bluuebunny/crossref_metadata_2025 huggingface dataset:
Trajectory-tracking control based on backstepping hyperbolic tangent sliding mode control for aerial manipulators
Authors: Yang Bin , Miao Xinghua , Chen Xiaokang
Published: December 2024

Aerial manipulators, as a novel robotic system combining the flexibility of drones and the operational capability of robotic arms, offer significant potential for complex manipulation tasks in diverse environments. However, achieving precise operation tasks with these systems is challenging due to system uncertainty and external disturbances. This paper presents a novel trajectory-tracking control strategy for aerial manipulators using a combination of backstepping and hyperbolic tangent sliding mode control. The backstepping design decomposes the aerial manipulator’s complex system into subsystems, allowing for the step-by-step design of control laws for each subsystem. This method ensures the stability of each step. Additionally, the integration of a hyperbolic tangent sliding surface into each control law ensures smooth transitions and robust performance against disturbances. Simulation results demonstrate that the composite controller exhibits superior tracking control performance when facing external disturbances.
Round fruit picking system based on machine vision
Authors: Fang Xiumei , Zhu Haiyang , Li Sanyan , Zhang Qilong
Published: December 2024

Traditional fruit quality selection mainly relies on manual labor, which is costly and time-consuming, and the results are difficult to meet the accuracy requirements. To solve this problem, this paper proposes a fruit-picking system based on machine vision technology using MATLAB as a software tool. It takes round fruits as the research object, introducing Zhang’s camera calibration method, making the target picture reach the ideal state through image pre-processing, such as edging processing, filtering and denoising, binary processing, size eigenvalue extraction, etc. Then, the fruit size grade is evaluated by using the Sobel edge detection algorithm. The fruit color grade is evaluated using the HSV detection algorithm to assess the fruit color grade, and a feature extraction method is used to assess the relative score of the defect degree. Finally, a weighted composite score is used to evaluate the fruit quality grade. This paper also designed a visualized GUI interface. The results prove that the system can accurately and quickly perform fruit selection and quality rating.
The Effect of Structural Strengthening On The Dynamic Behavior of Irregular Buildings
Authors: Prasetiyo Dwi , Sangadji Senot , Saifullah Halwan Alfisa
Published: December 2024

Many buildings have sustained damage due to earthquakes. Buildings with irregularities (asymmetrical structures) are particularly hazardous in seismic zones, where points of stiffness changes, mass changes, and/or strength changes represent weak points. A low level of lateral stiffness makes such structures vulnerable to deformation and eventual structural failure. This study investigates the dynamic behavior of asymmetric structures subjected to earthquake loads. Reinforced concrete asymmetric structures were strengthened with steel bracing placed in various configurations as an evaluation of existing buildings or structures. The method used was linear time history analysis, supported by finite element-based software. The earthquake loads applied were from Imperial Valley 06, Iwate Off, and Chile, matched to the study location. The results of this study indicate that buildings with asymmetrical plans and various bracing configuration placements improve global lateral stiffness. This research is expected to provide valuable insights for determining the optimal placement of bracing to strengthen both new and existing structures.
Comparison of site classification using SPT and seismic downhole survey to evaluate liquefaction severity: A Case study in Serang-Panimbang Section III Toll Road Project
Authors: Heykal Muhammad , Ismanti Sito , Setiawan Hendy
Published: December 2024

Evaluating liquefaction risk, as an indirect consequence of seismic events, is crucial for mitigating geohazards and achieving sustainable developments in infrastructure projects. The Serang-Panimbang Toll Road, a National Strategic Project in Banten, Indonesia, aims to connect intra-districts, bolster local tourism and establish a new industrial region. In this context, site classification plays a substantial role in determining the impact of earthquakes on soil behavior. This study compared the site classification of two soil investigations, including the Standard Penetration Test (SPT) and the downhole seismic (Vs
) survey at eleven sites along the toll route. A marginal sensitivity was observed in the classification as small variations in field measurements could lead to a shift in site class, resulting in significant changes in the surface-level seismic wave amplification. Notably, the correlation between SPT N-values and Vs
is often weak. Studies have confirmed the superior reliability of Vs
for soil profiling, suggesting that its adoption as a mandatory practice should be considered. Analysis of the investigation data classified the sites as belonging to site classes SD, SE, and SF. The Simplified Procedure method was employed to evaluate the liquefaction factor of safety, by considering the Cyclic Stress Ratio (CSR) and the Cyclic Resistance Ratio (CRR). The evaluation utilized parameters derived from the Indonesia Seismic Code, with a 7% likelihood of exceedance in 75 years. The analysis revealed that most areas, predominantly clayey soils, exhibited no liquefaction potential. However, specific sections containing sand lenses displayed a low-level Liquefaction Severity Index (LSI) as identified in three boreholes.
Liquefaction potential analysis using simplified procedure (Case study: Stadium construction project in North Sumatra, Indonesia)
Authors: Mulrony Brian Priadana , Ismanti Sito , Rifa’i Ahmad
Published: December 2024

