bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and validation of a ferroptosis-related genes based prognostic signature for prostate cancer
Authors: Liu Huan , Gao Lei , Li Jie , Zhai Tingshuai , Xie Tiancheng , Xu Yunfei 
Published: October 2020

AbstractFerroptosis, an iron-dependent form of selective cell death, involves in the development of many cancers. However, systematic analysis of ferroptosis related genes (FRGs) in prostate cancer (PCa) remains to be clarified. In our research, we collected the mRNA expression profiles and clinical information of PCa patients from TCGA and MSKCC databases. The univariate, LASSO and multivariate Cox regression method were performed to construct prognostic signature in TCGA cohort. Seven FRGs, AKR1C3, ALOXE3, ATP5MC3, CARS1, MT1G, PTGS2, TFRC, were included to establish the risk model, which was validated in MSKCC dataset. Subsequently, we found that high risk group was strongly correlated with copy number alteration load, tumor burden mutation, immune cell infiltration, mRNAsi, immuetherapy and bicalutamide response. Finally, it was identified that overexpression of TFRC could induce proliferation and invasion in PCa cell linesin vitro.These results demonstrated that this risk model based on recurrence free survival (RFS) could accurately predict prognosis in PCa patients, suggesting that FRGs are promising prognostic biomarkers and drug target genes for PCa patients.
Shortcomings of human-in-the-loop optimization for an ankle-foot prosthesis: a case series
Authors: Welker Cara G. , Voloshina Alexandra S. , Chiu Vincent L. , Collins Steven H. 
Published: October 2020

ABSTRACTHuman-in-the-loop optimization allows for individualized device control based on measured human performance. This technique has been used to produce large reductions in energy expenditure during walking with exoskeletons but has not yet been applied to prosthetic devices. In this series of case studies, we applied human-in-the-loop optimization to the control of an active ankle-foot prosthesis used by participants with unilateral transtibial amputation. We optimized the parameters of five control architectures that captured aspects of successful exoskeletons and commercial prostheses, but none resulted in significantly lower metabolic rate than generic control. In one control architecture, we increased the exposure time per condition by a factor of five, but the optimized controller still resulted in higher metabolic rate. Finally, we optimized for self-reported comfort instead of metabolic rate, but the resulting controller was not preferred. There are several reasons why human-in-the-loop optimization may have failed for people with amputation. Control architecture is an unlikely cause given the variety of controllers tested. The lack of effect likely relates to adaptation protocol or differences in the learning mechanisms or objectives of people with amputation. Future work should investigate these causes to determine whether human-in-the-loop optimization for prostheses could be successful.
Fine tuning cyclic-di-GMP signaling inPseudomonas aeruginosausing the type 4 pili alignment complex
Authors: Webster Shanice S. , Lee Calvin K. , Schmidt William C. , Wong Gerard C. L. , O’Toole George A. 
Published: October 2020

AbstractTo initiate biofilm formation it is critical for bacteria to sense a surface and respond precisely. Type 4 pili (T4P) have been shown to be important in surface sensing, however, mechanism(s) driving downstream changes important for the switch to biofilm growth have not been clearly defined. Here, using macroscopic bulk assays and single cell tracking analyses ofPseudomonas aeruginosa, we uncover a new role of the T4P alignment complex protein, PilO, in modulating the activity of the diguanylate cyclase (DGC) SadC. Two hybrid and bimolecular fluorescence complementation assays show that PilO physically interacts with SadC and that the PilO-SadC interaction inhibits SadC’s activity resulting in decreased biofilm formation and increased motility. We show that disrupting the PilO-SadC interaction contributes to greater variation of cyclic-di-GMP levels among cells, thereby increasing cell-to-cell heterogeneity in the levels of this signal. Thus, this work shows thatP. aeruginosauses a component of the T4P scaffold to fine-tune the levels of this nucleotide signal during surface commitment. Finally, given our previous findings linking SadC to the flagellar machinery, we propose that this DGC acts as a bridge to integrate T4P and flagellar-derived input signals during initial surface engagement.Significance StatementT4P ofP. aeruginosaare important for surface sensing and regulating intracellular cyclic-di-GMP levels. This work identifies a new role for the T4P alignment complex, previously known for its role in supporting pili biogenesis, in surface-dependent signaling. Furthermore, our findings indicate thatP. aeruginosauses a single DGC, via a complex web of protein-protein interactions, to integrate signaling through the T4P and the flagellar motor to fine-tune cyclic-di-GMP levels. A key implication of this work is that more than just regulating signal levels, cells must modulate the dynamic range of cyclic-di-GMP to precisely control the transition to a biofilm lifestyle.
Progenesis as an intrinsic factor of ecological opportunity in a polyphenic amphibian
Authors: Lejeune Benjamin , Bissey Lucie , Didaskalou Emilie Alexia , Sturaro Nicolas , Lepoint Gilles , Denoël Mathieu 
Published: October 2020

