bluuebunny/crossref_metadata_2025_split huggingface dataset:
First evidence of introgressive hybridization of apple snails (Pomacea spp.) in their native range
Authors: Glasheen Paul M , Burks Romi L , Campos Sofia R , Hayes Kenneth A 
Published: December 2019

Abstract
Genetic variation facilitates both natural range expansions and anthropogenic invasions. Contrary to expectations, hybridization does not always impact negatively on biodiversity. Increasing evidence indicates advantageous roles for introgressive hybridization in maintaining standing genetic variation. Hypothesizing that hybridization may contribute to the evolutionary and invasive success of a diverse group of freshwater snails (Ampullariidae, commonly known as apple snails), we estimated the frequency of hybridization between two globally invasive species of Pomacea, Pomacea canaliculata (Lamarck, 1822) and P. maculata Perry, 1810, in their native range. While previous work in Asia has uncovered the occurrence of extensive hybridization, we provide the first phylogenetic evidence of a high degree of hybridization (30%) between these species in Uruguay and Brazil. Hybrids carried both heterozygous and homozygous combinations of elongation factor 1-α (EF1α) nuclear alleles in both mating directions, indicating that hybridization has occurred over multiple generations and likely preceded introductions outside the native range. Among the five sites in Brazil previously documented as containing only P. maculata, one far northern population (Careiro Castanho), which is thousands of kilometres from the northern range of P. canaliculata, unexpectedly contained hybrids. This may be the result of human-facilitated introductions. Together with recent work from Asia, our investigations in the native range of apple snails support a reframing of historical perspectives of hybridization as a driver of extinction and diversity loss towards a modern paradigm where hybridization may promote diversification and contribute to the survival of evolutionary lineages such as molluscs.
53BP1/RIF1 signaling promotes cell survival after multifractionated radiotherapy
Authors: Eke Iris , Zong Dali , Aryankalayil Molykutty J , Sandfort Veit , Bylicky Michelle A , Rath Barbara H , Graves Edward E , Nussenzweig André , Coleman C Norman 
Published: December 2019

Abstract
Multifractionated irradiation is the mainstay of radiation treatment in cancer therapy. Yet, little is known about the cellular DNA repair processes that take place between radiation fractions, even though understanding the molecular mechanisms promoting cancer cell recovery and survival could improve patient outcome and identify new avenues for targeted intervention. To address this knowledge gap, we systematically characterized how cells respond differentially to multifractionated and single-dose radiotherapy, using a combination of genetics-based and functional approaches. We found that both cancer cells and normal fibroblasts exhibited enhanced survival after multifractionated irradiation compared with an equivalent single dose of irradiation, and this effect was entirely dependent on 53BP1-mediated NHEJ. Furthermore, we identified RIF1 as the critical effector of 53BP1. Inhibiting 53BP1 recruitment to damaged chromatin completely abolished the survival advantage after multifractionated irradiation and could not be reversed by suppressing excessive end resection. Analysis of the TCGA database revealed lower expression of 53BP1 pathway genes in prostate cancer, suggesting that multifractionated radiotherapy might be a favorable option for radio-oncologic treatment in this tumor type. We propose that elucidation of DNA repair mechanisms elicited by different irradiation dosing regimens could improve radiotherapy selection for the individual patient and maximize the efficacy of radiotherapy.
Integrative analyses of noncoding RNAs reveal the potential mechanisms augmenting tumor malignancy in lung adenocarcinoma
Authors: Shih Jou-Ho , Chen Hsin-Yi , Lin Shin-Chih , Yeh Yi-Chen , Shen Roger , Lang Yaw-Dong , Wu Dung-Chi , Chen Chien-Yu , Chen Ruey-Hwa , Chou Teh-Ying , Jou Yuh-Shan 
Published: December 2019

