bluuebunny/crossref_metadata_2025_split huggingface dataset:
GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids
Authors: Ebmeyer Stefan , Coertze Roelof Dirk , Berglund Fanny , Kristiansson Erik , Larsson D G Joakim 
Published: December 2021

Abstract

Summary
Comparing genomic loci of a given bacterial gene across strains and species can provide insights into their evolution, including information on e.g. acquired mobility, the degree of conservation between different taxa or indications of horizontal gene transfer events. While thousands of bacterial genomes are available to date, there is no software that facilitates comparisons of individual gene loci for a large number of genomes. GEnView (Genetic Environment View) is a Python-based pipeline for the comparative analysis of gene–loci in a large number of bacterial genomes, providing users with automated, taxon-selective access to the &gt;800.000 genomes and plasmids currently available in the NCBI Assembly and RefSeq databases, and is able to process local genomes that are not deposited at NCBI, enabling searches for genomic sequences and to analyze their genetic environments through the interactive visualization and extensive metadata files created by GEnView.

Availability and implementation
GEnView is implemented in Python 3. Instructions for download and usage can be found at https://github.com/EbmeyerSt/GEnView under GLP3.

Supplementary information
Supplementary data are available at Bioinformatics online.
Disruption of amygdalaTsc2in adolescence leads to changed prelimbic cellular activity and generalized fear responses at adulthood in rats
Authors: Joly Fanny , Jeckel Pauline , Kriebel Martin , Raut Sanket , El Massioui Nicole , Vaillend Cyrille , Johnson Luke R , Volkmer Hansjürgen , Doyère Valérie 
Published: December 2021

AbstractAdolescence constitutes a period of vulnerability in the emergence of fear-related disorders (FRD), as a massive reorganization occurs in the amygdala-prefrontal cortex network, critical to regulate fear behavior. Genetic and environmental factors during development may predispose to the emergence of FRD at the adult age, but the underlying mechanisms are poorly understood. In the present study, we tested whether a partial knock-down of tuberous sclerosis complex 2 (Tsc2, Tuberin), a risk gene for neurodevelopmental disorders, in the basolateral amygdala (BLA) from adolescence could alter fear-network functionality and create a vulnerability ground to FRD appearance at adulthood. Using bilateral injection of a lentiviral vector expressing a miRNA against Tsc2 in the BLA of early (PN25) or late adolescent (PN50) rats, we show that alteration induced specifically from PN25 resulted in an increased c-Fos activity at adulthood in specific layers of the prelimbic cortex, a resistance to fear extinction and an overgeneralization of fear to a safe, novel stimulus. A developmental dysfunction of the amygdala could thus play a role in the vulnerability to FRD emergence at adulthood. We propose our methodology as an alternative to model the developmental vulnerability to FRD, especially in its comorbidity with TSC2-related autism syndrome.
The performance of cooperation strategies for enhancing the efficiency of international oil trade networks
Authors: Wei Na , Xie Wen-Jie , Zhou Wei-Xing 
Published: December 2021

Abstract
The efficiency of the international oil trade networks (iOTNs) is an important measure of the efficient redistribution of oil resources among various economies. Adopting cooperation strategies between economies can enhance the efficiency of the iOTNs. We design a series of trade cooperation strategies based on trade volumes, geographic locations and local similarities of economies, and quantitatively analyse the impact of new trade relations on the efficiency of the iOTNs under different trade cooperation strategies. We find that the oil trade system rapidly developed into a more efficient system for the flows of resources and market information. When the proportion of newly added trade relationships is fairly large, the win–win strategy can improve the network efficiency the most; otherwise, the common neighbour strategy performs the best.
A holistic analysis of web-based public key infrastructure failures: comparing experts' perceptions and real-world incidents
Authors: Hadan Hilda , Serrano Nicolas , Camp L Jean 
Published: December 2021

