bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compositionally Constrained Sites Drive Long-Branch Attraction
Authors: Szánthó Lénárd L , Lartillot Nicolas , Szöllősi Gergely J , Schrempf Dominik 
Published: March 2023

Abstract
Accurate phylogenies are fundamental to our understanding of the pattern and process of evolution. Yet, phylogenies at deep evolutionary timescales, with correspondingly long branches, have been fraught with controversy resulting from conflicting estimates from models with varying complexity and goodness of fit. Analyses of historical as well as current empirical datasets, such as alignments including Microsporidia, Nematoda, or Platyhelminthes, have demonstrated that inadequate modeling of across-site compositional heterogeneity, which is the result of biochemical constraints that lead to varying patterns of accepted amino acids along sequences, can lead to erroneous topologies that are strongly supported. Unfortunately, models that adequately account for across-site compositional heterogeneity remain computationally challenging or intractable for an increasing fraction of contemporary datasets. Here, we introduce “compositional constraint analysis,” a method to investigate the effect of site-specific constraints on amino acid composition on phylogenetic inference. We show that more constrained sites with lower diversity and less constrained sites with higher diversity exhibit ostensibly conflicting signals under models ignoring across-site compositional heterogeneity that lead to long-branch attraction artifacts and demonstrate that more complex models accounting for across-site compositional heterogeneity can ameliorate this bias. We present CAT-posterior mean site frequencies (PMSF), a pipeline for diagnosing and resolving phylogenetic bias resulting from inadequate modeling of across-site compositional heterogeneity based on the CAT model. CAT-PMSF is robust against long-branch attraction in all alignments we have examined. We suggest using CAT-PMSF when convergence of the CAT model cannot be assured. We find evidence that compositionally constrained sites are driving long-branch attraction in two metazoan datasets and recover evidence for Porifera as the sister group to all other animals. [Animal phylogeny; cross-site heterogeneity; long-branch attraction; phylogenomics.]
The Good, The Bad, and The Misleading: How to Improve the Quality of ‘Genome Announcements’?
Authors: Kusch Stefan , Vaghefi Niloofar , Kiss Levente 
Published: March 2023

When comparing the requirements of diverse journals to publish microbial ‘Genome Reports,’ we noticed that some mostly focus on benchmarking universal single-copy orthologs scores as a quality measure, while the exclusion of possible contaminating sequences from genomic resources and the possible misidentification of the target microbes receive less attention. To deal with these quality issues, we suggest that DNA barcodes that are widely accepted for the identification of the target microbe species should be extracted from newly reported genome resources and included in phylogenetic analyses to confirm the identity of the sequenced microorganisms before Genome Reports are published. This approach, applied, for example, by the journal IMA Fungus, largely prevents the misidentification of the microbes that are targeted for whole-genome sequencing (WGS). In addition, contig similarity values, including GC content, remapping coverage of WGS reads, and BLASTN searches against the National Center for Biotechnology Information nucleotide database, would also reveal contamination issues. The values of these two recommendations to improve the publication criteria for microbial Genome Reports in diverse journals are demonstrated here through analyses of a draft genome published in Molecular Plant-Microbe Interactions and then retracted due to contaminations. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Combining Air Sampling and DNA Metabarcoding to Monitor Plant Pathogens
Authors: Reich Jonathan , Chen Wen , Radford Devon , Turkington Kelly , Yevtushenko Dmytro , Hamelin Richard , Chatterton Syama 
Published: March 2023

