bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence
Authors: Fukushima Kenji , Pollock David 
Published: April 2022

Abstract
On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask the signals of genotype-phenotype associations underlying convergent evolution. To overcome this problem, we extended the widely used framework of nonsynonymous-to-synonymous substitution rate ratios and developed the novel metric ωC, which measures the error-corrected convergence rate of protein evolution. While ωC distinguishes natural selection from genetic noise and phylogenetic errors in simulation and real examples, its accuracy allows an exploratory genome-wide search of adaptive molecular convergence without phenotypic hypothesis or candidate genes. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes. We further extended our method with a heuristic algorithm to detect highly repetitive convergence among computationally nontrivial higher-order phylogenetic combinations. Our approach allows bidirectional searches for genotype-phenotype associations, even in lineages that diverged for hundreds of millions of years.
Assessment of groundwater quality and human health risk impact on fluoride concentration: A case study of Namakkal district, South India
Authors: Kaliyan Kalaivanan , Karuppaiah Sankar , Duraisamy Shanthi 
Published: April 2022

Abstract
This study evaluates the health hazards of fluoride contamination of groundwater in the Namakkal district of south India based on the water quality index. The samples were collected during the NEM season from bore wells and analysed for major anion and cation. There is generally no smell or colour to the groundwater in the study area. The pH of the groundwater samples is acidic to alkaline in nature. Higher EC was noted at 7650 µS/cm during the NEM season. Na+ is the most abundant ion in groundwater, followed by Ca2+, Mg2+, K+, then Cl-, SO42- > HCO3-, and then F-. The majority of ions like Sodium, Potassium, Calcium, Magnesium, Cl-, SO4-, HCO3, and F- recorded higher concentrations during NEM seasons, representing the action of leaching, dissolution, and weathering anthropogenic influences on the groundwater quality. Hill-Piper plot showed the majority of the groundwater samples fall in CaHCO3, NaCl, and Mixed CaNaHCO3, CaMgCl, with minor representations in CaCl and NaHCO3 being noted during the NEM. The Gibbs plot shows all the water samples belonging to rock dominance. The WQI value varies between 22.08 and 211.64 throughout the NEM seasons, with a mean of 78.90. According to the Water Quality Index (WQI), 26%, 33%, and 14% of water types have good, poor, and extremely poor quality, respectively. The average F- level is 1.12 mg/l and ranges from 0.27 to 0.39 mg/l. There is excessive fluoride concentration in 76 % of the groundwater samples (WHO 2011). Children, women, and men should undergo health risk assessments based on non-carcinogenic risk estimates for fluoride oral and dermal pathways. The health risk assessment for this study is that children are the most susceptible to fluoride intake. Consequently, more treatments must be initiated to appraise the water as good quality, and government organizations need to select and provide appropriate groundwater for the inhabitants.
Metabolic framework of spontaneous and synthetic sourdough metacommunities to unravel microbial players implying resilience and performance
Authors: Calabrese Francesco Maria , Ameur Hana , Nikoloudaki Olga , Celano Giuseppe , Vacca Mirco , Junior Wilson J F Lemos , Manzari Caterina , Vertè Fabienne , Cagno Raffaella Di , Pesole Graziano , De Angelis Maria , Gobbetti Marco 
Published: April 2022

Abstract
Background: In nature, microbial communities undergo changes in composition threatening their resilient behaviour. Here, we interrogated sourdough, a natural cereal-fermenting metacommunity, as challenging ecosystem, where players undergo continuous environmental and spatiotemporal stimuli. Results: Inspecting meta-genomes and -transcriptomes, spontaneous sourdoughs harboured dominant, sub-dominant and satellite players differently engaged in functional pathways. The highest microbial richness bared the highest number of gene copies per pathway. Merging meta-24 omics data or using the same microbiota of a spontaneous sourdough, we de novo reconstructed two synthetic microbial communities, respectively, SDG and SMC-SD43. In vitro, the KEGG number of dominant players in SDG was not affected by single player depletion; that of sub-dominants and satellites fluctuated but showed unique contributions. Compared to SMC-SD43, SDG ensured broader transcriptome redundancy. After in situ long-time back slopping, SDG kept stable, with constant volatilome. SMC-SD43 lost many members. Dominant, sub-dominant and satellite players altogether ensured gene and transcript redundancy. Conclusions: Our study demonstrates how starting from spontaneous sourdoughs and by reconstructing the synthetic community it was possible to unravel the metabolic contribution of individual players. To be resilient and performing, the sourdough metacommunity had to comprise dominant, sub-dominant and satellite players, which, only altogether, ensured gene and transcript redundancy. Overall, our study changed the paradigm and introduced theoretical foundations for steering food fermentations.
LncRNA NEAT1 regulates apoptosis in Parkinson's disease via sponging miR-132-3p
Authors: Xie Anmu , Liu Yumei , Yao Weichao , Gao Jing , Yang Liying 
Published: April 2022

