bluuebunny/crossref_metadata_2025 huggingface dataset:
Combining convolutional neural networks and self-attention for fundus diseases identification
Authors: Wang Keya , Xu Chuanyun , Li Gang , Zhang Yang , Zheng Yu , Sun Chengjie
Published: January 2023

Early detection of lesions is of great significance for treating fundus diseases. Fundus photography is an effective and convenient screening technique by which common fundus diseases can be detected. In this study, we use color fundus images to distinguish among multiple fundus diseases. Existing research on fundus disease classification has achieved some success through deep learning techniques, but there is still much room for improvement in model evaluation metrics using only deep convolutional neural network (CNN) architectures with limited global modeling ability; the simultaneous diagnosis of multiple fundus diseases still faces great challenges. Therefore, given that the self-attention (SA) model with a global receptive field may have robust global-level feature modeling ability, we propose a multistage fundus image classification model MBSaNet which combines CNN and SA mechanism. The convolution block extracts the local information of the fundus image, and the SA module further captures the complex relationships between different spatial positions, thereby directly detecting one or more fundus diseases in retinal fundus image. In the initial stage of feature extraction, we propose a multiscale feature fusion stem, which uses convolutional kernels of different scales to extract low-level features of the input image and fuse them to improve recognition accuracy. The training and testing were performed based on the ODIR-5k dataset. The experimental results show that MBSaNet achieves state-of-the-art performance with fewer parameters. The wide range of diseases and different fundus image collection conditions confirmed the applicability of MBSaNet.
High performance antenna-on-chip inspired by SIW and metasurface technologies for THz band operation
Authors: Alibakhshikenari Mohammad , Virdee Bal S. , Rajaguru Renu Karthick , Iqbal Amjad , Al‑Hasan Muath , See Chan H. , Falcone Francisco
Published: January 2023

In this paper, a high-performance antenna-on-chip (AoC) is implemented on gallium arsenide (GaAs) wafer based on the substrate integrated waveguide (SIW) and metasurface (MTS) technologies for terahertz band applications. The proposed antenna is constructed using five stacked layers comprising metal-GaAs-metal-GaAs-metal. The conductive electromagnetic radiators are implemented on the upper side of the top GaAs layer, which has a metallic ground-plane at its underside. The metallic feedline is implemented at the underside of the bottom GaAs layer. Dual wrench-shaped radiators are framed by metallic vias connected to the ground-plane to create SIW cavity. This technique mitigates the surface waves and the substrate losses, thereby improving the antenna’s radiation characteristics. The antenna is excited by a T-shaped feedline implemented on the underside of the bottom GaAs substrate layer. Electromagnetic (EM) energy from the feedline is coupled to the radiating elements through the circular and linear slots etched in the middle ground-plane layer. To mitigate the surface-wave interactions and the substrate losses in the bottom GaAs layer, the feedline is contained inside a SIW cavity. To enhance the antenna’s performance, the radiators are transformed into a metamaterial-inspired surface (i.e., metasurface), by engraving periodic arrangement of circular slots of sub-wavelength diameter and periodicity. Essentially, the slots act as resonant scatterers,which control the EM response of the surface. The antenna of dimensions of 400 × 400 × 8 μm3is demonstrated to operate over a wide frequency range from 0.445 to 0.470 THz having a bandwidth of 25 GHz with an average return-loss of − 27 dB. The measured average gain and radiation efficiency are 4.6 dBi and 74%, respectively. These results make the proposed antenna suitable for AoC terahertz applications.
Expanded genetic testing of GIST patients identifies high proportion of non-syndromic patients with germline alterations
Authors: Mandelker Diana , Marra Antonio , Mehta Nikita , Selenica Pier , Yelskaya Zarina , Yang Ciyu , Somar Joshua , Mehine Miika , Misyura Maksym , Basturk Olca , Latham Alicia , Carlo Maria , Walsh Michael , Stadler Zsofia K. , Offit Kenneth , Bandlamudi Chaitanya , Hameed Meera , Chi Ping , Reis-Filho Jorge S. , Ceyhan-Birsoy Ozge
Published: January 2023

Traditional genetic testing for patients with gastrointestinal stromal tumors (GISTs) focus on those with syndromic features. To assess whether expanded genetic testing of GIST patients could identify hereditary cancer predisposition, we analyzed matched tumor-germline sequencing results from 103 patients with GISTs over a 6-year period. Germline pathogenic/likely pathogenic (P/LP) variants in GIST-associated genes (SDHA, SDHB, SDHC, NF1, KIT) were identified in 69% of patients with KIT/PDGFRA-wildtype GISTs, 63% of whom did not have any personal or family history of syndromic features. To evaluate the frequency of somatic versus germline variants identified in tumor-only sequencing of GISTs, we analyzed 499 de-identified tumor-normal pairs. P/LP variants in certain genes (e.g., BRCA1/2, SDHB) identified in tumor-only sequencing of GISTs were almost exclusively germline in origin. Our results provide guidance for genetic testing of GIST patients and indicate that germline testing should be offered to all patients with KIT/PDGFRA-wildtype GISTs regardless of their history of syndromic features.
Friction hysteretic behavior of supported atomically thin nanofilms
Authors: Xu Chaochen , Ye Zhijiang , Egberts Philip
Published: January 2023

