bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative analysis of pathogenic variants in glucose-6-phosphatase based on an AlphaFold2 model
Authors: Sinclair Matt , Stein Richard A , Sheehan Jonathan H , Hawes Emily M , O’Brien Richard M , Tajkhorshid Emad , Claxton Derek P 
Published: January 2024

Abstract
Mediating the terminal reaction of gluconeogenesis and glycogenolysis, the integral membrane protein glucose-6-phosphate catalytic subunit 1 (G6PC1) regulates hepatic glucose production by catalyzing hydrolysis of glucose-6-phosphate (G6P) within the lumen of the endoplasmic reticulum. Consistent with its vital contribution to glucose homeostasis, inactivating mutations in G6PC1 causes glycogen storage disease (GSD) type 1a characterized by hepatomegaly and severe hypoglycemia. Despite its physiological importance, the structural basis of G6P binding to G6PC1 and the molecular disruptions induced by missense mutations within the active site that give rise to GSD type 1a are unknown. In this study, we determine the atomic interactions governing G6P binding as well as explore the perturbations imposed by disease-linked missense variants by subjecting an AlphaFold2 G6PC1 structural model to molecular dynamics simulations and in silico predictions of thermodynamic stability validated with robust in vitro and in situ biochemical assays. We identify a collection of side chains, including conserved residues from the signature phosphatidic acid phosphatase motif, that contribute to a hydrogen bonding and van der Waals network stabilizing G6P in the active site. The introduction of GSD type 1a mutations modified the thermodynamic landscape, altered side chain packing and substrate-binding interactions, and induced trapping of catalytic intermediates. Our results, which corroborate the high quality of the AF2 model as a guide for experimental design and to interpret outcomes, not only confirm the active-site structural organization but also identify previously unobserved mechanistic contributions of catalytic and noncatalytic side chains.
Application of the Adverse Childhood Experiences Framework to the NICU
Authors: Malin Kathryn J. , Vittner Dorothy , Darilek Umber , McGlothen-Bell Kelly , Crawford Allison , Koerner Rebecca , Pados Britt Frisk , Cartagena Diana , McGrath Jacqueline M. , Vance Ashlee J. 
Published: January 2024

Background:
Infants and families requiring neonatal intensive care unit (NICU) care often experience significant stress and trauma during the earliest period of the infant's life, leading to increased risks for poorer infant and family outcomes. There is a need for frameworks to guide clinical care and research that account for the complex interactions of generational stress, pain, toxic stress, parental separation, and lifelong health and developmental outcomes for infants and families.

Purpose:
Apply the Adverse Childhood Experiences (ACEs) framework in the context of the NICU as a usable structure to guide clinical practice and research focused on infant neurodevelopment outcomes and parental attachment.

Methods:
An overview of ACEs is provided along with a detailed discussion of risk at each level of the ACEs pyramid in the context of the NICU. Supportive and protective factors to help mitigate the risk of the ACEs in the NICU are detailed.

Results:
NICU hospitalization may be considered the first ACE, or potentially an additional ACE, resulting in an increased risk for poorer health outcomes. The promotion of safe, stable, and nurturing relationships and implementation of trauma-informed care and individualized developmental care potentially counter the negative impacts of stress in the NICU.

Implications for Practice and Research:
Nurses can help balance the negative and positive stimulation of the NICU through activities such as facilitated tucking, skin-to-skin care, mother's milk, and active participation of parents in infant care. Future research can consider using the ACEs framework to explain cumulative risk for adverse health and well-being in the context of NICU care.
Reliable Prediction of Discharge Disposition Following Cervical Spine Surgery With Ensemble Machine Learning and Validation on a National Cohort
Authors: Feng Rui , Valliani Aly A. , Martini Michael L. , Gal Jonathan S. , Neifert Sean N. , Kim Nora C. , Geng Eric A. , Kim Jun S. , Cho Samuel K. , Oermann Eric K. , Caridi John M. 
Published: January 2024

Study Design:
A retrospective cohort study.

Objective:
The purpose of this study is to develop a machine learning algorithm to predict nonhome discharge after cervical spine surgery that is validated and usable on a national scale to ensure generalizability and elucidate candidate drivers for prediction.

