bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression Profiling of Fibroblasts in Chronic and Acute Disease Models Reveals Novel Pathways in Kidney Fibrosis
Authors: Higashi Atsuko Y. , Aronow Bruce J. , Dressler Gregory R. 
Published: December 2018

Background
Renal interstitial fibrosis results from activation and proliferation of fibroblasts to myofibroblasts, secretion and accumulation of extracellular matrix, and displacement of normal renal tubules. In contrast to chronic renal disease, acute injury may be repaired, a process that includes a decrease in the number of myofibroblasts in the interstitium and degradation of the accumulated extracellular matrix, leaving little evidence of prior injury.

Methods
To investigate whether activated fibroblasts demonstrate changes in gene expression that correspond with regression after acute injury but are not observed in chronic models of fibrosis, we used microarrays to analyze gene expression patterns among fibroblast populations at different stages of injury or repair. We then mined the data for signaling pathways in fibroblasts corresponding to the acute proliferative, regression, and chronic phases of renal injury.

Results
We identified multiple gene clusters with changes that correlate with the three phases of renal injury, including changes in levels of receptors for the antifibrotic factor PGE2. In adult renal fibroblast cultures, PGE2 was able to upregulate many genes that are suppressed by the profibrotic cytokine TGF-β, whereas many PGE2-downregulated genes were activated by TGF-β. High levels of TGF-β suppressed expression of a subset of PG receptors in fibroblast cultures, making these cells resistant to any effects of PGE2.

Conclusions
Inherent gene expression changes in activated fibroblasts accompany the transition from AKI to repair and regeneration. In chronic models, however, activated fibroblasts are resistant to the antifibrotic effects of PGE2 due to suppression of a subset of PGE receptors.
Ceramic Industry Wastewater Treatment By Chemical Coagulation Process: A Statistical Optimization of Operating Parameters
Authors: SARI ERKAN Hanife 
Published: December 2018

This study deals with chemical
oxygen demand (COD) removal from ceramic industry wastewater by chemical coagulation
using alum and ferric chloride (FeCl3) as coagulants. The study also
focuses on the capillary suction time (CST) of sludge samples which is an
important sludge dewatering parameter. Response surface methodology (RSM)
approach was employed to evaluate the effects and interactions of the operating
variables and to optimize the performance of the process. Significant quadratic
polynomial models were obtained (R2 = 96.26% for alum and R2=89.15%
for FeCl3 for COD removal; R2
= 96.6% for alum and R2=90.9% for FeCl3 for CST of
sludge, respectively). Alum was more effective coagulant for ceramic industry
wastewater treatment as compared with FeCl3. Numerical optimization
based on desirability function was employed; in a 36 min trial 95.2% of COD
removal was achieved at alum dosage of 3.3 g/L and pH 5. The optimization study
shows that the minimum CST of sludge was found 17.4 s at alum dosage of 5 g/L
and pH 5 in a reaction time of 16 min. The results indicate that the RSM is
suitable for the design and optimization of chemical coagulation process using
alum as a coagulant fort he treatment of ceramic industry wastewater.
A study on the outcome of various methods of administration of intratympanic dexamethasone in tinnitus of cochlear pathology
Authors: Vivek M. , Gowri Shankar M. , Ponraj Kumar N. , Suresh V. 
Published: December 2018

<p class="abstract"><strong>Background:</strong> The aim of the study was to compare the outcome of various methods of injecting intra tympanic steroids in patients with tinnitus of cochlear pathology.</p><p class="abstract"><strong>Methods:</strong> A prospective study was conducted on 56 patients with subjective tinnitus of cochlear pathology who were then divided into three groups. After thorough otological and audiological evaluation using standard questionnaire, ENT examination, pure tone audiometry, tone decay test, tinnitogram, CT scans of temporal bone and brain. Each patient underwent one of the three chosen methods of intra tympanic steroids administration randomly. The methods are 1-Tympanomeatal flap elevationand application of steroid soaked gelfoam sponge; 2-Transtympanic steroid injection; 3-Grommet insertion followed by steroid administration. These methods were performed for subjects with tinnitus of cochlear pathology from 2009 to 2011 at a neurotological clinic at Chennai. After following up on 1st, 3rd and 6 months the observations were statistically analysed. </p><p class="abstract"><strong>Results:</strong> Success rate for techniques viz tympanomeatal flap was 70%, transtympanic - 63%, grommet - 50%. But when comparing statistically all the three methods were equally successful.</p><p class="abstract"><strong>Conclusions:</strong> Intratympanic steroids for tinnitus (cochlear pathology) are a safe, simple and promising treatment option. Though all the methods of intra tympanic steroids injection had similar success rate, the tympanomeatal flap elevation method may be preferred since it can be done in a single sitting. However transtympanic injection remains the easiest and cost effective compared to the other two methods.</p>
The impact of dental anxiety and dental fear on the periodontal status and quality of life among dental patients
Authors: Penteado Luiz Alexandre Moura , Pinho Roberto Carlos Mourão , Santos Natanael Barbosa dos , Vajgel Bruna de Carvalho Farias , Cimões Renata 
Published: December 2018

