bluuebunny/crossref_metadata_2025_split huggingface dataset:
The environments and hosts of metal absorption at z &gt; 5
Authors: Doughty Caitlin C , Finlator Kristian M 
Published: November 2022

ABSTRACT
A growing population of metal absorbers are observed at z &gt; 5, many showing strong evolution in incidence approaching the epoch of hydrogen reionization. Follow-up surveys examining fields around these metals have resulted in galaxy detections but the direct physical relationship between the detected galaxies and absorbers is unclear. Upcoming observations will illuminate this galaxy–absorber relationship, but the theoretical framework for interpreting these observations is lacking. To inform future z &gt; 5 studies, we define the expected relationship between metals and galaxies using the Technicolor Dawn simulation to model metal absorption from z = 5 to 7, encompassing the end of reionization. We find that metal absorber types and strengths are slightly better associated with their environment than with the traits of their host galaxies, as absorption system strengths are more strongly correlated with the local galaxy overdensity than the stellar mass of their host galaxy. For redshifts prior to the end of the epoch of reionization, strong high-ionization transitions like C iv are more spatially correlated with brighter galaxies on scales of a few hundred proper kpc than are low-ionization systems, due to the former’s preference for environments with higher ultraviolet background amplitudes and those ions’ relative rarity at z &gt; 6. Post-reionization, the galaxy counts near these high-ionization ions are reduced, and increase surrounding certain low-ionization ions due to a combination of their relative abundances and preferred denser gas phase. We conclude that galaxy–absorber relationships are expected to evolve rapidly such that high-ionization absorbers are better tracers of galaxies pre-reionization, while low-ionization absorbers are better post-reionization.
DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology
Authors: Zhang Yuxin , Jiang Jie , Ma Jiongming , Wei Zhen , Wang Yue , Song Bowen , Meng Jia , Jia Guifang , de Magalhães João Pedro , Rigden Daniel J , Hang Daiyun , Chen Kunqi 
Published: November 2022

Abstract
With advanced technologies to map RNA modifications, our understanding of them has been revolutionized, and they are seen to be far more widespread and important than previously thought. Current next-generation sequencing (NGS)-based modification profiling methods are blind to RNA modifications and thus require selective chemical treatment or antibody immunoprecipitation methods for particular modification types. They also face the problem of short read length, isoform ambiguities, biases and artifacts. Direct RNA sequencing (DRS) technologies, commercialized by Oxford Nanopore Technologies (ONT), enable the direct interrogation of any given modification present in individual transcripts and promise to address the limitations of previous NGS-based methods. Here, we present the first ONT-based database of quantitative RNA modification profiles, DirectRMDB, which includes 16 types of modification and a total of 904,712 modification sites in 25 species identified from 39 independent studies. In addition to standard functions adopted by existing databases, such as gene annotations and post-transcriptional association analysis, we provide a fresh view of RNA modifications, which enables exploration of the epitranscriptome in an isoform-specific manner. The DirectRMDB database is freely available at: http://www.rnamd.org/directRMDB/.
Passing the buck!—how credible are self-reported measures of confidence in public institutions?
Authors: Chatterjee Somdeep 
Published: November 2022

Abstract
Measures of confidence in public institutions are self-reported and therefore, susceptible to heterogeneity arising out of individual perceptions. In this article, I explore the possibility of individuals reporting lower levels of confidence in public institutions depending on their personal economic conditions, for which these institutions cannot be solely held responsible. Using nationally representative Indian data, I exploit exogenous sources of indebtedness in an instrumental variables regression approach to identify the causal effects of personal economic hardships on confidence in public institutions. The identification strategy relies on exogenous variation in the measure of indebtedness generated by a large monetary loss arising out of natural calamities such as accident, fire, or drought. I find that estimated coefficients from two-stage least square regressions are negative and statistically significant suggesting that an increase in indebtedness is associated with an erosion in confidence measures.
Academic achievements and brain volume development in children and adolescents
Authors: Hashimoto Teruo , Matsuzaki Yutaka , Yokota Susumu , Kawashima Ryuta 
Published: November 2022