Abstract
Emerging studies have indicated that dysregulation of long non-coding RNA nuclear-enriched assembly transcript 1 (lncRNA NEAT1) is closely associated with development of Parkinson’s disease (PD). But the potential mechanism of NEAT1 is unclear. SH-SY5Y cells were treated with MPP+ to mimic PD, transfected sh-NEAT1 to mediate NEAT1 level. Cell viability was detected by CCK-8 assays. Apoptotic cytokines were detected by qRT-PCR and western blot. TargetScan6.2 database and dual-luciferase reporter assay were conducted to validate the interaction between indicated molecules. The expression of Bim, Bax and cleaved caspase-3 was increased, while the expression of miR-132-3p, p-FOXO3a and Bcl-2 was reduced. Knockdown of NEAT1 retrain apoptosis and increased miR-132-3p expression. Besides, NEAT1 was verified as a direct target of miR-132-3p. NEAT1 knockdown suppressed apoptosis in PD through regulating the miR-132-3p/FOXO3a/Bim/caspase and miR-132-3p/Bax/Bcl-2/caspase 3 pathways, providing a promising therapeutic intervention strategy for PD.
Impact of baseline versus intercurrent steroids administration on upfront chemo- immunotherapy for advanced non-small cell lung cancer (NSCLC)
Authors: De Giglio Andrea , Aprile Marta , Federico Alessandro , Sperandi Francesca , Melotti Barbara , Gelsomino Francesco , Ardizzoni Andrea 
Published: April 2022

Abstract
Background: The baseline use of steroids has been associated with worse survival outcomes in patients with metastatic non-small cell lung cancer (NSCLC) treated with single-agent immune-checkpoint inhibitors.Objective: We investigated the impact of baseline versus intercurrent corticosteroid therapy on the efficacy of chemotherapy plus pembrolizumab (CT-ICI) as first-line treatment for advanced NSCLC patients.Methods: We conducted a retrospective study on metastatic NSCLC patients treated with upfront CT-ICI at our institution between March 2020 and December 2021. The use of steroids was considered as the administration of at least 10 mg of prednisone equivalent. Results: Of 101 patients, 36 (35.6%) received steroid therapy at baseline, and 18 (17.8%) started steroids on treatment. Overall, median progression-free survival (mPFS) was 6.5 months (95% CI, 5.9-8.9) and median overall survival (mOS) was 18.2 months (95% CI, 8.9-NR). Patients taking baseline steroids had significantly shorter survival than those not taking them (mPFS 5.0 vs. 8.9 months, p=0.00011; mOS 7.0 months vs. not reached, p <0.0001). Intercurrent steroid administration was associated to prolonged OS (not reached vs. 8.9 months, p = 0.0057) but not PFS (6.1 vs. 9.2 months, p = 0.098). Baseline steroids were significantly associated with poorer survival outcomes in the multivariate model. Conversely, intercurrent prescription did not reach a significant value regardless of other pivotal variables included in the model. Conclusions: Baseline steroid administration was associated with a detrimental effect on survival outcomes in NSCLC patients treated with CT-ICI. The role of intercurrent steroid administration should be further explored in larger studies.
Association between Ivermectin treatment and mortality in Covid-19: A hospital-based case-control study
Authors: Ravikirti  , Ranjan Alok , Porel Rajdeep , Agarwal Ketan , Tahaseen SM , Shyama  , Kumar Anjani 
Published: April 2022