AbstractPrecise noncoding RNA (ncRNA)-based network prediction is necessary to reveal ncRNA functions and pathological mechanisms. Here, we established a systemic pipeline to identify prognostic ncRNAs, predict their functions and explore their pathological mechanisms in lung adenocarcinoma (LUAD). After in silico and experimental validation based on evaluations of prognostic value in multiple LUAD cohorts, we selected the PTTG3P pseudogene from among other prognostic ncRNAs (MIR497HG, HSP078, TBX5-AS1, LOC100506990 and C14orf64) for mechanistic studies. PTTG3P upregulation in LUAD cells shortens the metaphase to anaphase transition in mitosis, increases cell viability after cisplatin or paclitaxel treatment, facilitates tumor growth that leads to poor survival in orthotopic lung models, and is associated with a poor survival rate in LUAD patients in the TCGA cohort who received chemotherapy. Mechanistically, PTTG3P acts as an ncRNA that interacts with the transcription factor FOXM1 to regulate the transcriptional activation of the mitotic checkpoint kinase BUB1B, which augments tumor growth and chemoresistance and leads to poor outcomes for LUAD patients. Overall, we established a systematic strategy to uncover prognostic ncRNAs with functional prediction methods suitable for pan-cancer studies. Moreover, we revealed that PTTG3P, due to its upregulation of the PTTG3P/FOXM1/BUB1B axis, could be a therapeutic target for LUAD patients.
AtFKBP53: a chimeric histone chaperone with functional nucleoplasmin and PPIase domains
Authors: Singh Ajit Kumar , Datta Aritreyee , Jobichen Chacko , Luan Sheng , Vasudevan Dileep 
Published: December 2019

AbstractFKBP53 is one of the seven multi-domain FK506-binding proteins present in Arabidopsis thaliana, and it is known to get targeted to the nucleus. It has a conserved PPIase domain at the C-terminus and a highly charged N-terminal stretch, which has been reported to bind to histone H3 and perform the function of a histone chaperone. To better understand the molecular details of this PPIase with histone chaperoning activity, we have solved the crystal structures of its terminal domains and functionally characterized them. The C-terminal domain showed strong PPIase activity, no role in histone chaperoning and revealed a monomeric five-beta palm-like fold that wrapped over a helix, typical of an FK506-binding domain. The N-terminal domain had a pentameric nucleoplasmin-fold; making this the first report of a plant nucleoplasmin structure. Further characterization revealed the N-terminal nucleoplasmin domain to interact with H2A/H2B and H3/H4 histone oligomers, individually, as well as simultaneously, suggesting two different binding sites for H2A/H2B and H3/H4. The pentameric domain assists nucleosome assembly and forms a discrete complex with pre-formed nucleosomes; wherein two pentamers bind to a nucleosome.
A versatile cis-acting element reporter system to study the function, maturation and stability of ribosomal RNA mutants in archaea
Authors: Jüttner Michael , Weiß Matthias , Ostheimer Nina , Reglin Corinna , Kern Michael , Knüppel Robert , Ferreira-Cerca Sébastien 
Published: December 2019

AbstractGeneral molecular principles of ribosome biogenesis have been well explored in bacteria and eukaryotes. Collectively, these studies have revealed important functional differences and few similarities between these processes. Phylogenetic studies suggest that the information processing machineries from archaea and eukaryotes are evolutionary more closely related than their bacterial counterparts. These observations raise the question of how ribosome synthesis in archaea may proceed in vivo. In this study, we describe a versatile plasmid-based cis-acting reporter system allowing to analyze in vivo the consequences of ribosomal RNA mutations in the model archaeon Haloferax volcanii. Applying this system, we provide evidence that the bulge-helix-bulge motif enclosed within the ribosomal RNA processing stems is required for the formation of archaeal-specific circular-pre-rRNA intermediates and mature rRNAs. In addition, we have collected evidences suggesting functional coordination of the early steps of ribosome synthesis in H. volcanii. Together our investigation describes a versatile platform allowing to generate and functionally analyze the fate of diverse rRNA variants, thereby paving the way to better understand the cis-acting molecular determinants necessary for archaeal ribosome synthesis, maturation, stability and function.
Protein unties the pseudoknot: S1-mediated unfolding of RNA higher order structure
Authors: Lund Paul E , Chatterjee Surajit , Daher May , Walter Nils G 
Published: December 2019