Abstract
Public key infrastructure (PKI) is the foundation of secure and trusted transactions across the Internet. This paper presents an evaluation of web-based PKI incidents in two parts. We began with a qualitative study where we captured security and policy experts' perceptions of PKI in a set of interviews. We interviewed 18 experts in two conferences who include security academics and practitioners. We describe their perceptions of PKI failures. To evaluate whether perceived failures match real documented failures, we conducted a quantitative analysis of real-world PKI incidents on the web since 2001. Our data comprise reports from Bugzilla, root program operators, academic literature, security blogs, and the popular press. We determined the underlying causes of each and reported the results. We identified a gap between experts' perceptions and real-world PKI incidents. We conclude that there are significant sources of failures of PKI that neither the usability nor traditional computer security community is engaging, nor can arguably engage separately. Specifically, we found incidents illustrate systematic weaknesses of organizational practices that create risks for all who rely upon PKI. More positively, our results also point to organizational and configuration choices that could avoid or mitigate some of these risks. Thus, we also identify immediate mitigation strategies (where feasible).
Interpretation and actionability of genetic variants in cardiomyopathies: a position statement from the European Society of Cardiology Council on cardiovascular genomics
Authors: Arbustini Eloisa , Behr Elijah R , Carrier Lucie , van Duijn Cornelia , Evans Paul , Favalli Valentina , van der Harst Pim , Haugaa Kristina Hermann , Jondeau Guillaume , Kääb Stefan , Kaski Juan Pablo , Kavousi Maryam , Loeys Bart , Pantazis Antonis , Pinto Yigal , Schunkert Heribert , Di Toro Alessandro , Thum Thomas , Urtis Mario , Waltenberger Johannes , Elliott Perry 
Published: December 2021

Abstract
This document describes the contribution of clinical criteria to the interpretation of genetic variants using heritable Mendelian cardiomyopathies as an example. The aim is to assist cardiologists in defining the clinical contribution to a genetic diagnosis and the interpretation of molecular genetic reports. The identification of a genetic variant of unknown or uncertain significance is a limitation of genetic testing, but current guidelines for the interpretation of genetic variants include essential contributions from clinical family screening that can establish a de novo assignment of the variant or its segregation with the phenotype in the family. A partnership between clinicians and patients helps to solve major uncertainties and provides reliable and clinically actionable information.
Classification of volcanic tremors and earthquakes based on seismic correlation: application at Sakurajima volcano, Japan
Authors: Permana Theodorus , Nishimura Takeshi , Nakahara Hisashi , Shapiro Nikolai 
Published: December 2021

SUMMARY
Classification of volcanic tremors and earthquakes is an important part of volcano monitoring. Conventional classification technique relies on visual characterization of the amplitudes, frequency, or duration of seismic signals. In some cases, such classification is difficult to be maintained continuously, especially during high eruptive activities. In the present study, we develop a classification technique based on analyses of seismic wave correlation. The technique is based on a measure of spatial coherence using the distribution width of eigenvalues from the seismic covariance matrix that is referred to as ‘spectral width’. We use the spectral width characteristics to extract the frequencies where the seismic signals are the most spatially coherent. We analyse 6-month continuous seismic data at six seismic stations deployed on Sakurajima volcano, Japan. The classification is performed every 10 min to recognize volcanic tremor and B-type earthquakes, both of which show unclear onsets and are dominant at around 1–4 Hz. Their frequencies of high spatial coherence are different from each other, providing a basis for automatic classification of both types of seismic events. Our classification results show that an increase in seismic activity, particularly volcanic tremors, occurred during high eruptive activity and is well matched with the events that are routinely determined by the Japan Meteorological Agency (JMA) based on visual examination of the data. We discuss the volcanic activities by combining our classification results with those from detections and location methods based on seismic correlation. Most of the source locations of volcanic tremor and B-type earthquakes are distributed at the same region with depths of less than 4 km beneath the active craters, which are almost consistent with the source locations of explosion earthquakes and B-type earthquakes determined from P-wave onsets in the previous studies. Also, the distribution of horizontal locations is spatially elongated at shallow depths above a dyke that is inferred to extend from Aira caldera at a depth of 7–9 km. We obtain deep and shallow sources for the tremor that occurred before and after an explosive eruption, respectively. We also obtain shallow sources beneath the active crater during a continuous tremor that accompanies increasing eruptive activity. The source locations of the classified volcanic tremor and B-type earthquakes may represent the movement of magma and gas from the shallow magma chamber at 5 km depth to the active craters.
Diffusion delay centrality: decelerating diffusion processes across networks
Authors: Leone Sciabolazza Valerio , Riccetti Luca 
Published: December 2021

