bluuebunny/crossref_metadata_2025_split huggingface dataset:
De Novo Genome Assembly Highlights the Role of Lineage-Specific Gene Duplications in the Evolution of Venom in Fea's Viper (Azemiops feae)
Authors: Myers Edward A , Strickland Jason L , Rautsaw Rhett M , Mason Andrew J , Schramer Tristan D , Nystrom Gunnar S , Hogan Michael P , Yooseph Shibu , Rokyta Darin R , Parkinson Christopher L 
Published: June 2022

AbstractDespite the medical significance to humans and important ecological roles filled by vipers, few high-quality genomic resources exist for these snakes outside of a few genera of pitvipers. Here we sequence, assemble, and annotate the genome of Fea’s Viper (Azemiops feae). This taxon is distributed in East Asia and belongs to a monotypic subfamily, sister to the pitvipers. The newly sequenced genome resulted in a 1.56 Gb assembly, a contig N50 of 1.59 Mb, with 97.6% of the genome assembly in contigs &gt;50 Kb, and a BUSCO completeness of 92.4%. We found that A. feae venom is primarily composed of phospholipase A2 (PLA2) proteins expressed by genes that likely arose from lineage-specific PLA2 gene duplications. Additionally, we show that renin, an enzyme associated with blood pressure regulation in mammals and known from the venoms of two viper species including A. feae, is expressed in the venom gland at comparative levels to known toxins and is present in the venom proteome. The cooption of this gene as a toxin may be more widespread in viperids than currently known. To investigate the historical population demographics of A. feae, we performed coalescent-based analyses and determined that the effective population size has remained stable over the last 100 kyr. This suggests Quaternary glacial cycles likely had minimal influence on the demographic history of A. feae. This newly assembled genome will be an important resource for studying the genomic basis of phenotypic evolution and understanding the diversification of venom toxin gene families.
Random Peptides Rich in Small and Disorder-Promoting Amino Acids Are Less Likely to Be Harmful
Authors: Kosinski Luke J , Aviles Nathan R , Gomez Kevin , Masel Joanna 
Published: June 2022

Abstract
Proteins are the workhorses of the cell, yet they carry great potential for harm via misfolding and aggregation. Despite the dangers, proteins are sometimes born de novo from noncoding DNA. Proteins are more likely to be born from noncoding regions that produce peptides that do little to no harm when translated than from regions that produce harmful peptides. To investigate which newborn proteins are most likely to “first, do no harm,” we estimate fitnesses from an experiment that competed Escherichia coli lineages that each expressed a unique random peptide. A variety of peptide metrics significantly predict lineage fitness, but this predictive power stems from simple amino acid frequencies rather than the ordering of amino acids. Amino acids that are smaller and that promote intrinsic structural disorder have more benign fitness effects. We validate that the amino acids that indicate benign effects in random peptides expressed in E. coli also do so in an independent data set of random N-terminal tags in which it is possible to control for expression level. The same amino acids are also enriched in young animal proteins.
Press tack needle stimulation for blunt chest trauma: a randomized double-blind control trial
Authors: Kao Pei-Yu , Lottering Bernice , Lu Ting-Yu , Ho Wen-Chao , Lin Yu-Sen , Huang Tzu-Min , Chen Chien-Kuang , Chen Jian-Xun , Lee Yu-Chen , Chen Fang-Pey , Ben-Arie Eyal 
Published: June 2022

Abstract

OBJECTIVES
Blunt chest trauma is often associated with severe pain, reduced lung function and decreased sleep quality. This study aims to investigate the immediate and long-term effect of acupuncture on these factors using a randomized control double-blind design.

METHODS
A total of 72 patients were randomized into 2 groups: treatment group (press tack acupuncture) and control group (press tack placebo). The face rating scale, numerical rating scale (NRS), portable incentive spirometer and Verran Snyder-Halpern sleep scale were measured at baseline, immediately after the intervention, and at the 4th day, with 2-weeks and 3-months follow-ups.

RESULTS
There were no significant changes between the groups at the baseline measurements, with the exception of hypertension comorbidity. Immediately after the intervention and on the 4th day follow-up, the patients in the treatment group showed a significantly lower face rating scale when compared to the control (P &lt; 0.05). There were no significant changes in any of the other measurements between the groups (P &gt; 0.05). Subgroup analysis revealed that the NRS for turn over on the 4th day was reduced significantly in the treatment group of patients without lung contusion (P &lt; 0.05). For patients without pleural drainage, cough NRS in the treatment group was significantly reduced in the 2-week follow-up (P &lt; 0.05).

