bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemoradiotherapy by intensity-modulated radiation therapy with simultaneous integrated boost in locally advanced or oligometastatic non-small-cell lung cancer—a two center experience
Authors: Mantel Frederick , Müller Elena , Kleine Philip , Zimmermann Marcus , Exner Florian , Richter Anne , Weick Stefan , Ströhle Serge , Polat Bülent , Höcht Stefan , Flentje Michael 
Published: March 2021

Abstract
Purpose
Integrating moderate hypofractionation to the macroscopic tumor with elective nodal irradiation while sparing the organs at risk (OAR) in chemoradiotherapy of locally advanced non-small-cell lung cancer.

Methods
From 2010–2018, treatment, patient and tumor characteristics of 138 patients from two radiation therapy centers were assessed. Chemoradiotherapy by intensity-modulated radiation therapy (IMRT) with a simultaneous integrated boost (SIB) to the primary tumor and macroscopic lymph node metastases was used.

Results
A total of 124 (90%) patients received concurrent chemotherapy. 106 (76%) patients had UICC (Union for International Cancer Control) stage ≥IIIB and 21 (15%) patients had an oligometastatic disease (UICC stage IV). Median SIB and elective total dose was 61.6 and 50.4 Gy in 28 fractions, respectively. Furthermore, 64 patients (46%) had an additional sequential boost to the primary tumor after the SIB-IMRT main series: median 6.6 Gy in median 3 fractions. The median cumulative mean lung dose was 15.6 Gy (range 6.2–29.5 Gy). Median follow-up and radiological follow-up for all patients was 18.0 months (range 0.6–86.9) and 16.0 months (range 0.2–86.9), respectively. Actuarial local control rates at 1, 2 and 3 years were 80.4, 68.4 and 57.8%. Median overall survival and progression-free survival was 30.0 months (95% confidence interval [CI] 23.5–36.4) and 12.1 months (95% CI 8.2–16.0), respectively. Treatment-related toxicity was moderate. Radiation-induced pneumonitis grade 2 and grade 3 occurred in 13 (9.8%) and 3 (2.3%) patients.

Conclusions
Chemoradiotherapy using SIB-IMRT showed promising local tumor control rates and acceptable toxicity in patients with locally advanced and in part oligometastatic lung cancer. The SIB concept, resulting in a relatively low mean lung dose, was associated with low numbers of clinically relevant pneumonitis. The overall survival appears promising in the presence of a majority of patients with UICC stage ≥IIIB disease.
The Himalayan Onion (Allium wallichii Kunth) Harbors Unique Spatially Organized Bacterial Communities
Authors: Chen Xiaoyulong , Krug Lisa , Yang Maofa , Berg Gabriele , Cernava Tomislav 
Published: March 2021

AbstractPlant-associated microorganisms are known to contribute with various beneficial functions to the health and productivity of their hosts, yet the microbiome of most plants remains unexplored. This especially applies to wild relatives of cultivated plants, which might harbor beneficial microorganisms that were lost during intensive breeding. We studied bacterial communities of the Himalayan onion (Allium wallichii Kunth), a wild relative of onion native to mountains in East Asia. The bacterial community structure was assessed in different plant microhabitats (rhizosphere, endosphere, anthosphere) by sequencing of 16S rRNA gene fragment amplicons. Targeted bioinformatic analyses were implemented in order to identify unique features in each habitat and to map the overall community in the first representative of the Amaryllidaceae plant family. The highest bacterial diversity was found for bulk soil (Shannon index, H′ 9.3) at the high-altitude sampling location. It was followed by the plant rhizosphere (H′ 8.9) while communities colonizing flowers (H′ 6.1) and the endosphere (H′ 6.5 and 5.6) where less diverse. Interestingly, we observed a non-significant rhizosphere effect. Another specificity of the microbiome was its high evenness in taxonomic distribution, which was so far not observed in plant microbiomes. Pseudomonas was identified among additional 10 bacterial genera as a plant-specific signature. The first insights into the microbiome of a plant in the widespread Allium genus will facilitate upcoming comparisons with its domesticated relatives while additionally providing a detailed microbiome mapping of the plant’s microhabitats to facilitate bioresource mining.
Genetic barcodes allow traceability of CRISPR/Cas9-derived Aspergillus niger strains without affecting their fitness
Authors: Garrigues Sandra , Kun Roland S. , de Vries Ronald P. 
Published: March 2021

