bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSL-Recommender: Protein Subcellular Localization Prediction using Recommender System
Authors: Jamali Ruhollah , Jahangiri-Tazehkand Soheil , Eslahchi Changiz 
Published: September 2021

Abstract
Identifying a protein’s subcellular location is of great interest for understanding its function and behavior within the cell. In the last decade, many computational approaches have been proposed as a surrogate for expensive and labor-intensive wet-lab methods that are used for protein subcellular localization. Yet, there is still much room for improving the prediction accuracy of these methods. In this article, we meant to develop a customized computational method rather than using common machine learning predictors, which are used in the majority of computational research on this topic. The neighbourhood regularized logistic matrix factorization technique was used to create PSL-Recommender (Protein subcellular location recommender), a GO-based predictor. We declared statistical inference as the driving force behind the PSL-Recommender here. Following that, it was benchmarked against twelve well-known methods using five different datasets, demonstrating outstanding performance. Finally, we discussed potential research avenues for developing a comprehensive prediction tool for protein subcellular location prediction. The datasets and codes are available at: https://github.com/RJamali/PSL-Recommender
Differences in distribution and community structure of plant-parasitic nematodes in pecan orchards between two ecoregions of Georgia
Authors: Jagdale Ganpati B. , Brenneman Timothy B. , Severns Paul M. , Shapiro-Ilan David 
Published: September 2021

Abstract
In Georgia, pecans are commercially grown in the Piedmont and Coastal Plain ecoregions which are characterized by sandy-loam, sandy, and/or clay soils. If well-drained, these soils are suitable for pecan production, but the soil characteristics differ enough between ecoregions in which the plant-parasitic nematode (PPN) communities could differ substantially. We studied PPN communities in pecan orchards to evaluate the potential for ecoregion differences. In total, 11 genera (Helicotylenchus, Hemicycliophora, Heterodera, Hoplolaimus, Meloidogyne, Mesocriconema, Pratylenchus, Paratylenchus, Paratrichodorus, Tylenchorhynchs, Xiphenema) were recovered from pecan orchards in the Piedmont and Coastal Plain ecoregions. However, Non-Metric Multi-Dimensional Scaling ordination, Multi-Rank Permutation Procedure, and Indicator Species Analyses indicated that the pecan PPN communities strongly differed between ecoregions and that different genera were strongly associated with different ecoregions. For 9 of the 11 PPN genera, the maximum counts occurred in Coastal Plain locations, suggesting that the well-drained sandy soils of the Coastal Plain and comparatively ill-drained red clay soils of the Piedmont may be conducive and unfavorable for movement/reproduction of PPNs, respectively.
Community management does not equate to participation: fostering community participation in rural water supplies
Authors: Shields Katherine F. , Moffa Michelle , Behnke Nikki L. , Kelly Emma , Klug Tori , Lee Kristen , Cronk Ryan , Bartram Jamie 
Published: September 2021

Abstract
Community management has remained the dominant paradigm for managing rural water supplies in sub-Saharan Africa. There is a widespread perception that community participation principles are inherently embedded in the community management model. In this paper, we analyze how an international nongovernmental organization engages rural communities in their rural water projects, and the ways in which community members are able to participate in the management and governance of their water supplies. Qualitative data were collected in 18 study communities – six each in Ghana, Kenya, and Zambia – through interviews, focus group discussions, and participatory mapping with community and water committee members. We argue that community management does not inherently lead to broader community participation, but rather that fostering community participation requires intentionality. We recommend implementers use collaborative planning processes and explicitly engage with intra-community diversity and inequalities in order to facilitate the opportunity for all community members to meaningfully participate in decision-making. Collaborative planning with diverse groups will also allow community members to realize their rights to transparency and accountability once community management structures are in place.
Cost minimization of groundwater supply to a central tank
Authors: Nagkoulis Nikolaos , Katsifarakis Konstantinos L. 
Published: September 2021