Indonesia’s Seismic Design Standards determine that soils in high-seismicity areas with layers of loose sandy soil and a shallow groundwater level require the calculation of liquefaction potential. According to the Indonesian Liquefaction Vulnerability Zone, North Sumatra is categorized as a liquefaction area. Based on these requirements, this research investigates the liquefaction potential of the Stadium Construction Project in North Sumatra. The study area consists mostly of sand with shallow groundwater levels and high seismic zones associated with the Renun-A fault. Soil investigation data, such as Standard Penetration Test, SPT and groundwater level served as the main data for liquefaction potential analyses. The calculation was done using the SPT-based liquefaction triggering analysis by Idriss and Boulanger method for 3 boreholes with a depth of 40 m. This method considered factors such as the Cyclic Stress Ratio and Cyclic Resistance Ratio to determine the safety factor against liquefaction. Peak ground acceleration was obtained from probabilistic seismic hazard analysis, PSHA and deterministic seismic hazard analysis, DSHA. The PSHA is based on the Indonesian earthquake hazard map from the National Earthquake Study Centre of Indonesia with a probability exceeding 2% in 50 years. The DSHA is calculated based on earthquake sources around the research location according to the Seismic Hazard Deaggregation Map of Indonesia. Based on this analysis, the PGA used is 0.303 g. It is concluded that the presence of liquefaction layers was identified at depths ranging from 4 to 17 meters for three bore-hole locations.
Utilization of Portland Cement and Fly Ash for Treatment of Mercury Polluted Soil through Stabilization/Solidification
Authors: Rachman Ranno Marlany , Faisal Suciati , Trihadiningrum Yulinah , Aswad Nini Hasriyani , Ahmad Fatimah
Published: December 2024

Traditional gold mining contributes significantly to soil mercury pollution. Stabilization/Solidification (S/S) Technology offers a remediation solution for soils contaminated with heavy metals. Besides the low cost of the technology, the S/S technology can be carried out in situ and ex-situ with material pozzolanic properties, such as Portland cement and fly ash, effectively bind these metals. This study aims to identify the proportion of mercury-contaminated soil mixed with a combination of Portland cement and fly ash. Artificial soil samples with a mercury content of 150 mg/kg were used, and test specimens were formed into 5 cm cubes. In the first phase, different ratios of Portland cement to fly ash were tested: 100:0, 90:10, 80:20, 70:30, 60:40, and 50:50. The second phase focused on the optimal mix ratio based on compressive strength tests for combinations of Portland cement and fly ash with mercury-contaminated soil, with the same ratios as in the first phase. Subsequent compressive strength and specimens were tested using the Toxicity Characteristic Leaching Procedure (TCLP). The first phase identified the optimal 50:50 ratio of Portland cement to fly ash, achieving a compressive strength of 5559 tons/m2. In the second phase, the same 80:20 ratio for the mix of Portland cement, fly ash, and mercury-contaminated soil yielded a compressive strength of 2902 tons/m2 and a TCLP result of 0.0062 mg/L. All samples met the criteria set by the United States Environmental Protection Agency (US EPA), with variations ranging from 17 MPa for residential concrete to 28 MPa and the TCLP-B quality standard. According to Regulation by Government No. 22 of 2021, the permissible concentration is 0.05 mg/L. The study concludes that increasing the proportion of soil and fly ash Included in the mixture reduces the quality of S/S products.
Land subsidence analysis in Bekasi City and Bekasi Regency using differential interferometric synthetic aperture radar method
Authors: Ihsani Tazkia Tiara , Sutoyo  , Saptomo Satyanto Krido , Suharnoto Yuli , Syafiudin Moh. Fifik
Published: December 2024

Land subsidence is a problem faced by many countries worldwide due to massive urbanization over the past few decades, especially in countries with dense populations, including Indonesia. Bekasi became the study’s main subject because, besides being one of Indonesia’s economic support areas, the northern part of Bekasi Regency is directly adjacent to the Java Sea, increasing the potential for seawater intrusion. Furthermore, the presence of land subsidence and the sloping topography in the area contribute to the severity of the losses caused by this potential danger. Hence, this study aims to examine the land subsidence phenomenon in Bekasi between the years 2019 and 2023. This subsidence analysis is performed by using DInSAR method that used SAR images that corrected with DEM so it can produce a final result as a differential interferogram. Bekasi is geographically separated into two administrative regions: Bekasi City and Bekasi Regency. Bekasi City contains nine fringes, while Bekasi Regency contains five fringes. The subsidence rate in Bekasi City varies between 3.4 and 4.3 centimeters per year. Meanwhile, the subsidence rate in Bekasi Regency ranges from 3.8 cm/year to 4.6 cm/year.
Implementation of digital twins to investigate the condition of the bandung state polytechnic student dormitory building
Authors: Labibah Amira , Tamariska Deony , Krisnandi Andri , Astor Yackob , Syaputra Master Jimmy Dekha
Published: December 2024

The Bandung State Polytechnic (Polban) Student Dormitory, built in 1982, has been standing for over 40 years, nearing the building life expectancy recommended by the Ministry of Public Works and Housing (PUPR), which is 50 years. This condition has been exacerbated by the COVID-19 pandemic, which left the building vacant for three years, halting its maintenance. The student dormitory is an important facility but has not received adequate annual maintenance funding, resulting in various damages and non-functional facilities. This study investigates building damage using Terrestrial Laser Scanner (TLS) technology to create a 3D model aimed at expediting the investigation at the research site, which includes three dormitory buildings, each with 3 floors and 24 rooms. The investigation results indicate that the Polban Student Dormitory falls into the Moderate Damage category. Non-destructive tests, such as the Hammer Test, Ultrasonic Pulse Velocity (UPV), and Rebar Scanner, were conducted and processed using ETABS software to assess the condition of the building structure. The results showed that the Polban Student Dormitory has concrete with a column compressive strength of 28.42 MPa, beams at 25.2 MPa, and floor plates at 25.25 MPa, as well as reinforcement with U24 quality.
Eco-friendly concrete bricks with tetris-t model
Authors: Susanti Riza , Fauziyah Shifa , Khoerunissa Nadya , Hapsari Adinda Nur
Published: December 2024

