bluuebunny/crossref_metadata_2025 huggingface dataset:
Research on Deceleration Technology of Rocket Sled Double Track Sled
Authors: Xiao Jun , Zhang Lin-rui , Xue Qiang , Geng Qiang
Published: July 2023

Aiming at the shortcomings of water brake in the deceleration recovery test of double-track sled, the reverse rocket deceleration was applied to the recovery of double-track sled. A deceleration scheme of rocket sled double track sled car is designed to improve the safety of double track sled car. Firstly, according to the requirements of sliding distance and water entry speed of sled, the deceleration resistance is designed and calculated, and the reverse rocket is selected. However, the sled car is designed according to the dimensions of the reverse thrust rocket, and the installation position and way of the reverse thrust rocket are determined. At last, according to the deceleration trajectory and the parameters of recoil rocket, the control mode and ignition position of recoil rocket are designed. The simulation results show that the deceleration effect of reverse rocket is obvious. This control method is simple and feasible. The reverse rocket deceleration method can be applied to the recovery of double track sled.
Study on flame cutting process of thick stainless-clad steel
Authors: Deng Chunyin , Chen Guoxing , Wu Shuhui , Lu Zhuang , Liu Shengyong , Su Liangliang , Zhao Ying , Gao Wenju
Published: July 2023

In general, three different types of processes can be utilized to cut thick stainless-clad steel: waterjet cutting, mechanical cutting, and thermal cutting (plasma, flame, and EDM cutting). Because stainless steel contains a lot of Cr, Ni, and other elements with high ignition and melting temperatures, flame cutting is not recommended for direct cutting of stainless steel. Three different stainless-clad steel specimen thicknesses were prepared for this study, and cutting experiments were conducted utilizing the flame-cutting procedure. The tests demonstrate that using suitable flame-cutting parameters can yield the optimal cutting process parameters and successfully cut thick stainless-clad steel.
Simulation Study of Aircraft Active-Active Hydroelectric Hybrid Power Drive Unit
Authors: Mo Wei , Li Wei , Lu Yueliang
Published: July 2023

The Power Drive Unit (PDU) is the power source of the aircraft high-lift system (HLS), which converts hydraulic or electric energy into mechanical energy for output, and deflects the flap/slat through the transmission lines to increase the wing area to improve lift. Two sets of hydraulic motor subsystems working simultaneously are used in the Active-Active PDU of traditional aircraft to improve the reliability of the system. In this paper, an Active-Active Hydroelectric Hybrid Power Drive Unit (HPDU) is designed with a fixed-displacement hydraulic motor and a permanent magnet synchronous motor, the fundamental composition of the HPDU is introduced, the mathematical model of main components is analyzed, the HPDU is modeled based on AMESim, and the function and operation performance are investigated by simulation. The results show that the HPDU can realize the functional design requirements such as forward and reverse rotation and the performance design requirements such as withstanding sudden load within the rated load range during running.
A Novel Design of a Built-in V-Rotor Ultra-Efficient PMSM Based on Multiple Air Slots
Authors: Liu Xin , Wang Bulai , Yang Mengzhen
Published: July 2023

According to indicators, the New V-Rotor Permanent Magnet Motor (NVRPM) for compressors with a rated power of 22 kW and a rated speed of 3000 rpm is optimally designed. Because of the large number of permanent magnets in the V-type PM motor, the magnetic leakage between rotor poles will increase, and its air gap magnetic field contains large harmonic components, which is easy to increase the loss and reduce the efficiency. The structure of the initial V-shaped rotor was optimized by adding multiple air slots and cosine non-uniform air gaps on the rotor surface. Through the finite element simulation of electromagnetic characteristics of NVRPM, it is proved that the improvement of the new motor structure can reduce the loss, weaken the cogging torque, and decrease the torque ripple, and the simulation efficiency is up to 96%, and its operation area is wide and efficient. Finally, the results show that the optimization design of the NVRPM structure is feasible.
08 steel numerical simulation study on the cold forging of buffer seat
Authors: Lv Longlong , Cai Yujun , Dong Xiaochuan , Wu Chuan
Published: July 2023

For the problem of uneven hardness in the specified area of the buffer seat, we analyze the reasons for this problem. With the goal of promoting hardness uniformity in the specified area of the product, the friction coefficient and punch pressing speed were selected as the influencing factors, simulation experiments were designed, and the results were obtained through multiple simulations. The simulation results show that the processing conditions are that the friction coefficient is not greater than 0.2 and the pressing speed of the punch is 0.2 mm/sec, which are the process solutions to make the hardness of the product uniform. Moreover, compared to the effects of several other variables, the pressing speed has the greatest influence on the hardness deviation of the final product.
Mesh Stiffness Models for Modified Straight Bevel Gears without and with Slice Coupling
Authors: Shu Ruizhi , Chen Siyu , Ge Shuaishuai , Tan Rulong , Yin Qin
Published: July 2023

