bluuebunny/crossref_metadata_2025_split huggingface dataset:
An improved Lagrangian relaxation algorithm based SDN framework for industrial internet hybrid service flow scheduling
Authors: Song Yan , Luo Wenjing , Xu Panfeng , Wei Jianwei , Qi Xiangbo 
Published: March 2022

AbstractThe Industrial Internet is the key for Industry 4.0, and network control in the industrial internet usually requires high reliability and low latency. The industrial internet ubiquitously connects all relevant Internet of things (IoT) sensing and actuating devices, allowing for monitoring and control of multiple industrial systems. Unfortunately, guaranteeing very low end-to-end wait times is particularly challenging because the transmissions must be articulated in time. In the industrial internet, there usually coexist multiple streams. The amount of data for controlling business flows is small, while other business flows (e.g., interactive business flows, sensing business flows) typically transmit large amounts of data across the network. These data flows are mainly processed in traditional switches using a queue-based "store-and-forward" mode for data exchange, consuming much bandwidth and filling up the network buffers. This causes delays in the control flow. In our research, we propose an Software Defined Networking (SDN) framework to reduce such delays and ensure real-time delivery of mixed service flows. The scheduling policy is performed through the northbound Application Programming Interface (API) of the SDN controller so that the dynamic network topology can be satisfied. We use the concept of edge and intermediate switches, where each switch port sends data at a specific time to avoid queuing intermediate switches. We also introduce an improved Langerian relaxation algorithm to select the best path to ensure low latency. Finally, the path rules are deployed to the switches in flow tables through the SDN controller. Our mathematical analysis and simulation evaluation demonstrates that the proposed scheme is more efficient.
Noise-assisted variational quantum thermalization
Authors: Foldager Jonathan , Pesah Arthur , Hansen Lars Kai 
Published: March 2022

AbstractPreparing thermal states on a quantum computer can have a variety of applications, from simulating many-body quantum systems to training machine learning models. Variational circuits have been proposed for this task on near-term quantum computers, but several challenges remain, such as finding a scalable cost-function, avoiding the need of purification, and mitigating noise effects. We propose a new algorithm for thermal state preparation that tackles those three challenges by exploiting the noise of quantum circuits. We consider a variational architecture containing a depolarizing channel after each unitary layer, with the ability to directly control the level of noise. We derive a closed-form approximation for the free-energy of such circuit and use it as a cost function for our variational algorithm. By evaluating our method on a variety of Hamiltonians and system sizes, we find several systems for which the thermal state can be approximated with a high fidelity. However, we also show that the ability for our algorithm to learn the thermal state strongly depends on the temperature: while a high fidelity can be obtained for high and low temperatures, we identify a specific range for which the problem becomes more challenging. We hope that this first study on noise-assisted thermal state preparation will inspire future research on exploiting noise in variational algorithms.
Three-dimensional modelling of the choroidal angioarchitecture in a multi-ethnic Asian population
Authors: Cheong Kai Xiong , Teo Kelvin Yi Chong , Tham Yih Chung , Sim Ralene , Majithia Shivani , Lee Jia Min , Tan Anna Cheng Sim , Cheng Ching-Yu , Cheung Chui Ming Gemmy , Agrawal Rupesh 
Published: March 2022

AbstractThis study aimed to describe the topographic variation of the macula’s choroidal angioarchitecture using three-dimensional (3D) choroidal vascularity index (CVI) of healthy eyes from an Asian population and to investigate the associations of CVI. 50 participants were recruited via stratified randomisation based on subfoveal choroidal thickness from the Singapore Epidemiology of Eye Diseases Study. Macular volume scans were acquired using spectral-domain optical coherence tomography with enhanced depth imaging. CVI was assessed based on B-scan binarisation and choroid segmentation. The 3D CVI of the whole, superior, central, and inferior macula were 62.92 ± 1.57%, 62.75 ± 1.93%, 63.35 ± 1.72%, and 62.66 ± 1.70%, respectively, pairwise comparisons P all > 0.05). 3D CVI (Whole Macula) and 2D CVI (Subfoveal) were associated only with each other and not with other ocular and systemic factors. 2D CVI (Subfoveal) had a moderate agreement with 3D CVI (Central Macula) [intraclass corelation coefficient (ICC) = 0.719], and had poorer agreement with 3D CVI of the whole macula, superior, and inferior macula (ICC = 0.591, 0.483, and 0.394, respectively). Scanning volume did not influence 3D CVI measurements. In conclusion, 3D CVI demonstrated no significant topographic variation. CVI was not correlated with demographic or ocular structural features. 2D CVI of the fovea is partially representative of 3D CVI of the macula.
GOntoSim: a semantic similarity measure based on LCA and common descendants
Authors: Kamran Amna Binte , Naveed Hammad 
Published: March 2022

