bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical forces guide curvature sensing and cell migration mode bifurcating
Authors: Feng Luyi , Zhao Tiankai , Xu Hongmei , Shi Xuechen , Li Changhao , Hsia K Jimmy , Zhang Sulin 
Published: August 2023

Abstract
The ability of cells to sense and adapt to curvy topographical features has been implicated in organ morphogenesis, tissue repair, and tumor metastasis. However, how individual cells or multicellular assemblies sense and differentiate curvatures remains elusive. Here, we reveal a curvature sensing mechanism in which surface tension can selectively activate either actin or integrin flows, leading to bifurcating cell migration modes: focal adhesion formation that enables cell crawling at convex front edges and actin cable assembly that pulls cells forward at concave front edges. The molecular flows and curved front morphogenesis are sustained by coordinated cellular tension generation and transmission. We track the molecular flows and mechanical force transduction pathways by a phase-field model, which predicts that multicellular curvature sensing is more efficient than individual cells, suggesting collective intelligence of cells. The unique ability of cells in curvature sensing and migration mode bifurcating may offer insights into emergent collective patterns and functions of living active systems at different length scales.
Single-molecule FRET and molecular diffusion analysis characterize stable oligomers of amyloid-β 42 of extremely low population
Authors: Meng Fanjie , Kim Jae-Yeol , Gopich Irina V , Chung Hoi Sung 
Published: August 2023

AbstractSoluble oligomers produced during protein aggregation have been thought to be toxic species causing various diseases. Characterization of these oligomers is difficult because oligomers are a heterogeneous mixture, which is not readily separable, and may appear transiently during aggregation. Single-molecule spectroscopy can provide valuable information by detecting individual oligomers, but there have been various problems in determining the size and concentration of oligomers. In this work, we develop and use a method that analyzes single-molecule fluorescence burst data of freely diffusing molecules in solution based on molecular diffusion theory and maximum likelihood method. We demonstrate that the photon count rate, diffusion time, population, and Förster resonance energy transfer (FRET) efficiency can be accurately determined from simulated data and the experimental data of a known oligomerization system, the tetramerization domain of p53. We used this method to characterize the oligomers of the 42-residue amyloid-β (Aβ42) peptide. Combining peptide incubation in a plate reader and single-molecule free-diffusion experiments allows for the detection of stable oligomers appearing at various stages of aggregation. We find that the average size of these oligomers is 70-mer and their overall population is very low, less than 1 nM, in the early and middle stages of aggregation of 1 µM Aβ42 peptide. Based on their average size and long diffusion time, we predict the oligomers have a highly elongated rod-like shape.
Development and validation of a predictive model for pulmonary hemorrhage in computed tomography–guided percutaneous lung biopsy
Authors: Yang Song , Li Jie , Wang Wangjia , Lou Lejing , Jin Xiao , Wang Shijia , Cai Jihao , Cai Chang 
Published: July 2023

Abstract

Purpose
This study aimed to identify risk factors for pulmonary hemorrhage (PH) and higher-grade PH that complicate computed tomography (CT)-guided percutaneous lung biopsy (CT-PNLB) and establish predictive models to quantify the risk.

Methods
A total of 2653 cases of CT-PNLB were enrolled. Multivariate logistic regression was used to identify independent risk factors to develop a nomogram prediction model. The model was assessed using the area under the curve (AUC) of the receiver operator characteristic (ROC) and calibration curves and validated in the validation group.

Results
PH occurred in 23.52% (624/2653) of cases, and higher-grade PH occurred in 7.09% (188/2653) of cases. The parameters of lesion size, puncture depth, and contact to pleura were identified as risk factors of PH and higher-grade PH in the logistic regression model, besides the position as a risk factor for PH. The AUC of the PH prediction model was 0.776 [95% confidence interval (CI): 0.752–0.800], whereas that of the validation group was 0.743 (95% CI: 0.706–0.780). The AUC of the higher-grade PH prediction model was 0.782 (95% CI: 0.742–0.832), whereas that of the validation group was 0.769 (95% CI: 0.716–0.822). The calibration curves of the model showed good agreement between the predicted and actual probability in the development and validation groups.

