bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression pattern and prognostic value of N6-methyladenosine RNA methylation key regulators in hepatocellular carcinoma
Authors: Deng Min , Fang Lin , Li Shao-Hua , Zhao Rong-Ce , Mei Jie , Zou Jing-Wen , Wei Wei , Guo Rong-Ping 
Published: September 2021

Abstract
Hepatocellular carcinoma (HCC) is still one of the most common malignancies worldwide. The accuracy of biomarkers for predicting the prognosis of HCC and the therapeutic effect is not satisfactory. N6-methyladenosine (m6A) methylation regulators play a crucial role in various tumours. Our research aims further to determine the predictive value of m6A methylation regulators and establish a prognostic model for HCC. In this study, the data of HCC from The Cancer Genome Atlas (TCGA) database was obtained, and the expression level of 15 genes and survival was examined. Then we identified two clusters of HCC with different clinical factors, constructed prognostic markers and analysed gene set enrichment, proteins’ interaction and gene co-expression. Three subgroups by consensus clustering according to the expression of the 13 genes were identified. The risk score generated by five genes divided HCC patients into high-risk and low-risk groups. In addition, we developed a prognostic marker that can identify high-risk HCC. Finally, a novel prognostic nomogram was developed to accurately predict HCC patients’ prognosis. The expression levels of 13 m6A RNA methylation regulators were significantly upregulated in HCC samples. The prognosis of cluster 1 and cluster 3 was worse. Patients in the high-risk group show a poor prognosis. Moreover, the risk score was an independent prognostic factor for HCC patients. In conclusion, we reveal the critical role of m6A RNA methylation modification in HCC and develop a predictive model based on the m6A RNA methylation regulators, which can accurately predict HCC patients’ prognosis and provide meaningful guidance for clinical treatment.
AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation
Authors: Hur Jeong Hwan , Kang Chan Young , Lee Sungjin , Parveen Nazia , Yu Jihyeon , Shamim Amen , Yoo Wanki , Ghosh Ambarnil , Bae Sangsu , Park Chin-Ju , Kim Kyeong Kyu 
Published: September 2021

Abstract
I-motif or C4 is a four-stranded DNA structure with a protonated cytosine:cytosine base pair (C+:C) found in cytosine-rich sequences. We have found that oligodeoxynucleotides containing adenine and cytosine repeats form a stable secondary structure at a physiological pH with magnesium ion, which is similar to i-motif structure, and have named this structure ‘adenine:cytosine-motif (AC-motif)’. AC-motif contains C+:C base pairs intercalated with putative A+:C base pairs between protonated adenine and cytosine. By investigation of the AC-motif present in the CDKL3 promoter (AC-motifCDKL3), one of AC-motifs found in the genome, we confirmed that AC-motifCDKL3 has a key role in regulating CDKL3 gene expression in response to magnesium. This is further supported by confirming that genome-edited mutant cell lines, lacking the AC-motif formation, lost this regulation effect. Our results verify that adenine-cytosine repeats commonly present in the genome can form a stable non-canonical secondary structure with a non-Watson–Crick base pair and have regulatory roles in cells, which expand non-canonical DNA repertoires.
Reinforcement of transcriptional silencing by a positive feedback between DNA methylation and non-coding transcription
Authors: Rothi M Hafiz , Tsuzuki Masayuki , Sethuraman Shriya , Wierzbicki Andrzej T 
Published: September 2021

Abstract
Non-coding transcription is an important determinant of heterochromatin formation. In Arabidopsis thaliana a specialized RNA polymerase V (Pol V) transcribes pervasively and produces long non-coding RNAs. These transcripts work with small interfering RNA to facilitate locus-specific establishment of RNA-directed DNA methylation (RdDM). Subsequent maintenance of RdDM is associated with elevated levels of Pol V transcription. However, the impact of DNA methylation on Pol V transcription remained unresolved. We found that DNA methylation strongly enhances Pol V transcription. The level of Pol V transcription is reduced in mutants defective in RdDM components working downstream of Pol V, indicating that RdDM is maintained by a mutual reinforcement of DNA methylation and Pol V transcription. Pol V transcription is affected only on loci that lose DNA methylation in all sequence contexts in a particular mutant, including mutants lacking maintenance DNA methyltransferases, which suggests that RdDM works in a complex crosstalk with other silencing pathways.
Consciousness in active inference: Deep self-models, other minds, and the challenge of psychedelic-induced ego-dissolution
Authors: Deane George 
Published: September 2021