AbstractThe Gene Ontology (GO) is a controlled vocabulary that captures the semantics or context of an entity based on its functional role. Biomedical entities are frequently compared to each other to find similarities to help in data annotation and knowledge transfer. In this study, we propose GOntoSim, a novel method to determine the functional similarity between genes. GOntoSim quantifies the similarity between pairs of GO terms, by taking the graph structure and the information content of nodes into consideration. Our measure quantifies the similarity between the ancestors of the GO terms accurately. It also takes into account the common children of the GO terms. GOntoSim is evaluated using the entire Enzyme Dataset containing 10,890 proteins and 97,544 GO annotations. The enzymes are clustered and compared with the Gold Standard EC numbers. At level 1 of the EC Numbers for Molecular Function, GOntoSim achieves a purity score of 0.75 as compared to 0.47 and 0.51 GOGO and Wang. GOntoSim can handle the noisy IEA annotations. We achieve a purity score of 0.94 in contrast to 0.48 for both GOGO and Wang at level 1 of the EC Numbers with IEA annotations. GOntoSim can be freely accessed at (http://www.cbrlab.org/GOntoSim.html).
Using Sentinel-1 and GRACE satellite data to monitor the hydrological variations within the Tulare Basin, California
Authors: Vasco Donald W. , Kim Kyra H , Farr Tom G. , Reager J. T. , Bekaert David , Sangha Simran S. , Rutqvist Jonny , Beaudoing Hiroko K. 
Published: March 2022

AbstractSubsidence induced by groundwater depletion is a grave problem in many regions around the world, leading to a permanent loss of groundwater storage within an aquifer and even producing structural damage at the Earth’s surface. California’s Tulare Basin is no exception, experiencing about a meter of subsidence between 2015 and 2020. However, understanding the relationship between changes in groundwater volumes and ground deformation has proven difficult. We employ surface displacement measurements from Interferometric Synthetic Aperture Radar (InSAR) and gravimetric estimates of terrestrial water storage from the Gravity Recovery and Climate Experiment (GRACE) satellite pair to characterize the hydrological dynamics within the Tulare basin. The removal of the long-term aquifer compaction from the InSAR time series reveals coherent short-term variations that correlate with hydrological features. For example, in the winter of 2018–2019 uplift is observed at the confluence of several rivers and streams that drain into the southeastern edge of the basin. These observations, combined with estimates of mass changes obtained from the orbiting GRACE satellites, form the basis for imaging the monthly spatial variations in water volumes. This approach facilitates the quick and effective synthesis of InSAR and gravimetric datasets and will aid efforts to improve our understanding and management of groundwater resources around the world.
Forest soil biotic communities show few responses to wood ash applications at multiple sites across Canada
Authors: Smenderovac Emily , Emilson Caroline , Porter Teresita , Morris Dave , Hazlett Paul , Diochon Amanda , Basiliko Nathan , Bélanger Nicolas , Markham John , Rutherford P. Michael , van Rees Ken , Jones Trevor , Venier Lisa 
Published: March 2022