The development of construction has resulted in a higher demand for construction materials, especially concrete bricks. However, cement as one of the main components in concrete bricks has several problems. The process of cement making requires SiO2 and CaCO3 from natural sources, which can cause environmental damage. More environmentally friendly materials are needed to substitute the use of cement especially in concrete bricks. One of the materials rich in SiO2 is sugarcane Fiber ash, and materials rich in CaCO3 include eggshell powder. So, both materials are possible to be used as cement substitution materials. Innovation in form is also needed to reduce the use of cement in implementation as well as to speed up implementation time. The purpose of this research is to produce eco-friendly concrete bricks with a new design (Tetris-T model). The method used in this study is an experimental method based on SNI 03-0349-1989. The comparison of the brick mixture used is 1 pc: 6 sands with 4 variations of comparison between sugarcane Fiber ash: eggshell powder, namely variation A (0%:0%), variation B (5%: 10%), variation C (7.5%:7.5%), and variation D (10%:5%). The results of the study show that test specimen C has a compressive strength of 117.227 kg/cm2 and a water absorption of 4.87%. Based on the test results, it can be seen that variation C meets the standard requirements for SNI 03-0349-1989 quality III. The test of the effectiveness of installation on a wall measuring 1 × 1 meter shows that Tetris T innovation bricks take 38.85% less time to install compared to conventional bricks. Based on this research, reducing cement used about 15% can help the implementation of green projects to support sustainable development.
Electrospun microfibers to enhance nutrient supply in bioinks and 3D-bioprinted tissue precursors
Authors: Neuhäusler A , Rogg K , Schröder S , Spiehl D , Zora H , Arefaine E , Schettler J , Hartmann H , Blaeser A
Published: December 2024

3D-bioprinting is a promising technique to mimic the complex anatomy of natural tissues, as it comprises a precise and gentle way of placing bioinks containing cells and hydrogel. Although hydrogels expose an ideal growth environment due to their extracellular matrix (ECM)-like properties, high water amount and tissue like microstructure, they lack mechanical strength and possess a diffusion limit of a couple of hundred micrometers. Integration of electrospun fibers could hereby benefit in multiple ways, for instance by controlling mechanical characteristics, cell orientation, direction of diffusion and anisotropic swelling behavior. The aim of this study was to create an advanced ECM-biomimicking scaffold material for tissue engineering, which offers enhanced diffusion properties. PCL bulk membranes were successfully electrospun and fragmented using a cryo cutting technique. Subsequently, these short single fibers (<400 µm in length and ∼5–10 µm in diameter) were embedded in an agarose-based hydrogel after hydrophilization of the short single fibers by O2 plasma treatment. Fiber-filled bioinks exhibit significantly improved biomolecule diffusion (>500 µm), swelling properties (20%–60% of control), and higher mechanical strength, while its viscosity (5–30 mPas*s) and gelation kinetics (28 °C) remained almost unaffected. The diffusion tests indicate a high level of size selectivity, which can be utilized for targeted biomolecule transport in the future. Finally, applying 3D-bioprinting technology (drop-on-demand vs. microextrusion) a print setting dependent post-dispensing orientation of the fibers could be induced, which ultimately paves way for the fabrication of metamaterials with anisotropic material properties. As expected, the fiber-filled bioink was found to be non-cytotoxic in cell culture trials using HUVECs and HepG2 (>80% viability). In summary, microfiber integration holds great promise for 3D-bioprinting of tissue percursors with advanced metamaterial properties and thus offers high applicability in various fields of research, such as in-vitro tissue models, tissue engineered implants or cultivated meat.
A reinforcement learning model for autonomous vehicles with realistic car simulation in urban using Unity
Authors: M Mamdouh Abdulla , Farouk Mohamed , A Khater Hatem , F Hassan Yasser
Published: December 2024

Simulator training with reinforcement learning (RL) for autonomous vehicles (AVs) offers advantages over supervised learning. However, transferring the learned behaviours to the real world is a challenging task due to the inconsistencies between the data captured by the vehicle’s sensors in the simulated environment and the real world. Additionally, some of the sensors that the AVs rely on are sensitive to weather and lighting conditions. Our proposed model addresses the challenges of sensor data disparity and environmental variation. It utilizes three sensing components which are radio detection and ranging (RADAR), inertial measurement units (IMUs), and global positioning systems (GPSs) to overcome the addressed drawbacks. The proposed model incorporates a carefully designed reward system and prioritizes computational efficiency by using fewer number of sensors and ensures safe and efficient driving. The chosen sensors enable easier knowledge transfer from the simulator to the real-world due to their consistent data representation. The model leverages the Unity engine and ML agent to train AVs for both urban and highway environments. The experimental results show that our suggested model effectively trained AVs to navigate through complex urban areas without collisions while keeping them in their lanes. The demonstration video is provided in the following link: https://youtu.be/YCOjli7lrCM
Quadrature rules for splines of high smoothness on uniformly refined triangles
Authors: Eddargani Salah , Manni Carla , Speleers Hendrik
Published: December 2024

