bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools
Authors: Garcia-Prieto Carlos A , Martínez-Jiménez Francisco , Valencia Alfonso , Porta-Pardo Eduard 
Published: May 2022

AbstractMotivationThe analysis of cancer genomes provides fundamental information about its etiology, the processes driving cell transformation or potential treatments. While researchers and clinicians are often only interested in the identification of oncogenic mutations, actionable variants or mutational signatures, the first crucial step in the analysis of any tumor genome is the identification of somatic variants in cancer cells (i.e. those that have been acquired during their evolution). For that purpose, a wide range of computational tools have been developed in recent years to detect somatic mutations in sequencing data from tumor samples. While there have been some efforts to benchmark somatic variant calling tools and strategies, the extent to which variant calling decisions impact the results of downstream analyses of tumor genomes remains unknown.ResultsHere, we quantify the impact of variant calling decisions by comparing the results obtained in three important analyses of cancer genomics data (identification of cancer driver genes, quantification of mutational signatures and detection of clinically actionable variants) when changing the somatic variant caller (MuSE, MuTect2, SomaticSniper and VarScan2) or the strategy to combine them (Consensus of two, Consensus of three and Union) across all 33 cancer types from The Cancer Genome Atlas. Our results show that variant calling decisions have a significant impact on these analyses, creating important differences that could even impact treatment decisions for some patients. Moreover, the Consensus of three calling strategy to combine the output of multiple variant calling tools, a very widely used strategy by the research community, can lead to the loss of some cancer driver genes and actionable mutations. Overall, our results highlight the limitations of widespread practices within the cancer genomics community and point to important differences in critical analyses of tumor sequencing data depending on variant calling, affecting even the identification of clinically actionable variants.Availability and implementationCode is available at https://github.com/carlosgarciaprieto/VariantCallingClinicalBenchmark.Supplementary informationSupplementary data are available at Bioinformatics online.
The Colour of Eco-Crime
Authors: Bertenthal A 
Published: May 2022

AbstractIn taking up the mantle of ‘green,’ criminologists concerned with environmental harm have succeeded in shifting criminology away from its anthropocentric focus on crime and harms committed to and by humans. While this framework has generated a large body of scholarship, it has also occluded important discussions about the significance of race and racial ideologies in the ongoing construction of crime, even—and especially—when depictions of crime do not explicitly reference humans. This article employs semiotic analysis of media images of eco-crime to demonstrate that the ways in which we see eco-crime—like ways of seeing crime more generally—construct images of race and contribute to the establishment of racialized relations. By placing eco-crime in a visual context and deconstructing the implicit and explicit racial imagery of eco-crime, I prompt criminologists to consider more critically issues of race and racialization in green criminology.
Long-term exposure to air pollutants and increased risk of chronic kidney disease in a community-based population using a fuzzy logic inference model
Authors: Lin Hsueh-Chun , Hung Peir-Haur , Hsieh Yun-Yu , Lai Ting-Ju , Hsu Hui-Tsung , Chung Mu-Chi , Chung Chi-Jung 
Published: May 2022

ABSTRACT

Background
Fuzzy inference systems (FISs) based on fuzzy theory in mathematics were previously applied to infer supplementary points for the limited number of monitoring sites and improve the uncertainty of spatial data. Therefore we adopted the FIS method to simulate spatiotemporal levels of air pollutants [particulate matter &lt;2.5 μm (PM2.5), sulfur dioxide (SO2) and (NO2)] and investigated the association of levels of air pollutants with the community-based prevalence of chronic kidney disease (CKD).

Methods
A Complex Health Screening program was launched during 2012–2013 and a total of 8284 community residents in Chiayi County, which is located in southwestern Taiwan, received a series of standard physical examinations, including measurement of estimated glomerular filtration rate (eGFR). CKD cases were defined as eGFR &lt;60 mL/min/1.73 m2 and were matched for age and gender in a 1:4 ratio of cases:controls. Data on air pollutants were collected from air quality monitoring stations during 2006–2016. The longitude, latitude and recruitment month of the individual case were entered into the trained FIS. The defuzzification process was performed based on the proper membership functions and fuzzy logic rules to infer the concentrations of air pollutants. In addition, we used conditional logistic regression and the distributed lag nonlinear model to calculate the prevalence ratios of CKD and the 95% confidence interval. Confounders including Framingham Risk Score (FRS), diabetes, gout, arthritis, heart disease, metabolic syndrome and vegetables consumption were adjusted in the models.

