bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased microenvironment stiffness leads to altered aldehyde metabolism and DNA damage in mammary epithelial cells through a RhoA-dependent mechanism
Authors: Wood Amber , Sun Heyuan , Jones Matthew , Percival Hannah , Broadberry Eleanor , Zindy Egor , Lawless Craig , Streuli Charles , Swift Joe , Brennan Keith , Gilmore Andrew P. 
Published: October 2020

SummaryMicroenvironmental stiffness regulates the behaviour of both normal and cancer cells. In breast tissue, high mammographic density (HMD), which reflects greater organisation and stiffness of the periductal collagen, represents a significant risk factor for cancer. However, the mechanistic link between extracellular matrix (ECM) stiffness and increased risk of breast tumour initiation remains unclear. In particular, how increased ECM stiffness might promote genomic damage, leading to the acquisition of transforming mutations, remains to be determined. Here we determine that ECM stiffness induces changes in mammary epithelial cell (MEC) metabolism that drive genomic damage. Using a 3D-culture model, we demonstrate that genome-wide transcriptional changes in response to increased ECM stiffness impair the ability of MECs to remove reactive aldehyde species, resulting in greater accumulation of DNA damage in a RhoA-dependent manner. Together, our results provide a mechanistic link between increased ECM stiffness and the genomic damage required for breast cancer initiation.
Development of a three-compartmentin vitrosimulator of the Atlantic Salmon GI tract and associated microbial communities: SalmoSim
Authors: Kazlauskaite R. , Cheaib B. , Heys C. , Ijaz U. , Connelly S. , Sloan W.T. , Russell J. , Martinez-Rubio L. , Sweetman J. , Kitts A. , McGinnity P. , Lyons P. , Llewellyn M. 
Published: October 2020

AbstractAtlantic salmon are a species of major economic importance. Intense innovation is underway to improve salmon feeds and feed additives to enhance fish performance, welfare, and the environmental sustainability of the industry. Several gut models targeted at monogastric vertebrates are now in operation. Here we report progress in the development of an Atlantic salmonin vitrogut model, SalmoSim, to simulate three gut compartments (stomach, pyloric caecum and mid gut) and associated microbial communities. The artificial gut model was established in a series of linked bioreactors seeded with biological material derived for adult marine phase salmon. In biological triplicate, the response of thein vitrosystem to two distinct dietary formulations (fish meal and fish meal free) was compared to a parallelin vivotrial over forty days. 16S rDNA sequencing, qPCR, ammoniacal nitrogen and volatile fatty acid measurements were undertaken to survey microbial community dynamics and function. SalmoSim communities were indistinguishable (p=0.230) from their founding inocula at 20 days and most abundant genera (e.g.Psycrobacter, Staphylococcus, Pseudomonas) proliferated thein vitrosystem. Real salmon and SalmoSim responded similarly to the introduction of the novel feed, with most taxa (96% Salmon, 97% SalmoSim) unaffected, while a subset of taxa was affected non-identically across both systems. Consistent with a low impact of the novel feed on microbial community function, VFA profiles were not significantly different in SalmoSim pre and post the switch feed. This study represents an important first-step in the development of anin vitrogut system as a tool for the improvement of salmon nutrition.
The transcription factor BCL11A defines a distinctive subset of dopamine neurons in the developing and adult midbrain
Authors: Tolve Marianna , Ulusoy Ayse , Islam Khondker Ushna Sameen , Bodea Gabriela O. , Öztürk Ece , Broske Bianca , Mentani Astrid , Wagener Antonia , van Loo Karen , Britsch Stefan , Liu Pengtao , Khaled Walid , Baader Stephan , Di Monte Donato A. , Blaess Sandra 
Published: October 2020

