bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lowering DNA binding affinity of SssI DNA methyltransferase does not enhance the specificity of targeted DNA methylation in E. coli
Authors: Ślaska-Kiss Krystyna , Zsibrita Nikolett , Koncz Mihály , Albert Pál , Csábrádi Ákos , Szentes Sarolta , Kiss Antal 
Published: July 2021

AbstractTargeted DNA methylation is a technique that aims to methylate cytosines in selected genomic loci. In the most widely used approach a CG-specific DNA methyltransferase (MTase) is fused to a sequence specific DNA binding protein, which binds in the vicinity of the targeted CG site(s). Although the technique has high potential for studying the role of DNA methylation in higher eukaryotes, its usefulness is hampered by insufficient methylation specificity. One of the approaches proposed to suppress methylation at unwanted sites is to use MTase variants with reduced DNA binding affinity. In this work we investigated how methylation specificity of chimeric MTases containing variants of the CG-specific prokaryotic MTase M.SssI fused to zinc finger or dCas9 targeting domains is influenced by mutations affecting catalytic activity and/or DNA binding affinity of the MTase domain. Specificity of targeted DNA methylation was assayed in E. coli harboring a plasmid with the target site. Digestions of the isolated plasmids with methylation sensitive restriction enzymes revealed that specificity of targeted DNA methylation was dependent on the activity but not on the DNA binding affinity of the MTase. These results have implications for the design of strategies of targeted DNA methylation.
2D–3D reconstruction of distal forearm bone from actual X-ray images of the wrist using convolutional neural networks
Authors: Shiode Ryoya , Kabashima Mototaka , Hiasa Yuta , Oka Kunihiro , Murase Tsuyoshi , Sato Yoshinobu , Otake Yoshito 
Published: July 2021

AbstractThe purpose of the study was to develop a deep learning network for estimating and constructing highly accurate 3D bone models directly from actual X-ray images and to verify its accuracy. The data used were 173 computed tomography (CT) images and 105 actual X-ray images of a healthy wrist joint. To compensate for the small size of the dataset, digitally reconstructed radiography (DRR) images generated from CT were used as training data instead of actual X-ray images. The DRR-like images were generated from actual X-ray images in the test and adapted to the network, and high-accuracy estimation of a 3D bone model from a small data set was possible. The 3D shape of the radius and ulna were estimated from actual X-ray images with accuracies of 1.05 ± 0.36 and 1.45 ± 0.41 mm, respectively.
Importance of methylammonium iodide partial pressure and evaporation onset for the growth of co-evaporated methylammonium lead iodide absorbers
Authors: Heinze Karl L. , Dolynchuk Oleksandr , Burwig Thomas , Vaghani Jaykumar , Scheer Roland , Pistor Paul 
Published: July 2021

AbstractVacuum-based co-evaporation promises to bring perovskite solar cells to larger scales, but details of the film formation from the physical vapor phase are still underexplored. In this work, we investigate the growth of methylammonium lead iodide (MAPbI$$_3$$

3

) absorbers prepared by co-evaporation of methylammonium iodide (MAI) and lead iodide (PbI$$_2$$

2

) using an in situ X-ray diffraction setup. This setup allows us to characterize crystallization and phase evolution of the growing thin film. The total chamber pressure strongly increases during MAI evaporation. We therefore assume the total chamber pressure to be mainly built up by an MAI atmosphere during deposition and use it to control the MAI evaporation. At first, we optimize the MAI to PbI$$_2$$

2

impingement ratios by varying the MAI pressure at a constant PbI$$_2$$

2

flux rate. We find a strong dependence of the solar cell device performance on the chamber pressure achieving efficiencies > 14$$\%$$
%
in a simple n-i-p structure. On the road to further optimizing the processing conditions we vary the onset time of the PbI$$_2$$

2

and MAI deposition by delaying the start of the MAI evaporation by t = 0/8/16 min. This way, PbI$$_2$$

2

nucleates as a seed layer with a thickness of up to approximately 20 nm during this initial stage. Device performance benefits from these PbI$$_2$$

