bluuebunny/crossref_metadata_2025 huggingface dataset:
A Stochastic Algorithm Based on Cable-stayed Bridges Model for Stochastic Optimization in Machine Learning
Authors: Tai Linguang , Shan Feng , Wang Ruibin , Wu Yulun , Li Xinjian , Yao Qinmin , Yan Gang , Ouyang Chen , Yuan Gonglin
Published: October 2023

This paper takes the economic cost of road design as the objective function to study the optimization of road construction cost. It is well-know that stochastic optimization is widely regarded as one of the most important and difficult problems in optimization and machine learning. It is noted that various methods for stochastic optimization problems are sensitive to the learning rate (step-size), which is usually underestimated. Therefore, two new stochastic conjugate gradient algorithms are proposed in this paper. We adapt two modified line search techniques to set the stochastic optimization. One uses the modified Armijo line search technology, the other uses the modified weak Wolfe-Powell line search technology. The new search direction has the properties of sufficient descent and trust region, which makes the establishment of global convergence of the two algorithms very understandable and clear. Finally, numerical experiments show that the two new stochastic conjugate gradient methods are competitive compared with other classical methods.
Binary search of the optimal cut-point value in ROC analysis using the F1 score
Authors: Tan Swee Chuan , Zhu Siying
Published: October 2023

This paper introduces a binary search algorithm for determining the optimal probability cut-point value (C) of binary classifiers. Cut-points are operating points on the receiver operating characteristic curve that divide positive and negative predictions. Compared to the traditional exhaustive search for optimal C value, the proposed method offers execution time efficiency (O(log2(k))) and a small cut-point error of 1/2
n
after k steps of binary search. Traditionally, the optimal C value is determined by stepping through all possible C values. This search is uninformed because there is no indication of the search direction. To address this issue, we derive the expectation of the F-Measure (aka F1 score); and use it to guide the search process. Specifically, by comparing the F-Measure at the current cut-point with the F-Measure at expected cut-point, we can use the information to adjust C dynamically towards the optimal cut-point, resulting in optimal model performance. Our results on two classifiers trained from disease classification datasets suggest that the algorithm is robust and efficient, as compared to the traditional methods.
An effective mathematical model of cardiac electrical activities for Bundle Branch Blocks
Authors: Elkaranshawy Hesham , Mohammed Hala , Elabsy Hanaa
Published: October 2023

In this paper a mathematical model of cardiac induction system is developed. Sinoatrial node (SA), atrioventricular node (AV) and His Purkinje system (HP) are represented by modified Van der Pol-type oscillators (VDP) connected with time-delay coupling. Atrial and ventricular muscles are modeled using modified Aliev-Panfilov equations (AP), with stimulation current from the related pacemakers, to represent the P, QRS, Ta, and T waves. The main aim of this paper is to model bundle branch blocks (BBBs) for right (RBBB) and left (LBBB) branches. In fact, the right and left ventricles are directly affected by these blocks since the HP bundle is composed of right and left bundle branches that provide electrical signals, respectively, to the right and left ventricles. Four VDP oscillators are utilized, one for each of SA, AV, right HP, and left HP. The depolarization of the right and left ventricular muscles are represented by two systems of AP equations to produce right QRS and left QRS waves. The results of the simulation are compared with real normal and pathological electrocardiograms (ECGs) to show the effectiveness and the accuracy of the proposed model. The simulation proves that the model can reproduce the blocks in the HP bundle branches.
Flow Prediction for Hydropower Generation using LMST Neural Networks
Authors: Achig Roberto Salazar , Gonzales J A , Hidalgo C A
Published: October 2023

The objective of this investigation is to predict the necessary flow to satisfy the demand in order to guarantee the generation of energy in a hydropower, for which the artificial neural network LMST (Long Short-Term Memory) was used. In this context, in this article, historical data from the years 2010 to 2019 of flow and power of the plant was used, which were provided by it, in the first instance the data was purified to group them and graph the heat diagram with which the variables of interest were determined, then the training was carried out with which the network was structured with 10 neurons, 2 hidden layers, 2 freezing layers and 1 output layer. In addition, the RMSprop optimizer was selected with 10 numbers of delays with which an absolute error of 5.12% was obtained, finally tests were made comparing the results obtained in the training with data from one day after those that were used in the training and testing database. It is worth mentioning that by predicting the flow for the production of electrical energy, it contributes to the National Development Plan “Toda una Vida” of Ecuador, which is why it focuses on optimizing the use of water resources for required production levels.
Negative thermal expansion mechanical metamaterial using the swastika shape
Authors: Lim Teik-Cheng
Published: October 2023

