bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yeast mtDNA transcription initiation in single nucleotide addition steps
Authors: Das Kalyan , Goovaerts Quinten , Shen Jiayu , De Wijngaert Brent , Basu Urmimala , Patel Smita 
Published: September 2022

Abstract
Transcription initiation catalyzed by the RNA polymerase is a multistep process involving promoter binding, transcription bubble formation, abortive RNA synthesis, and transition into elongation following promoter escape. We report cryo-EM structures of yeast mitochondrial RNA polymerase initiation complexes (ICs) with transcription factor MTF1 catalyzing RNA synthesis from de novo initiation to 6-mer synthesis at single-nucleotide steps on fully-resolved transcription bubbles. The growing RNA:DNA hybrid is accommodated by continuous scrunching of the template strand while the non-template and MTF1 C-tail in the polymerase cleft are structurally reorganized. Each nucleotide addition accumulates stress energy, which drives abortive RNA synthesis during early transcription initiation steps and promoter release later. The non-template scrunches as loops in IC2/IC3, and unscrunching assists abortive synthesis of 2-/3-mer RNAs. Subsequently, in IC5 and IC6, the non-template strand assumes a stable structure by stacking its bases into a spiral staircase-like structure that supports processive synthesis. In IC6, the template scrunches to the maximum and places the -1 nucleotide in a pocket near the thumb domain. Subsequently, the -1 nucleotide acts as a pivot point for promoter escape ushering the IC into the elongation phase. The structural snapshots visualize the interplay between abortive and productive synthesis regulating transcription initiation.
Comparative Study of Diversity and Community Characteristics of Trees in Natural (NFS) and Planted (PFS) Forest stands of Patharia Hills Reserve Forest (PHRF), Assam
Authors: Nath Sutashree , Yumnam J. Y. 
Published: September 2022

Abstract

An investigation was undertaken to compare the diversity and community characteristics of trees in natural (NFS) and planted (PFS) forest stands of Patharia Hills Reserve Forest of Barak Valley (PHRF), Assam by random quadrat method. A total of 68 tree species belonging to 50 genera and 30 families were recorded from the two stands. Out of which, 67 species (49 genera and 29 families) were recorded from the NFS and 7 species (7 genera and 6 families) were recorded from the PFS respectively. The IVI revealed that in the NFS,Artocarpus lakoochaRoxb. (31.70) was the most dominant species and in the PFS,Tectona grandisL.f. (175.39) was the most dominant species. The total density was recorded to be 740 trees ha-1 and 770 trees ha-1in the NFS and PFS respectively. The Shannon-Weiner index, Simpson index, Margalef’s richness index and Pielou’s evenness index were recorded to be 3.7, 0.04, 11.16 and 0.88 respectively for the NFS; and 1.41, 0.37, 1.10 and 0.72 respectively for the PFS. The disturbance index was 32.22% in the PFS. The Sorensen’s similarity index was 16%. Population dynamics of trees revealed that the regeneration status of the NFS was much better than that of the PFS. Hutchenson’st-test revealed that the NFS and the PFS were significantly different (P<0.001) in terms of tree species diversity. To avoid the rapid destruction of the forest in general and planted forest in particular, implementation of strict regulations and protective measures is urgent.
Vitamin C and curcumin supplementation protects laboratory mice from buprofezin-induced toxicity
Authors: Sadia Haleema , Qureshi Irfan Zia 
Published: September 2022

Abstract
Purpose
Buprofezin is a type-1 chitin synthesis inhibitor insecticide used to control a variety of insect pests at immature stages but potential adverse effects on non-target organisms and humans have been raised. The present study determined buprofezin toxicity after 4 weeks exposure to Balb/c mice and investigated the role of vitamin C and curcumin as possible protective agents.
Methods
Mice were exposed orally for 28 days to low, medium and high buprofezin doses (50, 100 and 250 mg.kg-1 bw respectively). Only high dose animals were co-treated with vitamin C and curcumin (100 mg.kg-1bw dose each), alone or in combination. Data were analyzed statistically; P<0.05.
Results
Results demonstrated that medium and high buprofezin doses were toxic to mammalian tissues. Supplementation with vitamin C and curcumin alleviated toxicity by significant (P<0.001) lowering of ROS and TBARS whilst increasing the levels of antioxidant enzymes SOD, POD and CAT. Similarly, serum ALT, AST, ALP, triglycerides, total cholesterol, LDH, creatinine and urea levels that were significantly elevated (P<0.05) and decreased tissue proteins upon exposure to buprofezin were restored to near normal values with vitamin C and curcumin. Similar protective effect was obtained (P<0.001) for hematological parameters. Histology and comet assay of liver and kidney further confirmed reduction in buprofezin-induced cellular and DNA damage and preservation of tissue integrity with vitamin C and curcumin.
Conclusion
Both vitamin C and curcumin are therefore effective remedial measures against buprofezin-induced toxicity but in combination, they are more effective.
Strong nanostructured films and effective lead (II) removal capacity based on nitro oxidized cellulose nanofibrils prepared from banana rachis
Authors: Rwegasila Edward , Mushi Ngesa Ezekiel , Berglund Lars A 
Published: September 2022