2

seed layers, which also induce strong preferential thin film orientation as evidenced by grazing incidence wide angle X-ray scattering (GIWAXS) measurements. Our insights into the growth of MAPbI$$_3$$

3

thin films from the physical vapor phase help to understand the film formation mechanisms and contribute to the further development of MAPbI$$_3$$

3

and related perovskite absorbers.
Rabphilin silencing causes dilated cardiomyopathy in a Drosophila model of nephrocyte damage
Authors: Selma-Soriano Estela , Casillas-Serra Carlos , Artero Rubén , Llamusi Beatriz , Navarro Juan Antonio , Redón Josep 
Published: July 2021

AbstractHeart failure (HF) and the development of chronic kidney disease (CKD) have a direct association. Both can be cause and consequence of the other. Many factors are known, such as diabetes or hypertension, which can lead to the appearance and/or development of these two conditions. However, it is suspected that other factors, namely genetic ones, may explain the differences in the manifestation and progression of HF and CKD among patients. One candidate factor is Rph, a gene expressed in the nervous and excretory system in mammals and Drosophila, encoding a Rab small GTPase family effector protein implicated in vesicular trafficking. We found that Rph is expressed in the Drosophila heart, and the silencing of Rph gene expression in this organ had a strong impact in the organization of fibers and functional cardiac parameters. Specifically, we observed a significant increase in diastolic and systolic diameters of the heart tube, which is a phenotype that resembles dilated cardiomyopathy in humans. Importantly, we also show that silencing of Rabphilin (Rph) expression exclusively in the pericardial nephrocytes, which are part of the flies' excretory system, brings about a non-cell-autonomous effect on the Drosophila cardiac system. In summary, in this work, we demonstrate the importance of Rph in the fly cardiac system and how silencing Rph expression in nephrocytes affects the Drosophila cardiac system.
Text mining of gene–phenotype associations reveals new phenotypic profiles of autism-associated genes
Authors: Li Sijie , Guo Ziqi , Ioffe Jacob B. , Hu Yunfei , Zhen Yi , Zhou Xin 
Published: July 2021

AbstractAutism is a spectrum disorder with wide variation in type and severity of symptoms. Understanding gene–phenotype associations is vital to unravel the disease mechanisms and advance its diagnosis and treatment. To date, several databases have stored a large portion of gene–phenotype associations which are mainly obtained from genetic experiments. However, a large proportion of gene–phenotype associations are still buried in the autism-related literature and there are limited resources to investigate autism-associated gene–phenotype associations. Given the abundance of the autism-related literature, we were thus motivated to develop Autism_genepheno, a text mining pipeline to identify sentence-level mentions of autism-associated genes and phenotypes in literature through natural language processing methods. We have generated a comprehensive database of gene–phenotype associations in the last five years’ autism-related literature that can be easily updated as new literature becomes available. We have evaluated our pipeline through several different approaches, and we are able to rank and select top autism-associated genes through their unique and wide spectrum of phenotypic profiles, which could provide a unique resource for the diagnosis and treatment of autism. The data resources and the Autism_genpheno pipeline are available at: https://github.com/maiziezhoulab/Autism_genepheno.
Molecular fingerprinting of bovine mastitis-associated Staphylococcus aureus isolates from India
Authors: Annamanedi Madhavi , Sheela P. , Sundareshan Srinivasaiah , Isloor Shrikrishna , Gupta Priya , Jasmeen Pagala , Gargi Madhuranjana , Mallick Sathi , Hegde Nagendra R. 
Published: July 2021