Summary of Background Data:
Excessive length of hospital stay can be attributed to delays in postoperative referrals to intermediate care rehabilitation centers or skilled nursing facilities. Accurate preoperative prediction of patients who may require access to these resources can facilitate a more efficient referral and discharge process, thereby reducing hospital and patient costs in addition to minimizing the risk of hospital-acquired complications.

Methods:
Electronic medical records were retrospectively reviewed from a single-center data warehouse (SCDW) to identify patients undergoing cervical spine surgeries between 2008 and 2019 for machine learning algorithm development and internal validation. The National Inpatient Sample (NIS) database was queried to identify cervical spine fusion surgeries between 2009 and 2017 for external validation of algorithm performance. Gradient-boosted trees were constructed to predict nonhome discharge across patient cohorts. The area under the receiver operating characteristic curve (AUROC) was used to measure model performance. SHAP values were used to identify nonlinear risk factors for nonhome discharge and to interpret algorithm predictions.

Results:
A total of 3523 cases of cervical spine fusion surgeries were included from the SCDW data set, and 311,582 cases were isolated from NIS. The model demonstrated robust prediction of nonhome discharge across all cohorts, achieving an area under the receiver operating characteristic curve of 0.87 (SD=0.01) on both the SCDW and nationwide NIS test sets. Anterior approach only, age, elective admission status, Medicare insurance status, and total Elixhauser Comorbidity Index score were the most important predictors of discharge destination.

Conclusions:
Machine learning algorithms reliably predict nonhome discharge across single-center and national cohorts and identify preoperative features of importance following cervical spine fusion surgery.
The Oxygen Therapy Tube as a Tool for Breast Squeezing during Pedicle De-epithelialization in Reduction Mammaplasty
Authors: Pau Alberto , Torresetti Matteo , Dragonetti Pietro , Di Benedetto Giovanni 
Published: January 2024

Summary:
During breast reduction, pedicle de-epithelialization, as meticulous as possible, is necessary to ensure satisfying breast sculpting and to avoid any epidermoid cyst. To perform an effective and rapid de-epithelialization, a good tension of the skin is mandatory. Several techniques to improve skin tension of the breast are described in the literature. We report a cheap, effective, and easily reproducible method, based on the use of an oxygen tube with nasal cannula.
A Modified Suturing Technique to Produce Temporary Scleral Buckling Effect for Noncomplex Rhegmatogenous Retinal Detachment
Authors: Zhang Zhaotian 
Published: January 2024

Purpose:
To introduce a surgical technique for temporary scleral buckling (SB) of noncomplex rhegmatogenous retinal detachment (RRD) using a combination of non-absorbable and absorbable sutures that would induce minimal permanent refractive changes.

Method:
Twenty consecutive patients (20 eyes) with noncomplex RRD were prospectively included. SB was performed in all eligible subjects, and encircling buckling (EB) was added when necessary. The silicone elements were fixed on the sclera with 5-0 non-absorbable sutures and tightened to form a ridge with 6-0 absorbable sutures. Best-corrected visual acuity (BCVA), scleral ridge status, axial length (AL), spherical diopter (SD), and cylinder diopter (CD) were collected.

Results:
All patients achieved primary retinal re-attachment with significant improvement of BCVA after surgery. Scleral ridge was obvious and in situ at the one-month follow-up but diminished at the three-month follow-up. At the one-month follow-up, AL increased from 24.78±2.14 mm preoperatively to 25.22±2.11 mm, and CD increased from –1.99±1.03 to –2.95±1.55 (both p<0.001). At the three-month follow-up, AL, SD, and CD decreased significantly compared with the values at the one-month follow-up (all p<0.05). No obvious complications were observed during the whole follow-up. Patients who underwent additional EB exhibited greater changes in AL and CD at the one-month follow-up (both P<0.001).