In this paper, we identify families of quadrature rules that are exact for sufficiently smooth spline spaces on uniformly refined triangles in

R

2

\mathbb {R}^2

. Given any symmetric quadrature rule on a triangle

T
T

that is exact for polynomials of a specific degree

d
d

, we investigate if it remains exact for sufficiently smooth splines of the same degree

d
d

defined on the Clough–Tocher 3-split or the (uniform) Powell–Sabin 6-split of

T
T

. We show that this is always true for

C

2
r
−
1

C^{2r-1}

splines having degree

d
=
3
r

d=3r

on the former split or

d
=
2
r

d=2r

on the latter split, for any positive integer

r
r

. Our analysis is based on the representation of the considered spline spaces in terms of suitable simplex splines.
Randomized Runge-Kutta-Nyström methods for unadjusted Hamiltonian and kinetic Langevin Monte Carlo
Authors: Bou-Rabee Nawaf , Kleppe Tore
Published: December 2024

We introduce

5

/

2

5/2

- and

7

/

2

7/2

-order

L
2

L^2

-accurate randomized Runge-Kutta-Nyström methods, tailored for approximating Hamiltonian flows within non-reversible Markov chain Monte Carlo samplers, such as unadjusted Hamiltonian Monte Carlo and unadjusted kinetic Langevin Monte Carlo. We establish quantitative

5

/

2

5/2

-order

L
2

L^2

-accuracy upper bounds under gradient and Hessian Lipschitz assumptions on the potential energy function. The numerical experiments demonstrate the superior efficiency of the proposed unadjusted samplers on a variety of well-behaved, high-dimensional target distributions.
Providence and Colonial Slavery
Authors: King Benjamin J
Published: December 2024

The same Tractarian leaders who gave the laity a role in the Church demanded the enslaved remain subservient to the established social order. Countering historians who argue that it is incoherent to distinguish in the early nineteenth century between proslavery and anti-abolitionism, this chapter critically lays out the latter’s theological foundation in Joseph Butler’s doctrine of providence. In addition, Newman used John Chrysostom’s interpretation of 1 Corinthians 7:20–1, and Froude’s firsthand accounts from Barbados, to express concern about what effects manmade abolition would have on the enslaved. Tractarians thought providence was acting through the Church to bring slavery to an end faster than a previous generation of High Churchmen thought, and argued that conditions for the enslaved would be better if ameliorated by catholic Anglicanism than by the liberal Anglicanism exhibited by T. F. Buxton or Richard Whately. The connection of some prominent Tractarians to the slave economy (Manning, Gladstone, Robert Wilson, John Bowden) and others to abolitionism (Acland, Allies, Robert and Henry Wilberforce) will be revealed.
Consensus Fidelium and Synods
Authors: King Benjamin J
Published: December 2024

The first section will expound the doctrine of the common mind of the faithful (consensus fidelium). Its historical origins, including its use by the Church Fathers, will be discussed as these shaped Newman’s theological writings and the Keble brothers’ depiction of the exemplary layperson in the ‘Richard Nelson’ numbers of the Tracts for the Times. The second section will use their theology of consensus fidelium as the lens through which to view the subsequent development of synods in the Church of England. When Tractarian laymen such as Alexander Beresford Hope and Francis Dickinson wanted to make lay consent part of synodal decision-making, the theology of consensus fidelium provided them with a justification for their campaign, even as Keble and Pusey argued against lay participation. A call for Church democracy was not on these Tractarian laymen’s minds, however, any more than on Newman’s when he said the Church ‘must look to the people’.
Two Revolutions: Einstein’s Relativity and Quantum Physics
Authors: Vishveshwara Smitha , Vishveshwara C V
Published: December 2024

“Can you kick apart a black hole?” “What about electrons?” As a child, quantum-physicist Smitha Vishveshwara pondered such questions with her astrophysicist father, C. V. Vishveshwara (Vishu); decades later, their musings grew into a series of letter exchanges in Two Revolutions: Einstein’s Relativity and Quantum Physics. The letters between father and daughter lead the scientifically curious reader through these two remarkable branches of physics that dramatically changed our perception of Nature. From the subatomic to the astronomical realms, they weave a rich tapestry of scientific insight, history, personal anecdotes, philosophy, and wonder. The book traces Einstein’s tenacious journey in formulating the theory of relativity, in which space and time merge, and gravitation warps spacetime, forming the very fabric of the Universe. The book reveals how black holes and gravitational waves emerge as bizarre and awe-inspiring offspring of this theory. In the quantum realm, the book mulls over conundrums posed by wave-particle duality, Schrödinger’s curious cat, the beautiful dance of electrons in atoms, and entanglement. It explores communities of particles acting in marvelous concert in magnetic resonance imaging, superfluids, and more. Fate took unforeseen twists while the book was still in the making. In 2016, after decades of work by numerous researchers, the detection of gravitational waves—Vishu’s lifelong dream—finally came to pass. Emanating from two inspiraling black holes a billion light years away, the waves’ signals even showed hints of Vishu’s pioneering predictions on black hole ringdowns from the 1970s. But soon after that glorious culmination, Vishu fell critically ill. Smitha concludes their story by recreating the euphoria of scientific discovery against the intimate backdrop of life and death.
Prologue: Contemplating the quantum revolution, commencing the dialogue
Authors: Vishveshwara Smitha , Vishveshwara C V
Published: December 2024

