bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential of the C Genome of Different Variants of Brassica oleracea for the Improvement of Agronomic and Seed Quality Traits of B. napus Canola
Authors: Nikzad Azam , Kebede Berisso , Pinzon Jaime , Bhavikkumar Jani , Yang Rong‐Cai , Rahman Habibur 
Published: October 2019

ABSTRACTThe narrow genetic base of Brassica napus L. canola, especially of its C genome, is an impediment for continued improvement of this crop. We investigated the gene pools of different variants of B. oleracea L. to improve agronomic and seed quality traits of B. napus canola. For this, B. napus canola inbred populations were developed from six interspecific crosses, involving a single B. napus canola line and six accessions of B. oleracea belonging to four variants of this species, following two breeding techniques (F2– and BC1–derived lines). Among these, the population derived from crossing with var. italica gave the greatest seed yield and also had shorter duration of flowering than most of the other populations. The population developed using var. botrytis had the highest seed oil content, and seed yield was comparable with the population developed using var. italica. Populations based on var. capitata had the lowest oil but greater protein content than most of the populations. Several lines from these interspecific crosses exceeded seed yield of the B. napus parent and also had acceptable agronomic and seed quality traits. Comparing the two breeding techniques, the F2–derived population gave greater yield than the BC1–derived population, whereas the BC1–derived population flowered and matured earlier than the F2–derived population. Genetic distance of the inbred lines from the B. napus parent showed positive correlation of r ≥ 0.4 with days to flowering and seed protein content and negative correlation with seed oil content, whereas correlation with seed yield was negative and weak (r = −0.18). Thus, the results showed that the B. oleracea gene pool, especially var. italica and botrytis, can be used to improve spring B. napus canola, as well as to broaden the genetic base of this crop.
Shade Effects on Overseeded Bermudagrass Athletic Fields: II. Rooting, Species Composition, and Traction
Authors: Richardson Michael D. , Mattina Girolamo , Sarno Mauro , McCalla John H. , Karcher Douglas E. , Thoms Adam W. , Dickson Kyley H. , Sorochan John C. 
Published: October 2019

ABSTRACTShade from athletic stadium structures can be a significant detriment to turfgrass performance. The objective of this study was to determine the effects of shade on rooting and playing surface stability, measured as traction, on overseeded or non‐overseeded bermudagrass (Cynodon spp.) turf. An experiment was established in 2013 on a mature bermudagrass [Cynodon dactylon (L.) Pers. cv. Riviera] turf that was either overseeded with perennial ryegrass (Lolium perenne L.) or non‐overseeded. Shade structures were installed to create four light level treatments, including 0%, 30%, 60%, or 90% light‐reducing shade cloth. The light treatments resulted in average daily light integrals (DLI) of 40.8, 26.2, 14.8, and 3.3 mol m–2 d–1, respectively. Data were collected on rooting characteristics, species composition, and two forms of traction measurements. Moderate levels of shading (30%) caused a significant decline in rooting characteristics in non‐overseeded turf, while rooting of overseeded turf was not significantly affected until a 60% light reduction. Rotational resistance and peak horizontal force, measurements of athlete traction, were affected by increasing shade in both overseeded and non‐overseeded turf, but the association between traction and a minimum DLI was not conclusive. The persistence of bermudagrass in overseeded turf was significantly reduced at all shade levels studied. This study clearly demonstrates that rooting, bermudagrass persistence and traction of overseeded and non‐overseeded bermudagrass athletic fields are negatively affected by even modest levels of shade.
Quantifying Physical Properties of Three Sphagnum‐Based Growing Media as Affected by Drying–Wetting Cycles
Authors: Turunen M. , Hyväluoma J. , Heikkinen J. , Keskinen R. , Kaseva J. , Koestel J. , Rasa K. 
Published: October 2019