The analysis of the dynamics of gear systems is based on the determination of the time-varying mesh stiffness (TVMS). The infinitesimal approach was used to slice the straight bevel gear’s teeth. After that, the beam deformation theory was combined to determine the stiffness components of each tooth segment. On this basis, the meshing stiffness models with and without slice coupling were constructed using the methods of accumulative integral potential energy and slice coupling, respectively. Lastly, the results of the suggested methodology were compared to those of the finite element analysis to ensure accuracy. The result shows that both analytical methods can solve the TVMS of straight bevel gears accurately and quickly.
Design of a high-accuracy time-to-digital converter based on dual-edge signals
Authors: Xiao Yuan , Liang Huaguo , Jin Liyu , Wang Yuchuan , Shao Zhiwei , Wang Yue , Lu Yingchun
Published: July 2023

Among numerous time-to-digital converters (TDC), tapped
delay line (TDL) is the most commonly used architecture. However,
its dead time of more than two cycles is inefficient for
applications with high measurement rates. Limited by the device
process, the delay of each cell in the TDL exhibits a random and
uneven distribution, degrading the linearity of the TDC. In this
study, a dual-edge TDL structure is proposed. By improving original
pulse-holding circuit, the propagated signal injected into the fine
measurement chain is alternately switched between rising and falling
edge signals to decrease the dead time to one cycle. The
nonlinearity problem is alleviated by an enhanced tapped sampling
sequence circuit. A dual-edge “1” count encoder is introduced to
effectively simplify the difficulty of addressing the bubble
problem. Bit-by-bit calibration and a moving average filter are
adopted to improve accuracy. The proposed scheme has been verified
on a Xilinx Kintex-7 FPGA platform. The resolution (least
significant bit, LSB1) is 12.07 ps when the
propagated signal in the TDL is the rising edge. The differential
nonlinearity (DNL) is [-0.81,0.93] LSB1, and the
integral nonlinearity (INL) is between
[-2.33,2.19] LSB1. At the falling edge, the
resolution (LSB0) is 11.90 ps, between
[-0.73,0.98] LSB0 and
[-2.46,1.83] LSB0 for DNL and INL, respectively. In
addition, the accuracy reaches 15.25 ps after multiple measurements
for different time intervals separately.
Adiabatic bunch compression in storage rings from self wakes generated in Cherenkov waveguides
Authors: Antipov S.A. , Agapov I. , Zagorodnov I. , Lemery F.
Published: July 2023

Equilibrium bunch lengths typical to modern day light sources of tens of picoseconds limit the spectral reach of superradiant approaches for exploring materials and biological samples. In particular, generation of terahertz radiation seems appealing for pump-probe experiments.
Taking advantage of self-wakes generated by carefully chosen structure one can control the bunch length and shape the bunch profile to increase significantly the high-frequency spectral components. Numerical analysis indicates the presence of self-consistent steady states that can be obtained with passive corrugated or dielectric structures. This approach has potential applications for generating superradiant terahertz radiation and pulse shaping in circular accelerators.
Contact feedback helps snake robots propel against uneven terrain using vertical bending
Authors: Fu Qiyuan , Li Chen
Published: July 2023

Snakes can bend their elongate bodies in various forms to traverse various environments. We understand well how snakes use lateral body bending to push against asperities on flat ground for propulsion, and snake robots can do so effectively. However, snakes can also use vertical bending to push against uneven terrain of large height variation for propulsion, and they can adjust this bending to adapt to novel terrain presumably using mechano-sensing feedback control. Although some snake robots can traverse uneven terrain, few have used vertical bending for propulsion, and how to control this process in novel environments is poorly understood. Here we systematically studied a snake robot with force sensors pushing against large bumps using vertical bending to understand the role of sensory feedback control. We compared a feedforward controller and four feedback controllers that use different sensory information and generate distinct bending patterns and body-terrain interaction. We challenged the robot with increasing backward load and novel terrain geometry that break its contact with the terrain. We further varied how much the feedback control modulated body bending to conform to or push against the terrain to test their effects. Feedforward propagation of vertical bending generated large propulsion when the bending shape matched terrain geometry. However, when perturbations caused loss of contact, the robot easily lost propulsion or had motor overload. Contact feedback control resolved these issues by helping the robot regain contact. Yet excessive conformation interrupted shape propagation and excessive pushing stalled motors frequently. Unlike that using lateral bending, for propulsion generation using vertical bending, body weight that can help maintain contact with the environment but may also overload motors. Our results will help snake robots better traverse uneven terrain with large height variation and can inform how snakes use sensory feedback to control vertical body bending for propulsion.
Multistate transition dynamics by strong time-dependent perturbation in NISQ era
Authors: Wang Yulun , Krstić Predrag S
Published: July 2023

We develop a quantum computing scheme utilizing McLachlan variational principle in a hybrid quantum–classical algorithm to accurately calculate the transition dynamics of a closed quantum system with many excited states subject to a strong time-dependent perturbation. A systematic approach for optimal construction of a general N-state ansatz with unary N-qubit encoding is refined. We also use qubit efficient encoding in McLachlan variational quantum algorithm to reduce the number of qubits to

log

2

N

, simultaneously diminishing depths of the quantum circuits. The significant reduction of the number of time steps is achieved by use of the second order marching method. Instrumental in obtaining high accuracy are adaptations of the circuits to include time-dependent global phase correction. We illustrated, tested and optimized our quantum computing algorithm on a set of 16 bound hydrogenic eigenstates exposed to a strong laser attosecond pulse. Results for transition probabilities are obtained with accuracy better than 1%, as established by comparison to the benchmark data. Use of interaction representation of the Hamiltonian reduces the noise accumulation while the quantum system evolves in time.
Auxetic mechanical metamaterials: from soft to stiff
Authors: Li Xiang , Peng Weitao , Wu Wenwang , Xiong Jian , Lu Yang
Published: July 2023

Highlights

Mechanical design methods and theoretical models of soft and hard mechanical metamaterials are reviewed based on deformation mechanisms.