Aim: The aim of the study was to investigate levels of Dental Fear (DF) and Dental Anxiety (DA) among individuals awaiting appointments at the clinics of two courses in dentistry and determine the impact on oral health status and quality of life. Methods: An observational study was conducted with a sample of adult dental patients. Levels of DF and DA and the perception of quality of life were determined using questionnaires and periodontal data. Results: Among the 287 subjects, 71.4% were female, 7.3% were classified as very anxious and 16% were classified as anxious. Gender was significantly associated with DA (p = 0.001); 20% of the female volunteers and 6.1% of the males were classified as anxious. The frequency of moderate and extreme fear was 42.9% and was not significantly correlated with gender (p = 0.071). The prevalence of a negative impact from oral health status on quality of life (measured using the OHIP-14 scale) was 38.3% and income was significantly associated with this outcome (p = 0.000). Conclusion: Levels of DA and DF were substantial among the individuals analyzed. Women with a lower education were susceptible to anxiety. DA and DF were associated with periodontal status or impact on quality of life.
Vascular Parameters of Normal Cynomolgus Macaques by Fundus Fluorescence Angiography and Optical Coherence Tomography Angiography
Authors: Peng Jingyi , Zhong Liuxueying , Ma Li , Jin Jiayi , Zheng Yongxin 
Published: December 2018

Abstract
Background: To provide normal vascular parameters for cynomolgus macaques. Compare the advantages and disadvantages of Fundus fluorescence angiography (FFA) and Optical coherence tomography angiography (OCT-A) in angiography. To establish an eye parameter database for cynomolgus macaques.
Methods: Five normal cynomolgus macaques were studied for the collection of data, with a mean age of 4.6±0.55 years. The Heldelberg Spectralis® HRA+OCT was used to obtain parameters for Fundus fluorescence angiography (FFA). The vessel density was measured using the RTVue XR with AngioVue (software version 2017.1.0.155; Optovue, Inc., Fremont, CA, USA); the scan sizes of the macular and optic discs were 3×3mm and 4.5×4.5mm, respectively.
Results: Cynomolgus macaque's fundus fluorescence angiography had similar stages as those found in humans. Optical coherence tomography can image the superficial, deep capillary plexus and the radial peripapillary capillary network. The highest whole En-face mean vessel density (VD) in the macular area was 68.19±0.75 % in the choroid capillary layer. In both layers of the optic disc, the vessel density in the Nasal quadrant was lower than in the inferior-tempo quadrant.
Conclusions: This is a rare research, where we have collected the normal FFA and the novel OCT-A parameters for cynomolgus macaques. This study provides normal vascular parameters of cynomolgus macaques via Fundus fluorescence angiography (FFA) and Optical coherence tomography angiography (OCT-A), helping to establish an optical parameter database for cynomolgus macaques, promoting choroid-retinopathy research.
Nitrogen Source and Rate Effects on Irrigated Potato in Tropical Sandy Soils
Authors: Souza Emerson F. C. , Soratto Rogério P. , Fernandes Adalton M. , Rosen Carl J. 
Published: December 2018

