bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detect the Water Flow Characteristic of the Tigris River by Using HFC-RAS Program
Authors: Dhafer Abed Ali , Maythem Jaafer Sumyah 
Published: April 2021

Abstract
The Tigris River has recently suffered from a significant decrease in water levels, in addition to the scarcity of drainage and the velocity of water entering the river from Syria, Turkey and Iran. These decreases in the levels leads gradually to drying of some parts of the banks, raising the level of the riverbed, and the appearance of dry areas in the middle of the river. This led to a decrease in the width of the river and hindering the movement of river navigation. Also, the decrease in water levels leads to an impact on the water levels needed by the liquefaction plants to secure the drinking water needed by the city of Baghdad. So, it is necessary to find a technique in which the flow characteristics of the Tigris River are revealed in periods of scarcity, in order to create planning solutions that increase the water height to levels that ensure uninterrupted water supply in the liquefaction plants all over the river. Therefore, this research aims to simulate the movement of water in the Tigris River to detect flow characteristics in times of scarcity by building a one-dimensional hydraulic model (for steady flow) using the HEC-RAS program. Where the simulation will be done based on the geometric data for the shape of the river, as well as the initial and boundary conditions that represent the levels and drainages of water for the river at periods of scarcity, in addition to identifying the values of the Manning coefficient. The model will produce results that are longitudinal and cross sections, flow charts, tables and values, on the basis of which planning solutions are proposed to raise the water level to the required level, restore the natural properties of flow, and examine the compatibility of the proposed solution with the reality of the situation. It was concluded that raising the water level would be by proposing an (Ungated Inline wirs) dam. The proposed dam was tested at a minimum level in times of scarcity, ensuring its ability to raise water levels to the height required for all liquefaction plants installed along the river that required a minimum level of 28.5 m.
Tourist development of heritage in Algeria: case of the Hypone site -ANNABA-
Authors: Ahmed Soufiane Sid , Alkinani Amer shakir , saddek Guerfia , Alrikabi Nada khaleefah 
Published: April 2021

Abstract
In a world where tourism has become the leading industry on the market, sustainable tourism has found its place and is becoming a major player in the network of traveling Internet users. Hospitality, solidarity and conviviality are essential are giving meaning to sharing. This “extra soul” has the capacity to enrich moments, places, attractions and heritage. Archaeological heritage sites constitute an important factor for the economic and social life of a large number of countries, the development policy came to emphasize the safeguard and the preservation of landscapes and natural or man-made sites, against the attacks which have impoverished the cultural heritage, this heritage which represents a historic imprint for future generations. Archaeological sites exert major tourist attractions. Successfully managed cultural tourism can capture the appeal of archaeological heritage and generate significant funds which will then be used to finance studies, conservation, maintenance and the presentation of this heritage to the public. This is how tourism has become, according to the World Tourism Organization (UNWTO), the world’s leading industry. Algeria contains archaeological sites which are classified as world cultural heritage by UNESCO. Unfortunately, reality shows that most of these sites are left to deteriorate without any real intervention. It is important to point out the importance of putting in place a work plan aimed at developing tourism that preserves archaeological sites considering social, environmental, cultural dimensions, etc. We will conduct this analysis based on a problem built around this main question: How to preserve our cultural heritage to achieve sustainable tourism? Through this research work, it is a question of examining the problem of integrating the conservation and enhancement of archaeological sites in the context of producing sustainable tourism for the city of Annaba and for Algeria. a global way.
Reality analysis of the state of spatial distribution of green areas using geographic information systems (GIS) – The holy city of Najaf as a case study
Authors: Kh Alrikabi Nada , Almosherefawi Osama J 
Published: April 2021

