bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continuous Automated Model EvaluatiOn (CAMEO)—Perspectives on the future of fully automated evaluation of structure prediction methods
Authors: Robin Xavier , Haas Juergen , Gumienny Rafal , Smolinski Anna , Tauriello Gerardo , Schwede Torsten 
Published: August 2021

AbstractThe Continuous Automated Model EvaluatiOn (CAMEO) platform complements the biennial CASP experiment by conducting fully automated blind evaluations of three‐dimensional protein prediction servers based on the weekly prerelease of sequences of those structures, which are going to be published in the upcoming release of the Protein Data Bank. While in CASP14, significant success was observed in predicting the structures of individual protein chains with high accuracy, significant challenges remain in correctly predicting the structures of complexes. By implementing fully automated evaluation of predictions for protein–protein complexes, as well as for proteins in complex with ligands, peptides, nucleic acids, or proteins containing noncanonical amino acid residues, CAMEO will assist new developments in those challenging areas of active research.
The role of collective sensemaking and science curriculum development within a research–practice partnership
Authors: Marshall Stefanie L. , Nazar Christina Restrepo , Ibourk Amal , McElhaney Kevin W. 
Published: August 2021

AbstractThis study examines how researchers can better understand the instructional and practical realities of teachers through collective sensemaking. Traditional approaches to curriculum design engage learning models without accounting for the needed flexibility of teachers. This approach has resulted in tension and gatekeeping—inhibiting the implementation of curriculum. Teachers are often considered relatively autonomous; however, this study sheds light on the constrained autonomy teachers experience resulting from internal and external pressures. This study examines the collective sensemaking process of researchers while developing a high school genetics curriculum. By examining the collective sensemaking of the areas of tension that arose during the curriculum design process, the problem space of researchers expanded and became more aligned with the problem space of teachers. Collective sensemaking encouraged the humanizing of teachers by centering their content, contextual, and social needs. In addition, this study suggests that gatekeeping can result from many factors; but through collective sensemaking, researchers can intentionally design to resolve said factors.
Range‐separated multiconfigurational density functional theory methods
Authors: Pernal Katarzyna , Hapka Michał 
Published: August 2021

AbstractRange‐separated multiconfigurational density functional theory (RS MC‐DFT) rigorously combines density functional (DFT) and wavefunction (WFT) theories. This is achieved by partitioning of the electron interaction operator into long‐ and short‐range components and modeling them with WFT and DFT, respectively. In contrast to other methods, mixing wavefunctions with density functionals, RS MC‐DFT is free from electron correlation double counting. The general formulation of RS MC‐DFT allows for merging any ab initio approximation with density functionals. Implementations of RS MC‐DFT aim at increasing both versatility and accuracy of the underlying methods, while reducing the computational cost of the ab initio problem. Variants of the RS MC‐DFT approach can be divided into single‐determinant‐based range‐separated methods and range‐separated multideterminantal WFT methods. In these approaches the electron correlation energy is described both by a pertinent short‐range density functional and by the wavefunction theory. We review the short‐range functionals and correlated wavefunction theories employed in the framework of RS MC‐DFT. We discuss applications of the RS MC‐DFT methods to ground‐state properties of molecules and to noncovalent interactions. Time‐dependent linear‐response theory and direct approaches to excited states are also presented. For each area of applications, we assess advantages of RS MC‐DFT over conventional DFT and ab initio methods.This article is categorized under:
Electronic Structure Theory > Ab Initio Electronic Structure Methods
Electronic Structure Theory > Density Functional Theory
Future Vision, Summary and Outlook
Authors: Habyarimana Ephrem 
Published: August 2021