Abstract
Children are expected to acquire both basic and numeric skills. Achievement of higher levels of reading, writing, arithmetic, and vocabulary are favorable and desirable. The relationship between each literacy skill and neural development has been investigated; however, association between brain development and the 4 literacy skills has not been examined. This longitudinal, structural, neuroimaging study explored the contribution of higher academic achievement in reading, writing, arithmetic, and vocabulary to neural development. The brain volumes of children and adolescents aged 9–16 years were measured in the first test. Approximately 2.6 years later, the brain volumes and 4 academic achievement scores of 77 participants were measured in the second test. Changes in the gray matter volume in the left fusiform gyrus were associated with vocabulary scores, whereas those in the left striatum were associated with arithmetic scores. The reading and writing scores showed no statistically significant relationship with changes in brain volume. The current vocabulary score correlated with current gray matter volume, while brain volumes in the first test showed no association with any achievement scores. These results suggest that academic achievement may modulate brain plasticity in various ways.
Complete Genome Sequence Resource of the Pathogen Pectobacterium cacticida CFCC 10813T Causing Soft Rot Diseases of Cactus Plants
Authors: Xie Ting , Zhu Huajie , Liao Tianlan , Liang Yan , An Qianli 
Published: November 2022

Pectobacterium cacticida (formerly Erwinia cacticida) causes soft rot disease of cactus plants. Its taxonomic status within the genus Pectobacterium remains questionable because no whole genome sequence of this species is available in public databases for reliable taxonomic analyses. Here, we present the complete genome sequence of the P. cacticida type strain CFCC 10813T (=1-12T = ATCC 49481T). P. cacticida can be classified into the genus Pectobacterium because it is on the deepest basal phylogenomic branch of the genus Pectobacterium, and its genome relatedness to other Pectobacterium species is at the border for the genus delimitation boundaries. This complete genome sequence provides the genome resource for elucidating P. cacticida pathogenicity and adaptation to plant hosts and environments. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Ventilation Strategies During Extracorporeal Membrane Oxygenation for Neonatal Respiratory Failure: Current Approaches Among Level IV Neonatal ICUs
Authors: Ibrahim John , Mahmood Burhan , DiGeronimo Robert , Rintoul Natalie E. , Hamrick Shannon E. , Chapman Rachel , Keene Sarah , Seabrook Ruth B. , Billimoria Zeenia , Rao Rakesh , Daniel John , Cleary John , Sullivan Kevin , Gray Brian , Weems Mark , Dirnberger Daniel R. ,   for the CHNC ECMO Focus Group
Published: November 2022

OBJECTIVES:
To describe ventilation strategies used during extracorporeal membrane oxygenation (ECMO) for neonatal respiratory failure among level IV neonatal ICUs (NICUs).

DESIGN:
Cross-sectional electronic survey.

SETTING:
Email-based Research Electronic Data Capture survey.

PATIENTS:
Neonates undergoing ECMO for respiratory failure at level IV NICUs.

INTERVENTIONS:
A 40-question survey was sent to site sponsors of regional referral neonatal ECMO centers participating in the Children’s Hospitals Neonatal Consortium. Reminder emails were sent at 2- and 4-week intervals.

MEASUREMENTS AND MAIN RESULTS:
Twenty ECMO centers responded to the survey. Most primarily use venoarterial ECMO (65%); this percentage is higher (90%) for congenital diaphragmatic hernia. Sixty-five percent reported following protocol-based guidelines, with neonatologists primarily responsible for ventilator management (80%). The primary mode of ventilation was pressure control (90%), with synchronized intermittent mechanical ventilation (SIMV) comprising 80%. Common settings included peak inspiratory pressure (PIP) of 16–20 cm H2O (55%), positive end-expiratory pressure (PEEP) of 9–10 cm H2O (40%), I-time 0.5 seconds (55%), rate of 10–15 (60%), and Fio
2 22–30% (65%). A minority of sites use high-frequency ventilation (HFV) as the primary mode (5%). During ECMO, 55% of sites target some degree of lung aeration to avoid complete atelectasis. Fifty-five percent discontinue inhaled nitric oxide (iNO) during ECMO, while 60% use iNO when trialing off ECMO. Nonventilator practices to facilitate decannulation include bronchoscopy (50%), exogenous surfactant (25%), and noninhaled pulmonary vasodilators (50%). Common ventilator thresholds for decannulation include PEEP of 6–7 (45%), PIP of 21–25 (55%), and tidal volume 5–5.9 mL/kg (50%).