Results
Participants with a high FRS (&gt;10%), diabetes, heart disease, gout, arthritis or metabolic syndrome had significantly increased CKD prevalence. After adjustment for confounders, PM2.5 levels were significantly increased in CKD cases in both single- and two-pollutant models (prevalence ratio 1.31–1.34). There was a positive association with CKD in the two-pollutant models for NO2. However, similar results were not observed for SO2.

Conclusions
FIS may be helpful to reduce uncertainty with better interpolation for limited monitoring stations. Meanwhile, long-term exposure to ambient PM2.5 appears to be associated with an increased prevalence of CKD, based on a FIS model.
Tailoring the dialysate bicarbonate eliminates pre-dialysis acidosis and post-dialysis alkalosis
Authors: Cuadrado Elena , Broseta José Jesús , Rodríguez-Espinosa Diana , Montagud-Marrahi Enrique , Rodas Lida , Fontseré Néstor , Arias-Guillén Marta , Rico Naira , Maduell Francisco 
Published: May 2022

ABSTRACT

Background
Both metabolic acidosis and alkalosis increase hospitalizations, haemodynamic instability and mortality in haemodialysis patients. Unfortunately, current practices opt for a one-size-fits-all approach, leaving many patients either acidotic before or alkalotic after dialysis sessions. Therefore an individualized adjustment of these patients’ dialysate bicarbonate prescriptions could reduce these acid–base imbalances.

Methods
This is a prospective single-cohort study of patients on a chronic haemodiafiltration programme. The dialysate bicarbonate prescription was modified according to the pre- and post-dialysis total carbon dioxide (TCO2) values of 19–25 mEq/L and ≤29 mEq/L, respectively, with an adjustment formula calculated with the data obtained from previously published work by our group. In addition, we analysed this adjustment's effect on plasma sodium, potassium, phosphorus, parathyroid hormone (PTH) and calcium.

Results
At baseline, only 67.9% of patients were within the desired pre- and post-dialysis TCO2 target range. As of the first month, every followed patient met the TCO2 target range objective in pre-dialysis measurements and ˃95% met the post-dialysis TCO2 target. At the end of the study, 75% of the patients were on dialysate bicarbonate of 32–34 mEq/L. There were no clinically significant changes in calcium, phosphate, PTH, sodium or potassium levels. Also, we did not notice any increase in intradialytic adverse events.

Conclusions
We suggest an individualized adjustment of the dialysate bicarbonate concentration according to the pre- and post-dialysis TCO2 values. With it, nearly every patient in our cohort reached the established range, potentially reducing their mortality risk.
On Log-Algebraic Identities for Anderson t-Modules and Characteristic p Multiple Zeta Values
Authors: Green Nathan , Ngo Dac Tuan 
Published: May 2022

Abstract
Based on the notion of Stark units, we present a new approach that obtains refinements of log-algebraic identities for Anderson $t$-modules. As a consequence, we use our techniques to recover many earlier results and prove stronger results in some cases. Further, we devise a direct and conceptual way to get logarithmic interpretations for multiple zeta values in positive characteristic. This generalizes the work of Anderson and Thakur for Carlitz zeta values.
As right as rain: deciphering drought-related metabolic flexibility in the C4–CAMPortulaca
Authors: Reyna-Llorens Ivan , Aubry Sylvain 
Published: May 2022

This article comments on:Ferrari RC, Kawabata AB, Ferreira SS, Hartwell J, Freschi L. 2022. A matter of time: regulatory events behind the synchronization of C4 and crassulacean acid metabolism gene expression in Portulaca oleracea. Journal of Experimental Botany 73,4867–4885.
On the relation of host properties and environment of AGN galaxies across the standard optical diagnostic diagram
Authors: Perez Noelia R , Coldwell Georgina 
Published: May 2022