Abstract

Paedomorphosis, a developmental heterochrony involving the retention of larval traits at the adult stage, is considered a major evolutionary process because it can generate phenotypic variation without requiring genetic modifications. Two main processes underlie paedomorphosis: neoteny, a slowdown of somatic development, and progenesis, a precocious maturation associated with body size reduction. Being essentially a truncation of ontogeny, progenesis has often been deemed an evolutionary dead end with advantages attributed to precocious reproduction or small body size required in specific environmental contexts (e.g. parasitism, interstitial life), but there is a lack of studies on the immediate ecological consequences of progenesis.

Because body size is a key factor determining trophic ecology in animals, we hypothesized that progenesis might intrinsically promote ecological opportunity via body size reduction (i.e. ‘the trophic advantage of progenesis’ hypothesis). We tested this hypothesis in facultatively progenetic palmate newts Lissotriton helveticus using stable isotope niche modelling and diet reconstruction in conjunction with traditional stomach content analyses and body condition (BC) assessment.

We show that not only did progenetic individuals occupy a different trophic niche than metamorphic individuals in all populations, but the smaller they were compared to metamorphs due to progenesis, the more different they were in terms of trophic ecology, with no negative effect on their BC.

Altogether, the results suggest that via body size reduction, progenesis may generally act as an intrinsic factor of ecological opportunity, allowing the use of existing but previously unavailable resources, even in habitats where seemingly little opportunity exists. We argue that beyond the classically recognized fitness advantages of progenetic development, this process may also generally bring an immediate trophic advantage via body size reduction, which would have important implications to understand the evolution and adaptiveness of this process in many different taxa, from marine meiofauna to primates.

A free Plain Language Summary can be found within the Supporting Information of this article.
Physician trajectories of abandoning long‐course breast radiotherapy and their cost impact
Authors: Xu Xiao , Soulos Pamela R. , Herrin Jeph , Wang Shi‐Yi , Pollack Craig Evan , Evans Suzanne B. , Yu James B. , Gross Cary P. 
Published: October 2020

AbstractObjectiveTo examine variation in trajectories of abandoning conventionally fractionated whole‐breast irradiation (CF‐WBI) for adjuvant breast radiotherapy among physician peer groups and the associated cost implications.Data SourcesMedicare claims data were obtained from the Chronic Conditions Data Warehouse for fee‐for‐service beneficiaries with breast cancer in 2011‐2014.Study DesignWe used social network methods to identify peer groups of physicians that shared patients. For each physician peer group in each time period (T1 = 2011‐2012 and T2 = 2013‐2014), we calculated a risk‐adjusted rate of CF‐WBI use among eligible women, after adjusting for patient clinical characteristics. We applied a latent class growth analysis to these risk‐adjusted rates to identify distinct trajectories of CF‐WBI use among physician peer groups. We further estimated potential savings to the Medicare program by accelerating abandonment of CF‐WBI in T2 using a simulation model.Data Collection/Extraction MethodsUse of conventionally fractionated whole‐breast irradiation was determined from Medicare claims among women ≥ 66 years of age who underwent adjuvant radiotherapy after breast conserving surgery.Principal FindingsAmong 215 physician peer groups caring for 16 988 patients, there were four distinct trajectories of abandoning CF‐WBI: (a) persistent high use (mean risk‐adjusted utilization rate: T1 = 94.3%, T2 = 90.6%); (b) decreased high use (T1 = 81.3%, T2 = 65.3%); (c) decreased medium use (T1 = 60.1%, T2 = 44.0%); and (d) decreased low use (T1 = 31.6%, T2 = 23.6%). Peer groups with a smaller proportion of patients treated at free‐standing radiation facilities and a larger proportion of physicians that were surgeons tended to follow trajectories with lower use of CF‐WBI. If all physician peer groups had practice patterns in T2 similar to those in the “decreased low use” trajectory, the Medicare program could save $83.3 million (95% confidence interval: $58.5 million‐$112.2 million).ConclusionsPhysician peer groups had distinct trajectories of abandoning CF‐WBI. Physician composition and setting of radiotherapy were associated with the different trajectories. Distinct practice patterns across the trajectories had important cost implications.
Comparing propofol with placebo for early resolution of acute migraine in adult emergency department patients: A double‐blind randomised controlled trial
Authors: Meek Robert , Graudins Andis , McDonald Micah , McGannon Daniel , Limm Ezra 
Published: October 2020

