bluuebunny/crossref_metadata_2025_split huggingface dataset:
Converting single nucleotide variants between genome builds: from cautionary tale to solution
Authors: Ormond Cathal , Ryan Niamh M , Corvin Aiden , Heron Elizabeth A 
Published: February 2021

Abstract
Next-generation sequencing studies are dependent on a high-quality reference genome for single nucleotide variant (SNV) calling. Although the two most recent builds of the human genome are widely used, position information is typically not directly comparable between them. Re-alignment gives the most accurate position information, but this procedure is often computationally expensive, and therefore, tools such as liftOver and CrossMap are used to convert data from one build to another. However, the positions of converted SNVs do not always match SNVs derived from aligned data, and in some instances, SNVs are known to change chromosome when converted. This is a significant problem when compiling sequencing resources or comparing results across studies. Here, we describe a novel algorithm to identify positions that are unstable when converting between human genome reference builds. These positions are detected independent of the conversion tools and are determined by the chain files, which provide a mapping of contiguous positions from one build to another. We also provide the list of unstable positions for converting between the two most commonly used builds GRCh37 and GRCh38. Pre-excluding SNVs at these positions, prior to conversion, results in SNVs that are stable to conversion. This simple procedure gives the same final list of stable SNVs as applying the algorithm and subsequently removing variants at unstable positions. This work highlights the care that must be taken when converting SNVs between genome builds and provides a simple method for ensuring higher confidence converted data. Unstable positions and algorithm code, available at https://github.com/cathaloruaidh/genomeBuildConversion
ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome
Authors: Song Bowen , Chen Kunqi , Tang Yujiao , Wei Zhen , Su Jionglong , de Magalhães João Pedro , Rigden Daniel J , Meng Jia 
Published: February 2021

AbstractMotivation N6-methyladenosine (m6A) is the most prevalent RNA modification on mRNAs and lncRNAs. Evidence increasingly demonstrates its crucial importance in essential molecular mechanisms and various diseases. With recent advances in sequencing techniques, tens of thousands of m6A sites are identified in a typical high-throughput experiment, posing a key challenge to distinguish the functional m6A sites from the remaining ‘passenger’ (or ‘silent’) sites. Results: We performed a comparative conservation analysis of the human and mouse m6A epitranscriptomes at single site resolution. A novel scoring framework, ConsRM, was devised to quantitatively measure the degree of conservation of individual m6A sites. ConsRM integrates multiple information sources and a positive-unlabeled learning framework, which integrated genomic and sequence features to trace subtle hints of epitranscriptome layer conservation. With a series validation experiments in mouse, fly and zebrafish, we showed that ConsRM outperformed well-adopted conservation scores (phastCons and phyloP) in distinguishing the conserved and unconserved m6A sites. Additionally, the m6A sites with a higher ConsRM score are more likely to be functionally important. An online database was developed containing the conservation metrics of 177 998 distinct human m6A sites to support conservation analysis and functional prioritization of individual m6A sites. And it is freely accessible at: https://www.xjtlu.edu.cn/biologicalsciences/con.
Making #BlackLivesMatter in the Shadow of Selma: Collective Memory and Racial Justice Activism in U.S. News
Authors: Jackson Sarah J 
Published: February 2021

Abstract
It is clear in news coverage of recent uprisings for Black life that journalists and media organizations struggle to reconcile the fact of ongoing racism with narratives of U.S. progress. Bound up in this struggle is how collective memory—or rather whose collective memory—shapes the practices of news-making. Here I interrogate how television news shapes collective memory of Black activism through analysis of a unique moment when protests over police abuse of Black people became newsworthy simultaneous with widespread commemorations of the civil rights movement. I detail the complex terrain of nostalgia and misremembering that provides cover for moderate and conservative delegitimization of contemporary Black activism. At the same time, counter-memories, introduced most often by members of the Black public sphere, offer alternative, actionable, and comprehensive interpretations of Black protest.
State-of-charge estimation for second-life lithium-ion batteries based on cell difference model and adaptive fading unscented Kalman filter algorithm
Authors: Du Banghua , Yu Zhang , Yi Shuhao , He Yanlin , Luo Yulin 
Published: February 2021