ABSTRACT
We study the host properties and environment of active galactic nuclei (AGNs) galaxies, taken from SDSS-DR12, across the [O iii]/H β versus [N ii]/H α diagnostic diagram. We select AGN subsamples defined as parallel and perpendicular to the star-forming locus on the BPT diagram based on the Kauffmann et al. and Schawinski et al. criteria. For parallel subsamples we find that AGN host properties exhibit a morphological evolution as they become more distant to the star-forming sequence. The local density environment shows a more evident morphology–density relationship for subsamples mainly formed by Composite and Spiral galaxies than those containing LINERs and Seyferts, where the AGN emission is the dominant source. We also analyse the properties of the five closest AGN neighbours observing no significant differences in the environment, although the AGN host properties of every subsample have noticeable variations. The AGNs belonging to perpendicular subsamples show clear differences on their host properties from left top to right bottom on the diagram. However, the analysis of the local density environment do not reflect strong dependency with the host AGN properties. This result is reinforced by the characteristics of the AGN neighbouring galaxies. These findings suggest that mixed AGN/star-forming galaxies present environmental features more similar to that of non-active galaxies. However, as AGNs at the centre of the more evolved galaxies become the dominant source, the environment tends to provide suitable conditions for the central black hole feeding with an increasing content of gas and likelihood of a higher merger rate.
CO excitation and line energy distributions in gas-selected galaxies
Authors: Klitsch A , Christensen L , Valentino F , Kanekar N , Møller P , Zwaan M A , Fynbo J P U , Neeleman M , Prochaska J X 
Published: May 2022

ABSTRACT
While emission-selected galaxy surveys are biased towards the most luminous part of the galaxy population, absorption selection is a potentially unbiased galaxy selection technique with respect to luminosity. However, the physical properties of absorption-selected galaxies are not well characterized. Here, we study the excitation conditions in the interstellar medium (ISM) in damped Ly α (DLA) absorption-selected galaxies. We present a study of the CO spectral-line energy distribution (SLED) in four high-metallicity absorption-selected galaxies with previously reported CO detections at intermediate (z ∼ 0.7) and high (z ∼ 2) redshifts. We find further evidence for a wide variety of ISM conditions in these galaxies. Two out of the four galaxies show CO SLEDs consistent with that of the Milky Way inner disc. Interestingly, one of these galaxies is at z ∼ 2 and has a CO SLED below that of main-sequence galaxies at similar redshifts. The other two galaxies at z &gt; 2 show more excited ISM conditions, with one of them showing thermal excitation of the mid-J (J = 3, 4) levels, similar to that seen in two massive main-sequence galaxies at these redshifts. Overall, we find that absorption selection traces a diverse population of galaxies.
Polarization, polarizing efficiency, and grain alignment towards the direction of the cluster NGC 2345
Authors: Singh Sadhana , Pandey Jeewan C , Hoang Thiem 
Published: May 2022

ABSTRACT
We have investigated the grain alignment and dust properties towards the direction of the cluster NGC 2345 using the multiband optical polarimetric observations. For the majority of the stars, the observed polarization is found to be due to the interstellar medium with average values of maximum polarization and wavelength corresponding to it as 1.55 per cent and 0.58 $\mu$m, respectively. This reveals a similar size distribution of dust grains to that in the general interstellar medium in the direction of NGC 2345. Alteration of dust properties near the distance of 1.2 kpc towards the direction of NGC 2345 has been noticed. The dust grains located beyond this distance are found to be aligned with the Galactic magnetic field, whereas a dispersion in the orientation of the dust grains lying in the foreground of this distance is found. Polarizing efficiency of grains in this direction is found to be close to the average efficiency for our Galaxy. The decreased grain size along with the increased polarizing efficiency towards the core region of the cluster indicates the local radiation field is higher within the cluster, which is responsible for the increased alignment efficiency of small grains. The wavelength of maximum polarization (associated with the average size of aligned grains) is also found to increase with extinction and reduces with the increase in polarizing efficiency, which can be explained by the radiative torque alignment mechanism.
High-resolution X-ray study of supernova remnant J0453.6−6829 with unusually high forbidden-to-resonance ratio
Authors: Koshiba Yosuke , Uchida Hiroyuki , Tanaka Takaaki , Amano Yuki , Sano Hidetoshi , Tsuru Takeshi Go 
Published: May 2022