Multifunctional mechanical benefits and limitations of soft and hard mechanical metamaterials are reviewed, and comprehensive performances optimization methods are categorized.

Industrial applications of soft and hard mechanical metamaterials are reviewed, perspectives and challenges are discussed.
Textile electronics for wearable applications
Authors: Pu Junhong , Ma Kitming , Luo Yonghui , Tang Shengyang , Liu Tongyao , Liu Jin , Leung Manyui , Yang Jing , Hui Ruomu , Xiong Ying , Tao Xiaoming
Published: July 2023

Textile electronics have become an indispensable part of wearable applications because of their large flexibility, light-weight, comfort and electronic functionality upon the merge of textiles and microelectronics. As a result, the fabrication of functional fibrous materials and the integration of textile electronic devices have attracted increasing interest in the wearable electronic community. Challenges are encountered in the development of textile electronics in a way that is electrically reliable and durable, without compromising on the deformability and comfort of a garment, including processing multiple materials with great mismatches in mechanical, thermal, and electrical properties and assembling various structures with the disparity in dimensional scales and surface roughness. Equal challenges lie in high-quality and cost-effective processes facilitated by high-level digital technology enabled design and manufacturing methods. This work reviews the manufacturing of textile-shaped electronics via the processing of functional fibrous materials from the perspective of hierarchical architectures, and discusses the heterogeneous integration of microelectronics into normal textiles upon the fabric circuit board and adapted electrical connections, broadly covering both conventional and advanced textile electronic production processes. We summarize the applications and obstacles of textile electronics explored so far in sensors, actuators, thermal management, energy fields, and displays. Finally, the main conclusions and outlook are provided while the remaining challenges of the fabrication and application of textile electronics are emphasized.
A deep neural network approach for parameterized PDEs and Bayesian inverse problems
Authors: Antil Harbir , Elman Howard C , Onwunta Akwum , Verma Deepanshu
Published: July 2023

We consider the simulation of Bayesian statistical inverse problems governed by large-scale linear and nonlinear partial differential equations (PDEs). Markov chain Monte Carlo (MCMC) algorithms are standard techniques to solve such problems. However, MCMC techniques are computationally challenging as they require a prohibitive number of forward PDE solves. The goal of this paper is to introduce a fractional deep neural network (fDNN) based approach for the forward solves within an MCMC routine. Moreover, we discuss some approximation error estimates. We illustrate the efficiency of fDNN on inverse problems governed by nonlinear elliptic PDEs and the unsteady Navier–Stokes equations. In the former case, two examples are discussed, respectively depending on two and 100 parameters, with significant observed savings. The unsteady Navier–Stokes example illustrates that fDNN can outperform existing DNNs, doing a better job of capturing essential features such as vortex shedding.
Antibacterial efficacy of surface aluminum oxide nanostructures produced by hot water treatment
Authors: Smith Quinshell , Burnett Kenneth , Ali Nawab , Bush John , Karabacak Tansel
Published: July 2023

This study utilizes a hot water treatment (HWT) method for introducing antibacterial properties to aluminum (Al) surfaces, which has relevance in several industries ranging from food packaging and ventilation systems to biomedical materials. The HWT process can produce a nanostructured oxide layer on a wide range of metallic materials by simply immersing the metal in water at temperatures ranging from 75 °C to 95 °C. In this work, Al foil was treated in deionized (DI) water for 5 min at various temperatures, including 75 °C, 85 °C, and 95 °C. Concentrations of Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus epidermidis (S. epidermidis) were placed on Al foil for different times, ranging from 30 seconds to 60 min The survival time was measured, and the analysis of the results indicates a direct correlation between when the bacteria was exposed to HWT Al foil and the number of bacteria killed. As the temperature of the HWT increased, there was an increase in antibacterial activity. This finding is consistent with our expectations; at higher HWT temperatures, more prominent nanostructures are produced, causing increased inactivation of bacteria. Our results show the nanostructured HWT Al foil was superior at inactivating Gram-negative (E. coli) and Gram-positive (S. epidermidis) bacteria compared to the untreated control Al foil. HWT Al foil treated at 75 °C, 85 °C, and 95 °C was 58%, 64%, and 73% more effective in killing the Gram-negative bacteria, respectively, after only 30 seconds of contact time compared to untreated control Al foil, while the antibacterial efficacy was enhanced 88%, 92%, and 94% for the Gram-positive bacteria, respectively. The HWT nanostructures synthesized at 95 °C, after 60 min of contact time, were able to inactivate 97% of the gram-negative bacteria and 100% of the gram-positive bacteria, demonstrating the efficacy of its antibacterial properties. This research presents a novel, inexpensive, and environmentally friendly method of producing nanostructures that inhibit bacterial activity.
The association between high ambient temperature and risk of hospitalization: a time-series study in eight ecological regions in Vietnam
Authors: Tran Nu Quy Linh , Ngo Hieu K T , Tuong Vy Nguyen Thi , Dang Tran Ngoc , Nghiem Son , Nguyen Huu Quyen , Phung Dung
Published: July 2023

