bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for Layer-Specific Connectional Heterogeneity in the Mouse Auditory Corticocollicular System
Authors: Yudintsev Georgiy , Asilador Alexander R. , Sons Stacy , Vaithiyalingam Chandra Sekaran Nathiya , Coppinger Macey , Nair Kavya , Prasad Masumi , Xiao Gang , Ibrahim Baher A. , Shinagawa Yoshitaka , Llano Daniel A. 
Published: October 2021

The auditory cortex (AC) sends long-range projections to virtually all subcortical auditory structures. One of the largest and most complex of these—the projection between AC and inferior colliculus (IC; the corticocollicular pathway)—originates from layer 5 and deep layer 6. Though previous work has shown that these two corticocollicular projection systems have different physiological properties and network connectivities, their functional organization is poorly understood. Here, using a combination of traditional and viral tracers combined within vivoimaging in both sexes of the mouse, we observed that layer 5 and layer 6 corticocollicular neurons differ in their areas of origin and termination patterns. Layer 5 corticocollicular neurons are concentrated in primary AC, while layer 6 corticocollicular neurons emanate from broad auditory and limbic areas in the temporal cortex. In addition, layer 5 sends dense projections of both small and large (>1 µm2area) terminals to all regions of nonlemniscal IC, while layer 6 sends small terminals to the most superficial 50–100 µm of the IC. These findings suggest that layer 5 and 6 corticocollicular projections are optimized to play distinct roles in corticofugal modulation. Layer 5 neurons provide strong, rapid, and unimodal feedback to the nonlemniscal IC, while layer 6 neurons provide heteromodal and limbic modulation diffusely to the nonlemniscal IC. Such organizational diversity in the corticocollicular pathway may help to explain the heterogeneous effects of corticocollicular manipulations and, given similar diversity in corticothalamic pathways, may be a general principle in top-down modulation.SIGNIFICANCE STATEMENTWe demonstrate that a major descending system in the brain is actually two systems. That is, the auditory corticocollicular projection, which exerts considerable influence over the midbrain, comprises two projections: one from layer 5 and the other from layer 6. The layer 6 projection is diffusely organized, receives multisensory inputs, and ends in small terminals; while the layer 5 projection is derived from a circumscribed auditory cortical area and ends in large terminals. These data suggest that the varied effects of cortical manipulations on the midbrain may be related to effects on two disparate systems. These findings have broader implications because other descending systems derive from two layers. Therefore, a duplex organization may be a common motif in descending control.
Effect of preoperative glycemic status on postoperative complications of coronary artery bypass graft surgery in patients with diabetes
Authors: Andishmand Abbas , Froozannia Seyed Khalil , Namayandeh Seyedeh-Mahdieh , Mirhosseini Seyed Jalil , Salami Maryamalsadat , Mohamedi Farnaz 
Published: October 2021

Objectives: Diabetes mellitus is one of the major risk factors for cardiovascular disease, and increases the risk of postoperative mortality. HbA1c is a measure of glycemic control. This study aimed to determine the effect of glycemic status on the complications of coronary artery bypass graf (CABG) surgery in diabetic patients.
Methods: This cross-sectional study was performed on 300 diabetic patients including 186 (62%) men and 114 (38%) women who underwent CABG from March 2010 to August 2011 and selected via census method. Preoperative blood glucose control status was determined using HbA1c levels, and the patients were evaluated for postoperative in-hospital complications.
Results: The mean age of the patients was 62.3± 6.9 years. In-hospital mortality was 1.0% (3/300). New-onset atrial fibrillation was the most common complication (35%). HbA1c level above 7.5% was a predictor of in-hospital mortality after CABG (unadjusted odds ratio 1.9, 95٪ CI: 1.1-3.2, p = 0.006). After stratifying analysis with Chi-sqaure test we found that gender history of myocardial infarction had no significant relationship with HbA1c level in two groups with or without complication.
Conclusions: Long-term uncontrolled blood glucose before CABG is associated with increased postoperative complications. Preoperative HbA1c measurement can be a predictor of high-risk patients.
Parameters of arterial stiffness in hypertensive patients with and without subclinical carotid atherosclerosis
Authors: Gumerova V. E. , Sayganov S. A. , Gomonova V. V. 
Published: October 2021

