bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rehabilitative Training Interacts with Ischemia-Instigated Spine Dynamics to Promote a Lasting Population of New Synapses in Peri-Infarct Motor Cortex
Authors: Clark Taylor A. , Sullender Colin , Jacob Daron , Zuo Yi , Dunn Andrew K. , Jones Theresa A. 
Published: September 2019

After subtotal infarcts of primary motor cortex (M1), motor rehabilitative training (RT) promotes improvements in paretic forelimb function that have been linked with its promotion of structural and functional reorganization of peri-infarct cortex, but how the reorganization unfolds is scantly understood. Cortical infarcts also instigate a prolonged period of dendritic spine turnover in peri-infarct cortex. Here we investigated the possibility that synaptic structural responses to RT in peri-infarct cortex reflect, in part, interactions with ischemia-instigated spine turnover. This was tested after artery-targeted photothrombotic M1 infarcts or Sham procedures in adult (4 months) C57BL/6 male and female GFP-M line (n= 24) and male yellow fluorescent protein-H line (n= 5) mice undergoing RT in skilled reaching or no-training control procedures. Regardless of training condition, spine turnover was increased out to 5 weeks postinfarct relative to Sham, as was the persistence of new spines formed within a week postinfarct. However, compared with no-training controls, new spines formed during postinfarct weeks 2–4 in mice undergoing RT persisted in much greater proportions to later time points, by a magnitude that predicted behavioral improvements in the RT group. These results indicate that RT interacts with ischemia-instigated spine turnover to promote preferential stabilization of newly formed spines, which is likely to yield a new population of mature synapses in peri-infarct cortex that could contribute to cortical functional reorganization and behavioral improvement. The findings newly implicate ischemia-instigated spine turnover as a mediator of cortical synaptic structural responses to RT and newly establish the experience dependency of new spine fates in the postischemic turnover context.SIGNIFICANCE STATEMENTMotor rehabilitation, the main treatment for motor impairments after stroke, is far from sufficient to normalize function. A better understanding of neural substrates of rehabilitation-induced behavioral improvements could be useful for understanding how to optimize it. Here, we investigated the nature and time course of synaptic responses to motor rehabilitative trainingin vivo. Focal ischemia instigated a period of synapse turnover in peri-infarct motor cortex of mice. Rehabilitative training increased the stability of new synapses formed during the initial weeks after the infarct, the magnitude of which was correlated with improvements in skilled motor performance. Therefore, the maintenance of new synapses formed after ischemia could represent a structural mechanism of rehabilitative training efficacy.
Transformation with Artificial Chromosomes in Oxytricha trifallax and Their Applications
Authors: Clay Derek M , Kim Hoyon , Landweber Laura F 
Published: September 2019

Abstract
Oxytricha trifallax, like other ciliates, has separate germline and somatic nuclei. The diploid germline genome in the micronucleus is composed of long conventional chromosomes. The macronucleus contains a somatic genome which is naturally fragmented into thousands of kilobase-sized chromosomes. Here, we develop a method to stably incorporate artificial chromosomes into the macronucleus. We report two cases of successful transformation and demonstrate the use of somatic transformation to investigate gene regulation and gene function in Oxytricha. We show that the transformed artificial chromosomes are maintained through multiple asexual divisions. Furthermore, they support the transcriptional regulation of the native chromosome from which they were derived and are translated to produce functional proteins. To test if transformed chromosomes are amenable to practical applications, we generated a tagged version of a representative gene (AL1) and used it to co-precipitate associated proteins. This revealed an association with nucleic acid binding proteins, specifically RNA-binding proteins, and RNA immunoprecipitation of AL1 revealed its association with multiple RNAs. The use of artificial chromosomes in Oxytricha enables an array of genetic and molecular biological assays, as well as new avenues of inquiry into the epigenetic programming of macronuclear development and genome rearrangement.
Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize
Authors: Anderson Sarah N , Stitzer Michelle C , Zhou Peng , Ross-Ibarra Jeffrey , Hirsch Cory D , Springer Nathan M 
Published: September 2019