AbstractStaphylococcus aureus is a major etiological agent of clinical and subclinical bovine mastitis. Owing to the mostly backyard dairy practices, we hypothesized that genetic diversity among mastitis-associated S. aureus from India would be high, and investigated 166 isolates obtained mostly from the Southern State of Karnataka, but also from a few other states. The results revealed (a) 8 to 13 fragments in pulsed-field gel electrophoresis (PFGE), forming 31 distinct patterns, and (b) 34 spa types, of which three (t17680, t18314, and t18320) were newly identified. Multi-locus sequencing typing (MLST) identified 39 sequence types (STs), with ST2454 (34.4%) and ST2459 (24%) being the most commonly represented, which clustered to clonal complexes (CC) CC9 and CC97, respectively; 12 STs were newly identified. Thirty-four (20.5%) of the 166 isolates displayed oxacillin resistance. On the other hand, whereas none were mecC+, 44 (26.5%) isolates were mecA+, with a predominance of SCCmecIVb (26/32 isolates, others being untypeable); 24 isolates (14.46%) were oxacillin-susceptible methicillin-resistant S. aureus (OS-MRSA; mecA+ but OS). Integrated analysis revealed that CC9-ST2454- and CC97-ST2459-SCCmecIVb were the predominant MRSA, although the distribution of CC9 and CC97 was similar between methicillin-resistant and -susceptible isolates. By PCR, 56.25%, 28.75% and 47.5% of the 166 isolates were positive for hlg, tsst and pvl genes, respectively. Our results, for the first time describe the application of a combination of various molecular methods to bovine mastitis-associated S. aureus isolates from India, corroborate the worldwide distribution of CC97 and CC9, and suggest pathogenic potential of the isolates.
Microbiome pattern of Lucilia sericata (Meigen) (Diptera: Calliphoridae) and feeding substrate in the presence of the foodborne pathogen Salmonella enterica
Authors: Iancu Lavinia , Angelescu Iulia Roxana , Paun Victoria Ioana , Henríquez-Castillo Carlos , Lavin Paris , Purcarea Cristina 
Published: July 2021

AbstractThe microbial diversity and quantitative dynamics during the insect’s development stages constitute recently developed putative tools in forensic and medical studies. Meanwhile, little is known on the role of insects in spreading foodborne pathogenic bacteria and on the impact of these pathogens on the overall insects and feeding substrate microbiome composition. Here, we provide the first characterization of the bacterial communities harbored in adult and immature stages of Lucilia sericata, one of the first colonizers of decomposed human remains, in the presence of the foodborne pathogen Salmonella enterica using 16S rRNA Illumina sequencing and qPCR. The pathogen transmission from the wild adults to the second generation was observed, with a 101.25× quantitative increase. The microbial patterns from both insect and liver samples were not influenced by the artificial introduction of this pathogenic foodborne bacteria, being dominated by Firmicutes and Proteobacteria. Overall, our results provided a first detailed overview of the insect and decomposed substrate microbiome in the presence of a human pathogen, advancing the knowledge on the role of microbes as postmortem interval estimators and the transmission of pathogenic bacteria.
Uniqueness of gait kinematics in a cohort study
Authors: Park Gunwoo , Lee Kyoung Min , Koo Seungbum 
Published: July 2021

AbstractGait, the style of human walking, has been studied as a behavioral characteristic of an individual. Several studies have utilized gait to identify individuals with the aid of machine learning and computer vision techniques. However, there is a lack of studies on the nature of gait, such as the identification power or the uniqueness. This study aims to quantify the uniqueness of gait in a cohort. Three-dimensional full-body joint kinematics were obtained during normal walking trials from 488 subjects using a motion capture system. The joint angles of the gait cycle were converted into gait vectors. Four gait vectors were obtained from each subject, and all the gait vectors were pooled together. Two gait vectors were randomly selected from the pool and tested if they could be accurately classified if they were from the same person or not. The gait from the cohort was classified with an accuracy of 99.71% using the support vector machine with a radial basis function kernel as a classifier. Gait of a person is as unique as his/her facial motion and finger impedance, but not as unique as fingerprints.
Taxonomic and phylogenetic characterizations reveal four new species of Simplicillium (Cordycipitaceae, Hypocreales) from Guizhou, China
Authors: Chen Wan-Hao , Han Yan-Feng , Liang Jian-Dong , Liang Zong-Qi 
Published: July 2021