Abstract
Ribosomal protein S1 plays important roles in the translation initiation step of many Escherichia coli mRNAs, particularly those with weak Shine-Dalgarno sequences or structured 5′ UTRs, in addition to a variety of cellular processes beyond the ribosome. In all cases, the RNA-binding activity of S1 is a central feature of its function. While sequence determinants of S1 affinity and many elements of the interactions of S1 with simple secondary structures are known, mechanistic details of the protein's interactions with RNAs of more complex secondary and tertiary structure are less understood. Here, we investigate the interaction of S1 with the well-characterized H-type pseudoknot of a class-I translational preQ1 riboswitch as a highly structured RNA model whose conformation and structural dynamics can be tuned by the addition of ligands of varying binding affinity, particularly preQ1, guanine, and 2,6-diaminopurine. Combining biochemical and single molecule fluorescence approaches, we show that S1 preferentially interacts with the less folded form of the pseudoknot and promotes a dynamic, partially unfolded conformation. The ability of S1 to unfold the RNA is inversely correlated with the structural stability of the pseudoknot. These mechanistic insights delineate the scope and limitations of S1-chaperoned unfolding of structured RNAs.
Stereotactic radiosurgery for non-functioning pituitary adenomas: meta-analysis and International Stereotactic Radiosurgery Society practice opinion
Authors: Kotecha Rupesh , Sahgal Arjun , Rubens Muni , De Salles Antonio , Fariselli Laura , Pollock Bruce E , Levivier Marc , Ma Lijun , Paddick Ian , Regis Jean , Sheehan Jason , Yomo Shoji , Suh John H 
Published: December 2019

Abstract

Background
This systematic review reports on outcomes and toxicities following stereotactic radiosurgery (SRS) for non-functioning pituitary adenomas (NFAs) and presents consensus opinions regarding appropriate patient management.

Methods
Using the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses, a systematic review was performed from articles of ≥10 patients with NFAs published prior to May 2018 from the Medline database using the key words “radiosurgery” and “pituitary” and/or “adenoma.” Weighted random effects models were used to calculate pooled outcome estimates.

Results
Of the 678 abstracts reviewed, 35 full-text articles were included describing the outcomes of 2671 patients treated between 1971 and 2017 with either single fraction SRS or hypofractionated stereotactic radiotherapy (HSRT). All studies were retrospective (level IV evidence). SRS was used in 27 studies (median dose: 15 Gy, range: 5–35 Gy) and HSRT in 8 studies (median total dose: 21 Gy, range: 12–25 Gy, delivered in 3–5 fractions). The 5-year random effects local control estimate after SRS was 94% (95% CI: 93.0–96.0%) and 97.0% (95% CI: 93.0–98.0%) after HSRT. The 10-year local control random effects estimate after SRS was 83.0% (95% CI: 77.0–88.0%). Post-SRS hypopituitarism was the most common treatment-related toxicity observed, with a random effects estimate of 21.0% (95% CI: 15.0–27.0%), whereas visual dysfunction or other cranial nerve injuries were uncommon (range: 0–7%).

Conclusions
SRS is an effective and safe treatment for patients with NFAs. Encouraging short-term data support HSRT for select patients, and mature outcomes are needed before definitive recommendations can be made. Clinical practice opinions were developed on behalf of the International Stereotactic Radiosurgery Society (ISRS).
A Forced-Choice Procedure to Assess the Acute Relative Reinforcing Effects of Nicotine Dose per se in Humans
Authors: Perkins Kenneth A , Karelitz Joshua L 
Published: December 2019

Abstract

Introduction
A method to assess acute reinforcement due to nicotine may aid identification of doses needed to maintain dependence. After describing development of a forced-choice procedure, results are presented from two studies using it to determine the relative reinforcing effects of nicotine dose per se.

Aims and Methods
Choice between a higher versus a very low or no nicotine option, via smoking (Study 1, n = 59) and via nasal spray (Study 2, n = 42), was assessed in nontreatment-seeking dependent smokers abstinent overnight. Using a within-subject design, different nicotine levels for each product were administered under blind conditions, initially to assess their discriminability (Study 1: 1.3–17 mg/g each vs. 0.4 mg/g nicotine Spectrum cigarettes; Study 2: 2.5 µg/kg vs. 0 µg/kg nicotine per spray). At the end of sessions for each study, participants engaged in forced-choice trials to assess preference, requiring a fixed number of puffs/sprays for one and/or the other.