CONCLUSIONS
This study showed that press tack acupuncture effects on pain reduction were inconclusive. However, future studies on the effect of acupuncture on blunt chest trauma patients are needed.

Clinical trial registration
clinicaltirl.gov: NCT04318496.
Gradual Decline of Japanese Beetle (Coleoptera: Scarabaeidae) Populations in Michigan Follows Establishment of Ovavesicula popilliae (Microsporidia)
Authors: Smitley D , Hotchkiss E , Buckley K , Piombiono M , Lewis P , Studyvin J 
Published: June 2022

Abstract
The purpose of this research was to document the incidence of Japanese beetle, Popillia japonica Newman (Coleoptera: Scarabaeidae), infection by the microsporidian pathogen, Ovavesicula popilliae Andreadis & Hanula (Microsporida: Pleistophoridae) while monitoring Japanese beetle populations at nine golf courses in Michigan from 1999 to 2018. We also compared the current distribution of the pathogen in Michigan to the known distribution in 1999. Beetles were sampled a total of seven different years, in three time periods: 1999–2000, 2005–2007, and 2015–2018. At these nine golf courses, O. popilliae infection rates of adults increased from 0.39% in 2000 to 29.5% in 2018, while Japanese beetle adult populations declined 73.2%, and Japanese beetle larval density declined 78.6% (from 1999 to 2018). In previous research, larval infection rates averaged at least twice the infection rates of adults, because all infections originate in the larval stage, and at least 75% of infected larvae die before pupation. This means that an adult infection rate of 29.5%, combined with previously observed 50% reductions in egg production by infected females, are consistent with the observed population declines. The current distribution of O. popilliae in southern Michigan was determined by sampling Japanese beetle larvae and adults at 38 sites in 2017 and 2018. Ovavesicula popilliae was found at 21 of 38 sites and in 16 of 21 counties, compared with two sites in one of 16 counties when it was first detected in Michigan in 1999 and 2000.
Osteofibrous dysplasia-like adamantinoma of isolated fibula in a child mimicking chronic osteomyelitis with pathological fracture
Authors: Goetz Pierre-Emmanuel , Dumitriu Dana , Galant Christine , Docquier Pierre-Louis 
Published: June 2022

Abstract
The occurrence of a pathological fracture in children requires a rigorous diagnostic approach in order to establish the etiology and to develop a precise therapeutic strategy. Several causes are associated with these fractures, the most frequent being benign tumors in children in developed countries and chronic osteomyelitis in developing countries. More rarely, malignant tumors must however always be considered. The differential diagnosis on imaging may be difficult to establish between bone tumors and chronic infection. Surgical biopsy is therefore often performed to establish the precise origin of the fracture. We report the case of an adamantinoma (osteofibrous dysplasia-like) of the fibula in a 7-year-old child, discovered during the management of a pathologic fracture. The presumed diagnosis before biopsy was chronic osteomyelitis. A 14-cm-resection of the affected fibula was performed with good functional result. Differential diagnosis between adamantinoma, osteofibrous dysplasia and osteofibrous dysplasia-like adamantinoma remains very challenging.
Diagnostic Accuracy of the Boston Assessment of Traumatic Brain Injury-Lifetime Clinical Interview Compared to Department of Defense Medical Records
Authors: Kim Sahra , Currao Alyssa , Fonda Jennifer R , Beck Brigitta , Kenna Alexandra , Fortier Catherine B 
Published: June 2022

ABSTRACT

Introduction
Since 2006, efforts have been made to increase the accurate identification of traumatic brain injuries (TBIs) in post-9/11 military personnel. The Boston Assessment of TBI-Lifetime (BAT-L) is the first validated instrument designed specifically to diagnose TBIs throughout the life span in post-9/11 Veterans. The objective was to compare the diagnostic accuracy of the BAT-L with medical records from the Department of Defense (DoD).

