bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pan-cancer analyses reveal regulation and clinical outcome association of the shelterin complex in cancer
Authors: Luo Zhenhua , Liu Weijin , Sun Panpan , Wang Feng , Feng Xuyang 
Published: December 2020

Abstract
Shelterin, a protective complex at telomeres, plays essential roles in cancer. In addition to maintain telomere integrity, shelterin functions in various survival pathways. However, the detailed mechanisms of shelterin regulation in cancer remain elusive. Here, we perform a comprehensive analysis of shelterin in 9125 tumor samples across 33 cancer types using multi-omic data from The Cancer Genome Atlas, and validate some findings in Chinese Glioma Genome Atlas and cancer cell lines from Cancer Cell Line Encyclopedia. In the genomic landscape, we identify the amplification of TRF1 and POT1, co-amplification/deletion of TRF2–RAP1–TPP1 as the dominant alteration events. Clustering analysis based on shelterin expression reveals three cancer clusters with different degree of genome instability. To measure overall shelterin activity in cancer, we derive a shelterin score based on shelterin expression. Pathway analysis shows shelterin is positively correlated with E2F targets, while is negatively correlated with p53 pathway. Importantly, shelterin links to tumor immunity and predicts response to PD-1 blockade immune therapy. In-depth miRNA analysis reveals a miRNA–shelterin interaction network, with p53 regulated miRNAs targeting multiple shelterin components. We also identify a significant amount of lncRNAs regulating shelterin expression. In addition, we find shelterin expression could be used to predict patient survival in 24 cancer types. Finally, by mining the connective map database, we discover a number of potential drugs that might target shelterin. In summary, this study provides broad molecular signatures for further functional and therapeutic studies of shelterin, and also represents a systemic approach to characterize key protein complex in cancer.
Incident Non-AIDS Comorbidity Burden Among Women With or at Risk for Human Immunodeficiency Virus in the United States
Authors: Collins Lauren F , Sheth Anandi N , Mehta C Christina , Naggie Susanna , Golub Elizabeth T , Anastos Kathryn , French Audrey L , Kassaye Seble , Taylor Tonya N , Fischl Margaret A , Adimora Adaora A , Kempf Mirjam-Colette , Palella Frank J , Tien Phyllis C , Ofotokun Ighovwerha 
Published: December 2020

Abstract

Background
Human immunodeficiency virus (HIV) infection may accelerate development of aging-related non-AIDS comorbidities (NACMs). The incidence of NACMs is poorly characterized among women living with HIV (WLWH).

Methods
WLWH and HIV-seronegative participants followed in the Women’s Interagency HIV Study (WIHS) through 2009 (when &gt;80% of WLWH used antiretroviral therapy) or onward were included, with outcomes measured through 31 March 2018. Sociodemographics, clinical covariates, and prevalent NACM were determined at enrollment. We used Poisson regression models to determine incident NACM burden (number of NACMs accrued through most recent WIHS visit out of 10 total NACMs assessed) by HIV serostatus and age.

Results
There were 3129 participants (2239 WLWH, 890 HIV seronegative) with 36 589 person-years of follow-up. At enrollment, median age was 37 years, 65% were black, and 47% currently smoked. In fully adjusted analyses, WLWH had a higher incident NACM rate compared with HIV-seronegative women (incidence rate ratio, 1.36 [95% confidence interval (CI), 1.02–1.81]). Incident NACM burden was higher among WLWH vs HIV-seronegative women in most age strata (HIV × age interaction: P = .0438), and women &lt;25 years old had the greatest incidence rate ratio by HIV serostatus at 1.48 (95% CI, 1.19–1.84) compared with those in older age groups. Incident NACM burden was associated with traditional comorbidity risk factors but not HIV-specific indices.