In the opening chapter on relativity, C. V. Vishveshwara (Vishu) takes the reader through an excursion on how Einstein laid down the remarkable foundations of special relativity. The chapter begins with an early treatment of relativity, namely Galilean relativity, which while successful with classical mechanics was not tenable with electromagnetism. Working in the seclusion of a patent office, Einstein thought deeply and despairingly of relativity that would encompass electromagnetism. He realized that not only spatial measures but also time varied among inertial observers moving with constant relative velocities. Thus, Einstein’s special theory of relativity came to be, and along with it, his celebrated equation, E = mc2. The chapter then surveys bizarre, observable consequences of this special relativity and how they all beautifully fit into a mathematical framework created by Minkowski in which space and time become united. The chapter concludes by describing physicists’ reactions to this radical new theory and its role in different areas, such as elementary particle physics and astrophysics. In the opening chapter of quantum physics, Smitha describes the circuitous historic path taken by many a physicist explorer that led to the establishment of its mind-boggling fundamentals. This revolutionary branch of physics was seeded by puzzles posed in the late 1800s related to the behavior of light from radiating objects. The chapter begins by exploring the nature of light and the story of blackbody radiation that led to Planck introducing the notion of the quantum. It then surveys the photoelectric effect, which heralds the concept of the photon, and wave-particle duality, which applies both to light and matter. The excursion continues into Schrödinger’s description of matter acting as a wave and its consequences, including energy quantization and quantum tunneling. The chapter then explains Heisenberg’s uncertainty principle from multiple angles. Finally, it presents the quantum picture of the atom and how it resolved some of the deep puzzles, a crowning testament to quantum theory.
On the electrodynamics of moving bodies: Foundations of special relativity
Authors: Vishveshwara Smitha , Vishveshwara C V
Published: December 2024

Sample
Matter: Is it a particle? Is it a wave?
Authors: Vishveshwara Smitha , Vishveshwara C V
Published: December 2024

Sample
Response to relativity
Authors: Vishveshwara Smitha , Vishveshwara C V
Published: December 2024

Sample
Final formulation
Authors: Vishveshwara Smitha , Vishveshwara C V
Published: December 2024

Sample
Gravitational waves and Quasimodo
Authors: Vishveshwara Smitha , Vishveshwara C V
Published: December 2024

Sample
Phase transitions
Authors: Vishveshwara Smitha , Vishveshwara C V
Published: December 2024

Sample
Nitrogen deficiency influences strigolactone levels in basal parts of shoots and shoot branching phenotype in Arabidopsis thaliana
Authors: Sakioka Riko , Yoneyama Kaori
Published: December 2024

Strigolactones (SLs) are allelochemicals attracting both symbiotic arbuscular mycorrhizal (AM) fungi and root parasitic plants and a novel class of phytohormones inhibiting lateral shoot branching. In general, nutrient deficiency significantly promotes SL production in roots and exudation into the rhizosphere, and also induces suppressed shoot branching phenotype in host plants of AM fungi, including rice, tomato, and maize. Nutrient deficiencies also inhibit the shoot branching in Arabidopsis thaliana (hereafter Arabidopsis), a nonhost of AM fungi, while the level of carlactone, a noncanonical SL and the SL precursor for the other SLs, was reported to be unaffected. Because Arabidopsis SLs, including CL and methyl carlactonoate, are highly unstable, relationships between SL levels and shoot branching in Arabidopsis remain elusive. Herein, we demonstrate that nitrogen deficiency increases SL levels in the basal part of shoots in Arabidopsis and lateral shoot branching appears to be strongly regulated by these SLs.
VSS-Hi-C: variance-stabilized signals for chromatin contacts
Authors: Kenari Neda Shokraneh , Bayat Faezeh , Libbrecht Maxwell W
Published: December 2024

Motivation

The genome-wide chromosome conformation capture assay Hi-C is widely used to study chromatin 3D structures and their functional implications. Read counts from Hi-C indicate the strength of chromatin contact between each pair of genomic loci. These read counts are heteroskedastic: that is, a difference between the interaction frequency of 0 and 100 is much more significant than a difference between the interaction frequency of 1000 and 1100. This property impedes visualization and downstream analysis because it violates the Gaussian variable assumption of many computational tools. Thus heuristic transformations aimed at stabilizing the variance of signals like the shifted-log transformation are typically applied to data before its visualization and inputting to models with Gaussian assumption. However, such heuristic transformations cannot fully stabilize the variance because of their restrictive assumptions about the mean–variance relationship in the data.

Results

Here, we present VSS-Hi-C, a data-driven variance stabilization method for Hi-C data. We show that VSS-Hi-C signals have a unit variance improving visualization of Hi-C, for example in heatmap contact maps. VSS-Hi-C signals also improve the performance of subcompartment callers relying on Gaussian observations. VSS-Hi-C is implemented as an R package and can be used for variance stabilization of different genomic and epigenomic data types with two replicates available.