Materials and structures operating under thermal fluctuation encounter thermal expansion and/or thermal stresses, which require components that allow expansion compensation in certain directions and zero expansion in other directions. A 2D mechanical metamaterial with negative thermal expansion and zero thermal expansion in the in-plane and out-of-plane directions, respectively, is established herein by inspiration from the swastika shape. The swastika units are rigid and are interconnected to each other by positioning the connecting materials, which possess high thermal expansion, at the inner surfaces of the swastika arms. In this way, thermal expansion of the connecting materials tends to draw the swastika units towards each other, thereby generating an overall thermal contraction. Theoretical results indicate that the negativity of the thermal expansion is enhanced by the size of the connecting materials, but suppressed by the size of the swastika units. The results also reveal that the connecting material thickness and the swastika arm length exert major roles while the connecting material length and the swastika arm width play minor roles in influencing the effective thermal expansion coefficient of the metamaterial. These observations offer solutions for quick coarse-tuning and slow fine-tuning of the metamaterial’s CTE. Although swastikas have cultural, religious, and even political connotations, the author would like to clarify that the swastika considered herein has been used purely for its geometric shape. The author does not intend to convey any cultural or ideological meaning by its use in this article.
Optimization of a punch shape with a doubly connected contact domain
Authors: Shyshkanova G , Walther A
Published: October 2023

The objective is to optimize the distribution of the normal pressure under a rigid punch (indenter) having a doubly connected contact domain close to a circular ring and interacting with a homogeneous isotropic elastic half-space. In the problem considered here, the required design variable is the punch shape. The functional to be minimized is the root-mean-square deviation of the present pressure distribution from some given distribution. An analytical technique is developed for solving the problem for the punches with doubly connected shape, by reducing to a sequence of similar problems for the circular ring punches using expansions of the simple layer potential. The method of expansion in terms of a small parameter is used. The simple layer potential expansion is proposed when mapping a doubly connected integration domain onto a circular ring by transforming the integration variables and transforming the coordinates of the pole of the kernel. As a result, a set of similar problems was obtained for a circular ring to determine the functions characterizing the normal pressure distribution over a non-circular ring contact domain under the punch, as well as the normal displacements, from where the optimal punch shape is determined.
A lubrication model and static characteristics analysis for bubbly oil lubricated journal bearings based on theory of multiphase mixtures
Authors: Li Shaohua , Jiang Shuyun , Lin Xiaohui
Published: October 2023

A bubbly oil lubrication model is established in this paper. Interface effect is included in this new model. Two single-component coupled nonlinear generalized Reynolds-type equations are derived based on the theory of multiphase-mixture flow and the second law of thermodynamics. The static characteristics of the finite journal bearings with bubbly oil lubrication are predicted using this theoretical model. The results show that the friction torque is significantly reduced compared to pure oil lubrication at a higher initial bubble volume fraction, and the sidle leakage are significantly increased compared to pure oil lubrication.
Design and Analysis of Brake Drum using Finite Element Analysis
Authors: Choy H Y , Siaw M G , Pung K Q
Published: October 2023

Because of the need for safety, braking performance has become a very important factor for automotive manufacturers and passengers. Despite all the stresses experienced by the drum brake doesn’t damage the drum due to high tensile strength but the drum may fail under fatigue loading. The critical region of concentrated stress is determined, and appropriate modifications are being made to improve it. The distribution of stress and the heat dissipation obtained from the result of the analysis are employed as input for the failure region. The findings of stress and thermal analysis are crucial for improving the component design at the first stage of development. The objectives of this study are to modify and improve the circumferential strength and heat dissipation and to optimize the design of the drum brake with simulation using Finite Element Analysis. The simulation was run on the initial model and modified on its to make it better. it shows that 27.33% decrease in maximum von Mises stress. Thermal analysis for heat flux on the material will show the ability of heat dissipation. Overall, It has been determined that aluminium alloy is the optimum material for drum brake design in terms of total heat flux.
Gelatin scaffold ameliorates proliferation & stem cell differentiation into the hepatic like cell and support liver regeneration in partial-hepatectomized mice model
Authors: Kumari Kshama , Tandon Simran , Ghosh Sourabh , Baligar Prakash
Published: October 2023

Stem cell-based tissue engineering is an emerging tool for developing functional tissues of choice. To understand pluripotency and hepatic differentiation of mouse embryonic stem cells (mESCs) on a three-dimensional (3D) scaffold, we established an efficient approach for generating hepatocyte-like cells (HLCs) from hepatoblast cells. We developed porous and biodegradable scaffold, which was stimulated with exogenous growth factors and investigated stemness and differentiation capacity of mESCs into HLCs on the scaffold in-vitro. In animal studies, we had cultured mESCs-derived hepatoblast-like cells on the scaffold and then, transplanted them into the partially hepatectomized C57BL/6 male mice model to evaluate the effect of gelatin scaffold on hepatic regeneration. The 3D culture system allowed maintenance of stemness properties in mESCs. The step-wise induction of mESCs with differentiation factors leads to the formation of HLCs and expressed liver-specific genes, including albumin, hepatocyte nucleic factor 4 alpha, and cytokeratin 18. In addition, cells also expressed Ki67, indicating cells are proliferating. The secretome showed expression of albumin, urea, creatinine, alanine transaminase, and aspartate aminotransferase. However, the volume of the excised liver which aids regeneration has not been studied. Our results indicate that hepatoblast cells on the scaffold implanted in PH mouse indicates that these cells efficiently differentiate into HLCs and cholangiocytes, forming hepatic lobules with central and portal veins, and bile duct-like structures with neovascularization. The gelatin scaffold provides an efficient microenvironment for liver differentiation and regeneration both in-vitro and in-vivo. These hepatoblasts cells would be a valuable source for 3D liver tissue engineering/transplantation in liver diseases.
Assumptions about prior fossil fuel inventories impact our ability to estimate posterior net CO2 fluxes that are needed for verifying national inventories
Authors: Oda Tomohiro , Feng Liang , Palmer Paul I , Baker David F , Ott Lesley E
Published: October 2023