AbstractMidbrain dopaminergic (mDA) neurons are diverse in their projection targets, impact on behavior and susceptibility to neurodegeneration. Little is known about the molecular mechanisms that establish this diversity in mDA neurons during development. We find that the transcription factor Bcl11a defines a subset of mDA neurons in the developing and adult murine brain. By combining intersectional labeling and viral-mediated tracing we show that Bcl11a-expressing mDA neurons form a highly specific subcircuit within the dopaminergic system. We demonstrate that Bcl11a-expressing mDA neurons in the substantia nigra (SN) are particularly vulnerable to neurodegeneration in an α-synuclein overexpression model of Parkinson’s disease. Inactivation of Bcl11a in developing mDA neurons results in anatomical changes, deficits in motor learning and a dramatic increase in the susceptibility to α-synuclein-induced degeneration in SN-mDA neurons. In summary, we identify an mDA subpopulation with highly distinctive characteristics defined by the expression of the transcription factor Bcl11a already during development.
RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding
Authors: Mazumder Abhishek , Wang Anna , Uhm Heesoo , Ebright Richard H. , Kapanidis Achillefs N. 
Published: October 2020

AbstractThe RNA polymerase (RNAP) clamp, a mobile structural element conserved in RNAP from all domains of life, has been proposed to play critical roles at different stages of transcription. In previous work, we demonstrated using single-molecule Förster resonance energy transfer (smFRET) that RNAP clamp interconvert between three short-lived conformational states (lifetimes ∼ 0.3-0.6 s), that the clamp can be locked into any one of these states by small molecules, and that the clamp stays closed during initial transcription and elongation. Here, we extend these studies to obtain a comprehensive understanding of clamp dynamics under conditions RNAP may encounter in living cells. We find that the RNAP clamp can populate long-lived conformational states (lifetimes >1.0 s) and can switch between these long-lived states and the previously observed short-lived states. In addition, we find that clamp motions are increased in the presence of molecular crowding, are unchanged in the presence of elevated monovalent-cation concentrations, and are reduced in the presence of elevated divalent-cation concentrations. Finally, we find that RNAP bound to non-specific DNA predominantly exhibits a closed clamp conformation. Our results raise the possibility of additional regulatory checkpoints that could affect clamp dynamics and consequently could affect transcription and transcriptional regulation.
North American fireflies host low bacterial diversity
Authors: Green Emily A. , Smedley Scott R. , Klassen Jonathan L. 
Published: October 2020

ABSTRACTAlthough there are numerous studies of firefly mating flashes, lantern bioluminescence, and anti-predation lucibufagin metabolites, almost nothing is known about their microbiome. We therefore used 16S rRNA community amplicon sequencing to characterize the gut and body microbiomes of four North American firefly taxa:Ellychnia corrusca, thePhoturis versicolorspecies complex,Pyractomena borealis, andPyropyga decipiens. These firefly microbiomes all have very low species diversity, often dominated by a single species, and each firefly type has a characteristic microbiome. Although the microbiomes of male and female fireflies did not differ from each other,Ph. versicolorgut and body microbiomes did, with their gut microbiomes being enriched inPseudomonasandAcinetobacter.Ellychnia corruscaegg and adult microbiomes were unique except for a single egg microbiome that shared a community type withE.corruscaadults, which could suggest microbial transmission from mother to offspring. Mollicutes that had been previously isolated from fireflies were common in our firefly microbiomes. These results set the stage for further research concerning the function and transmission of these bacterial symbionts.
Helicobacter pyloriaccelerates KRAS-dependent gastric dysplasia
Authors: O’Brien Valerie P. , Koehne Amanda , Dubrulle Julien , Rodriguez Armando E. , Leverich Christina K. , Kong Paul , Campbell Jean S. , Pierce Robert H. , Goldenring James R. , Choi Eunyoung , Salama Nina R. 
Published: October 2020