Abstract
Banana rachis is an abundant and renewable source of cellulose from agricultural wastes. The main focus of the current work is the nanostructured aspects and the potential for removing heavy metals from wastewater using banana rachis cellulose. Highly individualized cellulose nanofibrils, CNF (length = 1231 nm, diameter = 5.26 nm) with negatively charged carboxylic groups at the C6 position of different degrees of oxidations (DO) were developed through nitro oxidation (NO) followed by simple mechanical treatment. The possibility of understanding the nanostructured aspects and tailoring high purification efficiency is discussed. A film prepared through vacuum filtration of the hydrocolloid suspension was strong (tensile strength = 254 MPa, Young modulus = 10.7 GPa, tensile strain = 5.7%), with the highest strength reaching 334 MPa. The highest purification efficiency (compared to other adsorbents in the literature data) was reached at DO = 1.466 mmol/g using an initial Pb (II) concentration of 1000 ppm and followed pseudo-second-order kinetics. A good relationship between an increased Pb (II) removal to the DO (0.455–1.466 mmol/g) and the NOCNF concentration was observed whereby chemisorption is the primary adsorption mechanism. The NOCNF shows a maximum adsorption capacity of 1667 mg/g at the DO = 0.455 mmol/g based on the Langmuir equilibrium adsorption isotherm. The film formation property and high Pb (II) removal behavior were attributed to a well-individualized NOCNF, good dispersion, and high nanofibril interaction. The stiff cellulose crystal was successfully preserved even at a high DO with the crystallinity index = 72%.
A New Binary Arithmetic Optimization Algorithm For Uncapacitated Facility Location Problem
Authors: BAŞ Emine , YILDIZDAN Gülnur 
Published: September 2022

Abstract
Arithmetic Optimization Algorithm (AOA) is a heuristic method developed in recent years. The original version was developed for continuous optimization problems. Its success on different optimization problems has not yet been tested. In this paper, the binary form of AOA (BinAOA) has been proposed. In addition, the candidate solution production scene of BinAOA is developed with the xor logic gate and the BinAOAX method was proposed. Both methods have been tested for success on well-known uncapacitated facility location problems (UFLPs) in the literature. The UFL problem is a binary optimization problem whose optimum results are known. The results of BinAOA and BinAOAX methods were compared and discussed according to best, worst, mean, standard deviation, and gap values. The results of BinAOA and BinAOAX on UFLP are compared with binary heuristic methods used in the literature. As a second application, the performances of BinAOA and BinAOAX algorithms are also tested on classical benchmark functions. The binary forms of AOA, AOAX, Jaya, Tree Seed Algorithm (TSA), and Gray Wolf Optimization (GWO) algorithms were compared in different candidate generation scenarios. The results showed that the binary form of AOA is successful and can be preferred as an alternative binary heuristic method.
Protective Effect of Bruton Tyrosine Kinase Inhibitor in Murine Model of Chronic Demyelination
Authors: Pol Suyog , Dhanraj Ravendra , Ding YingYing , Taher Anissa , Zivadinov Robert 
Published: September 2022