Hysteretic friction behavior has been observed on varied 2D nanofilms. However, no unanimous conclusion has yet been drawn on to the exact mechanism or relative contribution of each mechanism to the observed behavior. Here we report on hysteretic friction behavior of supported atomically thin nanofilms studied using atomic force microscopy (AFM) experiments and molecular dynamics (MD) simulations. Load dependent friction measurements were conducted on unheated and heated samples of graphene, h-BN, and MoS2 supported by silica substrates. Two diverging friction trends are reported: the unheated samples showed higher friction during unloading than during loading, and the heated samples showed a reversed hysteresis. Further, the friction force increased sub-linearly with normal force for heated samples, compared with unheated samples. Tapping mode AFM suggested that the interaction strength of the substrate was increased with heating. Roughened substrates in the MD simulations that mimicked strong/weak interaction forces reproduced the experimental observations and revealed that the evolution of real contact area in different interface interaction situation caused the diverging behaviors. Surface roughness and interaction strength were found to be the key parameters for controlling the out-of-plane deformation of atomically thin nanofilms.
Synthesis of trans-1,2-dimetalloalkenes through reductive anti-dimagnesiation and dialumination of alkynes
Authors: Takahashi Fumiya , Kurogi Takashi , Yorimitsu Hideki
Published: January 2023

Polar reactive organometallic species have been key reagents in synthesis for more than a century. Stereodefined 1,2-dimetallated alkenes offer promising synthetic utility; however, few methods are available for their preparation due to their relatively low stability. Here we report the reductive anti-1,2-dimetallation of alkynes to stereoselectively generate trans-1,2-dimagnesio- and 1,2-dialuminoalkenes, which are stable and have been demonstrated in organic synthesis. These stereodefined 1,2-dimetallated alkenes are prepared through the use of a sodium dispersion as a reducing agent, and organomagnesium and organoaluminium halides as reduction-resistant electrophiles. Highly nucleophilic 1,2-dimagnesioalkenes serve as dual Grignard reagents and have been demonstrated to react with various electrophiles to afford anti-difunctionalized alkenes. The 1,2-dialuminoalkenes react with paraformaldehyde with dearomatization of the aryl moieties to form the corresponding dearomatized 1,4-diols, with the overall reaction being regarded as alkynyl-directed dearomatization of arenes. X-ray crystallographic analysis further supports the formation of trans-1,2-dimagnesio- and 1,2-dialuminoalkenes, with computational studies providing insight into the mechanism of dearomative difunctionalization.
Fabrication and development of a microfluidic paper-based immunosorbent assay platform (μPISA) for colorimetric detection of hepatitis C
Authors: Ozefe Fatih , Arslan Yildiz Ahu
Published: January 2023

A portable and disposable microfluidic paper-based immunosorbent assay platform (μPISA) was utilized for the qualitative and quantitative detection of HCV protein in human blood plasma.
SERS-based error calibration of a TMB–H2O2 colorimetric system
Authors: Wan Jianhui , Liu Qixin , Tang Ping , Ji Yinuo , Zhong Wanqing , Cheng Wendai , Xing Xinyue , Lu Xiaoxu , Zhong Liyun
Published: January 2023

SERS spectrum-based error calibration method of TMB–H2O2 colorimetric system to achieve the actual process information during TMB oxidation and open a new horizon for enzyme-linked immunosorbent assays and other biomedical applications.
Fluorescent glyco-gold nanocluster induced EGFR mediated targeting of cancer cells
Authors: Chandra Ankita , Bhoge Preeti Ravindra , K. R. Remya , Shanthamurthy Chethan D. , Kikkeri Raghavendra
Published: January 2023

Sulfated oligo-iduronic acid ligand engineered fluorescent gold nanoclusters show EGF receptor-regulated cancer cell homing ability in both 2D and 3D cell culture systems, opening a new avenue for a practical and direct imaging tool for carbohydrate research.
Synthesis of benzo[b][1,5]diazocin-6(5H)-one derivatives via the Cu-catalysed oxidative cyclization of 2-aryl-1H-indoles with 1,1-enediamines
Authors: Chen Yi-Hua , Yang Jing , Lu Zi-Han , Zhao Ke-Hua , Xie Qi-Ying , Yan Sheng-Jiao
Published: January 2023

A novel protocol for the synthesis of highly functionalized benzo[b][1,5]diazocin-6(5H)-one derivatives (BDCOs, 4 and 5) from 2-aryl-1H-indoles and 1,1-enediamines was developed via a complex cascade of reactions.
Journeys in crystal energy landscapes: actual and virtual structures in polymorphic 5-nitrobenzo[c][1,2,5]thiadiazole
Authors: Gentile Francesco Silvio , Parisi Emmanuele , Centore Roberto
Published: January 2023

Few crystal structures are observed, out of the many possible ones, because of strong selection playing at the level of prenucleation clusters.
Unraveling the contributions to the spectral shape of flexible dyes in solution: insights on the absorption spectrum of an oxyluciferin analogue
Authors: Cerezo Javier , García-Iriepa Cristina , Santoro Fabrizio , Navizet Isabelle , Prampolini Giacomo
Published: January 2023

The experimental shape of the absorption spectrum in water of 5,5-spirocyclopropyl-oxyluciferin is rationalized in terms of homogeneous and inhomogeneous broadening contributions by means of a mixed quantum classical computational approach.
Deep eutectic solvothermal NiS2/CdS synthesis for the visible-light-driven valorization of the biomass intermediate 5-hydroxymethylfurfural (HMF) integrated with H2 production
Authors: Liu Shuzi , Zhang Baolong , Yang Zhaohui , Xue Zhimin , Mu Tiancheng
Published: January 2023