AbstractMore than 80% of gastric cancer is attributable to stomach infection withHelicobacter pylori(Hp), even though the bacterium is not always present at time of diagnosis. Infection is thought to lead to cancer by promoting the accumulation of oncogenic mutations downstream of inflammation; once oncogenic pathways become activated, infection may become dispensable for cancer development. Gastric preneoplastic progression involves sequential changes to the tissue, including loss of parietal cells, spasmolytic polypeptide-expressing metaplasia (SPEM), intestinal metaplasia (IM) and dysplasia. In mice, active KRAS expression recapitulates these tissue changes in the absence ofHpinfection. This model provides an experimental system to investigate whetherHpinfection has additional roles in preneoplastic progression, beyond initiating inflammation. Mice were assessed by evaluating tissue histology, gene expression changes, the immune cell repertoire, and expression of metaplasia and dysplasia markers. Compared toHp-/KRAS+ mice,Hp+/KRAS+ mice had i) severe T cell infiltration and altered macrophage polarization; ii) altered expression of metaplasia markers, including increased expression of CD44v9 (SPEM) and decreased expression of TFF3 (IM); iii) more dysplastic (TROP2+) glands; and iv) greater proliferation of metaplastic and dysplastic glands.Hpwas able to persistently colonize the stomach during the onset of these tissue changes, and eradication ofHpwith antibiotics prevented metaplastic, dysplastic and proliferation marker changes. Collectively, these results suggest that gastric preneoplastic progression differs betweenHp+ andHp-cases, and that sustainedHpinfection can promote the later stages of gastric preneoplastic progression, in addition to its established role in initiating chronic inflammation.
Effective resource utilization in Arkansas public schools
Authors: Sanders Ryan , Zhang Shengfan 
Published: October 2020

PurposeTeacher pay in Arkansas public schools varies widely from district to district across the state. This pay discrepancy is driven by both the funds available to a district and by how these funds are allocated. A standard per student budget is given to districts across the state, but this budget can be supplemented by additional property taxes collected on property within a district. This leaves districts with more highly valued property at an advantage. Districts are free to allocate their budget for teacher pay as they see fit, with constraints on number of students per teacher and minimum teacher salary.Design/methodology/approachUsing public data available through the Arkansas Department of Education, this research investigates what variables affect student performance in Arkansas public schools using feature selection and predictive modelling and determine the cost-effectiveness associated with changing possible decision variables in terms of improving student performance.FindingsIt was found that the most cost-effective ways for districts to increase student performance are to (1) increase average teacher salary and (2) increase average years of teacher experience. This result is validated by education research, as both of these methods have been identified in literature as being effective ways to increase teacher quality and increase student performance. Furthermore, districts should consider increasing student–teacher ratio and applying the resulting savings toward teacher salaries.Originality/valueThis methodology gives a fresh perspective on the most cost-effective use of resources in publicly funded schools.
Contractual procurement alternatives of air force contingency pharmaceuticals: a cost-benefit analysis
Authors: Brubakken Adam J. , Dickens John M. , Anderson Jason , Cunningham William 
Published: October 2020

Purpose
This paper aims to explore effective supply chain principles, through the theory of transaction cost economics, as measures to improve current contingency pharmaceutical item shortfalls in the Air Force Medical Service (AFMS) Contingency Pharmaceutical Programme.

Design/methodology/approach
In this research, AFMS contingency pharmaceutical data was collected from various databases, including the Joint Medical Asset Repository, Medical Contingency Requirements Workflow and the Medical Requirements List. Through the methodology of cost-benefit analysis, alternative sourcing and fulfilment practices are evaluated.

Findings
The findings of this research indicate that the application of centralized purchasing principles, in an effort to leverage prime vendor contract fill rates for shortage items, can lead to 12%–17% increases in pharmaceutical material availability across the programme.

Originality/value
This research clearly shows that consolidating demand for shortage items across Active Duty War Reserve Material assemblages, though applications of centralized purchasing principles that leverage prime vendor contract fill rates, can lead to substantial increases in material availability at costs that justify the calculated benefits.
Interpreting plant root responses to nutrients, neighbours and pot volume depends on researchers’ assumptions
Authors: McNickle Gordon G. 
Published: October 2020

Abstract

Some plants respond to both neighbours and nutrient levels below‐ground independently, while others respond only to nutrients. These responses have important ecological implications, but debate about the appropriate control treatments used in experiments has led many to debate results.

When plants ignore neighbours, and only respond to nutrient levels this is sometimes called an ideal‐free distribution (IFD). When individual plants respond to neighbours by increasing root production to pre‐empt the uptake of neighbours, and do so at the expense of reproduction, this has become known as a tragedy of the commons (TOC). Here, I describe how the history of competition experiments has largely been a history of experiments that only control two of three critical variables: (a) total nutrients per plant; (b) soil nutrient concentration and (c) pot volume. These confounding effects are the source of debate about results.