Abstract
Lithium-ion batteries retired from electric vehicles can provide considerable economic benefits when they are retired for secondary use. However, retired batteries after screening and restructuring still face the problem of inaccurate battery pack state-of-charge (SOC) estimation due to the existence of extreme inconsistency. To solve this problem, an adaptive fading unscented Kalman filtering (AFUKF) algorithm based on the cell difference model (CDM) is proposed in this paper for improving the accuracy of SOC estimation of retired lithium-ion battery packs. Firstly, an improved CDM based on a hypothetical Rint model is developed based on a second-order resistor/capacitor equivalent circuit model. Secondly, an AFUKF algorithm is developed to improve the adaptability and robustness of local state estimation against process modelling errors. Finally, characteristic data are obtained by conducting discharge tests on the screened retired lithium-ion batteries under specific operating conditions. The proposed method can improve the accuracy of SOC estimation of retired lithium-ion battery packs and provide a new idea for SOC estimation of retired lithium-ion battery packs, as shown by the simulated real experimental data.
Effects of Nicotine and Tobacco-Related Products on the Feeding Behavior of the German Cockroach (Blattodea: Blattellidae)
Authors: Di Ilio Vincenzo , Birkett Michael A , Pickett John A 
Published: February 2021

AbstractAnimals use olfaction to detect developmentally significant volatile organic compounds (VOCs) in their local environment. As part of a wider study aiming to demonstrate that the olfactory responses of animals to VOCs can be modified through the creation of a drug-addicted status and association with a selected VOC, we investigated nicotine and tobacco smoke particulate (TSP) extract as possible addictive compounds for male German cockroaches, Blattella germanica (Linnaeus). In feeding experiments using an artificial food stimulus, food treated with TSP extract was preferred over untreated food. Surprisingly, nicotine, which was expected to be the most important addictive tobacco component, did not induce noticeable effects on cockroach behavior. Both TSP extract and nicotine were shown to be phagostimulants. Olfactometry assays that measured odor-mediated insect behavior demonstrated that male B. germanica did not choose TSP-extract-treated food even when attempts were made specifically to train them via this modality. These results support a hypothesis that B. germanica needs to consume TSP-containing food to show a clear preference for this stimulus and that gustatory mechanisms are involved due to compounds present in the TSP extract.
Thyroid paraganglioma in a patient with a history of carotid and vagal paraganglioma: metastatic or primary tumor?
Authors: Yepuri Natesh , Vanga Gautam R , Naous Rana , Kinthala Sudhakar 
Published: February 2021

Abstract
Paragangliomas (PGs) are extremely rare multicentric neoplasms. Hereditary or familial PGs are associated with germline mutations in succinate dehydrogenase genes, seen in one-third of cases. Primary PGs of the thyroid are uncommon neuroendocrine neoplasms that account for 0.012% of all head and neck lesions. Although majority of these tumors are solitary, familial PGs are associated with synchronous tumors (carotid/vagal). We report an interesting case of primary thyroid PG in a patient with a previous history of a right carotid body, right vagal PGs and positive familial history, confining the differential diagnosis to recurrent lesions, which is the most common occurrence or new primary or a metastatic lesion. However, long interval and surgical anatomy suggests the diagnosis to be a primary lesion. In conclusion, although these lesions present multicentrically present at varying intervals, their occurrence at anatomically distinct sites should raise the concern for a new primary PG.
H i-MaNGA: tracing the physics of the neutral and ionized ISM with the second data release
Authors: Stark David V , Masters Karen L , Avila-Reese Vladimir , Riffel Rogemar , Riffel Rogerio , Boardman Nicholas Fraser , Zheng Zheng , Weijmans Anne-Marie , Dillon Sean , Fielder Catherine , Finnegan Daniel , Fofie Patricia , Goddy Julian , Harrington Emily , Pace Zachary , Rujopakarn Wiphu , Samanso Nattida , Shamsi Shoaib , Sharma Anubhav , Warrick Elizabeth , Witherspoon Catherine , Wolthuis Nathan 
Published: February 2021