Conclusion
We identified risk factors associated with PH and higher-grade PH after PNLBs. Furthermore, we developed and validated two risk prediction models for PNLB-related PH and higher-grade PH risk prediction and clinical decision support.
Key messages What is already known on this topic Pulmonary hemorrhage (PH) and other hemorrhagic complications are the most common complication in CT-guided percutaneous lung biopsy (CT-PNLB), except pneumothorax. However, the risk factors associated with PH remain controversial, and research on models of PH and higher-grade PH is also limited. What this study adds The parameters of lesion size, puncture depth, and contact to pleura were identified as risk factors of PH and higher-grade PH in the logistic regression model, besides the position as a risk factor for PH. In addition, we developed and validated two risk prediction models for PNLB-related PH and higher-grade PH risk prediction and clinical decision support. How this study might affect research, practice, or policy Of all the predictors, the position is the key factor to be considered by the operator. Moreover, two risk prediction models show good discrimination and calibration characteristics to identify patients at high risk of hemorrhage and higher-grade PH after PNLB, so these could assist clinicians in avoiding risk factors in advance.
Long-Term Safety of Bone Regeneration Using Autologous Stromal Vascular Fraction and Calcium Phosphate Ceramics: A 10-Year Prospective Cohort Study
Authors: Wu Vivian , Klein-Nulend Jenneke , Bravenboer Nathalie , ten Bruggenkate Christiaan M , Helder Marco N , Schulten Engelbert A J M 
Published: August 2023

Abstract
This prospective cohort study aimed to assess long-term safety, dental implant survival, and clinical and radiological outcomes after maxillary sinus floor elevation (MSFE; lateral window technique) using freshly isolated autologous stromal vascular fraction (SVF) combined with calcium phosphate ceramics. All 10 patients previously participating in a phase I trial were included in a 10-year follow-up. They received either β-tricalcium phosphate (β-TCP; n = 5) or biphasic calcium phosphate (BCP; n = 5) with SVF-supplementation on one side (study). Bilaterally treated patients (6 of 10; 3 β-TCP, 3 BCP) received only calcium phosphate on the opposite side (control). Clinical and radiological assessments were performed on 44 dental implants at 1-month pre-MSFE, and 0.5- to 10-year post-MSFE. Implants were placed 6 months post-MSFE. No adverse events or pathology was reported during a 10-year follow-up. Forty-three dental implants (98%) remained functional. Control and study sides showed similar peri-implant soft-tissue quality, sulcus bleeding index, probing depth, plaque index, keratinized mucosa width, as well as marginal bone loss (0-6 mm), graft height loss (0-6 mm), and graft volume reduction. Peri-implantitis was observed around 6 implants (control: 4; study: 2) in 3 patients. This study is the first to demonstrate the 10-year safety of SVF-supplementation in MSFE for jawbone reconstruction. SVF-supplementation showed enhanced bone regeneration in the short term (previous study) and led to no abnormalities clinically and radiologically in the long term.
Beef color and tenderness response to production systems utilizing additive combinations of growth-promotant technologies
Authors: Webb Megan J , Block Janna J , Jaeger John R , Funston Rick N , Gonda Michael G , Underwood Keith R , Grubbs Judson K , Olson Kenneth C , Blair Amanda D 
Published: August 2023