Availability and implementation

https://github.com/nedashokraneh/vssHiC.
Perioperative patient safety recommendations: systematic review of clinical practice guidelines
Authors: Martinez-Nicolas Ismael , Arnal-Velasco Daniel , Romero-García Eva , Fabregas Neus , Sanduende Otero Yolanda , Leon Irene , Bartakke Ashish A , Silva-Garcia Javier , Rodriguez Anna , Valli Claudia , Zamarian Sandro , Zaludek Adam , Meneses-Echavez Jose , Loaiza-Betancur Andrés F , Sousa Paulo , Orrego Carola , Soria-Aledo Victor ,   SAFEST Consortium, Baneres Joaquim , Carrasco Genis , Sunol Rosa , Vall Helena , Calsbeek Hiske , Emond Yvette , Heideveld-Chevalking Anita , Casaca-Carvalho Pedro , Leite Andreia , Nunes Ana Beatriz , Seyfulayeva Ayshe , De Robertis Edoardo , Weynants Cathy , Wittman Maria , Garel Pascal , Nabbe Marie , Groene Oliver , Wang Sophie , Kangasniemi Mari , Kommusaar Janne , Kristensen Kaja , Polluste Kaja , Pühvel Janne , Starkopf Joel , Marx David , Vlcek Frantisek , Schäfer Willemijn , Schlinkert Caroline , van der Schoot Nina , Van Tuyl Lilian , Voshaar Marieke , Wagner Cordula
Published: December 2024

Background

Surgical-related incidents are a common cause of in-hospital adverse events. Surgical patient safety would benefit from evidence-based practices, but a comprehensive collection of patient safety recommendations is still lacking. This study aimed to compile and assess the perioperative patient safety recommendations for adults.

Method

A systematic review of clinical practice guidelines was conducted using Medline, Embase, Cochrane, Virtual Health Library Regional Portal, and Trip Database from 2012 to 2022. Eligibility criteria followed a PICAR strategy for patient safety recommendations in the perioperative care continuum. Guidelines were appraised for quality, particularly focusing on the ‘rigour of development’ domain of the AGREE-II tool for those containing strong recommendations. Descriptive analyses were conducted, emphasizing guideline quality, recommendation strength, and the supporting level of evidence.

Results

From the 267 guidelines, 4666 perioperative patient safety recommendations were extracted, of which 44.9% (2095) were strongly recommended. Of these, 322 had the highest level of evidence, but only 18 guidelines met high standards in the AGREE-II ‘rigour of development’ domain. A subset of 78 recommendations ranked the highest in the strength of recommendation, level of evidence, and rigour of development of their guidelines. A gap was found within pre-admission and post-discharge care recommendations.

Discussion

This review highlights the noteworthy variability in the methodological quality of the guidelines, and a discordance between strength of recommendation and evidence level of the available perioperative patient safety recommendations. These findings provide valuable information for advising policy decisions and promoting best practices to enhance global surgical safety.

Registration

PROSPERO (CRD42022347449).
Extra-axial inflammatory signal and its relationship to peripheral and central immunity in depression
Authors: Eiff Brandi , Bullmore Edward T , Clatworthy Menna R , Fryer Tim D , Pariante Carmine M , Mondelli Valeria , Maccioni Lucia , Hadjikhani Nouchine , Loggia Marco L , Moskowitz Michael A , Bruner Emiliano , Veronese Mattia , Turkheimer Federico E , Schubert Julia J
Published: December 2024

Although both central and peripheral inflammation have been observed consistently in depression, the relationship between the two remains obscure. Extra-axial immune cells may play a role in mediating the connection between central and peripheral immunity. This study investigates the potential roles of calvarial bone marrow and parameningeal spaces in mediating interactions between central and peripheral immunity in depression.

PET was used to measure regional TSPO expression in the skull and parameninges as a marker of inflammatory activity. This measure was correlated with brain TSPO expression and peripheral cytokine concentrations in a cohort enriched for heightened peripheral and central immunity comprising 51 individuals with depression and 25 healthy controls.

The findings reveal a complex relationship between regional skull TSPO expression and both peripheral and central immunity. Facial and parietal skull bone TSPO expression showed significant associations with both peripheral and central immunity. TSPO expression in the confluence of sinuses was also linked to both central and peripheral immune markers. Group-dependent elevations in TSPO expression within the occipital skull bone marrow were also found to be significantly associated with central inflammation.

Significant associations between immune activity within the skull, parameninges, parenchyma and periphery highlight the role of the skull bone marrow and venous sinuses as pivotal sites for peripheral and central immune interactions.
Optimizing treatment of cardiovascular risk factors in cerebral small vessel disease using genetics
Authors: Koohi Fatemeh , Harshfield Eric L , Gill Dipender , Ge Wenjing , Burgess Stephen , Markus Hugh S
Published: December 2024

Cerebral small vessel disease (cSVD) causes lacunar stroke (LS), intracerebral haemorrhage, and is the most common pathology underlying vascular dementia. However, there are few trials examining whether treating conventional cardiovascular risk factors reduce stroke risk in cSVD, as opposed to stroke as a whole. We used Mendelian randomization techniques to investigate which risk factors are causally related to cSVD and to evaluate whether specific drugs may be beneficial in cSVD prevention.