Objective. To assess the relationship between arterial stiffness parameters in hypertensive patients with and without atherosclerotic lesions.Design and methods. We included 127 subjects who were divided into 3 groups: patients with hypertension (HTN) without atherosclerosis (n = 42); patients with HTN and subclinical atherosclerosis (SА) (n = 52) and control group which consisted of individuals without HTN, SA, or coronary artery disease (n = 33). All groups matched by age and gender. All subjects underwent following examinations: ultrasonography of extracranial segments of carotid arteries, 24-hour blood pressure monitoring with the assessment of arterial stiffness parameters.Results. In subjects with HTN compared to controls, pulse wave velocity in aorta (PWVao) was significantly higher (11,3 ± 1,5; 12,3 ± 1,8 vs 10,4 ± 1,3 m/s; p < 0,05), as well as pulse pressure (PP) (46,4 ± 9,8; 45,6 ± 10,6 vs 39,9 ± 6,5 mmHg; p < 0,05), central pulse pressure (PPао) (35,5 ± 8,5; 34,9 ± 8,5 vs 30,9 ± 5,4 mmHg; p < 0,05), and arterial stiffness index (ASI) (141 (127, 159); 139 (128,5, 160,5) vs 126 (118, 138) mmHg; p < 0,05). In subjects with HTN and SA, PWVao was significantly higher compared to other groups (p < 0,05). No significant difference in augmentation index was found (–32,5 (–45, –12); –22 (–36, –12); –37 (–50, –17); p = 0,25). Аmbulatory arterial stiffness index was higher in controls (0,5 ± 0,2) compared to HTN group (0,4 ± 0,2; p = 0,05), while HTN and SA group did not differ significantly (0,5 ± 0,2; p = 0,3). PWVao above 11,15 m/s is associated with 4,3 (2,3–8,2) times higher rate of atherosclerosis plaque detection.Conclusions. In HTN patients, arterial stiffness is changed compared to healthy individuals. PWVao above 11,15 m/s is associated with 4,3 (2,3–8,2) times higher rate of atherosclerosis plaque detection. In patients with HTN and SA arterial stiffness is higher, which might have additional predictive value in risk stratification.
Gender and cardiovascular risk in rotational shift workers in the Arctic
Authors: Shurkevich N. P. , Vetoshkin A. S. , Gapon L. I. , Simonyan A. A. , Dyachkov S. M. 
Published: October 2021