Abstract
Minimization of groundwater exploitation cost is examined, considering: (a) pumping from a system of wells up to a central water tank, including friction losses along the connecting pipe network and (b) amortization of network construction. Assuming that the wells are located symmetrically around the tank and directly connected to it, we derived analytically the distance between tank and wells, which minimizes the total cost. Then we compared the minimum cost of this well layout, with that of placing one well at the location of the tank and the rest symmetrically around it. Finally, we dropped any assumption on well layout, we considered that wells are connected to the tank using a minimum spanning tree and we optimized well locations and flow rates using genetic algorithms. For up to 8 wells, the resulting minimum cost is comparable to that of the symmetrical cases, even when the optimal well layout is quite different. Moreover, the analytical solution, derived for the symmetrical case, can serve to evaluate solutions achieved by sophisticated optimization techniques.
Microporous activated carbon developed from KOH activated biomass waste: surface mechanistic study of methylene blue dye adsorption
Authors: Jawad Ali H. , Abdulhameed Ahmed Saud , Bahrudin Noor Nazihah , Hum Nurul Nadiah Mohd Firdaus , Surip S. N. , Syed-Hassan Syed Shatir A. , Yousif Emad , Sabar S. 
Published: September 2021

Abstract
In this work, sugarcane bagasse waste (SBW) was used as a lignocellulosic precursor to develop a high-surface-area activated carbon (AC) by thermal treatment of the SBW impregnated with KOH. This SBW activated carbon (SBWAC) was characterized by crystallinity, porosity, surface morphology and functional groups availability. The SBWAC exhibited Type I isotherm which corresponds to microporosity with high specific surface area of 709.3 m2/g and 6.6 nm of mean pore diameter. Further application of SBWAC as an adsorbent for methylene blue (MB) dye removal demonstrated that the adsorption process closely followed the pseudo-second order kinetic and Freundlich isotherm models. Conversely, a thermodynamic study revealed the endothermic nature and spontaneity of MB dye adsorption on SBWAC with high acquired adsorption capacity (136.5 mg/g). The MB dye adsorption onto SBWAC possibly involved electrostatic interaction, H-bonding and π–π interaction. This work demonstrates SBW as a potential lignocellulosic precursor to produce high-surface-area AC that can potentially remove more cationic dyes from the aqueous environment.
Mechanistic insights into the adsorption of methylene blue by particulate durian peel waste in water
Authors: Sudrajat Hanggara , Susanti Ari , Putri Ditta Kharisma Yolanda , Hartuti Sri 
Published: September 2021

Abstract
This study aims to investigate the adsorption of methylene blue (MB) over particulate durian peel waste, which is chemically activated with hydrogen peroxide. The equilibrium data are well described by the Freundlich isotherm model, which indicates that the MB adsorption takes place predominantly on multilayers and heterogeneous surfaces of the biosorbent. The Freundlich adsorption constants, KF and n, are 11.06 L/g and 2.94, respectively. Thermodynamic data suggest that the MB adsorption occurs spontaneously and endothermically. The enthalpy and entropy for the MB adsorption are obtained as 10.26 kJ/mol and 0.058 kJ/mol K, respectively, in the temperature range of 303–323 K. Based on the stepwise desorption method, the adsorption of MB is dominated by physical interactions, particularly hydrogen bonding.
Fabricating novel PVDF-g-IBMA copolymer hydrophilic ultrafiltration membrane for treating papermaking wastewater with good antifouling property
Authors: Tong Yujia , Ding Wenlong , Shi Lijian , Li Weixing 
Published: September 2021

Abstract
Ultrafiltration membranes are widely used for the treatment of papermaking wastewater. The antifouling performance of polyvinylidene fluoride (PVDF) ultrafiltration membranes can be improved by changing the hydrophilicity. Here, a novel amphiphilic copolymer material, PVDF grafted with N-isobutoxy methacrylamide (PVDF-g-IBMA), was prepared using ultraviolet-induced Cu(II)-mediated reversible deactivation radical polymerization. The amphipathic copolymer was used to prepare ultrafiltration membrane via NIPS. The prepared PVDF-g-IBMA ultrafiltration membrane was estimated using 1H NMR, FT-IR, and DSC. The contact angle, casting viscosity, and the permeation performance of the PVDF-g-IBMA ultrafiltration membrane were also determined. The pure water flux, bovine serum albumin removal rate, and pure water flux recovery rate of the PVDF-g-IBMA ultrafiltration membrane were 432.8 L·m−2·h−1, 88.4%, and 90.8%, respectively. Furthermore, for the treatment of actual papermaking wastewater, the chemical oxygen demand and turbidity removal rates of the membrane were 61.5% and 92.8%, respectively. The PVDF-g-IBMA amphiphilic copolymer ultrafiltration membrane exhibited good hydrophilicity and antifouling properties, indicating its potential for treating papermaking wastewater.
Omega-3 Fatty Acid Treatment Combined with Chemotherapy to Prevent
Toxicity, Drug Resistance, and Metastasis in Cancer
Authors: Soni Sneha , Torvund Meaghan , Mandal Chandi C. 
Published: September 2021