Viet Nam is among the countries most threatened by and vulnerable to climate change and extreme weather events. However, research on the temperature-morbidity relationship at the national scale has been scarce. This study aimed to assess the impact of high temperatures on the risk of hospital admissions for all causes and heat-sensitive diseases across eight ecological regions in Vietnam. The study utilized a longitudinal dataset that included hospitalization and meteorological data from eight provinces representing eight regions in Vietnam. A time series analysis was applied using the generalized linear and distributed lag models with a quasi-Poisson family to examine the temperature-hospitalization association in each province. A random-effects meta-analysis was used to calculate the pooled estimate of risk for the national scale. The country-level pooled effects (%, [95% CI]) indicated that a 1 °C increase above the threshold temperature (19 °C) increased the hospitalization risk for all causes and infectious diseases by 0.8% [0.4%–1.2%] and 2.4% [1.02%–1.03%], respectively at lag 0–3 d. The effects of heat on respiratory diseases and mental health disorders were not significant. At the regional level, the association varied across eight regions, of which the Northern parts tended to have a higher risk than the Southern. This is among very few national-scale studies assessing hospitalization risk associated with high temperatures across eight ecological regions of Vietnam. These findings would be useful for developing evidence-based heat-health action plans.
Adaptation as Process: A Genetic Edition of Andrew Davies’ Middlemarch (BBC/WGBH, 1994)
Authors: Smith Justin , Hobbs Lucy
Published: July 2023

This article reports on an interdisciplinary project to produce the first genetic edition of a television adaptation, drawing on the papers of screenwriter Andrew Davies who adapted George Eliot’s Middlemarch for the BBC in 1994. Combining methodologies from digital humanities, television history, and archival theory and practice, the digital resource places Xtensible Mark-up Language versions of Eliot’s novel and Davies’ scripts at the centre of an intertextual framework which enables close cross-referencing. Supported by primary sources derived from thorough production history research, the genetic edition opens up a potentially productive approach to adaptation which foregrounds the creative practice of the screenwriter at the heart of the collaborative process of producing television adaptations of classic novels. Following an outline of the case history, the project and the resource, the article then illustrates some preliminary findings based on new editorial commentary. It concludes that this genetic edition will not only be of interest to Eliot scholars, television historians, and adaptations studies, but might have potential beyond the academy in the development of resources for education and heritage sites.
Socioeconomic Inequalities and Molecular Risk for Aging in Young Adulthood
Authors: Potente Cecilia , Chumbley Justin , Xu Wenjia , Levitt Brandt , Cole Steven W , Ravi Sudharshan , Bodelet Julien Stephane , Gaydosh Lauren , Harris Kathleen Mullan , Shanahan Michael J
Published: July 2023

Diverse manifestations of biological aging often reflect disparities in socioeconomic status (SES). In this paper, we examine associations between indicators of SES and an mRNA-based aging signature during young adulthood, before clinical indications of aging are common. We use data from wave V (2016–2018) of the National Longitudinal Study of Adolescent to Adult Health, a nationally representative study of adults aged 33–43 years, with transcriptomic data from a subset of 2,491 participants. Biological aging is measured using 1) a composite transcriptomic aging signature previously identified by Peters et al.’s out-of-sample meta-analysis (Nat Commun. 2015;6:8570) and 2) 9 subsets that represent functional pathways of coexpressed genes. SES refers to income, education, occupation, subjective social status, and a composite measure combining these 4 dimensions. We examine hypothesized mechanisms through which SES could affect aging: body mass index, smoking, health insurance status, difficulty paying bills, and psychosocial stress. We find that SES—especially the composite measure and income—is associated with transcriptomic aging and immune, mitochondrial, ribosomal, lysosomal, and proteomal pathways. Counterfactual mediational models suggest that the mediators partially account for these associations. The results thus reveal that numerous biological pathways associated with aging are already linked to SES in young adulthood.
Impact of enhanced pharmacy services on adherence for patients with hypertension
Authors: Garcia Paloma , Zolekar Ashwini , Donnelly Andrew , Nagelli Anitha
Published: July 2023

Purpose

To evaluate the impact of UI TEAM RX, a pharmacy-based enhanced services and care model, on adherence in patients with hypertension and prescribed a renin-angiotensin system antagonist (RASA).

Methods

A single-center, retrospective, observational cohort study was conducted in an academic health system, University of Illinois Hospital & Health Sciences System (UI Health). The cohort consisted of patients who utilized UI Health’s outpatient pharmacies between May 2016 and December 2018 to fill RASA prescriptions. Patients who were not part of the UI TEAM RX care model served as the control group, while patients enrolled in UI TEAM RX formed the intervention group. The control and intervention groups were matched based on index date, age, gender, and race. The primary outcome was mean change in a rolling 6-month calculation of proportion of days covered (PDC). The secondary outcome was the percentage of patients who had reached their blood pressure goal at follow-up at 12 months.