AbstractSafe use of genetically modified organisms (GMOs) in biotechnology requires the ability to track the presence of these strains in any environment in which they are applied. For this, introduction of genetic barcodes within the editing site represents a valuable tool for the identification of microbial strains that have undergone genetic modifications. However, it is not known whether these barcodes would have any unexpected effect in the resulting strains or affect the efficiency of the genetic modification. CRISPR/Cas9 has become one of the fastest-growing technologies for genome editing in a range of organisms, including fungi. However, this technology enables the generation of scarless GMOs that are very difficult to distinguish from naturally occurring mutants or other modified organisms. In this study, we address this issue using the industrial workhorse Aspergillus niger as a test case. We applied CRISPR/Cas9 technology to delete the genes encoding the transcriptional regulators XlnR and AraR, involved in the production of plant biomass-degrading enzymes. We generated 20-bp barcoded and non-barcoded ΔxlnR and ΔaraR mutants and analyzed the traceability and fitness of the resulting strains, as well as the efficiency of the genetic modification. Results showed that both barcoded and non-barcoded mutants can be traced by routine PCR reactions when the specific CRISPR/Cas9 modification is known. Additionally, barcodes neither affected the efficiency of the genetic modification nor the growth or protein production of the resulting strains. These results confirm the suitability of genetic barcodes to trace CRISPR-derived GMOs without affecting the performance of the resulting strains.
Quantification of dual-energy CT-derived functional parameters as potential imaging markers for progression of idiopathic pulmonary fibrosis
Authors: Scharm Sarah C. , Vogel-Claussen Jens , Schaefer-Prokop Cornelia , Dettmer Sabine , Knudsen Lars , Jonigk Danny , Fuge Jan , Apel Rosa-Marie , Welte Tobias , Wacker Frank , Prasse Antje , Shin Hoen-oh 
Published: March 2021

Abstract
Objectives
The individual course of disease in idiopathic pulmonary fibrosis (IPF) is highly variable. Assessment of disease activity and prospective estimation of disease progression might have the potential to improve therapy management and indicate the onset of treatment at an earlier stage. The aim of this study was to evaluate whether regional ventilation, lung perfusion, and late enhancement can serve as early imaging markers for disease progression in patients with IPF.

Methods
In this retrospective study, contrast-enhanced dual-energy CT scans of 32 patients in inspiration and delayed expiration were performed at two time points with a mean interval of 15.4 months. The pulmonary blood volume (PBV) images obtained in the arterial and delayed perfusion phase served as a surrogate for arterial lung perfusion and parenchymal late enhancement. The virtual non-contrast (VNC) images in inspiration and expiration were non-linearly registered to provide regional ventilation images. Image-derived parameters were correlated with longitudinal changes of lung function (FVC%, DLCO%), mean lung density in CT, and CT-derived lung volume.

Results
Regional ventilation and late enhancement at baseline preceded future change in lung volume (R - 0.474, p 0.006/R - 0.422, p 0.016, respectively) and mean lung density (R - 0.469, p 0.007/R - 0.402, p 0.022, respectively). Regional ventilation also correlated with a future change in FVC% (R - 0.398, p 0.024).

Conclusion
CT-derived functional parameters of regional ventilation and parenchymal late enhancement are potential early imaging markers for idiopathic pulmonary fibrosis progression.