Abstract
Recent high-resolution X-ray spectroscopy has revealed that several supernova remnants (SNRs) in the Large Magellanic Cloud (LMC) show unusually high forbidden-to-resonance (f/r) line ratios. While their origin is still uncertain and debated, most of these SNRs have asymmetric morphology and/or show evidence of interaction with dense material, which may hint at the true nature of the anomalous f/r ratios. Here we report on a detailed spectral analysis of the LMC SNR J0453.6−6829 with the Reflection Grating Spectrometer (RGS) onboard XMM-Newton. We find that the f/r ratio of O vii ($=1.06^{+0.09}_{-0.10}$) is significantly higher than expected from the previously reported thermal model. The spectrum is suitably explained by taking into account a charge exchange (CX) emission in addition to the thermal component. Analyzing archival ATCA and Parkes radio data, we also reveal that an H i cloud is possibly interacting with J0453.6−6829. These results support the presence of CX in J0453.6−6829, as the origin of the obtained high f/r ratio. Although a contribution of the resonance scattering (RS) cannot be ruled out at this time, we conclude that CX seems more likely than RS considering the relatively symmetric morphology of this remnant.
Real-time processing pipeline for automatic streak detection in astronomical images implemented in a multi-GPU system
Authors: Cegarra Polo Manuel , Yanagisawa Toshifumi , Kurosaki Hirohisa 
Published: May 2022

Abstract
Detecting and tracking objects in low Earth orbit is an increasingly important task. Telescope observations contribute to its accomplishment, and telescope imagers produce a large amount of data for this task. Thus, it is convenient to use fast computer-aided processes to analyze it. Telescopes tracking at the sidereal rate usually detect these objects in their imagers as streaks, their lengths depending on the exposure time and the slant range to the object. We have developed a processing pipeline to automatically detect streaks in astronomical images in real time (i.e., faster than the images are produced) by a graphics processing unit parallel processing system. After the detection stage, streak photometric information is obtained, and object candidate identification is provided through matches with a two-line element set database. The system has been tested on a large set of images, consisting of two hours of observation time, from the Tomo-e Gozen camera of the 105 cm Schmidt telescope at Kiso Observatory in Japan. Streaks were automatically detected in approximately 0.5% of the images. The process detected streaks down to a minimum apparent magnitude of +11.3 and matched the streaks with objects from the space-track catalog in 78% of the cases. We believe that this processing pipeline can be instrumental in detecting new objects and tracking existing ones when processing speed is important, for instance, when a short handover time is required between follow-up observation stations, or when there is a large number of images to process. This study will contribute to consolidating optical observations as an effective way to control and alleviate the space debris problem.
ON THE ASSESSMENT OF EXPOSURE FROM LTE 800-MHZ DOWNLINK FREQUENCY BAND THROUGH THE TIME-AVERAGED AND INTEGRAL-BASED MEASURE
Authors: Šuka Darko , Simić-Pejović Mirjana , Pejović Predrag 
Published: May 2022

AbstractExposure assessment should consider the stochastic nature of the emitted signals. Therefore, the long-term temporal variability of E-field strength, obtained by band selective measurements for long-term evolution in a real mobile network environment, is considered in this paper. Intensive measurements were carried out 24 h a day for 2 weeks at an indoor location in the urban area. The repeatability of the measurement results was achieved through descriptive statistics of the 24-h instantaneous, time-averaged and integral-based values. More specifically, we addressed the uncertainties on the temporal variability of the instantaneous exposure levels and the effects of duration of averaging and time-integrating on it. To this aim, a huge amount of signal levels (120 960 samples) was collected during the measurement campaign by considering three operators in the 800 MHz downlink band. Results have shown how some factors, such as the time interval in which the measurements are taken, can significantly affect the measurement results and their repeatability. Furthermore, in some cases, such effects become comparable to, or even larger than typical measurement uncertainty. By applying both the 24-h time-averaged and integral-based measure, the variability of daily exposure levels could be reduced to values lower than the measurement uncertainty (i.e. lower than ± 20% of the mean week value obtained with either measure). Based on such results, an indicator depending on the exposure duration should better quantify the far-field exposure in each location.
Oldest fossil loon documents a pronounced ecomorphological shift in the evolution of gaviiform birds
Authors: Mayr Gerald , Kitchener Andrew C 
Published: May 2022