Objective. To study gender differences in potential risk factors (RF) for cardiovascular diseases in rotational shift workers in the Arctic.Design and methods.Out of 213 examined patients, 183 individuals were enrolled in groups within 6 days of September 2019, in the polar settlement of Yamburg (68 N), on the basis of Health Service LLC “Gazprom Dobycha Yamburg” medical unit. They were comparable by age: 99 were males (M) aged 48 years (41,5; 58,5) and 81 were females (F) aged 49 years (43,6; 58,1) (p = 0,441); by number of years of rotational shift work: 16,5 (9,0; 26,4) years in M and 16,3 (8,5; 26,9) years in F (p = 0,635); by number of individuals with hypertension: 49,5% were M, 43,9% were F (p = 0,344) and normotensive individuals (p = 0,544). Office blood pressure was 149,4 (119,1; 180,2) mmHg in M group, 149,6 (128,5; 178,5) mmHg in F group (p = 0,250). All patients underwent ultrasound examination of carotid arteries (CA) for the detection of atherosclerotic plaque (ASP), and assessment of local stiffness parameters of CA and femoral arteries (FA); cardio-ankle vascular index, and pulse wave velocity. In addition, ambulatory blood pressure monitoring, echocardiography with calculation of HFpEF probability using H2FPEF score (Heavy; Hypertensive; Atrial Fibrillation; Pulmonary Hypertension; Elder; Filling Pressure); blood tests (lipid spectrum, levels of high-sensitivity C-reactive protein (hs-CRP), homocysteine, C-peptide, insulin, brain natriuretic propeptide (NT-pro-BNP)) were performed. The following RF were assessed: smoking, physical activity, and perceived stress level.Results. Overweight (p = 0,039), smoking (p = 0,014) were more common in M than in F. Low self-esteem level of psychosocial stress was more frequently registered in F: 93% vs 54 % (p < 0,0001), while mean level was more often found in M: 46% vs 7 % (p < 0,0001). In M group, there was a significant increase in homocysteine (p < 0,001), which was associated with higher stiffness index β in CA (p = 0,004) and FA (p = 0,004), Peterson’s elastic modulus Ep CA (p = 0,009), higher detection rate of ASP in CA (p = 0,021). F group showed significant increase in hs-CRP (p = 0,03), and NT-pro-BNP, (p < 0,001). Odds ratio of gender-related indicators showed association of male sex with arterial stiffness, formation of ASP in CA, while female sex was associated with markers of systemic inflammation and neurohumoral activation. There were no significant differences between M and F regarding HFpEF probability, assessed by H2FPEF score (p = 0,303).Conclusions. Our data will allow for identifying the most significant factors with high gender-specific cardiovascular risk in rotating shift-workers in the Arctic which can play role in cardiovascular prevention and early diagnosis with the focus on economic efficiency.
Is foliar Cl- concentration the cause of photosynthetic decline in grapevine during mild salinity?
Authors: Baggett John P. , Habibsadeh Saied , Toups Haley S. , Cochetel Noé , Ghan Ryan , Robinson M.L. , Barrios-Masias Felipe H. , Cramer Grant R. 
Published: October 2021

Moderate levels of Cl- have been associated with grapevine salt tolerance. The hypothesis to be tested in this work is: photosynthesis in grapevine is negatively correlated with foliar Cl- concentration. To further test this hypothesis, multiple mild salinity experiments on four different Vitis genotypes (Cabernet-Sauvignon, Riparia Gloire, Ramsey and SC2) were conducted and photosynthesis, ion concentrations and gene expression responses were quantified. The salt-tolerant rootstock Ramsey had greater Cl- exclusion capabilities than V. vinifera cultivars both during rooted cutting greenhouse experiments and three years of field-grafted experiments; SC2 also excluded Cl-. Differential gene expression indicated that salinity affected transcript abundance more in salt-sensitive genotypes (97.7 % of DEGs in the dataset), especially chloroplast-related transcripts. The transcript abundances of known anion transporters were determined and a family of putative B transporters was associated with the Cl- exclusion phenotype. Photosynthesis and growth were maintained in Ramsey and SC2 under mild salinity. However, photosynthesis declined in Cabernet-Sauvignon with isosmotic 20 mM salt concentrations of NaCl, KCl or NaNO3, independent of the salt type. While foliar Cl- concentrations did correlate with salt tolerance during control and NaCl conditions, it was not found to be the cause of photosynthetic decline in Vitis during mild salinity.
Composición y estructura vegetal de una parcela de vegetación en un relicto de bosque seco tropical en el Caribe colombiano
Authors: Londoño Lemos Viviana , Escobar-Hadechini Orlando , Tapasco-García Juan , Madriñán Santiago 
Published: October 2021

El bosque seco tropical (bs-T) es uno de los ecosistemas más amenazados a nivel mundial debido a la conversión histórica de sus tierras hacia pastos y cultivos. El bs-T del Jardín Botánico de Cartagena “Guillermo Piñeres” (JBGP) es un fragmento de 3 ha, aislado ubicado en un enclave húmedo donde nace el arroyo Matute, uno de los principales afluentes de Cartagena. Con el objetivo de estudiar la composición y estructura vegetal en uno de los últimos remanentes de bs-T cercanos a Cartagena, se construyó una parcela permanente de 1 ha y se censó la vegetación leñosa con diámetro a la altura del pecho (DAP) ≥ 2.5 cm. Se registraron 1568 individuos y 2023 tallos de 62 especies distribuidas en 34 familias. El 85 % de los individuos registrados fueron árboles y arbustos, el 11 % lianas y el 4 % palmas. La familia con mayor riqueza de especies fue Sapindaceae, con cuatro, seguida de Apocynaceae, Arecaceae, Fabaceae, Meliaceae, Moraceae, Nyctaginaceae y Urticaceae, cada una con tres. Se concluye que el bosque se encuentra en un estado de sucesión secundaria tardía, y que su ubicación e historial de perturbaciones son factores importantes en la determinación de su composición y estructura.
Physics Inspired Machine Learning for Solving Fluid Flow in Porous Media: A Novel Computational Algorithm for Reservoir Simulation
Authors: Sambo Chico , Feng Yin 
Published: October 2021