Abstract
The objective of this study was to compare the influence of beef production systems using additive combinations of growth-promotant technologies on meat quality. Steer calves (n = 120) were assigned to 1 of 4 treatments: 1) no technology (NT; control), 2) antibiotic treated (ANT; NT plus therapeutic antibiotics, monensin, and tylosin), 3) implant treated (IMP; ANT plus a series of three implants), and 4) beta-agonist treated (BA; IMP plus ractopamine-HCl). Muscle biopsy samples from the longissimus lumborum were extracted from a subset (n = 4 per treatment) of steers to evaluate expression of calpain-1, calpain-2, and calpastatin using real-time RT-PCR. Following carcass chilling, objective color (L*, a*, and b*) was evaluated. The right strip loin was removed from each carcass, portioned into 2.54-cm steaks, and designated to 7, 14, or 21 d postmortem aging periods for analysis of cook loss and Warner–Bratzler shear force (WBSF). The anterior face of each strip loin was used for analysis of crude fat and moisture. Treatment influenced (P &lt; 0.001) L*, a*, and b*. The NT and IMP treatments had greater (P &lt; 0.01) L* values, ANT was intermediate, and BA had the lowest (P &lt; 0.01) L* values. The NT and IMP treatments had higher (P &lt; 0.01) a* and b* values compared with ANT, which were higher (P &lt; 0.01) than BA. Steaks from implanted steers (IMP and BA) tended (P ≤ 0.067) to exhibit higher a* and b* than steaks from nonimplanted steers. Cattle in the NT and ANT treatments produced steaks with increased (P &lt; 0.01) crude fat percentage compared with the IMP and BA treatments, which were similar (P &gt; 0.05). Percent moisture of NT steaks was lower (P &lt; 0.01) than all other treatments, ANT was intermediate, and IMP and BA were similar (P &gt; 0.05) and had the highest (P &lt; 0.01) moisture content. Cook loss tended to be greater (P = 0.088) for implanted steers (IMP and BA) compared to nonimplanted steers (NT and ANT). Steaks from NT and ANT treatments were more tender (P &lt; 0.05) than IMP and BA, which were similar (P &gt; 0.05). Thus, WBSF was lower (P &lt; 0.001) in nonimplanted than implanted steaks. Expression of calpastatin was increased (P ≤ 0.025) in ANT and BA treatments, and there was a tendency for expression of calpain-2 to be increased (P = 0.081) in ANT compared to NT. These results suggest that production systems with limited use of growth promoting technology produced strip loins with more crude fat, less moisture and cook loss, and improved tenderness.
Preoperative dexamethasone administration in hepatectomy of 25-minute intermittent Pringle’s maneuver for hepatocellular carcinoma: a randomized controlled trial
Authors: Huang Yang , Xu Liangliang , Wang Ning , Wei Yonggang , Wang Wentao , Xu Mingqing , Jiang Li 
Published: August 2023

Background:
A previous randomized controlled trial (RCT) demonstrated that intermittent Pringle’s maneuver (IPM) with a 25-minute ischemic interval can be applied safely and efficiently in hepatectomy for patients with hepatocellular carcinoma (HCC). But prolonging the hepatic inflow clamping time will inevitably aggravate the ischemia-reperfusion injury (IRI). Therefore, we aimed to evaluate the effect of prophylactic dexamethasone on alleviating the surgical stress for HCC patients with a 25-minute ischemic interval.

Methods:
From December 2022 to April 2023, patients met the inclusion criteria were randomly assigned to dexamethasone group or control group. Perioperative data and short-term survival outcomes between the two groups were recorded and compared, and subgroup analysis was performed.

Results:
Two hundred and seventy patients were allocated to the dexamethasone group (n=135) and control group (n=135). Patients in dexamethasone group had lower area under the curve of serial alanine aminotransferase (AUCALT) (P=0.043) and aspartate aminotransferase (AUCAST) (P=0.009), total bilirubin (TB) (P=0.018), procalcitonin (PCT) (P=0.012), interleukin-6 (IL-6) (P=0.006), incidence of major complication (P=0.031) and shorter postoperative hospital stay (P=0.046) than those in control group. Subgroup analysis showed that the dexamethasone group experienced milder hepatocellular injury than the control group for patients with cirrhosis, and for patients without cirrhosis, the dexamethasone group experienced milder inflammatory response. Moreover, the dexamethasone group preserved better liver function and experienced milder inflammatory response for patients undergoing major hepatectomy, although hepatocellular injury was not significantly improved.

