bluuebunny/crossref_metadata_2025 huggingface dataset:
CAVE: a cloud-based platform for analysis and visualization of metabolic pathways
Authors: Mao Zhitao , Yuan Qianqian , Li Haoran , Zhang Yue , Huang Yuanyuan , Yang Chunhe , Wang Ruoyu , Yang Yongfu , Wu Yalun , Yang Shihui , Liao Xiaoping , Ma Hongwu
Published: May 2023

Flux balance analysis (FBA) is an important method for calculating optimal pathways to produce industrially important chemicals in genome-scale metabolic models (GEMs). However, for biologists, the requirement of coding skills poses a significant obstacle to using FBA for pathway analysis and engineering target identification. Additionally, a time-consuming manual drawing process is often needed to illustrate the mass flow in an FBA-calculated pathway, making it challenging to detect errors or discover interesting metabolic features. To solve this problem, we developed CAVE, a cloud-based platform for the integrated calculation, visualization, examination and correction of metabolic pathways. CAVE can analyze and visualize pathways for over 100 published GEMs or user-uploaded GEMs, allowing for quicker examination and identification of special metabolic features in a particular GEM. Additionally, CAVE offers model modification functions, such as gene/reaction removal or addition, making it easy for users to correct errors found in pathway analysis and obtain more reliable pathways. With a focus on the design and analysis of optimal pathways for biochemicals, CAVE complements existing visualization tools based on manually drawn global maps and can be applied to a broader range of organisms for rational metabolic engineering. CAVE is available at https://cave.biodesign.ac.cn/.
Forkhead box protein D2 suppresses colorectal cancer by reprogramming enhancer interactions
Authors: Kim Hyo-Min , Kang Byunghee , Park Sohyun , Park Hyorim , Kim Chan Johng , Lee Hyeonji , Yoo Mijoung , Kweon Mi-Na , Im Sin-Hyeog , Kim Tae Il , Roh Tae-Young
Published: May 2023

Somatic stem cells contribute to normal tissue homeostasis, and their epigenomic features play an important role in regulating tissue identities or developing disease states. Enhancers are one of the key players controlling chromatin context-specific gene expression in a spatial and temporal manner while maintaining tissue homeostasis, and their dysregulation leads to tumorigenesis. Here, epigenomic and transcriptomic analyses reveal that forkhead box protein D2 (FOXD2) is a hub for the gene regulatory network exclusive to large intestinal stem cells, and its overexpression plays a significant role in colon cancer regression. FOXD2 is positioned at the closed chromatin and facilitates mixed-lineage leukemia protein-4 (MLL4/KMT2D) binding to deposit H3K4 monomethylation. De novo FOXD2-mediated chromatin interactions rewire the regulation of p53-responsive genes and induction of apoptosis. Taken together, our findings illustrate the novel mechanistic details of FOXD2 in suppressing colorectal cancer growth and suggest its function as a chromatin-tuning factor and a potential therapeutic target for colorectal cancer.
Attenuation of a DNA cruciform by a conserved regulator directs T3SS1 mediated virulence in Vibrio parahaemolyticus
Authors: Getz Landon J , Brown Justin M , Sobot Lauren , Chow Alexandra , Mahendrarajah Jastina , Thomas Nikhil A
Published: May 2023

Pathogenic Vibrio species account for 3–5 million annual life-threatening human infections. Virulence is driven by bacterial hemolysin and toxin gene expression often positively regulated by the winged helix-turn-helix (wHTH) HlyU transcriptional regulator family and silenced by histone-like nucleoid structural protein (H-NS). In the case of Vibrio parahaemolyticus, HlyU is required for virulence gene expression associated with type 3 Secretion System-1 (T3SS1) although its mechanism of action is not understood. Here, we provide evidence for DNA cruciform attenuation mediated by HlyU binding to support concomitant virulence gene expression. Genetic and biochemical experiments revealed that upon HlyU mediated DNA cruciform attenuation, an intergenic cryptic promoter became accessible allowing for exsA mRNA expression and initiation of an ExsA autoactivation feedback loop at a separate ExsA-dependent promoter. Using a heterologous E. coli expression system, we reconstituted the dual promoter elements which revealed that HlyU binding and DNA cruciform attenuation were strictly required to initiate the ExsA autoactivation loop. The data indicate that HlyU acts to attenuate a transcriptional repressive DNA cruciform to support T3SS1 virulence gene expression and reveals a non-canonical extricating gene regulation mechanism in pathogenic Vibrio species.
IRSOM2: a web server for predicting bifunctional RNAs
Authors: Postic Guillaume , Tav Christophe , Platon Ludovic , Zehraoui Farida , Tahi Fariza
Published: May 2023

Recent advances have shown that some biologically active non-coding RNAs (ncRNAs) are actually translated into polypeptides that have a physiological function as well. This paradigm shift requires adapted computational methods to predict this new class of ‘bifunctional RNAs’. Previously, we developed IRSOM, an open-source algorithm to classify non-coding and coding RNAs. Here, we use the binary statistical model of IRSOM as a ternary classifier, called IRSOM2, to identify bifunctional RNAs as a rejection of the two other classes. We present its easy-to-use web interface, which allows users to perform predictions on large datasets of RNA sequences in a short time, to re-train the model with their own data, and to visualize and analyze the classification results thanks to the implementation of self-organizing maps (SOM). We also propose a new benchmark of experimentally validated RNAs that play both protein-coding and non-coding roles, in different organisms. Thus, IRSOM2 showed promising performance in detecting these bifunctional transcripts among ncRNAs of different types, such as circRNAs and lncRNAs (in particular those of shorter lengths). The web server is freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr.
svCapture: efficient and specific detection of very low frequency structural variant junctions by error-minimized capture sequencing
Authors: Wilson Thomas E , Ahmed Samreen , Higgins Jake , Salk Jesse J , Glover Thomas W
Published: May 2023

