bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrophobicity-Driven Increases in Editing in Mitochondrial mRNAs during the Evolution of Kinetoplastids
Authors: Rusman Fanny , Floridia-Yapur Noelia , Díaz Anahí G , Ponce Tatiana , Diosque Patricio , Tomasini Nicolás 
Published: April 2023

Abstract
Kinetoplastids are a diverse group of flagellates which exhibit editing by insertion/deletion of Us in the mitochondrial mRNAs. Some mRNAs require editing to build most of their coding sequences, a process known as pan-editing. Evidence suggests that pan-editing is an ancestral feature in kinetoplastids. Here, we investigate how the transition from nonedited to pan-edited states occurred. The mitochondrial mRNAs and protein sequences from nine kinetoplastids and related groups (diplonemids, euglenids, and jakobids) were analyzed. RNA editing increased protein hydrophobicity to extreme values by introducing Us in the second codon position, despite the absence of editing preferences related to codon position. In addition, hydrophobicity was maintained by purifying selection in species that lost editing by retroposition of the fully edited mRNA. Only a few hydrophobic to hydrophilic amino acid changes were inferred for such species. In the protein secondary structure, these changes occurred spatially close to other hydrophilic residues. The analysis of coevolving sites showed that multiple changes are required together for hydrophobicity to be lost, which suggest the proteins are locked into extended hydrophobicity. Finally, an analysis of the NAD7 protein–protein interactions showed they can also influence hydrophobicity increase in the protein and where editing can occur in the mRNA. In conclusion, our results suggest that protein hydrophobicity has influenced editing site selection and how editing expanded in mRNAs. In effect, the hydrophobicity increase was entrenched by a neutral ratchet moved by a mutational pressure to introduce Us, thus helping to explain both RNA editing increase and, possibly, persistence.
Surgery and proton radiation therapy for pediatric base of skull chordomas: Long-term clinical outcomes for 204 patients
Authors: Ioakeim-Ioannidou Myrsini , Niemierko Andrzej , Kim Daniel W , Tejada Athena , Urell Tobias , Leahy Shannon , Adams Judy , Fullerton Barbara , Nielsen G Petur , Hung Yin P , Shih Angela R , Patino Manuel , Buch Karen , Rincon Sandra , Kelly Hilary , Cunnane Mary Beth , Tolia Maria , Widemann Brigitte C , Wedekind Mary F , John Liny , Ebb David , Shin John H , Cote Gregory , Curry William , MacDonald Shannon M 
Published: April 2023

Abstract

Background
Data on clinical outcomes for base of skull (BOS) chordomas in the pediatric population is limited. We report patient outcomes after surgery and proton radiotherapy (PRT).

Methods
Pediatric patients with BOS chordomas were treated with PRT or combined proton/photon approach (proton-based; for most, 80% proton/20% photon) at the Massachusetts General Hospital from 1981 to 2021. Endpoints of interest were overall survival (OS), disease-specific survival, progression-free survival (PFS), freedom from local recurrence (LC), and freedom from distant failure (DC).

Results
Of 204 patients, median age at diagnosis was 11.1 years (range, 1–21). Chordoma location included 59% upper and/or middle clivus, 36% lower clivus, 4% craniocervical junction, and 1% nasal cavity. Fifteen (7%) received pre-RT chemotherapy. Forty-seven (23%) received PRT, and 157 (77%) received comboRT. Median total dose was 76.7 Gy (RBE) (range, 59.3–83.3). At a median follow-up of 10 years (interquartile range, 5–16 years), 56 recurred. Median OS and PFS were 26 and 25 years, with 5-, 10-, and 20-year OS and PFS rates of 84% and 74%, 78% and 69%, and 64% and 64%, respectively. Multivariable actuarial analyses showed poorly differentiated subtype, radiographical progression prior to RT, larger treatment volume, and lower clivus location to be prognostic factors for worse OS, PFS, and LC. RT was well tolerated at a median follow-up of 9 years (interquartile range, 4–16 years). Side effects included 166 patients (80%) with mild/moderate acute toxicities, 24 (12%) patients with late toxicities, and 4 (2%) who developed secondary radiation-related malignancies.

