bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutation rate and spectrum in obligately outcrossing Caenorhabditis elegans mutation accumulation lines subjected to RNAi-induced knockdown of the mismatch repair gene msh-2
Authors: Katju Vaishali , Konrad Anke , Deiss Thaddeus C , Bergthorsson Ulfar 
Published: October 2021

Abstract
DNA mismatch repair (MMR), an evolutionarily conserved repair pathway shared by prokaryotic and eukaryotic species alike, influences molecular evolution by detecting and correcting mismatches, thereby protecting genetic fidelity, reducing the mutational load, and preventing lethality. Herein we conduct the first genome-wide evaluation of the alterations to the mutation rate and spectrum under impaired activity of the MutSα homolog, msh-2, in Caenorhabditis elegans male–female fog-2(lf) lines. We performed mutation accumulation (MA) under RNAi-induced knockdown of msh-2 for up to 50 generations, followed by next-generation sequencing of 19 MA lines and the ancestral control. msh-2 impairment in the male–female background substantially increased the frequency of nuclear base substitutions (∼23×) and small indels (∼328×) relative to wildtype hermaphrodites. However, we observed no increase in the mutation rates of mtDNA, and copy-number changes of single-copy genes. There was a marked increase in copy-number variation of rDNA genes under MMR impairment. In C. elegans, msh-2 repairs transitions more efficiently than transversions and increases the AT mutational bias relative to wildtype. The local sequence context, including sequence complexity, G + C-content, and flanking bases influenced the mutation rate. The X chromosome exhibited lower substitution and higher indel rates than autosomes, which can either result from sex-specific mutation rates or a nonrandom distribution of mutable sites between chromosomes. Provided the observed difference in mutational pattern is mostly due to MMR impairment, our results indicate that the specificity of MMR varies between taxa, and is more efficient in detecting and repairing small indels in eukaryotes relative to prokaryotes.
Chromosome-level genome assemblies of Channa argus and Channa maculata and comparative analysis of their temperature adaptability
Authors: Ou Mi , Huang Rong , Yang Cheng , Gui Bin , Luo Qing , Zhao Jian , Li Yongming , Liao Lanjie , Zhu Zuoyan , Wang Yaping , Chen Kunci 
Published: October 2021

Abstract

Background
Channa argus and Channa maculata are the main cultured species of the snakehead fish family, Channidae. The relationship between them is close enough that they can mate; however, their temperature adaptability is quite different.

Results
In this study, we sequenced and assembled the whole genomes of C. argus and C. maculata and obtained chromosome-level genome assemblies of 630.39 and 618.82 Mb, respectively. Contig N50 was 13.20 and 21.73 Mb, and scaffold N50 was 27.66 and 28.37 Mb, with 28,054 and 24,115 coding genes annotated for C. argus and C. maculata, respectively. Our analyses showed that C. argus and C. maculata have 24 and 21 chromosomes, respectively. Three pairs of chromosomes in C. argus correspond to 3 chromosomes in C. maculata, suggesting that 3 chromosomal fusion events occurred in C. maculata. Comparative analysis of their gene families showed that some immune-related genes were unique or expandable to C. maculata, such as genes related to herpes simplex infection. Analysis of the transcriptome differences related to temperature adaptation revealed that the brain and liver of C. argus rapidly produced more differentially expressed genes than C. maculata. Genes in the FoxO signalling pathway were significantly enriched in C. argus during the cooling process (P &lt; 0.05), and the expression of 3 transcription factor genes in this pathway was significantly different between C. argus and C. maculata (P &lt; 0.01).

Conclusions
C. maculata may have higher resistance to certain diseases, whereas C. argus has a faster and stronger response to low-temperature stress and thus has better adaptability to a low-temperature environment. This study provides a high-quality genome research platform for follow-up studies of Channidae and provides important clues regarding differences in the low-temperature adaptations of fish.
Studying mutation rate evolution in primates—a need for systematic comparison of computational pipelines
Authors: Bergeron Lucie A , Besenbacher Søren , Schierup Mikkel H , Zhang Guojie 
Published: October 2021