Abstract
Transposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in the maize genome. Due to their repetitive nature, genomic studies of TEs are complicated by the difficulty of properly attributing multi-mapped short reads to specific genomic loci. Here, we utilize a method to attribute RNA-seq reads to TE families rather than particular loci in order to characterize transcript abundance for TE families in the maize genome. We applied this method to assess per-family expression of transposable elements in &gt;800 published RNA-seq libraries representing a range of maize development, genotypes, and hybrids. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. A large number of TE families were specifically detected in pollen and endosperm, consistent with reproductive dynamics that maintain silencing of TEs in the germ line. We find that B73 transcript abundance is a poor predictor of TE expression in other genotypes and that transcript levels can differ even for shared TEs. Finally, by assessing recombinant inbred line and hybrid transcriptomes, complex patterns of TE transcript abundance across genotypes emerged. Taken together, this study reveals a dynamic contribution of TEs to maize transcriptomes.
Pharmaco-Genetic Screen To Uncover Actin Regulators Targeted by Prostaglandins DuringDrosophilaOogenesis
Authors: Spracklen Andrew J , Lamb Maureen C , Groen Christopher M , Tootle Tina L 
Published: September 2019

AbstractProstaglandins (PGs) are lipid signaling molecules with numerous physiologic functions, including pain/inflammation, fertility, and cancer. PGs are produced downstream of cyclooxygenase (COX) enzymes, the targets of non-steroidal anti-inflammatory drugs (NSAIDs). In numerous systems, PGs regulate actin cytoskeletal remodeling, however, their mechanisms of action remain largely unknown. To address this deficiency, we undertook a pharmaco-genetic interaction screen during late-stage Drosophila oogenesis. Drosophila oogenesis is as an established model for studying both actin dynamics and PGs. Indeed, during Stage 10B, cage-like arrays of actin bundles surround each nurse cell nucleus, and during Stage 11, the cortical actin contracts, squeezing the cytoplasmic contents into the oocyte. Both of these cytoskeletal properties are required for follicle development and fertility, and are regulated by PGs. Here we describe a pharmaco-genetic interaction screen that takes advantage of the fact that Stage 10B follicles will mature in culture and COX inhibitors, such as aspirin, block this in vitro follicle maturation. In the screen, aspirin was used at a concentration that blocks 50% of the wild-type follicles from maturing in culture. By combining this aspirin treatment with heterozygosity for mutations in actin regulators, we quantitatively identified enhancers and suppressors of COX inhibition. Here we present the screen results and initial follow-up studies on three strong enhancers – Enabled, Capping protein, and non-muscle Myosin II Regulatory Light Chain. Overall, these studies provide new insight into how PGs regulate both actin bundle formation and cellular contraction, properties that are not only essential for development, but are misregulated in disease.
Germline Maintenance Through the Multifaceted Activities of GLH/Vasa inCaenorhabditis elegansP Granules
Authors: Marnik Elisabeth A , Fuqua J Heath , Sharp Catherine S , Rochester Jesse D , Xu Emily L , Holbrook Sarah E , Updike Dustin L 
Published: September 2019

AbstractVasa homologs are ATP-dependent DEAD-box helicases, multipotency factors, and critical components that specify and protect the germline. They regulate translation, amplify piRNAs, and act as RNA solvents; but, the limited availability of mutagenesis-derived alleles and their wide...Vasa homologs are ATP-dependent DEAD-box helicases, multipotency factors, and critical components that specify and protect the germline. They regulate translation, amplify piwi-interacting RNAs (piRNAs), and act as RNA solvents; however, the limited availability of mutagenesis-derived alleles and their wide range of phenotypes have complicated their analysis. Now, with clustered regularly interspaced short palindromic repeats (CRISPR/Cas9), these limitations can be mitigated to determine why protein domains have been lost or retained throughout evolution. Here, we define the functional motifs of GLH-1/Vasa in Caenorhabditis elegans using 28 endogenous, mutant alleles. We show that GLH-1’s helicase activity is required to retain its association with P granules. GLH-1 remains in P granules when changes are made outside of the helicase and flanking domains, but fertility is still compromised. Removal of the glycine-rich repeats from GLH proteins progressively diminishes P-granule wetting-like interactions at the nuclear periphery. Mass spectrometry of GLH-1-associated proteins implies conservation of a transient piRNA-amplifying complex, and reveals a novel affinity between GLH-1 and three structurally conserved PCI (26S Proteasome Lid, COP9, and eIF3) complexes or “zomes,” along with a reciprocal aversion for assembled ribosomes and the 26S proteasome. These results suggest that P granules compartmentalize the cytoplasm to exclude large protein assemblies, effectively shielding associated transcripts from translation and associated proteins from turnover. Within germ granules, Vasa homologs may act as solvents, ensuring mRNA accessibility by small RNA surveillance and amplification pathways, and facilitating mRNA export through germ granules to initiate translation.
MetaCrowd: Crowdsourcing Biomedical Metadata Quality Assessment
Authors: Zaveri Amrapali , Hu Wei , Dumontier Michel 
Published: September 2019