AbstractThere is interest in utilizing wood ash as an amendment in forestry operations as a mechanism to return nutrients to soils that are removed during harvesting, with the added benefit of diverting this bioenergy waste material from landfill sites. Existing studies have not arrived at a consensus on what the effects of wood ash amendments are on soil biota. We collected forest soil samples from studies in managed forests across Canada that were amended with wood ash to evaluate the effects on arthropod, bacterial and fungal communities using metabarcoding of F230, 16S, 18S and ITS2 sequences as well as enzyme analyses to assess its effects on soil biotic function. Ash amendment did not result in consistent effects across sites, and those effects that were detected were small. Overall, this study suggests that ash amendment applied to managed forest systems in amounts (up to 20 Mg ha−1) applied across the 8 study sties had little to no detectable effects on soil biotic community structure or function. When effects were detected, they were small, and site-specific. These non-results support the application of wood ash to harvested forest sites to replace macronutrients (e.g., calcium) removed by logging operations, thereby diverting it from landfill sites, and potentially increasing stand productivity.
In vitro effects of 5-Hydroxy-L-tryptophan supplementation on primary bovine mammary epithelial cell gene expression under thermoneutral or heat shock conditions
Authors: Field Sena L. , Ouellet Véronique , Sheftel Celeste M. , Hernandez Laura L. , Laporta Jimena 
Published: March 2022

AbstractSerotonin (5-HT) is an autocrine-paracrine molecule within the mammary gland regulating homeostasis during lactation and triggering involution after milk stasis. Exposure of dairy cows to hyperthermia during the dry period alters mammary gland involution processes leading to reduced subsequent yields. Herein, primary bovine mammary epithelial cells (pBMEC) under thermoneutral (TN, 37 °C) or heat shock (HS, 41.5 °C) conditions were cultured with either 0, 50, 200, or 500 μM 5-Hydroxy-L-tryptophan (5-HTP; 5-HT precursor) for 8-, 12- or 24-h. Expression of 95 genes involved in 5-HT signaling, involution and tight junction regulation were evaluated using a Multiplex RT-qPCR BioMark Dynamic Array Circuit. Different sets of genes were impacted by 5-HTP or temperature, or by their interaction. All 5-HT signaling genes were downregulated after 8-h of HS and then upregulated after 12-h, relative to TN. After 24-h, apoptosis related gene, FASLG, was upregulated by all doses except TN-200 μM 5-HTP, and cell survival gene, FOXO3, was upregulated by HS-50, 200 and 500 μM 5-HTP, suggesting 5-HTP involvement in cell turnover under HS. Supplementing 5-HTP at various concentrations in vitro to pBMEC modulates the expression of genes that might aid in promoting epithelial cell turn-over during involution in dairy cattle under hyperthermia.
MTAP loss correlates with an immunosuppressive profile in GBM and its substrate MTA stimulates alternative macrophage polarization
Authors: Hansen Landon J. , Yang Rui , Roso Kristen , Wang Wenzhe , Chen Lee , Yang Qing , Pirozzi Christopher J. , He Yiping 
Published: March 2022

AbstractGlioblastoma (GBM) is a lethal brain cancer known for its potent immunosuppressive effects. Loss of Methylthioadenosine Phosphorylase (MTAP) expression, via gene deletion or epigenetic silencing, is one of the most common alterations in GBM. Here we show that MTAP loss in GBM cells is correlated with differential expression of immune regulatory genes. In silico analysis of gene expression profiles in GBM samples revealed that low MTAP expression is correlated with an increased proportion of M2 macrophages. Using in vitro macrophage models, we found that methylthioadenosine (MTA), the metabolite that accumulates as a result of MTAP loss in GBM cells, promotes the immunosuppressive alternative activation (M2) of macrophages. We show that this effect of MTA on macrophages is independent of IL4/IL3 signaling, is mediated by the adenosine A2B receptor, and can be pharmacologically reversed. This study suggests that MTAP loss in GBM cells may contribute to the immunosuppressive tumor microenvironment, and that MTAP status should be considered for characterizing GBM immune states and devising immunotherapy-based approaches for treating MTAP-null GBM.
Computational identification of new potential transcriptional partners of ERRα in breast cancer cells: specific partners for specific targets
Authors: Cerutti Catherine , Zhang Ling , Tribollet Violaine , Shi Jing-Ru , Brillet Riwan , Gillet Benjamin , Hughes Sandrine , Forcet Christelle , Shi Tie-Liu , Vanacker Jean-Marc 
Published: March 2022