AbstractThe DataBio’s agriculture pilots were carried out through a multi-actor whole-farm management approach using information technology, satellite positioning and remote sensing data as well as Internet of Things technology. The goal was to optimize the returns on inputs while reducing environmental impacts and streamlining the CAP monitoring. Novel knowledge was delivered for a more sustainable agriculture in line with the FAO call to achieve global food security and eliminate malnutrition for the more than nine billion people by 2050. The findings from the pilots shed light on the potential of digital agriculture to solve Europe’s concern of the declining workforce in the farming industry as the implemented technologies would help run farms with less workforce and manual labor. The pilot applications of big data technologies included autonomous machinery, mapping of yield, variable rate of applying agricultural inputs, input optimization, crop performance and in-season yields prediction as well as the genomic prediction and selection method allowing to cut cost and duration of cultivar development. The pilots showed their potential to transform agriculture, and the improved predictive analytics is expected to play a fundamental role in the production environment. As AI models are retrained with more data, the decision support systems become more accurate and serve the farmer better, leading to faster adoption. Adoption is further stimulated by cooperation between farmers to share investment costs and technological platforms allowing farmers to benchmark among themselves and across cropping season.
Conclusions and Outlook—Summary of Big Data in Forestry
Authors: Miettinen Jukka , Tergujeff Renne 
Published: August 2021

AbstractIn this chapter, we summarize the findings from the forestry pilots conducted during the DataBio project. Although the pilots demonstrated the functionality of big data in forestry through several practical applications and services, they also highlighted areas where further development is needed. More effort is needed particularly in ensuring smooth connections between the technical components of the processing pipelines, as well as designing the best business solutions within the big data service chain and between the service providers and users. Overall, the challenge for the coming years is to establish operational big data processing pipelines that meet the requirements and expectations of forestry stakeholders.
Kaliumhydroxid-5 %-Lösung bei aktinischer Keratose
Authors: Reinhold U. , Bai-Habelski J. , Abeck D. , Denfeld R. , Dominicus R. , Fischer T. , Radny P. 
Published: August 2021

Zusammenfassung
Hintergrund
Die aktinische Keratose (AK) ist ein epitheliales Carcinoma in situ der Haut. Aufgrund des Risikos einer malignen Transformation besteht ein frühzeitiger Behandlungsbedarf. Gerade die initiale Therapie sollte neben der Wirksamkeit eine gute Verträglichkeit und Anwenderfreundlichkeit aufweisen. Kaliumhydroxid (KOH)-Lösung ist als keratolytische Behandlungsoption bei hyperkeratotischen Hauterkrankungen, wie z. B. Mollusca contagiosa, bereits etabliert.

Methodik
Wirksamkeit und Verträglichkeit von KOH-5 %-Lösung zur Behandlung der leichten bis moderaten AK wurden in einer prospektiven, einarmigen, multizentrischen Medizinproduktestudie (Treatment of AK with KOH [TAKKOH]) untersucht. Die KOH-Lösung wurde 2‑mal täglich über 14 Tage aufgetragen mit anschließender Behandlungspause von 14 Tagen (≙ 1 Behandlungszyklus) für maximal 3 Behandlungszyklen oder mindestens bis zum Behandlungserfolg. Das primäre Zielkriterium „Behandlungserfolg“ wurde als komplette Remission (CR) aller AK-Läsionen eines Patienten definiert. Sekundäre Zielkriterien beinhalteten die Beurteilung der partiellen Remission (PR), der Anzahl an AK-Läsionen in Remission, die Wirksamkeitsbeurteilung anhand von Schulnoten durch Prüfärzte und Patienten sowie sicherheitsrelevante Endpunkte.

Ergebnisse
Es wurden 73 Patienten in die Studie eingeschlossen. Eine CR wurde von 54,9 % der Patienten erreicht, eine PR von 64,8 % bei einer Reduktion der Gesamtzahl an Läsionen um 69,9 %. Bei 46,6 % der Patienten wurden unerwünschte Ereignisse beobachtet. Diese überwiegend unerwünschten Wirkungen (82,6 %) stellten ausnahmslos transiente und milde lokale Hautreaktionen dar.

Schlussfolgerung
Die Studie liefert Hinweise auf die Wirksamkeit und Sicherheit von KOH-5 %-Lösung zur läsionsgerichteten topischen Therapie der AK.
Cones and sleeves present good survival and clinical outcome in revision total knee arthroplasty: a meta-analysis
Authors: Fischer Laura Theresa , Heinecke Markus , Röhner Eric , Schlattmann Peter , Matziolis Georg 
Published: August 2021

Abstract
Purpose
The fixation of revision total knee arthroplasties (rTKA) tends to be difficult, leading to a reduction in implant survival. One option for achieving a more stable anchorage is to use metaphyseal cones and sleeves. The objective of the present paper is to provide a current comparative meta-analysis on survival and clinical results of cones vs. sleeves, with a differentiation between the short- and long-term outcome.