To reuse the enormous amounts of biomedical data available on the Web, there is an urgent need for good quality metadata. This is extremely important to ensure that data is maximally Findable, Accessible, Interoperable and Reusable. The Gene Expression Omnibus (GEO) allow users to specify metadata in the form of textual key: value pairs (e.g. sex: female). However, since there is no structured vocabulary or format available, the 44,000,000+ key: value pairs suffer from numerous quality issues. Using domain experts for the curation is not only time consuming but also unscalable. Thus, in our approach, MetaCrowd, we apply crowdsourcing as a means for GEO metadata quality assessment. Our results show crowdsourcing is a reliable and feasible way to identify similar as well as erroneous metadata in GEO. This is extremely useful for data consumers and producers for curating and providing good quality metadata.
The Roots of Violence in Western Social Theories: In Search of Solution for Islam and Modernity
Authors: Matin Usep Abdul 
Published: September 2019

I argue that if we recognize the roots of violence in modern social theories, we may have at least a picture of how to solve the problem of violence for both Islam and modernity. I use the term “violence” to refer to an idea or an action that explicitly endorses revolt or physical conflict in attaining a goal. I will review fourteen social theories of the colonial and post-colonial period from the beginning to the end of the Twentieth Century, as presented by Charles Lemert in his book, Social Theory: The Multicultural & Classic Readings (1993). I refer my understanding of violence and its solutions for Islam and modernity on my interpretation of the types of abuse that I took from Lemert’s book. I discuss my argument in the following subtitles. The first subtitle is an introduction to capitalism as the answer to Islam and modernity. The second item is my finding of the notion of violence as a concept that is originated in the Western social theories of the colonial period. The third point is the degree to which I find that the roots of violence are also originated in the Western social methods of the post-colonial period. The fourth point of my article conveys the term “violence” used in linguistics by two French philosophers: Jacques Derrida and Michelle Foucault. The fifth element concludes this article by strengthening the above-mentioned assumption.
Outcome analysis of acute myeloid leukemia patients treated with high dose daunorubicin
Authors: Dolatkhah Roya , Jam Effat Irani , Nikanfar Alireza , Esfahani Ali , Chavooshi Sayed Hadi , Nejati Babak , Sanaat Zohreh 
Published: September 2019

Abstract: Acute Myeloid Leukemia (AML) is a malignant hematopoietic disease caused by the presence of a malignant clone in the bone marrow. The classic AML treatment includes a combination of an Anthracycline and Cytarabine. This study aimed to evaluate the effect of high doses of Daunorubicin on patients' outcome.
Methods: During the study period, 16 AML patients received induction therapy with Cytarabine (100 mg/m2/d) for 7 days and Daunorubicin (90 mg/m2/d) for 3 days. Outcome analysis was performed to evaluate the overall survival (OS) and disease-free survival (DFS) during 2 years of study.
Results: The mean age of patients was 38+/-12.38 years, with the age range between 16 and 54 years old. Seven patients (43.8%) were females, and 9 cases (56.3%) were males. OS was 81.3%, with a mean of 396.88 days. (95% CI: 306.99-486.77). DFS was 83.3%, with a mean of 383.57 days (95% CI: 299.88-467.26). The log-rank test showed a significant difference in DFS of AML sub-types, as M1 subtypes had lower DFS (P log-rank= 0.013). Although M1 subtypes had a lower OS, there was no significant difference in OS between subgroups (P log-rank= 0.067).
Conclusion: Although disease-free survival was improved by increasing the dose of daunorubicin, there was no difference in the overall survival between the AML subgroups and sexes.
Reducing Streptococcal Testing in Patients &lt;3 Years Old in an Emergency Department
Authors: Ahluwalia Tania , Jain Shobhit , Norton Laura , Meade Jennifer , Etherton-Still Jana , Myers Angela 
Published: September 2019