Abstract
Introduction
: This study was designed to test the hypothesis that exposure to ivermectin in early disease prevents mortality due to COVID-19. A secondary objective was to see if the drug has any impact on the length of hospital stay among the survivors.
Methods
It was a hospital-based retrospective case control Study conducted at a tertiary teaching hospital in India. All patients with a diagnosis of COVID-19 who were admitted between 1st April and 15th May 2021 and received inpatient care were included. Important variables like demographic details, dates of admission and discharge or death, symptoms at the time of admission, comorbidities, severity of illness at the time of admission, whether ivermectin was administered or not during the course of the illness and other treatments received as part of the standard of care were retrieved from the medical records.
Results
Of the 965 patients who received inpatient care, 307 died during their hospital stay while 658 were successfully discharged. The proportion of cases treated with ivermectin was 17.26% among the non-survivors (53/307) and 17.93% among the survivors (118/658). The effect was statistically insignificant (crude OR = 0.954 ;95% CI: 0.668–1.364, p = 0.80). Among the survivors, the median length of stay was 11 days for patients who received ivermectin (IQR: 7–15) as well as for those who did not (IQR 7–16).
Conclusion
This study did not show any effect of ivermectin on in-patient mortality in patients with COVID-19 and there was no effect of the drug on the length of hospital stay among the survivors.
Meta-analysis of the endocrine and metabolic effects of probiotics on polycystic ovary syndrome
Authors: Xu Lian-Hua , Zhang Fang 
Published: April 2022

Abstract
Objective Systematic evaluation of the application of probiotics in the treatment of polycystic ovary syndrome (PCOS).Methods Computer searches of PubMed, The Cochrane Library, Web of Science, Medline, Embase, Ovid, CNKI, Wan Fang Data, and VIP databases were conducted to retrieve RCT studies on probiotics for the treatment of patients with PCOS from the time of database creation to March 2021. Meta-analysis was performed by two researchers after screening, extracting, and evaluating the literature using revman 5.3 software.Results A total of 13 studies were included, and the results of Meta-analysis showed that compared with the placebo group, probiotic supplementation increased sex hormone binding globulin (SHBG) and insulin sensitivity testing index (QUICKI) and decreased fasting insulin (INS), total testosterone (TT), insulin resistance index (HOMA-IR), fasting blood glucose (FPG), low-density lipoprotein (LDL-C), triglyceride (TG), and total cholesterol (TC) levels in PCOS patients (P<0.05); there was no significant effect on deoxyepiandrosterone sulfate (DHEAS), high-density lipoprotein (HDL-C), and hyper-sensitive c-reactive protein (HS-CRP) levels in PCOS patients (P>0.05).Conclusions Probiotics may improve serum levels of endocrine and metabolism-related indicators in patients with PCOS, but further investigation and validation in large samples and high-quality RCT studies are needed.
ANALISA PERILAKU KONSUMSI PERSPEKTIF EKONOMI ISLAM PADA MASYARAKAT DESA SIDOKERTO, KECAMATAN BUDURAN, KABUPATEN SIDOARJO
Authors: Qoriani Hersa Farida 
Published: April 2022

The purpose of this study is to determine the consumption patterns of the majority of the population of Sidokerto Village, Buduran Subdistrict, Sidoarjo and to find out the factors that influence the consumption behavior patterns of Sidokerto villagers, Buduran Subdistrict, Sidoarjo. This type of research is a qualitative study using a case study approach study. The results of the study show that it is undeniable that with the increasing economic conditions in the family, the consumption patterns of the family of Indonesian Migrant Workers (TKI) in Sidokerto Village, Buduran District, Sidoarjo will change. There is a difference in consumption patterns before and after a family member who becomes a TKI (Indonesian Worker) abroad is becoming more consumptive. Where before there were family members who became migrant workers income was only enough to meet their daily food needs. The principles of consumption in Islam include several things, namely: the principle of justice, the principle of lawfulness, the principle of cleanliness, moral principles, the principle of generosity
Keywords : Consumption, Sidokerto, Islamic Economics
EFEKTIVITAS PRODUCT KNOWLEDGE DAN PERSEPSI KUALITAS DALAM MENINGKATKAN MINAT BERZAKAT PELAKU UMKM TULUNGAGUNG
Authors: Shidiqy Dhiya'u , Nurhayati Wina 
Published: April 2022