Conclusion:
The modified technique of SB with/without EB using both non-absorbable and absorbable sutures offers a safe and effective option to repair noncomplex RRD, which would offer an adequate temporary SB effect and induce minimal permanent refractive changes.
A Novel Reconstruction Technique to Reduce Stair-Step Artifacts in Sequential Mode Coronary CT Angiography
Authors: Moser Lukas Jakob , Mergen Victor , Allmendinger Thomas , Manka Robert , Eberhard Matthias , Alkadhi Hatem 
Published: January 2024

Purpose
Prospective electrocardiography-triggering is one of the most commonly used cardiac computed tomography (CT) scan modes but can be susceptible to stair-step artifacts in the transition areas of an acquisition over multiple cardiac cycles. We evaluated a novel reconstruction algorithm to reduce the occurrence and severity of such artifacts in sequential coronary CT angiography.

Materials and Methods
In this institutional review board–approved, retrospective study, 50 consecutive patients (16 females; mean age, 58.9 ± 15.2) were included who underwent coronary CT angiography on a dual-source photon-counting detector CT in the sequential ultra-high-resolution mode with a detector collimation of 120 × 0.2 mm. Each scan was reconstructed without (hereafter called standard reconstruction) and with the novel ZeeFree reconstruction algorithm, which aims to minimize stair-step artifacts. The presence and extent of stair-step artifacts were rated by 2 independent, blinded readers on a 4-point discrete visual scale. The relationship between the occurrences of artifacts was correlated with the average and variability of heart rate and with patient characteristics.

Results
A total of 504 coronary segments were included into the analyses. In standard reconstructions, reader 1 reported stair-step artifacts in 40/504 (7.9%) segments, from which 12/504 led to nondiagnostic image quality (2.4% of all segments). Reader 2 reported 56/504 (11.1%) stair-step artifacts, from which 11/504 lead to nondiagnostic image quality (2.2% of all segments). With the ZeeFree algorithm, 9/12 (75%) and 8/11 (73%) of the nondiagnostic segments improved to a diagnostic quality for readers 1 and 2, respectively. The ZeeFree reconstruction algorithm significantly reduced the frequency and extent of stair-step artifacts compared with standard reconstructions for both readers (P < 0.001, each). Heart rate variability and body mass index were significantly related to the occurrence of stair-step artifacts (P < 0.05).

Conclusions
Our study demonstrates the feasibility and effectiveness of a novel reconstruction algorithm leading to a significant reduction of stair-step artifacts and, hence, a reduction of coronary segments with a nondiagnostic image quality in sequential ultra-high-resolution coronary photon-counting detector CT angiography.
Comparative Efficacy of Drug Interventions for Keloids
Authors: Yang Hsi-An , Jheng Wun-Long , Yu Jiaxin , Huang Jhao-Yu , Cheng Kai-Yuan , Lee Jian-Jr 
Published: January 2024

Background
Keloids are common benign skin lesions originating from a disorganized fibroproliferative collagen response; these lesions often lead to both physical and psychological problems. The optimal treatment for keloids is yet to be standardized. Intralesional injection, which is simple and nontraumatic, is one of the most commonly used treatment modalities for these lesions. In this study, we compared 5 different drugs (intralesional injections) for the treatment of keloids in terms of efficacy.

Methods
We systemically searched relevant studies on PubMed, EMBASE, and Cochrane Library. Randomized clinical trials on the safety and efficacy of triamcinolone acetonide (TAC), 5-fluorouracil (5-FU), botulinum toxin A (BTA), verapamil, and bleomycin were included in this study.

Results
This network meta-analysis included a total of 1114 patients from 20 randomized controlled trials. Botulinum toxin A alone and TAC plus 5-FU exhibited significantly better efficacy than did 5-FU, TAC, and verapamil. No significant difference in efficacy between BTA alone and TAC combined with 5-FU was observed. No significant differences were noted in the adverse event rate between BTA, TAC plus 5-FU, 5-FU, and TAC. Furthermore, we performed surface under the cumulative ranking curve analyses to predict the rank of each intervention (by efficacy and adverse event rate). The predicted ranking by efficacy was as follows: TAC plus 5-FU, BTA, bleomycin, TAC, 5-FU, and verapamil; the predicted ranking by adverse events was as follows: TAC, 5-FU, TAC plus 5-FU, and BTA. Funnel plot analysis revealed no publication bias.