BACKGROUND:
Although pharyngitis is common, group A Streptococcus is an uncommon etiology, and sequelae are rare in patients &lt;3 years old. Inappropriate testing leads to increased cost of health care and unnecessary exposure to antibiotics. Rapid streptococcal tests (RSTs) for group A Streptococcus pharyngitis are not routinely indicated in this age group. At our urban, tertiary pediatric emergency department (ED), on average, 20 RSTs were performed each month for patients &lt;3 years of age. Our objective was to reduce RSTs in the ED in patients aged &lt;3 years by 50% in 18 months.

METHODS:
We initiated this project in October 2016 at an urban, tertiary pediatric ED. We surveyed pertinent multidisciplinary stakeholders to identify factors leading to RSTs in children &lt;3 years of age. We conducted multiple interventions and collected weekly data on the number of RSTs in children aged &lt;3 years (outcome measure) and the number of family complaints and return visits for complications of pharyngitis (balancing measure). We used statistical process control for analysis.

RESULTS:
The mean number of RSTs ordered per month in patients aged &lt;3 years declined by 52% in 10 months. The majority of tests during the study phase were ordered by nurse practitioners (62%) for patients aged 25 to 36 months (66%). There has been 1 family grievance and no patient complications attributable to the project.

CONCLUSIONS:
Our interventions led to a successful and sustained reduction of RSTs in patients aged &lt;3 years. A local clinical practice guideline was developed, and the project was expanded to other acute care settings.
Serious Illness Treatment Preferences for Older Adults with Advanced CKD
Authors: Baddour Nicolas Awad , Siew Edward D. , Robinson-Cohen Cassianne , Salat Huzaifah , Mason Olivia J. , Stewart Thomas G. , Karlekar Mohana , El-Sourady Maie H. , Lipworth Loren , Abdel-Kader Khaled 
Published: September 2019

Significance Statement
Effective advance care planning is a national priority for nephrologists. Yet, multiple barriers stymie patient–provider communication about treatment goals and patient preferences, including limited provider time and reluctance to initiate these conversations. This study examined a single-item measure eliciting patients’ treatment preference when confronted with a serious illness. This simple measure associated with two validated tools measuring health outcome priorities as well as acceptability of hypothetical end-of-life scenarios, including chronic dialysis. These results suggest that the serious illness treatment preference question is an efficient measure that can serve as an important point of entry for initiating goals-of-care communication and discussing the trade-offs of aggressive treatments (e.g., dialysis) with respect to patients’ overarching goals.

Background
Patient-centered care for older adults with CKD requires communication about patient’s values, goals of care, and treatment preferences. Eliciting this information requires tools that patients understand and that enable effective communication about their care preferences.

Methods
Nephrology clinic patients age ≥60 years with stage 4 or 5 nondialysis-dependent CKD selected one of four responses to the question, “If you had a serious illness, what would be important to you?” Condensed versions of the options were, “Live as long as possible;” “Try treatments, but do not suffer;” “Focus on comfort;” or “Unsure.” Patients also completed a validated health outcome prioritization tool and an instrument determining the acceptability of end-of-life scenarios. Patient responses to the three tools were compared.

Results
Of the 382 participants, 35% (n=134) selected “Try treatments, but do not suffer;” 33% (n=126) chose “Focus on comfort;” 20% (n=75) opted for “Live as long as possible;” and 12% (n=47) selected “Unsure.” Answers were associated with patients’ first health outcome priority and acceptability of end-of-life scenarios. One third of patients with a preference to “Focus on comfort” reported that a life on dialysis would not be worth living compared with 5% of those who chose “Live as long as possible” (P<0.001). About 90% of patients agreed to share their preferences with their providers.