Material and Methods
Traumatic brain injury diagnosis for 153 Veterans deployed in 2011 enrolled in the Translational Research Center for TBI and Stress Disorder longitudinal cohort study from the BAT-L clinical interview was compared to DoD online medical records to determine diagnostic prevalence and injury severity for all head injury cases during deployment. Sensitivity, specificity, Cohen’s kappa, and Kendall’s tau-b were calculated for TBI diagnosis and severity. Concordant TBI cases and discordant TBI cases were compared using chi-square and t-test analyses. This study has been approved by VA Boston by Institutional Review Boards for human participants’ protection.

Results
Correspondence of TBI diagnoses from the BAT-L with DoD records was fair (κ = 0.42; sensitivity = 72.7%; specificity = 82.8%). Comparison of injury severity also showed fair correspondence (κ = 0.41). Missing TBI diagnostic data from DoD records were frequent; 43% of TBIs reported on the BAT-L did not have any documentation of assessment or diagnoses in DoD records.

Conclusion
This study addresses a critical gap in research by comparing the diagnostic accuracy of a validated, semi-structured clinical interview with available medical records. Diagnosis of TBIs via the BAT-L was both sensitive and specific when compared to DoD records, supporting the validity of the BAT-L for retrospective assessment of military TBI. However, diagnostic correspondence was only fair. This lack of diagnostic agreement was related to multiple factors including lack of documentation at the time of injury by DoD, differences in assessment and goals, and other combat-related motivational factors associated with failure to report injuries while deployed. Several policies have been implemented to address underreporting and under-documentation of TBIs, yet challenges remain. Recommendations for evaluating TBI are presented. Accurate diagnosis of TBI is necessary for appropriate treatment planning, as well as service-related compensation.
Realistic synthetic integral field spectroscopy with RealSim-IFS
Authors: Bottrell Connor , Hani Maan H 
Published: June 2022

ABSTRACT
The most direct way to confront observed galaxies with those formed in numerical simulations is to forward-model simulated galaxies into synthetic observations. Provided that synthetic galaxy observations include similar constraints and limitations as real observations, they can be used to (1) carry out even-handed comparisons of observation and theory and (2) map the observable characteristics of simulated galaxies to their a priori known origins. In particular, integral field spectroscopy (IFS) expands the scope of such comparisons and mappings to an exceptionally broad set of physical properties. We therefore present RealSim-IFS, a tool for forward-modelling galaxies from hydrodynamical simulations into synthetic IFS observations. The core components of RealSim-IFS model the detailed spatial sampling mechanics of any fibre-bundle, image slicer, or lenslet array IFU and corresponding observing strategy, real or imagined, and support the corresponding propagation of noise adopted by the user. The code is highly generalized and can produce cubes in any light- or mass-weighted quantity (e.g. specific intensity, gas/stellar line-of-sight velocity, stellar age/metallicity, etc.). We show that RealSim-IFS exactly reproduces the spatial reconstruction of specific intensity and variance cubes produced by the MaNGA survey Data Reduction Pipeline using the calibrated fibre spectra as input. We then apply RealSim-IFS by producing a public synthetic MaNGA stellar kinematic survey of 893 galaxies with log (M⋆/M⊙) &gt; 10 from the TNG50 cosmological hydrodynamical simulation.
Lensing in the darkness: a Bayesian analysis of 22 Chandra sources at z ≳ 6 shows no evidence of lensing
Authors: Pacucci Fabio , Foord Adi , Gordon Lucia , Loeb Abraham 
Published: June 2022

ABSTRACT
More than 200 quasars have been detected so far at z &gt; 6, with only one showing clear signs of strong gravitational lensing. Some studies call for a missing population of lensed high-z quasars, but their existence is still in doubt. A large fraction of high-z quasars being lensed would have a significant effect on the shape of the intrinsic quasar luminosity function (QLF). Here, we perform the first systematic search for lensed X-ray-detected quasars at z ≳ 6 employing a Bayesian analysis, with the code baymax, to look for morphological evidence of multiple images that may escape a visual inspection. We analysed a sample of 22 quasars at z &gt; 5.8 imaged by the Chandra X-ray observatory and found none with statistically significant multiple images. In the sub-sample of the eight sources with photon counts &gt;20, we exclude multiple images with separations r &gt; 1 arcsec and count ratios f &gt; 0.4, or with separations as small as 0.7 arcsec and f &gt; 0.7 at $95{{\ \rm per\ cent}}$ confidence level. Comparing this non-detection with predictions from theoretical models suggesting a high- and a low-lensed fraction, we placed upper limits on the bright-end slope, β, of the QLF. Using only the sub-sample with eight sources, we obtain, in the high-lensing model, a limit β &lt; 3.38. Assuming no multiple source is present in the full sample of 22 sources, we obtain β &lt; 2.89 and β &lt; 3.53 in the high- and low-lensing models, respectively. These constraints strongly disfavour steep QLF shapes previously proposed in the literature.
A machine learning approach to infer the accreted stellar mass fractions of central galaxies in the TNG100 simulation
Authors: Shi Rui , Wang Wenting , Li Zhaozhou , Han Jiaxin , Shi Jingjing , Rodriguez-Gomez Vicente , Peng Yingjie , Li Qingyang 
Published: June 2022