Monitoring national and global greenhouse gas (GHG) emissions is a critical component of the Paris Agreement, necessary to verify collective activities to reduce GHG emissions. Top-down approaches to infer GHG emission estimates from atmospheric data are widely recognized as a useful tool to independently verify emission inventories reported by individual countries under the United Nation Framework Convention on Climate Change. Conventional top-down atmospheric inversion methods often prescribe fossil fuel CO2 emissions (FFCO2) and fit the resulting model values to atmospheric CO2 observations by adjusting natural terrestrial and ocean flux estimates. This approach implicitly assumes that we have perfect knowledge of FFCO2 and that any gap in our understanding of atmospheric CO2 data can be explained by natural fluxes; consequently, it also limits our ability to quantify non-FFCO2 emissions. Using two independent FFCO2 emission inventories, we show that differences in sub-annual emission distributions are aliased to the corresponding posterior natural flux estimates. Over China, for example, where the two inventories show significantly different seasonal variations in FFCO2, the resulting differences in national-scale flux estimates are small but are significant on the subnational scale. We compare natural CO2 flux estimates inferred from in-situ and satellite observations. We find that sparsely distributed in-situ observations are best suited for quantifying natural fluxes and large-scale carbon budgets and less suitable for quantifying FFCO2 errors. Satellite data provide us with the best opportunity to quantify FFCO2 emission errors; a similar result is achievable using dense, regional in-situ measurement networks. Enhancing the top-down flux estimation capability for inventory verification requires a coordinated activity to (a) improve GHG inventories; (b) extend methods that take full advantage of measurements of trace gases that are co-emitted during combustion; and (c) improve atmospheric transport models.
Distinguishing the main climatic drivers to the variability of gross primary productivity at global FLUXNET sites
Authors: Zhou Hao , Yue Xu , Wang Bin , Tian Chenguang , Lu Xiaofei , Zhu Jun , Cao Yang
Published: October 2023

Climate exerts both short-term and long-term impacts on the ecosystem carbon assimilation. However, the main climatic drivers for the variability of gross primary productivity (GPP) remain unclear across various timescales and vegetation types. Here, we combine the state-of-the-art machine learning algorithms with a well-established explanatory method to explore the impacts of climatic factors on long-term GPP variability at global FLUXNET sites across four timescales and six plant functional types. Results show that diffuse shortwave radiation (SWdif) dominates GPP variability at the sub-daily (half-hourly to three hourly) timescales especially for the tree species, and acts as the secondary contributor after air temperature at the daily or longer timescales. Attribution analyses further showed that the main effects of SWdif are much higher than their interactive effects with other climatic factors in regulating the GPP variability. By identifying the main climatic drivers, this study improves the understanding of the climate-driven GPP variability and provides important implications for the future projection of ecosystem carbon assimilation under global climate change.
Thermal form-factor expansion of the dynamical two-point functions of local operators in integrable quantum chains
Authors: Göhmann Frank , Kozlowski Karol K , Minin Mikhail D
Published: October 2023

Evaluating a lattice path integral in terms of spectral data and matrix elements pertaining to a suitably defined quantum transfer matrix, we derive form-factor series expansions for the dynamical two-point functions of arbitrary local operators in fundamental Yang–Baxter integrable lattice models at finite temperature. The summands in the series are parameterised by solutions of the Bethe Ansatz equations associated with the eigenvalue problem of the quantum transfer matrix. We elaborate on the example of the XXZ chain for which the solutions of the Bethe Ansatz equations are sufficiently well understood in certain limiting cases. We work out in detail the case of the spin-zero operators in the antiferromagnetic massive regime at zero temperature. In this case the thermal form-factor series turn into series of multiple integrals with fully explicit integrands. These integrands factorize into an operator-dependent part, determined by the so-called Fermionic basis, and a part which we call the universal weight as it is the same for all spin-zero operators. The universal weight can be inferred from our previous work. The operator-dependent part is rather simple for the most interesting short-range operators. It is determined by two functions ρ and ω for which we obtain explicit expressions in the considered case. As an application we rederive the known explicit form-factor series for the two-point function of the magnetization operator and obtain analogous expressions for the magnetic current and the energy operators.
Characterisation of weld bead and microhardness of SS316L weld overlays on S355J2+N steel using GTAW under E-type magnet
Authors: Raj Prem , Gill Jaspal Singh
Published: October 2023