Error-corrected sequencing of genomic targets enriched by probe-based capture has become a standard approach for detecting single-nucleotide variants (SNVs) and small insertion/deletions (indels) present at very low variant allele frequencies. Less attention has been given to comparable strategies for rare structural variant (SV) junctions, where different error mechanisms must be addressed. Working from samples with known SV properties, we demonstrate that duplex sequencing (DuplexSeq), which demands confirmation of variants on both strands of a source DNA molecule, eliminates false SV junctions arising from chimeric PCR. DuplexSeq could not address frequent intermolecular ligation artifacts that arise during Y-adapter addition prior to strand denaturation without requiring multiple source molecules. In contrast, tagmentation libraries coupled with data filtering based on strand family size greatly reduced both artifact classes and enabled efficient and specific detection of single-molecule SV junctions. The throughput of SV capture sequencing (svCapture) and base-level accuracy of DuplexSeq provided detailed views of the microhomology profile and limited occurrence of de novo SNVs near the junctions of hundreds of newly created SVs, suggesting end joining as a possible formation mechanism. The open source svCapture pipeline enables rare SV detection as a routine addition to SNVs/indels in properly prepared capture sequencing libraries.
Effects of Disease Resistance and Fungicide Application on Management of Tar Spot on Corn in the North Central United States
Authors: Ross Tiffanna J. , Chilvers Martin I. , Byrne Adam M. , Smith Damon L. , Mueller Brian , Shim Sujoung , Telenko Darcy E. P.
Published: May 2023

Tar spot, caused by Phyllachora maydis, is the most significant disease of corn in the North Central United States. Elucidating an integrated management approach to protect grain yield is a high priority. The integration of tillage, hybrid, and fungicide application on tar spot severity, canopy greenness, and grain yield was assessed in Indiana in 2019, 2020, and 2021. A split-plot arrangement of two tillage treatments as main plots with factorial arrangement of subplots with three hybrids (tar spot susceptible and two partially resistant) and fungicide application (propiconazole + benzovindiflupyr + azoxystrobin) were evaluated. Furthermore, a multistate study comparing two hybrids (susceptible and partially resistant) and fungicide application (propiconazole + benzovindiflupyr + azoxystrobin) was conducted in Indiana, Michigan, and Wisconsin in 2020. This research demonstrates that partially resistant hybrids with a standardized area under the disease progress curve of 2.5 and 3.0 had significantly less tar spot than a susceptible hybrid with a standardized area under the disease progress curve of 10.1 and increased canopy greenness ratings of 48.1 and 51.5%, which were significantly higher than the susceptible hybrid at 13.0% at maturity. Tar spot severity was further reduced and canopy greenness increased with a fungicide application in the susceptible hybrid. These results suggest that partial resistance alone may be used to manage tar spot. Yields did not differ significantly across hybrids with or without a fungicide application. However, a general trend of preserved yield potential was observed in the treatments with fungicide, indicating that knowledge of genetics and yield potential will be necessary to achieve the greatest benefit from partially resistant hybrids and judicious fungicide applications.
Comparison of Sequencing Methods for Obtaining a Whole Genome of Pea Necrotic Yellow Dwarf Virus from U.K. Peas
Authors: Fowkes A. R. , Duffy S. , McGreig S. , Vazquez-Iglesias I. , Alraiss K. , Barrett B. , Conyers C. , Webster G. , Ward R. , Chisnall K. , Mynett M. , Adams I. P. , Macarthur R. , Howard B. , Fox A.
Published: May 2023

During a project investigating pea viruses in the United Kingdom and developing a workflow for high-throughput sequencing in crop surveillance, pea necrotic yellow dwarf virus (PNYDV) was identified at one site, along with pea enation mosaic virus-1, pea enation mosaic virus-2, pea enation mosaic virus satellite RNA, pea seedborne mosaic virus, and turnip yellows virus. Following an initial finding of small PNYDV contigs by an RNA sequencing protocol on MiSeq (Illumina), confirmation and prevalence testing by PCR and Sanger sequencing determined the average PNYDV prevalence to be 3%. This is the first report of PNYDV, and a nanovirus, in the United Kingdom. Initial characterization of the octopartite genome by PCR revealed that component DNA N had a truncated sequence that differed from those previously reported. This led to confirmation testing using rolling circle amplification (RCA) into MiSeq and then MinION (Oxford Nanopore). Sequences were obtained by both RCA-MiSeq and RCA-MinION, with MinION producing more complete genomes than RCA-MiSeq. Data obtained from sequencing were used to provide an initial estimation of the genomic formula of PNYDV. Previous work has looked into comparing each method; however, this study shows how these methods can be used together. The truncated sequence for DNA N was also found by RCA-MiSeq and RCA-MinION and confirmed by specific primers, but further work is required to understand the impact of this truncation.