AbstractPredictive processing approaches to brain function are increasingly delivering promise for illuminating the computational underpinnings of a wide range of phenomenological states. It remains unclear, however, whether predictive processing is equipped to accommodate a theory of consciousness itself. Furthermore, objectors have argued that without specification of the core computational mechanisms of consciousness, predictive processing is unable to inform the attribution of consciousness to other non-human (biological and artificial) systems. In this paper, I argue that an account of consciousness in the predictive brain is within reach via recent accounts of phenomenal self-modelling in the active inference framework. The central claim here is that phenomenal consciousness is underpinned by ‘subjective valuation’—a deep inference about the precision or ‘predictability’ of the self-evidencing (‘fitness-promoting’) outcomes of action. Based on this account, I argue that this approach can critically inform the distribution of experience in other systems, paying particular attention to the complex sensory attenuation mechanisms associated with deep self-models. I then consider an objection to the account: several recent papers argue that theories of consciousness that invoke self-consciousness as constitutive or necessary for consciousness are undermined by states (or traits) of ‘selflessness’; in particular the ‘totally selfless’ states of ego-dissolution occasioned by psychedelic drugs. Drawing on existing work that accounts for psychedelic-induced ego-dissolution in the active inference framework, I argue that these states do not threaten to undermine an active inference theory of consciousness. Instead, these accounts corroborate the view that subjective valuation is the constitutive facet of experience, and they highlight the potential of psychedelic research to inform consciousness science, computational psychiatry and computational phenomenology.
A Novel Weave Tether Technique for Proximal Junctional Kyphosis Prevention in 71 Adult Spinal Deformity Patients: A Preliminary Case Series Assessing Early Complications and Efficacy
Authors: Rabinovich Emily P , Buell Thomas J , Sardi Juan P , Lazaro Bruno C R , Shaffrey Christopher I , Smith Justin S 
Published: September 2021

Abstract

BACKGROUND
Proximal junctional kyphosis (PJK) rates may be as high as 69.4% after adult spinal deformity (ASD) surgery. PJK is one of the greatest unsolved challenges in long-segment fusions for ASD and remains a common indication for costly and impactful revision surgery. Junctional tethers may help to reduce the occurrence of PJK by attenuating adjacent-segment stress.

OBJECTIVE
To report our experience and assess early safety associated with a novel “weave-tether technique” (WTT) for PJK prophylaxis in a large series of patients.

METHODS
This single-center retrospective study evaluated consecutive patients who underwent ASD surgery including WTT between 2017 and 2018. Patient demographics, operative details, standard radiographic measurements, and complications were analyzed.

RESULTS
A total of 71 patients (mean age 66 ± 12 yr, 65% women) were identified. WTT included application to the upper-most instrumented vertebrae (UIV) + 1 and UIV + 2 in 38(53.5%) and 33(46.5%) patients, respectively. No complications directly attributed to WTT usage were identified. For patients with radiographic follow-up (96%; mean duration 14 ± 12 mo), PJK occurred in 15% (mean 1.8 ± 1.0 mo postoperatively). Proximal junctional angle increased an average 4° (10° to 14°, P = .004). Rates of symptomatic PJK and revision for PJK were 8.8% and 2.9%, respectively.

CONCLUSION
Preliminary results support the safety of the WTT for PJK prophylaxis. Approximately 15% of patients developed radiographic PJK, no complications were directly attributed to WTT usage, and the revision rate for PJK was low. These early results warrant future research to assess longer-term efficacy of the WTT for PJK prophylaxis in ASD surgery.
Quantitative Anatomic Comparison of Microsurgical Transcranial, Endoscopic Endonasal, and Transorbital Approaches to the Spheno-Orbital Region
Authors: Agosti Edoardo , Turri-Zanoni Mario , Saraceno Giorgio , Belotti Francesco , Karligkiotis Apostolos , Rocca Gregorio , Buffoli Barbara , Raffetti Elena , Hirtler Lena , Rezzani Rita , Rodella Luigi Fabrizio , Ferrari Marco , Nicolai Piero , Bresson Damien , Herman Philippe , Dallan Iacopo , Castelnuovo Paolo , Locatelli Davide , Fontanella Marco Maria , Doglietto Francesco 
Published: September 2021

Abstract

BACKGROUND
The spheno-orbital region (SOR) is a complex anatomic area that can be accessed with different surgical approaches.