Abstract
The Physics Inspired Machine Learning (PIML) is emerging as a viable numerical method to solve partial differential equations (PDEs). Recently, the method has been successfully tested and validated to find solutions to both linear and non-linear PDEs. To our knowledge, no prior studies have examined the PIML method in terms of their reliability and capability to handle reservoir engineering boundary conditions, fractures, source and sink terms. Here we explored the potential of PIML for modelling 2D single phase, incompressible, and steady state fluid flow in porous media.
The main idea of PIML approaches is to encode the underlying physical law (governing equations, boundary, source and sink constraints) into the deep neural network as prior information.
The capability of the PIML method in handling reservoir engineering boundary including no-flow, constant pressure, and mixed reservoir boundary conditions is investigated. The results show that the PIML performs well, giving good results comparable to analytical solution. Further, we examined the potential of PIML approach in handling fluxes (sink and source terms). Our results demonstrate that the PIML fail to provide acceptable prediction for no-flow boundary conditions. However, it provides acceptable predictions for constant pressure boundary conditions.
We also assessed the capability of the PIML method in handling fractures. The results indicate that the PIML can provide accurate predictions for parallel fractures subjected to no-flow boundary. However, in complex fractures scenario its accuracy is limited to constant pressure boundary conditions. We also found that mixed and adaptive activation functions improve the performance of PIML for modeling complex fractures and fluxes.
Adding GPU Acceleration to an Industrial CPU-Based Simulator, Development Strategy and Results
Authors: Cao Hui , Zaydullin Rustem , Liao Terrence , Gohaud Neil , Obi Eguono , Darche Gilles 
Published: October 2021

Abstract
Running multi-million cell simulation problems in minutes has been a dream for reservoir engineers for decades. Today, with the advancement of Graphic Processing Unit (GPU), we have a real chance to make this dream a reality. Here we present our experience in the step-by-step transformation of a fully developed industrial CPU-based simulator into a fully functional GPU-based simulator. We also demonstrate significant accelerations achieved through the use of GPU technology.
To achieve the best performance possible, we choose to use CUDA (NVIDIA GPU’s native language), and offload as much computations to GPU as possible. Our CUDA implementation covers all reservoir computes, which include property calculation, linearization, linear solver, etc. The well and Field Management still reside on CPU and need minor changes for their interaction with GPU-based reservoir. Importantly, there is no change to the nonlinear logic. The GPU and CPU parts are overlapped, fully utilizing the asynchronous nature of GPU operations. Each reservoir computation can be run in three modes, CPU_only (existing one), GPU_only, CPU followed by GPU. The latter is only used for result checking and debugging.
In early 2019, we prototyped two reservoir linearization operations (mass accumulation and mass flux) in CUDA; both showed very strong runtime speed-up of several hundred times, 1 P100-GPU (NVIDIA) vs 1 POWER8NVL CPU core rated at 2.8 GHz (IBM). Encouraged by this success, we moved into linear solver development and managed to move the entire linear solver module into GPU. Again, strong speed-up of ~50 times was achieved (1 GPU vs 1 CPU). The focus for 2019 has been on standard Black-Oil cases. Our implementation was tested with multiple "million-cell range" models (SPE10 and other real field cases). In early 2020, we managed to put SPE10 fully on GPU, and finished the entire 2000 day time-stepping in ~35 sec with a single P100 card. After that our effort has switched to compositional AIM (Adaptive Implicit Method), with focus on compositional flash and AIM implementation for reservoir linearization and linear solver, both show early promising results.
GPU-based reservoir simulation is a future trend for HPC. The development of a reservoir simulator is complex, multi-discipline and time-consuming work. Our paper demonstrates a clear strategy to add tremendous GPU acceleration into an existing CPU-based simulator. Our approach fully utilizes the strength of the existing CPU simulator and minimizes the GPU development effort. This paper is also the first publication targeting GPU acceleration for compositional AIM models.
A Similarity Solution for Imbibition Process and its Adaptation in Finite Difference Simulation of Fractured Reservoirs
Authors: Du Song , Lee Seong , Wen Xian-Huan , Efendiev Yalchin 
Published: October 2021