[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 .
Innovations in Learning
Authors: DeBrew Jacqueline , Lindsey Karen
Published: May 2023

Because of a dearth of available resources, faculty faced with creating a Foundations of Nursing course aligned with the revised American Association of Colleges of Nursing Essentials for a new accelerated baccalaureate program struggled to design an innovative way to integrate concepts that demonstrate the role of the professional nurse. With the help of a colleague from the Communications Department, an innovative assignment was developed that engaged students throughout the semester. The assignment created a foundation for students’ practice as professional nurses.
Costs of Surgery in Adult Spinal Deformity
Authors: Joujon-Roche Rachel , Dave Pooja , Tretiakov Peter , Mcfarland Kimberly , Mir Jamshaid , Williamson Tyler K. , Imbo Bailey , Krol Oscar , Lebovic Jordan , Schoenfeld Andrew J , Vira Shaleen , Lafage Renaud , Lafage Virginie , Passias Peter G.
Published: May 2023

Study Design.

Retrospective

Objective.

To assess impact of surgical costs on patient reported outcomes in ASD.

Summary of Background Data.

With increased focus on delivering cost effective healthcare, interventions with high resource utilization, such as adult spinal deformity (ASD) surgery, have received greater scrutiny.

Methods.

ASD patients≥18 years with BL and 2Y data were included. Surgical costs were calculated using 2021 average Medicare reimbursement by CPT code. Costs of complications and reoperations were intentionally excluded. Patients were ranked into tertiles by surgical cost: highest surgical costs (HC) and lowest surgical costs (LC). They were propensity score matched (PSM) to account for differences in baseline age and deformity. Bivariate logistic regressions assessed odds of achieving outcomes.

Results.

421 patients met inclusion (60.7 y, 81.8% female, CCI: 1.6, 27.1 kg/m2), 139 LC and 127 HC patients. After PSM, 102 patients remained in each cost group with an average reimbursement of LC: $12,494 versus HC: $29,248. Matched cohorts had similar demographics and baseline HRQLs. Matched groups had similar baseline SVA (HC: 59.0 vs. LC: 56.7 mm), PI-LL (HC: 13.1 vs. LC: 13.4°), and PT (HC: 25.3 vs. LC: 22.4°). Rates of complications were not significantly different between the cost groups. Compared to LC group, by 2Y HC patients had higher odds of reaching SCB in ODI (OR: 2.356, [1.220, 4.551], P=0.011), in SRS-Total (OR: 2.988, [1.515, 5.895], P=0.002), and in NRS Back (OR: 2.739, [1.105, 6.788], P=0.030). Similar findings were appreciated for HC patients in the setting of Schwab deformity outcome criteria.

Conclusions.

Although added cost did not guarantee an ideal outcome, HC patients experienced superior patient reported outcomes compared to LC patients. While cost efficiency remains an important priority for health policy, isolating cost reduction may compromise outcomes and add to future costs of re-intervention, particularly with more severe baseline deformity.

Level of Evidence.

III
Interleukin-1 Blockers for the Treatment of Recurrent Pericarditis: Pathophysiology, Patient-Reported Outcomes, and Perspectives
Authors: Thomas Georgia K. , Bonaventura Aldo , Vecchié Alessandra , van Tassell Benjamin , Imazio Massimo , Klein Allan , Luis Sushil Allen , Abbate Antonio
Published: May 2023

Recurrent pericarditis (RP) is the most troublesome complication of acute pericarditis reflecting an unresolving inflammation of the pericardial sac around the heart and associated with significant morbidity. Recent studies have shown interleukin-1 (IL-1) signaling to be central to the pathophysiology of cases of RP with evidence of activation of systemic inflammation. We herein review the literature and clinical trials discussing the utility of IL-1 blockade for RP. The early experience of IL-1 blockade with anakinra (Kineret) and its favorable safety profile paved the way for the clinical development of rilonacept (Arcalyst) and subsequent approval by the US FDA for RP. In patients with RP who have become colchicine-resistant and glucocorticoid-dependent, IL-1 blockade with rilonacept or anakinra effectively treats recurrences and prevents future flares and significantly improves quality of life.
Quality Matters: Examining the Impact of Nurse Staffing Challenges on Clinical Outcomes
Authors: Polancich Shea , Miltner Rebecca , Montgomery Aoyjai , Dick Tracey , Poe Terri , Brown Daran , Patrician Patricia A.
Published: May 2023

Goal:

The purpose of this study was to examine nurse staffing while describing the relationships that exist in staffing and quality associated with nursing care during the COVID-19 pandemic, a significantly challenging time for nurse staffing. We examined the relationship between permanent registered nurse (RN) and travel RN staffing during the pandemic and the nursing-sensitive outcomes of catheter-associated urinary tract infections (CAUTIs), central line-associated bloodstream infections (CLABSIs), falls, and hospital-acquired pressure injuries (HAPIs) and length of stay and compared the cost of CAUTIs, CLABSIs, falls, and HAPIs in fiscal years 2021 and 2022.

Methods:

We used a descriptive, observational design to retrospectively examine permanent nurse staffing volume and CAUTI, CLABSI, HAPI, and fall counts from October 1, 2019, to February 28, 2022, and travel nurse volume for the most current 12 months, April 1, 2021, to March 31, 2022. Descriptive statistics, Pearson correlation, and statistical process control analyses were completed.