ABSTRACT
We present the second data release for the H i-MaNGA programme of H i follow-up observations for the SDSS-IV MaNGA survey. This release contains measurements for 3669 unique galaxies, combining 2108 Green Bank Telescope observations with an updated crossmatch of the MaNGA sample with the ALFALFA survey. We combine these data with MaNGA spectroscopic measurements to examine relationships between H i-to-stellar mass ratio (${\rm M_{H\, {\small I}}/{M_*}}$) and average ISM/star formation properties probed by optical emission lines. ${\rm M_{H\, {\small I}}/{M_*}}$ is very weakly correlated with the equivalent width of H α, implying a loose connection between the instantaneous star formation rate and the H i reservoir, although the link between ${\rm M_{H\, {\small I}}/{M_*}}$ and star formation strengthens when averaged even over only moderate time-scales (∼30 Myr). Galaxies with elevated H i depletion times have enhanced [O i]/H α and depressed H α surface brightness, consistent with more H i residing in a diffuse and/or shock-heated phase that is less capable of condensing into molecular clouds. Of all optical lines, ${\rm M_{H\, {\small I}}/{M_*}}$ correlates most strongly with oxygen equivalent width, EW(O), which is likely a result of the existing correlation between ${\rm M_{H\, {\small I}}/{M_*}}$ and gas-phase metallicity. Residuals in the ${\rm M_{H\, {\small I}}/{M_*}}$−EW(O) relation are again correlated with [O i]/H α and H α surface brightness, suggesting they are also driven by variations in the fraction of diffuse and/or shock-heated gas. We recover the strong anticorrelation between ${\rm M_{H\, {\small I}}/{M_*}}$ and gas-phase metallicity seen in previous studies. We also find a relationship between ${\rm M_{H\, {\small I}}/{M_*}}$ and [O i]6302/H α, suggesting that higher fractions of diffuse and/or shock-heated gas are more prevalent in gas-rich galaxies.
Cosmic filaments in galaxy cluster outskirts: quantifying finding filaments in redshift space
Authors: Kuchner Ulrike , Aragón-Salamanca Alfonso , Rost Agustín , Pearce Frazer R , Gray Meghan E , Cui Weiguang , Knebe Alexander , Rasia Elena , Yepes Gustavo 
Published: February 2021

ABSTRACT
Inferring line-of-sight distances from redshifts in and around galaxy clusters is complicated by peculiar velocities, a phenomenon known as the ‘Fingers of God’ (FoG). This presents a significant challenge for finding filaments in large observational data sets as these artificial elongations can be wrongly identified as cosmic web filaments by extraction algorithms. Upcoming targeted wide-field spectroscopic surveys of galaxy clusters and their infall regions, such as the WEAVE Wide-Field Cluster Survey, motivate our investigation of the impact of FoG on finding filaments connected to clusters. Using zoom-in resimulations of 324 massive galaxy clusters and their outskirts from the three hundred project, we test methods typically applied to large-scale spectroscopic data sets. This paper describes our investigation of whether a statistical compression of the FoG of cluster centres and galaxy groups can lead to correct filament extractions in the cluster outskirts. We find that within 5R200 (∼15 h−1 Mpc) statistically correcting for FoG elongations of virialized regions does not achieve reliable filament networks compared to reference filament networks based on true positions. This is due to the complex flowing motions of galaxies towards filaments in addition to the cluster infall, which overwhelm the signal of the filaments relative to the volume that we probe. While information from spectroscopic redshifts is still important to isolate the cluster regions, and thereby reduce background and foreground interlopers, we expect future spectroscopic surveys of galaxy cluster outskirts to rely on 2D positions of galaxies to extract cosmic filaments.
Constraining the circumbinary disc tilt in the KH 15D system
Authors: Poon Michael , Zanazzi J J , Zhu Wei 
Published: February 2021

ABSTRACT
KH 15D is a system that consists of a young, eccentric binary, and a circumbinary disc that obscures the binary as the disc precesses. We develop a self-consistent model that provides a reasonable fit to the photometric variability that was observed in the KH 15D system over the past 60 yr. Our model suggests that the circumbinary disc has an inner edge rin ≲ 1 au, an outer edge rout ∼ a few au, and that the disc is misaligned relative to the stellar binary by ∼5–16°, with the inner edge more inclined than the outer edge. The difference between the inclinations (warp) and longitude of ascending nodes (twist) at the inner and outer edges of the disc are of order ∼10 and ∼15°, respectively. We also provide constraints on other properties of the disc, such as the precession period and surface density profile. Our work demonstrates the power of photometric data in constraining the physical properties of planet-forming circumbinary discs.
The obstructed jet in Mrk 231
Authors: Wang Ailing , An Tao , Jaiswal Sumit , Mohan Prashanth , Wang Yuchan , Baan Willem A , Zhang Yingkang , Yang Xiaolong 
Published: February 2021