Conclusion
This is the largest cohort of BOS chordomas in the literature, pediatric and/or adult. High-dose PRT following surgical resection is effective with low rates of late toxicity.
Bone Metastases Detection in Patients with Breast Cancer: Does Bone Scintigraphy Add Information to PET/CT?
Authors: Cristo Santos Joana , Henriques Abreu Miguel , Seoane Santos Miriam , Duarte Hugo , Alpoim Tiago , Próspero Inês , Sousa Susana , Henriques Abreu Pedro 
Published: April 2023

Abstract

Background
Positron emission tomography/computed tomography (PET/CT) has become in recent years a tool for breast cancer (BC) staging. However, its accuracy to detect bone metastases is classically considered inferior to bone scintigraphy (BS). The purpose of this work is to compare the effectiveness of bone metastases detection between PET/CT and BS.

Materials and Methods
Prospective study of 410 female patients treated in a Comprehensive Cancer Center between 2014 and 2020 that performed PET/CT and BS for staging purposes. The image analysis was performed by 2 senior nuclear medicine physicians. The comparison was performed based on accuracy, sensitivity, and specificity on a patient and anatomical region level and was assessed using McNemar’s Test. An average ROC was calculated for the anatomical region analysis.

Results
PET/CT presented higher values of accuracy and sensitivity (98.0% and 93.83%), surpassing BS (95.61% and 81.48%) in detecting bone disease. There was a significant difference in favor of PET/CT (sensitivity 93.83% vs. 81.48%), however, there is no significant difference in eliminating false positives (specificity 99.09% vs. 99.09%). PET/CT presented the highest accuracy and sensitivity values for most of the bone segments, only surpassed by BS for the cranium. There was a significant difference in favor of PET/CT in the upper limb, spine, thorax (sternum) and lower limb (pelvis and sacrum), and in favor of BS in the cranium. The ROC showed that PET/CT has a higher sensitivity and consistency across the bone segments.

Conclusion
With the correct imaging protocol, PET/CT does not require BS for patients with BC staging.
Geographically consistent hybridization dynamics between the Black-crested and Tufted titmouse with evidence of hybrid zone expansion
Authors: Semenov Georgy A , Curry Claire M , Patten Michael A , Weir Jason T , Taylor Scott A 
Published: April 2023

Abstract
We studied hybridization between the Black-crested and Tufted titmouse across two geographically distinct transects that differ in the timing of secondary contact by hundreds to thousands of years. We found that hybridization patterns correspond to localized hybrid swarms and that the titmouse hybrid zone is likely slowly expanding over time, a product of short post-natal dispersal distances coupled with weak or absent selection against admixture. We show the southern part of the hybrid zone located in Texas is four times wider than the northern region of hybridization in Oklahoma, which is likely due to geographic differences in hybrid zone age. Despite differences in width, most individuals in both transects are advanced-generation hybrids and backcrosses, suggesting geographically consistent hybridization dynamics. We documented a strong correlation between genotypes and plumage index, suggesting that hybridization has not yet resulted in the decoupling of plumage and genome-wide ancestry as observed in some other avian hybrid zones. Although our results suggest the ongoing expansion of the hybrid zone, the rate of expansion appears to be slow, on the scale of tens of meters a year, and it will likely take hundreds of thousands to millions of years before homogenization of the parental populations. While we did not find support for partial reproductive isolation in the hybrid zone itself, there is the possibility that ecological or sexual selection limits introgression into allopatric regions. Broadly, the results of our study highlight the value of multiple, geographically distant, transects across a hybrid zone for assessing the evolutionary dynamics of hybridizing lineages.
Conditions, Actions and Purposes (CAP): A Dynamic Model for Community Policing in Europe
Authors: O’Neill Megan , van der Giessen Mark , Bayerl Petra Saskia , Hail Yvonne , Aston Elizabeth , Houtsonen Jarmo 
Published: April 2023