Key Points
• Functional CT parameters at baseline (regional ventilation and late enhancement) correlate with future structural changes of the lung as measured with loss of lung volume and increase in lung density in serial CT scans of patients with idiopathic pulmonary fibrosis.
• Functional CT parameter measurements in high-attenuation areas (- 600 to - 250 HU) are significantly different from normal-attenuation areas (- 950 to - 600 HU) of the lung.
• Mean regional ventilation in functional CT correlates with a future change in forced vital capacity (FVC) in pulmonary function tests.
Besnoitiosis in donkeys: an emerging parasitic disease of equids in Italy
Authors: Villa Luca , Gazzonis Alessia Libera , Diezma-Diaz Carlos , Perlotti Chiara , Zanzani Sergio Aurelio , Ferrucci Francesco , Álvarez-García Gema , Manfredi Maria Teresa 
Published: March 2021

AbstractBesnoitiosis is an emerging parasitic disease of equids. Italy is one of the few European countries where the circulation of Besnoitia spp. antibodies was demonstrated. In this study, a case of clinical besnoitiosis in two donkeys in northern Italy is reported. The two animals were clinically examined. Serum and blood samples were analyzed for the detection of Besnoitia spp. antibodies and for hematology, biochemistry, and enzyme activity, respectively. ITS-1 PCR and sequencing were carried out on DNA extracted from skin biopsies. Clinical examination revealed numerous scleral pearls in eyes of both animals; alopecia and hyperkeratosis with skin nodules in the region of the neck, hind leg, and on the pinnae were detected. No cysts were evidenced by endoscopy in respiratory and genital tracts. Both animals resulted seropositive to Besnoitia spp. antibodies by Western Blot. Hematology evidenced light anemia, leukocytosis with eosinophilia, and lymphocytosis; biochemistry and enzyme activity revealed hypoalbuminemia with decreased albumin/globulin ratio and elevated alkaline phosphatase values. Parasitic DNA extracted from skin biopsies of both donkeys demonstrated a homology of 100% with Besnoitia spp. This first clinical case of besnoitiosis in two donkeys in Italy both confirms the circulation of Besnoitia spp. in Italian equids and demonstrates that the distribution area of equine besnoitiosis in Europe could be wider than expected. Further studies are needed to infer its relevance, in relation to seroprevalence and clinical disease, and to identify the species of Besnoitia infecting donkeys. Besnoitiosis may be a neglected disease of donkeys in Europe: an early and accurate diagnosis is fundamental to implement adequate control measures to prevent a “silent” spread of Besnoitia spp. infection in equids populations.
Deep learning-based high-throughput phenotyping can drive future discoveries in plant reproductive biology
Authors: Warman Cedar , Fowler John E. 
Published: March 2021

AbstractKey messageAdvances in deep learning are providing a powerful set of image analysis tools that are readily accessible for high-throughput phenotyping applications in plant reproductive biology.High-throughput phenotyping systems are becoming critical for answering biological questions on a large scale. These systems have historically relied on traditional computer vision techniques. However, neural networks and specifically deep learning are rapidly becoming more powerful and easier to implement. Here, we examine how deep learning can drive phenotyping systems and be used to answer fundamental questions in reproductive biology. We describe previous applications of deep learning in the plant sciences, provide general recommendations for applying these methods to the study of plant reproduction, and present a case study in maize ear phenotyping. Finally, we highlight several examples where deep learning has enabled research that was previously out of reach and discuss the future outlook of these methods.
Mechanics of tubular helical assemblies: ensemble response to axial compression and extension
Authors: Quaglierini Jacopo , Lucantonio Alessandro , DeSimone Antonio 
Published: March 2021

Abstract
Nature and technology often adopt structures that can be described as tubular helical assemblies. However, the role and mechanisms of these structures remain elusive. In this paper, we study the mechanical response under compression and extension of a tubular assembly composed of 8 helical Kirchhoff rods, arranged in pairs with opposite chirality and connected by pin joints, both analytically and numerically. We first focus on compression and find that, whereas a single helical rod would buckle, the rods of the assembly deform coherently as stable helical shapes wound around a common axis. Moreover, we investigate the response of the assembly under different boundary conditions, highlighting the emergence of a central region where rods remain circular helices. Secondly, we study the effects of different hypotheses on the elastic properties of rods, i.e., stress-free rods when straight versus when circular helices, Kirchhoff’s rod model versus Sadowsky’s ribbon model. Summing up, our findings highlight the key role of mutual interactions in generating a stable ensemble response that preserves the helical shape of the individual rods, as well as some interesting features, and they shed some light on the reasons why helical shapes in tubular assemblies are so common and persistent in nature and technology.