CONCLUSIONS:
The majority of level IV NICUs follow internal protocols for ventilator management during neonatal respiratory ECMO, and neonatologists primarily direct management in the NICU. While most centers use pressure-controlled SIMV, there is considerable variability in the range of settings used, with few centers using HFV primarily. Future studies should focus on identifying respiratory management practices that improve outcomes for neonatal ECMO patients.
Assessment of visual field progression in glaucoma
Authors: Chen Rebecca I. , Gedde Steven J. 
Published: November 2022

Purpose of review
Perimetry plays an important role in the diagnosis and management of glaucoma. This article discusses the assessment of visual field progression in patients with glaucoma.

Recent findings
Selecting the best visual field test strategy and establishing a baseline of visual fields will assist clinicians in the detection of glaucomatous progression. Repeat testing serves to confirm or refute changes on visual field testing. More frequent testing after initial diagnosis is recommended to establish a baseline and to identify patients with rapid progression who may need more aggressive management. Statistically significant changes on event analysis can prompt examination of a patient's trend analysis to determine whether clinically significant deterioration may be occurring. Future applications of machine learning can complement existing methods of visual field interpretation.

Summary
Many treated patients with glaucoma will experience visual field progression. Optimal utilization of visual field testing strategy and analytical software can help clinicians identify patients with glaucomatous progression likely to cause functional visual disability.
Hybrid Ga-68 prostate-specific membrane antigen PET/MRI in the detection of skeletal metastasis in patients with newly diagnosed prostate cancer: Contribution of each part to the diagnostic performance
Authors: Asa Sertac , Ozgur Eren , Uslu-Besli Lebriz , Ince Burak , Sager Sait , Demirdag Cetin , Guner Ekrem , Sayman Haluk B. , Bakir Baris , Sonmezoglu Kerim 
Published: November 2022

Purpose
Bone metastasis is essential in patients with prostate cancer (PCa) as it determines prognosis and survival. Hybrid PET/MRI allows simultaneous acquisition of PET and MRI data, thus combining the strength of both technologies allows the detection of bone marrow metastases that are missed by PET/CT. In this retrospective study, we aimed to evaluate the diagnostic efficiency of hybrid PET/MRI with Ga-68 prostate-specific membrane antigen (PSMA) in detecting skeletal metastases in newly diagnosed PCa patients and compared the effectiveness of stand-alone PSMA PET reviewing versus stand-alone whole-body (WB) MRI evaluation. We also investigated the effect of the interpretation of all PET/MR data together on clinical management.

Methods
We studied 74 newly diagnosed PCa patients who underwent PSMA PET/MRI for staging purposes. At first, PET and MRI were evaluated separately for bone lesions on a patient-and-lesion basis and then a further joint PSMA PET/MRI interpretation was made.

Results
Patient-based sensitivity, specificity, positive predictive value, negative predictive value and accuracy analysis for bone metastasis was, respectively, 1.0, 0.83, 0.54, 1.0, 0.86 for PET; 0.75, 0.96, 0.81, 0.95, 0.93 for WB MRI and 0.91, 0.95, 0.78, 0,98, 0.94 for PET/MRI. The combined PET/MRI evaluation changed the clinical impact in 13.5% of patients (eight correct and two wrong decisions) compared to PET stand-alone interpretation.