Principal Findings:

Pearson correlation showed a statistically significant, moderately strong negative correlation (r = −0.568, p = .001) between the active registered nurse full-time equivalents (RN FTEs) and average length of stay (ALOS), and a moderately strong positive correlation (r = 0.688, p = .013) between the travel RN FTEs and ALOS. Pearson correlations were not statistically significant, with low to moderate negative correlations for CAUTIs (r = −0.052, p = .786), CLABSIs (r = −0.207, p = .273), and falls (r = −0.056, p = .769). Pearson correlation for active RN and HAPI showed a moderately strong, statistically significant positive correlation (r = 0.499, p = .003). We observed common cause variation in CAUTIs and CLABSIs, with HAPIs and falls showing special cause variation via statistical process control.

Practical Applications:

Despite the challenges associated with the lack of available nurse staffing accompanied by increasing responsibilities including unlicensed tasks, positive clinical outcomes can be maintained by staff adherence to evidence-based quality improvement.
The Patient Experience of Adolescents With Traumatic Injuries: Recommendations for Improvement
Authors: McCord Emma , Ballard Joseph H. , Mills Carol A. , Bandali Elhaam , Bell Teresa M. , Mazurenko Olena
Published: May 2023

Goal:

Positive patient experience is associated with less healthcare utilization, better treatment adherence, increased likelihood of returning to the same hospital, and fewer complaints. However, hospitals have been able to collect few insights into the experiences of pediatric patients due to age limitations. As an exception to that reality, adolescents (aged 12–20 years) are able to share their experiences and recommend improvements, yet little is known about their hospital experiences with traumatic injuries. We examined the patient experience of adolescents with traumatic injuries and collected their recommendations for improving care.

Methods:

We conducted 28 semistructured interviews with English-speaking adolescents hospitalized at two trauma Level 1 hospitals (pediatric and adult) for physical injuries from July 2018 to June 2021. Interviews were transcribed and analyzed using modified thematic analysis.

Principal Findings:

The patients expressed three basic desires: (1) autonomy and active involvement in their care, (2) human connections with their clinicians, and (3) minimal discomfort. Study participants provided actionable recommendations for improving the patient experience for adolescents with traumatic injuries.

Practical Applications:

Hospital administrators and clinicians can improve the patient experience for adolescents in their care by sharing information, expectations, and goals with them. Hospital administrators can also empower the clinical staff to connect with adolescents with traumatic injuries on a personal level.
Transoral endoscopic thyroidectomy vestibular approach as a safe and feasible alternative to open thyroidectomy: a systematic review and meta-analysis
Authors: Oh Moon Young , Chai Young Jun , Yu Hyeong Won , Kim Su-Jin , Choi June Young , Lee Kyu Eun
Published: May 2023

Background:

Transoral endoscopic thyroidectomy vestibular approach (TOETVA) is a scarless alternative to open thyroidectomy (OT). This systematic review and meta-analysis aimed to synthesize evidence comparing the intraoperative and postoperative outcomes of TOETVA and OT.

Methods:

A systematic literature search of PubMed, Web of Science, the Cochrane Library, and Google Scholar was performed to identify studies comparing the outcomes of TOETVA and OT published before February 2023. The outcomes of interest were operative time, intraoperative blood loss, hospital stay, postoperative pain, number of central lymph nodes retrieved, number of metastatic central lymph nodes, and incidences of transient and permanent recurrent laryngeal nerve injury, transient and permanent hypocalcemia, hematoma, and infection.

Results:

Thirteen studies published between 2016 and 2022, involving a total of 2889 patients (TOETVA, n=1085; OT, n=1804) were included in this systematic review and meta-analysis. Meta-analysis showed that the TOETVA group had a significantly longer overall operative time (weighted mean difference [WMD] 55.19; 95% CI, 39.15, 71.23; P<0.001), longer hospital stay (WMD, 0.27; 95% CI, 0.14, 0.39; P<0.001), and lower pain scores on postoperative day 1 (WMD, −1.41; 95% CI, −2.79, −0.03; P=0.04) than the OT group. Other intraoperative and postoperative outcomes were not significantly different between the groups.

Conclusion:

TOETVA has a similar safety profile to OT with less postoperative pain, making it an appropriate and more cosmetically appealing alternative to OT for select patients.
Postoperative infectious complications following laparoscopic versus open hepatectomy for hepatocellular carcinoma: a multicenter propensity score analysis of 3876 patients
Authors: Pu Jia-Le , Xu Xiao , Chen Lan-Lan , Li Chao , Jia Hang-Dong , Fan Zhong-Qi , Li Ju-Dong , Guan Ming-Cheng , Liang Ying-Jian , Zhou Ya-Hao , Wang Xian-Ming , Gu Wei-Min , Wang Hong , Li Jie , Chen Zhi-Yu , Chen Ting-Hao , Zhang Yao-Ming , Chen Zi-Xiang , Yao Lan-Qing , Diao Yong-Kang , Wang Ming-Da , Shen Feng , Pawlik Timothy M. , Lau Wan Yee , Chen Zhong , Yang Tian , Lv Guo-Yue
Published: May 2023

Objectives:

Hepatocellular carcinoma (HCC) is a common indication for hepatectomy that is often complicated by postoperative complication. The authors sought to investigate the relationship between the open with laparoscopic approach of hepatectomy and incidences of postoperative infectious complications.