Results

Patients receiving UI TEAM RX intervention showed significant improvement in mean PDC at 6-month follow-up compared to control patients (P < 0.01). The proportion of patients with a PDC above 0.8 was higher in the intervention group, but this difference was not statistically significant. There was also a 16.4% increase in the proportion of patients who reached their blood pressure goal in the intervention group, although this increase was not statistically significant.

Conclusion

The UI TEAM RX program had a statistically significant impact on patients’ mean PDCs. An increase in the number of patients reaching their blood pressure goal was also seen.
Does the unity of reason imply that epistemic justification is factive?
Authors: Hirvelä Jaakko
Published: July 2023

Some externalists have recently argued that the unity of theoretical and practical reason implies that epistemic justification is factive. It is argued that arguments for the factivity of epistemic justification either (i) equate two actions that are in fact different, or (ii) make the unwarranted assumption that the by-relation transmits justification. The unity of reason does not imply that epistemic justification is factive.
Three-Dimensional Photography and Computer Modeling as a Reconstructive Surgical Training Tool
Authors: Singh Prateush , Chan Kayen , Dhar Shivani , Krumhuber Eva , Mosahebi Afshin , Ponniah Allan
Published: July 2023

Background

Reconstructive surgery operations are often complex, staged, and have a steep learning curve. As a vocational training requiring thorough three-dimensional (3D) understanding of reconstructive techniques, the use of 3D photography and computer modeling can accelerate this learning for surgical trainees.

Objectives

The authors illustrate the benefits of introducing a streamlined reconstructive pathway that integrates 3D photography and computer modeling, to create a learning database for use by trainees and patients alike, to improve learning and comprehension.

Methods

A computer database of 3D photographs and associated computer models was developed for 35 patients undergoing reconstructive facial surgery at the Royal Free Hospital, London, UK. This was used as a training and teaching tool for 20 surgical trainees, with an MCQ questionnaire assessing knowledge and a Likert scale questionnaire assessing satisfaction with the understanding of core reconstructive techniques, given before and after teaching sessions. Data were analyzed using the Mann–Whitney U test for trainee knowledge and Wilcoxon rank sum test for trainee satisfaction.

Results

Trainee (n = 20) knowledge showed a statistically significant improvement, P < .01, as did trainee satisfaction, P < .05, after a teaching session using 3D photography and computer models for facial reconstruction.

Conclusions

Three-dimensional photography and computer modeling are useful teaching and training tools for reconstructive facial surgery. The authors advocate the implementation of an integrated pathway for patients with facial defects to include 3D photography and computer modeling wherever possible, to develop internal databases for training trainees as well as patients. This algorithm can be extrapolated to other aspects of reconstructive surgery.

Level of Evidence: 5
ZooPathWeb: a comprehensive web resource for zoonotic pathogens
Authors: Hu Rui-Si , Zhang Xin , Wei Yanming
Published: July 2023

Motivation

Zoonotic pathogens, such as viruses, bacteria, fungi and parasites, can be transmitted from animals to humans, causing a wide range of diseases that can vary from mild to life-threatening. These pathogens typically exhibit a broad host range, infecting domestic and/or wild animals, which serve as reservoirs of infection. Human infection can occur through direct contact with infected animals or their body fluids, consumption of contaminated food or water, or via bites from infected arthropod vectors. Understanding the epidemiological characteristics and population structure of zoonotic pathogens is of paramount importance for preventing and controlling the spread of zoonotic diseases.

Results

Here, we present ZooPathWeb, a comprehensive online resource for zoonotic pathogens. ZooPathWeb provides essential information on pathogens that are particularly relevant to public health and includes a literature collection organized by pathogen classification, such as lineage, host, country or region and publication year. Moreover, we have developed four web-based utility tools for this release: SeqNHandle, PaPhy-ML, TreeView and BLAST. These tools are specifically designed to facilitate the identification of population structure and adaptive evolution in relation to zoonotic pathogens.

Availability and implementation

The ZooPathWeb website is accessed via http://lab.malab.cn/~hrs/zoopathweb/. The source code for AKINND, which is used for collecting pathogen-related literature, can be found at https://github.com/RuiSiHu/AKINND. Additionally, the source code for PaPhy-ML, utilized for phylogenetic analysis, can be found at https://github.com/RuiSiHu/PaPhy-ML.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Counting pseudoalignments to novel splicing events
Authors: Borozan Luka , Rojas Ringeling Francisca , Kao Shao-Yen , Nikonova Elena , Monteagudo-Mesas Pablo , Matijević Domagoj , Spletter Maria L , Canzar Stefan
Published: July 2023

Motivation

Alternative splicing (AS) of introns from pre-mRNA produces diverse sets of transcripts across cell types and tissues, but is also dysregulated in many diseases. Alignment-free computational methods have greatly accelerated the quantification of mRNA transcripts from short RNA-seq reads, but they inherently rely on a catalog of known transcripts and might miss novel, disease-specific splicing events. By contrast, alignment of reads to the genome can effectively identify novel exonic segments and introns. Event-based methods then count how many reads align to predefined features. However, an alignment is more expensive to compute and constitutes a bottleneck in many AS analysis methods.