Conclusions
Botulinum toxin A and TAC plus 5-FU appear to have outstanding therapeutic efficacy for keloids. The rate of adverse events was similar among BTA, TAC, 5-FU, and TAC plus 5-FU. Nonetheless, additional reviews of rigorous, large-scale randomized controlled trials are warranted for further validation of our findings.
Surgical Navigation Applied in Removal of Glass Located Under Zygomatic Arch
Authors: Liu Jaehong , Lee Jun Won , Jeong Hii Sun 
Published: January 2024

The limited detection rate of plain radiography (as low as 75%) for glass particles within the softs renders the conventional C-arm visualization method ineffective in intraoperative scenarios. The authors report the successful use of intraoperative navigation to visualize and extract multiple small glass fragments located deep within the temporal fossa and beneath the zygomatic arch. A 25-year-old man presented with a deep facial laceration, suspected injury to the temporal branch of the facial nerve, and a 2×2 cm foreign body beneath the sphenoid bone near the left zygomatic arch. The initial surgery removed most of the glass; however, two 4 mm fragments remained near the skull base. Using intraoperative navigation, a 3 cm incision was made, and a navigating stylet was used to locate and remove the foreign bodies. In conclusion, intraoperative navigation is a precise method for removing small, imperceptible glass fragments from challenging anatomic areas, thus reducing the need for extensive dissection compared to conventional approaches.
A proof of Specker’s principle
Authors: Bacciagaluppi Guido 
Published: January 2024

Specker’s principle, the condition that pairwise orthogonal propositions must be jointly orthogonal (or rather, the ‘exclusivity principle’ that follows from it), has been much investigated recently within the programme of finding physical principles to characterize quantum mechanics. Specker’s principle, however, largely appears to lack a physical justification. In this paper, I present a proof of Specker’s principle from three assumptions (made suitably precise): the existence of ‘maximal entanglement’, the existence of ‘non-maximal measurements’ and no-signalling. I discuss these three assumptions and describe canonical examples of non-Specker sets of propositions satisfying any two of them. These examples display analogies with various approaches to the interpretation of quantum mechanics, including retrocausation. I also discuss connections with the work of Popescu & Rohrlich. The core of the proof (and the main example violating no-signalling) is illustrated by a variant of Specker’s tale of the seer of Nineveh, with which I open the paper.
This article is part of the theme issue ‘Quantum contextuality, causality and freedom of choice’.
The quantum maxima for the basic graphs of exclusivity are not reachable in Bell scenarios
Authors: Porto Lucas E. A. , Rabelo Rafael , Terra Cunha Marcelo , Cabello Adán 
Published: January 2024

A necessary condition for the probabilities of a set of events to exhibit Bell non-locality or Kochen–Specker contextuality is that the graph of exclusivity of the events contains induced odd cycles with five or more vertices, called odd holes, or their complements, called odd antiholes. From this perspective, events whose graph of exclusivity are odd holes or antiholes are the building blocks of contextuality. For any odd hole or antihole, any assignment of probabilities allowed by quantum theory can be achieved in specific contextuality scenarios. However, here we prove that, for any odd hole, the probabilities that attain the quantum maxima cannot be achieved in Bell scenarios. We also prove it for the simplest odd antiholes. This leads us to the conjecture that the quantum maxima for any of the building blocks cannot be achieved in Bell scenarios. This result sheds light on why the problem of whether a probability assignment is quantum is decidable, while whether a probability assignment within a given Bell scenario is quantum is, in general, undecidable. This also helps to understand why identifying principles for quantum correlations is simpler when we start by identifying principles for quantum sets of probabilities defined with no reference to specific scenarios.
This article is part of the theme issue ‘Quantum contextuality, causality and freedom of choice’.
Observer effect, quasi-probabilities and generalized Specker’s boxes
Authors: Onggadinata K. , Kaszlikowski D. , Kurzyński P. 
Published: January 2024