Conclusions
Older adults with advanced CKD have diverse treatment preferences and want to share them. A single treatment preference question correlated well with longer, validated health preference tools and may provide a point of entry for discussions about patient’s treatment goals.
Content Validation of the Arabic Translation of the Practice Environment Scale of the Nursing Work Index-Revised
Authors: Ambani Zainab , Al-Hamdan Zaid , Al-Touby Salem , Ghanim Amani , Al Jarameez Faiza , Squires Allison 
Published: September 2019

Background and PurposeThere is no reliable and valid version of the Practice Environment Scale of the Nursing Work Index-Revised (PES-NWI-R) in Arabic. The purpose of this study was to describe the systematic instrument translation and validation of the PES-NWI-R.MethodsUsing the Content Validity Indexing-based approach, 32 expert nurses from four countries in the Eastern Mediterranean Region (Jordan, Oman, Saudi Arabia, and United Arab Emirates) participated in the validation of this translation.ResultsThe content validity index score of the overall scale was excellent (0.87 for the relevancy, and 0.95 for the quality of Arabic translation).ConclusionOur study supported the content validity of the Arabic version of the instrument which provided the first valid Arabic translation of the instrument.
Development of a Tool for the Assessment of Nurses' Attitudes Toward Delirium
Authors: Papastavrou Evridiki , Papaioannou Maria , Evripidou Melina , Tsangari Haritini , Kouta Christiana , Merkouris Anastasios 
Published: September 2019

Background and PurposeThe prevalence of delirium during hospitalization is high in older patients and there is evidence of staff regarding them as unpopular or a burden. This study aims to develop an instrument examining nurses' attitudes toward patients with delirium.MethodsStages included (a) content identification, (b) content development, (c) content critique, (e) pilot study with a test–retest reliability, (f) field study consisting of psychometric testing of the internal consistency and construct validity.ResultsThe Cronbach's alpha was 0.89 and the stability reliability was acceptable. The factor analysis resulted in three factors explaining a total of 56.5% of the variance. hese factors are “beliefs,” “behavior,” and “emotions,” explaining 37.025%, 12.792%, and 5.652% of variance.ConclusionsThe Attitude Tool of Delirium (ATOD) is a reliable and valid instrument for the assessment of attitudes toward delirium.
A Comparison of Missing-Data Imputation Techniques in Exploratory Factor Analysis
Authors: Xiao Canhua , Bruner Deborah W. , Dai Tian , Guo Ying , Hanlon Alexandra 
Published: September 2019

Background and PurposeTo compare the effects of missing-data imputation techniques, mean imputation, group mean imputation, regression imputation, and multiple imputation (MI), on the results of exploratory factor analysis under different missing assumptions.MethodsMissing data with different missing assumptions were generated from true data. The quality of imputed data was examined by correlation coefficients. Factor structures were compared indirectly by coefficients of congruence and directly by factor structures.ResultsMI had the best quality and matching factor structure to the true data for all missing assumptions with different missing rates. Mean imputation had the least favorable results in factor analysis. The imputation techniques revealed no important differences with 10% of data missing.ConclusionMI showed the best results, especially with larger proportions of missing data.
Validation of the Brazilian Moral Distress Scale in Nurses
Authors: Ramos Flavia Regina Souza , Barlen Edison Luis Devos , Brito Maria José Menezes , Vargas Mara Ambrosina , Schneider Dulcineia Ghizoni , de Farias Brehmer Laura Cavalcanti 
Published: September 2019

Background and PurposeTo determine the psychometric properties of the Brazilian Moral Distress Scale in Nurses (MDSN-BR).DesignIn this methodological, cross-sectional study, the criterion, content, and construct validation stages were presented.MethodA 57-item questionnaire was applied to 1,227 brazilian nurses through an online form. The exploratory factor analyses revealed significant conceptual relations among its items in six constructs, expressing the consistency of the scale.ResultsThe validated version of the instrument consists of six constructs and 49 items—Cronbach's alpha .980 (instrument) and of constructs: (a) (.942) Acknowledgment, power, and professional identity; (b) (.961) Safe and qualified care; (c) (.924) Defense of values and rights; (d) (.944) Work conditions; (e) (.933) Ethical infractions; (f) (.914) Work teams.ConclusionThe results provide evidence supporting the reliability and trustworthiness of the scale in the selected population.