OBJECTIVE
To quantitatively compare, in a preclinical setting, microsurgical transcranial approaches (MTAs), endoscopic endonasal transpterygoid approach (EEA), and endoscopic transorbital approaches (ETOAs) to the SOR.

METHODS
These approaches were performed in 5 specimens: EEA, ETOAs (superior eyelid and inferolateral), anterolateral MTAs (supraorbital, minipterional, pterional, pterional-transzygomatic, and frontotemporal-orbitozygomatic), and lateral MTAs (subtemporal and subtemporal transzygomatic). All specimens underwent high-resolution computed tomography; an optic neuronavigation system with dedicated software was used to quantify working volume and exposed area for each approach. Mixed linear models with random intercepts were used for statistical analyses.

RESULTS
Anterolateral MTAs offer a direct route to the greater wings (GWs) and lesser wings (LWs); only they guarantee exposure of the anterior clinoid. Lateral MTAs provide access to a large area corresponding to the GW, up to the superior orbital fissure (SOF) anteriorly and the foramen rotundum medially. ETOAs also access the GW, close to the lateral portion of SOF, but with a different angle of view as compared to lateral MTAs. Access to deep and medial structures, such as the lamina papyracea and the medial SOF, is offered only by EEA, which exposes the LW and GW only to a limited extent.

CONCLUSION
This is the first study that offers a quantitative comparison of the most used approaches to SOR. A detailed knowledge of their advantages and limitations is paramount to choose the ideal one, or their combination, in the clinical setting.
Medicago SPX1 and SPX3 regulate phosphate homeostasis, mycorrhizal colonization, and arbuscule degradation
Authors: Wang Peng , Snijders Roxane , Kohlen Wouter , Liu Jieyu , Bisseling Ton , Limpens Erik 
Published: September 2021

Abstract
To acquire sufficient mineral nutrients such as phosphate (Pi) from the soil, most plants engage in symbiosis with arbuscular mycorrhizal (AM) fungi. Attracted by plant-secreted strigolactones (SLs), the fungi colonize the roots and form highly branched hyphal structures called arbuscules inside inner cortex cells. The host plant must control the different steps of this interaction to maintain its symbiotic nature. However, how plants sense the amount of Pi obtained from the fungus, and how this determines the arbuscule lifespan, are far from understood. Here, we show that Medicago truncatula SPX-domain containing proteins SPX1 and SPX3 regulate root Pi starvation responses, in part by interacting with PHOSPHATE RESPONSE REGULATOR2, as well as fungal colonization and arbuscule degradation. SPX1 and SPX3 are induced upon Pi starvation but become more restricted to arbuscule-containing cells upon the establishment of symbiosis. This induction in arbuscule-containing cells is associated with the presence of cis-regulatory AW-boxes and transcriptional regulation by the WRINKLED1-like transcription factor WRI5a. Under Pi-limiting conditions, SPX1 and SPX3 facilitate the expression of the SL biosynthesis gene DWARF27, which could help explain the increased fungal branching in response to root exudates. Later, in arbuscule-containing cells, SPX1 and SPX3 redundantly control arbuscule degradation. Thus, SPX proteins play important roles as phosphate sensors to maintain a beneficial AM symbiosis.
Woodland strawberry axillary bud fate is dictated by a crosstalk of environmental and endogenous factors
Authors: Andrés Javier , Caruana Julie , Liang Jiahui , Samad Samia , Monfort Amparo , Liu Zhongchi , Hytönen Timo , Koskela Elli A 
Published: September 2021

