Miracle-dz/UniFAR-FTUs huggingface dataset:
Chloramine Disinfection-Induced Nitrification Activities and Their Potential Public Health Risk Indications within Deposits of a Drinking Water Supply System

Microsensors were applied to study the diffusion reaction and activity of a nitrogen species of deposit sediment from a drinking water supply system. Microprofiles of dissolved oxygen (DO), NH4+-N, NO3−-N, and NO2−N in the sediment indicated that the DO concentration decreased from the highest at the sediment surface to zero at the bottom of the sediment. Similarly, with the increase of depth, NH4+-N initially increased rapidly and then decreased slowly, while the concentration of NO3−-N reached a maximum at around 6000 μm and then decreased to about 0.1 mg·L−1 near the bottom of the sediment. Almost no change was observed for NO2−-N. The decrease of NH4+-N and DO corresponded well with the increase of NO3−-N. Furthermore, based on a consumption and production rate analysis, DO has always been consumed; the NH4+-N consumption rate increased rapidly within 0–1000 μm, reaching about 14 mg·L−1·S−1·10−9. A small amount of NH4+-N was produced in 2000–6000 μm, which could be attributed to denitrification activity. There was no change deeper than 6000 μm, while NO3−-N was produced at a depth between 0 and 6000 μm and was consumed in the deeper zone. At the depth of 9000 μm, the NO3−-N consumption reached a maximum of 5 mg·L−1·S−1·10−9. The consumption of DO and NH4+-N, which corresponded with the production of NO3−-N in a specific microscale range within the sediment, demonstrated nitrification and denitrification activities. In addition, the time required for the diffusion of only DO, NH4+-N, NO3−-N, and NO2−-N was estimated as 14 days; however, in the practical, even after 60 days of operation, there was still a continuous reaction, which provided further evidence towards microbial activities within the sediment.
A novel biochemical marker -OKL38- with its apoptotic and antioxidant properties for the development of PCOS and its related clinical implications

Abstract Aim: To investigate the role of serum OKL38 levels in the development of polycystic ovary syndrome (PCOS) and clinical implications related to PCOS. Method: PCOS (n = 33) and ovulatory controls (n = 48) were recruited for the study. Anthropometric measurements were recorded, and blood samples for hormonal and biochemical parameters including serum OKL38 levels were obtained. The potential role of OKL38 on the development of PCOS, metabolic syndrome and cardiovascular disease (CVD) were investigated. Framingham risk score (FRS) was used for the determination of CVD risk. Results: Mean Ferriman–Gallway (FG) score, insulin, low-density lipoprotein (LDL), total cholesterol (TC) levels, and the homeostasis model assessment of insulin resistance index (HOMA-IR) were significantly increased (p < .05) in women with PCOS compared to controls. PCOS group had lower mean OKL38 level compared to controls (p < .0001) and OKL38 was negatively predictive for the diagnosis of PCOS after adjustment of variables that were significantly different between two groups. A negative association between OKL38 and metabolic syndrome in PCOS women was evident after adjustment for age, obesity, and abdominal obesity. OKL38 level was also negatively correlated with body mass index, waist-to-hip-ratio, fat composition, serum TC, LDL, free testosterone levels, FRS, and FG scores. Conclusion: OKL38 may have a partial role in the etiopathogenesis of PCOS and may protect development of metabolic syndrome and CVD in women with PCOS.
Environmental heterogeneity and commodity sharing in smallholder agroecosystems

Smallholder farmers undertake a number of strategies to cope with climate shocks in a community. The sharing of resources across households constitutes one coping mechanism when environmental shocks differentially impact households. This paper investigates commodity sharing dynamics among households in eight communities in an environmentally heterogeneous highland-lowland area in central Kenya. We use survey data and meteorological data to test whether commodity sharing, measured at the household level by net inflow of commodities, varies across a regional precipitation gradient, and we reveal how sharing fluctuates with rainfall over the course of a year. We find both precipitation and income to be significant predictors of households’ net value of shared commodities. Specifically, farmers who live in drier areas with less income are more likely to receive more commodities than they give. We also find that the length of time a household has been established in the area is significantly related to commodity sharing. Further, commodity sharing follows the pattern of harvest and food storage over the course of the year, with households giving the most commodities at times when food storage levels are higher, that is, post-harvest. The study sheds light on the relationship between commodity sharing as a coping mechanism and environmental heterogeneity in a region prone to seasonal food insecurity.
Adaptive Ultrasound Tissue Harmonic Imaging Based on an Improved Ensemble Empirical Mode Decomposition Algorithm