Patients and methods:

Using a multicenter database, HCC patients who underwent laparoscopic hepatectomy (LH) or open hepatectomy (OH) were reviewed and analyzed. Propensity score matching (PSM), inverse probability of treatment weight (IPTW), and multivariate logistic regression analyses were utilized to assess the association of the operative approach with postoperative infectious complications, including incisional surgical site infection (SSI), organ/space SSI, and remote infection (RI).

Results:

Among 3876 patients, 845 (21.8%) and 3031 (78.2%) patients underwent LH and OH, respectively. The overall incidence of infection was 6.9versus14.6% among patients who underwent LHversusOH, respectively (P<0.001). Of note, the incidences of incisional SSI (1.8 vs. 6.3%,P<0.001), organ/space SSI (1.8 vs. 4.6%,P<0.001), and RI (3.8 vs. 9.8%,P<0.001) were all significantly lower among patients who underwent LHversusOH. After PSM (6.9, 1.8, 1.8, and 3.8% vs. 18.5, 8.4, 5.2, and 12.8%, respectively) and IPTW (9.5, 2.3, 2.1, and 5.5% vs. 14.3, 6.3, 4.5, and 9.8%, respectively), LH remained associated with statistically lower incidences of all types of infectious complications. After adjustment for other confounding factors on multivariate analyses, LH remained independently associated with lower incidences of overall infection, incisional SSI, organ/space SSI, and RI in the overall, PSM, and IPTW cohorts, respectively.

Conclusion:

Compared with open approach, laparoscopic approach was independently associated with lower incidences of postoperative infectious complications following hepatectomy for HCC.
Comparisons of different new-generation transcatheter aortic valve implantation devices for patients with severe aortic stenosis: a systematic review and network meta-analysis
Authors: Yang Yi-Xing , Liu Xin-Ming , Fu Yuan , Li Chuang , Wang Hong-Jiang , Xu Li , Xia Kun , Zhang Zhi-Yong , Zhong Jiu-Chang , Chen Mu-Lei , Su Pi-Xiong , Wang Le-Feng
Published: May 2023

Background:

Whether there are differences among the new-generation transcatheter aortic valve implantation (TAVI) devices for patients with aortic stenosis remains unclear. The aim of the study was to compare the efficiency and safety of different new-generation TAVI devices for patients with aortic stenosis.

Materials and methods:

A comprehensive search of PubMed, Embase and Web of Science from their inception to 1 February 2022. Randomized clinical trials and observational studies that compared two or more different TAVI devices were enroled. Pairwise meta-analysis and frequentist network meta-analysis were conducted to pool the outcome estimates of interest.

Results:

A total of 79 studies were finally included. According to the surface under the cumulative ranking, the top two ranked valves for lower rates of events were as follows: direct flow medical (DFM) (4.6%) and Lotus (48.8%) for lower rate of device success; Sapien 3 (16.8%) and DFM (19.7%) for lower mortality; DFM (8.6%) and Sapien 3 (25.5%) for lower rates of stroke; Evolut (27.6%) and DFM (35.8%) for lower rates of major and life-threatening bleeding; Portico (22.6%) and Sapien 3 (41.9%) for lower rates of acute kidney injury; Acurate (8.6%) and DFM (13.2%) for lower rates of permanent pacemaker implantation; Lotus (0.3%) and Sapien 3 (22.7%) for lower rates of paravalvular leak; Evolut (1.4%) and Portico (29.1%) for lower rates of mean aortic valve gradients.

Conclusions:

The findings of the present study suggested that the device success rates were comparable among these new-generation valves except for DFM. After excluding DFM, Sapien 3 might be the best effective for decreased mortality and stroke; Lotus might be the best effective for decreased paravalvular leak; Evolut might be the best effective for decreased major and life-threatening bleeding and mean aortic valve gradients; Acurate and Portico might be the best effective for decreased permanent pacemaker implantation and acute kidney injury, respectively.
Quantification of institutional and professional impact of a professional advancement program for advanced practice registered nurses and physician assistants
Authors: Kuriakose Clair , Chan Garrett K. , Haven Angela , Remer Lauren , Milliken Amy , Majabo Baker Anita , Sen Krishneel , Tippett Vicki
Published: May 2023

Professional advancement programs, also known as career or clinical ladders, have proliferated for advanced practice registered nurses (APRNs) and physician assistants (PAs) and recognize clinical and/or professional contributions within clinical agencies. Although the literature is rich in describing the benefits of these programs on job satisfaction and staff retention, there is a dearth of literature on the effect of these programs on clinical practice, institutions, and the respective professions. This article quantifies the impact on the institution and profession of APRNs and PAs who have been promoted through an institution's career ladder.
Early allograft dysfunction after living donor liver transplantation—current concepts and future directions
Authors: Agrawal Dhiraj , Saigal Sanjiv
Published: May 2023

Early allograft dysfunction (EAD) after liver transplantation is a significant clinical problem that negatively impacts graft and patient outcomes. The rising incidence of EAD and what it means concerning living donor liver transplantation (LDLT) is an area of great interest. However, EAD after LDLT is a complex research topic yet to be reviewed comprehensively. Most of the literature on EAD is based on experience in deceased donor liver transplantation, and limited information is available in the context of LDLT. Thus, in this review, we present an overview of EAD after LDLT and have attempted to present balanced points of view on all its aspects, such as definitions, pathogenesis, risk factors, predictive markers, and management. The review aims to broadly overview the nature and extent of ongoing research evidence on this complex topic and inform practice in the field by identifying key concepts and knowledge gaps and highlighting areas that require further inquiry.
Zhu Fan Zhi and the Maritime Road of Aromatic Medicine in the Song Dynasty
Authors: Zhilin YU , ZHANG Yuan
Published: May 2023