Core Ideas
A suitable nitrogen source and optimum nitrogen rate can improve potato yield and nitrogen‐use efficiency in tropical sandy soils.
Regardless of the nitrogen source, the nitrogen fertilization increased the potato tuber yield up to rates between 136 kg nitrogen ha−1 and at least 160 kg nitrogen ha−1.
Ammonium sulfate nitrate plus DMPP promoted greater total and marketable tuber yields than urea and higher agronomic efficiency compared to urea and ammonium sulfate.
There is a potential for ammonium sulfate nitrate plus DMPP to improve the synchronization between soil nitrogen availability and potato nitrogen demand when potato is cultivated in a tropical sandy soil.
A suitable N source and an optimal application rate can improve the N‐use efficiency of potato (Solanum tuberosum L.) while minimizing N losses, especially when potato is grown in sandy soils. Three experiments were conducted at irrigated sandy soil sites in São Paulo State, Brazil, to evaluate the effects of ammonium sulfate (AMS), ammonium sulfate nitrate with the nitrification inhibitor 3,4‐dimethylpyrazole phosphate (ASN+DMPP), and urea applied at three N rates (80, 120, and 160 kg ha−1), as well as a zero‐N control on potato (cv. Agata). Leaf N and S concentrations, tuber yield, and agronomic efficiency (AE) were measured. The 80 kg N ha−1 rate was applied in the furrow at planting, and the other rates were split‐applied, with 40 kg N ha−1 in the furrow at planting and the remainder applied at hilling. Regardless of the N source, the N fertilizer rates increased the potato leaf N concentration and tuber bulking of the potato crop, which in turn increased the tuber yield up to rates between 136 kg N ha−1 and at least 160 kg N ha−1. Among the N sources, ASN+DMPP fertilizer resulted in a higher potato tuber set and yield than urea and led to the highest AE compared to AMS and urea. Overall, these results suggest the potential for ASN+DMPP to improve the synchronization between soil N availability and potato N demand and provide a more appropriate balance of N forms in the soil when potato is cultivated in sandy soils in a tropical climate.
Three Two‐Dimensional Approaches for Simulating the Water Flow Dynamics in a Heterogeneous Tile‐Drained Agricultural Field in Denmark
Authors: Varvaris Ioannis , Børgesen Christen Duus , Kjærgaard Charlotte , Iversen Bo V. 
Published: December 2018

Core Ideas
Simulating water flow dynamics in a clayey subsurface drained agricultural field.
Three two‐dimensional models incorporating preferential water flow were used.
All models produced a reasonably good fit to the hydrograph features.
Examine models' capabilities and weaknesses for simulating the drainage dynamics.
Non‐equilibrium preferential flow has received increasing attention in modeling water flow dynamics across tile‐drained agricultural fields. The HYDRUS‐2D software package was used in this study to generate a hydrogeological model for simulating the water flow dynamics across hydro‐topographical gradients and drainage sequences at drainage subcatchment (western part of Norsminde catchment in Denmark). The selected study area is characterized by spatial variability in the geological, stratified heterogeneity. Three two‐dimensional models incorporating preferential water flow were used to examine the ability of each approach to predict the drainage dynamics and water balance in a clayey subsurface drained agricultural field: (i) a single‐porosity model, (ii) a dual‐porosity model, and (iii) a dual‐permeability model. The initial parameterization of the models relied on in situ observations of soil structure, soil hydraulic property maps of Denmark and pedotransfer functions. The models, once calibrated against observed drainage data, were used for the reproduction of the subsurface drainage water dynamics for different time periods for the specific agricultural landscape. The different conceptual approaches gave a fairly good fit to the hydrograph features for both the calibration and validation datasets. The predictive ability of all models for the calibration dataset was fairly similar, while for the first and second validation datasets better results were obtained with the dual‐porosity and dual‐permeability models, respectively. The calibrated values of the effective parameters had been examined using laboratory data and in situ measurements of the groundwater level to evaluate how well these parameters physically represent the flow domain.
Long-term streamflow forecasting for the Cascade Reservoir System of Han River using SWAT with CFS output
Authors: Liu Tian , Chen Yuanfang , Li Binquan , Hu Yiming , Qiu Hui , Liang Zhongmin 
Published: December 2018