Monitoring the air for airborne plant pathogens is an increasingly common method for the management of economically important plant diseases. In Alberta, Canada, several commodity clusters, including dry bean, canola, potato, and wheat, currently support air monitoring research programs for airborne pathogens of interest. In this study, we assessed the feasibility of monitoring for these, and more, plant fungal pathogens simultaneously using two different sampler types (cyclone versus rotation impaction) and by metabarcoding the ITS1 region using the Illumina sequencing platform. We collected air samples from four geographically distant sites across Alberta and monitored four crop types in southern Alberta. Overall, we found weak, but statistically significant, effects of geographic location and crop type on the aeromycobiota community composition. A few common taxa, such as Ramularia, Alternaria, and Epicoccum, constituted the vast majority of reads across all samples. Nevertheless, in each sample, we identified many plant pathogens of interest and organisms that previous research has found antagonistic to those pathogens, highlighting the utility of these approaches in understanding the pathobiome. In assessing the real-world implications of read counts, we discovered that they were only weakly correlated with spore counts quantified by qPCR. The two types of samplers collected different community profiles, reinforcing the importance of carefully considering which sampler type to use in monitoring programs. Taken together, our results show promise for the future of monitoring the air pathobiome, although much more work is required to understand the relationship of airborne communities to their in-field impact on disease development. [Formula: see text] Copyright © 2023 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada. This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Prospective Evaluation of the Safety and Efficacy of Thermomechanical Fractional Injury for Perioral Rhytides
Authors: Wang Jordan V. , Bajaj Shirin , Steuer Alexa , Orbuch David , Geronemus Roy G. 
Published: March 2023

BACKGROUND:
Perioral rhytides can be treated with laser and energy-based devices. More recently, a novel fractional thermomechanical skin rejuvenation system was developed to cause controlled thermal injury through direct heat transfer.

OBJECTIVE:
A prospective clinical trial evaluated the safety and efficacy of a thermomechanical fractional injury device (Tixel 2, Novoxel, Netanya, Israel) for perioral rhytides.

MATERIALS AND METHODS:
Subjects with moderate-to-severe perioral rhytides were enrolled and underwent 4 monthly treatments.

RESULTS:
Twenty-three subjects were enrolled and completed all study visits. Mean age was 62.5 years, and 100.0% were women. Fitzpatrick Skin Types I-IV were included. For Fitzpatrick Wrinkle Classification System (FWCS), mean baseline score was 6.9. Per investigator, there was a mean 1.9-grade improvement in FWCS at 3-month follow-up (p < .0001). At 3-month follow-up, 8.7% (n = 2) of subjects had a 3-grade improvement, 69.6% (n = 16) had a 2-grade improvement, and 21.7% (n = 5) had a 1-grade improvement. For physician Global Aesthetics Improvement Scale at 3-month follow-up, 69.6% (n = 16) had 76% to 100% improvement, 13.0% (n = 3) had 51% to 75% improvement, and 17.4% (n = 4) had 26% to 50% improvement. There were no severe adverse events, and subjects experienced minimal pain.

CONCLUSION:
A novel device using thermomechanical fractional injury was demonstrated to be safe and effective in the treatment of perioral rhytides.
Combined Fractional CO2 Laser With Intradermal Platelet-Rich Plasma versus Fractional CO2 Laser Alone in the Treatment of Striae Distensae
Authors: Sayed Doaa S. , Badary Daila M. , Ali Rania A. , Abou-Taleb Doaa A. E. 
Published: March 2023

BACKGROUND:
Striae distensae (SD) or stretch marks are common cutaneous conditions that occur because of the stretching of the dermis.

OBJECTIVE To evaluate and compare the efficacy of fractional carbon dioxide (CO2) laser alone versus combined fractional CO2 laser with platelet-rich plasma (PRP) in SD treatment.

METHODS AND MATERIALS:
Thirty adult female patients with SD (SR and SA) were enrolled. In each patient, a split-lesion design was conducted as follows: pairs of SD on both sides of the midline were selected and allocated to groups A and B. Group A: was treated with combined fractional CO2 laser with intradermal PRP. Group B: was treated with fractional CO2 laser alone. Skin biopsies were taken from the lesions before and after treatment for histopathologic evaluation.

RESULTS:
In group A, a significant excellent improvement of the SD was achieved more than in group B (p = .007) and the mean of improvement was significantly higher (60.33 ± 26.49) than that in group B (43.80 ± 27.43) (p-value = .001). Group A was also associated with a more significant dermal deposition of collagen and elastic fibers.