ABSTRACT
We propose a random forest (RF) machine learning approach to determine the accreted stellar mass fractions (facc) of central galaxies, based on various dark matter halo and galaxy features. The RF is trained and tested using 2710 galaxies with stellar mass log10M*/M⊙ &gt; 10.16 from the TNG100 simulation. Galaxy size is the most important individual feature when calculated in 3-dimensions, which becomes less important after accounting for observational effects. For smaller galaxies, the rankings for features related to merger histories increase. When an entire set of halo and galaxy features are used, the prediction is almost unbiased, with root-mean-square error (RMSE) of ∼0.068. A combination of up to three features with different types (galaxy size, merger history, and morphology) already saturates the power of prediction. If using observable features, the RMSE increases to ∼0.104, and a combined usage of stellar mass, galaxy size plus galaxy concentration achieves similar predictions. Lastly, when using galaxy density, velocity, and velocity dispersion profiles as features, which approximately represent the maximum amount of information extracted from galaxy images and velocity maps, the prediction is not improved much. Hence, the limiting precision of predicting facc is ∼0.1 with observables, and the multicomponent decomposition of galaxy images should have similar or larger uncertainties. If the central black hole mass and the spin parameter of galaxies can be accurately measured in future observations, the RMSE is promising to be further decreased by ∼20 per cent.
A simple analytical model of magnetic jets
Authors: Zdziarski Andrzej A , Stawarz Łukasz , Sikora Marek , Nalewajko Krzysztof 
Published: June 2022

ABSTRACT
We propose a simple analytical jet model of magnetic jets, in which radially averaged profiles of main physical quantities are obtained based on conservation laws and some results of published general relativistic magnetohydrodynamic jet simulations. We take into account conversion of the magnetic energy flux to bulk acceleration in jets formed around rotating black holes assuming the mass continuity equation and constant jet power, which leads to the Bernoulli equation. For assumed profiles of the bulk Lorentz factor and the radius, this gives us the profile of the toroidal magnetic field component along the jet. We then consider the case where the poloidal field component is connected to a rotating black hole surrounded by an accretion disc. Our formalism then recovers the standard formula for the power extracted from a rotating black hole. We find that the poloidal field strength dominates over the toroidal one in the comoving frame up to large distances, which means that jets should be more stable to current-driven kink modes. The resulting magnetic field profiles can then be used to calculate the jet synchrotron emission.
Iso-FRET: an isothermal competition assay to analyze quadruplex formation in vitro
Authors: Luo Yu , Verga Daniela , Mergny Jean-Louis 
Published: June 2022