Abstract
Green areas are an essential component of city planning, as they serve as an outlet for them to spend their free time, in addition to the environmental role that these green areas play in improving the city’s climate by purifying the air and beautifying the city. The study’s problem is summarized in identifying the appropriateness of the current spatial distribution of green areas in the city of Najaf with the current population densities and the pattern in which green areas are distributed using GIS and knowing the per capita share of those green areas in the city, the research assumes that the inconsistency of spaces between regions Green and residential neighbourhoods need to conform to the standards for the individual share. The research also aims to know the reality of the green areas in the holy city of Najaf using GIS to take advantage of the capabilities provided by the program in the field of entering and analysing information related to its spatial distribution, as well as identifying the pattern in which the green areas are distributed in the city of Najaf, and come up with recommendations and proposals to address the existing imbalance. The research found that more than half of the neighbourhoods in the region do not conform to the standard followed in assessing the individual’s share, where the individual’s share ranged between (0.4-3.9) square meters, and there are neighbourhoods completely devoid of green areas, and this is due to poor planning in those areas. On the neighbourhood link index, the pattern of distribution of these green areas was aggregated to random. As for the Moran coefficient, its value departed from one frequently, indicating a weak spatial and random correlation of green areas, The area reached by the impact area of the green areas reached (5512) hectares, which is equivalent to (83.32%) of the total area of the Holy City of Najaf, and the neighbourhoods near the middle centre and surrounding it are the most intersecting neighbourhoods in the impact area.
Changes in Land Use and Its Impact on the Hierarchy of Roads in Ramadi City
Authors: Ahmed N A , Mahmood T S 
Published: April 2021

Abstract
Well-consideration should be given to the change in land use since it has a significant impact on the hierarchy of roads in terms of traffic congestion, traffic accidents, and low efficiency of roads as they serve traffic volumes higher than what has been planned for the master plans of cities. Therefore, this research investigates the impact of change in land uses on the hierarchy of roads in Ramadi city by utilizing Geographically Weighted Regression (GWR) in the Geographic Information System (GIS) to analyze the relationship between changes in land uses and road class according to the functional classification system of Ramadi city. The GWR analysis method was adopted because it provides an accurate description of the study area and takes into account the spatial dimension of the phenomenon. It was concluded that all classes of roads (major arterial, minor arterial, collector, and local roads) have a linear relationship with changes in land uses. Moreover, results show that the secondary arterial roads are the most affected by changes in land uses while the local roads are uselessly affected.
Climatic Treatments for Housing in the Traditional Holy Cities: A Comparison between Najaf and Yazd Cities
Authors: Jasim Ihsan A. , Farhan Sabeeh L. , Al-Maliki Laheab A. , AL-Mamoori Sohaib K. 
Published: April 2021

AbstractThe hot, dry environmental conditions prevailing in Al-Najaf and Yazd cities - a modern old problem-must be studied with some detail to come up with new solutions to adapt to the current environmental conditions of the two cities. the research aims to compare the methods used by the residents of Al-Najaf and Yazd cities to handle the hard-environmental conditions in the past and the way to adapt to them. Eight criteria were compared and discussed to investigate the ways and methods to improve the environmental situation in the two cities. The research concluded that there is a great similarity in the environment of the two cities, as well as the environment responding to the treatments that human life adapts. This necessitates the need to preserve the environmental design vocabulary for these two cities (Yazd and Najaf) such as the central courtyard of the aligned residential units to soften the atmosphere within the one unit and increase the family bonding.in addition to preserving the side Shanasheel and local privacy. Yazd city overpass Al-Najaf city by maintaining climate treatments for the historical centre and developing them in line with the development of building methods and construction materials.
Urban Centralization and Its Effect on the Kinetic Nodes of the Passengers in the Path of Transferring Bayaa-Bab Al-Moazam
Authors: Ali K S , Abid N M 
Published: April 2021

Abstract
In urban areas, there are many centres containing activities, events and residents. They may be main or secondary centres. However, there are centres related to urban transport. We also assume that there are urban centres called kinetic nodes that differ from each other along the transport line. In this paper, we aim to identify the causes of the discrepancy between these kinetic nodes. The problem is to find a solution to identify transmission stations that are more important than others along the al-Baya – Bab al-Moazam transport line.
Developing and establishing a geospatial database of the religious endowments in Hilla, Iraq
Authors: Husain Hashim Ali , Zakariya Jasim Oday , Mejbel Salih Mohammed 
Published: April 2021