Abstract
Due to the large uncertainties of long-term precipitation prediction and reservoir operation, it is difficult to forecast long-term streamflow for large basins with cascade reservoirs. In this paper, a framework coupling the original Climate Forecasting System (CFS) precipitation with the Soil and Water Assessment Tool (SWAT) was proposed to forecast the nine-month streamflow for the Cascade Reservoir System of Han River (CRSHR) including Shiquan, Ankang and Danjiangkou reservoirs. First, CFS precipitation was tested against the observation and post-processed through two machine learning algorithms, random forest and support vector regression. Results showed the correlation coefficients between the monthly areal CFS precipitation (post-processed) and observation were 0.91–0.96, confirming that CFS precipitation post-processing using machine learning was not affected by the extended forecast period. Additionally, two precipitation spatio-temporal distribution models, original CFS and similar historical observation, were adopted to disaggregate the processed monthly areal CFS precipitation to daily subbasin-scale precipitation. Based on the reservoir restoring flow, the regional SWAT was calibrated for CRSHR. The Nash–Sutcliffe efficiencies for three reservoirs flow simulation were 0.86, 0.88 and 0.84, respectively, meeting the accuracy requirement. The experimental forecast showed that for three reservoirs, long-term streamflow forecast with similar historical observed distribution was more accurate than that with original CFS.
A Nonmathematical Review of Optimal Operator and Experimental Design for Uncertain Scientific Models with Application to Genomics
Authors: Dougherty Edward R. 
Published: December 2018

Introduction:
The most basic aspect of modern engineering is the design of operators to act on physical systems in an optimal manner relative to a desired objective – for instance, designing a
control policy to autonomously direct a system or designing a classifier to make decisions regarding
the system. These kinds of problems appear in biomedical science, where physical models are created
with the intention of using them to design tools for diagnosis, prognosis, and therapy.

Methods:
In the classical paradigm, our knowledge regarding the model is certain; however, in
practice, especially with complex systems, our knowledge is uncertain and operators must be designed
while taking this uncertainty into account. The related concepts of intrinsically Bayesian robust
operators and optimal Bayesian operators treat operator design under uncertainty. An objective-based
experimental design procedure is naturally related to operator design: We would like to perform an
experiment that maximally reduces our uncertainty as it pertains to our objective.

Results & Discussion:
This paper provides a nonmathematical review of optimal Bayesian operators
directed at biomedical scientists. It considers two applications important to genomics, structural
intervention in gene regulatory networks and classification.

Conclusion:
The salient point regarding intrinsically Bayesian operators is that uncertainty is
quantified relative to the scientific model, and the prior distribution is on the parameters of this model.
Optimization has direct physical (biological) meaning. This is opposed to the common method of
placing prior distributions on the parameters of the operator, in which case there is a scientific gap between
operator design and the phenomena.
Accurate and Unbiased Quantitation of Amyloid-β Fluorescence Images Using ImageSURF
Authors: O'Mara Aidan R. , Collins Jessica M. , King Anna E. , Vickers James C. , Kirkcaldie Matthew T.K. 
Published: December 2018

Background:
Images of amyloid-β pathology characteristic of Alzheimer’s disease are difficult
to consistently and accurately segment, due to diffuse deposit boundaries and imaging variations.

Methods:
We evaluated the performance of ImageSURF, our open-source ImageJ plugin, which considers
a range of image derivatives to train image classifiers. We compared ImageSURF to standard image
thresholding to assess its reproducibility, accuracy and generalizability when used on fluorescence images
of amyloid pathology.

Results:
ImageSURF segments amyloid-β images significantly more faithfully, and with significantly
greater generalizability, than optimized thresholding.

Conclusion:
In addition to its superior performance in capturing human evaluations of pathology images,
ImageSURF is able to segment image sets of any size in a consistent and unbiased manner, without requiring
additional blinding, and can be retrospectively applied to existing images. The training process
yields a classifier file which can be shared as supplemental data, allowing fully open methods and data,
and enabling more direct comparisons between different studies.
Outcomes of Perilla Seed Oil as an Additional Neuroprotective Therapy in Patients with Mild to Moderate Dementia: A Randomized Control Trial
Authors: Kamalashiran Chuntida , Sriyakul Kusuma , Pattaraarchachai Junya , Muengtaweepongsa Sombat 
Published: December 2018

Background:
Dementia is a common medical disorder in the elderly. Oxidative stress plays a
major role in the process of cognitive decline in dementia. Perilla seed oil demonstrates its neuroprotective
effects via anti-oxidative mechanisms against dementia. We investigate neuroprotective effects of
perilla seed oil as an additional treatment in patients with mild to moderate dementia.
</P><P>
Method: A double-blind, randomized-control trial (perilla seed oil versus placebo) in patients with mild
to moderate dementia was conducted. Perilla seed oil or placebo was added on with standard treatment
for six months. Cognitive function was compared at nine months after enrollment.
</P><P>
Result: 182 patients, with 94 in the experimental group and 88 in the placebo group, were able to complete
the study. Cognitive function is not significantly different compared between groups. However, the
total cholesterol and LDL cholesterol were significantly lower in the experimental group. Perilla seed oil
had no adverse effect to kidney, liver, blood components or glucose metabolism.