AbstractObjectiveTo compare propofol with placebo in adult ED patients with acute migraine. Primary outcome was headache resolution by 1 h. Secondary outcome was reduction in headache severity by two or more points on a numerical rating scale.MethodsDouble‐blind randomised controlled clinical trial comparing propofol (10 mg/mL) with placebo (20% intralipid). Adults with acute migraine without aura were included. The study drug was administered as an initial dose of 4 mL followed by up to five doses of 2 mL, delivered 5 min apart. Pain scores were taken prior to each dose and further administration was ceased when either the pain score was zero or the maximum dosage reached (140 mg of propofol or 14 mL of 20% intralipid).ResultsOf 40 recruited patients, 21 received propofol and 19 placebo. Headache resolution occurred for 5 (24%, 95% CI 13–57) and 6 (32%, 95% CI 13–57) patients, respectively, difference 8% (95% CI −20 to 36). Headache severity reduction by two or more numerical rating scale points was reported by 17 (81%, 95% CI 58–95) and 7 (37%, 95% CI 16–62) patients, respectively, difference 44% (95% CI 17–71).ConclusionsPropofol was not superior to placebo for the primary outcome of early headache resolution. Superiority of propofol for the secondary outcome of headache severity reduction suggests that further research may be warranted.
Impact of national lockdown towards emergency department visits and admission rates during the COVID‐19 pandemic in Thailand: A hospital‐based study
Authors: Wongtanasarasin Wachira , Srisawang Thanchanok , Yothiya Wanwisa , Phinyo Phichayut 
Published: October 2020

AbstractObjectiveTo evaluate the impact of the national lockdown because of the 2019 coronavirus (COVID‐19) pandemic towards the ED visits and admission rates in Thailand.MethodsWe retrospectively reviewed the electronic medical database of patients presenting to the ED during the national lockdown period (from 26 March to 30 June 2020). We used the same time interval in the year 2019 as the control period in our analysis. We collected baseline characteristics and outcomes of each patient in the ED. The primary outcome was the incidence rate ratio (IRR) with a 95% confidence interval (CI) of the average daily ED visits. Secondary outcomes included the IRR with 95% CI of total admissions and intensive care unit (ICU) admissions.ResultsThe average number of daily ED visits decreased significantly from 89.1 to 57.0 (−36.0%, IRR 0.69, 95% CI 0.67–0.70). However, the proportions of ‘Resuscitation’ and ‘Emergency’ triage level were increased (29.1% vs 19.2%, P < 0.001). Total ED admission rate and ICU admission rate were also increased (33.5% vs 28.3%, P < 0.001 and 10.2% vs 7.5%, P < 0.001, respectively). The IRR for the admission rate was 1.18 (95% CI 1.11–1.26), and the IRR for the ICU admission rate was 1.35 (95% CI 1.21–1.52).ConclusionThe national lockdown in Thailand was associated with a significant reduction in average daily ED visits across traumatic and non‐traumatic patients. Communication from healthcare professionals and public health officers is necessary to reinforce the importance of timely ED visits for acute health conditions.
TOA: A software package for automated functional annotation in non‐model plant species
Authors: Mora‐Márquez Fernando , Chano Víctor , Vázquez‐Poletti José Luis , López de Heredia Unai 
Published: October 2020