NiS2/CdS photocatalyst produced from deep eutectic solvothermal technique is efficient for visible-light-driven dehydrogenation of 5-hydroxymethylfurfural into H2 and 2,5-diformylfuran at rates of up to 519.64 and 476.60 μmol g−1 h−1, respectively.
Reproduction of super-multicomponent self-assembled structures and their functionality using coarse-grained molecular simulation – the example of cleansing agents
Authors: Yokoyama Takahiro , Miwake Hideki , Hamaguchi Masugu , Nakatake Ryoichi , Arai Noriyoshi
Published: January 2023

Our aim is to link the macroscopic properties of multi-component systems with the mesoscale structures to elucidate the molecular evidence of functions.
A xanthene-based probe with dual reaction sites enables fluorescence turn-on detection of thiophenol in an aqueous medium
Authors: Priya Bhanu , Kumar Naresh , Mishra Deepak , Roopa
Published: January 2023

A xanthene-derived fluorescent probe has been reported to detect and discriminate thiophenol from hydrogen sulfide.
Cyanine-based [18F]F-C-glycosyl dual imaging probe: synthesis, physico-chemical characterization, in vitro binding evaluation and direct [18F]fluorination
Authors: Vucko Timothé , Ariztia Julen , Jouad Kamal , Chapeau Dylan , Mourot Benjamin , Jouan-Hureaux Valérie , Collet Charlotte , Boura Cédric , Selmeczi Katalin , Pellegrini Moïse Nadia , Lamandé-Langle Sandrine
Published: January 2023

Efficient synthesis of a [18F]F-C-glycosyl dual imaging probe displaying a cyanine for fluorescence imaging (FLI) and a robust [18F]F–C bond for positron emission tomography (PET) imaging.
Leveraging Pd(100)/SnO2interfaces for highly efficient electrochemical formic acid oxidation
Authors: Huang Haiyan , Yang Tianyi , Sun Fang , Liu Zhaohui , Tang Qing , Liu Lingmei , Han Yu , Huang Jianfeng
Published: January 2023

A novel Pd/SnO2nanocomposite with abundant Pd(100)/SnO2interfaces shows a record-high mass activity of 14.55 A mgPd−1towards electrochemical formic acid oxidation.
Dual-mode frequency multiplier in graphene-base hot electron transistor
Authors: Liang Bor-Wei , Li Min-Fang , Lin Hung-Yu , Li Kai-Shin , Chen Jyun-Hong , Shieh Jia-Min , Wu Chien-Ting , Simbulan Kristan Bryan , Su Ching-Yuan , Kuan Chieh-Hsiung , Lan Yann-Wen
Published: January 2023

A graphene-base hot electron transistor integrated with a 2D material heterojunction is demonstrated as a frequency modulator. Our device can operate as a doubler or tripler with AC signals from 100 kHz to 10 MHz in single tunneling transistor.
Analysis of a method to compute mixed-mode stress intensity factors for non-planar cracks in three-dimensions
Authors: Grossman-Ponemon Benjamin E. , Negri Matteo , Lew Adrian J.
Published: January 2023

In this work, we present and prove results underlying a method which uses functionals derived from the interaction integral to approximate the stress intensity factors along a three-dimensional crack front. We first prove that the functionals possess a pair of important properties. The functionals are well-defined and continuous for square-integrable tensor fields, such as the gradient of a finite element solution. Furthermore, the stress intensity factors are representatives of such functionals in a space of functions over the crack front. Our second result is an error estimate for the numerical stress intensity factors computedviaour method. The latter property of the functionals provides a recipe for numerical stress intensity factors; we apply the functionals to the gradient of a finite element approximation for a specific set of crack front variations, and we calculate the stress intensity factors by inverting the mass matrix for those variations.
Advances in Exploring Cyclopentadienyl (Cp) Rhodium Catalysts Featuring Diastereotopic or Enantiotopic Cp Faces for Asymmetric C–H Activation
Authors: Wang Jun , Yan Xiaoqiang
Published: January 2023

Chiral cyclopentadienyl rhodium (CpRh) complexes have emerged as a class of powerful catalysts for enantioselective C–H activation reactions. In terms of Cp ligand development, the mainstream is to design chiral ligands with C
2 symmetry in order to avoid the problem of Cp face selectivity during their metalation with rhodium. In recent years, CpRh catalysts with diastereotopic or enantiotopic Cp faces were also revealed and successfully applied in asymmetric C–H activation. These advances are summarized in this short review together with perspectives for their future development.