In this study, a three-pole (E-type) electromagnet with magnetic configurations north-south-north (NSN) and south-north-south (SNS) was installed in the GTAW process to generate a combination of two symmetrically transverse external magnetic fields around the weld arc and the molten pool. The effects of magnetic fields obtained by these two types of magnetic configurations (NSN and SNS) on the weld bead characteristics and microhardness in GTAW were analysed. In these experiments, high-strength low alloy (HSLA) S355J2+N grade with a thickness of 10 mm was selected as the substrate material and S316L as the filler wire. Using magnetic fields during the welding process successfully enhanced the weld bead appearance and shape and improved the mechanical characteristics of weld overlays. It was also observed that for different values of excitation current, magnetic fields generated with both configurations ( i.e., NSN and SNS) provide greater bead width, a higher penetration shape factor, and higher microhardness values in comparison to specimens welded with conventional GTAW. The NSN and SNS configurations of the E-type magnet improve the penetration shape factor by 58% and 46%, respectively. These configurations were more suitable for weld overlays (cladding) and hardfacing. However, the observations indicated an enhancement in microhardness for all excitation current values by employing the NSN and SNS magnetic configurations.
Experimental and numerical simulation studies of CuO thin films based solar cells
Authors: Benaissa N , Garmim T , El Boughdadi M , El Jouad Z , Louardi A , Hartiti B , Monkade M
Published: October 2023

This study presents an experimental investigation into the solar performance of copper oxide (CuO) thin films. These CuO films were fabricated using the spray pyrolysis technique, and their structural, morpholigical, optical, and electrical properties were examined in relation to the effect of layer thickness. Additionally, we employed SCAPS-1D software to perform numerical simulations of CuO-based solar cells. Moreover, the band gap energy was discovered to be between 1.14 eV, 1.53 eV and 1.61. Using the four-point probe, the electrical resistivity was computed and the high conductivity found corresponds to the sample generated with a film thickness of t = 292 nm, is 7.52 (×10−3 Ω.cm)−1. The CuO/TiO2/FTO solar cell configuration showed a potential efficiency of 13.38% when the absorber layer thickness is 292 nm and the band gap value is 1.53 eV. Furthermore, based on the band gap energy value of 1.53 eV the investigation has been deepened by expanding the range of absorber layer thickness and temperature to thoroughly examine their impact on solar cell performance. Moreover, the CuO/TiO2 solar cells curves of external quantum efficiency (EQE) for various CuO layer thicknesses were determined.
CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides
Authors: Li Zhongshen , Jin Junru , He Wenjia , Long Wentao , Yu Haoqing , Gao Xin , Nakai Kenta , Zou Quan , Wei Leyi
Published: October 2023

NcRNA-encoded small peptides (ncPEPs) have recently emerged as promising targets and biomarkers for cancer immunotherapy. Therefore, identifying cancer-associated ncPEPs is crucial for cancer research. In this work, we propose CoraL, a novel supervised contrastive meta-learning framework for predicting cancer-associated ncPEPs. Specifically, the proposed meta-learning strategy enables our model to learn meta-knowledge from different types of peptides and train a promising predictive model even with few labeled samples. The results show that our model is capable of making high-confidence predictions on unseen cancer biomarkers with only five samples, potentially accelerating the discovery of novel cancer biomarkers for immunotherapy. Moreover, our approach remarkably outperforms existing deep learning models on 15 cancer-associated ncPEPs datasets, demonstrating its effectiveness and robustness. Interestingly, our model exhibits outstanding performance when extended for the identification of short open reading frames derived from ncPEPs, demonstrating the strong prediction ability of CoraL at the transcriptome level. Importantly, our feature interpretation analysis discovers unique sequential patterns as the fingerprint for each cancer-associated ncPEPs, revealing the relationship among certain cancer biomarkers that are validated by relevant literature and motif comparison. Overall, we expect CoraL to be a useful tool to decipher the pathogenesis of cancer and provide valuable information for cancer research. The dataset and source code of our proposed method can be found at https://github.com/Johnsunnn/CoraL.
Multi-shelled ECIF: improved extended connectivity interaction features for accurate binding affinity prediction
Authors: Shiota Koji , Akutsu Tatsuya
Published: October 2023

Motivation

Extended connectivity interaction features (ECIF) is a method developed to predict protein–ligand binding affinity, allowing for detailed atomic representation. It performed very well in terms of Comparative Assessment of Scoring Functions 2016 (CASF-2016) scoring power. However, ECIF has the limitation of not being able to adequately account for interatomic distances.

Results

To investigate what kind of distance representation is effective for P-L binding affinity prediction, we have developed two algorithms that improved ECIF’s feature extraction method to take distance into account. One is multi-shelled ECIF, which takes into account the distance between atoms by dividing the distance between atoms into multiple layers. The other is weighted ECIF, which weights the importance of interactions according to the distance between atoms. A comparison of these two methods shows that multi-shelled ECIF outperforms weighted ECIF and the original ECIF, achieving a CASF-2016 scoring power Pearson correlation coefficient of 0.877.