AbstractThe increase of sequencing capacity provided by high‐throughput platforms has made it possible to routinely obtain large sets of genomic and transcriptomic sequences from model and non‐model organisms. Subsequent genomic analysis and gene discovery in next‐generation sequencing experiments are, however, bottlenecked by functional annotation. One common way to perform functional annotation of sets of sequences obtained from next‐generation sequencing experiments, is by searching for homologous sequences and accessing the related functional information deposited in genomic databases. Functional annotation is especially challenging for non‐model organisms, like many plant species. In such cases, existing free and commercial general‐purpose applications may not offer complete and accurate results. We present TOA (Taxonomy‐oriented annotation), a Python‐based user‐friendly open source application designed to establish functional annotation pipelines geared towards non‐model plant species that can run in Linux/Mac computers, HPCs and cloud servers. TOA performs homology searches against proteins stored in the PLAZA databases, NCBI RefSeq Plant, Nucleotide Database and Non‐Redundant Protein Sequence Database, and outputs functional information from several ontology systems: Gene Ontology, InterPro, EC, KEGG, Mapman and MetaCyc. The software performance was validated by comparing the runtimes, total number of annotated sequences and accuracy of the functional information obtained for several plant benchmark data sets with TOA and other functional annotation solutions. TOA outperformed the other software in terms of number of annotated sequences and accuracy of the annotation and constitutes a good alternative to improve functional annotation in plants. TOA is especially recommended for gymnosperms or for low quality sequence data sets of non‐model plants.
Is there any association between psoriasis, psoriatic arthritis and thyroid autoimmunity?
Authors: Vastarella Maria , Megna Matteo , Lupoli Gelsy Arianna , Napolitano Maddalena , Gallo Lucia , Balato Anna , Tasso Marco , Costa Luisa , Fabbrocini Gabriella , Peluso Rosario 
Published: October 2020

AbstractBackgroundAutoimmune diseases share a significant part of their genetic background and tend to coexist in the same patient. Some studies have investigated the possible association between autoimmune thyroiditis and psoriasis or psoriatic arthritis (PsA), with conflicting results. This study aimed to investigate the prevalence of autoimmune thyroiditis in psoriatic patients with (PsA) or without (PsC) joint involvement.Methods208 patients with psoriasis and/or PsA were recruited. These patients were divided into two groups: psoriasis patients (without PsA) (PsC group: 100 patients; mean age of 50.1 ± 11.7 years) and subjects with psoriasis and psoriatic arthritis (PsA group: 108 subjects: mean age of 39.8 ± 10.8 years). Assessment of psoriasis severity was conducted using the Psoriasis Area and Severity Index (PASI) score. The diagnosis of psoriatic arthritis was made according to CASPAR criteria. All patients had thyroid evaluation through evaluation of thyroid function, thyroperoxidase antibodies and thyroid ultrasound examination.ResultsA statistically significant difference was found between the prevalence of autoimmune thyroiditis in the PsA group than the PsC group (25.9 vs 9.0 %; P = 0.018) with higher trends to hypothyroidism in the PsA group compared to the PsC group (13.9% vs 2.0%, P = 0.0018).ConclusionsThe higher prevalence of autoimmune thyroiditis in the PsA group may be due to an immune dysfunction pathway in patients with psoriatic arthritis with a higher risk to develop other autoimmune diseases. This evidence confirms that psoriatic arthritis is an autoimmune disease with an overactive immune system that can involve multiple organs. Thyroid function evaluation should be part of the clinical and laboratory examination of patients with psoriatic arthritis.
Effectiveness of water as the neutralising agent for glycolic acid peels in skin phototypes IV‐V
Authors: Sitohang Irma Bernadette S. , Rahmayunita Githa , Hosfiar Vashty Amanda , Ninditya Shafira , Augustin Maureen 
Published: October 2020

AbstractThe aim of the study is to evaluate the effectiveness of water as a substitute for sodium bicarbonate plus solution in the neutralisation process of chemical peeling using a 35% glycolic acid solution. This randomised, double‐blind, split‐face, controlled trial was conducted in an outpatient setting. A total of 126 healthy patients with skin phototypes IV–V aged between 18 and 60 years old were recruited. Chemical peeling was performed with 35% glycolic acid solution. One side of the face was neutralised with water, and the other side of the face was neutralised with a sodium bicarbonate plus solution. The main outcome of this study was measured by the degree of erythema, pruritus and pain scores. Significant difference in the pain score immediately after the neutralisation process of the chemical peeling with glycolic acid was seen. However, there were no significant differences in the degree of erythema or the pruritus score. These results indicate that water can be used as a substitute for sodium bicarbonate plus solution in the neutralisation process of chemical peeling with 35% glycolic acid in patients with skin phototypes IV–V.
Alteration of systemic and uterine endometrial immune populations in patients with endometriosis
Authors: Le Nhung X. H. , Loret de Mola Julio R. , Bremer Pamela , Groesch Kathleen , Wilson Teresa , Diaz‐Sylvester Paula , Braundmeier‐Fleming Andrea G. 
Published: October 2020