Conclusion
PSMA PET imaging showed superior sensitivity to WB MRI in detecting bone metastases in newly diagnosed PCa patients, whereas WB MRI has superior specificity and PPV. Furthermore, the specificity and PPV of joint PET/MRI evaluation are better than PSMA PET alone. Despite the longer acquisition period, adding WB MRI sequences to PSMA PET imaging appears beneficial for PCa patient management.
The great team: A recipe
Authors: Rosengart Matthew R. 
Published: November 2022

ABSTRACT
When do the many become one? Why does one join with others? In his political writings of self-government, Rousseau proposes “when the obstacles to their self-preservation in the state of nature are too great to be overcome by the forces each individual is capable of exerting to maintain himself in that state.” Few obstacles are more threatening to an individual than disease and death, and our response as a civilization is the institution of healthcare. The impetus for this perspective piece budded from personal experience and a resultant sentiment that emerged from more deliberate contemplation. It is purposed to conjure in the reader a certain joy of that which can be accomplished through collaboration, but concomitantly, to offer perspective as to characteristics opined to be vital to creating and maintaining a great team.
Non-parametric GWAS: Another View on Genome-wide Association Study
Authors: Hu Xiaoyue , Yu Shizhou , Jiang Hangjin 
Published: November 2022

AbstractGenome-wide association study (GWAS) is a fundamental step for understanding the genetic link to traits (phenotypes) of interest, such as disease, BMI and height. Typically, GWAS estimates the effect of SNP on the phenotype using a linear model by coding SNP as working code, {0, 1, 2}, according to the minor allele frequency. Looking inside the linear model, we find that the coding strategy of SNP plays a key role in detecting SNPs contributed to the phenotype. Specifically, a partial mismatch between the order of the working code and that of the underlying true code will lead to false negatives, which has been ignored for a long time. Motivated by this phenomenon, we propose an indicator of possible false negatives and several non-parametric GWAS methods independent of coding strategy. Results from both simulations and real data analysis show the advantages of new methods in identifying significant loci, indicating their important complementary role in GWAS.
Buffering role of HSP shapes the molecular evolution of mammalian and human genomes at short and long-term scales
Authors: Timonina Valeriia , Tretiakov Evgenii , Goncharov Andrey , Gunbin Konstantin , Fellay Jacques , Popadin Konstantin 
Published: November 2022

ABSTRACTHeat shock proteins in parallel with their main and originally discovered function – maintenance of folded proteins under stressful conditions, can play also background buffering role – by folding proteins with an excess of slightly-deleterious nonsynonymous variants (SDNV). Here we tested several scenarios of this buffering role. On the comparative species scale, we demonstrated that low-Ne species are characterized by a higher expression level of hsp90 which can be explained by the excess of SDNV. On the comparative tissue level, we showed that long-lived tissues have also a higher hsp90 expression level, which can be advantageous to maintain the functionality of proteins. On the comparative gene level, we demonstrated that purifying selection of hsp90 in low-Ne-species did not relax as strongly as it happens for control genes, similar to hsp90. Additionally, we demonstrated that hsp clients versus non-clients are characterised by decreased level of selective constraints; demonstrate stronger relaxation of purifying selection in low-Ne species; have an excess of slightly-deleterious variants associated with complex disease phenotypes in humans; have an excess of pathological variants associated with clinical phenotypes in humans, suggesting that clients, being buffered by hsp90 can degenerate a bit more as compared to non-clients. Altogether, our results show that the secondary role of hsp, buffering of SDNV, is widespread and universal affecting properties of species, tissues and genes. A deep understanding of the buffering role of hsp90 will help to predict the deleterious effect of each variant in the human genome more precisely as well as will extend the application of the effectively-neutral theory of molecular evolution.
Computational Design of a New Aflatoxin B1 Aptamerin lieuof SELEX Technique
Authors: Ahmad Ghazy Mohamad Yasser 
Published: November 2022