Availability and implementation

All the codes and data are available on GitHub (https://github.com/koji11235/MSECIFv2).
stVAE deconvolves cell-type composition in large-scale cellular resolution spatial transcriptomics
Authors: Li Chen , Chan Ting-Fung , Yang Can , Lin Zhixiang
Published: October 2023

Motivation

Recent rapid developments in spatial transcriptomic techniques at cellular resolution have gained increasing attention. However, the unique characteristics of large-scale cellular resolution spatial transcriptomic datasets, such as the limited number of transcripts captured per spot and the vast number of spots, pose significant challenges to current cell-type deconvolution methods.

Results

In this study, we introduce stVAE, a method based on the variational autoencoder framework to deconvolve the cell-type composition of cellular resolution spatial transcriptomic datasets. To assess the performance of stVAE, we apply it to five datasets across three different biological tissues. In the Stereo-seq and Slide-seqV2 datasets of the mouse brain, stVAE accurately reconstructs the laminar structure of the pyramidal cell layers in the cortex, which are mainly organized by the subtypes of telencephalon projecting excitatory neurons. In the Stereo-seq dataset of the E12.5 mouse embryo, stVAE resolves the complex spatial patterns of osteoblast subtypes, which are supported by their marker genes. In Stereo-seq and Pixel-seq datasets of the mouse olfactory bulb, stVAE accurately delineates the spatial distributions of known cell types. In summary, stVAE can accurately identify spatial patterns of cell types and their relative proportions across spots for cellular resolution spatial transcriptomic data. It is instrumental in understanding the heterogeneity of cell populations and their interactions within tissues.

Availability and implementation

stVAE is available in GitHub (https://github.com/lichen2018/stVAE) and Figshare (https://figshare.com/articles/software/stVAE/23254538).
KDM6A/UTX promotes spermatogenic gene expression across generations and is not required for male fertility
Authors: Walters Benjamin W , Rainsford Shannon R , Heuer Rachel A , Dias Nicolas , Huang Xiaofang , de Rooij Dirk , Lesch Bluma J
Published: October 2023

Paternal chromatin undergoes extensive structural and epigenetic changes during mammalian spermatogenesis, producing sperm with an epigenome optimized for the transition to embryogenesis. Lysine demethylase 6a (KDM6A, also called UTX) promotes gene activation in part via demethylation of H3K27me3, a developmentally important repressive modification abundant throughout the epigenome of spermatogenic cells and sperm. We previously demonstrated increased cancer risk in genetically wild-type mice derived from a paternal germ line lacking Kdm6a (Kdm6a cKO), indicating a role for KDM6A in regulating heritable epigenetic states. However, the regulatory function of KDM6A during spermatogenesis is not known. Here, we show that Kdm6a is transiently expressed in spermatogenesis, with RNA and protein expression largely limited to late spermatogonia and early meiotic prophase. Kdm6a cKO males do not have defects in fertility or the overall progression of spermatogenesis. However, hundreds of genes are deregulated upon loss of Kdm6a in spermatogenic cells, with a strong bias toward downregulation coinciding with the time when Kdm6a is expressed. Misregulated genes encode factors involved in chromatin organization and regulation of repetitive elements, and a subset of these genes was persistently deregulated in the male germ line across two generations of offspring of Kdm6a cKO males. Genome-wide epigenetic profiling revealed broadening of H3K27me3 peaks in differentiating spermatogonia of Kdm6a cKO mice, suggesting that KDM6A demarcates H3K27me3 domains in the male germ line. Our findings highlight KDM6A as a transcriptional activator in the mammalian male germ line that is dispensable for spermatogenesis but important for safeguarding gene regulatory state intergenerationally.
Update of the international HerniaSurge guidelines for groin hernia management
Authors: Stabilini Cesare , van Veenendaal Nadine , Aasvang Eske , Agresta Ferdinando , Aufenacker Theo , Berrevoet Frederik , Burgmans Ine , Chen David , de Beaux Andrew , East Barbora , Garcia-Alamino Jose , Henriksen Nadia , Köckerling Ferdinand , Kukleta Jan , Loos Maarten , Lopez-Cano Manuel , Lorenz Ralph , Miserez Marc , Montgomery Agneta , Morales-Conde Salvador , Oppong Chris , Pawlak Maciej , Podda Mauro , Reinpold Wolfgang , Sanders David , Sartori Alberto , Tran Hanh Minh , Verdaguer Mireia , Wiessner Reiko , Yeboah Michael , Zwaans Willem , Simons Maarten
Published: October 2023

Background

Groin hernia repair is one of the most common operations performed globally, with more than 20 million procedures per year. The last guidelines on groin hernia management were published in 2018 by the HerniaSurge Group. The aim of this project was to assess new evidence and update the guidelines. The guideline is intended for general and abdominal wall surgeons treating adult patients with groin hernias.

Method

A working group of 30 international groin hernia experts and all involved stakeholders was formed and examined all new literature on groin hernia management, available until April 2022. Articles were screened for eligibility and assessed according to GRADE methodologies. New evidence was included, and chapters were rewritten. Statements and recommendations were updated or newly formulated as necessary.