Results
Confirming the procedure’s validity, the choice of the higher nicotine option was significantly greater than that for the very low or no nicotine option in both studies. In Study 1, choice relative to 0.4 mg/g was greater for cigarettes 5.3 mg/g or more but not 2.3 mg/g or less (p = .003 for the interaction of higher content vs. 0.4 mg/g comparison). In Study 2, choice was greater for the nicotine versus placebo spray (p &lt; .005), as nicotine was preferred nearly twice as much as the placebo.

Conclusion
This forced-choice procedure may efficiently determine the relative reinforcing value of a nicotine dose per se.

Implications
The forced-choice procedure described here may identify nicotine doses that are acutely reinforcing in dependent smokers. A priori research of choice comparisons between small versus zero nicotine doses could inform clinical research in larger and more diverse samples to determine nicotine contents in cigarettes, and perhaps in other commercial products, that are not reinforcing and, thus, likely to reduce the risk of their addictiveness. This procedure may also be applicable to assessing changes in acute nicotine reinforcement due to different product formulations, novel drugs, or other manipulations, perhaps helping inform development of new interventions for cessation or harm reduction.
Current explorations of nutrition and the gut microbiome: a comprehensive evaluation of the review literature
Authors: Frame Leigh A , Costa Elise , Jackson Scott A 
Published: December 2019

AbstractContextThe ability to measure the gut microbiome led to a surge in understanding and knowledge of its role in health and disease. The diet is a source of fuel for and influencer of composition of the microbiome.ObjectiveTo assess the understanding of the interactions between nutrition and the gut microbiome in healthy adults.Data SourcesPubMed and Google Scholar searches were conducted in March and August 2018 and were limited to the following: English, 2010–2018, healthy adults, and reviews.Data ExtractionA total of 86 articles were independently screened for duplicates and relevance, based on preidentified inclusion criteria.Data AnalysisResearch has focused on dietary fiber – microbiota fuel. The benefits of fiber center on short-chain fatty acids, which are required by colonocytes, improve absorption, and reduce intestinal transit time. Contrastingly, protein promotes microbial protein metabolism and potentially harmful by-products that can stagnate in the gut. The microbiota utilize and produce micronutrients; the bidirectional relationship between micronutrition and the gut microbiome is emerging.ConclusionsNutrition has profound effects on microbial composition, in turn affecting wide-ranging metabolic, hormonal, and neurological processes. There is no consensus on what defines a “healthy” gut microbiome. Future research must consider individual responses to diet.
Sentinel approach to detect emerging causes of work-related respiratory diseases
Authors: Zhou A Y , Seed M , Carder M , Money A , Van Tongeren M , Agius R 
Published: December 2019

Abstract

Background
The world of work is continually changing, and this could result in new and emerging risks being introduced, including those that may cause work-related respiratory diseases (WRRD).

Aims
To describe recently emerging and new cases of WRRD and the relevant methodology using data in a national occupational respiratory disease surveillance scheme in the UK.

Methods
Incident cases of respiratory diseases reported by physicians to the Surveillance of Work-related and Occupational Respiratory Disease (SWORD) between January 2015 and December 2017 were included. Potentially emerging respiratory hazards manifesting in SWORD data were identified with the following hierarchical approach: (i) new respiratory disease not previously associated with work, (ii) specific exposure/agent not previously associated with WRRD and (iii) industry and/or occupation not previously associated with WRRD.

Results
A total of 1215 cases of WRRD were reported to SWORD between January 2015 and December 2017. No new WRRD were identified. Thirteen potentially emerging causes of occupational asthma were identified, including exposures to agents such as ninhydrin. Four potential new causes were identified for interstitial pneumonia, which included wood and brass dust. Two potentially emerging causes of WRRD were identified for inhalational accidents (green coffee and nitrocellulose), hypersensitivity pneumonitis (diphenylmethane diisocyanate and salami mould), rhinitis (morphine and Amaranthus quitensis) and sarcoidosis (prions and horses).