AbstractThe lack of consensus methods to estimate germline mutation rates from pedigrees has led to substantial differences in computational pipelines in the published literature. Here, we answer Susanne Pfeifer's opinion piece discussing the pipeline choices of our recent article estimating the germline mutation rate of rhesus macaques (Macaca mulatta). We acknowledge the differences between the method that we applied and the one preferred by Pfeifer. Yet, we advocate for full transparency and justification of choices as long as rigorous comparison of pipelines remains absent because it is the only way to conclude on best practices for the field.
Regression of oesophageal varices in total anomalous pulmonary venous connection
Authors: Takahara Shingo , Masaki Naoki , Tatewaki Hideki , Sai Sadahiro 
Published: October 2021

Abstract
The coexisting of oesophageal varices with total anomalous pulmonary venous connection is extremely rare but contains a potential leading to a lethal haemorrhage. The fate of the oesophageal varices after total anomalous pulmonary vein connection repair remains largely unknown. We herein report a case with infracardiac type total anomalous pulmonary venous connection with remarkable oesophageal varices. In the present case, of note, the oesophageal varices were completely regressed after total anomalous pulmonary venous connection repair without any intervention. This case might help a surgical team reduce the hesitation to repair the total anomalous pulmonary venous connection regardless of oesophageal varices, a potentially fatal condition.
Hindgut fermentation of starch is greater for pulse grains than cereal grains in growing pigs
Authors: Tan Felina P Y , Wang Li Fang , Gao Jun , Beltranena Eduardo , Vasanthan Thava , Zijlstra Ruurd T 
Published: October 2021

AbstractThe nutritive value of starch, the major source of dietary energy in pigs, varies depending on its susceptibility for digestion. The botanical origin of starch determines starch structure, and therefore, digestibility. To compare digestibility of starch, fiber, gross energy (GE), crude protein, and amino acid (AA), and to characterize undigested starch of grains in growing pigs, seven ileal-cannulated barrows (initial body weight, 30 kg) were fed six diets containing 96% of one of six test ingredients (three pulse grains: zero-tannin faba bean, green field pea, or mixed-cultivar chickpea; three cereal grains: hulled barley, hard red spring wheat, or hybrid yellow, dent corn), or a N-free diet in a 7 × 7 Latin square at 2.8 × maintenance digestible energy. Grain samples were ground with a hammer mill through a 2.78-mm screen. Amylose content ranged from 29% to 34% for pulse grains and from 22% to 25% for cereal grains. The apparent ileal digestibility (AID) of starch was greater (P &lt; 0.05) in cereal (94% to 97%) than pulse grains (85% to 90%) and was lowest (P &lt; 0.05) in faba bean (85.3%) followed by field pea (87.2%) and chickpea (90.1%). However, apparent total tract digestibility (ATTD) of starch of all tested grains was close to 100%. Apparent hindgut fermentability (AHF, as ATTD − AID) of starch was greater (P &lt; 0.05) in pulse grains (9.9% to 15%) than cereal grains (3.3% to 4.8%). The AHF of total dietary fiber tended to be the greatest (P &lt; 0.10) for corn (43.5%) and lowest for wheat (25.3%). The AHF of GE was greater (P &lt; 0.05) in pulse grains (17% to 20%) than in cereal grains (9% to 11%) and resulted in greater (P &lt; 0.05) digestible energy (DE) contribution from hindgut fermentation for pulse grains than cereal grains (0.9 vs. 0.5 Mcal/kg). Wheat had the greatest standardized ileal digestibility of total AA (90.2%; P &lt; 0.05). Confocal laser scanning microscopy images revealed that 20% to 30% of starch granules of pulse grains were entrapped in protein matrixes. In scanning electron microscopy images, starch granules were larger in faba bean and field pea than cereal grains. Digesta samples revealed pin holes and surface cracks in starch granules of corn and wheat, respectively. In conclusion, hindgut fermentation of starch and fiber was greater in pulse grains than cereal grains resulting in a greater DE value despite lower ileal DE for pulse grain than cereal grains. Defining the digestible and fermentable fractions of starch may enhance the accuracy of equations to predict the net energy value of these feedstuffs.
The National Cancer Institute and Cannabis and Cannabinoids Research
Authors: Ellison Gary L , Alejandro Salicrup L , Freedman Andrew N , Fu Yali , Ross Sharon , Johnson Ronald L , Bakos Alexis , White Jeffrey D 
Published: October 2021