AbstractDespite its popularity as a policing method and evidence of its positive affect on communities, community policing has defied attempts to establish a clear definition and replicable form. Often regarded as an Anglo-American policing method in origin, community policing is now found across the world and is growing in influence. The need for differentiated local implementation raises important questions regarding the core features of community policing to guide the work of practitioners. Integrating insights from the existing literature and a trans-European project involving 323 interviews with community members and police officers across eight countries, we propose a dynamic model for community policing. In this original model, we differentiate between the conditions, actions and purposes of community policing (CAP) and describe how these core components are required for effective community policing, interrelated, and flexible enough for local implementation. Accordingly, we show how the CAP model is adaptable while at the same time retaining a sense of what makes ‘community policing’ a unique and identifiable policing method. We conclude our study with a discussion of the implications for research and practice internationally.
Police Use of Twitter During a Sporting Mega-Event
Authors: Aitken Adam , Ralph Liam , Robinson Paul 
Published: April 2023

Abstract
There exists a range of sporting mega-event security case studies from respective Olympic Games, Commonwealth Games, International Association Football Federation (FIFA) World Cup, and Union of European Football Associations (UEFA) Championships. This literature tends to focus on outlining the policing and physical security arrangements at respective Games and the social consequences of these. However, no studies have examined police use of social media at a mega-event. This article addresses this gap by analysing the Twitter activities of social media accounts from police forces and units within Glasgow and London during the Euro 2020 Finals. The article makes an empirical contribution to the mega-events and policing literature by identifying that the police used Twitter in five strategic ways: security spectacle, demonstration of effective partnership working, responsibilization of citizens, public feedback and reporting, and real-time crowd management. Such findings have important implications for the use of social media by police practitioners at future mega-events and for football policing.
Quantitative Susceptibility Mapping MRI in Deep-Brain Nuclei in First-Episode Psychosis
Authors: García Saborit Marisleydis , Jara Alejandro , Muñoz Néstor , Milovic Carlos , Tepper Angeles , Alliende Luz María , Mena Carlos , Iruretagoyena Bárbara , Ramirez-Mahaluf Juan Pablo , Diaz Camila , Nachar Ruben , Castañeda Carmen Paz , González Alfonso , Undurraga Juan , Crossley Nicolas , Tejos Cristian 
Published: April 2023

Abstract

Background
Psychosis is related to neurochemical changes in deep-brain nuclei, particularly suggesting dopamine dysfunctions. We used an magnetic resonance imaging-based technique called quantitative susceptibility mapping (QSM) to study these regions in psychosis. QSM quantifies magnetic susceptibility in the brain, which is associated with iron concentrations. Since iron is a cofactor in dopamine pathways and co-localizes with inhibitory neurons, differences in QSM could reflect changes in these processes.

Methods
We scanned 83 patients with first-episode psychosis and 64 healthy subjects. We reassessed 22 patients and 21 control subjects after 3 months. Mean susceptibility was measured in 6 deep-brain nuclei. Using linear mixed models, we analyzed the effect of case-control differences, region, age, gender, volume, framewise displacement (FD), treatment duration, dose, laterality, session, and psychotic symptoms on QSM.

Results
Patients showed a significant susceptibility reduction in the putamen and globus pallidus externa (GPe). Patients also showed a significant R2* reduction in GPe. Age, gender, FD, session, group, and region are significant predictor variables for QSM. Dose, treatment duration, and volume were not predictor variables of QSM.

Conclusions
Reduction in QSM and R2* suggests a decreased iron concentration in the GPe of patients. Susceptibility reduction in putamen cannot be associated with iron changes. Since changes observed in putamen and GPe were not associated with symptoms, dose, and treatment duration, we hypothesize that susceptibility may be a trait marker rather than a state marker, but this must be verified with long-term studies.
Shared and Disorder-Specific Alterations of Brain Temporal Dynamics in Obsessive-Compulsive Disorder and Schizophrenia
Authors: Luo Lekai , Li Qian , Wang Yaxuan , He Ning , Wang Yuxia , You Wanfang , Zhang Qian , Long Fenghua , Chen Lizhou , Zhao Youjin , Yao Li , Sweeney John A , Gong Qiyong , Li Fei 
Published: April 2023

Abstract

Background
Obsessive-compulsive disorder (OCD) and schizophrenia have distinct but also overlapping symptoms. Few studies have examined the shared and disorder-specific disturbances in dynamic brain function in the 2 disorders.

Study Design
Resting-state functional magnetic resonance imaging data of 31 patients with OCD and 49 patients with schizophrenia, all untreated, and 45 healthy controls (HCs) were analyzed using spatial group independent component (IC) analysis. Time-varying degree centrality patterns across the whole brain were clustered into 3 reoccurring states, and state transition metrics were obtained. We further explored regional temporal variability of degree centrality for each IC across all time windows.