AbstractProblemEndometriosis is defined as growth of endometrial tissue in ectopic locations; it is associated with infertility and chronic pain and affects ~12% of reproductive‐aged women. Although inflammation is known to play a key role in endometriosis, knowledge related to immune phenotypes associated with this disease is lacking. This study aimed to characterize immune profiles in patients with endometriosis, to assess inflammatory mediators, to and determine if surgical and/or hormonal therapies restore immune homeostasis.Methods of studySamples from nine controls and 20 histologically confirmed endometriosis patients were collected upon surgery and ~1‐3 weeks post‐surgical intervention. Subjects were either not utilizing hormonal suppression or were currently on monophasic hormonal therapy. Tolerant regulatory T cells (Tregs = natural [nTregs] +inducible [iTregs]) and inflammatory T helper 17 (Th17) cells were identified in peripheral blood via flow cytometry and within the eutopic/ectopic endometrial tissues via immunohistochemistry and real‐time‐qPCR. Cytokines were assessed via 10‐plex‐ELISA.ResultsPatients with endometriosis not utilizing hormonal therapy exhibited lower iTregs (tolerant), greater Th17 (inflammatory), and a reduction in Treg/Th17 ratio (P < .05), indicative of systemic inflammation. Treg and Th17 localizations were enhanced within the ectopic endometrial implant, which promotes lesion development. Hormonal therapy decreased systemic and local inflammation (eutopic/ectopic endometrium) via decreased iTregs and Th17 cells in patients with endometriosis (P < .05). Thus, imbalance within immune populations correlated with increased inflammation in patients with endometriosis, which was mitigated by hormonal therapy.ConclusionsPatients with endometriosis exhibited systemic and localized inflammation within ectopic and endometrial tissues. Hormonal therapy dampened inflammation caused by disease.
QT correction using Bazett’s formula remains preferable in long QT syndrome type 1 and 2
Authors: Dahlberg Pia , Diamant Ulla‐Britt , Gilljam Thomas , Rydberg Annika , Bergfeldt Lennart 
Published: October 2020

AbstractBackgroundThe heart rate (HR) corrected QT interval (QTc) is crucial for diagnosis and risk stratification in the long QT syndrome (LQTS). Although its use has been questioned in some contexts, Bazett's formula has been applied in most diagnostic and prognostic studies in LQTS patients. However, studies on which formula eliminates the inverse relation between QT and HR are lacking in LQTS patients.We therefore determined which QT correction formula is most appropriate in LQTS patients including the effect of beta blocker therapy and an evaluation of the agreement of the formulae when applying specific QTc limits for diagnostic and prognostic purposes.MethodsAutomated measurements from routine 12‐lead ECGs from 200 genetically confirmed LQTS patients from two Swedish regions were included (167 LQT1, 33 LQT2). QT correction was performed using the Bazett, Framingham, Fridericia, and Hodges formulae. Linear regression was used to compare the formulae in all patients, and before and after the initiation of beta blocking therapy in a subgroup (n = 44). Concordance analysis was performed for QTc ≥ 480 ms (diagnosis) and ≥500 ms (prognosis).ResultsThe median age was 32 years (range 0.1–78), 123 (62%) were female and 52 (26%) were children ≤16 years. Bazett's formula was the only method resulting in a QTc without relation with HR. Initiation of beta blocking therapy did not alter the result. Concordance analyses showed clinically significant differences (Cohen's kappa 0.629–0.469) for diagnosis and prognosis in individual patients.ConclusionBazett's formula remains preferable for diagnosis and prognosis in LQT1 and 2 patients.
Successful trans‐septal ablation of a left concealed accessory pathway in a patient receiving surgical mitral valve repair and mechanical aortic valve replacement
Authors: Huang Ting‐Chun , Tsai Jing‐Hsiung , Chen Ju‐Yi 
Published: October 2020

AbstractWe presented a case of severe aortic regurgitation and moderate mitral regurgitation s/p aortic valve replacement and mitral valve repair. Deterioration of tachyarrhythmia attacks was noted. In EP study, left lateral accessory pathway with orthodromic atrioventricular reentrant tachycardia was identified. We successfully ablated the accessory pathway by trans‐septal approach. Even though trans‐septal approach currently is a daily routine of invasive interventional electrophysiologists, in this case, we want to emphasize and illustrate the distance between true mitral annulus and coronary sinus. Unrecognizing this concept could result in efficacy and safety of catheter‐based therapy.