Conclusion:
Preoperative dexamethasone administration can help improve perioperative outcomes for HCC patients when applying IPM with a 25-minute ischemic interval in hepatectomy.
Preoperative low muscle mass and early postoperative outcomes in children undergoing living donor liver transplantation: A retrospective study
Authors: Jeong Daun , Lee Sang-Wook , Jang Hwa-Young , Kwon Hye-Mee , Shin Won-Jung , Song In-Kyung 
Published: August 2023

Low skeletal muscle mass may develop in children with end-stage liver disease, affecting postoperative outcomes. We retrospectively investigated whether preoperative low muscle mass was associated with early postoperative outcomes in pediatric patients undergoing living donor liver transplantation (LDLT). Electronic medical records of children (age below 12 y) who underwent LDLT between February 1, 2007, and January 31, 2018, were reviewed. The cross-sectional areas of psoas, quadratus lumborum, and erector spinae muscles at the level of fourth-fifth lumbar intervertebral disks were measured using abdominal CT images, divided by the square of the height and were added to obtain the total skeletal muscle index (TSMI). The patients were divided into two groups according to the median TSMI in the second quintile (1859.1 mm2/m2). Complications in the early postoperative period (within 30 d after surgery) classified as Clavien-Dindo grade 3 or higher were considered major complications. Logistic regression analyses were performed to determine the association between preoperative low muscle mass and early postoperative outcomes. In the study population of 123 patients (median age, 14 mo; range, 8–38 mo) who underwent LDLT, 29% and 71% were classified in the low (mean TSMI, 1642.5 ± 187.0 mm2/m2) and high (mean TSMI 2188.1 ± 273.5 mm2/m2) muscle mass groups, respectively. The rates of major complications, mechanical ventilation >96 hours, intensive care unit stay >14 days, hospital stay >30 days, and in-hospital mortality were not significantly different between the 2 groups. Additionally, adverse outcomes according to pediatric end-stage liver disease scores and sex were not significantly different between the 2 groups. In conclusion, preoperative low muscle mass defined by TSMI was not associated with early postoperative outcomes in pediatric patients undergoing LDLT.
Binucleated Myocytes and Heart Weight
Authors: Gadsby Zeena , Garland Jack , Thompson Melissa , Ondruschka Benjamin , Da Broi Ugo , Tse Rexson 
Published: August 2023

Abstract
Hypertrophy of the heart is assessed by heart weight (and dimensions) and myocyte hypertrophy. Establishing an association between the two may be useful in assessing hypertrophy in cases where there are limitations in assessing the heart weight. This preliminary study explored the association between the number of binucleated myocytes (a feature of myocyte hypertrophy) in a randomly chosen single high-power field of the left ventricular free wall and heart weight in an adult White population. It also compared the number of binucleated myocytes between cases with increased heart weight (>400 g in female and >500 g in male) and cases with normal heart weight. Heart weight and number of binucleated myocytes correlated significantly in male only. Increased heart weight had a significantly higher number of binucleated myocytes, with 8.5 binucleated myocytes being able to segregate cases with increased heart weight (74% sensitivity and 79% specificity). The results of this study showed the number of binucleated myocytes may have a complementary role in assessing hypertrophy of the heart.
Entanglement and indistinguishability: facing some challenges from a new perspective
Authors: Lombardi Olimpia 
Published: July 2023

While entanglement in the case of distinguishable particles is clearly understood, in the case of indistinguishable particles, there is still a wide debate regarding basic conceptual issues. Here, I will address two such issues. First, the debate almost always rests on a differentiated treatment of the cases of distinguishability and indistinguishability, even with respect to the definition of the concept of entanglement. Second, the fact that symmetrized and antisymmetrized states of indistinguishable particles are non-factorizable leads to certain perplexities about the very nature of entanglement. In the present work, both issues will be addressed from the perspective of an ontology of properties, which finds its natural expression in the algebraic formalism of quantum mechanics. The final goal will be to show that the proposed ontology allows a unified treatment of entanglement in the distinguishability and indistinguishability cases and offers a straightforward way out to perplexities.
This article is part of the theme issue 'Identity, individuality and indistinguishability in physics and mathematics'.
Entanglement and discernibility of identical particles
Authors: Bigaj Tomasz 
Published: July 2023