Conclusions
Incident NACM burden was higher among WLWH than HIV-seronegative women. This difference was most dramatic among women aged &lt;25 years, a group for whom routine comorbidity screening is not prioritized. Established non-HIV comorbidity risk factors were significantly associated with incident NACM burden. More data are needed to inform best practices for NACM screening, prevention, and management among WLWH, particularly young women.
Expression of the ace operon in Escherichia coli is triggered in response to growth rate-dependent flux-signal of ATP
Authors: El-Mansi Mansi , Phue Je-Nie , Shiloach Joseph 
Published: December 2020

ABSTRACT
The signal that triggers the expression of the ace operon and, in turn, the transition of central metabolism's architecture from acetogenic to gluconeogenic in Escherichia coli remains elusive despite extensive research both in vivo and in vitro. Here, with the aid of flux analysis together with measurements of the enzymic activity of isocitrate lyase (ICL) and its aceA-messenger ribonucleuc acid (mRNA) transcripts, we provide credible evidence suggesting that the expression of the ace operon in E. coli is triggered in response to growth rate-dependent threshold flux-signal of adenosine triphosphate (ATP). Flux analysis revealed that the shortfall in ATP supply observed as the growth rate ($\mu $) diminishes from µmax to ≤ 0.43h−1 ($ \pm 0.02;n4)\ $is partially redressed by up-regulating flux through succinyl CoA synthetase. Unlike glycerol and glucose, pyruvate cannot feed directly into the two glycolytic ATP-generating reactions catalyzed by phosphoglycerokinase and pyruvate kinase. On the other hand, glycerol, which upon its conversion to D-glyceraldehyde, feeds into the phosphorylation and dephosphorylation parts of glycolysis including the substrate-level phosphorylation-ATP generating reactions, thus preventing ATP flux from dropping to the critical threshold signal required to trigger the acetate-diauxic switch until glycerol is fully consumed. The mRNA transcriptional patterns of key gluconeogenic enzymes, namely, ackA, acetate kinase; pta, phosphotransacetylase; acs, acetyl CoA synthetase and aceA, ICL, suggest that the pyruvate phenotype is better equipped than the glycerol phenotype for the switch from acetogenic to gluconeogenic metabolism.
Development and Testing of a New Simplified Endoscopic Mucosal Assessment for Crohn’s Disease: The SEMA-CD
Authors: Adler Jeremy , Eder Sally J , Gebremariam Acham , French Kelley Rose , Moncion Ila , Singer Andrew A M , Bass Lee M , Moran Christopher J , Picoraro Joseph A , Moses Jonathan , Lewis Jeffery D , Sandberg Kelly C , Mar Shuemein J , Ebach Dawn R , Saeed Shehzad A , Rosh Joel R , Neef Haley C , Kaplan Jess L , Goyal Alka , del Rosario J Fernando , Zacur George M 
Published: December 2020

Abstract

Objectives
Endoscopic mucosal improvement is the gold standard for assessing treatment efficacy in clinical trials of Crohn’s disease. Current endoscopic indices are not routinely used in clinical practice. The lack of endoscopic information in large clinical registries limits their use for research. A quick, easy, and accurate method is needed for assessing mucosal improvement for clinicians in real-world practice. We developed and tested a novel simplified endoscopic mucosal assessment for Crohn’s disease (SEMA-CD).

Methods
We developed a 5-point scale for ranking endoscopic severity of ileum and colon based on Simple Endoscopic Score for Crohn’s disease (SES-CD). Central readers were trained to perform SES-CD and SEMA-CD. Pediatric patients with Crohn’s disease undergoing colonoscopy were enrolled. Video recordings of colonoscopies were de-identified and randomly assigned to blinded central readers. The SES-CD and SEMA-CD were scored for each video. The SES-CD was considered the validated standard for comparison. Correlation was assessed with Spearman rho, inter- and intrarater reliability with kappa statistics.

Results
Fifty-seven colonoscopies were read a total of 212 times. Correlation between SEMA-CD and SES-CD was strong (rho = 0.98, P &lt; 0.0001). Inter-rater reliability for SEMA-CD was 0.80, and intrarater reliability was 0.83. Central readers rated SEMA-CD as easier than SES-CD.