:
Despite advances in treatment, individuals diagnosed with cancer are often at risk of suffering
from metastasis, tumor recurrence, therapy resistance, and off-target toxicities from conventional
chemo-, radio-, and endocrine- therapies. Drugs with potent anticancer and antimetastatic activity
but with milder side effects can be combined with conventional therapies to increase efficacy,
reduce therapy resistance, and decrease toxicity. Substantial data from epidemiological, cell culture,
animal, and clinical studies have established the anticancer potential of nontoxic omega-3 fatty
acids. This paper highlights the beneficial effects of omega-3 fatty acid treatment when used in
combination with conventional therapies to protect against metastasis, enhance therapeutic efficacy,
and prevent the off-target toxicity caused by conventional therapies. These omega-3 fatty acids
target therapy-induced central players, NF-κB and ROS, to prevent drug-associated metastasis, therapy
resistance, and off-target toxicities.
Evaluation of the Expression Pattern of 4 microRNAs and their Correlation
with Cellular/viral Factors in PBMCs of Long Term Non-progressors
and HIV Infected Naïve Individuals
Authors: Bokharaei-Salim Farah , Jamshidi Sogol , Nahand Javid Sadri , Monavari Seyed Hamidreza , Moghoofei Mohsen , Garshasbi Saba , Kalantari Saeed , Esghaei Maryam , Mirzaei Hamed 
Published: September 2021

Background:
Long-term non-progressors (LTNPs) are small subsets of HIV-infected
subjects that can control HIV-1 replication for several years without receiving ART. The exact
mechanism of HIV-1 suppression has not yet been completely elucidated. Although the modulatory
role of microRNAs (miRNAs) in HIV-1 replication has been reported, their importance in LTNPs
is unclear.

Objective:
The aim of this cross-sectional study was to assess the expression pattern of miR-27b,
-29, -150, and -221, as well as their relationship with CD4+ T-cell count, HIV-1 viral load, and nef
gene expression in peripheral blood mononuclear cells (PBMCs) of untreated viremic patients and
in LTNPs.

Methods:
MiRNAs expression levels were evaluated with real-time PCR assay using RNA isolated
from PBMCs of LTNPs, HIV-1 infected naive patients, and healthy people. Moreover, CD4 T-cell
count, HIV viral load, and nef gene expression were assessed.

Results:
The expression level of all miRNAs significantly decreased in the HIV-1 patient group
compared to the control group, while the expression pattern of miRNAs in the LNTPs group was
similar to that in the healthy subject group. In addition, there were significant correlations between
some miRNA expression with viral load, CD4+ T-cell count, and nef gene expression.

Conclusion:
The significant similarity and difference of the miRNA expression pattern between
LNTPs and healthy individuals as well as between elite controllers and HIV-infected patients, respectively,
showed that these miRNAs could be used as diagnostic biomarkers. Further, positive
and negative correlations between miRNAs expression and viral/cellular factors could justify the
role of these miRNAs in HIV-1 disease monitoring.
Synthesis, Characterization and Screening of Some Novel 2-Methyl-N'-
[(Z)-Substituted-Phenyl ethylidene] Imidazo [1, 2-a] Pyridine-3-Carbohy
drazide Derivatives as DPP-IV Inhibitors for the Treatment of Type 2 Diabetes
Mellitus
Authors: Chavan Prerana A. , Jadhav Shailaja B. 
Published: September 2021

Background:
One of the leading global metabolic diseases marked by insulin resistance and
chronic hyperglycemia is type 2 diabetes mellitus (T2DM). Since the last decade, DPP-4 enzyme inhibition
has proven to be a successful, safe, and well-established therapy for the treatment of T2DM.

Objective:
The present work reports the synthesis, characterization, and screening of some novel 2-
methyl-N'-[(Z)-substituted-phenyl ethylidene] imidazo [1, 2-a] pyridine-3-carbohydrazide derivatives as
DPP-IV inhibitors for the treatment of T2DM.