Results

Ten chapters of the original HerniaSurge inguinal hernia guidelines were updated. In total, 39 new statements and 32 recommendations were formulated (16 strong recommendations). A modified Delphi method was used to reach consensus on all statements and recommendations among the groin hernia experts and at the European Hernia Society meeting in Manchester on October 21, 2022.

Conclusion

The HerniaSurge Collaboration has updated the international guidelines for groin hernia management. The updated guidelines provide an overview of the best available evidence on groin hernia management and include evidence-based statements and recommendations for daily practice. Future guideline development will change according to emerging guideline methodology.
When mass culture meets high culture: reality television and big data at the art museum
Authors: Griffin Hollis
Published: October 2023

This article examines cultural beliefs related to reality television and social media, using a museum installation as a point of departure for examining the persistence of particular ideas about taste and aesthetic value as they relate to mass media in a historical moment when audiences are more frequently small and specialized. Its case study is an artwork that creates a data visualization from social media analytics related to American Idol, America’s Got Talent, America’s Next Top Model, and America’s Best Dance Crew. Using discourse analysis, the article unpacks how the installation establishes connections between televised contests, social media activity, and U.S. national identity. The author argues that the installation predicates its critique of reality television and social media on collapsing the differences between disparate programs, animating hierarchies of taste between various publics, and simplifying emergent industry practices related to big data.
Relational hinterlands in the USA have become disconnected from major global centres
Authors: Buchholz Maximilian , Bathelt Harald
Published: October 2023

Research identifies strong concentrations of economic activity in dynamic, major city regions, whereas shifts in economic linkages between these and smaller, less-advantaged city regions have been less investigated. Using data on firms’ investment/disinvestment decisions between 1993 and 2017, we show that the majority of ‘relational hinterlands’ (smaller, non-contiguous city regions with at least 1 investment tie to a global centre in 1993) in the USA have become disconnected from major US ‘global centres’ (globally integrated city regions). Relational hinterlands which lost connectivity to the global centres are also disadvantaged in many other ways. While global centres have become increasingly connected to other global centres in the USA and abroad, relational hinterlands have become increasingly disconnected from centres of economic growth.
Framework for converting mechanistic network models to probabilistic models
Authors: Goyal Ravi , De Gruttola Victor , Onnela Jukka-Pekka
Published: October 2023

There are two prominent paradigms for the modelling of networks: in the first, referred to as the mechanistic approach, one specifies a set of domain-specific mechanistic rules that are used to grow or evolve the network over time; in the second, referred to as the probabilistic approach, one describes a model that specifies the likelihood of observing a given network. Mechanistic models (models developed based on the mechanistic approach) are appealing because they capture scientific processes that are believed to be responsible for network generation; however, they do not easily lend themselves to the use of inferential techniques when compared with probabilistic models. We introduce a general framework for converting a mechanistic network model (MNM) to a probabilistic network model (PNM). The proposed framework makes it possible to identify the essential network properties and their joint probability distribution for some MNMs; doing so makes it possible to address questions such as whether two different mechanistic models generate networks with identical distributions of properties, or whether a network property, such as clustering, is over- or under-represented in the networks generated by the model of interest compared with a reference model. The proposed framework is intended to bridge some of the gap that currently exists between the formulation and representation of mechanistic and PNMs. We also highlight limitations of PNMs that need to be addressed in order to close this gap.
Anorectal Manometry in Patients With Fecal Incontinence After Ileal Pouch–Anal Anastomosis for Ulcerative Colitis: A Cohort Study
Authors: Young Sigrid , Lee Briton , Smukalla Scott , Axelrad Jordan , Chang Shannon
Published: October 2023

Background

Fecal incontinence commonly occurs in patients with ulcerative colitis and ileal pouch–anal anastomosis. There is a paucity of manometric data in pouch patients. We aimed to better define manometric parameters in pouch patients with fecal incontinence.

Methods

We compared clinical and manometric variables in ulcerative colitis patients with pouch and fecal incontinence to ulcerative colitis patients with pouch without fecal incontinence and to non-ulcerative colitis patients with fecal incontinence. Manometric data for the 3 cohorts were compared to established normative data. An independent-samples t-test was performed for continuous variables, and chi-square test was used for categorical variables. Logistic regression was performed to identify predictors of incontinence in pouch patients (P < .05).

Results

Among 26 pouch patients with fecal incontinence (73% female), 26 pouch patients without fecal incontinence (35% female), and 84 patients with fecal incontinence without ulcerative colitis (68% female), there were no differences in anorectal pressures between patients with fecal incontinence. Lower pressures were observed in pouch patients with fecal incontinence compared to those without fecal incontinence. Resting pressure was similar between pouch patients with fecal incontinence and healthy controls (60.9 ± 36.1 mmHg vs. 66.9 ± 3.2 mmHg, P = .40). Female sex (P = .019) and defecatory disorders (P = .033) each independently predicted fecal incontinence in pouch patients.