Zhao Rukuo’s Zhu Fan Zhi in the Southern Song dynasty was the first book in the history of China to systematically describe the “Maritime Silk Road”, recording the geography, products, customs, trade, etc. of more than 50 foreign countries and regions. The book included a large amount of medical literature, introducing medical customs and the production of drugs in various places, as well as the efficacy of some medicine. These materials are of unique value for understanding the medicine trade in the Song dynasty, and even the medical culture along the “Maritime Road of Aromatic Medicine”.
Asynchronous Learning Module for Pediatric Emergency Medicine Physicians on How to Manage Vaginal Birth and Neonatal Resuscitation in the Emergency Department
Authors: Nickerson Jillian , McCollum Nichole , Abdulrahman Eiman , Marko Kathryn , Soghier Lamia , Rucker Alexandra , Madati Jamil , Zhao Xian
Published: May 2023

Objectives

Newborn deliveries and neonatal resuscitation events are rare but essential skills for pediatric emergency medicine (PEM) physicians. We sought to evaluate the effect of an online module on PEM physicians' knowledge and confidence in managing newborn deliveries and neonatal resuscitation.

Methods

A team of experts in PEM, obstetrics, neonatology, and medical education developed a self-directed, 1-hour online module on managing newborn deliveries with neonatal resuscitation. The module was designed to address the learning needs of the targeted group. The module was piloted before dissemination to PEM faculty. A 10-question multiple choice test was given to assess knowledge of the material covered. A 10-point Likert scale questions survey was used to evaluate confidence. Measures were administered before initiation, after module completion, and 6 months after completion. Pairedttests were used to compare mean knowledge scores, and rank sum tests were used to compare median confidence levels.

Results

Most (n = 47, 89%) of the PEM faculty members completed the module. The majority (n = 43, 91%) thought the information was relevant to their practice. After completing the module, physicians' overall knowledge scores improved by 18% (mean [SD]: 74% [14.7] vs 92% [8.0],P< 0.01). Self-assessed confidence improved after the module in terms of managing uncomplicated vaginal deliveries (median 5 vs 7,P< 0.01), care of patients with complicated vaginal deliveries (2 vs 5,P< 0.01), and managing neonatal resuscitation (7 vs 8,P< 0.01). During the 6-month follow-up, there was sustained improvement in physicians' overall knowledge score (82% [16.9],P= 0.007) and self-assessed confidence in managing complicated vaginal deliveries (median 2 vs 4,P= 0.0012); however, other measures were not statistically significant.

Conclusions

An online module is an appropriate method for training PEM providers about rarely used but essential skills such as managing vaginal deliveries and neonatal resuscitation.
“Frailty Indices Outperform Historic Risk Proxies as Predictors of Post-Abdominoplasty Complications: An Analysis of a National Database”
Authors: Akhavan Arya A. , Liu Helen , Alerte Eric , Ibelli Taylor , Etigunta Suhas K. , Katz Abigail , Kuruvilla Annet S. , Taub Peter J.
Published: May 2023

Background:

While age, BMI, and major comorbidities were historically used as predictors of surgical risk, recent literature supports patient frailty as a more accurate predictor. Database studies and chart reviews support the modified Charlson Comorbidity Index (mCCI) and the Modified 5-Item Frailty Index (mFI-5) as predictors of postsurgical complications in plastic surgery. The authors hypothesized that the mFI-5 and mCCI are more predictive of abdominoplasty complications than historic risk proxies.

Methods:

A retrospective review of the NSQIP database was performed, for abdominoplasty patients from 2013 to 2019. Demographics, comorbidities, and complications were gathered. The mFI-5 and mCCI scores were calculated per patient. Age, BMI, major comorbidities, ASA class, mFI-5 score, and mCCI score were compared as predictors of all-cause 30-day complications, 30-day surgical site complications, length of stay, and aggregate Clavien-Dindo complication severity score.

Results:

Of 421 patients, the strongest predictors for all-cause complications and complication severity were mCCI score ≥ 3 and mFI-5 score ≥2. mFI-5 score was the strongest predictor of unplanned reoperation. Length of stay was best predicted by age ≥ 65. The only predictor of surgical site complications was BMI ≥ 30.0. Smoking was predictive of complication severity, but not any other outcome.