Methods
A search of the literature was conducted systematically to include original papers from 2010 to June 2021. The following parameters were taken into account: revision for aseptic loosening, revision for any reason, periprosthetic joint infections (PJI), KSS as well as KSFS. Studies with a mean follow-up of at least 60 months were defined to be long-term follow-up studies (LT). All other studies were included in the short-term (ST) study analysis. A pooled incidence was used as a summary statistic using a random intercept logistic regression model.

Results
The present meta-analysis included 43 publications with 3008 rTKA. Of these, 23 publications with 1911 cases were allocated to the sleeve group (SG) and 20 papers with 1097 cases to the cone group (CG). CG showed overall numerically higher complication rates in short- and long-term follow-up, compared with SG. Aseptic loosening occurred at a rate of 0.4% in SG (LT) and 4.1% in CG (LT) (p = 0.09). Periprosthetic joint infection (PJI) was more frequent in the cone group (7% in ST and 11.7% in LT) than in the sleeve group (3.4% in ST and 4.9% in LT, p = 0.02 both). The total revision rate was 5.5% in SG (LT) and 14.4% in CG (LT) (p = 0.12). The clinical scores were also comparable between the two groups. Hinged prothesis were used more frequent in the cone group (ST p < 0.001; LT p = 0.10), whereas CC type protheses were used more frequently in the sleeve group (ST p < 0.001; LT p < 0.11).

Conclusions
This meta-analysis takes into account the longest follow-up periods covered to date. Both cones and sleeves represent a reliable fixation method in the case of severe bone loss in rTKA, although the higher rate of PJI after cone fixation remains a source of concern. A metaphyseal fixation of hinged implants should be taken into account.

Level of evidence
II (meta-analysis).
Modeling the infrared cascade spectra of small PAHs: the 11.2 μm band
Authors: Mackie Cameron J. , Candian Alessandra , Lee Timothy J. , Tielens Alexander G. G. M. 
Published: August 2021

AbstractThe profile of the 11.2 μm feature of the infrared (IR) cascade emission spectra of polycyclic aromatic hydrocarbon (PAH) molecules is investigated using a vibrational anharmonic method. Several factors are found to affect the profile including: the energy of the initially absorbed ultraviolet (UV) photon, the density of vibrational states, the anharmonic nature of the vibrational modes, the relative intensities of the vibrational modes, the rotational temperature of the molecule, and blending with nearby features. Each of these factors is explored independently and influence either the red or blue wing of the 11.2 μm feature. The majority impact solely the red wing, with the only factor altering the blue wing being the rotational temperature.
Inhibition of interferon I induction by non-structural protein NSs of Puumala virus and other vole-associated orthohantaviruses: phenotypic plasticity of the protein and potential functional domains
Authors: Binder Florian , Gallo Giulia , Bendl Elias , Eckerle Isabella , Ermonval Myriam , Luttermann Christine , Ulrich Rainer G. 
Published: August 2021

AbstractThe orthohantavirus Puumala virus (PUUV), which is transmitted by bank voles (Clethrionomys glareolus), and other vole-borne hantaviruses contain in their small (S) genome segment two overlapping open reading frames, coding for the nucleocapsid protein and the non-structural protein NSs, a putative type I interferon (IFN-I) antagonist. To investigate the role of NSs of PUUV and other orthohantaviruses, the expression pattern of recombinant NSs constructs and their ability to inhibit human IFN-I promoter activity were investigated. The NSs proteins of PUUV and related cricetid-borne orthohantaviruses showed strong inhibition of IFN-I promoter induction. We identified protein products originating from three and two methionine initiation codons in the NSs ORF of PUUV during transfection and infection, respectively. The three putative start codons are conserved in all PUUV strains analysed. Translation initiation at these start codons influenced the inhibitory activity of the NSs products, with the wild-type (wt) construct expressing two proteins starting at the first and second methionine and showing strong inhibition activity. Analysis of in vitro-generated variants and naturally occurring PUUV NSs proteins indicated that amino acid variation in the NSs protein is well tolerated, suggesting its phenotypic plasticity. The N-terminal 20-amino-acid region of the NSs protein was found to be associated with strong inhibition and to be highly vulnerable to amino acid exchanges and tag fusions. Infection studies using human, bank vole, and Vero E6 cells did not show obvious differences in the replication capacity of PUUV Sotkamo wt and a strain with a truncated NSs protein (NSs21Stop), showing that the lack of a full-length NSs might be compensated by its N-terminal peptide, as seen in transfection experiments. These results contribute to our understanding of virus-host interactions and highlight the importance of future innate immunity studies in reservoir hosts.
Genomic landscape of a mouse model of diffuse-type gastric adenocarcinoma
Authors: Zhang Menghua , Sugita Itsuki , Komura Daisuke , Katoh Hiroto , Shimada Shu , Inazawa Johji , Tanaka Shinji , Ishikawa Shumpei 
Published: August 2021