Results

Here, we propose fortuna, a method that guesses novel combinations of annotated splice sites to create transcript fragments. It then pseudoaligns reads to fragments using kallisto and efficiently derives counts of the most elementary splicing units from kallisto’s equivalence classes. These counts can be directly used for AS analysis or summarized to larger units as used by other widely applied methods. In experiments on synthetic and real data, fortuna was around 7× faster than traditional align and count approaches, and was able to analyze almost 300 million reads in just 15 min when using four threads. It mapped reads containing mismatches more accurately across novel junctions and found more reads supporting aberrant splicing events in patients with autism spectrum disorder than existing methods. We further used fortuna to identify novel, tissue-specific splicing events in Drosophila.

Availability and implementation

fortuna source code is available at https://github.com/canzarlab/fortuna.
Unravelling spatial gene associations with SEAGAL: a Python package for spatial transcriptomics data analysis and visualization
Authors: Wang Linhua , Liu Chaozhong , Gao Yang , Zhang Xiang H -F , Liu Zhandong
Published: July 2023

In the era where transcriptome profiling moves toward single-cell and spatial resolutions, the traditional co-expression analysis lacks the power to fully utilize such rich information to unravel spatial gene associations. Here, we present a Python package called Spatial Enrichment Analysis of Gene Associations using L-index (SEAGAL) to detect and visualize spatial gene correlations at both single-gene and gene-set levels. Our package takes spatial transcriptomics datasets with gene expression and the aligned spatial coordinates as input. It allows for analyzing and visualizing genes’ spatial correlations and cell types’ colocalization within the precise spatial context. The output could be visualized as volcano plots and heatmaps with a few lines of code, thus providing an easy-yet-comprehensive tool for mining spatial gene associations.

Availability and implementation

The Python package SEAGAL can be installed using pip: https://pypi.org/project/seagal/. The source code and step-by-step tutorials are available at: https://github.com/linhuawang/SEAGAL.
Evaluation of intraoperative neuromonitoring (IONM) data with the Mainz IONM Quality Assurance and Analysis tool
Authors: Musholt Thomas J , Staubitz Julia I , Musholt Petra B
Published: July 2023

Background

Intraoperative neuromonitoring is widely used in thyroid and parathyroid surgery to prevent unilateral and especially bilateral recurrent nerve paresis. Reference values for amplitude and latency for the recurrent laryngeal nerve and vagus nerve have been published. However, data quality measures that exclude errors of the underlying intraoperative neuromonitoring (IONM) data (immanent software errors, false data labelling) before statistical analysis have not yet been implemented.

Methods

The authors developed an easy-to-use application (the Mainz IONM Quality Assurance and Analysis tool) using the programming language R. This tool allows visualization, automated and manual correction, and statistical analysis of complete raw data sets (electromyogram signals of all stimulations) from intermittent and continuous neuromonitoring in thyroid and parathyroid surgery. The Mainz IONM Quality Assurance and Analysis tool was used to evaluate IONM data generated and exported from ‘C2’ and ‘C2 Xplore’ neuromonitoring devices (inomed Medizintechnik GmbH) after surgery. For the first time, reference values for latency and amplitude were calculated based on ‘cleaned’ IONM data.

Results

Intraoperative neuromonitoring data files of 1935 patients consecutively operated on from June 2014 to May 2020 were included. Of 1921 readable files, 34 were excluded for missing data labelling. Automated plausibility checks revealed: less than 3 per cent device errors for electromyogram signal detection; 1138 files (approximately 60 per cent) contained potential labelling errors or inconsistencies necessitating manual review; and 915 files (48.5 per cent) were indeed erroneous. Mean(s.d.) reference onset latencies for the left vagus nerve, right vagus nerve, recurrent laryngeal nerve, and external branch of the superior laryngeal nerve were 6.8(1.1), 4.2(0.8), 2.5(1.1), and 2.1(0.5) ms, respectively.

Conclusion

Due to high error frequencies, IONM data should undergo in-depth review and multi-step cleaning processes before analysis to standardize scientific reporting. Device software calculates latencies differently; therefore reference values are device-specific (latency) and/or set-up-specific (amplitude). Novel C2-specific reference values for latency and amplitude deviate considerably from published values.
Beta-triggered adaptive deep brain stimulation during reaching movement in Parkinson’s disease
Authors: He Shenghong , Baig Fahd , Merla Anca , Torrecillos Flavie , Perera Andrea , Wiest Christoph , Debarros Jean , Benjaber Moaad , Hart Michael G , Ricciardi Lucia , Morgante Francesca , Hasegawa Harutomo , Samuel Michael , Edwards Mark , Denison Timothy , Pogosyan Alek , Ashkan Keyoumars , Pereira Erlick , Tan Huiling
Published: July 2023