AbstractThis study is to determine the effect of product knowledge of zakat and perceptions of the quality of zakat on the interest in zakat. The population in this study were entrepreneurs who were members of FORKOM UMKM Tulungagung. There is also a sample measurement guideline using a saturated sample technique with a sample of 42 people. The research instrument for data collection in this study used a questionnaire with a Likert scale with data analysis techniques in this study, including descriptive statistical techniques, inferential statistical analysis with classical assumption tests, and hypothesis testing using the F test and t test with the SPSS 23 application. The t test in this study shows that product knowledge has no effect on respondents' interest in giving zakat. Perceptions of the quality of zakat are also proven to have no effect on respondents' interest in paying zakat. The results of the F test in this study also prove that simultaneously there is no effect of product knowledge on zakat and perceived quality on respondents' interest in zakat.Keywords: zakat, product knowledge, perceived quality, interest in zakat
Abstrak
Penelitian ini untuk mengetahui pengaruh pengetahuan produk (product knowledge) zakat dan persepsi kualitas zakat terhadap minat berzakat. Populasi pada penelitian ini adalah para pengusaha yang tergabung dalam FORKOM UMKM Tulungagung. Ada pun pedoman pengukuran sampel menggunakan teknik sampel jenuh dengan sampel sejumlah 42 orang. Instrumen penelitian untuk pengumpulan data dalam penelitian ini menggunakan kuesioner dengan skala likert dengn teknik analisis data pada penelitian ini antara lain dengan teknik statistik deskiptif, analisis statistik inferensial dengan uji asumsi klasik, serta pengujian hipotesis dengan uji F dan uji t dengan aplikasi SPSS 23. Hasil uji t pada penelitian ini menunjukkan bahwa product knowledge tidak berpengaruh terhadap minat responden dalam berzakat. Persepsi tentang kualitas zakat juga terbukti tidak berpengaruh terhadap minat responden dalam membayar zakat. Hasil uji F pada penelitian ini juga membuktian bahwa secara simultan tidak ada pengaruh product knowledge zakat dan persepsi kualitas terhadap minat berzakat responden.
Kata kunci : zakat, product knowledge, persepsi kualitas, minat berzakat
Water quality of springs and lakes in the Kumaon Lesser Himalayan Region of Uttarakhand, India
Authors: Chhimwal Monika , Kaur Simran , Srivastava Rajeev Kumar , Hagare Dharma , Shiva Prasad Halkurike Jayadevaish 
Published: April 2022

AbstractThe scarcity of drinking water has become a bitter reality in many countries. The gap between demand and supply of water has been increasing exponentially year by year. Deforestation, vigorous use of groundwater for agricultural practices, and pollution of our present water resources such as rivers, lakes, and wells are triggering the freshwater scarcity problem. Ninety percent of people in Uttarakhand depend on springs for their daily life activities. In such a case, the quality and quantity of spring water should be a prime topic to be focussed on. In the Kumaon region of Uttarakhand, spring water quality is good but there is an issue with its availability, especially in summer. This review paper details the studies that have been conducted on nutrient status, hardness, heavy metals, and the presence of microbiological diversity in spring water. It also uncovers information on some critical springs, geological settings of their aquifers, and the steps that have been adopted to rejuvenate the spring. Some other measures have been carried out by the government and local communities for springs’ revival and their improvement in discharge rate, including the construction of percolation pits, contour trenches, check dams, and improvement of water resources. It has been observed among the analyzed sample that the Kumaon region is dominated by arsenic, cadmium, chromium, and lead, whereas aluminum, barium, cobalt, and manganese are more in the Garhwal region. Apart from springs, this review paper also reveals the physicochemical characteristics of the spring-fed rivers and lakes of the Kumaon region.
Study on auxiliary operation control of machine learning in multiobjective complex drainage system
Authors: Li Pengcheng , Zhou Shihua , Cao Jing , Xu Wenzheng , Zhou Juanjuan 
Published: April 2022