ABSTRACT
Mrk 231 is the closest radio-quiet quasar known and one of the most luminous infrared galaxies in the local Universe. It is characterized by the co-existence of a radio jet and powerful multiphase multiscale outflows, making it an ideal laboratory to study active galactic nucleus (AGN) feedback. We analyse the multi-epoch very long baseline interferometry data of Mrk 231 and estimate the jet head advance speed to be ≲0.013 c, suggesting a sub-relativistic jet flow. The jet position angle changes from −113○ in the inner parsec to −172○ at a projected distance of 25 pc. The jet structure change might result from either a jet bending following the rotation of the circum-nuclear disc or the projection of a helical jet on the plane of the sky. In the large opening angle (∼60○) cone, the curved jet interacts with the interstellar medium and creates wide-aperture-angle shocks that subsequently dissipate a large portion of the jet power through radiation and contribute to powering the large-scale outflows. The low power and bent structure of the Mrk 231 jet, as well as extensive radiation dissipation, are consistent with the obstruction of the short-length jet by the host galaxy’s environment.
Social Determinants of Health and Neurosurgical Outcomes: Current State and Future Directions
Authors: Glauser Gregory , Detchou Donald K , Dimentberg Ryan , Ramayya Ashwin G , Malhotra Neil R 
Published: February 2021

Abstract
The relationship between social determinants of health (SDOH) and neurosurgical outcomes has become increasingly relevant. To date, results of prior work evaluating the impact of social determinants in neurosurgery have been mixed, and the need for robust data on this subject remains. The present review evaluates how gender, race, and socioeconomic status (SES) influence outcomes following various brain tumor resection procedures. Results from a number of prior studies from the senior author's lab are summarized, with all data acquired using the EpiLog tool (Epilog Laser). Separate analyses were performed for each procedure, evaluating the unique, isolated impact of gender, race, and SES on outcomes. A comprehensive literature review identified any prior studies evaluating the influence of these SDOH on neurosurgical outcomes. The review presented herein suggests that the effect of gender and race on outcomes is largely mitigated when equal access to care is attained, and socioeconomic factors and comorbidities are controlled for. Furthermore, when patients are matched upon for a number of clinically relevant covariates, SES impacts postoperative mortality. Elucidation of this disparity empowers surgeons to initiate actionable change to equilibrate future outcomes.
A BLUS1 kinase signal and a decrease in intercellular CO2 concentration are necessary for stomatal opening in response to blue light
Authors: Hosotani Sakurako , Yamauchi Shota , Kobayashi Haruki , Fuji Saashia , Koya Shigekazu , Shimazaki Ken-ichiro , Takemiya Atsushi 
Published: February 2021

Abstract
Light-induced stomatal opening stimulates CO2 uptake and transpiration in plants. Weak blue light under strong red light effectively induces stomatal opening. Blue light-dependent stomatal opening initiates light perception by phototropins, and the signal is transmitted to a plasma membrane H+-ATPase in guard cells via BLUE LIGHT SIGNALING 1 (BLUS1) kinase. However, it is unclear how BLUS1 transmits the signal to H+-ATPase. Here, we characterized BLUS1 signaling in Arabidopsis thaliana, and showed that the BLUS1 C-terminus acts as an auto-inhibitory domain and that phototropin-mediated Ser-348 phosphorylation within the domain removes auto-inhibition. C-Terminal truncation and phospho-mimic Ser-348 mutation caused H+-ATPase activation in the dark, but did not elicit stomatal opening. Unexpectedly, the plants exhibited stomatal opening under strong red light and stomatal closure under weak blue light. A decrease in intercellular CO2 concentration via red light-driven photosynthesis together with H+-ATPase activation caused stomatal opening. Furthermore, phototropins caused H+-ATPase dephosphorylation in guard cells expressing constitutive signaling variants of BLUS1 in response to blue light, possibly for fine-tuning stomatal opening. Overall, our findings provide mechanistic insights into the blue light regulation of stomatal opening.
Linking AM-PAC Mobility and Daily Activity to the PROMIS Physical Function Metric
Authors: Thackeray Anne , Hanmer Janel , Yu Lan , McCracken Polly , Marcus Robin 
Published: February 2021

Abstract

Objective
The purpose of this study was to link Activity Measure for Post-Acute Care (AM-PAC) Mobility and Daily Activity scales to the PROMIS Physical Function (PF) allowing for a common metric across scales.