AbstractPlant architecture is defined by fates and positions of meristematic tissues and has direct consequences on yield potential and environmental adaptation of the plant. In strawberries (Fragaria vesca L. and F. × ananassa Duch.), shoot apical meristems can remain vegetative or differentiate into a terminal inflorescence meristem. Strawberry axillary buds (AXBs) are located in leaf axils and can either remain dormant or follow one of the two possible developmental fates. AXBs can either develop into stolons needed for clonal reproduction or into branch crowns (BCs) that can bear their own terminal inflorescences under favorable conditions. Although AXB fate has direct consequences on yield potential and vegetative propagation of strawberries, the regulation of AXB fate has so far remained obscure. We subjected a number of woodland strawberry (F. vesca L.) natural accessions and transgenic genotypes to different environmental conditions and growth regulator treatments to demonstrate that strawberry AXB fate is regulated either by environmental or endogenous factors, depending on the AXB position on the plant. We confirm that the F. vesca GIBBERELLIN20-oxidase4 (FvGA20ox4) gene is indispensable for stolon development and under tight environmental regulation. Moreover, our data show that apical dominance inhibits the outgrowth of the youngest AXB as BCs, although the effect of apical dominance can be overrun by the activity of FvGA20ox4. Finally, we demonstrate that the FvGA20ox4 is photoperiodically regulated via FvSOC1 (F. vesca SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1) at 18°C, but at higher temperature of 22°C an unidentified FvSOC1-independent pathway promotes stolon development.
Early Identification of Deep-Tissue Pressure Injury Using Long-Wave Infrared Thermography: A Blinded Prospective Cohort Study
Authors: Simman Richard , Angel Carol 
Published: September 2021

ABSTRACT

BACKGROUND
The current clinical standard for diagnosing deep-tissue pressure injury (DTPI) is visual inspection. This method is subjective and only presents to the observer the external “picture;” deeper tissues are disguised from the observer. In contrast, long-wave infrared thermography (LWIT) can capture an image of the area of concern and detect tissue temperature relative to the level of tissue perfusion.

OBJECTIVE
To determine the efficacy of a handheld LWIT device and software solution as an adjunct to the current clinical standard of visual skin assessment to detect nonvisual pathophysiologic changes of DTPI.

METHODS
Investigators performed a blinded, prospective cohort study scanning participants’ sacral area and bilateral heels with the LWIT device. Follow-up imaging took place throughout patient stays (on admission and 3, 7, 14, and 25 days thereafter). Clinicians were blinded to the LWIT images, and all participants received standard care for the prevention and treatment of wounds.

RESULTS
Among the 70 participants enrolled in this study, there were 131 anatomical areas with intact skin at the time of admission. Four areas with initially intact skin progressed to visually identifiable DTPI. On all four of these areas, the LWIT device identified a previsual temperature anomaly before there existed a visually identifiable DTPI.

CONCLUSIONS
The outcomes of this study suggest objective and quantitative documentation of temperature change using the LWIT device can serve as an indication of DTPI formation before visual identification is possible. Accordingly, it may allow for earlier detection of DTPI, decreasing the risk of associated complications to the patient and allowing for earlier, targeted intervention.
Abdominal Ultrasound Assists the Diagnosis and Management of Necrotizing Enterocolitis
Authors: Chan Belinda , Gordon Sasha , Yang Michelle , Weekes Jennifer , Dance Logan 
Published: September 2021

Background:
Abdominal x-ray (KUB) routinely aids in detecting necrotizing enterocolitis (NEC), one of the most serious neonatal intestinal diseases. However, a KUB may miss up to 50% of the early signs of NEC. Recent advances in abdominal ultrasound (AUS) can expedite this diagnosis and improve clinical management.

Purposes:
To illustrate AUS findings that suggest NEC through 3 case examples. To review current literature regarding advantages and limitations of AUS compared with KUB.

Results:
The added visualization of intra-abdominal structures with AUS compared with KUB improves the diagnosis and management of NEC. Some AUS features are highly suggestive of impending bowel perforation, while others can confirm bowel perforation despite a negative radiograph.

Implications for Practice:
AUS expedites time to diagnosis of NEC and helps to stratify patients who may fail medical management and require surgical intervention.

Implications for research:
More quality improvement studies are needed to validate an AUS protocol for the management of NEC. Advances in technology, such as contrast-enhanced ultrasound, may improve NEC detection with AUS in the future.