Graphic Abstract
We study the mechanical response under compression/extension of an assembly composed of 8 helical rods, pin-jointed and arranged in pairs with opposite chirality. In compression we find that, whereas a single rod buckles (a), the rods of the assembly deform as stable helical shapes (b). We investigate the effect of different boundary conditions and elastic properties on the mechanical response, and find that the deformed geometries exhibit a common central region where rods remain circular helices. Our findings highlight the key role of mutual interactions in the ensemble response and shed some light on the reasons why tubular helical assemblies are so common and persistent.
The Polito Surface Wave flat-file Database (PSWD): statistical properties of test results and some inter-method comparisons
Authors: Passeri Federico , Comina Cesare , Foti Sebastiano , Socco Laura Valentina 
Published: March 2021

AbstractThe compilation and maintenance of experimental databases are of crucial importance in all research fields, allowing for researchers to develop and test new methodologies. In this work, we present a flat-file database of experimental dispersion curves and shear wave velocity profiles, mainly from active surface wave testing, but including also data from passive surface wave testing and invasive methods. The Polito Surface Wave flat-file Database (PSWD) is a gathering of experimental measurements collected within the past 25 years at different Italian sites. Discussion on the database content is reported in this paper to evaluate some statistical properties of surface wave test results. Comparisons with other methods for shear wave velocity measurements are also considered. The main novelty of this work is the homogeneity of the PSWD in terms of processing and interpretation methods. A common processing strategy and a new inversion approach were applied to all the data in the PSWD to guarantee consistency. The PSWD can be useful for further correlation studies and is made available as a reference benchmark for the validation and verification of novel interpretation procedures by other researchers.
Ethnic Identity and Genome Wide Runs of Homozygosity
Authors: Fieder Martin , Mitchell Brittany L. , Gordon Scott , Huber Susanne , Martin Nicholas G. 
Published: March 2021

AbstractIt is long known that inbreeding increases the detrimental effects of recessive sequence variants in “Runs of Homozygosity” (ROHs). However, although the phenotypic association of ROH has been investigated for a variety of traits, the statistical power of the results often remains limited as a sufficiently high number of cases are available for only a restricted number of traits. In the present study, we aim to analyze the association of runs of homozygosity with the trait “in-group ethnic favoritism”. This analysis assumes that if ethnic identity is important for an individual, that individual may tend to marry more frequently within their own group and therefore ROH are expected to increase. We hypothesize that an attitude preferring one’s own ethnic group may be associated with a stronger tendency of inbreeding and, as a result, with more and longer ROHs. Accordingly, we investigated the association between the attitude to someone’s own ethnicity and ROH, using the Wisconsin Longitudinal data (WLS, total N ~ 9000) as discovery data set and the Brisbane Twin data as replication data set (N ~ 8000). We find that both the number as well as the total length of homozygous segments are significantly positively associated with “in-group ethnic favoritism”, independent of the method used for ROH calculation.
On the necessity of explicit cross-layer data formats in near-data processing systems
Authors: Weber Lukas , Vinçon Tobias , Knödler Christian , Solis-Vasquez Leonardo , Bernhardt Arthur , Petrov Ilia , Koch Andreas 
Published: March 2021