1 Introduction

2 Cp Ligands with Diastereotopic Cp Faces

3 Cp Ligands with Enantiotopic Cp Faces

4 Conclusion and Outlook
A Mn(OAc)3-Triggered Formation of Cyclopropanes from Ugi Adducts
Authors: El Kaïm Laurent , Cheibas Cristina , Vieu Emilie , Casaretto Nicolas , Vitale Maxime , Grimaud Laurence
Published: January 2023

Ugi adducts involving malonic acid monoesters and dialkoxy-substituted aromatic aldehydes can undergo an oxidative dearomatization when treated with Mn(OAc)3 leading to the formation of fused cyclopropanes as observed in the Buchner reaction of diazo compounds.
Addition of Alcohols onto Electron-Deficient Heteroarenium Salts: A Reversible Covalent Bonding Process under Basic Conditions
Authors: Chen Baoli , Li En , Chen Jiean , Huang Yong , Song Feifei , Guimond Nicolas
Published: January 2023

The reversible addition of benzyl alcohol onto heteroarenium salts under basic conditions was studied. Fine-tuning of the nature of the arenium and substituents allowed the discovery of a range of pyrimidinium substrates that can undergo C6-selective alcohol addition. Crossover experiments were also performed to confirm the addition-elimination equilibrium under basic conditions.
Frustrated Lewis Pair Catalyzed Reactions
Authors: Zhou Rundong , Tavandashti Zoleykha Pirhadi , Paradies Jan
Published: January 2023

In recent years, frustrated Lewis pairs have been widely used for the activation of small molecules and in catalytic transformations. This graphical review aims to provide a fundamental understanding of frustrated Lewis pair reactivity and the exploitation thereof in catalytic reactions.
Anti-glutamatergic Effects of Three Lignan Compounds: Arctigenin, Matairesinol and Trachelogenin – An ex vivo Study on Rat Brain Slices
Authors: Koech Peter Kiplangʼat , Jócsák Gergely , Boldizsár Imre , Moldován Kinga , Borbély Sándor , Világi Ildikó , Dobolyi Arpád , Varró Petra
Published: January 2023

Arctigenin is a bioactive dibenzylbutyrolactone-type lignan exhibiting various pharmacological activities. The neuroprotective effects of arctigenin were demonstrated to be mediated via
inhibition of AMPA and KA type glutamate receptors in the somatosensory cortex of the rat brain. The aim of this study was to compare the effects of arctigenin with matairesinol and
trachelogenin on synaptic activity in ex vivo rat brain slices. Arctigenin, matairesinol and trachelogenin were isolated from Arctium lappa, Centaurea scabiosa and Cirsium
arvense, respectively, and applied on brain slices via perfusion medium at the concentration range of 0.5 – 40 µM. The effects of the lignans were examined in the CA1 hippocampus and the
somatosensory cortex by recording electrically evoked field potentials. Arctigenin and trachelogenin caused a significant dose-dependent decrease in the amplitude of hippocampal population
spikes (POPS) and the slope of excitatory postsynaptic potentials (EPSPs), whereas matairesinol (1 µM and 10 µM) decreased EPSP slope but had no effect on POPS amplitude. Trachelogenin
effect (0.5 µM, 10 µM, 20 µM) was comparable to arctigenin (1 µM, 20 µM, 40 µM) (p > 0.05). In the neocortex, arctigenin (10 µM, 20 µM) and trachelogenin (10 µM) significantly decreased
the amplitude of evoked potential early component, while matairesinol (1 µM and 10 µM) had no significant effect (p > 0.05). The results suggest that trachelogenin and arctigenin act via
inhibition of AMPA and KA receptors in the brain and trachelogenin has a higher potency than arctigenin. Thus, trachelogenin and arctigenin could serve as lead compounds in the development
of neuroprotective drugs.
Stem Cells in the Periodontium—Anatomically Related Yet Physiologically Diverse
Authors: Ponnaiyan Deepa , Rughwani Roshan R. , Victor Dhayanand John , Shetty Ganesh
Published: January 2023

Periodontitis is a complex chronic disease discernible by the deterioration of periodontal tissue. The goal of periodontal therapy is to achieve complete tissue regeneration, and one of the most promising treatment options is to harness the regenerative potential of stem cells available within the periodontal complex. Periodontal ligament stem cells, gingival mesenchymal stem cells, oral periosteal stem cells, and dental follicle stem cells have structural similarities, but their immunological responses and features differ. The qualities of diverse periodontal stem cells, their immune-modulatory effects, and variances in their phenotypes and characteristics will be discussed in this review. Although there is evidence on each stem cell population in the periodontium, understanding the differences in markers expressed, the various research conducted so far on their regenerative potential, will help in understanding which stem cell population will be a better candidate for tissue engineering. The possibility of selecting the most amenable stem cell population for optimal periodontal regeneration and the development and current application of superior tissue engineering treatment options such as autologous transplantation, three-dimensional bioengineered scaffolds, dental stem cell-derived extracellular vesicles will be explored.
What Is the Safest Intersurgical Interval between Staged Bilateral Total Knee Arthroplasty? A Nationwide Analysis of 20,279 Patients
Authors: Pan Xuankang , Emara Ahmed K. , Zhou Guangjin , Koroukian Siran , Klika Alison K. , Molloy Robert M. , Piuzzi Nicolas S.
Published: January 2023