CONCLUSION:
Combined fractional CO2 laser with PRP was more effective than fractional CO2 laser alone for the treatment of SD.
Retrospective Review of the Laser Removal of Facial Cosmetic Tattoos
Authors: Hartman Nina , Loyal Jameson , Borsack Summer , Goldman Mitchel P. , Boen Monica 
Published: March 2023

BACKGROUND
Cosmetic facial tattoos have proven difficult to remove despite advancements in laser technology.

OBJECTIVE
Review safety and efficacy of picosecond laser removal of cosmetic facial tattoos.

METHODS & MATERIALS
Retrospective chart review from January 2015 to January 2022 of patients undergoing tattoo removal of facial cosmetic tattoos.

RESULT
A total of 33 patients were included in the review. The average number of treatments to obtain satisfactory results was 3. Sixty 6 percent of subjects were rated as “very much improved” with 76% to 100% of the tattoo removed and 34% of subjects were rated “much improved” with 51% to 75% of the tattoo removed. Thirty percent of subjects experienced unexpected changes in the tattoo color after initial treatment with 1,064-nm picosecond laser.

CONCLUSION
Picosecond laser is an effective and safe treatment for cosmetic tattoos, and it highlights the underreported unmasking of an orange color postlaser treatment that can be successfully treated with a 532-nm PS laser.
Pain Management and Substance Use Disorders
Authors: Sowicz Timothy Joseph , Compton Peggy , Matteliano Deborah , Oliver June , Strobbe Stephen , St. Marie Barbara , Turner Helen N. , Wilson Marian 
Published: March 2023

Abstract
The American Society for Pain Management Nursing and the International Nurses Society on Addictions hold the position that persons with co-occurring pain and substance use disorder have the right to be treated with dignity and respect and receive evidence-based, high-quality assessment and management for both conditions using an integrated, holistic, multidimensional approach. Nonopioid and nonpharmacological approaches to pain management are recommended. Opioids should not be withheld from anyone if necessary to treat pain, and a team-based approach, including pain and addiction specialists, should be utilized when possible. Pain management should include interventions aimed at minimizing the risk for relapse or escalation of problematic substance use and actively involve the person and their support persons in the plan of care. Institutions should establish policies and procedures that support this position statement.
Hospital Experiences of Dignity in People Who Inject Drugs
Authors: Dion Kimberly , Griggs Stephanie , Murray Jordan , Friedman Sarah 
Published: March 2023

Abstract

Background
Dignity is a complex concept necessary for the adequate treatment of patients in the healthcare setting. Autonomy, self-sufficiency, respect, and equality are concepts used to define dignity. Dignity has not been studied in people who inject drugs (PWID).

Objective
This study aimed to determine how PWID maintain or have their dignity threatened during hospitalization in an acute care unit.

Design
The qualitative descriptive study was a deductive thematic analysis of secondary data on PWID experiences with received nursing care. In-depth, semistructured interviews were conducted and transcribed verbatim with a constant comparison method for thematic analysis using NVivo. A priori codes of dignity concepts from the literature and dignity scales were used as a guide to examine the nine qualitative transcripts.

Findings
The three most common threats to dignity during hospitalization were lack of equality compared with other patients, not feeling valued as an individual, and not feeling respected by the healthcare workers providing care. The three most common protectors of dignity were feeling respected by healthcare workers, having autonomy in treatment choices, and feeling valued as an individual.