AbstractThis paper presents a new measure (the diffusion delay centrality—DDC) to identify agents who should be put into isolation to decelerate a diffusion process spreading throughout a network. We show that DDC assigns a high rank to agents acting as the gatekeepers of the fringe of the network. We also show that the ranking of nodes obtained from the DDC is predicted by the difference in the values of betweenness and eigenvector centrality of network agents. The findings presented might constitute a useful tool to reduce diffusion processes both for policy makers and for corporate managers in the organization of production.
Traffic control hand signal recognition using convolution and recurrent neural networks
Authors: Baek Taeseung , Lee Yong-Gu 
Published: December 2021

Abstract
Gesture understanding is one of the most challenging problems in computer vision. Among them, traffic hand signal recognition requires the consideration of speed and the validity of the commanding signal. The lack of available datasets is also a serious problem. Most classifiers approach these problems using the skeletons of target actors in an image. Extracting the three-dimensional coordinates of skeletons is simplified when depth information accompanies the images. However, depth cameras cost significantly more than RGB cameras. Furthermore, the extraction of the skeleton needs to be performed in prior. Here, we show a hand signal detection algorithm without skeletons. Instead of skeletons, we use simple object detectors trained to acquire hand directions. The variance in the time length of gestures mixed with random pauses and noise is handled with a recurrent neural network (RNN). Furthermore, we have developed a flag sequence algorithm to assess the validity of the commanding signal. In whole, the computed hand directions are sent to the RNN, which identifies six types of hand signals given by traffic controllers with the ability to distinguish time variations and intermittent randomly appearing noises. We constructed a hand signal dataset composed of 100 thousand RGB images that is made publicly available. We achieved correct recognition of the hand signals with various backgrounds at 91% accuracy. A processing speed of 30 FPS in FHD video streams, which is a 52% improvement over the best among previous works, was achieved. Despite the extra burden of deciding the validity of the hand signals, this method surpasses methods that solely use RGB video streams. Our work is capable of performing with nonstationary viewpoints, such as those taken from moving vehicles. To accomplish this goal, we set a higher priority for the speed and validity assessment of the recognized commanding signals. The collected dataset is made publicly available through the Korean government portal under the URL “data.go.kr/data/15075814/fileData.do.”
Posttraumatic Growth in Youth, Young Adults, and Caregivers Who Experienced Solid Organ Transplant
Authors: Triplett Kelli N , Mayersohn Gillian S , Masood Saba S , Pickwith Kristine , Mbroh Hayden , Killian Michael 
Published: December 2021

Abstract

Objective
To explore posttraumatic growth (PTG) in pediatric patients who have undergone solid organ transplant (SOT) and their caregivers, and to examine potential correlates of PTG.

Method
Youth and young adults with a history of SOT (heart, kidney, liver) at least 1 month prior to participation and caregivers completed measures of PTG, demographic, and medical factors. In total, 59 youth (M = 12.68 years, SD = 1.91), 21 young adults (M = 19.37, SD = 0.82), and 95 caregivers (M = 37.95 years, SD = 9.37) participated.

Results
Overall, 67% of youth, 76% of young adults, and 89% of caregivers reported PTG within the medium to very high range. Appreciation of Life was the highest PTG subscale across all groups. Youth and caregiver PTG scores were significantly positively correlated. Religious affiliation and religious coping were positively associated with PTG for caregivers, and the relationship yielded large effect sizes for young adults. Caregivers of children with kidney transplants endorsed lower PTG than other organ types and caregivers of children who had an acute medical condition endorsed greater PTG than caregivers of children who had chronic illness.