Abstract
The religious endowments (according to religious and legal contracts) are one of the important sources that acquire historical, cultural and economic importance in all countries of the world. For optimal management of real estate (non-transferable assets) of religious endowments, the proposed study introduces a new technical method for management, and under this method, a geospatial database is constructed: (satellite images, digital maps, and field survey data enhanced with GPS coordinates). Real estate that belongs to a religious institution in Iraq (Shiite endowment in Hilla city) will be investigated as a case study for the proposed research. In this proposed study, methods of statistical and spatial analysis are employed on the spatial database provided by Geographic Information Systems, in order to better manage and invest these properties.
The American Kestrel (Falco sparverius) genoscape: implications for monitoring, management, and subspecies boundaries
Authors: Ruegg Kristen C , Brinkmeyer Michaela , Bossu Christen M , Bay Rachael A , Anderson Eric C , Boal Clint W , Dawson Russell D , Eschenbauch Amber , McClure Christopher J W , Miller Karl E , Morrow Lance , Morrow Jill , Oleyar M David , Ralph Bill , Schulwitz Sarah , Swem Ted , Therrien Jean-Francois , Van Buskirk Rich , Smith Thomas B , Heath Julie A 
Published: April 2021

AbstractIdentifying population genetic structure is useful for inferring evolutionary process and comparing the resulting structure with subspecies boundaries can aid in species management. The American Kestrel (Falco sparverius) is a widespread and highly diverse species with 17 total subspecies, only 2 of which are found north of U.S./Mexico border (F. s. paulus is restricted to southeastern United States, while F. s. sparverius breeds across the remainder of the U.S. and Canadian distribution). In many parts of their U.S. and Canadian range, American Kestrels have been declining, but it has been difficult to interpret demographic trends without a clearer understanding of gene flow among populations. Here we sequence the first American Kestrel genome and scan the genome of 197 individuals from 12 sampling locations across the United States and Canada in order to identify population structure. To validate signatures of population structure and fill in sampling gaps across the U.S. and Canadian range, we screened 192 outlier loci in an additional 376 samples from 34 sampling locations. Overall, our analyses support the existence of 5 genetically distinct populations of American Kestrels—eastern, western, Texas, Florida, and Alaska. Interestingly, we found that while our genome-wide genetic data support the existence of previously described subspecies boundaries in the United States and Canada, genetic differences across the sampled range correlate more with putative migratory phenotypes (resident, long-distance, and short-distance migrants) rather than a priori described subspecies boundaries per se. Based on our results, we suggest the resulting 5 genetically distinct populations serve as the foundation for American Kestrel conservation and management in the face of future threats.
Asynchronous parallel Bayesian optimization for AI-driven cloud laboratories
Authors: Frisby Trevor S , Gong Zhiyun , Langmead Christopher James 
Published: April 2021

Abstract

Motivation
The recent emergence of cloud laboratories—collections of automated wet-lab instruments that are accessed remotely, presents new opportunities to apply Artificial Intelligence and Machine Learning in scientific research. Among these is the challenge of automating the process of optimizing experimental protocols to maximize data quality.

Results
We introduce a new deterministic algorithm, called PaRallel OptimizaTiOn for ClOud Laboratories (PROTOCOL), that improves experimental protocols via asynchronous, parallel Bayesian optimization. The algorithm achieves exponential convergence with respect to simple regret. We demonstrate PROTOCOL in both simulated and real-world cloud labs. In the simulated lab, it outperforms alternative approaches to Bayesian optimization in terms of its ability to find optimal configurations, and the number of experiments required to find the optimum. In the real-world lab, the algorithm makes progress toward the optimal setting.