Core Ideas
3D imaging and conventional observations revealed growing media physical properties.
Decomposition degree controlled porosity and pore‐size distributions.
Aeration was typically low when the amount of easily available water was sufficient.
Materials shrunk when desorbed but mostly recovered their structure during wetting.
It was shown how moisture retention, aeration, and shrinkage were interlinked.
The suitability of organic materials as growing media in plant production is largely dependent on their physical properties. However, the properties and impacts of different stress factors on Sphagnum‐based materials are not fully understood. This study aimed to quantify differences in water retention, aeration, and pore structure characteristics of three different low‐ or non‐humified Sphagnum‐based growing media using three‐dimensional (3D) X‐ray imaging and conventional physical measurements. In addition, we assessed the impacts of intense drying–wetting cycles on their pore structure. The imaged porosities of the materials differed significantly with decomposition degree. Drying curve observations showed that drying of the materials occurred in three phases with (i) large changes in the air‐filled porosity in the matric potential range 0.2 to 3.2 kPa, (ii) clearly smaller changes at 3.2 to 312 kPa, and (iii) large changes at 312 to 1585 kPa, comparable to the change in the wet end of the drying curves (0.2–3.2 kPa). The aeration of the materials was sufficient for plant growth in the second and third phases, where the amount of easily available water was low. This challenges the suitability of the materials under conditions without regular irrigation. The 3D imaging also revealed how pore‐size distributions shifted toward smaller pore‐size classes with increasing decomposition degree and stress impact of the drying–wetting cycles. However, unexpectedly most of the imaged porosity (≥97%) and height (96–98%) of the samples was recovered during rewetting. Overall, the results demonstrate how the water retention, aeration, and shrinkage properties of growing media are inherently interlinked.
Desenvolvimento Sustentável: um discurso em disputa
Authors: Sugahara Cibele Roberta , Rodrigues Eduardo Luiz 
Published: October 2019

Presente na agenda global durante praticamente toda a segunda metade do século XX e início do século XXI, e formalmente institucionalizado em 1987 pela Organização das Nações Unidas, o Desenvolvimento Sustentável é hoje uma das maiores preocupações da humanidade e um discurso em constante disputa. O conceito apresenta relação com os conceitos desenvolvimento e sustentabilidade, o Desenvolvimento Sustentável é importante para a compreensão e resolução de problemas enfrentados pela humanidade. A literatura aponta que é um conceito ainda em construção. Este artigo busca apresentar o Desenvolvimento Sustentável enquanto campo de disputa ideologica que enfrenta embates conceituais e políticos. É importante reconhecer que o Desenvolvimento Sustentável não está desvinculado dos níveis de consumo e produção de que trata o seu escopo conceitual. Por isso, as relações de poder rumo ao Desenvolvimento Sustentável precisam desembocar em um agenciamento coletivo. Assim, o objetivo deste estudo é descrever a disputa pelo conceito de Desenvolvimento Sustentável existente entre as teorias da Sustentabilidade Forte e da Sustentabilidade Fraca. Os resultados obtidos foram analisados pelos autores e ajudaram a traçar um panorama temporal dos embates travados entre estas duas linhas teóricas antagônicas.
Optimization method for joint operation of a double-reservoir-and-double-pumping-station system: a case study of Nanjing, China
Authors: Gong Zhihao , Jiang Xiaohong , Cheng Jilin , Gong Yi , Chen Xing , Cheng Haomiao 
Published: October 2019

Abstract
Double-reservoir-and-double-pumping-station systems are commonly used for irrigation water supply in hilly regions of southern China. An optimization model for this water supply system is proposed to minimize water shortage. The model features few coupling constraints, including available water in the system and pumping volume limited by regional water rights. Dynamic programming was adopted to solve the subsystem and aggregation models. The results with the model and that with the standard operation policy were compared; the total water shortage was reduced by 87.7%, total water replenishment from outside was reduced by 2.2%, and total water spill was reduced by 60.6% for a system in Nanjing, China. The method may provide a reference for optimal operation of water supply systems comprising reservoirs and pumping stations.
In Silico Drug Repositioning for Chagas Disease
Authors: Bellera Carolina L. , Alberca Lucas N. , Sbaraglini María L. , Talevi Alan 
Published: October 2019

:
Chagas disease is an infectious tropical disease included within the group of neglected tropical
diseases. Though historically endemic to Latin America, it has lately spread to high-income countries
due to human migration. At present, there are only two available drugs, nifurtimox and benznidazole,
approved for this treatment, both with considerable side-effects (which often result in treatment
interruption) and limited efficacy in the chronic stage of the disease in adults.