Subthalamic nucleus (STN) beta-triggered adaptive deep brain stimulation (ADBS) has been shown to provide clinical improvement comparable to conventional continuous DBS (CDBS) with less energy delivered to the brain and less stimulation induced side effects. However, several questions remain unanswered. First, there is a normal physiological reduction of STN beta band power just prior to and during voluntary movement. ADBS systems will therefore reduce or cease stimulation during movement in people with Parkinson’s disease and could therefore compromise motor performance compared to CDBS. Second, beta power was smoothed and estimated over a time period of 400 ms in most previous ADBS studies, but a shorter smoothing period could have the advantage of being more sensitive to changes in beta power, which could enhance motor performance. In this study, we addressed these two questions by evaluating the effectiveness of STN beta-triggered ADBS using a standard 400 ms and a shorter 200 ms smoothing window during reaching movements. Results from 13 people with Parkinson’s disease showed that reducing the smoothing window for quantifying beta did lead to shortened beta burst durations by increasing the number of beta bursts shorter than 200 ms and more frequent switching on/off of the stimulator but had no behavioural effects. Both ADBS and CDBS improved motor performance to an equivalent extent compared to no DBS. Secondary analysis revealed that there were independent effects of a decrease in beta power and an increase in gamma power in predicting faster movement speed, while a decrease in beta event related desynchronization (ERD) predicted quicker movement initiation. CDBS suppressed both beta and gamma more than ADBS, whereas beta ERD was reduced to a similar level during CDBS and ADBS compared with no DBS, which together explained the achieved similar performance improvement in reaching movements during CDBS and ADBS. In addition, ADBS significantly improved tremor compared with no DBS but was not as effective as CDBS. These results suggest that STN beta-triggered ADBS is effective in improving motor performance during reaching movements in people with Parkinson’s disease, and that shortening of the smoothing window does not result in any additional behavioural benefit. When developing ADBS systems for Parkinson’s disease, it might not be necessary to track very fast beta dynamics; combining beta, gamma, and information from motor decoding might be more beneficial with additional biomarkers needed for optimal treatment of tremor.
Addressing the gaps between socioeconomic disparities and biological models of dementia
Authors: Ibáñez Agustín , Legaz Agustina , Ruiz-Adame Manuel
Published: July 2023

How do socioeconomic disparities shape brain health and disease? Ibáñez et al. discuss the need for further research into how wealth and socioeconomic status affect biological models of dementia, highlighting the biological ripple effects of socioeconomic inequalities and the importance of globally inclusive brain health research.
Functional connectivity of the left inferior parietal lobule mediates the impact of anxiety and depression symptoms on sleep quality in healthy adults
Authors: Lai Mingfeng , Gao Yingxue , Lu Lu , Huang Xiaoqi , Gong Qiyong , Li Jing , Jiang Ping
Published: July 2023

Individuals with anxiety and depression symptoms are vulnerable to sleep disturbances. The current study aimed to explore the shared neuro-mechanisms underlying the effect of anxiety and depression symptoms on sleep quality. We recruited a cohort of 92 healthy adults who underwent functional magnetic resonance imaging scanning. We measured anxiety and depression symptoms using the Zung Self-rating Anxiety/Depression Scales and sleep quality using the Pittsburgh Sleep Quality Index. Independent component analysis was used to explore the functional connectivity (FC) of brain networks. Whole-brain linear regression analysis showed that poor sleep quality was associated with increased FC in the left inferior parietal lobule (IPL) within the anterior default mode network. Next, we extracted the covariance of anxiety and depression symptoms using principal component analysis to represent participants’ emotional features. Mediation analysis revealed that the intra-network FC of the left IPL mediated the association between the covariance of anxiety and depression symptoms and sleep quality. To conclude, the FC of the left IPL may be a potential neural substrate in the association between the covariance of anxiety and depression symptoms and poor sleep quality, and may serve as a potential intervention target for the treatment of sleep disturbance in the future.
The importance of graph databases and graph learning for clinical applications
Authors: Walke Daniel , Micheel Daniel , Schallert Kay , Muth Thilo , Broneske David , Saake Gunter , Heyer Robert
Published: July 2023

The increasing amount and complexity of clinical data require an appropriate way of storing and analyzing those data. Traditional approaches use a tabular structure (relational databases) for storing data and thereby complicate storing and retrieving interlinked data from the clinical domain. Graph databases provide a great solution for this by storing data in a graph as nodes (vertices) that are connected by edges (links). The underlying graph structure can be used for the subsequent data analysis (graph learning). Graph learning consists of two parts: graph representation learning and graph analytics. Graph representation learning aims to reduce high-dimensional input graphs to low-dimensional representations. Then, graph analytics uses the obtained representations for analytical tasks like visualization, classification, link prediction and clustering which can be used to solve domain-specific problems. In this survey, we review current state-of-the-art graph database management systems, graph learning algorithms and a variety of graph applications in the clinical domain. Furthermore, we provide a comprehensive use case for a clearer understanding of complex graph learning algorithms.