Conclusions
Protecting dignity significantly affects whether PWID are willing to seek healthcare in the hospital setting. Preserving dignity in PWID during their hospitalizations can encourage this population to seek care earlier. Nurses must be experienced in caring for PWID and provide nonjudgmental care for this population.
Predisposing, Reinforcing, and Enabling Factors of Nicotine Dependence Among Young Adults in a Rural Community
Authors: Garcia Norayda P. , Gamboa Aldrin Joseph Gio G. , Ganzalino Clynt Marc C. , Garcia Denzel C. , Garcia Gemcee Evan C. , Torres Gian Carlo S. 
Published: March 2023

Abstract

Objectives
The aim of this study was to determine the influence of predisposing, reinforcing, and enabling factors of nicotine dependence among young adults in a rural community.

Study Design
A quantitative, predictive–correlational cross-sectional study was done among 190 young adults in a rural community utilizing compact segmental sampling.

Methods
Data were collected from August to October 2018 utilizing a validated robotfoto, adapted determinants of smoking questionnaire, and Fagerström test to assess nicotine dependence. Stepwise multiple linear regression was used in predicting the relationship between the predictors and nicotine dependence.

Results
Reinforcing and enabling factors influenced nicotine dependency. The influence of other relatives (β = .179, p = .023) and radio advertisements (β = −.224, p = .008) as well as availability (access) to cigarettes (β = .228, p = .003) were significant predictors of nicotine dependency in the rural community.

Conclusion
Identified predictors can help form policies that can help address the availability of cigarettes and advertisements (radio) that can influence nicotine dependence among young adults in a rural community. Furthermore, the influence of other relatives (extended family) can be a factor that can increase the development of nicotine dependence.
Psychosexual responses to BRCA gene mutations in women of childbearing age
Authors: Hayes Alexis Elizabeth , Wardell Diane Wind , Engebretson Joan , LoBiondo-Wood Geri , Allicock Marlyn 
Published: March 2023

ABSTRACT

Background:
Diagnosis of a BRCA gene mutation presents a dilemma because life-changing medical decisions must be made to prevent breast and ovarian cancer. There is minimal evidence regarding how psychosexual functioning, psychological well-being with regard to body image and sexuality, affects the decision to have prophylactic treatment in women of childbearing age (WCBA; 18–49 years) with a BRCA gene mutation.

Purpose:
To explore, describe, and interpret the experience of women with a BRCA mutation during the treatment and decision-making process.

Methodology:
A qualitative descriptive design was used to recruit participants online through social media postings and from national and local BRCA support groups. Participants participated in semistructured interviews exploring their experience after BRCA diagnosis. Interpretive descriptive analysis was used to identify themes.

Results:
The purposive sample comprised 18 women aged 21–49 years. Four major themes, such as body image, sexuality, femininity, and childbearing/childrearing, were identified that influenced decisions related to the diagnosis and management of a BRCA mutation. All participants voiced that concerns regarding body image and sexuality caused hesitancy in their decision to have prophylactic surgery. Women who had undergone bilateral prophylactic mastectomy were concerned about the impact of the surgery, scarring, breast disfigurement, and the lack of sensation resulting from surgical intervention.

Conclusions:
Psychosexual concerns arise from internal and external influences that significantly affect the decision to undergo prophylactic measures. Therefore, body image, sexuality, and sexual orientation should all be addressed during the decision-making process.

Implications:
Provider communication and preparation for realistic surgical outcomes can be improved to assist WCBA throughout the decision-making process and enhance psychosexual functioning.
The Relationship Between Patient Safety Culture and the Intentions of the Nursing Staff to Report a Near-Miss Event During the COVID-19 Crisis
Authors: Idilbi Nasra , Dokhi Mohanad , Malka-Zeevi Helena , Rashkovits Sarit 
Published: March 2023

Background:
Reporting a near-miss event has been associated with better patient safety culture.

Purpose:
To examine the relationship between patient safety culture and nurses' intention to report a near-miss event during COVID-19, and factors predicting that intention.

Methods:
This mixed-methods study was conducted in a tertiary medical center during the fourth COVID-19 waves in 2020-2021 among 199 nurses working in COVID-19–dedicated departments.