:
Drug repositioning involves finding novel therapeutic indications for known drugs, including approved,
withdrawn, abandoned and investigational drugs. It is today a broadly applied approach to develop
innovative medications, since indication shifts are built on existing safety, ADME and manufacturing
information, thus greatly shortening development timeframes. Drug repositioning has been signaled as
a particularly interesting strategy to search for new therapeutic solutions for neglected and rare conditions,
which traditionally present limited commercial interest and are mostly covered by the public
sector and not-for-profit initiatives and organizations.

:
Here, we review the applications of computer-aided technologies as systematic approaches to drug
repositioning in the field of Chagas disease. In silico screening represents the most explored approach,
whereas other rational methods such as network-based and signature-based approximations have still
not been applied.
New Amine and Aromatic Substituted Analogues of Phencyclidine: Synthesis and Determination of Acute and Chronic Pain Activities
Authors: Shokrollahi Maryam , Samadizadeh Marjaneh , Khalili Mohsen , Sobhanian Seyed A. , Ahmadi Abbas 
Published: October 2019

Background:
Phencyclidine (PCP, I) is a synthetic drug with remarkable physiological
properties. PCP and its analogues exert many pharmacological activities and interact with some
neurotransmitter systems in the central nervous system like particular affinity for PCP sites in
NMDA receptors or dopamine uptake blocking or even both.

Aim and Objective:
The following research, methyl group with electron-donating and dipole
moment characters was added in different positions of phenyl ring along with the substitution of
benzylamine (with many pharmacological effects) instead of piperidine ring of I to produce new
compounds (II-V) of this family with more analgesic activities.

Materials and Methods:
Analgesic activities of these new compounds were measured by tail
immersion and formalin tests for acute and chronic pains, respectively. Also, the outcomes were
compared with control and PCP (10 mg/kg) groups.

Results:
The results indicate that compounds III, IV, and V have more acute and chronic
antinociceptive effects than PCP and compound II which may be concerned with more antagonizing
activities of these new painkillers for the blockage of dopamine reuptake as well as high affinity for
NMDA receptors PCP binding site.

Conclusion:
It can be concluded that the benzylamine derivative of phencyclidine with a methyl
group on the benzyl position on phenyl ring (V) is a more appropriate candidate to reduce acute and
chronic (thermal and chemical) pains compared to other substituted phenyl analogs (II-IV) and PCP.
Uptake of [¹⁸F]tetrafluoroborate in MCF-7 Breast Cancer Cells is Induced after Stimulation of the Sodium Iodide Symporter
Authors: Lehmacher Marc , Stolzenburg Antje , Samnick Samuel 
Published: October 2019

Background:
The human sodium iodide symporter (hNIS) has been the most important
target in nuclear medicine regarding thyroid-related diseases. Although hNIS-expression can also be
determined in extra-thyroidal tumors, imaging hNIS with positron emission tomography has not
been exploited clinically.

Objective:
Here, we evaluated the accumulation of the novel hNIS-substrate [18F]tetrafluoroborate
([18F]TFB) in the endogenously hNIS-expressing breast cancer cell line MCF-7 after an improved
radiosynthesis and pharmacological stimulation.

Methods:
[18F]TFB was prepared under mild reaction conditions (40°C, 25 min) and its uptake properties
were investigated in MCF-7 cells pretreated with a combination of all-trans retinoic acid plus
methasone-derivatives and compared to the clinically established tracers [131I]iodide and
[99mTc]pertechnetate. Specificity of the tracer accumulation was assessed by inhibition experiments
using NaBF4, KSO3F, KI and KIO3.

Results:
[18F]TFB was obtained with a radiochemical yield of 24.0 ± 6.6 % (n = 17) within 40 min
after high pressure liquid chromatography-separation and with 26.8 ± 6.2 % (n = 13) within 45 min
after adapting the procedure on a synthesis module using higher starting activities (> 10 GBq). After
pharmacological treatment, a 4-fold increase in hNIS-expression on the MCF-7 cell surface was
achieved, resulting in a significantly higher [18F]TFB uptake into the cells (up to 58-fold) as compared
to control experiments. Inhibition studies using various NIS-substrates confirmed the specificity
of [18F]TFB for hNIS.