Conclusions:

The mFI-5 and mCCI are stronger outcome predictors than historically-used factors, which showed little predictive value in this cohort. While the mCCI is a stronger predictor than the mFI-5, the mFI-5 is easily calculated during an initial consultation. Surgeons can apply these tools to aid in risk stratification for abdominoplasty.
Repair of Scars and Tissue Deficiency With Free Grafts of Full-thickness Scalp in Secondary Unilateral Cleft Lip Deformity
Authors: Wang Zi , Yu Baofu , Chen Xiaoxue , Li Qingfeng , Dai Chuanchang , Wei Jiao
Published: May 2023

Although surgical techniques have developed, the incidence of secondary cleft lip deformities after the primary repair is still high. Asymmetry of Cupid’s bow and philtrum is a common presentation and a technical challenge to reconstruct the upper lip. The authors introduce a technique to use the free grafts of the full-thickness scalp for the correction of scars and tissue deficiency in secondary unilateral cleft lip deformity. Thirty-seven patients with a prominent scar, tight upper lip, deformed Cupid’s bow and philtrum, and irregular vermillion border were included in this study. The specific points of interest were assessed before and after surgery by independent examiners with both subjective and objective methods. All surgeries were successfully completed, and the assessment results were satisfactory. The rating scores of philtrum improvement was 1.6±0.4, the POSAS result of patient scales was 13.48±3.21, and the observer scale result was 11.98±3.88. The asymmetry of Cupid’s bow was corrected (P=0.004), the central tubercle of vermilion was more natural (P=0.001), and the irregular vermillion border was improved (P=0.015). The results presented significant differences before and after surgery. This method could be an optional treatment for repairing scars and tissue deficiency in secondary unilateral cleft lip deformity.
Determining the educational impact of virtual patients on trauma team training during a multinational, large-scale civil military simulation exercise
Authors: Sonesson Linda , Boffard Kenneth D. , Örtenwall Per , Vekzsler Péter
Published: May 2023

BACKGROUND

With asymmetrical conflicts ongoing, many countries have an increasing number of major trauma events but limited capacity to cope with these events. Training for such events comprises primarily of simulations requiring significant resources and that are time-consuming and expensive. Virtual patients are defined as computer-based programs presenting authentic cases support training in trauma management.

HYPOTHESIS

Assisted learning technologies augment simulated trauma team training and can improve trauma team competencies. The aim was to investigate if virtual patients increased competencies in decision making required and to identify deficiencies in care for the management of trauma patients during a multinational civil military trauma exercise.

METHODS

A prospective educational intervention study with mixed methods, measuring the effects of a novel virtual patient model on trauma teams, was performed. The population consisted of surgeons, anesthesiologists, emergency department physicians, nurses, and paramedics (n = 30) and constituted six trauma teams from eight countries; three trauma teams formed the participating group, and three were allocated as control group. The participating group was exposed to virtual patients before, during, and after the live simulation exercise. Data sources were derived from individual preassessments and postassessments, evaluations made by experts in trauma, and video recordings of performance during the live simulation exercise and analyzed by the thematic analysis method.

RESULTS

Using virtual patients contributed to improved individual knowledge about the management of major trauma patients and improved teamwork. Virtual patients as support for reasoning in decision making were directly correlated to level of previous knowledge and experience. Two of the three participating trauma teams showed lower levels of existing knowledge and competence in managing major trauma patients and therefore made more efficient use of the virtual patients.

CONCLUSION

Results demonstrated advantages using virtual patients during a major civil military trauma live simulation exercise and appear to be supportive especially for teams who are not as experienced.

LEVEL OF EVIDENCE

Therapeutic/Care Management; Level IV.
Epigenetic opportunities for evolutionary computation
Authors: Yuen Sizhe , Ezard Thomas H. G. , Sobey Adam J.
Published: May 2023

Evolutionary computation is a group of biologically inspired algorithms used to solve complex optimization problems. It can be split into evolutionary algorithms, which take inspiration from genetic inheritance, and swarm intelligence algorithms, that take inspiration from cultural inheritance. However, much of the modern evolutionary literature remains relatively unexplored. To understand which evolutionary mechanisms have been considered, and which have been overlooked, this paper breaks down successful bioinspired algorithms under a contemporary biological framework based on the extended evolutionary synthesis, an extension of the classical, genetics focused, modern synthesis. Although the idea of the extended evolutionary synthesis has not been fully accepted in evolutionary theory, it presents many interesting concepts that could provide benefits to evolutionary computation. The analysis shows that Darwinism and the modern synthesis have been incorporated into evolutionary computation but the extended evolutionary synthesis has been broadly ignored beyond: cultural inheritance, incorporated in the sub-set of swarm intelligence algorithms, evolvability, through covariance matrix adaptation evolution strategy (CMA-ES), and multilevel selection, through multilevel selection genetic algorithm (MLSGA). The framework shows a gap in epigenetic inheritance for evolutionary computation, despite being a key building block in modern interpretations of evolution. This leaves a diverse range of biologically inspired mechanisms as low hanging fruit that should be explored further within evolutionary computation and illustrates the potential of epigenetic based approaches through the recent benchmarks in the literature.
Tail feather strength in tail-assisted climbing birds is achieved through geometric, not material change
Authors: Dickinson Edwin , Young Melody W. , DeLeon David , Bas Burcak , Zou Bettina , Ratkiewicz Aleksandra , Beatty Brian L. , Granatosky Michael C.
Published: May 2023

Birds encompass vast ecomorphological diversity and practise numerous distinct locomotor modes. One oft-cited feature seen in climbing birds is an increase in tail ‘stiffness’, yet it remains unclear to what extent these feathers are altered, and the specific mechanism by which differences in functional performance are attained. We collected a broad taxonomic sample of tail feathers (6525 total, from 774 species representing 21 avian orders and ranging in size from approximately 3 g to greater than 11 kg) and present data on their material properties, cross-sectional geometry and morphometrics. Ordinary and phylogenetic least-squares regressions of each variable versus body mass were conducted to assess scaling relationships and demonstrate that tail-supported climbers exhibit longer tail feathers with a wider rachis base and tip, and a greater second moment of area and maximum bending moment. However, no differences were observed in the material properties of the keratin itself. This suggests that tail-supported arboreal climbing birds of multiple orders have independently adopted similar morphologies. Moreover, these geometric relationships follow the same allometric scaling relationships as seen in the long bones of mammalian limbs, suggesting that the morphology of these developmentally and evolutionarily distinct structures are governed by similar functional constraints of weight support.
Virulence decomposition for bifurcating infections
Authors: Franz Mathias , Armitage Sophie A. O. , Rolff Jens , Regoes Roland R.
Published: May 2023