AbstractEstrogen related receptors are orphan members of the nuclear receptor superfamily acting as transcription factors (TFs). In contrast to classical nuclear receptors, the activities of the ERRs are not controlled by a natural ligand. Regulation of their activities thus relies on availability of transcriptional co-regulators. In this paper, we focus on ERRα, whose involvement in cancer progression has been broadly demonstrated. We propose a new approach to identify potential co-activators, starting from previously identified ERRα-activated genes in a breast cancer (BC) cell line. Considering mRNA gene expression from two sets of human BC cells as major endpoint, we used sparse partial least squares modeling to uncover new transcriptional regulators associated with ERRα. Among them, DDX21, MYBBP1A, NFKB1, and SETD7 are functionally relevant in MDA-MB-231 cells, specifically activating the expression of subsets of ERRα-activated genes. We studied SET7 in more details and showed its co-localization with ERRα and its ERRα-dependent transcriptional and phenotypic effects. Our results thus demonstrate the ability of a modeling approach to identify new transcriptional partners from gene expression. Finally, experimental results show that ERRα cooperates with distinct co-regulators to control the expression of distinct sets of target genes, thus reinforcing the combinatorial specificity of transcription.
Multiplex quantification of C-terminal alpha-1-antitrypsin peptides provides a novel approach for characterizing systemic inflammation
Authors: Bigalke Arite , Sponholz Christoph , Schnabel Claudia , Bauer Michael , Kiehntopf Michael 
Published: March 2022

AbstractC-terminal peptides (CAAPs) of the highly abundant serine protease alpha-1-antitrypsin (A1AT) have been identified at various lengths in several human materials and have been proposed to serve as putative biomarkers for a variety of diseases. CAAPs are enzymatically formed and these enzymatic activities are often associated with excessive immune responses (e.g. sepsis, allergies). However, most of those CAAPs have been either detected using in vitro incubation experiments or in human materials which are not easily accessible. To gain a comprehensive understanding about the occurrence and function of CAAPs in health and disease, a LC–MS/MS method for the simultaneous detection of nine CAAPs was developed and validated for human plasma (EDTA and lithium-heparin) and serum. Using this newly developed method, we were able to detect and quantify five CAAPs in healthy individuals thereby providing an initial proof for the presence of C36, C37, C40 and C44 in human blood. Concentrations of four CAAPs in a clinical test cohort of patients suffering from sepsis were significantly higher compared to healthy controls. These results reveal that in addition to C42 other fragments of A1AT seem to play a crucial role during systemic infections. The proposed workflow is simple, rapid and robust; thus this method could be used as diagnostic tool in routine clinical chemistry as well as for research applications for elucidating the diagnostic potential of CAAPs in numerous diseases. To this end, we also provide an overview about the current state of knowledge for CAAPs identified in vitro and in vivo.
Genic and non-genic SNP contributions to additive and dominance genetic effects in purebred and crossbred pig traits
Authors: Mohammadpanah Mahshid , Ayatollahi Mehrgardi Ahmad , Gilbert Hélène , Larzul Catherine , Mercat Marie-José , Esmailizadeh Ali , Momen Mehdi , Tusell Llibertat 
Published: March 2022

AbstractThe present research has estimated the additive and dominance genetic variances of genic and intergenic segments for average daily gain (ADG), backfat thickness (BFT) and pH of the semimembranosus dorsi muscle (PHS). Further, the predictive performance using additive and additive dominance models in a purebred Piétrain (PB) and a crossbred (Piétrain × Large White, CB) pig population was assessed. All genomic regions contributed equally to the additive and dominance genetic variations and lead to the same predictive ability that did not improve with the inclusion of dominance genetic effect and inbreeding in the models. Using all SNPs available, additive genotypic correlations between PB and CB performances for the three traits were high and positive (> 0.83) and dominance genotypic correlation was very inaccurate. Estimates of dominance genotypic correlations between all pairs of traits in both populations were imprecise but positive for ADG-BFT in CB and BFT-PHS in PB and CB with a high probability (> 0.98). Additive and dominance genotypic correlations between BFT and PHS were of different sign in both populations, which could indicate that genes contributing to the additive genetic progress in both traits would have an antagonistic effect when used for exploiting dominance effects in planned matings.
Mice recognize 3D objects from recalled 2D pictures, support for picture-object equivalence
Authors: Cohen Sarah J. , Cinalli David A. , Ásgeirsdóttir Herborg N. , Hindman Brandon , Barenholtz Elan , Stackman Robert W. 
Published: March 2022