Abstract
Background
Ibrutinib, a Bruton Tyrosine Kinase inhibitor (iBTK), binds with target protein to arrest B-cell development and decrease microglia activation. Considering the emerging role of B and microglial cells in multiple sclerosis (MS) pathology, BTK inhibition is being considered a novel therapeutic strategy.
Objective
To investigate the effects of Ibrutinib on the disease pathology and clinical disability of the Theiler’s Murine Encephalomyelitis Virus (TMEV) mouse model of MS.
Methods
Twenty-six TMEV injected mice were treated at 1-month post induction (mPI) with iBTK (n = 13) or vehicle control (n = 13). Clinical disability, weight and rotarod performance was recorded at 1, 2, 3, and 5 mPI. Histology analysis was performed on spinal cord tissue at 3 and 5 mPI with Iba1 staining. ELISA was conducted to confirm TMEV infection. CD19 expressing B-cell fraction of peripheral blood mono-nuclear cells was quantified.
Results
At functional level, iBTK showed lower clinical worsening (p < 0.001), higher body weights (p = 0.033) and longer rotarod retention (p = 0.048), compared to the vehicle treatment arm. CD19 expressing B-cell fraction was reduced in iBTK (6.65 ± 1.92%) relative to vehicle (12.51 ± 2.34%) (p = 0.043). Furthermore, CD3 density was lower both in grey matter (GM) (p = 0.013) and white matter (WM) (p = 0.025) lesions in the iBTK. IBTK presented lower density and activation of Iba1 positive cells within the spinal cord (p = 0.025). Additionally, at 3 mPI TMEV, spinal cord lesion area was lower in spinal WM (p = 0.016) and was trending lower in GM (p = 0.077) in iBTK.
Conclusions
Treatment with iBTK decreased B-cell fraction and microglia activation in TMEV model of MS, resulting in lower lesion burden and reduced clinical disability, body weight loss and motor dysfunction. It will be relevant to assess iBTK’s effect on neuroimaging measures of immune cell infiltration and the presence of neurodegeneration in the CNS and characterize resulting immune cell changes in future studies.
Isatin inhibits adhesion and Biofilm formation in Candida albicans Isatin as anti-Candida albicans agent
Authors: Jadhav Ashwini Khanderao , Chaugule Sayali Ashok , Parthasarathy Arun Kumar , Sawant Deepak , Karuppayil Sankunny Mohan 
Published: September 2022

Abstract
Background
Isatin possesses various biological activities. Isatin inhibit virulence factors in C. albicans.
Method
Micro broth dilution method was used to determine the minimum inhibitory concentration of Isatin against two strains of C. albicansATCC 90028 and GMC 3 clinical isolate. Biofilm was formed on 96 well polystyrene plates with different concentrations of Isatin (2 mg/ml to 0.062 mg/ml) and biofilm growth was quantified by using XTT-metabolic assay for both the strains. Light and scanning electron microscopy (SEM) were used to observe biofilm architecture. To study the effect of isatin on gene expression during biofilm formation qRT-PCR was used.
Results: Isatin exhibited concentration dependent inhibition against planktonic growth, adhesion and biofilm formation of C. albicans in both the strains. It inhibited the growth significantly (P < 0.05) at 0.5 mg/ml (MIC50) in ATCC 90028. Isatin exhibited anti-biofilm activity (MIC50) at 0.5 mg/ml and 1 mg/ml against ATCC 90028 and GMC3 respectively. Isatin treated (0.5 mg/ml) cells showed about 47 % increase in G2/M phase and 4 % increase in cell number in S phase compared to control. Down regulation of genes involved in Ras-cAMP-MAPK and Cek1-MAPK pathway except Tec 1 was found after treatment with Isatin.
Conclusion: The current study reveals that Isatin can be repositioned as an antifungal agent against C. albicanspathogenesis by confirming its potential by in vivo studies. It may represent a potential novel anti-virulence agent in C. albicans.
Neuroimmune proteins can differentiate between tauopathies
Authors: Cherry Jonathan D. , Baucom Zach H. , Eppich Kaleb G. , Kirsch Daniel , Dixon Erin R. , Tripodis Yorghos , Bieniek Kevin F. , Farrell Kurt , Whitney Kristen , Uretsky Madeline , Crary John F. , Dickson Dennis , McKee Ann C. 
Published: September 2022