In one study, split‐root pea plants were grown with and without a below‐ground neighbour at many pot volumes with equal total nutrients per‐plant. The researchers explicitly argued that plant growth responses would not be affected by the concentration of nutrients in soil, and therefore they explicitly confounded soil nutrient concentration with neighbour presence. Here, I reanalyse a subset of their data, controlling for soil nutrient concentration, but confounding pot volume with neighbour presence.

When I controlled for soil nutrient concentration, the presence of a below‐ground neighbour had no effects on plant size, or allocation, and the effects of volume also disappeared. The reanalysis suggests that the behaviour of peas in this study was consistent with an IFD model, and that the previously reported volume and neighbour responses may have been due to the confounding of nutrient concentration.

The results of the study in question depend very much on whether one does analyses that control for pot volume or whether one does analyses that control for soil nutrient concentration. Ultimately, these analyses lead to two different interpretations of the data. New experimental designs are emerging that fully control pot volume and nutrients across competition treatment, and I discuss possible paths forward in this ongoing debate.
The analysis of plant root responses to nutrient concentration, soil volume and neighbour presence: Different statistical approaches reflect different underlying basic questions
Authors: Chen Bin J. W. , During Heinjo J. , Vermeulen Peter J. , de Kroon Hans , Poorter Hendrik , Anten Niels P. R. 
Published: October 2020

Abstract

To investigate the responses of plants to their below‐ground neighbours independently of nutrient availability, experiments generally require a solitary treatment with one plant grown alone with one unit of nutrients, and a neighbour treatment with two plants grown together with two units of nutrients. This can either be done by doubling nutrient concentration (C) or by doubling soil volume (V) in the neighbour treatment as compared to the solitary treatment.

Statistically analysing the same dataset from an experiment that grew plants in solitary or neighbour treatment with a series of V given a fixed amount of nutrients per plant (e.g. 1 g), Chen et al. (2015a) found significant neighbour effects when they controlled for V, while McNickle (2020) found the effects to be insignificant when he controlled for C.

The discrepancy in the results of the two studies is caused by a difference in their analytical approaches. This includes (a) different choices of data transformation for the controlling factor, and (b) a mathematical deviation of model structures between V‐based and C‐based analyses, due to the different inversely proportional V‐C relationships between solitary and neighbour treatments.

Choices for either V or C as a controlling factor in the analyses for ‘neighbour effect’ are based on two different perspectives, focussing either on neighbour‐induced nutrient depletion (like McNickle, 2020) or on identity recognition (like Chen et al., 2015a).

We also raise concerns about the use of mesh‐divided root interaction design and replacement series design in the studies of plant–plant root interactions. We propose to adjust the experimental designs and analytical methods based on the focal perspectives of neighbour effect.
Comparison of 6‐mm and 11‐mm dental implants in the posterior region supporting fixed dental prostheses: 5‐year results of an open multicenter randomized controlled trial
Authors: Guljé Felix L. , Meijer Henny J. A. , Abrahamsson Ingemar , Barwacz Christopher A. , Chen Stephen , Palmer Paul J. , Zadeh Homayoun , Stanford Clark M. 
Published: October 2020

AbstractObjectiveThe aim of this multicenter, randomized controlled trial was to compare the clinical and radiographic outcomes of 6‐mm or 11‐mm implants, placed in the posterior maxilla and mandible, during a 5‐year follow‐up period.Materials and methodsNinety‐five patients with adequate bone height for 11‐mm implants, were randomly allocated to a 6‐mm group (test group with short implants) or an 11‐mm group (control group with standard‐length implants). Two or three implants of the same length were placed in each patient and after 6 weeks loaded with a splinted provisional restoration. This was followed by definitive splinted restoration 6 months after implant placement. Clinical and radiographic parameters, including the occurrence of complications were recorded.ResultsA total of 49 patients were enrolled to receive 6‐mm implants (n = 108) and 46 patients to receive 11‐mm implants (n = 101). Three implants (two of 6 mm and one of 11 mm in length) were lost before loading and one 6‐mm implant after 15 months of function, and one 11‐mm implant was lost during the first year of function. The 5‐year survival rates were 96.0% and 98.9% in the 6‐mm and 11‐mm group, respectively. The mean marginal bone level changes 5 years post‐loading were 0.01 ± 0.45 mm (bone gain) in the 6‐mm group and −0.12 ± 0.93 mm (bone loss) in the 11‐mm group (p = .7670). Clinical parameters, including plaque, bleeding on probing and pocket probing depth were not significantly different between the groups, and also technical complications were low.ConclusionThe clinical and radiographic outcomes of 6‐mm short and 11‐mm standard‐length implants were not different during a 5‐year evaluation period.
The evolution of reversed sex roles and classical polyandry: Insights from coucals and other animals
Authors: Safari Ignas , Goymann Wolfgang 
Published: October 2020