In staged bilateral total knee arthroplasty (BTKA), the intersurgical time is yet to be determined. This study aimed to (1) test for differences in in-hospital metrics between the index and contralateral TKA and (2) determine the safest intersurgical time interval to minimize adverse outcomes after the contralateral surgery. The National Readmissions Database was queried for patients who received staged BTKA (2016–2017). A total of 20,279 patients were included. Demographics, comorbidities, baseline determinants, and intersurgical time between index and contralateral TKAs (≤ 3 month, 4–6 months, 7–9 months, and 10–12 months intervals) were captured. Outcomes included healthcare utilization (length of stay [LOS] and nonhome discharge), in-hospital costs, and in-hospital complications. Outcomes were compared between index versus contralateral surgeries and among contralateral surgeries of various intersurgical intervals. Contralateral surgeries had shorter LOS (2.2 ± 1.9 vs. 2.4 ± 2.0 days; p < 0.001), lower nonhome discharge (n = 2692[13.2%] vs. n = 2963[14.7%]; p = 0.001), and in-hospital costs ($16,476 ± $7,404 vs. 16,774 ± $9,621; p < 0.001), but similar rates of nonmechanical (p = 0.40) complications compared with index TKA. Multivariable regression demonstrated that intersurgical time was not associated with nonmechanical complications or transfusion, or 30-day readmission (p > 0.05, each). Compared with the less than or equal to 3-month interval, the 4 to 6-month interval exhibited highest odds ratio (OR) of any infection (OR: 1.81; 95% confidence interval [CI]: [1.13–2.88]; p = 0.013), urinary tract infection (OR:1.81, 95%CI: [1.13–2.90]; p = 0.014), and any-cardiac complications (OR:1.17; 95%CI: [1.01–1.35]; p = 0.037). Patients in the 10–12-month cohort had lowest odds of posthemorrhagic anemia (OR: 0.84; 95% CI: [0.72–0.98]; p = 0.03). Overall, the second surgery of a staged BTKA has lower healthcare utilization despite similar complication rates. While patients in the 10 to 12-month intersurgical interval had the most favorable overall safety profile, no single interval exhibited consistently lower complications for all measured outcomes. Special care pathways should be optimized to care for patients undergoing staged BTKA.
Does Time Spent in the Post-Anesthesia Care Unit Affect Hospital Lengths of Stay following Primary Total Knee Arthroplasty?
Authors: Sayegh Michael J. , Garbarino Luke J. , Gold Peter A. , Anis Hiba K. , Chen Zhongming , Sodhi Nipun , Danoff Jonathan R. , Mont Michael A.
Published: January 2023

Given the current healthcare economic environment, substantial efforts have been made to help streamline the in-hospital care for total knee arthroplasty (TKA) patients. While potential cost-reducing factors have been identified in the literature, analyses specifically considering post-anesthesia care unit (PACU) lengths of stay (LOS) are lacking. Therefore, the purpose of this study was to identify factors associated with (1) longer PACU LOS as well as (2) longer Hospital LOS. Prospectively collected TKA data from seven participating hospitals within a large health system were evaluated for patient demographics, body mass indices, Charlson Comorbidity Indices (CCI), surgeon volumes/training, admission types, anesthesia types, PACU LOS, and overall hospital LOS. Complete data was available for 1,690 patients (1,082 females, mean age: 67 years). Univariate and multivariate analytical models were constructed to identify which factors were predictive of longer PACU and overall hospital LOS. Same-day admissions, higher volume surgeons (≥ 100 cases per year), fellowship-trained arthroplasty surgeons, and longer operative times were associated with longer PACU LOS (p < 0.05). Multivariate analyses found age more than or equal to 65 years (β= 0.124) and CCI more than or equal to 3 (β= 0.088) to be associated with longer hospital LOS (p < 0.001). Operative times, PACU LOS, and procedure times (operative time plus PACU LOS) were not associated with longer hospital LOS (p > 0.05). These data identify associative factors for PACU LOS, as well as the influence of time spent in the PACU on overall hospital LOS. Interestingly, this analysis revealed that patients of arthroplasty fellowship-trained and higher-volume surgeons had longer PACU LOS; however, this could be explained by the observation that these particular surgeons tend to perform more complex deformity cases. Also of importance, increased PACU LOS, meaning the patient spent more time in a high-monitored setting immediately after surgery, did not necessarily confer a longer overall hospital LOS. Based on these data, it may be more beneficial to identify alternate sources than time spent in the operating room or PACU to potentially help reduce overall hospital LOS.

Level of Evidence II, prospective cohort
One-electron self-interaction error and its relationship to geometry and higher orbital occupation
Authors: Lonsdale Dale R. , Goerigk Lars
Published: January 2023

Density Functional Theory (DFT) sees prominent use in computational chemistry and physics; however, problems due to the self-interaction error (SIE) pose additional challenges to obtaining qualitatively correct results. As an unphysical energy an electron exerts on itself, the SIE impacts most practical DFT calculations. We conduct an in-depth analysis of the one-electron SIE in which we replicate delocalization effects for simple geometries. We present a simple visualization of such effects, which may help in future qualitative analysis of the one-electron SIE. By increasing the number of nuclei in a linear arrangement, the SIE increases dramatically. We also show how molecular shape impacts the SIE. Two- and three-dimensional shapes show an even greater SIE stemming mainly from the exchange functional with some error compensation from the one-electron error, which we previously defined [D. R. Lonsdale and L. Goerigk, Phys. Chem. Chem. Phys. 22, 15805 (2020)]. Most tested geometries are affected by the functional error, while some suffer from the density error. For the latter, we establish a potential connection with electrons being unequally delocalized by the DFT methods. We also show how the SIE increases if electrons occupy higher-lying atomic orbitals; seemingly one-electron SIE free methods in a ground are no longer SIE free in excited states, which is an important insight for some popular, non-empirical density functional approximations (DFAs). We conclude that the erratic behavior of the SIE in even the simplest geometries shows that robust DFAs are needed. Our test systems can be used as a future benchmark or contribute toward DFT development.
Experimental analysis of shock smoothing design strategy for reducing cavitation erosion aggressiveness
Authors: Nahon Jeremy , Zangeneh Mehrdad , Tsuneda Tomoki , Nohmi Motohiko , Watanabe Hiroyoshi , Goto Akira
Published: January 2023