AbstractMassive data transfers in modern data-intensive systems resulting from low data-locality and data-to-code system design hurt their performance and scalability. Near-Data processing (NDP) and a shift to code-to-data designs may represent a viable solution as packaging combinations of storage and compute elements on the same device has become feasible. The shift towards NDP system architectures calls for revision of established principles. Abstractions such as data formats and layouts typically spread multiple layers in traditional DBMS, the way they are processed is encapsulated within these layers of abstraction. The NDP-style processing requires an explicit definition of cross-layer data formats and accessors to ensure in-situ executions optimally utilizing the properties of the underlying NDP storage and compute elements. In this paper, we make the case for such data format definitions and investigate the performance benefits under RocksDB and the COSMOS hardware platform.
Review of petroleum toxicity in marine reptiles
Authors: Ruberg Elizabeth J. , Williams Tony D. , Elliott John E. 
Published: March 2021

AbstractWorldwide petroleum exploration and transportation continue to impact the health of the marine environment through both catastrophic and chronic spillage. Of the impacted fauna, marine reptiles are often overlooked. While marine reptiles are sensitive to xenobiotics, there is a paucity of petroleum toxicity data for these specialized fauna in peer reviewed literature. Here we review the known impacts of petroleum spillage to marine reptiles, specifically to marine turtles and iguanas with an emphasis on physiology and fitness related toxicological effects. Secondly, we recommend standardized toxicity testing on surrogate species to elucidate the mechanisms by which petroleum related mortalities occur in the field following catastrophic spillage and to better link physiological and fitness related endpoints. Finally, we propose that marine reptiles could serve as sentinel species for marine ecosystem monitoring in the case of petroleum spillage. Comprehensive petroleum toxicity data on marine reptiles is needed in order to serve as a foundation for future research with newer, unconventional crude oils of unknown toxicity such as diluted bitumen.
The nature of build changes
Authors: Macho Christian , Beyer Stefanie , McIntosh Shane , Pinzger Martin 
Published: March 2021

AbstractBuild systems are an essential part of modern software projects. As software projects change continuously, it is crucial to understand how the build system changes because neglecting its maintenance can, at best, lead to expensive build breakage, or at worst, introduce user-reported defects due to incorrectly compiled, linked, packaged, or deployed official releases. Recent studies have investigated the (co-)evolution of build configurations and reasons for build breakage; however, the prior analysis focused on a coarse-grained outcome (i.e., either build changing or not). In this paper, we present BuildDiff, an approach to extract detailed build changes from Maven build files and classify them into 143 change types. In a manual evaluation of 400 build-changing commits, we show that BuildDiff can extract and classify build changes with average precision, recall, and f1-scores of 0.97, 0.98, and 0.97, respectively. We then present two studies using the build changes extracted from 144 open source Java projects to study the frequency and time of build changes. The results show that the top-10 most frequent change types account for 51% of the build changes. Among them, changes to version numbers and changes to dependencies of the projects occur most frequently. We also observe frequently co-occurring changes, such as changes to the source code management definitions, and corresponding changes to the dependency management system and the dependency declaration. Furthermore, our results show that build changes frequently occur around release days. In particular, critical changes, such as updates to plugin configuration parts and dependency insertions, are performed before a release day. The contributions of this paper lay in the foundation for future research, such as for analyzing the (co-)evolution of build files with other artifacts, improving effort estimation approaches by incorporating necessary modifications to the build system specification, or automatic repair approaches for configuration code. Furthermore, our detailed change information enables improvements of refactoring approaches for build configurations and improvements of prediction models to identify error-prone build files.
Natural Deduction Bottom Up
Authors: Zimmermann Ernst 
Published: March 2021

AbstractThe paper introduces a new type of rules into Natural Deduction, elimination rules by composition. Elimination rules by composition replace usual elimination rules in the style of disjunction elimination and give a more direct treatment of additive disjunction, multiplicative conjunction, existence quantifier and possibility modality. Elimination rules by composition have an enormous impact on proof-structures of deductions: they do not produce segments, deduction trees remain binary branching, there is no vacuous discharge, there is only few need of permutations. This new type of rules fits especially to substructural issues, so it is shown for Lambek Calculus, i.e. intuitionistic non-commutative linear logic and to its extensions by structural rules like permutation, weakening and contraction. Natural deduction formulated with elimination rules by composition from a complexity perspective is superior to other calculi.