Study Results
Patients with OCD and patients with schizophrenia both showed decreased occurrence of a state having the highest centrality in the sensorimotor and auditory networks. Additionally, patients with OCD and patients with schizophrenia both exhibited reduced dynamics of degree centrality in the superior frontal gyrus than controls, while dynamic degree centrality of the cerebellum was lower in patients with schizophrenia than with OCD and HCs. Altered dynamics of degree centrality nominally correlated with symptom severity in both patient groups.

Conclusions
Our study provides evidence of transdiagnostic and clinically relevant functional brain abnormalities across OCD and schizophrenia in neocortex, as well as functional dynamic alterations in the cerebellum specific to schizophrenia. These findings add to the recognition of overlap in neocortical alterations in the 2 disorders, and indicate that cerebellar alterations in schizophrenia may be specifically important in schizophrenia pathophysiology via impact on cerebellar thalamocortical circuitry.
Bidirectional associations between post-traumatic stress symptoms and sleep quality among older survivors of the 2011 Great East Japan Earthquake and Tsunami
Authors: Yazawa Aki , Shiba Koichiro , Okuzono Sakurako Shiba , Hikichi Hiroyuki , Kawachi Ichiro 
Published: April 2023

AbstractStudy ObjectivesWe sought to examine the bidirectional associations between post-traumatic stress symptoms (PTSS) and sleep quality in a sample of older disaster survivors.MethodsWe used 4 waves (2010, 2013, 2016, and 2020) of the Iwanuma Study, which included pre-disaster information and 9 years of follow-up data among older survivors of the 2011 Great East Japan Earthquake and Tsunami. Poisson regression analysis was used to examine the bidirectional associations between sleep problems and PTSS.ResultsIndividuals reporting sleep problems before the disaster were more likely to develop PTSS after exposure to disaster trauma, while there was no effect modification, i.e. prevalence ratio for sleep problems did not differ by the magnitude of disaster damages. Individuals reporting sleep problems after the disaster were less likely to recover from PTSS, and more likely to develop the delayed onset of PTSS 5 years after the disaster. While individuals who recovered from PTSS 9 years after the disaster were still at slightly higher risk of having sleep problems compared to those who never had PTSS, none of the sleeping problems were found to be significantly prevalent after the Bonferroni correction.ConclusionsPre-disaster sleep problems predicted PTSS onset independently of experiences of disaster trauma. The association between PTSS and sleep problems was bidirectional. Intervening to mitigate lingering sleep problems may benefit the recovery of disaster survivors from post-traumatic symptoms.
Sensitizing Blinders: Theorizing Theory in a Post-Colonial Era
Authors: Spickard James 
Published: April 2023

Abstract
Theories in the sociology of religion do more than identify the patterns that shape religious life. They also systematically hide other patterns from easy view. This often stems from the unexamined assumptions that each theory inherits from its cultural and historical context. This address presents three examples from the sociology of religion’s recent past. The first is an “underlying forces” theory that traces religious developments to long-term social trends. The second is an “individual-based modeling” theory that bases social outcomes on individual actions. The third is a “response-to-loss” theory, which connects religious innovation to unwanted social change. Each sees, and fails to see, different things. The address then examines some approaches to globalization, showing their presumption of the centrality of the developed West. Recent work on religions in the Global South, however, paints a different picture. The post-colonial patterns found there may well shape religion worldwide in ways that our current theories fail to see.
Neuroprotective Effects of Genome-Edited Human iPS Cell-Derived Neural Stem/Progenitor Cells on Traumatic Brain Injury
Authors: Imai Ryotaro , Tamura Ryota , Yo Masahiro , Sato Mizuto , Fukumura Mariko , Takahara Kento , Kase Yoshitaka , Okano Hideyuki , Toda Masahiro 
Published: April 2023