AbstractIn most animals, competition for mating opportunities is higher among males, whereas females are more likely to provide parental care. In few species, though, these "conventional" sex roles are reversed such that females compete more strongly for matings and males provide most or all parental care. This "reversal" in sex roles is often combined with classical polyandry—a mating system in which a female forms a harem with several males. Here, we review the major hypotheses relating such role reversals to evolutionary and behavioural traits (anisogamy, phylogenetic history, sexy males, parental care, genetic paternity, trade‐off between mating and parenting, adult sex ratio) and to ecological factors (food supply, offspring predation). We evaluate each hypothesis in relation to coucals (Centropodinae), a group of nesting cuckoos of great interest for mating system and parental care theory. The black coucal (Centropus grillii) is the only known bird combining classical polyandry with altricial development of young, a costly trait with regard to parental care. Our long‐term study offers a unique possibility to compare the strongly polyandrous black coucal with a monogamous close relative breeding in the same area and habitat, the white‐browed coucal (C. superciliosus). We show that the evolution of sex roles in coucals and other animals has many different facets. Whereas phylogenetic constraints are important, confidence in genetic paternity is not. In combination with facilitating ecological conditions, adult sex ratios are key to understanding sex roles in coucals, shorebirds, and most likely also other animals. We plead for more studies including experimental tests to understand how biased adult sex ratios emerge and whether they drive sexual selection or vice versa. How do sex ratios and sexual selection interact and feedback on each other? Answers to these questions will be fundamental for understanding the evolution of sex roles in mating and parenting in coucals and other species.
Cohort study of sleep quality in adult patients with acute pulmonary exacerbations of cystic fibrosis
Authors: Henderson Daniel , Moore Vanessa , MacMorran Kate , Castellini Julieta , Hay Karen , Keegan Vernon , Reid David , Curtin Deanne , Tay George 
Published: October 2020

AbstractBackgroundThe impact of an acute pulmonary exacerbation of cystic fibrosis (CF) on sleep quality has not been established. Patients have greater burden of symptoms, higher intensity of therapy and are often admitted to hospital outside of their usual sleeping environment.AimsTo evaluate the prevalence of, and factors associated with, poor sleep quality in adult patients admitted to hospital with an acute exacerbation of CF lung disease.MethodsThis prospective, observational study determined the prevalence of impaired sleep quality and associated factors in adult patients admitted to a single CF unit with an acute pulmonary exacerbation of CF. Sleep quality was defined by the Pittsburgh Sleep Quality Index (PSQI), with >5 indicating poor sleep quality. Data were obtained through patient questionnaires, chart review and examination.ResultsSixty‐six percent of patients had impaired sleep quality. Patients with poor sleep had more sleep disruption due to pain (median response ‘mild sleep disruption’ vs ‘no sleep disruption’; P = 0.003) and insomnia (mean Insomnia Severity Index (ISI) 13 vs 5; P < 0.001). In patients with symptoms of restless legs, poor sleepers had worse symptoms (mean International Restless Legs Severity Score (IRLSS) 15 vs 5; P = 0.029).Univariate modelling showed relationships between PSQI and symptoms of depression and anxiety as well as with sleep disruption due to pain, general noise and nursing observations. In a multivariable model, ISI was the only variable that remained significantly associated with PSQI. Mean PSQI score increased 0.58 units for each 1 unit increase in ISI (95% CI 0.42–0.73; P < 0.001).ConclusionsPoor sleep quality is common among patients admitted with an acute exacerbation of CF and is strongly associated with insomnia symptoms in this cohort.