This article follows an unorthodox approach to the individuation of quantum particles of the same type. According to this approach, individuation of the components of a composite system of identical particles is done not with the help of unphysical labels (indices) but physically meaningful projection operators. This unorthodox conception requires a modification of the standard notion of entanglement, in order to exclude states whose non-factorizability arises merely from the (anti)symmetrization of a product state. I will report several facts regarding the connections of the modified concept of entanglement with the issue of discernibility. I will also discuss recent experiments involving measurement-induced entanglement, and I will point out that they do not threaten the cogency of the new concept of entanglement. The statistical correlations observed in these experiments are explainable not by the entanglement of the initial state but by the creation of a new, genuinely entangled state by means of a pre-measurement selection. Finally, I will identify and discuss a genuine difference between non-entangled but non-factorizable states of identical particles and ordinary product states, which is that the former but not the latter admits an infinity of alternative and incompatible individuations by single-particle properties. This phenomenon can be accounted for using the concept of emergent particles proposed by Dennis Dieks.
This article is part of the theme issue 'Identity, individuality and indistinguishability in physics and mathematics'.
Emergence and identity of quantum particles
Authors: Dieks Dennis 
Published: July 2023

According to classical physics,particlesare basic constituents of the physical world. Quantum theory is much less friendly to particles; in particular, relativistic quantum field theory (RQFT) creates serious obstacles for the idea that particles are fundamental. Apparently, when moving from the domain of RQFT to that of classical mechanics (CM), particles have toemergeat some stage. It is standard to assume that this emergence has been completed at the level of quantum mechanics, halfway between RQFT and CM, even though particles of the same kind in many-particle quantum mechanics have the curious feature of being ‘entities without identity’. Against this ‘Received View’ about the nature of quantum particles we outline and defend anAlternative View(AV), in which the emergent character of particles is emphasized. According to this AV, the step to a particle theory has not yet been made in quantum mechanics: conditions have still to be satisfied in order to make the particle concept applicable. If these conditions are met, the quantum particles that emerge aredistinguishableindividuals possessing physically defined identities, in stark contrast to what the Received View asserts. We will compare and contrast the two Views, both from a physical and a logical/conceptual point of view.This article is part of the theme issue ‘Identity, individuality and indistinguishability in physics and mathematics’.
Indistinguishable entangled fermions: basics and future challenges
Authors: Majtey Ana P. , Valdés-Hernández Andrea , Cuestas Eloisa 
Published: July 2023

The study of entanglement in systems composed of identical particles raises interesting challenges with far-reaching implications in both, our fundamental understanding of the physics of composite quantum systems, and our capability of exploiting quantum indistinguishability as a resource in quantum information theory. Impressive theoretical and experimental advances have been made in the last decades that bring us closer to a deeper comprehension and to a better control of entanglement. Yet, when it involves composites of indistinguishable quantum systems, the very meaning of entanglement, and hence its characterization, still finds controversy and lacks a widely accepted definition. The aim of the present paper is to introduce, within an accessible and self-contained exposition, the basic ideas behind one of the approaches advanced towards the construction of a coherent definition of entanglement in systems of indistinguishable particles, with focus on fermionic systems. We also inquire whether the corresponding tools developed for studying entanglement in identical-fermion systems can be exploited when analysing correlations in distinguishable-party systems, in which the complete information of the individual parts is not available. Further, we open the discussion on the broader problem of constructing a suitable framework that accommodates entanglement in the presence of generalized statistics.
This article is part of the theme issue ‘Identity, individuality and indistinguishability in physics and mathematics’.
Star allele search: a pharmacogenetic annotation database and user-friendly search tool of publicly available 1000 Genomes Project biospecimens
Authors: Gharani N. , Calendo G. , Kusic D. , Madzo J. , Scheinfeldt L. 
Published: July 2023

AbstractHere we describe a new public pharmacogenetic (PGx) annotation database of a large (n=3202) and diverse biospecimen collection of 1000 Genomes Project cell lines and DNAs. The database is searchable with a user friendly, web-based tool (www.coriell.org/StarAllele/Search). This resource leverages existing whole genome sequencing data and PharmVar annotations to characterize *alleles for each biospecimen in the collection. This new tool is designed to facilitate in vitro functional characterization of *allele haplotypes and diplotypes as well as support clinical PGx assay development, validation, and implementation.