Data availability and implementation
PROTOCOL is available as both a stand-alone Python library, and as part of a R Shiny application at https://github.com/clangmead/PROTOCOL. Data are available at the same repository.

Supplementary information
Supplementary data are available at Bioinformatics online.
TITAN: T-cell receptor specificity prediction with bimodal attention networks
Authors: Weber Anna , Born Jannis , Rodriguez Martínez María 
Published: April 2021

Abstract

Motivation
The activity of the adaptive immune system is governed by T-cells and their specific T-cell receptors (TCR), which selectively recognize foreign antigens. Recent advances in experimental techniques have enabled sequencing of TCRs and their antigenic targets (epitopes), allowing to research the missing link between TCR sequence and epitope binding specificity. Scarcity of data and a large sequence space make this task challenging, and to date only models limited to a small set of epitopes have achieved good performance. Here, we establish a k-nearest-neighbor (K-NN) classifier as a strong baseline and then propose Tcr epITope bimodal Attention Networks (TITAN), a bimodal neural network that explicitly encodes both TCR sequences and epitopes to enable the independent study of generalization capabilities to unseen TCRs and/or epitopes.

Results
By encoding epitopes at the atomic level with SMILES sequences, we leverage transfer learning and data augmentation to enrich the input data space and boost performance. TITAN achieves high performance in the prediction of specificity of unseen TCRs (ROC-AUC 0.87 in 10-fold CV) and surpasses the results of the current state-of-the-art (ImRex) by a large margin. Notably, our Levenshtein-based K-NN classifier also exhibits competitive performance on unseen TCRs. While the generalization to unseen epitopes remains challenging, we report two major breakthroughs. First, by dissecting the attention heatmaps, we demonstrate that the sparsity of available epitope data favors an implicit treatment of epitopes as classes. This may be a general problem that limits unseen epitope performance for sufficiently complex models. Second, we show that TITAN nevertheless exhibits significantly improved performance on unseen epitopes and is capable of focusing attention on chemically meaningful molecular structures.

Availability and implementation
The code as well as the dataset used in this study is publicly available at https://github.com/PaccMann/TITAN.

Supplementary information
Supplementary data are available at Bioinformatics online.
Efficacy and Safety of Albendazole and High-Dose Ivermectin Coadministration in School-Aged Children Infected With Trichuris trichiura in Honduras: A Randomized Controlled Trial
Authors: Matamoros Gabriela , Sánchez Ana , Gabrie José Antonio , Juárez Marisa , Ceballos Laura , Escalada Andrés , Rodríguez Carol , Martí-Soler Helena , Rueda María Mercedes , Canales Maritza , Lanusse Carlos , Cajal Pamela , Álvarez Luis , Cimino Rubén O , Krolewiecki Alejandro 
Published: April 2021

Abstract

Background
The efficacy of currently available anthelminthics against Trichuris trichiura infections is significatively lower than for other soil-transmitted helminths. The combination of ivermectin (IVM) and albendazole (ALB) has shown significant improvements in efficacy.

Methods
Safety and efficacy randomized controlled clinical trial comparing 3 experimental regimens against ALB monotherapy for the treatment of T. trichiura infections in northern Honduras. Infected children were randomized to 4 treatment arms: arm 1, single-dose ALB (400 mg); arm 2, single-dose ALB (400 mg) plus IVM (600 μg/kg); arm 3, ALB (400 mg) for 3 consecutive days; or arm 4, ALB (400 mg) plus IVM (600 μg/kg) for 3 consecutive days. Efficacy was measured based on the egg reduction and cure rates, both assessed 14–21 days after treatment, using the Kato-Katz method. Safety was evaluated by analyzing the frequency and severity of adverse events.

Results
Of 176 children randomized to 1 of the 4 treatment arms, 117 completed treatment and follow-up. The egg reduction rates for arms 1, 2, 3, and 4 were 47.7%, 96.7%, 72.1%, and 100%, respectively; with P values &lt;.001 for comparisons between IVM groups and ALB-only arms. The cure rates were 4.2%, 88.6%, 33.3%, and 100%, respectively. A total of 48 adverse events (85.4% mild) were reported in 36 children.