Abstract
The landscape of both recreational and medicinal cannabis use has changed dramatically over the past decade; however, research examining the risks and benefits of cannabis and cannabinoid use has lagged significantly behind the increased media promotion and their use by the general public and cancer patients. The National Cancer Institute (NCI) has supported cannabis-related research projects and funding opportunity announcements. In addition, NCI organized a virtual symposium on December 15-18, 2020, to discuss recent research findings on the use of cannabis and cannabinoids in relationship to cancer risk, prevention, and care. Specifically, the symposium sought to highlight the state of the science regarding cannabis, including the chemical constituents of cannabis (eg, cannabinoids), and cancer research involving cannabis, including cancer epidemiology, use in cancer patients, cancer biology and prevention, and preclinical and clinical cancer symptom and treatment side effect management with cannabis and cannabinoids as therapeutics. The symposium identified promising areas of future study, current barriers to conducting the research, and strategies to overcome those barriers. The series of papers in this special edition provide a summary of the symposium sessions as well as a synopsis of opportunities and challenges related to conducting research in this area.
Safety verification of carbon-ion radiotherapy for patients with cardiac implantable electronic devices (CIEDs)
Authors: Okano Naoko , Sakai Makoto , Shibuya Kei , Tsuda Kazuhisa , Kanzaki Takao , Sano Masato , Kaneko Yoshiaki , Ohno Tatsuya 
Published: October 2021

Abstract
According to guidelines, carbon-ion beam therapy is considered to carry a high safety risk for patients with cardiac implantable electronic devices (CIEDs), although the actual impacts remain unclear. In this study, we investigated the safety of carbon-ion beam therapy in patients with CIEDs. Patients with CIEDs who underwent carbon-ion therapy at Gunma University Heavy Ion Medical Center between June 2010 and December 2019 were identified and investigated for abnormalities in the operation of their CIEDs, such as oversensing and resetting during irradiation, and abnormalities in operation after treatment. In addition, the risk of irradiation from carbon-ion beam therapy was evaluated by model simulations. Twenty patients (22 sites) with CIEDs were identified, 19 with pacemakers and one with an implantable cardioverter-defibrillator (ICD). Treatments were completed without any problems, except for one case in which the treatment was discontinued because of worsening of the primary disease. Monte Carlo simulation indicated that the carbon beam irradiation produced neutrons at a constant and high level in the irradiation field. Nevertheless, with the distances between the CIEDs and the irradiation fields in the analyzed cases, the quantity of neutrons at the CIEDs was lower than that within the irradiation. Although carbon-ion beam therapy can be safely administered to patients with CIEDs, it is advisable to perform the therapy with sufficient preparation and backup devices because of the risks involved.
HMDB 5.0: the Human Metabolome Database for 2022
Authors: Wishart David S , Guo AnChi , Oler Eponine , Wang Fei , Anjum Afia , Peters Harrison , Dizon Raynard , Sayeeda Zinat , Tian Siyang , Lee Brian L , Berjanskii Mark , Mah Robert , Yamamoto Mai , Jovel Juan , Torres-Calzada Claudia , Hiebert-Giesbrecht Mickel , Lui Vicki W , Varshavi Dorna , Varshavi Dorsa , Allen Dana , Arndt David , Khetarpal Nitya , Sivakumaran Aadhavya , Harford Karxena , Sanford Selena , Yee Kristen , Cao Xuan , Budinski Zachary , Liigand Jaanus , Zhang Lun , Zheng Jiamin , Mandal Rupasri , Karu Naama , Dambrova Maija , Schiöth Helgi B , Greiner Russell , Gautam Vasuk 
Published: October 2021

AbstractThe Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological, physiological and chemical properties since 2007. Over the past 15 years, the HMDB has grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in internet and computing technology. This year's update, HMDB 5.0, brings a number of important improvements and upgrades to the database. These should make the HMDB more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of metabolite entries (from 114 100 to 217 920 compounds); (ii) enhancements to the quality and depth of metabolite descriptions; (iii) the addition of new structure, spectral and pathway visualization tools; (iv) the inclusion of many new and much more accurately predicted spectral data sets, including predicted NMR spectra, more accurately predicted MS spectra, predicted retention indices and predicted collision cross section data and (v) enhancements to the HMDB’s search functions to facilitate better compound identification. Many other minor improvements and updates to the content, the interface, and general performance of the HMDB website have also been made. Overall, we believe these upgrades and updates should greatly enhance the HMDB’s ease of use and its potential applications not only in human metabolomics but also in exposomics, lipidomics, nutritional science, biochemistry and clinical chemistry.
Evaluation of the Warrior Programme intervention among UK ex-service personnel
Authors: Thandi G , Phillips A , Greenberg N , Maguire N , Fear N T 
Published: October 2021

Abstract

Background
Research has shown that of the myriad services available to veterans in the UK, very few have been independently evaluated. This report presents the results of a randomized controlled trial assessing the impact of Time Line Therapy™ delivered by the Warrior Programme (a third-sector organization).