Complete and accurate separation of harmonic components from the ultrasonic radio frequency (RF) echo signals is essential to improve the quality of harmonic imaging. There are limitations in the existing two commonly used separation methods, that is, the subjectivity for the high-pass filtering (S_HPF) method and motion artifacts for the pulse inversion (S_PI) method. A novel separation method called S_CEEMDAN, based on the complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) algorithm, is proposed to adaptively separate the second harmonic components for ultrasound tissue harmonic imaging. First, the ensemble size of the CEEMDAN algorithm is calculated adaptively according to the standard deviation of the added white noise. A set of intrinsic mode functions (IMFs) is then obtained by the CEEMDAN algorithm from the ultrasonic RF echo signals. According to the IMF spectra, the IMFs that contain both fundamental and harmonic components are further decomposed. The separation process is performed until all the obtained IMFs have been divided into either fundamental or harmonic categories. Finally, the fundamental and harmonic RF echo signals are obtained from the accumulations of signals from these two categories, respectively. In simulation experiments based on CREANUIS, the S_CEEMDAN-based results are similar to the S_HPF-based results, but better than the S_PI-based results. For the dynamic carotid artery measurements, the contrasts, contrast-to-noise ratios (CNRs), and tissue-to-clutter ratios (TCRs) of the harmonic images based on the S_CEEMDAN are averagely increased by 31.43% and 50.82%, 18.96% and 10.83%, as well as 34.23% and 44.18%, respectively, compared with those based on the S_HPF and S_PI methods. In conclusion, the S_CEEMDAN method provides improved harmonic images owing to its good adaptivity and lower motion artifacts, and is thus a potential alternative to the current methods for ultrasonic harmonic imaging.
Comparison between enzyme-linked immunosorbent assay and indirect immunofluorescence for detection of antineutrophil cytoplasmic antibodies

ABSTRACT Objective To evaluate the performance of enzyme-linked immunosorbent assay and indirect immunofluorescence methods for the detection of antineutrophil cytoplasmic antibodies in a routine clinical laboratory setting. Methods A total of 227 samples were tested by indirect immunofluorescence and enzyme-linked immunosorbent assay with antigen specificity for antiproteinase 3 and antimyeloperoxidase. The proportions of positive samples were compared by McNemar hypotheses and agreement was described by Cohen’s Kappa coefficient. Results The agreement of the tests was 96.5%, and the Kappa coefficient obtained was 0.70 (95%CI: 0.50-0.90; p<0.001). Considering indirect immunofluorescence as the gold standard, the sensitivity of the enzyme-linked immunosorbent assay was 0.62 and the specificity was 0.99, with diagnostic accuracy in 96% of cases. Some samples were negative in enzyme-linked immunosorbent assay and positive in indirect immunofluorescence. This situation occurred in all immunofluorescence patterns, but particularly in atypical patterns. Two samples with antiproteinase 3 positivity were considered negative in indirect immunofluorescence. Conclusion The enzyme-linked immunosorbent assay had high specificity but lower sensitivity. The performance of indirect immunofluorescence increases diagnostic sensitivity, while the search for antiproteinase 3 by enzyme-linked immunosorbent assay may also add diagnostic power.
B-Value Optimization in the Estimation of Intravoxel Incoherent Motion Parameters in Patients with Cervical Cancer

Objective This study aimed to find the optimal number of b-values for intravoxel incoherent motion (IVIM) imaging analysis, using simulated and in vivo data from cervical cancer patients. Materials and Methods Simulated data were generated using literature pooled means, which served as reference values for simulations. In vivo data from 100 treatment-naïve cervical cancer patients with IVIM imaging (13 b-values, scan time, 436 seconds) were retrospectively reviewed. A stepwise b-value fitting algorithm calculated optimal thresholds. Feed forward selection determined the optimal subsampled b-value distribution for biexponential IVIM fitting, and simplified IVIM modeling using monoexponential fitting was attempted. IVIM parameters computed using all b-values served as reference values for in vivo data. Results In simulations, parameters were accurately estimated with six b-values, or three b-values for simplified IVIM, respectively. In vivo data showed that the optimal threshold was 40 s/mm2 for patients with squamous cell carcinoma and a subsampled acquisition of six b-values (scan time, 198 seconds) estimated parameters were not significantly different from reference parameters (individual parameter error rates of less than 5%). In patients with adenocarcinoma, the optimal threshold was 100 s/mm2, but an optimal subsample could not be identified. Irrespective of the histological subtype, only three b-values were needed for simplified IVIM, but these parameters did not retain their discriminative ability. Conclusion Subsampling of six b-values halved the IVIM scan time without significant losses in accuracy and discriminative ability. Simplified IVIM is possible with only three b-values, at the risk of losing diagnostic information.
Senescence-associated genes and non-coding RNAs function in pancreatic cancer progression