Conclusions

Pouch patients with fecal incontinence have lower anorectal pressures compared to pouch patients without incontinence, though have similar pressures to non-ulcerative colitis patients with fecal incontinence. Pouch patients with fecal incontinence have similar resting pressures as healthy controls. Distinct manometric normative values for pouch patients are needed.
Is Occupation a Risk Factor for Developing Inflammatory Bowel Disease? A Case–Control Study
Authors: Mauriz-Barreiro Violeta , Ruano-Raviña Alberto , Ferreiro-Iglesias Rocío , Bastón-Rey Iria , Calviño-Suárez Cristina , Nieto-García Laura , Porto-Silva Sol , Martínez-Seara Xurxo , Domínguez-Munoz J Enrique , Barreiro-de Acosta Manuel
Published: October 2023

Background and aims

The role of occupation is uncertain in the onset of inflammatory bowel diseases. The aim of this study is to identify if there is a role of occupation in these diseases.

Materials and methods

A case–control study with incident cases with inflammatory bowel diseases was designed. Cases and controls were recruited simultaneously and controls followed a sex and age frequency matching with cases. A detailed questionnaire was completed by all the participants. To analyze the results, a logistic regression was used. A subgroup analysis was performed for each inflammatory bowel disease.

Results

A total of 141 patients with incident inflammatory bowel disease (80 ulcerative colitis, 55 Crohn’s disease, and 6 unclassified colitis) and 114 controls were included. There were no statistically significant differences in type of work, working hours, contact with animals, or physical activity at work between inflammatory bowel disease patients and controls. After stratifying results according to type of IBD, there were no statistically significant differences either.

Conclusions

There seems to be no risk for inflammatory bowel disease onset regarding the type of work, working hours, contact with animals, or sedentariness.
Imaging in patients with cardiovascular implantable electronic devices: part 1—imaging before and during device implantation. A clinical consensus statement of the European Association of Cardiovascular Imaging (EACVI) and the European Heart Rhythm Association (EHRA) of the ESC
Authors: Stankovic Ivan , Voigt Jens-Uwe , Burri Haran , Muraru Denisa , Sade Leyla Elif , Haugaa Kristina Hermann , Lumens Joost , Biffi Mauro , Dacher Jean-Nicolas , Marsan Nina Ajmone , Bakelants Elise , Manisty Charlotte , Dweck Marc R , Smiseth Otto A , Donal Erwan ,   Reviewers: This document was reviewed by members of the 2020-2022 EACVI Scientific Documents Committee:, Andreini Daniele , Bäck Magnus , Bertrand Philippe B , Keenan Niall , Neglia Danilo ,   by the 2020–2022 EACVI President:, Cosyns Bernard
Published: October 2023

More than 500 000 cardiovascular implantable electronic devices (CIEDs) are implanted in the European Society of Cardiology countries each year. The role of cardiovascular imaging in patients being considered for CIED is distinctly different from imaging in CIED recipients. In the former group, imaging can help identify specific or potentially reversible causes of heart block, the underlying tissue characteristics associated with malignant arrhythmias, and the mechanical consequences of conduction delays and can also aid challenging lead placements. On the other hand, cardiovascular imaging is required in CIED recipients for standard indications and to assess the response to device implantation, to diagnose immediate and delayed complications after implantation, and to guide device optimization. The present clinical consensus statement (Part 1) from the European Association of Cardiovascular Imaging, in collaboration with the European Heart Rhythm Association, provides comprehensive, up-to-date, and evidence-based guidance to cardiologists, cardiac imagers, and pacing specialists regarding the use of imaging in patients undergoing implantation of conventional pacemakers, cardioverter defibrillators, and resynchronization therapy devices. The document summarizes the existing evidence regarding the use of imaging in patient selection and during the implantation procedure and also underlines gaps in evidence in the field. The role of imaging after CIED implantation is discussed in the second document (Part 2).
The impact of genetic background during laboratory evolution of Pseudomonas aeruginosa in a cystic fibrosis-like environment
Authors: Filipow Nicole , Mallon Samantha , Shewaramani Sonal , Kassen Rees , Wong Alex
Published: October 2023

Genetic background has the potential to influence both the tempo and trajectory of adaptive change: Different genotypes of a given species may adopt varied solutions to the same environmental challenge, or they may approach the same solution at different rates. Laboratory selection has been widely used to experimentally examine the evolutionary consequences of variation in genetic background, although largely using genotypes differing by only a few mutations. Here, we leverage natural variation in the bacterium Pseudomonas aeruginosa to investigate whether different adaptive solutions are accessible from distant points of departure on an adaptive landscape. We evolved 17 diverse genotypes in a laboratory medium that partially mimics the lung sputum of cystic fibrosis patients, and we measured changes in 10 phenotypes as well as in fitness. Using phylogenetically informed analyses, we found that genetic background impacted the tempo, but not the trajectory, of phenotypic evolution: Different starting genotypes converged toward similar phenotypes, but at varying rates. Our findings add to a growing body of evidence supporting widespread diminishing return epistasis during adaptation. The importance of genetic background toward the trajectory of adaptation remains inconsistent across experimental systems and conditions.
Transcriptome analysis reveals molecular signature and cell-type difference of Homo sapiens endothelial-to-mesenchymal transition
Authors: Bronson Ronald , Lyu Junfang , Xiong Jianhua
Published: October 2023