Aims
This study was aimed to determine if the intervention is effective in reducing emotional and functional difficulties in ex-service personnel.

Methods
A mixed-design analysis of variance model was used to investigate whether the Warrior Programme had a statistically significant impact on self-reported scores. The intervention and control group provided data on measures prior to and immediately after the intervention, and at 3-month follow-up.

Results
Those in the intervention group (n = 23) reported statistically significant improvements in self-reported scores immediately following intervention: the Clinical Outcomes in Routine Evaluation (CORE) scores (CORE global distress mean difference [MD] = 45.0, 95% confidence interval [CI] 31–60) (CORE subjective well-being MD = 5.9, 95% CI 3.5–8.3) (CORE functioning MD = 16.7, 95% CI 11.4–21.9) (CORE problems/symptoms MD = 19.4, 95% CI 13.1–25.7), general self-efficacy (MD = −9.8, 95% CI −13.6 to –6.8), anxiety (MD = 8.6, 95% CI 5.2–12.1), depression (MD = 10, 95% CI 6.6–13.5), post-traumatic stress disorder (MD = 26.3, 95% CI 17–25) and functional impairment (MD = 11.1, 95% CI 5.3–16.8) over time, compared to the control group (n = 29). However, score improvement was not sustained over time or statistically significant at follow-up.

Conclusions
The Warrior Programme was effective in reducing emotional and functional difficulties in ex-service personnel immediately after the intervention, but the effect was not sustained at 3-month follow-up.
Suprabulbar Approach to Jugular Fossa Tumors: 2-Dimensional Operative Video
Authors: Wu Kyle C , Aboud Emad , Al-Mefty Ossama 
Published: October 2021

Abstract
Owing to their scarcity, location, and intricate neurovascular associations, jugular fossa tumors are among the most challenging pathologies encountered by the neurosurgeon.
1
While paragangliomas originate within and often occlude the jugular bulb, schwannomas and meningiomas are extra-bulbar and typically do not impede venous flow.
2
Schwannomas typically arise from an extradural origin, expanding the jugular foramen.
3-5
Meningiomas are intradural and cause hyperostosis of the jugular tubercle.
6
We described and have been exposing and resecting jugular fossa tumors through a presigmoid suprabulbar infralabyrinthine window
6
that has been detailed in cadaveric studies.
7,8
This approach maintains the patency of the jugular bulb without breaching the labyrinths or manipulating the facial nerve. It is applicable to cases with partially impaired hearing and intact lower cranial nerves. The carotid artery can be identified by neuronavigation and micro-Doppler ultrasonography. This approach provides a direct lateral trajectory with a short distance to the jugular fossa and cerebellopontine angle. Early exposure and central debulking of the tumor minimize manipulation of the exquisitely sensitive lower cranial nerves. The distal aspect of these tumors can be removed with endoscopic assisted techniques.
9
The first patient is a 49-yr-old woman with a previously irradiated schwannoma who presented with worsening neurologic deficits—an extradural suprabulbar approach was used to resect this tumor. The second patient is a 27-yr-old woman with an enlarging meningioma and associated neurological dysfunction; this tumor was resected using the suprabulbar approach with opening of the presigmoid dura. Both patients have consented to surgery and publication of images.
Image at 2:27 and 6:38 reprinted from Arnautović et al, with permission from JNSPG. Image at 2:50 and 6:45 ©Ossama Al-Mefty 1997, reused with permission.
Auxin-Responsive (Phospho)proteome Analysis Reveals Key Biological Processes and Signaling Associated with Shoot-Borne Crown Root Development in Rice
Authors: Singh Harshita , Singh Zeenu , Zhu Tingting , Xu Xiangyu , Waghmode Bhairavnath , Garg Tushar , Yadav Shivani , Sircar Debabrata , De Smet Ive , Yadav Shri Ram 
Published: October 2021