Conclusion
Findings suggest the pediatric SOT experience can yield positive changes such as a greater appreciation of life. Although small sample sizes may have led to reduced power for detecting significant findings for some analyses, results suggest religious, medical, and parent–child relationship factors are likely related to PTG in pediatric SOT and warrant future investigation.
The Complete Local-Volume Groups Sample – IV. Star formation and gas content in group-dominant galaxies
Authors: Kolokythas Konstantinos , Vaddi Sravani , O’Sullivan Ewan , Loubser Ilani , Babul Arif , Raychaudhury Somak , Lagos Patricio , Jarrett Thomas H 
Published: December 2021

ABSTRACT
Using multiband data, we examine the star formation activity of the nearby group-dominant early-type galaxies of the Complete Local-volume Groups Sample (CLoGS) and the relation between star formation, gas content, and local environment. Only a small fraction of the galaxies (13 per cent; 6/47) are found to be far-ultraviolet (FUV) bright, with FUV to near-infrared colours indicative of recent active star formation (NGC 252, NGC 924, NGC 940, NGC 1106, NGC 7252, and ESO 507-25). These systems are lenticulars presenting the highest FUV-specific star formation rates in the sample (sSFRFUV &gt; 5 × 1013 yr−1), significant cold gas reservoirs [M(H2) = 0.5-61 × 108 M⊙], reside in X-ray faint groups, and none hosts a powerful radio active galactic nucleus (AGN) (P$_{1.4\mathrm{ GHz}}\, \lt 10^{23}$ W Hz−1). The majority of the group-dominant galaxies (87 per cent; 41/47) are FUV faint, with no significant star formation, classified in most cases as spheroids based on their position on the infrared star-forming main sequence (87 per cent; 46/53). Examining the relationships between radio power, SFRFUV, and stellar mass, we find a lack of correlation that suggests a combination of origins for the cool gas in these galaxies, including stellar mass loss, cooling from the intra-group medium (IGrM) or galaxy halo, and acquisition through mergers or tidal interactions. X-ray bright systems, in addition to hosting radio powerful AGN, have a range of SFRs but, with the exception of NGC 315, do not rise to the highest rates seen in the FUV bright systems. We suggest that central group galaxy evolution is linked to gas mass availability, with star formation favoured in the absence of a group-scale X-ray halo, but AGN jet launching is more likely in systems with a cooling IGrM.
TOI-530b: a giant planet transiting an M-dwarf detected by TESS
Authors: Gan Tianjun , Lin Zitao , Wang Sharon Xuesong , Mao Shude , Fouqué Pascal , Fan Jiahao , Bedell Megan , Stassun Keivan G , Giacalone Steven , Fukui Akihiko , Murgas Felipe , Ciardi David R , Howell Steve B , Collins Karen A , Shporer Avi , Arnold Luc , Barclay Thomas , Charbonneau David , Christiansen Jessie , Crossfield Ian J M , Dressing Courtney D , Elliott Ashley , Esparza-Borges Emma , Evans Phil , Gnilka Crystal L , Gonzales Erica J , Howard Andrew W , Isogai Keisuke , Kawauchi Kiyoe , Kurita Seiya , Liu Beibei , Livingston John H , Matson Rachel A , Narita Norio , Palle Enric , Parviainen Hannu , Rackham Benjamin V , Rodriguez David R , Rose Mark , Rudat Alexander , Schlieder Joshua E , Scott Nicholas J , Vezie Michael , Ricker George R , Vanderspek Roland , Latham David W , Seager Sara , Winn Joshua N , Jenkins Jon M 
Published: December 2021