Video Abstract available at
https://journals.lww.com/advancesinneonatalcare/Pages/videogallery.aspx.
Operative Treatment of Cervical Spine Injuries Sustained in Youth Sports
Authors: Verhofste Bram P. , Hedequist Daniel J. , Birch Craig M. , Rademacher Emily S. , Glotzbecker Michael P. , Proctor Mark R. , Yen Yi-Meng 
Published: September 2021

Background:Little data exists on surgical outcomes of sports-related cervical spine injuries (CSI) sustained in children and adolescent athletes. This study reviewed demographics, injury characteristics, management, and operative outcomes of severe CSI encountered in youth sports.Methods:Children below 18 years with operative sports-related CSI at a Level 1 pediatric trauma center were reviewed (2004 to 2019). All patients underwent morden cervical spine instrumentation and fusion. Clinical, radiographic, and surgical characteristics were analyzed.Results:A total of 3231 patients (mean, 11.3±4.6 y) with neck pain were evaluated for CSI. Sports/recreational activities were the most common etiology in 1358 cases (42.0%). Twenty-nine patients (2.1%) with sports-related CSI (mean age, 14.5 y; range, 6.4 to 17.8 y) required surgical intervention. Twenty-five were males (86%). Operative CSI occurred in football (n=8), wrestling (n=7), gymnastics (n=5), diving (n=4), trampoline (n=2), hockey (n=1), snowboarding (n=1), and biking (n=1). Mechanisms were 27 hyperflexion/axial loading (93%) and 2 hyperextension injuries (7%). Most were cervical fractures (79%) and subaxial injuries (79%). Seven patients (24%) sustained spinal cord injury (SCI) and 3 patients (10%) cord contusion or myelomalacia without neurological deficits. The risk of SCI increased with age (P=0.03). Postoperatively, 2 SCI patients (29%) improved 1 American Spinal Injury Association Impairment Scale Grade and 1 (14%) improved 2 American Spinal Injury Association Impairment Scale Grades. Increased complications developed in SCI than non-SCI cases (mean, 2.0 vs. 0.1 complications;P=0.02). Bony fusion occurred in 26/28 patients (93%) after a median of 7.2 months (interquartile range, 6 to 15 mo). Ten patients (34%) returned to their baseline sport and 9 (31%) to lower-level activities.Conclusions:The incidence of sports-related CSI requiring surgery is low with differences in age/sex, sport, and injury patterns. Older males with hyperflexion/axial loading injuries in contact sports were at greatest risk of SCI, complications, and permanent disability. Prevention campaigns, education on proper tackling techniques, and neck strength training are required in sports at high risk of hyperflexion/axial loading injury.Level of Evidence:Level III—retrospective cohort study.
Effect of the Implementation of a Surgical Care Bundle in the Incidence of Surgical Site Infection in Spine Surgery
Authors: Vicente-Sánchez Gema , Alonso-García Marcos , Hijas-Gómez Ana Isabel , González-Díaz Rafael , Martinez-Martín Javier , Fahandezh-Saddi Homid , Durán-Poveda Manuel , Gil-de-Miguel Angel , Rodríguez-Caravaca Gil 
Published: September 2021

Study Design.
Quasi-experimental intervention study.

Objective.
To assess the effect of a clinical safety and quality improvement plan for patients undergoing spinal fusion surgery on the incidence of surgical site infection (SSI).

Summary of Background Data.
In recent years, infection surveillance and control programs based on care bundles have been included in surgical protocols. These have proven to be essential tools for the prevention and control of SSI, providing indicators for improvement and allowing the characterization of related risk factors.

Methods.
A quasi-experimental study was carried out with analysis before and after the introduction of a preventive care bundle (clinical safety and quality improvement plan). Patients who underwent spinal fusion surgery were included. The incidence of SSI up to 90 days after surgery (maximum incubation period) was assessed. The effect of the intervention was evaluated with the adjusted odds ratio (oR) using a logistic regression model.

Results.
A total of 1554 patients were included, 690 in the period 2007 to 2011 (before) and 864 during 2012 to 2018 (after). SSI incidence decreased from 4.2% to 1.9% after the plan (OR: 0.43; 95% confidence interval: 0.23–0.80; P
= 0.006). There was also an improvement in the adequacy of antibiotic prophylaxis, preoperative preparation, and hair removal procedure after the introduction of the care bundle.

Conclusion.
After implementation of the care bundle, the incidence of SSI in spine fusion surgery decreased significantly. Multivariate analysis showed that the care bundle was an independent protective factor. The implementation of these measures should be reinforced on the routine medical practice to reduce the SSI incidence.

Level of Evidence: 3