Conclusions
The combined use of ALB and high-dose IVM is a highly effective and well tolerated treatment for the treatment of T. trichiura infections, offering significantly improved treatment for the control of this infection.

Clinical Trials Registration
NCT04041453.
Reorganization of chromatin architecture during prenatal development of porcine skeletal muscle
Authors: Yuan Renqiang , Zhang Jiaman , Wang Yujie , Zhu Xingxing , Hu Silu , Zeng Jianhua , Liang Feng , Tang Qianzi , Chen Yaosheng , Chen Luxi , Zhu Wei , Li Mingzhou , Mo Delin 
Published: April 2021

Abstract
Myofibres (primary and secondary myofibre) are the basic structure of muscle and the determinant of muscle mass. To explore the skeletal muscle developmental processes from primary myofibres to secondary myofibres in pigs, we conducted an integrative three-dimensional structure of genome and transcriptomic characterization of longissimus dorsi muscle of pig from primary myofibre formation stage [embryonic Day 35 (E35)] to secondary myofibre formation stage (E80). In the hierarchical genomic structure, we found that 11.43% of genome switched compartment A/B status, 14.53% of topologically associating domains are changed intradomain interactions (D-scores) and 2,730 genes with differential promoter–enhancer interactions and (or) enhancer activity from E35 to E80. The alterations of genome architecture were found to correlate with expression of genes that play significant roles in neuromuscular junction, embryonic morphogenesis, skeletal muscle development or metabolism, typically, NEFL, MuSK, SLN, Mef2D and GCK. Significantly, Sox6 and MATN2 play important roles in the process of primary to secondary myofibres formation and increase the regulatory potential score and genes expression in it. In brief, we reveal the genomic reorganization from E35 to E80 and construct genome-wide high-resolution interaction maps that provide a resource for studying long-range control of gene expression from E35 to E80.
Impact of the implantation of one MitraClip on the mitral valve anatomy: NTR vs. XTR
Authors: Kassar M 
Published: April 2021

Abstract

Funding Acknowledgements
Type of funding sources: None.

Introduction
Percutaneous mitral repair using MitraClips (MC) for severe symptomatic regurgitation (MR) has emerge as an alternative treatment for selected high risk surgical patients. Despite the high number of cases treated with both iterations of the MC, the small NTR and the big XTR, the impact of the device size on the mitral valve area (MVA), the morphology of the annulus, the severity of the MR and the use of multiple device is still unknown.

Methods
High quality volume focused on the MV were acquired during each intervention. Using a dedicated 3-D analysis software the dimensions of the annulus, the MVA and the 3-D vena contracta area (VCA) were evaluated before and after clipping. After implantation, the area of both orifices were measured independently and summed.

Results
A total of 120 patients were included, 63 received a NTR and 57 a XTR. Before clipping, XTR cases had bigger MVA (5.9+/-1.7 vs. 4.9+/-1.3 cm2, p .001), a trend toward bigger VCA (0.56+/-0.7 vs. 0.51+/-0.9 cm2, p .073) and no difference in the anteroposterior (AP, 3.5 [3.1-4] vs. 3.5 [3.3-3.8] cm, p .47) and the lateromedial (LM, 4.2 [3.8-4.5] vs. 4.3 [4.0-4.5] cm) diameter of the annulus compared to NTR cases. One MC implantation produced a significant decrease of all these parameters but only MVA was significantly more reduce by XTR (Figure 1). The patients receiving a NTR as first MC did not need more often a second clip (31/63 vs. 26/57, p .072).

Conclusions
On average, both devices produce a MVA reduction of more than 50% and an indirect annuloplasty mainly in the anteroposterior direction. The use of an XTR as first MC do not decrease the probability of the necessity of a second one. All these parameters should be carefully taken into account when defining the implantation strategy. Abstract Figure.