This article presents the experimental analysis of cavitation erosion for two cascade hydrofoil profiles. The aim is to evaluate the change in erosive intensity between a conventional smooth blade surface and one generated by the means of inverse design specifically to reduce cavitation aggressiveness. The applied design strategy consists in imposing a reduced amplitude and gradient at the cavity closure pressure jump in order to bring down the potential energy contained in the vapor sheet. The result is a unique geometry that presents a surface kink located at cavity closure, which successfully smoothes the pressure jump according to computational fluid dynamics (CFD) verification analysis. Here, an experimental rig is constructed and equipped with a pressure sensing system and high-speed imaging to capture the flow field. The measurements for both geometries are first compared against a set of steady-state CFD solutions, which demonstrate the reliability of the inverse design solver for generating targeted flow characteristics in non-cavitating and cavitating conditions. Visual recordings also reveal significant changes in the aspect of the vapor sheet between the two blades indicating a shift in its dynamic behavior. Erosion intensity levels are then measured by paint method at identical conditions. The outcome of the experiment is highly conclusive as a marked reduction in paint erosion is observed for the design geometry. The measured data also serve as a benchmark test for predictive cavitation erosion models by comparing the measured erosion distributions for each blade to those obtained numerically from unsteady CFD.
TBMaLT, a flexible toolkit for combining tight-binding and machine learning
Authors: McSloy A. , Fan G. , Sun W. , Hölzer C. , Friede M. , Ehlert S. , Schütte N.-E. , Grimme S. , Frauenheim T. , Aradi B.
Published: January 2023

Tight-binding approaches, especially the Density Functional Tight-Binding (DFTB) and the extended tight-binding schemes, allow for efficient quantum mechanical simulations of large systems and long-time scales. They are derived from ab initio density functional theory using pragmatic approximations and some empirical terms, ensuring a fine balance between speed and accuracy. Their accuracy can be improved by tuning the empirical parameters using machine learning techniques, especially when information about the local environment of the atoms is incorporated. As the significant quantum mechanical contributions are still provided by the tight-binding models, and only short-ranged corrections are fitted, the learning procedure is typically shorter and more transferable as it were with predicting the quantum mechanical properties directly with machine learning without an underlying physically motivated model. As a further advantage, derived quantum mechanical quantities can be calculated based on the tight-binding model without the need for additional learning. We have developed the open-source framework—Tight-Binding Machine Learning Toolkit—which allows the easy implementation of such combined approaches. The toolkit currently contains layers for the DFTB method and an interface to the GFN1-xTB Hamiltonian, but due to its modular structure and its well-defined interfaces, additional atom-based schemes can be implemented easily. We are discussing the general structure of the framework, some essential implementation details, and several proof-of-concept applications demonstrating the perspectives of the combined methods and the functionality of the toolkit.
Fermionic-propagator and alternating-basis quantum Monte Carlo methods for correlated electrons on a lattice
Authors: Janković Veljko , Vučičević Jakša
Published: January 2023

Ultracold-atom simulations of the Hubbard model provide insights into the character of charge and spin correlations in and out of equilibrium. The corresponding numerical simulations, on the other hand, remain a significant challenge. We build on recent progress in the quantum Monte Carlo (QMC) simulation of electrons in continuous space and apply similar ideas to the square-lattice Hubbard model. We devise and benchmark two discrete-time QMC methods, namely the fermionic-propagator QMC (FPQMC) and the alternating-basis QMC (ABQMC). In FPQMC, the time evolution is represented by snapshots in real space, whereas the snapshots in ABQMC alternate between real and reciprocal space. The methods may be applied to study equilibrium properties within the grand-canonical or canonical ensemble, external field quenches, and even the evolution of pure states. Various real-space/reciprocal-space correlation functions are also within their reach. Both methods deal with matrices of size equal to the number of particles (thus independent of the number of orbitals or time slices), which allows for cheap updates. We benchmark the methods in relevant setups. In equilibrium, the FPQMC method is found to have an excellent average sign and, in some cases, yields correct results even with poor imaginary-time discretization. ABQMC has a significantly worse average sign, but also produces good results. Out of equilibrium, FPQMC suffers from a strong dynamical sign problem. On the contrary, in ABQMC, the sign problem is not time-dependent. Using ABQMC, we compute survival probabilities for several experimentally relevant pure states.
Accurate analytical calculation of the rate coefficient for the diffusion-controlled reactions due to hyperbolic diffusion
Authors: Traytak Sergey D.
Published: January 2023