ABSTRACT
We report the discovery of TOI-530b, a transiting Saturn-like planet around an M0.5V dwarf, delivered by the Transiting Exoplanet Survey Satellite (TESS). The host star is located at a distance of 147.7 ± 0.6 pc with a radius of R* = 0.54 ± 0.03 R⊙ and a mass of M* = 0.53 ± 0.02 M⊙. We verify the planetary nature of the transit signals by combining ground-based multiwavelength photometry, high-resolution spectroscopy from SPIRou as well as high-angular-resolution imaging. With V = 15.4 mag, TOI-530b is orbiting one of the faintest stars accessible by ground-based spectroscopy. Our model reveals that TOI-530b has a radius of 0.83 ± 0.05 RJ and a mass of 0.37 ± 0.08 MJ on a 6.39-d orbit. TOI-530b is the sixth transiting giant planet hosted by an M-type star, which is predicted to be infrequent according to core accretion theory, making it a valuable object to further study the formation and migration history of similar planets. Furthermore, we identify a potential dearth of hot massive giant planets around M-dwarfs with separation distance smaller than 0.1 au and planet-to-star mass ratio between 2 × 10−3 and 10−2. We also find a possible correlation between hot giant planet formation and the metallicity of its parent M-dwarf. We discuss the potential formation channel of such systems.
Unhoused Persons: Perspectives on Perceived Benefits of Music Therapy
Authors: Lahue Katie 
Published: December 2021

Abstract
There is limited literature to support the use of music therapy with unhoused persons and more research is needed to deepen the understanding of music therapy with this population. This researcher aimed to gather information from music therapists who work with unhoused persons to gain more perspective on the perceived benefits of the music therapy treatment process. Three music therapists were interviewed; interviews were then transcribed and coded to find themes regarding perceived benefits of music therapy with unhoused persons. The four themes derived from the data were increased resilience factors, facilitating connections, creating a safe space, and increased expression. Findings support music therapy attending to many levels of human need for unhoused individuals. These findings can be used as recommendation for practice and program development for the use of music therapy with unhoused persons and also point to a need for more research to understand the benefits of specific music therapy techniques and treatment methods with unhoused persons and subgroups of the unhoused community.
Vorinostat and isotretinoin with chemotherapy in young children with embryonal brain tumors: A report from the Pediatric Brain Tumor Consortium (PBTC-026)
Authors: Leary Sarah E S , Kilburn Lindsay , Geyer J Russell , Kocak Mehmet , Huang Jie , Smith Kyle S , Hadley Jennifer , Ermoian Ralph , MacDonald Tobey J , Goldman Stewart , Phillips Peter , Young Poussaint Tina , Olson James M , Ellison David W , Dunkel Ira J , Fouladi Maryam , Onar-Thomas Arzu , Northcott Paul A 
Published: December 2021

Abstract

Background
Embryonal tumors of the CNS are the most common malignant tumors occurring in the first years of life. This study evaluated the feasibility and safety of incorporating novel non-cytotoxic therapy with vorinostat and isotretinoin to an intensive cytotoxic chemotherapy backbone.

Methods
PBTC-026 was a prospective multi-institutional clinical trial for children &lt;48 months of age with newly diagnosed embryonal tumors of the CNS. Treatment included three 21-day cycles of induction therapy with vorinostat and isotretinoin, cisplatin, vincristine, cyclophosphamide, and etoposide; three 28-day cycles of consolidation therapy with carboplatin and thiotepa followed by stem cell rescue; and twelve 28-day cycles of maintenance therapy with vorinostat and isotretinoin. Patients with M0 medulloblastoma (MB) received focal radiation following consolidation therapy. Molecular classification was by DNA methylation array.

Results
Thirty-one patients with median age of 26 months (range 6-46) received treatment on study; 19 (61%) were male. Diagnosis was MB in 20 and supratentorial CNS embryonal tumor in 11. 24/31 patients completed induction therapy within a pre-specified feasibility window of 98 days. Five-year progression-free survival (PFS) and overall survival (OS) for all 31 patients were 55 ± 15 and 61 ± 13, respectively. Five-year PFS was 42 ± 13 for group 3 MB (n = 12); 80 ± 25 for SHH MB (n = 5); 33 ± 19 for embryonal tumor with multilayered rosettes (ETMR, n = 6).

Conclusion
It was safe and feasible to incorporate vorinostat and isotretinoin into an intensive chemotherapy regimen. Further study to define efficacy in this high-risk group of patients is warranted.