AbstractMycotoxins are extremely dangerous, and their detection in our environment, food and feed is becoming increasingly important. Biosensors are being implemented heavily in mycotoxin detection along with other significant applications. Aptamers have numerous beneficial advantages as biorecognition molecules and are being used as the biorecognition part of biosensors (Aptasensors). The development of aptamers does not require inducing immune response against the target, but the SELEX method is used. The SELEX method is laborious, time consuming and can be expensive at times. Various efforts were done to replace that method with a computational alternative to reduce the effort, time and money needed to develop and design aptamers. One of the most significant efforts to achieve that was the MAWS algorithm. We used the MAWS algorithm to develop a new aptamer against aflatoxin B1, the most dangerous mycotoxin. The MAWS algorithm failed to function properly, and molecular modelling and molecular docking was used alternatively to achieve the same goal. A new pipeline for predicting ssDNA aptamers was proposed, a new aptamer against aflatoxin B1 was obtained and recommendations for further future research directions were given.
Viral Airway Injury Promotes Cell Engraftment in anIn VitroModel of Cystic Fibrosis Cell Therapy
Authors: Lee Rhianna E. , Mascenik Teresa M. , Major Sidra C. , Lewis Catherine A. , Bear James E. , Pickles Raymond J. , Randell Scott H. 
Published: November 2022

AbstractCell therapy is a potential treatment for cystic fibrosis (CF). However, cell engraftment into the airway epithelium is challenging. Here, we model cell engraftmentin vitrousing the air-liquid interface (ALI) culture system by injuring well-differentiated CF ALI cultures and delivering non-CF cells at the time of peak injury. Engraftment efficiency was quantified by measuring chimerism by droplet digital PCR and functional ion transport in Ussing chambers. Using this model, we found that human bronchial epithelial cells (HBECs) engraft more efficiently when they are cultured by conditionally reprogrammed cell (CRC) culture methods. Cell engraftment into the airway epithelium requires airway injury, but the extent of injury needed is unknown. We compared three injury models and determined that severe injury with partial epithelial denudation facilitates long-term cell engraftment and functional CFTR recovery up to 20% of wildtype function. The airway epithelium promptly regenerates in response to injury, creating competition for space and posing a barrier to effective engraftment. We examined competition dynamics by time-lapse confocal imaging and found that delivered cells accelerate airway regeneration by incorporating into the epithelium. Irradiating the repairing epithelium granted engrafting cells a competitive advantage by diminishing resident stem cell proliferation. Intentionally causing severe injury to the lungs of people with CF would be dangerous. However, naturally occurring events like viral infection can induce similar epithelial damage with patches of denuded epithelium. We found that viral preconditioning promoted effective engraftment of cells primed for viral resistance.
Formation process of the twinning β-form anhydrous guanine platelets in the scallop eyes
Authors: Guo Dongmei , Liu Yiqun , Hou Xiubin , Wang Xubo , Fan Chenge , Bao Lixia , He Xinpeng , Zhang Hongmei , Ma Yurong 
Published: November 2022

AbstractSquare shaped twinning guanine microplates with high symmetry are assembled into highly ordered layered patterns and function as image-forming mirrors in the scallop eyes. However, the formation process and biomineralization mechanism of twinning guanine microplatelets are still unclear. Herein, the eyes of juvenileYessoscallops were investigated to understand the formation mechanism of the twinning β-form anhydrous guanine (β-AG) microplatelets exposing (100) plane. We find α form anhydrous guanine (α-AG) and single-crystal β-AG nanoplatelets in the very early stage of the eyes of the juvenile scallops, while the α-AG was supposed to be formed via amorphous guanine during the sample preparation process. Besides β-AG and α-AG, amorphous guanine was found in the eyes of juvenile scallops with size of 2.5 mm according to the Raman spectra. A formation mechanism was proposed for the biogenic twinning guanine platelets. Firstly, amorphous guanine is formed as an intermediate phase, which transforms into single crystalline β-AG nanoplatelets, or, dissolve and recrystallize to single crystalline β-AG nanoplatelets. Then, a second layer of β-AG forms on the top of the original single crystalline β-AG nanoplatelets, forming twinning β-AG nanoplatelets with twocaxes with a certain angle, 83° or 14°. Each layer of the β-AG nanoplatelets is calculated to be about 14 ± 2 nm. This is the first time to report the formation mechanism of biogenic twinning β-AG microplatelets. Uncovering the formation mechanism of twinning platelets of organic crystals may shed light on the formation of functional synthetic twinning organic crystals in the laboratories.