Using an approach based on the diffusion analog of the Cattaneo–Vernotte differential model, we find the exact analytical solution to the corresponding time-dependent linear hyperbolic initial boundary value problem, describing irreversible diffusion-controlled reactions under Smoluchowski’s boundary condition on a spherical sink. By means of this solution, we extend exact analytical calculations for the time-dependent classical Smoluchowski rate coefficient to the case that includes the so-called inertial effects, occurring in the host media with finite relaxation times. We also present a brief survey of Smoluchowski’s theory and its various subsequent refinements, including works devoted to the description of the short-time behavior of Brownian particles. In this paper, we managed to show that a known Rice’s formula, commonly recognized earlier as an exact reaction rate coefficient for the case of hyperbolic diffusion, turned out to be only its approximation being a uniform upper bound of the exact value. Here, the obtained formula seems to be of great significance for bridging a known gap between an analytically estimated rate coefficient on the one hand and molecular dynamics simulations together with experimentally observed results for the short times regime on the other hand. A particular emphasis has been placed on the rigorous mathematical treatment and important properties of the relevant initial boundary value problems in parabolic and hyperbolic diffusion theories.
Content and Engagement Among Plastic Surgeons on Instagram
Authors: Thawanyarat Kometh , Hinson Chandler , Gomez Diego A , Rowley Mallory A , Navarro Yelissa , Venditto Chelsea M
Published: January 2023

Background

Patients routinely use social media to locate providers, review before-and-after photographs, and discuss experiences, making it a powerful marketing tool for plastic surgeons. A few studies have systematically evaluated plastic surgery app content.

Objectives

This study aims to analyze engagement levels and content posted by top plastic surgeon influencers on Instagram (Menlo Park, CA).

Methods

The authors conducted a cross-sectional study in February 2022 to identify the top 10 global plastic surgeons on Instagram. Influencers were ranked based on the number of followers, and their latest 20 posts were analyzed. A total of 200 posts were categorized by 2 independent trainees as one of the following: marketing, education, personal, and miscellaneous. The number of likes was recorded as a proxy for engagement, and the average engagement for each category was calculated.

Results

The top 10 influencers work primarily in private practice focusing on aesthetic procedures. Out of 200 categorized posts on Instagram, marketing posts had the greatest presence (64.5%), followed by personal (20%), miscellaneous (11%), and educational (4.5%). More still images were posted (56.5%) than videos (43.5%). The highest average engagement was for personal content (P = .005). No significant differences in engagement levels were found between photo and video content (P = .24).

Conclusions

Although most content posted related to marketing efforts, many influencers were also using social media to post about their personal lives and promote their ancillary businesses. Although marketing content was the most common, engagement levels were the highest for personal and educational content, and no significant differences in engagement were found between videos and photos.
Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data
Authors: Rose Tim D , Köhler Nikolai , Falk Lisa , Klischat Lucie , Lazareva Olga E , Pauling Josch K
Published: January 2023

Lipidomics is of growing importance for clinical and biomedical research due to many associations between lipid metabolism and diseases. The discovery of these associations is facilitated by improved lipid identification and quantification. Sophisticated computational methods are advantageous for interpreting such large-scale data for understanding metabolic processes and their underlying (patho)mechanisms. To generate hypothesis about these mechanisms, the combination of metabolic networks and graph algorithms is a powerful option to pinpoint molecular disease drivers and their interactions. Here we present lipid network explorer (LINEX$^2$), a lipid network analysis framework that fuels biological interpretation of alterations in lipid compositions. By integrating lipid-metabolic reactions from public databases, we generate dataset-specific lipid interaction networks. To aid interpretation of these networks, we present an enrichment graph algorithm that infers changes in enzymatic activity in the context of their multispecificity from lipidomics data. Our inference method successfully recovered the MBOAT7 enzyme from knock-out data. Furthermore, we mechanistically interpret lipidomic alterations of adipocytes in obesity by leveraging network enrichment and lipid moieties. We address the general lack of lipidomics data mining options to elucidate potential disease mechanisms and make lipidomics more clinically relevant.
Systematic benchmarking of statistical methods to assess differential expression of circular RNAs
Authors: Buratin Alessia , Bortoluzzi Stefania , Gaffo Enrico
Published: January 2023

Circular RNAs (circRNAs) are covalently closed transcripts involved in critical regulatory axes, cancer pathways and disease mechanisms. CircRNA expression measured with RNA-seq has particular characteristics that might hamper the performance of standard biostatistical differential expression assessment methods (DEMs). We compared 38 DEM pipelines configured to fit circRNA expression data’s statistical properties, including bulk RNA-seq, single-cell RNA-seq (scRNA-seq) and metagenomics DEMs. The DEMs performed poorly on data sets of typical size. Widely used DEMs, such as DESeq2, edgeR and Limma-Voom, gave scarce results, unreliable predictions or even contravened the expected behaviour with some parameter configurations. Limma-Voom achieved the most consistent performance throughout different benchmark data sets and, as well as SAMseq, reasonably balanced false discovery rate (FDR) and recall rate. Interestingly, a few scRNA-seq DEMs obtained results comparable with the best-performing bulk RNA-seq tools. Almost all DEMs’ performance improved when increasing the number of replicates. CircRNA expression studies require careful design, choice of DEM and DEM configuration. This analysis can guide scientists in selecting the appropriate tools to investigate circRNA differential expression with RNA-seq experiments.
A Boolean algebra for genetic variants
Authors: Vis Jonathan K , Santcroos Mark A , Kosters Walter A , Laros Jeroen F J
Published: January 2023

Motivation

Beyond identifying genetic variants, we introduce a set of Boolean relations, which allows for a comprehensive classification of the relations of every pair of variants by taking all minimal alignments into account. We present an efficient algorithm to compute these relations, including a novel way of efficiently computing all minimal alignments within the best theoretical complexity bounds.