Conclusions:
[18F]TFB was shown to be a promising hNIS-substrate in our model using the human
MCF-7 breast cancer cell line mandating in vivo evaluations in xenografted studies and in patients.
Drug Choices and Advancements for Managing Depression in Parkinson's Disease
Authors: Assogna Francesca , Pellicano Clelia , Savini Cinzia , Macchiusi Lucia , Pellicano Gaia R. , Alborghetti Marika , Caltagirone Carlo , Spalletta Gianfranco , Pontieri Francesco E. 
Published: October 2019

:Depression is a frequent non-motor symptom of Parkinson’s disease (PD), and may even precede the onset of motor symptoms of parkinsonism. Beyond its negative influence on mood, depression in PD is frequently associated with other neuropsychiatric symptoms and with late-stage complications such as dementia. Despite its profound impact on the quality of life and cognitive functioning in PD, depression in PD is often under-recognized and poorly treated.:Pathophysiological studies demonstrated that depression in PD is associated with global dysfunction of interactions between discrete brain areas rather than focal structural or functional abnormalities, and that it is sustained by pathological changes of several neurotransmitter/receptor complexes.:In general, all traditional antidepressants and some dopamine agonists have been found to be safe and well-tolerated to treat depressive symptoms in PD, despite initial warning on worsening of parkinsonism. Available data suggest that the time-course of response differs among antidepressants. Efficacy results from clinical trials with antidepressant in PD are, however, rather uncertain, although pooled analysis suggests a moderate benefit. Several issues may critically impact the results of clinical trials with antidepressants in PD, including the correct psychiatric diagnosis, the overlap of symptoms between depression and PD, and the selection of appropriate end-points and rating scales.
Comparative Effectiveness of Agmatine and Choline Treatment in Rats with Cognitive Impairment Induced by AlCl3 and Forced Swim Stress
Authors: Rafi Hira , Ahmad Fahad , Anis Javaria , Khan Ruba , Rafiq Hamna , Farhan Muhammad 
Published: October 2019

Aim:Endogenous agmatine has a significant role in learning and memory processes as a neurotransmitter. Various studies described the physiological role of endogenous agmatine in learning and memory of multiple cognitive tasks suggesting elevated levels of agmatine during the learning process in the rat brain. Dietary intake of choline showed correlation with cognitive functions in human subjects and treatment with choline supplements validated the ability to diminish learning and cognitive impairment dementias.Methods:36 Albino rats were equally divided into three groups previously: a) control-water, b) Test I - AlCl3 (100 mg/Kg body weight), and c) Test II - Forced swim stress (FSS) for 14 days. On the next day of AlCl3 and FSS last administration, animals were allocated into further three groups and received the following treatments: a. water was given orally to the control group, b. Agmatine (100 mg/Kg Body Weight) group, and c. Choline (100 mg/Kg Body Weight) group for the next 14 days. Behaviors were assessed in Light/Dark Box, Open Field, Novel Object Recognition Test (NOR), T Maze Test, and Morris Water Maze Test.Results:Animals administered with agmatine demonstrated increased time spent in bright areas of light/dark box and square crossed while improved spatial memory in Morris water maze and T maze test and enhanced discrimination of novel object in NOR were observed in learning and memory paradigms along with choline.Conclusion:The present study determines that agmatine at the dose of (100 mg/kg body weight) attenuates memory and cognitive impairment in comparison with choline supplements.
SimExact – An Efficient Method to Compute Function Similarity Between Proteins Using Gene Ontology
Authors: Ikram Najmul , Qadir Muhammad Abdul , Afzal Muhammad Tanvir 
Published: October 2019

Background:
The rapidly growing protein and annotation databases necessitate the development
of efficient tools to process this valuable information. Biologists frequently need to
find proteins similar to a given protein, for which BLAST tools are commonly used. With the development
of biomedical ontologies, e.g. Gene Ontology, methods were designed to measure
function (semantic) similarity between two proteins. These methods work well on protein pairs,
but are not suitable for protein query processing.

Objective:
Our aim is to facilitate searching of similar proteins in an acceptable time.

Methods:
A novel method SimExact for high speed searching of functionally similar proteins has
been proposed.