Graphical abstract
Electropenetrography study of Euschistus heros (F.) (Heteroptera: Pentatomidae) nymphs feeding at different sites of the soybean pod
Authors: Lucini Tiago , Ricardo Panizzi Antônio , Arlindo Semeão Altair
Published: July 2023

This study aimed to characterize and correlate the stylet penetration behaviors of nymphs of the Neotropical brown stink bug, Euschistus heros (F.), on immature soybean pods. Waveforms were obtained using electropenetrography (EPG). The findings revealed that the nymphs exploited the xylem vessels and the seed tegument or endosperm. Primarily 4 phases were characterized: nonfeeding, pathway, salivation, and ingestion. The waveforms of each phase were similar in appearance across instars. The biological meanings of waveforms were based on visual observations, comparison with waveforms of adults, and histological studies. Np represents the insect resting or walking on soybean pod surface. Eh1 represents the first contact between the mouthparts (stylets) and plant tissue. Eh2 represents xylem sap ingestion, and Eh3 represents seed activities (including tegument and endosperm). The number of waveform events did not differ among instars for all waveforms. However, for Eh3, fifth instars performed more activities than other instars. The second instars had the smallest value, and third and fourth instars had intermediate values. For total duration, all waveforms differed among instars. Np duration was shorter for third compared with second and fourth instars and intermediate for fifth instar. For Eh1, second and third instars had the longest duration (1.5× to 2× greater) compared with fourth and fifth instars. For Eh2 and Eh3, the second-instar showed the longest (~2× greater) and shortest durations, respectively. Overall, this study provides important insights into the feeding behavior of E. heros nymphs so that effective pest management programs can be developed to contain this pest.
Desiccation tolerance of Termitidae termites in relation to their nest type
Authors: Wanthathaen Chatchaton , Chiu Chun-I , Chiu Ming-Chih , Leelayouthyotin Suchart , Krutmuang Patcharin , Li Hou-Feng , Sripontan Yuwatida
Published: July 2023

The family Termitidae is renowned for its diverse nesting behaviors, with the evolution of epigeal and arboreal nests hypothesized to increase desiccation stress due to greater exposure to air. However, these nests may also alleviate desiccation stress through humidity regulation. To explore the implications of acquiring epigeal and arboreal nests, we investigated desiccation tolerance traits in 16 Termitidae termite species with varying nest types and analyzed trait correlations. Principal component analysis revealed that termites constructing epigeal and arboreal nests exhibited reduced water loss rates and enhanced survival under desiccated conditions. Furthermore, termites building arboreal nests displayed a notably higher water content. Redundancy analysis demonstrated that nest types accounted for a substantial portion (57.2%) of the observed variation in desiccation tolerance. These findings support the hypothesis that epigeal and arboreal nests in termites are associated with increased desiccation stress and increased desiccation tolerance. These findings highlight the role of nest type in influencing desiccation tolerance mechanisms and water regulation strategies in termites.
Primary percutaneous closure of a traumatic ventricular septal defect after stab wound to the chest: a case report
Authors: Solórzano Vázquez Marco Alejandro , Medina Torres Oscar Samuel , Tiscareño Villanueva Ashby Daniel , Villar Valencia Cristian Adrián
Published: July 2023

Background

Traumatic ventricular septal defects (VSDs) are life-threatening complications of blunt or stab chest trauma. The standard of care is surgical closure or secondary percutaneous closure due to high surgical risk because of recent sternotomy.

Case summary

We present a 22-year-old male with an ice pick–related VSD. It was successfully closed by primary percutaneous approach. After 6 months, the echo Doppler shows no residual shunt, normal pulmonary artery pressure, and normal biventricular function.

Discussion

To our knowledge, this is one of the first primary percutaneous closures for knife-related VSD. Early diagnosis and treatment can prevent heart failure and long-term complications. Less necrotic tissue surrounding the VSD compared with post-infarction (PI) VSD allows for early and secure treatment. Percutaneous closure is a feasible and effective choice even in patients who had no prior sternotomy or who reject surgery as a primary treatment strategy.
Non-suppression of renin by renal cysts in a subset of patients with primary aldosteronism—a prospective observational single center study
Authors: Ylänen Antero , Pörsti Ilkka , Nevalainen Riikka , Hinkka Tero , Huhtala Heini , Matikainen Niina , Hämäläinen Esa , Niemelä Onni , Nevalainen Pasi I
Published: July 2023

Background

Screening for primary aldosteronism is based on measuring aldosterone-to-renin ratio. Non-suppressed renin may cause false negative screening results, and such patients may miss focused, potentially curable treatment. We investigated the association between renal cysts and non-suppressed plasma renin.

Methods

Altogether, 114 consecutive patients with confirmed primary aldosteronism undergoing adrenal vein sampling were prospectively recruited between October 7, 2020 and December 30, 2021. During the procedure, plasma samples for renin analyses were collected from the right and left renal veins and the inferior vena cava. Renal cysts were identified using contrast-enhanced computed tomography.

Results

Renal cysts were found in 58.2% of the 114 patients. Neither screening nor renal vein renin concentrations were significantly different in patients with and without cysts, or when the kidneys with and without cysts were evaluated. However, cysts were significantly more prevalent in the “high-normal renin” group (cut point 23.0 mU/L) than in the “low to low-normal renin” group (90.9%, n = 11 vs. 56.0%, n = 102, P = .027, respectively). All patients ≤50 years of age in the “high-normal renin” group had renal cysts. Strong correlations were found between renin concentrations in the right and left renal veins (r = .984), and between renin concentration and renin activity in the inferior vena cava (r = .817).

Conclusion

Renal cysts are found in the majority of patients with primary aldosteronism, and they may interfere with diagnostics, especially in patients aged 50 years or less. In patients with non-suppressed renin due to renal cysts, aldosterone-to-renin ratio below the diagnostic threshold does not always exclude the diagnosis of primary aldosteronism.