Quantum non-locality and contextuality can be simulated with quasi-probabilities, i.e. probabilities that take negative values. Here, we show that another quantum phenomenon, the observer effect, admits a quasi-probabilistic description too. We also investigate post-quantum observer effects based on the Specker’s triangle scenario. This scenario comprises three observables, with the possibility of measuring two simultaneously. Represented as three boxes with a hidden ball, this scenario exhibits counterintuitive behaviour: regardless of the chosen pair of boxes, one box always contains the ball. Moreover, the scenario demonstrates a strong observer effect. When an observer selects and opens the first box, finding it empty, the ball is guaranteed to be in the second box, thereby allowing the observer to determine the ball’s location among the remaining two boxes. We extend this scenario to include additional boxes and multiple balls. By employing negative probabilities, we demonstrate amplification of the observer effect.
This article is part of the theme issue ‘Quantum contextuality, causality and freedom of choice’.
Corrected Bell and non-contextuality inequalities for realistic experiments
Authors: Vallée Kim , Emeriau Pierre-Emmanuel , Bourdoncle Boris , Sohbi Adel , Mansfield Shane , Markham Damian 
Published: January 2024

Contextuality is a feature of quantum correlations. It is crucial from a foundational perspective as a non-classical phenomenon, and from an applied perspective as a resource for quantum advantage. It is commonly defined in terms of hidden variables, for which it forces a contradiction with the assumptions of parameter-independence and determinism. The former can be justified by the empirical property of non-signalling or non-disturbance, and the latter by the empirical property of measurement sharpness. However, in realistic experiments neither empirical property holds exactly, which leads to possible objections to contextuality as a form of non-classicality, and potential vulnerabilities for supposed quantum advantages. We introduce measures to quantify both properties, and introduce quantified relaxations of the corresponding assumptions. We prove the continuity of a known measure of contextuality, the contextual fraction, which ensures its robustness to noise. We then bound the extent to which these relaxations can account for contextuality, via corrections terms to the contextual fraction (or to any non-contextuality inequality), culminating in a notion of genuine contextuality, which is robust to experimental imperfections. We then show that our result is general enough to apply or relate to a variety of established results and experimental set-ups.This article is part of the theme issue ‘Quantum contextuality, causality and freedom of choice’.
Three novel Luteimonas species from a root and rhizosphere soil of Kalidium cuspidatum: Luteimonas endophytica sp. nov., Luteimonas rhizosphaericola sp. nov. and Luteimonas kalidii sp. nov.
Authors: Wei Hua-Mei , Xu Lian , Zhang Xu , Sun Ji-Quan 
Published: January 2024

Three Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated RD2P54T, M1R5S18T and M1R5S59T, were isolated from a root and rhizosphere soil of Kalidium cuspidatum, in Baotou, PR China. The three strains showed 94.1–98.7 % 16S rRNA gene sequence similarities to

Luteimonas

strains, indicating they belonged to the genus

Luteimonas

. The phylogenomic tree based on core genomes showed that strain RD2P54T tightly clustered with

Luteimonas salinisoli

SJ-92T, while strains M1R5S18T and M1R5S59T clustered with each other and with Luteimonas viscosa XBU10T and

Luteimonas saliphila

SJ-9T. Though strains M1R5S18T and M1R5S59T showed high 16S rRNA similarity (99.4 %) to each other, the low average nucleotide identity based on blast (ANIb; 88.6 %) and digital DNA–DNA hybridization (dDDH; 31.6 %) values between them indicated that they belonged to two different species. The ANIb and dDDH values of strains RD2P54T, M1R5S18T and M1R5S59T with their closely neighbours are well below the delineation threshold values for identifying strains as representing different species. All three strains take iso-C15 : 0 and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1
ω9c) as major fatty acids, and ubiquinone-8 as the sole respiratory quinone. The major polar lipids of all three strains are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on phenotypic and phylogenetic data, these three strains should be considered to represent three novel species of the genus

Luteimonas

, for which the names Luteimonas endophytica sp. nov. (type strain RD2P54T=CGMCC 1.61535T =KCTC 92470T), Luteimonas rhizosphaericola sp. nov. (type strain M1R5S18T=CGMCC 1.61537T =KCTC 92469T) and Luteimonas kalidii sp. nov. (type strain M1R5S59T=CGMCC 1.61536T =KCTC 92471T) are proposed.