and the macroscopic glaze color has been barely reported. In our work, the bright color strips (hare’s fur area) and black strips (black glaze area) of silver, gold and yellowish-brown hare’s fur glaze were morphologically and compositionally analyzed by SEM and EDS, respectively. The morphological features and compositional differences of three representative types of hare’s fur glaze samples were summarized, which indicated the differences in the size, distribution and coverage of crystals and the distribution and contents of materials. It was speculated that high-level of Fe2O3 and CaO with low-level of SiO2 and Al2O3 may relate to the crystallization of ε-Fe2O3. This work helps in laying the foundation of further explanation of the technological differences of hare’s fur glazes.
Quantitative imaging of bone remodeling in patients with a unicompartmental joint unloading knee implant (ATLAS Knee System)—effect of metal artifacts on a SPECT-CT-based quantification
Authors: Grosser Oliver S. , Klutzny Marcus , Wissel Heiko , Kupitz Dennis , Finger Michael , Schenke Simone , Wuestemann Jan , Lohmann Christoph H. , Hoeschen Christoph , Pech Maciej , Staerke Christian , Kreissl Michael C. 
Published: February 2021

Abstract
Background
SPECT-CT using radiolabeled phosphonates is considered a standard for assessing bone metabolism (e.g., in patients with osteoarthritis of knee joints). However, SPECT can be influenced by metal artifacts in CT caused by endoprostheses affecting attenuation correction. The current study examined the effects of metal artifacts in CT of a specific endoprosthesis design on quantitative hybrid SPECT-CT imaging.
The implant was positioned inside a phantom homogenously filled with activity (955 MBq 99mTc). CT imaging was performed for different X-ray tube currents (I = 10, 40, 125 mA) and table pitches (p = 0.562 and 1.375). X-ray tube voltage (U = 120 kVp) and primary collimation (16 × 0.625 mm) were kept constant for all scans. The CT reconstruction was performed with five different reconstruction kernels (slice thickness, 1.25 mm and 3.75 mm, each 512 × 512 matrix). Effects from metal artifacts were analyzed for different CT scans and reconstruction protocols. ROI analysis of CT and SPECT data was performed for two slice positions/volumes representing the typical locations for target structures relative to the prosthesis (e.g., femur and tibia). A reference region (homogenous activity concentration without influence from metal artifacts) was analyzed for comparison.

Results
Significant effects caused by CT metal artifacts on attenuation-corrected SPECT were observed for the different slice positions, reconstructed slice thicknesses of CT data, and pitch and CT-reconstruction kernels used (all, p < 0.0001). Based on the optimization, a set of three protocols was identified minimizing the effect of CT metal artifacts on SPECT data. Regarding the reference region, the activity concentration in the anatomically correlated volume was underestimated by 8.9–10.1%. A slight inhomogeneity of the reconstructed activity concentration was detected inside the regions with a median up to 0.81% (p < 0.0001). Using an X-ray tube current of 40 mA showed the best result, balancing quantification and CT exposure.

Conclusion
The results of this study demonstrate the need for the evaluation of SPECT-CT protocols in prosthesis imaging. Phantom experiments demonstrated the possibility for quantitative SPECT-CT of bone turnover in a specific prosthesis design. Meanwhile, a systematic bias caused by metal implants on quantitative SPECT data has to be considered.
Standard MRI-based attenuation correction for PET/MRI phantoms: a novel concept using MRI-visible polymer
Authors: Rausch Ivo , Valladares Alejandra , Sundar Lalith Kumar Shiyam , Beyer Thomas , Hacker Marcus , Meyerspeer Martin , Unger Ewald 
Published: February 2021

Abstract
Background
PET/MRI phantom studies are challenged by the need of phantom-specific attenuation templates to account for attenuation properties of the phantom material. We present a PET/MRI phantom built from MRI-visible material for which attenuation correction (AC) can be performed using the standard MRI-based AC.

Methods
A water-fillable phantom was 3D-printed with a commercially available MRI-visible polymer. The phantom had a cylindrical shape and the fillable compartment consisted of a homogeneous region and a region containing solid rods of different diameters. The phantom was filled with a solution of water and [18F]FDG. A 30 min PET/MRI acquisition including the standard Dixon-based MR-AC method was performed. In addition, a CT scan of the phantom was acquired on a PET/CT system.
From the Dixon in-phase, opposed-phase and fat images, a phantom-specific AC map (Phantom MR-AC) was produced by separating the phantom material from the water compartment using a thresholding-based method and assigning fixed attenuation coefficients to the individual compartments. The PET data was reconstructed using the Phantom MR-AC, the original Dixon MR-AC, and an MR-AC just containing the water compartment (NoWall-AC) to estimate the error of ignoring the phantom walls. CT-based AC was employed as the reference standard. Average %-differences in measured activity between the CT corrected PET and the PET corrected with the other AC methods were calculated.

Results
The phantom housing and the liquid compartment were both visible and distinguishable from each other in the Dixon images and allowed the segmentation of a phantom-specific MR-based AC. Compared to the CT-AC PET, average differences in measured activity in the whole water compartment in the phantom of −0.3%, 9.4%, and −24.1% were found for Dixon phantom MR-AC, MR-AC, and NoWall-AC based PET, respectively. Average differences near the phantom wall in the homogeneous region were −0.3%, 6.6%, and −34.3%, respectively. Around the rods, activity differed from the CT-AC PET by 0.7%, 8.9%, and −45.5%, respectively.

Conclusion
The presented phantom material is visible using standard MR sequences, and thus, supports the use of standard, phantom-independent MR measurements for MR-AC in PET/MRI phantom studies.