Methods:
The molecular docking was performed to study these derivatives' binding mode in the enzyme's
allosteric site. All the synthesized compounds were subjected for DPP-IV enzyme assay and in vivo antihyperglycemic
activity in STZ-induced diabetic rats.

Results:
The synthesized derivatives exhibited potent antidiabetic activity as compared to the standard
drug Sitagliptin. Out of sixteen compounds, A1, A4, B4, C2, C3, and D4 have shown promising antidiabetic
activity against the DPP-IV enzyme. The most promising compound, C2, showed a percentage inhibition
of 72.02±0.27 at 50 μM concentration. On the 21st-day, compound C2 showed a significant reduction
in serum blood glucose level, i.e., 156.16±4.87 mg/dL, then diabetic control, which was
280.00±13.29 mg/dL whereas, standard Sitagliptin showed 133.50±11.80 mg/dL. In the in vivo antihyperglycemic
activity, the compounds have exhibited good hypoglycemic potential in fasting blood glucose
in the T2DM animal model. All the docked molecules have exhibited perfect binding affinity towards
the active pocket of the enzyme. The synthesized derivatives were screened through Lipinski's rule
of five for better optimization, and fortunately, none of them violated the rule.

Conclusion:
The above results indicate that compound C2 is a relatively active and selective hit molecule
that can be structurally modified to enhance the DPP-IV inhibitor's potency and overall pharmacological
profile. From the present work, it has been concluded that substituted pyridine-3-carbohydrazide derivatives
possess excellent DPP-IV inhibitory potential and can be better optimized further by generating
more in vivo, in vitro models.
Impact of Nutrition in the Management of Nutritional Status of Covid-19
Patients
Authors: Soni Shashi , Noor Uroosa , Gupta Ena 
Published: September 2021

Abstract:
The second outbreak of severe acute respiratory syndrome coronavirus (SARS-CoV-2)
is of great concern due to its awful mortality and morbidity rate with decreasing nutritional status
and poor lifestyle as well as noteworthy food crisis and affected economy of the world. Increasing
food prices, food crisis, global hunger and decreasing availability and feasibility of food are the
foremost causes of decreasing nutritional status, which increases the risk of susceptibility to infection
and, in turn, leads to unfavorable outcomes of the diseases. Although, in times of the Covid-
19 pandemic, nutrition is of potential attention, and there is a requirement for more exploration in
the field of nutrition for the prevention of diseases arising from coronavirus infection. Elderly and
individuals with co-morbidity, such as respiratory diseases, cardiovascular diseases, diabetes mellitus
and metabolic diseases, are more prone towards getting infected with the coronavirus. Good
nutrition is mandatory for healthy immune responses, which can be improved by the inclusion of
vitamin A, B6, B12, C, D, E, zinc, selenium, iron, copper and an antioxidant-rich diet.
Wheatgrass: An Epitome of Nutritional Value
Authors: Minocha Neha , Sharma Nidhi , Pandey Parijat 
Published: September 2021

Background:
Plants having active constituents possess pharmaceutical use and nutritional
values. Herbal medicine or food supplement is gaining popularity, as well as scientific
research on wheatgrass as a “functional food”.

Objective:
The target behind accepting wheatgrass as a study for review is to have clinical and
non-clinical investigations on the wheatgrass plant at an equivalent stage. To let individuals,
think about different affirmed uses and activities of the plant.

Methods:
Plants having so many nutritional and therapeutic values have been selected for review
so that consumers or patients could be benefitted from their therapeutic uses. Recently,
the interests in the use of herbal products have grown dramatically in the western as well as
developing countries. The review was extracted from searches performed on Google Scholars,
Google Patents, etc. Data from sources have been collected and reported here at one place in
order to provide further research on wheatgrass.

Results :
Wheatgrass is a high source of various vitamins and minerals; it possesses many activities
like anti-oxidant, anti-inflammation, anti-bacterial and many more. Wheatgrass’ uses, benefits
and properties non-clinical data and clinical studies has been thoroughly studied. Patents
filed related to wheatgrass are mentioned here, so as to motivate other innovators to search for
new activities or molecules.