Conclusion:
Perilla seed oil as additional neuroprotective therapy in patients with mild to moderate dementia
does not improve cognitive function. Perilla seed oil significantly reduced total cholesterol and
LDL cholesterol. A clinical trial is needed to prove the benefit of cholesterol-lowering effects with perilla
seed oil in human.
Computational and In-Vitro Validation of Natural Molecules as Potential Acetylcholinesterase Inhibitors and Neuroprotective Agents
Authors: Kumar Ashwani , Mehta Vineet , Raj Utkarsh , Varadwaj Pritish Kumar , Udayabanu Malairaman , Yennamalli Ragothaman M. , Singh Tiratha Raj 
Published: December 2018

Background:
Cholinesterase inhibitors are the first line of therapy for the management of
Alzheimer’s disease (AD), however, it is now established that they provide only temporary and symptomatic
relief, besides, having several inherited side-effects. Therefore, an alternative drug discovery
method is used to identify new and safer ‘disease-modifying drugs’.

Methods:
Herein, we screened 646 small molecules of natural origin having reported pharmacological
and functional values through in-silico docking studies to predict safer neuromodulatory molecules with
potential to modulate acetylcholine metabolism. Further, the potential of the predicted molecules to inhibit
acetylcholinesterase (AChE) activity and their ability to protect neurons from degeneration was
determined through in-vitro assays.

Results:
Based on in-silico AChE interaction studies, we predicted quercetin, caffeine, ascorbic acid and
gallic acid to be potential AChE inhibitors. We confirmed the AChE inhibitory potential of these molecules
through in-vitro AChE inhibition assay and compared results with donepezil and begacestat. Herbal
molecules significantly inhibited enzyme activity and inhibition for quercetin and caffeine did not show
any significant difference from donepezil. Further, the tested molecules did not show any neurotoxicity
against primary (E18) hippocampal neurons. We observed that quercetin and caffeine significantly improved
neuronal survival and efficiently protected hippocampal neurons from HgCl2 induced neurodegeneration,
which other molecules, including donepezil and begacestat, failed to do.

Conclusion:
Quercetin and caffeine have the potential as “disease-modifying drugs” and may find application
in the management of neurological disorders such as AD.
The Temporal Relationship between Pain Intensity and Pain Interference and Incident Dementia
Authors: Ezzati Ali , Wang Cuiling , Katz Mindy J. , Derby Carol A. , Zammit Andrea R. , Zimmerman Molly E. , Pavlovic Jelena M. , Sliwinski Martin J. , Lipton Richard B. 
Published: December 2018

Background:
Chronic pain is common among older adults and is associated with cognitive
dysfunction based on cross-sectional studies. However, the longitudinal association between chronic
pain and incident dementia in community-based samples is unknown.

Objective:
We aimed to evaluate the association of pain intensity and pain interference with incident
dementia in a community-based sample of older adults.

Methods:
Participants were 1,114 individuals 70 years of age or older from Einstein Aging Study
(EAS), a longitudinal cohort study of community-dwelling older adults in the Bronx County, NY. The
primary outcome measure was incident dementia, diagnosed using DSM-IV criteria. Pain intensity and
interference in the month prior to first annual visit were measured using items from the SF-36 questionnaire.
Pain intensity and pain interference were assessed as predictors of time to incident dementia using
Cox proportionate hazards models while controlling for potential confounders.

Results:
Among participants, 114 individuals developed dementia over an average 4.4 years (SD=3.1) of
follow-up. Models showed that pain intensity had no significant effect on time to developing dementia,
whereas higher levels of pain interference were associated with a higher risk of dementia. In the model
that included both pain intensity and interference as predictors of incident dementia, pain interference
had a significant effect on incident dementia, and pain intensity remained non-significant.

Conclusion:
As a potential remediable risk factor, the mechanisms linking pain interference to cognitive
decline merit further exploration.