Conclusion
The SEMA-CD accurately and reproducibly correlates with the standard SES-CD. Central readers viewed SEMA-CD as easier than SES-CD. Use of SEMA-CD in practice should enable collecting mucosal improvement information in large populations of patients. This will improve the quality of research that can be conducted in clinical registries. External validation is needed.
Growth rates in a European eel Anguilla anguilla (L., 1758) population show a complex relationship with temperature over a seven-decade otolith biochronology
Authors: Vaughan Louise , Brophy Deirdre , O’Toole Ciar , Graham Conor , Ó Maoiléidigh Niall , Poole Russell 
Published: December 2020

Abstract
Environmental and habitat change can have profound and complex impacts on fish. We examined an unexploited population of European eel (Anguilla anguilla) from a West of Ireland catchment. The population is long-lived and slow-growing compared to many other European eel populations. Von Bertalanffy growth curves showed decadal changes, with a trend towards larger K, and t0 values in both males and females and a smaller L∞ in females. A growth biochronology spanning seven decades (1950s–2010s) was constructed using otolith annual increment measurements. We found evidence of high variability in growth over the course of the time series. A decrease in growth occurred after the early 2000s, potentially driven by habitat and climatic changes. Growth was negatively correlated with early spring and winter temperatures, providing strong evidence that the length of the growing season impacts eel growth. Growth was also positively correlated with summer temperatures and the number of days that exceeded 16˚C (GSL16˚C). The response to temperature was age-dependent; at age one the positive relationship with GSL16˚C was most pronounced and the negative relationship with winter temperatures was not evident. This study demonstrates the impact of climate change and highlights the complexities of eel growth strategies in a changing environment.
Infections after spine instrumentation: effectiveness of short antibiotic treatment in a large multicentre cohort
Authors: Benavent Eva , Rodríguez-Pardo Dolors , Ulldemolins Marta , Sobrino-Diaz Beatriz , Bustinduy María Jesús , Escudero-Sanchez Rosa , Nodar Andrés , Sorli Luisa , Del Toro López María Dolores , Bahamonde Alberto , Vilchez Helem H , Duran Joan , Muñez Elena , Rodriguez-Montserrat David , García-País María José , Pellisé Ferran , Núñez-Pereira Susana , Caballero-Martinez Luis F , Cobo Javier , Pérez-Rodríguez María Teresa , Ariza Javier , Pigrau Carlos , Murillo Oscar ,   the REIPI (Spanish Network for Research in Infectious Disease)/GEIO–SEIMC (Group for the Study of Osteoarticular Infections – Spanish Society of Infectious Diseases and Clinical Microbiology), Horcajada Juan P , Gómez Reinaldo Espíndola , Riera Melchor , Gasch Oriol , Blanco Silvia , Galindo Nieves Sopena , Rabuñal Ramón , Haddad Sleiman , Gómez-Junyent Joan , Iribarren Jose A , Sousa Adrián , Saló Guillem , Ferrer José Bravo , Ramos Antonio , Abos Sonia Molinos , Lombao Domingo , Garreta Iago , Mellado Juan Amador , Parrondo Susana Alvarez 
Published: December 2020

Abstract

Background and objectives
Available information about infection after spine instrumentation (IASI) and its management are scarce. We aimed to analyse DAIR (debridement, antibiotics and implant retention) prognosis and evaluate effectiveness of short antibiotic courses on early forms.

Methods
Multicentre retrospective study of patients with IASI managed surgically (January 2010–December 2016). Risk factors for failure were analysed by multivariate Cox regression and differences between short and long antibiotic treatment were evaluated with a propensity score-matched analysis.

Results
Of the 411 IASI cases, 300 (73%) presented in the first month after surgery, 48 in the second month, 22 in the third and 41 thereafter. Infections within the first 2 months (early cases) occurred mainly to older patients, with local inflammatory signs and predominance of Enterobacteriaceae, unlike those in the later periods. When managed with DAIR, prognosis of early cases was better than later ones (failure rate 10.4% versus 26.1%, respectively; P = 0.02). Risk factors for DAIR failure in early cases were female sex, Charlson Score, large fusions (&gt;6 levels) and polymicrobial infections (adjusted HRs of 2.4, 1.3, 2.6 and 2.26, respectively). Propensity score matching proved shorter courses of antibiotics (4–6 weeks) as effective as longer courses (failure rates 11.4% and 10.5%, respectively; P = 0.870).