Abstract
Background
There is a need for a model of diffuse-type gastric cancer that captures the features of the disease, facilitates the study of its mechanisms, and aids the development of potential therapies. One such model may be Cdh1 and Trp53 double conditional knockout (DCKO) mice, which have histopathological features similar to those of human diffuse-type gastric cancer. However, a genomic profile of this mouse model has yet to be completed.

Methods
Whole-genome sequences of tumors from eight DCKO mice were analyzed and their molecular features were compared with those of human gastric adenocarcinoma.

Results
DCKO mice gastric cancers harbored single nucleotide variations and indel patterns comparable to those of human genomically stable gastric cancers, whereas their copy number variation fraction and ploidy were more similar to human chromosomal instability gastric cancers (perhaps due to Trp53 knockout). Copy number variations dominated changes in cancer-related genes in DCKO mice, with typical high-level amplifications observed for oncogenic drivers, e.g., Myc, Ccnd1, and Cdks, as well as gastrointestinal transcription factors, e.g., Gata4, Foxa1, and Sox9. Interestingly, frequent alterations in gastrointestinal transcription factors in DCKO mice indicated their potential role in tumorigenesis. Furthermore, mouse gastric cancer had a reproducible but smaller number of mutational signatures than human gastric cancer, including the potentially acid-related signature 17, indicating shared tumorigenic etiologies in humans and mice.

Conclusions
Cdh1/Trp53 DCKO mice have similar genomic features to those found in human gastric cancer; hence, this is a suitable model for further studies of diffuse-type gastric cancer mechanisms and therapies.
Genomic selection in salmonids: new discoveries and future perspectives
Authors: D’Agaro Edo , Favaro Andea , Matiussi Stefano , Gibertoni Pier Paolo , Esposito Stefano 
Published: August 2021

AbstractOver the past 20 years, the introduction of new molecular techniques has given a new impetus to genetic and genomic studies of fishes. The main traits selected in the aquaculture sector conform to the polygenic model, and, thus far, effective breeding programmes based on genome-wide association studies (GWAS) and marker-assisted selection (MAS) have been applied to simple traits (e.g. disease resistance and sexual maturation of salmonids) and known Quantitative Trait Loci (QTLs). Genomic selection uses the genomic relationships between candidate loci and SNPs distributed over the entire genome and in tight linkage disequilibrium (LD) with genes that encode the traits. SNP (low and high density) arrays are used for genotyping thousands of genetic markers (single nucleotide polymorphisms, SNPs). The genomic expected breeding value (GEBV) of selection candidates is usually calculated by means of the GBLUP or ssGBLUP (single step) methods. In recent years, in several aquaculture breeding programmes, the genomic selection method has been applied to different fish and crustacean species. While routine implementation of genomic selection is now largely carried out in Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), it is expected that, in the near future, this method will progressively spread to other fish species. However, genomic selection is an expensive method, so it will be relevant mostly for traits of high economic value. In several studies (using different salmonid species), the accuracy of the GEBVs varied from 0.10 to 0.80 for different traits (e.g. growth rate and disease resistance) compared to traditional breeding methods based on geneology. Genomic selection applied to aquaculture species has the potential to improve selection programmes substantially and to change ongoing fish breeding systems. In the long term, the ability to use low-pass genome sequencing methods, low-cost genotyping and novel phenotyping techniques will allow genomic selection to be applied to thousands of animals directly at the farm level.
Computer-assisted sign language translation: a study of translators’ practice to specify CAT software
Authors: Kaczmarek Marion , Filhol Michael 
Published: August 2021