Results

We show that these relations are common, and many non-trivial, for variants of the CFTR gene in dbSNP. Ultimately, we present an approach for the storing and indexing of variants in the context of a database that enables efficient querying for all these relations.

Availability and implementation

A Python implementation is available at https://github.com/mutalyzer/algebra/tree/v0.2.0 as well as an interface at https://mutalyzer.nl/algebra.
Progressive MRI brain volume changes in ovine models of CLN5 and CLN6 neuronal ceroid lipofuscinosis
Authors: Murray Samantha J , Almuqbel Mustafa M , Felton Simon A , Palmer Nickolas J , Myall Daniel J , Shoorangiz Reza , Ella Arsène , Keller Matthieu , Palmer David N , Melzer Tracy R , Mitchell Nadia L
Published: January 2023

Neuronal ceroid lipofuscinoses (Batten disease) are a group of inherited lysosomal storage disorders characterized by progressive neurodegeneration leading to motor and cognitive dysfunction, seizure activity and blindness. The disease can be caused by mutations in 1 of 13 ceroid lipofuscinosis neuronal (CLN) genes. Naturally occurring sheep models of the CLN5 and CLN6 neuronal ceroid lipofuscinoses recapitulate the clinical disease progression and post-mortem pathology of the human disease. We used longitudinal MRI to assess global and regional brain volume changes in CLN5 and CLN6 affected sheep compared to age-matched controls over 18 months. In both models, grey matter volume progressively decreased over time, while cerebrospinal fluid volume increased in affected sheep compared with controls. Total grey matter volume showed a strong positive correlation with clinical scores, while cerebrospinal fluid volume was negatively correlated with clinical scores. Cortical regions in affected animals showed significant atrophy at baseline (5 months of age) and progressively declined over the disease course. Subcortical regions were relatively spared with the exception of the caudate nucleus in CLN5 affected animals that degenerated rapidly at end-stage disease. Our results, which indicate selective vulnerability and provide a timeline of degeneration of specific brain regions in two sheep models of neuronal ceroid lipofuscinoses, will provide a clinically relevant benchmark for assessing therapeutic efficacy in subsequent trials of gene therapy for CLN5 and CLN6 disease.
The effects of auricular acupressure on blood pressure, stress, and sleep in elders with essential hypertension: a randomized single-blind sham-controlled trial
Authors: Kim Bomi , Park Hyojung
Published: January 2023

Aims

Reduction of blood pressure and improvement of stress and sleep disorders in patients with essential hypertension were important factors. This study aimed to examine the effects of auricular acupressure on blood pressure, stress, and sleep quality among elderly with essential hypertension in Korea.

Methods and results

This study was a single-blind, randomized, placebo-controlled study. The experimental group (n = 23) received 8 weeks of auricular acupressure intervention on specific acupoints (superior triangular fossa, Shenmen, kidney, heart, and occiput) related to blood pressure, pulse rate, stress, and sleep, whereas the control group (n = 23) received auricular acupressure on non-specific acupoints. The primary outcomes were the systolic and diastolic blood pressure measured weekly. The secondary outcomes were the pulse rate, heart rate variability, actigraphy measured through Fitbit, and the Pittsburgh sleep quality index (PSQI) were measured before and after the experiment. There were statistically significant differences between two groups in systolic blood pressure (F = 5.67, P = 0.022), diastolic blood pressure (17.53, P < 0.001), and pulse rate (F = 6.78, P = 0.013) over time. Stress index (χ2 = 2.12, P = 0.040) and sleep efficiency (χ2 = 3.57, P = 0.001) were also significantly different before and after the experiment. However, there was no significant difference in the PSQI.

Conclusion

The findings showed that auricular acupressure leads to improvements in blood pressure, stress, and sleep in elderly people with essential hypertension. Therefore, auricular acupressure can be used as an alternative nursing intervention for hypertension prevention, stress, and sleep management.

Registration

WHO ICTRP KCT0007364
Immunogenicity evaluation of viral peptides via nonspecific interactions between anti-peptide IgYs and non-cognate peptides
Authors: Zhou Yuxi , Li Jingzhi , Wu Wenya , Chen Yanfei , Cheng Hu , Li Mengyu , Sun Yiyue , Yang Jiao , Peng Daxin , Xue Qinghong , Ma Hongwei
Published: January 2023

Immunogenicity can be evaluated by detecting antibodies (Abs) induced by an antigen. Presently deployed assays, however, do not consider the negative impacts of Ab poly-specificity, which is well established at the monoclonal antibody level. Here, we studied antibody poly-specificity at the serum level (i.e. nonspecific Ab–probe interactions, NSIs), and ended up establishing a new platform for viral peptide immunogenicity evaluation. We first selected three peptides of high, medium and low immunogenicity, using a ‘vaccine serum response rate’-based approach (i.e. the gold standard). These three peptides (Pi) in the bovine serum albumin–Pi form were used to immunize chickens, resulting in longitudinal serum samples for screening with a non-cognate peptide library. The signal intensity of Ab-peptide specific binding and ‘NSI count’ was used to evaluate the viral peptides’ immunogenicity. Only the NSI count agreed with the gold standard. The NSI count also provides more informative data on antibody production than the aggregated signal intensity by whole-protein-based indirect enzyme-linked immunosorbent assay.