Abstract
Recently, urban waterlogging prevention and treatment of black–odorous rivers have become a social concern and the upgradation of drainage system and the development of river runoff pollution control projects have accelerated. The use of deep tunnels to upgrade old drainage systems and achieve pollution control-related engineering designs has complicated the drainage system operation control. The traditional operation control mainly relies on human experience or model simulation. This study provides a perspective of machine learning for controlling the operation of the drainage system and exploring whether the operation suggestions regarding facilities in this system can be given in real time while relying only on real-time data and avoiding the complex model simulation process. Herein, five drainage systems were used as examples: the initial water level of a pipeline, key point water level flow, pump station front pool water level, and most unfavorable point water level were selected as relevant variables and four machine-learning discrimination methods were used for to analyze the weir-lowering operation of a deep tunnel. This study found that the average error rate of the linear discrimination method was &lt;10%, thereby exhibiting satisfactory performance. This study provides insights for improving the operation of complex drainage systems.
Domestic water use and water-saving countermeasures in the process of urbanization in 2021: Jiaozuo City case study
Authors: Shi Lei , Liu Zhongzheng , Yang Liangyan , Fan Wangtao 
Published: April 2022

Abstract
Water-saving scientifically proved measures are crucial to reduce the use of decreasing fresh water resources. In this study, we investigate the current situation of residents’ domestic water use, analyze the current situation of residents' water-saving measures, the current situation of residents' water-saving consciousness and its influencing factors. We performed a questionnaire survey and data obtained by relevant water supply departments, this paper used SPSS 19.0 and Excel 2020 software to conduct statistical analysis of survey data. Our results show that: (1) overall, the water consumption of urban residents in the central plains suburb is 18% higher than that of the original urban residents. (2) Among the residential water structures, washing, washing clothes and flushing toilets are the most frequent tasks, accounting for 87.3% of the total water consumption. (3) The implementation of water-saving measures by the original urban residents is better than that of the original suburban residents. (4) It is necessary to increase effective water-saving facilities and measures for urban water use.
Characterization of a Novel Protease Inhibitor from the Edible MushroomAgaricus bisporus
Authors: Vishvakarma Reena , Mishra Abha 
Published: April 2022

Background:Protease inhibitors inhibit the activity of protease enzymes, hence are essentially involved in the regulation of the metabolic processes involving protease enzymes and protection the host organism against external damage due to proteases. These inhibitors are abundantly present in all living organisms but have not been much reported in mushrooms. Mushrooms are one of the major food components of humans with delicious taste and high nutritional value. Mushrooms also have therapeutic and economic significance. The edible mushrooms with medicinal properties are much in commercial demand. To date, the presence of protease inhibitors has not been reported much in edible mushrooms. The present study reports the characterization of a protease inhibitor isolated from the common white button mushroom Agaricus bisporus.Objective:The objective of the present study is to characterize the novel protease inhibitor from Agaricus bisporus to determine its nature and activity at varying environmental conditions.Method:The protease inhibitor was characterized through SDS PAGE, gel filtration chromatography, and de novo sequencing to determine its molecular mass, and sequence respectively. The optimum pH and temperature, and the pH and thermal stability were studied to determine the optimum working range of the protease inhibitor. The protease inhibitory activity (%) was determined in presence of metal ions, surfactants, oxidizing agents, and reducing agents. The kinetic parameters and the type of inhibition exhibited by the protease inhibitor were determined using casein and trypsin protease enzyme.Results:The protease inhibitor was found to be a low molecular mass compound of 25 kDa. The de novo sequencing matched the inhibitor against a 227 amino acid containing peptide molecular mass of 24.6 kDa molecular mass. The protease inhibitory activity (%) was found highest at pH 7.0 and temperature 50 0C, and was stable from pH 4.0-9.0 and temperature 30-80 0C. In presence of metal ions, the residual protease inhibitory activity (%) enhanced in presence of Na+, Mg2+, and Fe3+. The residual activity increased in presence of the surfactant SDS slightly in comparison to control, while decreased in the case of Triton-X and Tween 20. The presence of oxidizing agents, hydrogen peroxide, and dimethyl sulfoxide decreased the residual inhibitory activity. The protease inhibitor was unaffected by the reducing agents: dithiothreitol and β-mercaptoethanol up to 2mM concentration but decreased at higher concentrations. The inhibitor exhibited uncompetitive inhibition against trypsin with an inhibitory constant of 166 nM, indicating a strong affinity towards the protease, with a half-life of 93.90 minutes at 37 0C.Conclusion:Protease inhibitors isolated from mushrooms are generally small in size, more stable, and tolerant towards varying external conditions. The protease inhibitor isolated from Agaricus bisporus also exhibited similar characteristics.