We identified genetic proxies for blood pressure traits, lipids, glycaemic markers, anthropometry measures, smoking, alcohol consumption, and physical activity from large-scale genome-wide association studies of European ancestry. We also selected genetic variants as proxies for drug target perturbation in hypertension, dyslipidaemia, hyperglycaemia, and obesity. Mendelian randomization was performed to assess their associations with LS from the GIGASTROKE Consortium (n = 6811) and in a sensitivity analysis in a cohort of patients with MRI-confirmed LS (n = 3306). We also investigated associations with three neuroimaging features of cSVD, namely, white matter hyperintensities (n = 55 291), fractional anisotropy (n = 36 460), and mean diffusivity (n = 36 012).

Genetic predisposition to higher systolic and diastolic blood pressure was associated with LS and cSVD imaging markers. Genetically predicted liability to diabetes, obesity, smoking, higher triglyceride levels, and the ratio of triglycerides to high density lipoprotein (HDL) also showed detrimental associations with LS risk, while genetic predisposition to higher HDL concentrations and moderate-to-vigorous physical activity showed protective associations. Genetically proxied blood pressure-lowering through calcium channel blockers (CCBs) was associated with cSVD imaging markers, while genetically proxied HDL-raising through Cholesteryl Ester Transfer Protein (CETP) inhibitors, triglyceride-lowering through lipoprotein lipase (LPL), and weight-lowering through gastric inhibitory polypeptide receptor (GIPR) were associated with lower risk of LS.

Our findings highlight the importance of some conventional cardiovascular risk factors, including blood pressure and BMI, in cSVD, but not other e.g. LDL. The findings further demonstrate the potential beneficial effects of CCBs on cSVD imaging markers and CETP inhibitors, LPL enhancement, and GIPR obesity-targeted drugs on LS. They provide useful information for initiating future clinical trials examining secondary prevention strategies in cSVD.
Rituximab versus placebo for chronic inflammatory demyelinating polyradiculoneuropathy: a randomized trial
Authors: Nobile-Orazio Eduardo , Cocito Dario , Manganelli Fiore , Fazio Raffaella , Lauria Pinter Giuseppe , Benedetti Luana , Mazzeo Anna , Peci Erdita , Spina Emanuele , Falzone Yuri , Dalla Bella Eleonora , Germano Francesco , Gentile Luca , Liberatore Giuseppe , Gallia Francesca , Collet-Vidiella Roger , Bianchi Elisa , Doneddu Pietro Emiliano
Published: December 2024

Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) often requires prolonged ongoing treatment to prevent worsening. The efficacy of rituximab in preventing worsening after the discontinuation of immunoglobulin therapy in patients with CIDP was assessed.

In this randomized, double-blind, placebo-controlled study, conducted at seven Italian hospitals, CIDP patients under immunoglobulin therapy were assigned to receive either rituximab (1 g on Days 1, 15 and 180 ± 7) or placebo. Both groups continued their regular immunoglobulin doses for 6 months post-intervention. The primary end point was the proportion of patients who worsened in any of the following three measures at Month 12, within 6 months after immunoglobulin discontinuation: a decrease of at least one point on the adjusted INCAT score, two points on the MRC sum score, or four points on the RODS centile score. Secondary end points included the proportion of patients deteriorating at Month 18 (within 12 months after immunoglobulin discontinuation), treatment cessation due to adverse events or voluntary reasons, and the time until deterioration after immunoglobulin discontinuation. This study was registered with ClinicalTrials.gov (NCT06325943) and EUDRACT (number 2017-005034-36), and is now complete.

From April 2019 to March 2022, 39 patients were recruited; two withdrew consent. The remaining 37 patients were assigned to rituximab (n = 19) or placebo (n = 18). Median age was 53 (interquartile range 45–64), with 11 (30%) females. A similar proportion of patients in both the rituximab (12/19, 63.2%) and placebo (12/18, 66.6%) groups worsened at Month 12 [odds ratio (OR) 0.86; 95% confidence interval (CI) 0.22–3.32]. No significant differences were noted at Month 18 (OR 0.62; 95% CI 0.14–2.70), or in the mean scores of each scale at Months 6, 12 and 18. The median time to worsening was 5 months for rituximab and 2 months for placebo (Log-rank P = 0.4372). Treatment was suspended due to adverse events in one rituximab patient.

In this study, rituximab was not more effective than placebo in preventing clinical deterioration following the discontinuation of immunoglobulin therapy in CIDP. Further studies might evaluate the efficacy of more frequent or earlier administration of rituximab.
Clinical characterization of a novel ATP1A2 p.Gly615Glu mutation in nine family members with familial hemiplegic migraine
Authors: Romozzi Marina , Spartano Serena , L’Erario Federica Francesca , Iannone Luigi Francesco , Trigila Vincenzo , Gentile Annalisa , Sanginario Pasquale , Calabresi Paolo , Tiziano Francesco Danilo , Vollono Catello
Published: December 2024

Familial hemiplegic migraine type 2 results from pathogenic variants in the ATP1A2 gene, which encodes for a catalytic subunit of sodium/potassium ATPase. This extremely rare autosomal dominant disorder manifests with a spectrum of symptoms, most commonly pure hemiplegic phenotype, epilepsy, and/or intellectual disability. In this study, we detail the clinical features and genetic analysis of nine patients from a large family spanning four generations, with all carrying a previously unreported likely pathogenic variant, p.Gly615Glu, in ATP1A2, compatible with a diagnosis of familial hemiplegic migraine type 2, fully penetrant with variable expressivity. This newly identified likely pathogenic variant primarily presented with psychiatric disturbances and a non-hemiplegic phenotype. Only one patient presented hemiplegic attacks, while seven were diagnosed with migraine with aura, including visual, sensory, and speech/language aura, and one with migraine without aura. The identification of the genes responsible for the more common forms of migraine, both with and without aura, remains a significant challenge in migraine genetics and is critical for advancing personalized medicine.
Acquired autoinflammatory disorders: a dermatologist’s perspective
Authors: Bishnoi Anuradha , Sharma Apoorva , Baskaran Narayanan , Mehta Hitaishi , Chatterjee Debajyoti , Vinay Keshavamurthy
Published: December 2024