Conclusions
Continuous monitoring and reporting of any new work-related disease is a critical function of any occupational disease reporting scheme. Potential emerging causes of work-related health risks have been identified by using a simple and systematic way of detecting emerging causes of WRRDs.
On Categories and the Countability of Things Bureaucratic: Turning From Wilson (Back) to Interpretation
Authors: Carpenter Daniel 
Published: December 2019

AbstractThe formulation and application of categories was the handiwork of frontier scholars of public management and remains the essential task of scholars of bureaucracy and regulation. These scholars, exemplified by James Q. Wilson, pioneered the development of categories in three domains: (1) the inductive assignment of observed objects to conceptual groups (a form of Weberian categorization), (2) the deductive assignment of incentives and styles to conceptual groups (type-dependent theorization), and (3) the empirical assignment of observed objects to applied analytic categories (behavioralist measurement). I find in Varieties of Police Behavior (1968) the origins of his enduring categories in Bureaucracy (1988). His classification of agency personnel into executives, managers, and operators remains perhaps his crowning achievement in administrative research. Yet Wilson examined these categories with greater care than is often demonstrated by his successors, as he was careful to condition his comparisons across and within categories. The extension of truly “Wilsonian” principles of analysis to bureaucratic organization requires not simply the development of conceptual structures and the careful consideration of bureaucratic incentives, but also a reappreciation of administrative routines, practices, concepts, and technologies. It may compel the admission that some quantitative and qualitative comparisons are literally, even mathematically, nonsensical.
Public Management in an Era of the Unprecedented: Dominant Institutional Logics as a Barrier to Organizational Sensemaking
Authors: Nowell Branda , Stutler Joseph 
Published: December 2019

AbstractIn an era when unprecedented events are occurring with increasing frequency, public management theory is challenged to consider whether it is possible to better prepare agencies to respond to situations previously neither expected, nor even seriously imagined. In this paper, we consider the case of the 2016 Chimney Tops 2 wildfire that contributed to the destruction of neighborhoods in and around Gatlinburg, TN. We argue this case illuminates a critical gap in extant organizational theory concerning the factors that impede sensemaking processes, which are fundamental to models of high reliability organizations during unprecedented events. Specifically, based on insights from this case considered through an institutional lens, we theorize that the nature of unprecedented events undermines an adaptive response through both structural and cultural/institutional processes. Structurally, we demonstrate how public agencies evolve to the contingencies of their normal task environment, which we should anticipate will be maladapted to the task demands of an unprecedented event. However, we theorize the greater challenge lies in the processes by which these structural features of the agency, over time, create, and reinforce a dominant institutional logic which can delay and weaken sensemaking processes, even when discrepant environmental cues are present. We conclude with a discussion of remedies that may facilitate earlier recognition, and thus more effective agency response, when the unprecedented is occurring.
Mineralized collagen-modified PMMA cement enhances bone integration and reduces fibrous encapsulation in the treatment of lumbar degenerative disc disease
Authors: Yang Long , Kong Jianjun , Qiu Zhiye , Shang Tieliang , Chen Siyu , Zhao Rui , Raucci Maria Grazia , Yang Xiao , Wu Zhanyong 
Published: December 2019

Abstract
As a minimally invasive surgery, percutaneous cement discoplasty (PCD) is now contemplated to treat lumbar disc degeneration disease in elder population. Here, we investigated whether the osteogenic mineralized collagen (MC) modified polymethylmethacrylate (PMMA) cement could be a suitable material in PCD surgery. Injectability, hydrophilicity and mechanical properties of the MC-modified PMMA (PMMA-MC) was characterized. The introduction of MC did not change the application and setting time of PMMA and was easy to be handled in minimally invasive operation. Hydrophilicity of PMMA-MC was greatly improved and its elastic modulus was tailored to complement mechanical performance of bone under dynamic stress. Then, PCD surgery in a goat model with induced disc degeneration was performed with implantation of PMMA-MC or PMMA. Three months after implantation, micro-computed tomography analysis revealed a 36.4% higher circumferential contact index between PMMA-MC and bone, as compared to PMMA alone. Histological staining confirmed that the surface of PMMA-MC was in direct contact with new bone, while the PMMA was covered by fibrous tissue. The observed gathering of macrophages around the implant was suspected to be the cause of fibrous encapsulation. Therefore, the interactions of PMMA and PMMA-MC with macrophages were investigated in vitro. We discovered that the addition of MC could hinder the proliferation and fusion of the macrophages. Moreover, expressions of fibroblast-stimulating growth factors, insulin-like growth factor, basic fibroblast growth factor and tumor necrosis factor-β were significantly down-regulated in the macrophages cocultured with PMMA-MC. Together, the promoted osteointegration and reduced fibrous tissue formation observed with PMMA-MC material makes it a promising candidate for PCD surgery.