Abstract
Despite developing neurosurgical procedures, few treatment options have achieved functional recovery from traumatic brain injury (TBI). Neural stem/progenitor cells (NS/PCs) may produce a long-term effect on neurological recovery. Although induced pluripotent stem cells (iPSCs) can overcome ethical and practical issues of human embryonic or fetal-derived tissues in clinical applications, the tumorigenicity of iPSC-derived populations remains an obstacle to their safe use in regenerative medicine. We herein established a novel treatment strategy for TBI using iPSCs expressing the enzyme-prodrug gene yeast cytosine deaminase-uracil phosphoribosyl transferase (yCD-UPRT). NS/PCs derived from human iPSCs displayed stable and high transgene expression of yCD-UPRT following CRISPR/Cas9-mediated genome editing. In vivo bioluminescent imaging and histopathological analysis demonstrated that NS/PCs concentrated around the damaged cortex of the TBI mouse model. During the subacute phase, performances in both beam walking test and accelerating rotarod test were significantly improved in the treatment group transplanted with genome-edited iPSC-derived NS/PCs compared with the control group. The injury area visualized by extravasation of Evans blue was smaller in the treatment group compared with the control group, suggesting the prevention of secondary brain injury. During the chronic phase, cerebral atrophy and ventricle enlargement were significantly less evident in the treatment group. Furthermore, after 5-fluorocytosine (5-FC) administration, 5-fluorouracil converted from 5-FC selectively eliminated undifferentiated NS/PCs while preserving the adjacent neuronal structures. NS/PCs expressing yCD-UPRT can be applied for safe regenerative medicine without the concern for tumorigenesis.
Functional Synthetic Biology
Authors: Aldulijan Ibrahim , Beal Jacob , Billerbeck Sonja , Bouffard Jeff , Chambonnier Gaël , Ntelkis Nikolaos , Guerreiro Isaac , Holub Martin , Ross Paul , Selvarajah Vinoo , Sprent Noah , Vidal Gonzalo , Vignoni Alejandro 
Published: April 2023

AbstractSynthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms. However, current paradigms in the field entangle sequence and functionality in a manner that makes abstraction difficult, reduces engineering flexibility and impairs predictability and design reuse. Functional Synthetic Biology aims to overcome these impediments by focusing the design of biological systems on function, rather than on sequence. This reorientation will decouple the engineering of biological devices from the specifics of how those devices are put to use, requiring both conceptual and organizational change, as well as supporting software tooling. Realizing this vision of Functional Synthetic Biology will allow more flexibility in how devices are used, more opportunity for reuse of devices and data, improvements in predictability and reductions in technical risk and cost.
Survey of the use of beef semen in dairy herds in Pennsylvania and nearby states
Authors: Felix T L , Emenheiser J C , Govoni K E , Zinn S A , Reed S A 
Published: April 2023

Abstract
Because dairies across the United States have rapidly adopted breeding to beef breed sires, the use of beef semen has increased dramatically in recent years. The objective of this survey was to gather information about the use of beef semen by dairy producers in the Northeast United States to generate beef × dairy cattle for beef markets. The survey was conducted using the services of the Center for Survey Research at the Pennsylvania State University—Harrisburg campus. Respondents had two options for returning their responses: 1) mail the paper survey to CSR in the postage-paid business-reply envelope included in the mailing, or 2) complete the survey online via an open-access web survey link. A total of 669 surveys were received and a final number of 617 surveys were included in the responses based on completeness and validity of the responses. Because of the broad electronic distribution, a true response rate cannot be calculated. Of these, 463 (75.0%) were completed via returned paper survey, and 154 (25.0%) were completed via web, between November 9, 2021 and February 16, 2022. Of the 617 respondents, 539 were from Pennsylvania. Due to the large variations in returned survey copies by state, results are reported without state separation. Across all respondents, 69.7% reported milking 100 or fewer cows and over 90% of collected responses reported Holsteins as the predominant dairy breed in the Northeast. Only 18.8% of the respondents did not currently, nor plan to, breed with beef semen. Deciding which beef bulls to use on Northeast dairy farms was primarily based on the recommendation of the semen sales representative (54.5%) and the price of the semen purchased (42.3%). In addition, 89.7% of respondents cited using Angus genetics in their beef bull selections. However, there was no difference in reported profitability of crossbreeding between respondents who indicated using other beef breeds vs. those who indicated just using Angus (P ≥ 0.19). In conclusion, using beef sires on dairy females, regardless of the breed of beef sire, adds value to the resulting progeny from dairy farms in the Northeast.