Conclusions
IASIs within the first 2 months could be managed effectively with DAIR and shorter antibiotic courses. Clinicians should be cautious when faced with patients with comorbidities, large fusions and/or polymicrobial infections.
Constraining cosmology using galaxy position angle-only cosmic shear
Authors: Whittaker Lee 
Published: December 2020

ABSTRACT
We investigate cosmological parameter inference from realistic simulated weak lensing image data using only galaxy position angles, as opposed to full-ellipticity information. We demonstrate that input shear fields can be accurately reconstructed using only the statistics of source galaxy position angles and that, from these shear fields, we can successfully recover power spectra and infer the input cosmology. This paper builds on previous work on angle-only weak lensing estimation by extending the method to deal with variable and anisotropic point spread function (PSF) convolution and variable shear fields. Previous work employed a weighting scheme to downweight the contribution to shear estimates from sources aligned with the PSF. This work removes the need to downweight sources by convolving them with an image of the PSF rotated by 90○. We show that this successfully undoes the rotation caused by PSF convolution, assuming we have reliable images of the PSF. We find that we can accurately recover the input shear signal from simulated weak lensing data, based loosely on current Stage III missions, using only the position angles to within an overall scale factor, and that the scale factor can be determined using a cosmology independent simulation with noise, galaxy, and PSF properties that match those of the simulated data set. We then demonstrate that we can constrain cosmological parameters using angle-only shear estimates with a constraining power comparable to a basic application of IM3SHAPE, which provides full-shape measurement information.
A comprehensive view of blackbody components in the X-ray spectra of GRBs
Authors: Valan Vlasta , Larsson Josefin 
Published: December 2020

Abstract
A small fraction of gamma-ray bursts (GRBs) exhibit blackbody emission in the X-ray spectra, the origin of which is debated. In order to gain a more complete understanding of this phenomenon, we present a search for blackbody components in 116 GRBs with known redshifts observed by Swift X-ray telescope (XRT). A time-resolved spectral analysis is carried out and the significance of the blackbody is assessed with respect to an absorbed power-law model. We report nine new detections and confirm the previously reported blackbody in GRB 171205A. Together with our previous results, there are a total of 19 GRBs with significant blackbody emission in a sample of 199 GRBs observed by Swift over 13 yr. The detections include one short GRB and two low-luminosity GRBs. We estimate fireball parameters from the blackbody components and note that the blackbody luminosity is correlated with the temperature and inferred Lorentz factor. There is a large spread in the properties of the blackbody components and the light curves, which points to different origins for the emission. In about a third of the GRBs, the blackbody is clearly associated with late prompt emission from the jet. The rest of the sample includes cases that are fully consistent with the expectations from a cocoon, as well cases that may be explained by high-latitude emission or more energetic cocoons. These results indicate that thermal emission is associated with all parts of the jet.
Interacting dark energy in a closed universe
Authors: Di Valentino Eleonora , Melchiorri Alessandro , Mena Olga , Pan Supriya , Yang Weiqiang 
Published: December 2020

ABSTRACT
Recent measurements of the Cosmic Microwave Anisotropies power spectra measured by the Planck satellite show a preference for a closed universe at more than $99 {{\ \rm per\ cent}}$ confidence level (CL). Such a scenario is however in disagreement with several low redshift observables, including luminosity distances of Type Ia supernovae. Here we show that interacting dark energy (IDE) models can ease the discrepancies between Planck and supernovae Ia data in a closed Universe, leading to a preference for both a coupling and a curvature different from zero above the 99 per cent CL. Therefore IDE cosmologies remain as very appealing scenarios, as they can provide the solution to a number of observational tensions in different fiducial cosmologies. The results presented here strongly favour broader analyses of cosmological data, and suggest that relaxing the usual flatness and vacuum energy assumptions can lead to a much better agreement among theory and observations.
Safeguarding Curricular Self-Experiences in Undergraduate Music Therapy Education and Training
Authors: Hiller James , Belt Courtney , Gardstrom Susan , Willenbrink-Conte Joy 
Published: December 2020