Abstract

BackgroundTauopathies are a group of neurodegenerative diseases where there is pathologic accumulation of hyperphosphorylated tau protein (ptau). The most common tauopathy is Alzheimer’s disease (AD), but chronic traumatic encephalopathy (CTE), progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), and argyrophilic grain disease (AGD) are significant health risks as well. Currently, it is unclear what specific molecular factors might drive each distinct disease and represent therapeutic targets. Additionally, there is a lack of biomarkers that can differentiate each disease in life. Recent work has suggested that neuroinflammatory changes might be specific among distinct diseases and offers a novel resource for mechanistic targets and biomarker candidates.MethodsTo better examine each tauopathy, a 71 immune-related protein multiplex ELISA panel was utilized to analyze anterior cingulate grey matter from 127 individuals neuropathologically diagnosed with AD, CTE, PSP, CBD, and AGD. A partial least square regression analysis was carried out to perform unbiased clustering and identify proteins that are distinctly correlated with each tauopathy correcting for age and gender. Receiver operator characteristic and binary logistic regression analyses were then used to examine the ability of each candidate protein to distinguish diseases. Validation in postmortem cerebrospinal fluid (CSF) from 15 AD and 14 CTE cases was performed to determine if candidate proteins could act as possible novel biomarkers.ResultsFive clusters of immune proteins were identified and compared to each tauopathy to determine if clusters were specific to distinct disease. Each cluster was found to correlate with either CTE, AD, PSP, CBD, or AGD. When examining which proteins were the strongest driver of each cluster, it was observed the most distinctive protein for CTE was 6Ckine, AD was FLT3L, and PSP was IL13. Individual proteins that were specific to CBD and AGD were not observed. 6Ckine was observed to be elevated in CTE CSF compared to AD cases (p = 0.02), further validating the use as possible biomarkers.ConclusionsOverall, these results highlight that different neuroinflammatory responses might underlie unique mechanisms in related neurodegenerative pathologies. Additionally, the use of distinct neuroinflammatory signatures could help differentiate between tauopathies and act as novel biomarker candidates.
Habitat Alteration Affects the Diversity and Assemblage of Amphibians in Rajah Sikatuna Protected Landscape of Bohol, Philippines
Authors: Aureo Wilbert A. , Decena Syrus Cesar P. 
Published: September 2022

Abstract

Anthropogenic habitat alteration is considered to be one of the major culprits of biodiversity loss worldwide. This paper presents an investigation on the response of tropical amphibian assemblage to a gradient of habitat alteration in Rajah Sikatuna Protected Landscape (RSPL) of Bohol, Philippines. The abundance, richness, diversity and composition of amphibians were compared among the different habitat types (lower montane forest, dipterocarp forest, riparian forest, grassland and agricultural areas), as well as their relationships with environmental or habitat characteristics were examined. A total of 318 amphibian individuals from 18 species, and belonging to 7 families were recorded. It was found that amphibian abundance, richness and diversity differed significantly between habitat types where it was generally higher in less disturbed habitats (e.g., forests and riparian) compared to highly altered habitats (e.g. grassland and agricultural areas). In relation to species composition pattern, forests and riparian habitats were strongly associated with rainforest and stream-dependent amphibian species while highly altered habitats such as grassland and agricultural areas were associated with those that were open-habitat specialist and disturbance tolerant species. Moreover, the most important environmental variables influencing the pattern of amphibian diversity in the area included grass cover, litter depth, ground relative humidity, temperature, and elevation. In summary, the assemblage of amphibians in the RSPL, Bohol was affected by habitat alteration, highlighting the importance of the sustained protection efforts of the landscape.
Fungus-synthesized nanoparticles and their target and nontarget effects on stored bean pest beetles and their parasitoid
Authors: Helmy Eman Ahmed Mohamed , San Phyu Phyu , Zhang Yao Zhuo , Adarkwah Charles , Tuda Midori 
Published: September 2022