Autoinflammatory disorders are characterized by a dysregulated and disproportionately heightened response by the innate immune system to PAMPs and DAMPs (pathogen- and damage-associated molecular patterns, respectively), with a crucial role played by neutrophils and macrophages in disease pathogenesis. Autoinflammatory disorders closely resemble connective tissue diseases (CTDs); however, tests for antinuclear antibodies, typically considered a marker of CTDs, are negative in autoinflammatory disorders. Many autoinflammatory disorders are monogenic and arise from inherited genetic mutations, resulting in autoinflammation. This is especially true for disorders presenting in childhood or early adulthood. However, with the relatively recent identification of VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome, the recognized genetic spectrum of these disorders has expanded, especially in the adult population, emphasizing that these mutations could either be inherited or acquired later in life. Additionally, many of the acquired autoinflammatory disorders, for example, adult-onset Still disease and Schnitzler syndrome, have a multifactorial pathogenesis and are typically polygenic. Many novel disorders are being described in this category, and the majority of them have prominent cutaneous manifestations – either at onset or during the course of disease – that are particularly important from a diagnostic point of view. In this review, we discuss the cutaneous findings of a few acquired autoinflammatory disorders, with a specific focus on adult-onset Still disease, VEXAS syndrome, Schnitzler syndrome, Kikuchi–Fujimoto disease and haemophagocytic lymphohistiocytosis.
Dioctyl-substituted dibenzotetracyanonaphthoquinodimethane for air-stable n-channel organic semiconductor
Authors: Yang Tengzhou , Xie Bing , Zhang Liang , Wei Haoming
Published: December 2024

In this study, a novel n-channel 11,11,12,12-tetracyanonaphtho-2,6-quinodimethane-based organic semiconductor C8-DBTNAP was synthesized. C8-DBTNAP had good solubility and low-lying lowest unoccupied molecular orbital level (−4.41 eV). The good thin-film formability of C8-DBTNAP made it produce continuous, strip-shaped and uniform crystalline films. C8-DBTNAP organic thin-film transistors demonstrated high electron mobility up to 0.4 cm2/Vs under air conditions. These findings revealed that DBTNAP skeleton can be expected as a potential building block for developing high-performance, air-stable n-channel organic semiconductors.
Recognition of mismatched sites in double-stranded DNA by a pair of partially noncomplementary peptide nucleic acids
Authors: Shibata Masanari , Shoji Osami , Aiba Yuichiro
Published: December 2024

We have successfully achieved efficient recognition of mismatched sites in double-stranded DNA through the formation of an invasion complex by using partially noncomplementary peptide nucleic acids (PNAs). Owing to mismatches between 2 PNAs used for invasion, the undesired PNA/PNA duplex, which inhibits invasion complex formation, was destabilized. This approach overcame an inherent challenge in PNA invasion, in particular, undesired PNA/PNA duplex formation resulting from PNA complementarity, thereby enhancing overall invasion efficiency.
A One Health Investigation into H5N1 Avian Influenza Virus Epizootics on Two Dairy Farms
Authors: Shittu Ismaila , Silva Diego , Oguzie Judith U , Marushchak Lyudmyla V , Olinger Gene G , Lednicky John A , Trujillo-Vargas Claudia M , Schneider Nicholas E , Hao Haiping , Gray Gregory C
Published: December 2024

Background

In early April 2024 we studied 2 Texas dairy farms that had suffered incursions of H5N1 highly pathogenic avian influenza virus (HPAIV) the previous month.

Methods

We employed molecular assays, cell and egg culture, Sanger and next generation sequencing to isolate and characterize viruses from multiple farm specimens (cow nasal swab, milk specimens, fecal slurry, and a dead bird).

Results

We detected H5N1 HPAIV in 64% (9/14) of milk specimens, 2.6% (1/39) of cattle nasal swab specimens, and none of 17 cattle worker nasopharyngeal swab specimens. We cultured and characterized virus from 8 H5N1-positive specimens. Sanger and next-generation sequencing revealed the viruses were closely related into other recent Texas epizootic H5N1 strains of clade 2.3.4.4b. Our isolates had multiple mutations associated with increased spillover potential. Surprisingly, we detected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a nasal swab from a sick cow. Additionally, 14.3% (2/14) of the farm workers who donated sera were recently symptomatic and had elevated neutralizing antibodies against a related H5N1 strain.

Conclusions

Although our sampling was limited, these data offer additional insight into the large H5N1 HPAIV epizootic, which has rapidly spread in the United States. Due to fears that research might damage dairy businesses, studies like this one have been few. We need to find ways to work with dairy farms in collecting more comprehensive epidemiological data that are necessary for the design of future interventions against H5N1 HPAIV on cattle farms.