Abstract
The rice root system is primarily composed of shoot-borne adventitious/crown roots (ARs/CRs) that develop from the coleoptile base, and therefore, it is an excellent model system for studying shoot-to-root trans-differentiation process. We reveal global changes in protein and metabolite abundance and protein phosphorylation in response to an auxin stimulus during CR development. The liquid chromatography–tandem mass spectrometry (LC–MS/MS) and gas chromatography–mass spectrometry (GC–MS) analyses of developing crown root primordia (CRP) and emerged CRs identified 334 proteins and 12 amino acids, respectively, that were differentially regulated upon auxin treatment. Gene ontology enrichment analysis of global proteome data uncovered the biological processes associated with chromatin conformational change, gene expression and cell cycle that were regulated by auxin signaling. Spatial gene expression pattern analysis of differentially abundant proteins disclosed their stage-specific dynamic expression pattern during CRP development. Further, our tempo-spatial gene expression and functional analyses revealed that auxin creates a regulatory module during CRP development and activates ethylene biosynthesis exclusively during CRP initiation. Further, the phosphoproteome analysis identified 8,220 phosphosites, which could be mapped to 1,594 phosphoproteins and of which 66 phosphosites were differentially phosphorylated upon auxin treatment. Importantly, we observed differential phosphorylation of the cyclin-dependent kinase G-2 (OsCDKG;2) and cell wall proteins, in response to auxin signaling, suggesting that auxin-dependent phosphorylation may be required for cell cycle activation and cell wall synthesis during root organogenesis. Thus, our study provides evidence for the translational and post-translational regulation during CR development downstream of the auxin signaling pathway.
DISTRIBUTION OF RADON AND URANIUM LEVELS IN GROUNDWATER OF DISTRICT PALWAL, SOUTHERN HARYANA, INDIA
Authors: Singh Bhupender , Kant Krishan , Garg Maneesha 
Published: October 2021

Abstract
Scintillation-detector-based SMART RnDuo (AQTEK System, India) and LED fluorimeter (Quantalase Instrument, India) were used for measurements of radon and uranium concentration in 54 groundwater samples collected from different locations in the Palwal district of Haryana (India). Radon in 26% and uranium in 54% of samples were found to be at higher levels than the maximum contamination limit (11 Bq l−1) for drinking water recommended by US Environmental Protection Agency and provisional guideline level (30 μg l−1) stated by World Health Organization.
Association between oral health and cardiovascular outcomes in patients with hypertension: a nationwide cohort study
Authors: Kim Jinkwon , Kim Hyung Jun , Jeon Jimin , Song Tae-Jin 
Published: October 2021

Objective:
Studies on the association of oral hygiene indicators with cardiovascular disease in hypertensive patients have been lacking. Oral hygiene is directly or indirectly associated with systemic inflammation, one of the essential mechanisms of cardiovascular disease. Therefore, we hypothesized that oral hygiene would be related to the risk of cardiovascular diseases in hypertensive patients.

Methods:
We included 52 677 hypertensive participants who completed oral health checkups from the Korean National Health Insurance Service-National Health Screening Cohort between 2003 and 2004. We collected data on periodontitis diagnosis and treatment history, number of teeth loss, number of dental caries, and frequency of tooth brushing from medical records of health claims and oral health examination. The primary outcome was defined as composite outcomes of stroke and myocardial infarction. Follow-up was done until the date of primary outcome, or 31 December 2015.

Results:
During the 11.26 ± 2.39 years (mean ± standard deviation) of the study follow-up, 3292 participants developed primary outcomes [stroke (n = 2430), myocardial infarction (n = 862)]. In multivariable Cox regression analyses, participants with dental caries (≥ 5) were independently associated with occurrence of a primary outcome [adjusted hazard ratio: 1.37; 95% confidence interval (CI):1.10–1.72; P = 0.006]. Frequent tooth brushing (≥ 2 times/day) was significantly related to lower risk of primary outcomes (adjusted hazard ratio: 0.88; 95% CI: 0.81–0.96; P = 0.002).

Conclusion:
Our study demonstrated that multiple dental caries were related to the risk of cardiovascular diseases in hypertensive patients. Better oral hygiene may attenuate the risk of cardiovascular events in hypertensive patients.