AbstractSimplicillium species are commonly found from soil, seawater, rock surface, decayed wood, air and as symbiotic, endophytic, entomopathogenic and mycoparasitic fungi. Minority insect-associated species was reported. Simplicillium coccinellidae, S. hymenopterorum, S. neolepidopterorum and S. scarabaeoidea were introduced as the newly insect-associated species. The phylogenetic analyses of two combined datasets (LSU + RPB1 + TEF and SSU + ITS + LSU) revealed that S. coccinellidae and S. hymenopterorum were both nested in an independent clade. S. neolepidopterorum and S. scarabaeoidea have a close relationship with S. formicidae and S. lepidopterorum, respectively. S. neolepidopterorum can be easily distinguished from S. formicidae by ellipsoidal to cylindrical, solitary conidia which occasionally gather in short imbricate chains. S. scarabaeoidea could be easily distinguished from S. lepodopterorum by having longer phialides and larger conidia. Based on the morphological and phylogenetic conclusion, we determine the four newly generated isolates as new species of Simplicillium and a new combination is proposed in the genus Leptobacillium.
Invasion dynamics of the European bumblebee Bombus terrestris in the southern part of South America
Authors: Fontúrbel Francisco E. , Murúa Maureen M. , Vieli Lorena 
Published: July 2021

AbstractInvasive species are one of the main biodiversity loss drivers. Some species can establish and thrive in novel habitats, impacting local communities, as is the case of managed pollinators. In this regard, an invasive species' expansion process over time is critical for its control and management. A good example is the European bumblebeeBombus terrestris, which has rapidly invaded the southern part of South America after being repeatedly introduced in Chile for crop pollination since 1997. We assessed the temporal dynamics ofB. terrestrisinvasion in Argentina and Chile by compiling 562 occurrence points from 2000 to 2019. We used two estimators (minimum convex polygon and 95% fixed kernel) to estimate the increase of the invaded area over time. We found that the area invaded byB. terrestrisin the southern part of South America presents a linear increase over time, which was consistent for both estimators. In this scenario, species traits, environmental characteristics, and introduction dynamics facilitate a rapid invasion process that will continue to expand, reaching other South American countries in the near future. As this bumblebee is a super-generalist, it probably will expand across South America, as climate niche modelling predicts, if no actions were taken.
Performance evaluation of a prescription medication image classification model: an observational cohort
Authors: Lester Corey A. , Li Jiazhao , Ding Yuting , Rowell Brigid , Yang Jessie ‘Xi’ , Kontar Raed Al 
Published: July 2021

AbstractTechnology assistance of pharmacist verification tasks through the use of machine intelligence has the potential to detect dangerous and costly pharmacy dispensing errors. National Drug Codes (NDC) are unique numeric identifiers of prescription drug products for the United States Food and Drug Administration. The physical form of the medication, often tablets and capsules, captures the unique features of the NDC product to help ensure patients receive the same medication product inside their prescription bottle as is found on the label from a pharmacy. We report and evaluate using an automated check to predict the shape, color, and NDC for images showing a pile of pills inside a prescription bottle. In a test set containing 65,274 images of 345 NDC classes, overall macro-average precision was 98.5%. Patterns of incorrect NDC predictions based on similar colors, shapes, and imprints of pills were identified and recommendations to improve the model are provided.
The Role of Faculty Advising, Mentoring, and Gatekeeping as Social Support for Undergraduate Communication Sciences and Disorders Students
Authors: Roos Brianne H. , Schreck Janet S. 
Published: July 2021