Endothelial-to-mesenchymal transition (EndoMT), a specific form of epithelial-to-mesenchymal transition, drives a growing number of human (Homo sapiens) pathological conditions. This emerging knowledge opens a path to discovering novel therapeutic targets for many EndoMT-associated disorders. Here, we constructed an atlas of the endothelial-cell transcriptome and demonstrated EndoMT-induced global changes in transcriptional gene expression. Our gene ontology analyses showed that EndoMT could be a specific checkpoint for leukocyte chemotaxis, adhesion, and transendothelial migration. We also identified distinct gene expression signatures underlying EndoMT across arterial, venous, and microvascular endothelial cells. We performed protein–protein interaction network analyses, identifying a class of highly connected hub genes in endothelial cells from different vascular beds. Moreover, we found that the short-chain fatty acid acetate strongly inhibits the transcriptional program of EndoMT in endothelial cells from different vascular beds across tissues. Our results reveal the molecular signature and cell-type difference of EndoMT across distinct tissue- and vascular-bed-specific endothelial cells, providing a powerful discovery tool and resource value. These results suggest that therapeutically manipulating the endothelial transcriptome could treat an increasing number of EndoMT-associated pathological conditions.
Chromosome-Level Genome Assembly for the Angiosperm Silene conica
Authors: Fields Peter D , Weber Melody M , Waneka Gus , Broz Amanda K , Sloan Daniel B
Published: October 2023

The angiosperm genus Silene has been the subject of extensive study in the field of ecology and evolution, but the availability of high-quality reference genome sequences has been limited for this group. Here, we report a chromosome-level assembly for the genome of Silene conica based on Pacific Bioscience HiFi, Hi-C, and Bionano technologies. The assembly produced 10 scaffolds (1 per chromosome) with a total length of 862 Mb and only ∼1% gap content. These results confirm previous observations that S. conica and its relatives have a reduced base chromosome number relative to the genus's ancestral state of 12. Silene conica has an exceptionally large mitochondrial genome (>11 Mb), predominantly consisting of sequence of unknown origins. Analysis of shared sequence content suggests that it is unlikely that transfer of nuclear DNA is the primary driver of this mitochondrial genome expansion. More generally, this assembly should provide a valuable resource for future genomic studies in Silene, including comparative analyses with related species that recently evolved sex chromosomes.
Critical view on oligo(dT)-based RNA-seq: bias arising, modeling, and mitigating
Authors: Su Qiang , Wang Jun , Kang Kang , Niu Yanqin , Li Shujin , Gou Deming
Published: October 2023

The precise biological interpretation of oligo(dT)-based RNA sequencing (RNA-seq) datasets, particularly in single-cell RNA-seq (scRNA-seq), is invaluable for understanding complex biological systems. However, the presence of biases can lead to misleading results in downstream analysis. This study has now identified two additional biases that are not accounted for in established bias models: poly(A)-tail length bias and fixed-position GC-content bias. These biases have a significant negative impact on the overall quality of oligo(dT)-based RNA-seq data. To address these biases, we have developed a universal bias-mitigating method based on the lower-affinity binding of short and nonanchored oligo(dT) primers to poly(A) tails. This method significantly reduces poly(A) length bias and completely eliminates fixed-position GC bias. Furthermore, the use of short oligo(dT) with impartial binding behavior toward the diverse poly(A) tails renders RNA-seq with more reliable measurements. The findings of this study are particularly beneficial for scRNA-seq datasets, where accurate benchmarking is critical.
Educational Influences on Late-Life Health: Genetic Propensity and Attained Education
Authors: Ericsson Malin , Finch Brian , Karlsson Ida K , Gatz Margaret , Reynolds Chandra A , Pedersen Nancy L , Mosing Miriam A
Published: October 2023

Objectives

The educational gradient in late-life health is well established. Despite this, there are still ambiguities concerning the role of underlying confounding by genetic influences and gene-environment (GE) interplay. Here, we investigate the role of educational factors (attained and genetic propensities) on health and mortality in late life using genetic propensity for educational attainment (as measured by a genome-wide polygenic score, PGSEdu) and attained education.

Methods

By utilizing genetically informative twin data from the Swedish Twin Registry (n = 14,570), we investigated influences of the educational measures, familial confounding as well as the possible presence of passive GE correlation on both objective and subjective indicators of late-life health, that is, the Frailty Index, Multimorbidity, Self-rated health, cardiovascular disease, and all-cause mortality.

Results

Using between-within models to adjust for shared familial factors, we found that the relationship between educational level and health and mortality later in life persisted despite controlling for familial confounding. PGSEdu and attained education both uniquely predicted late-life health and mortality, even when mutually adjusted. Between-within models of PGSEdu on the health outcomes in dizygotic twins showed weak evidence for passive GE correlation (prGE) in the education-health relationship.

Discussion

Both genetic propensity to education and attained education are (partly) independently associated with health in late life. These results lend further support for a causal education-health relationship but also raise the importance of genetic contributions and GE interplay.