Results:
The experiments of this study show that SimExact gives correct results required for protein
searching. A fully functional prototype of an online tool (www.datafurnish.com/protsem.php)
has been provided that generates a ranked list of the proteins similar to a query protein, with a response
time of less than 20 seconds in our setup. SimExact was used to search for protein pairs
having high disparity between function similarity and sequence similarity.

Conclusion:
SimExact makes such searches practical, which would not be possible in a reasonable
time otherwise.
Application of a Deep Matrix Factorization Model on Integrated Gene Expression Data
Authors: Hao Yong-Jing , Hou Mi-Xiao , Gao Ying-Lian , Liu Jin-Xing , Kong Xiang-Zhen 
Published: October 2019

Background:
Non-negative Matrix Factorization (NMF) has been extensively used in
gene expression data. However, most NMF-based methods have single-layer structures, which
may achieve poor performance for complex data. Deep learning, with its carefully designed hierarchical
structure, has shown significant advantages in learning data features.

Objective:
In bioinformatics, on the one hand, to discover differentially expressed genes in gene
expression data; on the other hand, to obtain higher sample clustering results. It can provide the
reference value for the prevention and treatment of cancer.

Method:
In this paper, we apply a deep NMF method called Deep Semi-NMF on the integrated
gene expression data. In each layer, the coefficient matrix is directly decomposed into the basic
and coefficient matrix of the next layer. We apply this factorization model on The Cancer Genome
Atlas (TCGA) genomic data.

Results:
The experimental results demonstrate the superiority of Deep Semi-NMF method in identifying
differentially expressed genes and clustering samples.

Conclusion:
The Deep Semi-NMF model decomposes a matrix into multiple matrices and multiplies
them to form a matrix. It can also improve the clustering performance of samples while digging
out more accurate key genes for disease treatment.
Protein Secondary Structure Prediction: A Review of Progress and Directions
Authors: Smolarczyk Tomasz , Roterman-Konieczna Irena , Stapor Katarzyna 
Published: October 2019

Background:
Over the last few decades, a search for the theory of protein folding has
grown into a full-fledged research field at the intersection of biology, chemistry and informatics.
Despite enormous effort, there are still open questions and challenges, like understanding the rules
by which amino acid sequence determines protein secondary structure.

Objective:
In this review, we depict the progress of the prediction methods over the years and
identify sources of improvement.

Methods:
The protein secondary structure prediction problem is described followed by the discussion
on theoretical limitations, description of the commonly used data sets, features and a review
of three generations of methods with the focus on the most recent advances. Additionally, methods
with available online servers are assessed on the independent data set.

Results:
The state-of-the-art methods are currently reaching almost 88% for 3-class prediction and
76.5% for an 8-class prediction.

Conclusion:
This review summarizes recent advances and outlines further research directions.
Immune-Inflammation in Atherosclerosis: A New Twist in an Old Tale
Authors: Talepoor Atefe Ghamar , Fouladseresht Hamed , Khosropanah Shahdad , Doroudchi Mehrnoosh 
Published: October 2019

Background and Objective:Atherosclerosis, a chronic and progressive inflammatory disease, is triggered by the activation of endothelial cells followed by infiltration of innate and adaptive immune cells including monocytes and T cells in arterial walls. Major populations of T cells found in human atherosclerotic lesions are antigen-specific activated CD4+ effectors and/or memory T cells from Th1, Th17, Th2 and Treg subsets. In this review, we will discuss the significance of T cell orchestrated immune inflammation in the development and progression of atherosclerosis.Discussion:Pathogen/oxidative stress/lipid induced primary endothelial wound cannot develop to a full-blown atherosclerotic lesion in the absence of chronically induced inflammation. While the primary inflammatory response might be viewed as a lone innate response, the persistence of such a profound response over time must be (and is) associated with diverse local and systemic T cell responses. The interplay between T cells and innate cells contributes to a phenomenon called immuneinflammation and has an impact on the progression and outcome of the lesion. In recent years immuneinflammation, an old term, has had a comeback in connecting the puzzle pieces of chronic inflammatory diseases.Conclusion:Taking one-step back and looking from afar at the players of immune-inflammation may help us provide a broader perspective of these complicated interactions. This may lead to the identification of new drug targets and the development of new therapies as well as preventative measures.