AbstractPicture-object equivalence or recognizing a three-dimensional (3D) object after viewing a two-dimensional (2D) photograph of that object, is a higher-order form of visual cognition that may be beyond the perceptual ability of rodents. Behavioral and neurobiological mechanisms supporting picture-object equivalence are not well understood. We used a modified visual recognition memory task, reminiscent of those used for primates, to test whether picture-object equivalence extends to mice. Mice explored photographs of an object during a sample session, and 24 h later were presented with the actual 3D object from the photograph and a novel 3D object, or the stimuli were once again presented in 2D form. Mice preferentially explored the novel stimulus, indicating recognition of the “familiar” stimulus, regardless of whether the sample photographs depicted radially symmetric or asymmetric, similar, rotated, or abstract objects. Discrimination did not appear to be guided by individual object features or low-level visual stimuli. Inhibition of CA1 neuronal activity in dorsal hippocampus impaired discrimination, reflecting impaired memory of the 2D sample object. Collectively, results from a series of experiments provide strong evidence that picture-object equivalence extends to mice and is hippocampus-dependent, offering important support for the appropriateness of mice for investigating mechanisms of human cognition.
Role of senescent cells in the motile behavior of active, non-senescent cells in confluent populations
Authors: Gabuardi Thamara Liz , Lee Hyun Gyu , Lee Kyoung J. 
Published: March 2022

AbstractCharacteristics of cell migration in a confluent population depend on the nature of cell-to-cell interactions as well as cell-intrinsic properties such as the directional persistence in crawling. In addition, biological tissues (or cell cultures) almost always carry anisotropies and they too can significantly affect cell motility. In the light of this viewpoint, the emergence of cellular senescences in a confluent population of active cells raises an interesting question. Cellular senescence is a process through which a cell enters a permanent growth-arrest state and generally exhibits a dramatic body expansion. Therefore, randomly emerging senescent cells transform an initially homogeneous cell population to a “binary mixture” of two distinct cell types. Here, using in vitro cultures of MDA-MB-231 cells we investigate how spatially localized cellular senescence affect the motility of active cells within a confluent population. Importantly, we estimate the intercellular surface energy of the interface between non-senescent and senescent MDA-MB-231 cells by combining the analysis on the motile behaviors of non-senescent cells encircling senescent cells and the result of extensive numerical simulations of a cellular Potts model. We find that the adhesion of normal cells to senescent cells is much weaker than that among normal cells and that the ‘arclength’ traveled by a normal cell along the boundary of a senescent cell, on average, is several times greater than the persistence length of normal cell in a densely packed homogeneous population. The directional persistent time of normal cell during its contact with a senescent cell also increases significantly. We speculate that the phenomenon could be a general feature associated with senescent cells as the enormous expansion of senescent cell’s membrane would inevitably decrease the density of cell adhesion molecules.
Buffering the impacts of extreme climate variability in the highly engineered Tigris Euphrates river system
Authors: Abdelmohsen Karem , Sultan Mohamed , Save Himanshu , Abotalib Abotalib Z. , Yan Eugene , Zahran Khaled H. 
Published: March 2022

AbstractMore extreme and prolonged floods and droughts, commonly attributed to global warming, are affecting the livelihood of major sectors of the world’s population in many basins worldwide. While these events could introduce devastating socioeconomic impacts, highly engineered systems are better prepared for modulating these extreme climatic variabilities. Herein, we provide methodologies to assess the effectiveness of reservoirs in managing extreme floods and droughts and modulating their impacts in data-scarce river basins. Our analysis of multiple satellite missions and global land surface models over the Tigris-Euphrates Watershed (TEW; 30 dams; storage capacity: 250 km3), showed a prolonged (2007–2018) and intense drought (Average Annual Precipitation [AAP]: < 400 km3) with no parallels in the past 100 years (AAP during 1920–2020: 538 km3) followed by 1-in-100-year extensive precipitation event (726 km3) and an impressive recovery (113 ± 11 km3) in 2019 amounting to 50% of losses endured during drought years. Dam reservoirs captured water equivalent to 40% of those losses in that year. Additional studies are required to investigate whether similar highly engineered watersheds with multi-year, high storage capacity can potentially modulate the impact of projected global warming-related increases in the frequency and intensity of extreme rainfall and drought events in the twenty-first century.