A fundamental goal in infection biology is to understand the emergence of variation in pathogen virulence—here defined as the decrease in host fitness caused by a pathogen. To uncover the sources of such variation, virulence can be decomposed into both host- and pathogen-associated components. However, decomposing virulence can be challenging owing to complex within-host pathogen dynamics such as bifurcating infections, which recently received increased empirical and theoretical attention. Bifurcating infections are characterized by the emergence of two distinct infection types: (i) terminal infections with high pathogen loads resulting in rapid host death, and (ii) persistent infections with lower loads and delayed host death. Here, we propose to use discrete mixture models to perform separate virulence decompositions for each infection type. Using this approach, we reanalysed a recently published experimental dataset on bacterial load and survival in
Drosophila melanogaster
. This analysis revealed several advantages of the new approach, most importantly the generation of a more comprehensive picture of the varying sources of virulence in different bacterial species. Beyond this application, our approach could provide valuable information for ground-truthing and improving theoretical models of within-host infection dynamics, which are developed to predict variation in infection outcome and pathogen virulence.
Protected fish spawning aggregations as self-replenishing reservoirs for regional recovery
Authors: Stock Brian C. , Mullen Andrew D. , Jaffe Jules S. , Candelmo Allison , Heppell Scott A. , Pattengill-Semmens Christy V. , McCoy Croy M. , Johnson Bradley C. , Semmens Brice X.
Published: May 2023

Dispersal of eggs and larvae from spawning sites is critical to the population dynamics and conservation of marine fishes. For overfished species like critically endangered Nassau grouper (
Epinephelus striatus
), recovery depends on the fate of eggs spawned at the few remaining aggregation sites. Biophysical models can predict larval dispersal, yet these rely on assumed values of key parameters, such as diffusion and mortality rates, which have historically been difficult or impossible to estimate. We used
in situ
imaging to record three-dimensional positions of individual eggs and larvae in proximity to oceanographic drifters released into egg plumes from the largest known Nassau grouper spawning aggregation. We then estimated a diffusion–mortality model and applied it to previous years' drifter tracks to evaluate the possibility of retention versus export to nearby sites within 5 days of spawning. Results indicate that larvae were retained locally in 2011 and 2017, with 2011 recruitment being a substantial driver of population recovery on Little Cayman. Export to a nearby island with a depleted population occurred in 2016. After two decades of protection, the population appears to be self-replenishing but also capable of seeding recruitment in the region, supporting calls to incorporate spawning aggregation protections into fisheries management.
Long term stability of patients undergoing endovascular parent artery occlusion of their intracranial artery
Authors: Koizumi Satoshi , Shojima Masaaki , Ota Takahiro , Dofuku Shogo , Miyawaki Satoru , Kiyofuji Satoshi , Maeda Keiichiro , Ochi Takashi , Ito Akihiro , Hidaka Yukihiro , Oya Soichi , Saito Akira , Yoshikawa Gakushi , Yanai Kei , Inoue Tomohiro , Tsunoda Sho , Hoya Katsumi , Saito Nobuhito
Published: May 2023

Background

Although endovascular parent artery occlusion (PAO) of the intracranial artery is a well-established treatment option, the long-term stability of cerebral blood flow remains a concern. This study aimed to evaluate the long-term clinical and radiological outcomes of patients who underwent PAO.

Methods

The patients who underwent endovascular PAO of their internal carotid or vertebral artery (VA) between April 2011 and March 2022 were included in this observational study. Information about patient characteristics, details of the endovascular treatment, and clinical and radiological follow-up were collected.

Results

The study included a total of 104 cases (average age 52.9±12.6 years old, male 73 (70.2%) cases, 95 (91.3%) VA PAO cases) from eight centers. Most cases were performed in an emergency condition, such as ruptured vertebral artery dissecting aneurysm (73 cases [70.2%]). PAO was successful in all cases. Early stroke (within 30 days) occurred in 33 (31.7%) cases (31 cases in VA PAO and two cases in internal carotid PAO) with ischemic stroke (29 cases) comprising the largest group. Clinical follow-up over 12 months was available in 78 cases. During an average follow-up period of 49.5 ± 24.3 months, one case in VA PAO experienced a stroke without functional deterioration. Imaging follow-up was performed in 73 cases. Recanalization of the occluded VA was observed in two cases. The remaining image change was contralateral VA stenosis after VA PAO. The incidence of clinical and radiological events was 0.95 and 1.1% per patient-year, respectively.

Conclusions

Once the patients surpass the acute phase after PAO, their mid-to-long term course was stable. The risk of late stroke or de novo aneurysm formation was lower than expected in the literature, and the direct comparison to novel reconstructiv techniques is warranted in future studies.

Registration

https://www.umin.ac.jp/ctr/index.html, trial ID: UMIN000045160