PurposeSocial support may be provided by undergraduate students' family and friends and by other members of the campus community, including faculty. The purpose of this review article was to review the existing literature about the roles of faculty members as advisors, mentors, and gatekeepers who provide social support for undergraduate students. Social support is a buffer for stress, and current undergraduate students are more stressed than their predecessors.MethodThe study is a narrative review of the literature about faculty as advisors, mentors, and gatekeepers. The concept of social support and its relationship to students' stress is explored, followed by a discussion of faculty advisors' roles, knowledge, and skills and a synthesis of literature about prescriptive, developmental, praxis, and appreciative advising. A discussion of faculty as mentors who focus on students' experiences before, during, and after college and as gatekeepers who look for signs of students in distress concludes the review.ConclusionsFaculty may provide social support to students inside and outside the classroom as advisors, mentors, and gatekeepers. Assuming these roles means faculty must consider students as whole people who have needs and experiences beyond academics. Students' stress was clear in the literature before COVID-19, and their concerns and needs are exacerbated during the pandemic. Additional research is needed to identify effective advising and mentoring programs for communication sciences and disorders undergraduate students. Increased institutional support for and recognition of the time, resources, and training faculty need to serve in this expanded role is also critical as faculty members attempt to manage their own stress.
A dynamic equivalent aggregation method of wind turbine systems with a full‐scale power converter for electromagnetic transient simulations
Authors: Xue Yicheng , Zhang Zheren , Xu Zheng 
Published: July 2021

AbstractWith the increasing exploitation of wind energy, the dynamic performances of large‐scale wind farms (WFs) are vital for the system design and stability analysis. However, a detailed WF model considering every wind turbine system (WTS) makes the electromagnetic transient simulation time‐consuming and computational‐demanding. Therefore, a dynamic equivalent aggregation method is proposed for WTS with a full‐scale power converter (WTS‐FSPC) in this paper, in order to reduce the computational complexity meanwhile maintaining the same accuracy as the detailed model. To improve the accuracy of the equivalent collector system, the collecting strings are decoupled based on the power flow distribution. Then the WTSs are clustered according to the output AC voltage distributions using a Louvain K‐means (LKM) algorithm, which innovatively determines the optimal solution automatically. Additionally, a centralized capacitor is set to represent the distributed capacitance of the collector system. Furthermore, to enhance the model adaptability during asymmetric short‐circuit faults, the equivalent method for the zero‐sequence collector system is introduced. Time‐domain simulation results demonstrate the effectiveness and robustness of the proposed method in reflecting the WF dynamics. The case study in a 2‐area system further verifies the superiority of the proposed method for the WF integrated power system stability analysis.
Granular mechanics simulations of collisions between chondritic aggregates
Authors: Umstätter Philipp , Urbassek Herbert M. 
Published: July 2021

Context. Collisions of dust aggregates are relevant for the evolution of protoplanetary disks.
Aims. While in the past interest focused on aggregates composed of monodisperse grains, here we study the collision of chondritic aggregates, in which – besides a majority of dust grains – larger chondrules are embedded.
Methods. We use granular-mechanics simulations to study collisions of chondritic aggregates.
Results. Low-velocity collisions lead to pancake-shaped deformations of the fused cluster accompanied by a compaction of the dust grains. Higher collision velocities fragment the aggregates. While some chondrules are almost laid bare after the collision, we find that the largest fragments typically contain chondrules; large fragments thus capture chondrules. Grain compaction is accompanied by an increase in grain – chondrule contacts and is maximum for intermediate velocities, just before aggregates start fragmenting.
Conclusions. The presence of chondrules considerably influences the fragmentation behavior of dust aggregates.
Cultural Divergence in popular music: the increasing diversity of music consumption on Spotify across countries
Authors: Bello Pablo , Garcia David 
Published: July 2021

AbstractThe digitization of music has changed how we consume, produce, and distribute music. In this paper, we explore the effects of digitization and streaming on the globalization of popular music. While some argue that digitization has led to more diverse cultural markets, others consider that the increasing accessibility to international music would result in a globalized market where a few artists garner all the attention. We tackle this debate by looking at how cross-country diversity in music charts has evolved over 4 years in 39 countries. We analyze two large-scale datasets from Spotify, the most popular streaming platform at the moment, and iTunes, one of the pioneers in digital music distribution. Our analysis reveals an upward trend in music consumption diversity that started in 2017 and spans across platforms. There are now significantly more songs, artists, and record labels populating the top charts than just a few years ago, making national charts more diverse from a global perspective. Furthermore, this process started at the peaks of countries’ charts, where diversity increased at a faster pace than at their bases. We characterize these changes as a process of Cultural Divergence, in which countries are increasingly distinct in terms of the music populating their music charts.