Abstract
The imbibition process due to capillary force is an important mechanism that controls fluid flow between the two domains, matrix and fracture, in naturally or hydraulically fractured reservoirs. Many simulation studies have been done in the past decades to understand the multi-phase flow in the tight and shale formation. Although significant advances have been made in large-scale modeling for both unconventional and conventional fields, the imbibition processes in the fractured reservoirs remains underestimated in numerical simulation, that limits confidence in long-term field production predictions. In the meanwhile, to simulate the near-fracture imbibition process, traditionally very-fine simulation grids have to be applied so that the physical phenomena of small-length scale could be captured. However, this leads to expensive computation cost to simulate full-field models with a large number of fractures. To improve numerical efficiency in field-scale modeling, we propose a similarity solution for the imbibition process that can be incorporated into the traditional finite difference formulation with coarse grid cells.
The semi-analytical similarity solutions are validated by comparing with numerical simulation results with fine-scale grids. The comparison clearly indicates that the proposed algorithm accurately represents the flow behaviors in complex fracture models. Furthermore, we adopt the semi-analytical study to hydraulic fracture models using Embedded Discrete Fracture Model (Lee et al., 2001) in our numerical studies at different scales to represent hydraulic fractures that are interconnected. We demonstrate: 1) the imbibition is critical in determining flow behavior in a capillary force dominant model, 2) conventional EDFM has its limitation in capturing sub-cell flow behaviors near fractures, 3) combining the proposed similarity solution and EDFM, we can accurately represent the multi-phase flow near fractures with coarser grids, and 4) it is straightforward to adapt the similarity solution concept in finite-difference simulations for fractured reservoirs
Upscaling of Realistic Discrete Fracture Simulations Using Machine Learning
Authors: Andrianov Nikolai 
Published: October 2021

Abstract
Upscaling of discrete fracture networks to continuum models such as the dual porosity/dual permeability (DPDP) model is an industry-standard approach in modelling of fractured reservoirs. While flow-based upscaling provides more accurate results than analytical methods, the application of flow-based upscaling is limited due to its high computational cost.
In this work, we parametrize the fine-scale fracture geometries and assess the accuracy of several convolutional neural networks (CNNs) to learn the mapping between this parametrization and the DPDP model closures such as the upscaled fracture permeabilities and the matrix-fracture shape factors. We exploit certain similarities between this task and the problem of image classification and adopt several best practices from the state-of-the-art CNNs used for image classification. By running a sensitivity study, we identify several key features in the CNN structure which are crucial for achieving high accuracy of predictions for the DPDP model closures, and put forward the corresponding CNN architectures.
Obtaining a suitable training dataset is challenging because i) it requires a dedicated effort to map the fracture geometries; ii) creating a conforming mesh for fine-scale simulations in presence of intersecting fractures typically leads to bad quality mesh elements; iii) fine-scale simulations are time-consuming. We alleviate some of these difficulties by pre-training a suitable CNN on a synthetic random linear fractures’ dataset and demonstrate that the upscaled parameters can be accurately predicted for a realistic fracture configuration from an outcrop data.
The accuracy of the DPDP results with the predicted model closures is assessed by a comparison with the corresponding fine-scale discrete fracture-matrix (DFM) simulation of a two-phase flow in a realistic fracture geometry. The DPDP results match well the DFM reference solution, while being significantly faster than the latter.