Conclusions:
Wheatgrass can be used in pharmaceutical formulations and can be used as nutritional
supplements due to its anti-oxidant nature, anti-microbial activity, anti-bacterial activity,
anti-fungal activity. It is also called “Panacea on Earth” owing to its wide range of nutritive
and medicinal aspects.
Integrated Computational Analysis on Some Indolo-quinoline Derivatives for the Development of Novel Antiplasmodium Agents: CoMFA, Pharmacophore Mapping, Molecular Docking and ADMET Studies
Authors: Mallick Chaitali , Mishra Mitali , Asati Vivek , Kashaw Varsha , Das Ratnesh , Iyer Arun K. , Kashaw Sushil Kumar 
Published: September 2021

Background:
The development of multi-resistant strains of the Plasmodium parasite has
become a global problem. Therefore, designing of new antimalarial agents is an exclusive solution.

Objective:
To improve the activity and identify potentially efficacious new antimalarial agents, integrated
computational perspectives such as pharmacophore mapping, 3D-QSAR and docking study
have been applied to a series of indolo-quinoline derivatives.

Methods:
The pharmacophore mapping generated various hypotheses based on key functional features
and the best hypothesis ADRRR_1 revealed that indolo-quinoline scaffold is essential for antimalarial
activity. 3D-QSAR model was established based on CoMFA and CoMSIA models by using
30 indolo-quinoline analogues as training set and the rest of 19 as test set.

Results:
The molecular field analysis (MFA) with PLS (partial least-squares) method was used to
develop significant CoMFA (q2=0.756, r2=0.996) and CoMSIA (q2=0.703, r2=0.812) models. The
CoMFA and CoMSIA models showed good predictive ability with r2
pred values of 0.9623 and 0.9214
respectively. Docking studies were performed by using pfLDH to identify structural insight into the
active site and results signify that the quinoline nitrogen acts as a hydrogen bond acceptor region to
facilitate interaction with Glu122. Finally, designed molecules were screened through the ADMET
tool to evaluate the pharmacokinetic and drug-likeness parameters.

Conclusion:
Thus, these studies suggested that established models have good predictability and
would help in the optimization of newly designed molecules that may produce potent antimalarial
activity.
TMT-Based Quantitative Proteomic Analysis Identified Proteins and Signaling Pathways
Involved in the Response to Xanthatin Treatment in Human HT-29 Colon Cancer
Cells
Authors: Shen Aizong , Zhang Lei , Geng Yadi , Li Lingli , Liu Ping , Chen Zhaolin 
Published: September 2021

Background:
Xanthatin is a plant-derived bioactive sesquiterpene lactone from the Xanthium strumarium
L., and it has been used as a traditional Chinese medicine. Recently, many studies have reported that xanthatin has
anticancer activity. However, a comprehensive understanding of the mechanism underlying the antitumor effects of
xanthatin is still lacking.

Objective:
To systematically and comprehensively identify the underlying mechanisms of xanthatin on cancer cells,
quantitative proteomic techniques were performed.

Methods:
Xanthatin induced HT-29 colon cancer cells death was detected by lactate dehydrogenase (LDH) release cell
death assay. Differentially abundant proteins in two groups (xanthatin treatment groups and control groups) of human
HT-29 colon cancer cells were identified using tandem mass tag (TMT) quantitative proteomic techniques. All the
significant differentially abundant proteins were generally characterized by performing hierarchical clustering, Gene
Ontology (GO) enrichment analyses and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses.
We chose Western blot analysis to validate the candidate proteins in the proteomics results.

Results:
A total of 5637 proteins were identified, of which 397 significantly differentially abundant proteins in the
groups were quantified. Based on the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses,
we found that p53-related signaling played an important role in xanthatin-treated HT-29 colon cancer cells. p53-
upregulated modulator of apoptosis (Puma), Sestrin-2 and p14ARF, which were selected from among p53-related
signaling proteins, were further validated, and the results were consistent with the tandem mass tag quantitative proteomic
results.

Conclusion:
We first investigated the molecular mechanism underlying the effects of xanthatin treatment on HT-29
colon cancer cells using tandem mass tag quantitative proteomic methods and provided a global comprehensive understanding
of the antitumor effects of xanthatin. However, it is necessary to further confirm the function of the differentially
abundant proteins and the potentially associated signaling pathways.