Abstract
Whether green nanotechnology can be effectively used with biological control agents in integrated pest management is currently unknown. We biosynthesized 8–33 nm nanoparticles (NPs) using extracts from the fungus Fusarium solani: silver (AgNPs), selenium (SeNPs), silicon dioxide (SiO2NPs), copper oxide, titanium dioxide (TiO2NPs) and zinc oxide (ZnONPs). They were applied to the adult, egg, and larval stages of Callosobruchus chinensis (Cc) and Callosobruchus maculatus (Cm) directly or via azuki beans Vigna angularis, and the adult stage of their parasitoid wasp Anisopteromalus calandrae. Susceptibility to the nanoparticles was species-dependent and differed among developmental stages; adults and eggs were more susceptible than larvae in the beetles except for Cc adults. Female adult longevity was shortened by SeNPs in A. calandrae and by SeNPs and AgNPs in Cm. In contrast, ZnONPs elongated Cc adult longevity and SeNPs elongated male Cm longevity. When eggs were treated, SeNPs and TiO2NPs reduced Cc egg hatchability and TiO2NPs reduced Cm larva-to-adult survivorship, leading to lower numbers of emerged adult offspring. When the bean surface was treated, there was a pronounced toxicity of SeNPs on the fecundity and egg hatchability of Cm and of SiO2NPs on egg hatchability of both beetle species. When beans containing beetle larvae were treated, no toxicity was detected. Cc adults were not negatively affected by any of the nanoparticles, which might be the consequence of endosymbiotic infection by Wolbachia that are abundant in the adults. The biosynthesized SeNPs demonstrated a strong potential for control of major stored bean pests but can also affect their biocontrol agent.
Pentraxin 3-Induced Fibrotic Scar Formation via Astrocytic Cebpd activation after Spinal Cord Injury
Authors: Wang Shao-Ming , Hsu Jung-Yu C , Ko Chiung-Yuan , Wu Hsiang-En , Hsiao Yu-Wei , Wang Ju-Ming 
Published: September 2022

Abstract
Astroglial-fibrotic scars after spinal cord injury affect motor and sensory function, leading to paralysis. Especially, fibrotic scar is a main barrier to disrupt neuronal regeneration after spinal cord injury. However, the association between astrocyte and fibrotic scar formation has not yet been understanding. According to our previous study showed that transcriptional factor Cebpd contributes to astrogliosis that promote glial scar formation after spinal cord injury. Herein, we show that fibrotic scar formation was decreased in epicenter region in Cebpd−/− mice after contusive spinal cord injury. Further, astrocytic Cebpd promotes fibroblast migration through secretion of Ptx3. We also found that expression of Mmp3 was increased under recombinant protein Ptx3 treatment in fibroblast by observing microarray data, resulting in fibroblast migration. Furthermore, regulation of Mmp3 is through NFκB signaling pathway by using an irreversible inhibitor of IκBα phosphorylation-pretreated fibroblast. Of note, we use synthetic peptide RI37 showing that block fibroblast migration and decrease fibroblast Mmp3 expression under IL-1β-treated astrocyte conditional media. Collectively, our data suggest that the fibroblast migration can be affected by astrocytic Cebpd through Ptx3/NFκB/Mmp3 axis pathway and RI37 peptide may act as a therapeutic medicine to inhibit fibrotic scar formation after spinal cord injury.
Construct validity of the COVID-19 Peritraumatic Distress Index (CPDI) in a Peruvian sample during COVID-19 lockdown and its relationship with anxiety and depression using structural equation modeling
Authors: Pedraz-Petrozzi Bruno , Böttcher Fabian , Arevalo-Flores Martin , Anculle-Arauco Victor , Krüger-Malpartida Hever 
Published: September 2022

Abstract

Background:The main aims of this study were to adapt the COVID-19 Peritraumatic Distress Index (CPDI) to the Peruvian population and to establish a model explaining depression using CPDI values and anxiety symptoms during the COVID-19 lockdown. Finally, we sought predictive values of the obtained CPDI factors for depression and anxiety as a secondary aim.Materials and Methods:An exploratory factor analysis (n = 300) was performed, followed by confirmatory factor analysis in a second phase (n = 1135). To explain depression scores during the COVID-19 pandemic, we performed structural equation modeling (SEM). Finally, we performed a hierarchical regression model (HRM) to evaluate the amount of explained variance of the CPDI factors above depression, anxiety, and sociodemographic variables.Results:A 2-factor solution (ruminationandstress) for the CPDI (p < 0.001; CFI = 0.99) was found. Concerning the SEM, our model was able to explain 81% of the depression scores (p < 0.001; CFI = 0.98). Finally, in the HRM,ruminationcould explain 17% additional variance in depression (p < 0.001) and 28% in anxiety (p < 0.001). However,stressshowed collinearity with depression and anxiety, not continuing for further HRM analysis.Conclusions:Our results showed a 2-factor solution for the CPDI. Moreover, our SEM model showed that female sex, younger age, and incomplete education (with high COVID-related stress and anxiety) lead to more depression symptoms during the COVID-19 lockdown. Finally, our HRM showed that people who frequently ruminate during the COVID-19 lockdown are more afraid and negatively affected.