Abstract
The purpose of this paper is to put forth a model to support the psychological safety of undergraduate students as they engage in a form of experiential learning called self-experiences (SEs). SEs pair active engagement in learning episodes with learner self-inquiry. The need to safeguard curricular SEs is grounded in the American Music Therapy Association’s Professional Competencies and Code of Ethics and the Certification Board for Music Therapists’ Board Certification Domains. We first explicate several types and benefits of SEs and identify potential risks and contraindications that may compromise learners’ psychological safety and even cause harm. Next, we describe the steps we took in developing the model and gaining administrative approval. We outline major tenets and describe specific safeguarding practices at various levels of implementation. We offer a hypothetical vignette to contextualize the information, address certain challenges in implementing this model, and offer recommendations for future research related to undergraduate experiential learning. Educators, clinical trainers, and supervisors who employ SEs are encouraged to implement safeguards toward upholding professional ethics and supporting learners’ personal and professional development.
Psychometric Properties of the Polish Version of the Self-care of Hypertension Inventory
Authors: Świątoniowska-Lonc Natalia , Polański Jacek , Jankowska-Polańska Beata 
Published: December 2020

Background
According to evidence-based guidelines, adherence to blood pressure–lowering medication and lifestyle modifications is a crucial part of hypertension management. Self-care is an effective method for secondary prevention. However, patients continue to exhibit major deficits in terms of adherence, self-control, and self-care. Standardized instruments for the effective monitoring of patients' self-care abilities are still lacking.

Objective
The objectives of this study were to produce a translation and cross-cultural adaptation of the Self-care of Hypertension Inventory (SC-HI) and to evaluate the psychometric properties of its Polish version.

Methods
The scale underwent translation and psychometric assessment using the standard methodology (forward-backward translation, review, psychometric analysis, criterion validity). The study included 250 patients, with a mean age of 61.23 ± 14.34 years, treated in a hypertension clinic.

Results
Mean self-care levels were evaluated in 3 domains: self-care maintenance (56.73 ± 18.57), self-care management (64.17 ± 21.18), and self-care confidence (62.47 ± 24.39). The Cronbach α for each domain showed satisfactory parameters: 0.755 for maintenance, 0.746 for management, and 0.892 for confidence. In the Polish version, the 3-factor structure of the SC-HI was not directly confirmed. Therefore, so-called modification indices were applied to obtain a standardized root mean square residual value less than 0.09 and a root mean square error of approximation value less than 0.06.

Conclusions
The SC-HI has been successfully translated and adapted for Polish settings, and is suitable for application among patients with hypertension.
Experiences of Parents of Infants Diagnosed With Mild or Severe Grades of Congenital Muscular Torticollis
Authors: Oledzka Magdalena M. , Sweeney Jane K. , Evans-Rogers Debbie L. , Coulter Colleen , Kaplan Sandra L. 
Published: December 2020

Purpose:
The primary purpose of this study was to describe the experiences of parents of infants diagnosed with congenital muscular torticollis (CMT). A secondary purpose was to compare the experiences of parents of infants with mild grades versus severe grades of involvement based on the CMT severity classification system.

Methods:
Through semistructured interviews, a qualitative phenomenological approach of inquiry was used to investigate the lived experiences of 12 parents.

Results:
Eight themes common to both groups of parents were identified. Findings indicated having an infant with CMT has a significant effect on the parents and other caregivers. Two themes were unique to parents of the infants with severe CMT.

Conclusions:
Parents are faced with a diagnosis that requires regular therapy visits and a challenging home program. A multimodal approach by clinicians for teaching and supporting parents during the episode of care may best address their unique challenges and stresses.
Associations Between Congenital Muscular Torticollis Severity and Physical Therapy Episode
Authors: Knudsen Kathryn C. R. , Jacobson Ryan P. , Kaplan Sandra L. 
Published: December 2020

Purpose:
To determine how physical therapy utilization varies with Congenital Muscular Torticollis (CMT) Severity Grading Scale, considering episode of care and clinical practice guidelines.

Methods:
A 3-year retrospective medical record review was conducted. Data were collected for 81 infants receiving physical therapy for CMT. Sample and service characteristics are described; 46 complete records (infants 6 months or younger) were analyzed to determine how physical therapy utilization varied across severity grades.

Results and Conclusions:
Of the 46 infants with complete care episodes, half had fully resolved all asymmetries. Units billed, episode duration, and total visits each increased across CMT severity grades 1 to 3. Cervical rotation restrictions correlated with total units billed, indicating a positive relationship between CMT severity and service utilization.

What This Adds to the Evidence:
This study supports that as CMT severity increases, physical therapy utilization increases for grades 1 to 3 of the 2018 CMT Severity Grading Scale.