Methods
Cross-sectional study of patients 18 years and older presenting to 1 of 8 outpatient rehabilitation clinics in southwestern Pennsylvania. Patients completed one survey with questions from the AM-PAC Daily Activity and Mobility short forms, and the PROMIS PF item bank. Using item response theory, 2 rounds of fixed-parameter calibration were performed. In the first, the AM-PAC Daily Activity and Mobility items were calibrated with 27 fixed item parameters from the PROMIS PF. Second, the AM-PAC Daily Activity items were calibrated with 11 PROMIS Upper Extremity fixed item parameters. This process uses the construct of physical function and equates AM-PAC items on the same underlying measurement scale for the PROMIS PF.

Results
Both scales measured a wide range of functioning and demonstrated good calibration. Data were appropriate for a fixed-parameter item response theory-based crosswalk. AM-PAC Daily Activity and Mobility raw scores were mapped onto the PROMIS PF metric. AM-PAC Daily Activity scores were also mapped onto the PROMIS PF Upper Extremity metric.

Conclusion
Question items from the AM-PAC Daily Activity, AM-PAC Mobility, and PROMIS PF similarly measure the construct of physical function. This consistency allows for a crosswalk of AM-PAC scores onto the PROMIS PF metric.

Impact
Crosswalk tables developed in this study allow for converting scores from the AM-PAC Daily Activity and Mobility scales to the PROMIS PF metric. This will facilitate monitoring of longitudinal change in function over time and across settings.
The potential toxicity of food-added sodium benzoate in mice is concentration-dependent
Authors: Olofinnade Anthony Tope , Onaolapo Adejoke Yetunde , Onaolapo Olakunle James , Olowe Olugbenga Adekunle 
Published: February 2021

Abstract
Sodium benzoate (NaB) is a versatile food preservative that has also found some applications in the treatment of medical disorders. However, till date, its possible widespread effects on the body are not well studied. We examined the likely effect of diet-added NaB on weight/food intake, haematological parameters, neurobehaviour, antioxidant status, lipid profile and anti-inflammatory/apoptotic markers in mice. Animals were assigned randomly into 4 groups of 10 mice each. Groups included normal control (fed rodent chow) and three groups fed NaB at 125 (0.0125%), 250 (0.025% and 500 (0.05%) mg/kg of feed added to diet, respectively, for eight weeks. Body weight and food intake were assessed. At the end of the experimental period animals were euthanized, blood was then taken for the assessment of haematological, biochemical and inflammatory/apoptotic markers. At the lowest concentration, NaB diet increased body weight and food intake. Decrease in haematological cell counts and total antioxidant capacity were observed, whereas serum malondialdehyde levels and superoxide dismutase activity were increased across the three concentrations. Serum tumour necrosis factor-alpha and interleukin-10 decreased, whereas caspase-3 levels showed no significant difference. Lipid profile and biochemical indices of kidney and liver function were also affected by NaB diet. In conclusion, our findings suggest that NaB may be harmful if regulations regarding its limit of consumption are mistakenly or deliberately ignored. Therefore, it is advisable that regulations on quantities to be added to food be enforced.
The Shieh Score as a Risk Assessment Tool for Hospital-Acquired Pressure Injuries: A Retrospective Cohort Study
Authors: Shieh David , Li Qiaowu , Shi Jiaxiao M. , Tovar Stephanie 
Published: February 2021

ABSTRACT

OBJECTIVE
To design a new risk assessment tool to identify patients at high risk for hospital-acquired pressure injuries.

METHODS
The researchers developed the Shieh Score using retrospective data of 406,032 hospital admissions from January 2014 to December 2016 with 1,299 pressure injury cases from the pressure injury registry. A decision tree and best subset logistic regression were used to select predictors from demographic and clinical candidate variables, which were then used to construct the Shieh Score.

RESULTS
The final Shieh Score included the following measures: sex, age, diabetes, glomerular filtration rate, albumin level, level of function, use of IV norepinephrine, mechanical ventilation, and level of consciousness. The Shieh Score had a higher Youden Index, specificity, and positive predictive value than the Braden Scale. However, the Braden Scale had a higher sensitivity compared with the Shieh Score.

CONCLUSIONS
The Shieh Score is an alternative risk assessment tool that may effectively identify a smaller number of patients at high risk for hospital-acquired pressure injuries with a higher specificity and positive predictive value than the Braden Scale.