AbstractProfessional Sign Language translators, unlike their text-to-text counterparts, are not equipped with computer-assisted translation (CAT) software. Those softwares are meant to ease the translators’ tasks. No prior study as been conducted on this topic, and we aim at specifying such a software. To do so, we based our study on the professional Sign Language translators’ practices and needs. The aim of this paper is to identify the necessary steps in the text-to-sign translation process. By filming and interviewing professionals for both objective and subjective data, we build a list of tasks and see if they are systematic and performed in a definite order. Finally, we reflect on how CAT tools could assist those tasks, how to adapt the existing tools to Sign Language and what is necessary to add in order to fit the needs of Sign Language translation. In the long term, we plan to develop a first prototype of CAT software for sign languages.
Identification of the causal agents of crazy root disease on hydroponically cultivated cucumber plants in Poland
Authors: Warabieda Michał , Mikiciński Artur , Oleszczak Marcin , Puławska Joanna 
Published: August 2021

AbstractIn April 2019, hydroponically cultivated cucumber plants with characteristic symptoms of crazy root disease were found in two different commercial production cucumber greenhouses in Poland. Due to excessive and inappropriate root growth, this disease led to a reduction in yield and deterioration of the general conditions of infected plants. Bacteria isolated from the roots were subjected to a morphological evaluation, as well as molecular, biochemical and pathogenicity tests. To identify the bacteria causing the disease, Agrobacterium-like colonies were subjected to PCR with primers complementary to the pathogenicity-related genes located on the crazy root-inducing plasmid (Ri-plasmid): the virD2A + virD2E primers complementary to the virD2 gene and the rolBF + rolBR primers complementary to the rolB gene. The pathogenicity of the isolated strains was studied in sunflowers and cucumbers. Twelve strains positive for the Ri plasmid, as determined by PCR, and pathogenic to sunflowers were identified based on sequence analysis of the 16S rRNA and recA genes. One strain was classified as belonging to the genus Pararhizobium, three to Rhizobium, and eight to Agrobacterium biovar 1, with the highest similarity to genomospecies G3. The results of the analyses suggest that these strains may belong to a new, thus far, undescribed species. To confirm this hypothesis, further phylogenetic studies are required.
A compact instrument for gamma-ray burst detection on a CubeSat platform I
Authors: Murphy David , Ulyanov Alexey , McBreen Sheila , Doyle Maeve , Dunwoody Rachel , Mangan Joseph , Thompson Joseph , Shortt Brian , Martin-Carrillo Antonio , Hanlon Lorraine 
Published: August 2021

AbstractThe Educational Irish Research Satellite 1 (EIRSAT-1) is a 2U CubeSat being developed under ESA’s Fly Your Satellite! programme. The project has many aspects, which are primarily educational, but also include space qualification of new detector technologies for gamma-ray astronomy and the detection of gamma-ray bursts (GRBs). The Gamma-ray Module (GMOD), the main mission payload, is a small gamma-ray spectrometer comprising a 25 mm × 25 mm × 40 mm cerium bromide scintillator coupled to an array of 16 silicon photomultipliers. The readout is provided by IDE3380 (SIPHRA), a low-power and radiation tolerant readout ASIC. GMOD will detect gamma-rays and measure their energies in a range from tens of keV to a few MeV. Monte Carlo simulations were performed using the Medium Energy Gamma-ray Astronomy Library to evaluate GMOD’s capability for the detection of GRBs in low Earth orbit. The simulations used a detailed mass model of the full spacecraft derived from a very high-fidelity 3D CAD model. The sky-average effective area of GMOD on board EIRSAT-1 was found to be 10 cm2at 120 keV. The instrument is expected to detect between 11 and 14 GRBs, at a significance greater than 10σ(and up to 32 at 5σ), during a nominal one-year mission. The shape of the scintillator in GMOD results in omni-directional sensitivity which allows for a nearly all-sky field of view.