Results:
Mean perception of patient safety culture was low overall. Although 77.4% of nurses intended to report a near-miss event, only 20.1% actually did. Five factors predicted nurses' intention to report a near-miss event; the model explains 20% of the variance. Poor departmental organization can adversely affect the intention to report a near-miss event.

Conclusions:
Organizational learning, teamwork between hospital departments, transfers between departments, and departmental disorganization can affect intention to report a near-miss event and adversely affect patient safety culture during a health crisis.
Factors Influencing Implementation Success of the Clinical Nurse Leader Care Delivery Model
Authors: Bender Miriam , Williams Marjory , Chandler Gianna 
Published: March 2023

Background:
The clinical nurse leader (CNL) care model has existed since 2007. However, there is limited understanding how the model can best be implemented.

Purpose:
A validated CNL Practice Survey measuring domains theorized to influence CNL implementation was used to examine the link between CNL domains and CNL implementation success.

Methods:
Mixed methods were used to analyze data from a nationwide 2015 survey administered to clinicians and administrators involved in CNL initiatives.

Results:
Of total respondents (n = 920), 543 (59%) provided success scores, with 349 (38%) providing comments. Respondents with negative comments gave significantly lower average CNL success scores. The majority of negative comments mapped onto Readiness and Structuring domains, providing details of barriers to CNL implementation success.

Conclusions:
Findings provide information about structural domains that can be strategically targeted to better prepare settings for CNL implementation and success.
Incontinence-Associated Dermatitis
Authors: Yüceler Kaçmaz Hatice , Kaplan Özlem , Kaplan Ali , Şahin Merve Gül , Cetinkaya Ali , Avci Atıl 
Published: March 2023

Background:
Incontinence-associated dermatitis (IAD) is a major concern among hospitals, especially in intensive care units (ICUs).

Purpose:
To describe ICU nurses' knowledge, attitudes, and practices of IAD and to examine the relationships with IAD prevalence in the ICU setting.

Methods:
A descriptive correlational design was used including the Knowledge, Attitudes and Practices of Incontinence-Associated Dermatitis Questionnaire and 1-month IAD prevalence data.

Results:
The prevalence of IAD in ICUs was 6.89%. A positive correlation was found between IAD prevalence and nurses' IAD knowledge and attitudes. Nurses working in the ICU for more than 7 years, caring for patients at high risk for or having IAD, and thinking IAD-related nursing practices were sufficient had significantly higher IAD knowledge, attitudes, and practices.

Conclusions:
Findings indicate that ICU nurses learned about IAD through clinical experience and have inadequate training on IAD. A standardized evidence-based care protocol for IAD should be developed.
Improving trunk postural control facilitates walking in children with cerebral palsy: a pilot study
Authors: Yan Shijun , Park Seoung Hoon , Keefer Renee , Dee Weena , Rojas Ana-Marie , Rymer William Zev , Wu Ming 
Published: March 2023

Abstract

Objective
The aim of this study was to determine the effects of bilateral trunk support during walking on trunk and leg kinematics and neuromuscular responses in children with cerebral palsy (CP).

Design
Fourteen children with spastic CP (GMFCS level I to III) participated in this study. Children walked on a treadmill under 4 different conditions, i.e., without support (BASELINE), with bilateral support applied to the upper trunk (UTS), the lower trunk (LTS), and combined upper and lower trunk (CTS). The trunk and leg kinematics and muscle activity were recorded.

Results
Providing bilateral support to the trunk had a significant impact on the displacement of the pelvis and trunk (p < 0.003) during walking. Children’s weaker leg showed greater step length (p = 0.032) and step height (p = 0.012) in CTS compared to BASELINE, and greater step length in UTS (p = 0.02) and CTS (p = 0.022) compared to LTS. Changes in soleus EMG activity during stance phase of gait mirrored the changes in step length across all conditions.

Conclusion
Providing bilateral upper or combined upper and lower trunk support during walking may induce improvements in gait performance, which may be due to improved pelvis kinematics. Improving trunk postural control may facilitate walking in children with CP.