AbstractWe describe a stem group representative of Gaviiformes (loons or divers) from the early Eocene London Clay of Walton-on-the-Naze (Essex, UK). The holotype of Nasidytes ypresianus gen. et sp. nov. is a partial skeleton including the mandible and all major limb bones. The new species is the oldest unambiguously identified loon and the most substantial Palaeogene fossil record of Gaviiformes. The mandible of Nasidytes is proportionally wider than that of extant loons and resembles that of extant coots (Fulica spp.), which indicates that the new taxon was less piscivorous than crown group Gaviiformes. Hypotarsus morphology suggests that N. ypresianus is the sister taxon of a clade including all other Cenozoic fossil loons and crown group Gaviiformes. According to its plesiomorphic leg morphology, and unlike extant loons, the new species was not a specialized pursuit predator of fishes. The evolution of advanced diving capabilities in the stem lineage of Gaviiformes is likely to have been correlated with an increased piscivory of loons, and the skeletal morphology of Nasidytes conforms to multiple independent origins of specialized piscivory and a highly aquatic ecology in the waterbird clade (Aequornithes).
An Evaluation of Audiovisual Discussion Boards in a Graduate-Level Nursing Course: Innovation During the Pandemic
Authors: Hodges Alexis , Powell Shannon , Williams Sarah 
Published: May 2022

Abstract
The COVID-19 pandemic challenged nurse educators to develop and implement effective learning environments at a distance and refine distance education instructional strategies that were used in the past. A quality improvement project implemented in a graduate-level nursing course incorporated audiovisual discussions as an innovative pedagogy. Students chose whether to participate in class discussions by either a narrative discussion board or an audiovisual discussion method with faculty feedback in the same format. Students who chose the audiovisual discussion board found the ability to see and hear others to be helpful, suggesting audiovisual methods may improve student satisfaction and learning outcomes.
The Influence of Sleep Quality on Patient Safety Learning of Nursing Students
Authors: Alenezi Atallah , Alquwez Nahed , Rivera Pedro P. , Catimbang Conrado C. , Alsolais Abdulellah , Cruz Jonas Preposi 
Published: May 2022

Abstract
We investigated the influence of nursing students’ sleep quality on their patient safety (PS) competence (i.e., knowledge of the dimensions of PS). The investigation surveyed 242 nursing students in a Saudi university. The majority of the surveyed students were characterized as having poor sleep quality. Notably, more male students experienced poor sleep quality than female students. The students reported the highest confidence in “culture of safety” and “managing safety risk”; they exhibited the poorest confidence in “working in teams.” Increased length of sleep latency decreased sleep efficiency, and increased daytime sleepiness-related dysfunction was associated with reduced PS competence.
Paid Mentors Develop Leadership Skills and Promote Socialization Into Nursing
Authors: Napierkowski Daria , Migliore Debra A. 
Published: May 2022

Abstract
Peer mentoring encourages relationships among novice and senior nursing students, provides emotional support, and develops leadership skills. The research design was a pretest/posttest, interventional study to evaluate a supervised peer-mentoring program among nursing students to determine socialization of mentees into the nursing discipline. The second purpose was to evaluate if financial reimbursement was an incentive for participation by mentors. The pretest mean was significantly lower than the posttest mean; the difference was statistically significant. Success was achieved for both mentors and mentees. A paid peer-mentoring program allows students to relinquish time that would otherwise be spent in outside employment.