Abstract
Algorithms have been widely used to predict G-quadruplexes (G4s)-prone sequences. However, an experimental validation of these predictions is generally required. We previously reported a high-throughput technique to evidence G4 formation in vitro called FRET-MC. This method, while convenient and reproducible, has one known weakness: its inability to pin point G4 motifs of low thermal stability. As such quadruplexes may still be biologically relevant if formed at physiological temperature, we wanted to develop an independent assay to overcome this limitation. To this aim, we introduced an isothermal version of the competition assay, called iso-FRET, based on a duplex-quadruplex competition and a well-characterized bis-quinolinium G4 ligand, PhenDC3. G4-forming competitors act as decoys for PhenDC3, lowering its ability to stabilize the G4-forming motif reporter oligonucleotide conjugated to a fluorescence quencher (37Q). The decrease in available G4 ligand concentration restores the ability of 37Q to hybridize to its FAM-labeled short complementary C-rich strand (F22), leading to a decrease in fluorescence signal. In contrast, when no G4-forming competitor is present, PhenDC3 remains available to stabilize the 37Q quadruplex, preventing the formation of the F22 + 37Q complex. Iso-FRET was first applied to a reference panel of 70 sequences, and then used to investigate 23 different viral sequences.
Availability of assisted peritoneal dialysis in Europe: call for increased and equal access
Authors: Brown Edwina A , Ekstrand Agneta , Gallieni Maurizio , Gorrín Maite Rivera , Gudmundsdottir Helga , Guedes Anabela Malho , Heidempergher Marco , Kitsche Benno , Lobbedez Thierry , Lundström Ulrika Hahn , McCarthy Kate , Mellotte George J , Moranne Olivier , Petras Dimitrios , Povlsen Johan V , Punzalan Sally , Wiesholzer Martin 
Published: June 2022

ABSTRACT

Background
Availability of assisted PD (asPD) increases access to dialysis at home, particularly for the increasing numbers of older and frail people with advanced kidney disease. Although asPD has been widely used in some European countries for many years, it remains unavailable or poorly utilized in others. A group of leading European nephrologists have therefore formed a group to drive increased availability of asPD in Europe and in their own countries.

Methods
Members of the group filled in a proforma with the following headings: personal experience, country experience, who are the assistants, funding of asPD, barriers to growth, what is needed to grow and their top three priorities.

Results
Only 5 of the 13 countries surveyed provided publicly funded reimbursement for asPD. The use of asPD depends on overall attitudes to PD, with all respondents mentioning the need for nephrology team education and/or patient education and involvement in dialysis modality decision making.

Conclusions and call to action
Many people with advanced kidney disease would prefer to have their dialysis at home, yet if the frail patient chooses PD most healthcare systems cannot provide their choice. AsPD should be available in all countries in Europe and in all renal centres. The top priorities to make this happen are education of renal healthcare teams about the advantages of PD, education of and discussion with patients and their families as they approach the need for dialysis, and engagement with policymakers and healthcare providers to develop and support assistance for PD.
Long-term outcomes and late toxicity of adult medulloblastoma treated with combined modality therapy: A contemporary single-institution experience
Authors: Saraf Anurag , Yock Torunn I , Niemierko Andrzej , Oh Kevin S , Curry William T , Butler William E , Forst Deborah A , Arrillaga-Romany Isabel , Ebb David H , Tarbell Nancy J , MacDonald Shannon , Loeffler Jay S , Shih Helen A 
Published: June 2022

Abstract

Background
Medulloblastoma (MB) is a rare central nervous system malignancy of adults, with limited contemporary studies to define treatment guidelines and expected late toxicity.

Methods
A single-center, retrospective study was conducted of patients age ≥18 years from 1997–2019 with MB and who were treated with postoperative radiotherapy. Late toxicity was defined as a minimum of 18 months from diagnosis. Overall survival (OS) and progression-free survival (PFS) were characterized using Kaplan-Meier and Cox regression analyses.

Results
Fifty-nine patients met criteria, with median age of 25 years (range 18–62 y) and median follow-up of 6.5 years (range 0.7–23.1 y). At diagnosis, 68% were standard-risk, 88% Chang M0, and 22% with anaplastic histology. Gross total resection was achieved in 75%; median craniospinal irradiation dose was 30.6 Gy (relative biological effectiveness [RBE]), median total dose was 54.0 Gy (RBE), 80% received proton radiotherapy; 81% received chemotherapy. 5 year PFS and OS were 86.5% and 95.8%, respectively; 10 year PFS and OS were 83.9% and 90.7%, respectively. Anaplastic histology was associated with worse PFS (P = .04). Among eight recurrences, 25% presented after 5 years. Most common grade ≥2 late toxicities were anxiety/depressive symptoms (30%), motor dysfunction (25%), and ototoxicity (22%). Higher posterior fossa radiation dose was associated with increased risk of late toxicity, including worse cognitive dysfunction (P = .05).

Conclusions
Adults with MB have favorable survival outcomes, but late failures and toxicity are not uncommon. Better understanding of prognostic factors, possibly from molecular subtyping, may help to define more personalized treatments for patients with high risk of recurrence and long-term treatment sequelae.