ABSTRACT Pancreatic cancer is a major cause of mortality with a poor diagnosis and prognosis that most often occurs in elderly patients. Few studies, however, focus on the interplay of age and pancreatic cancer at the transcriptional level. Here we evaluated the possible roles of age-dependent, differentially expressed genes (DEGs) in pancreatic cancer. These DEGs were used to construct a correlation network and clustered in six gene modules, among which two modules were highly correlated with patients’ survival time. Integrating different datasets, including ATAC-Seq and ChIP-Seq, we performed multi-parallel analyses and identified eight age-dependent protein coding genes and two non-coding RNAs as potential candidates. These candidates, together with KLF5, a potent functional transcription factor in pancreatic cancer, are likely to be key elements linking cellular senescence and pancreatic cancer, providing insights on the balance between them, as well as on diagnosis and subsequent prognosis of pancreatic cancer.
The relationship between intimate partner violence and probable depression among adolescent girls and young women in Lilongwe, Malawi

ABSTRACT This analysis estimates prevalence of intimate partner violence (IPV) and its association with probable depression among adolescent girls and young women (AGYW) in Lilongwe, Malawi, and whether partner’s controlling behaviour modifies this relationship. Baseline data was utilised from the Girl Power-Malawi study of 1000 15–24-year-old AGYW in Lilongwe. Emotional, physical, and sexual IPV experiences with a current or recent partner were measured using the modified Conflict Tactics Scale. Probable depression was measured by scoring ≥10 on the Centre for Epidemiologic Studies-Short Depression Scale (CES-D-10). Generalised linear models with log-link and binomial distribution estimated prevalence ratios (PR) and 95% confidence intervals (CI) for the association between IPV types and probable depression. Partner’s controlling behaviour was examined as an effect modifier. Participants’ mean age was 19.2 years, with 70% never-married. IPV prevalence varied for emotional (59%), physical (36%), sexual (46%), and all forms (20%). Prevalence of probable depression was 47%. AGYW who experienced each IPV type had a higher prevalence of probable depression: physical (PR:1.54, CI:1.28–1.86), sexual (1.46, CI:1.21–1.75), emotional (1.37, CI:1.14–1.64), all forms (1.72, CI:1.41–2.09). IPV and probable depression were prevalent and strongly associated, especially among AGYW reporting controlling behaviour. Interventions addressing IPV and controlling behaviour may positively impact depression among AGYW.
Periodontitis phenotypes and clinical response patterns to non-surgical periodontal therapy: reflections on the new periodontitis classification.

We aimed to identify response patterns to non-surgical periodontal therapy and to investigate whether the new classification system for periodontitis reflects response to treatment after 1 yr. At baseline, data on sociodemographic status, smoking, and diabetes were obtained from participants with periodontal disease. Clinical periodontal data and subgingival plaque were also collected. Participants underwent non-surgical periodontal therapy, and after 3 and 12 months, clinical data were reassessed. Factor analyses, group-based-trajectory modeling, and mixed-effects regression models were used for data analysis. Factor analysis of the baseline periodontal parameters revealed two different periodontitis dimensions: 'moderate' and 'severe'. Two response patterns for each of these periodontitis dimensions were identified. Periodontal therapy had a beneficial effect on both 'moderate' and 'severe' periodontitis; however, individuals with higher levels of disease at baseline experienced greater treatment effect. Regarding the new classification system, while the staging component distinguished different levels of 'moderate' and 'severe' periodontitis before and after treatment, the grading component did not. This study shows the beneficial effect of non-surgical periodontal therapy on both 'moderate' and 'severe' periodontitis. However, the benefit was limited among individuals with low levels of disease. The new classification system did not adequately reflect the periodontal response to therapy in this patient group.
RACK1 promotes cancer progression by increasing the M2/M1 macrophage ratio via the NF‐κB pathway in oral squamous cell carcinoma

Receptor for activated C kinase 1 (RACK1) has been shown to promote oral squamous cell carcinoma (OSCC) progression, and RACK1 expression levels have been negatively correlated with prognosis in patients with OSCC. Here, we investigated the impact of RACK1 OSCC expression on the recruitment and differentiation of tumor‐associated macrophages. High RACK1 expression in OSCC cells correlated with increased M2 macrophage infiltration in tumor samples from a clinical cohort study. Moreover, the combination of RACK1 expression and the M2/M1 ratio could successfully predict prognosis in OSCC. OSCC cells with high RACK1 expression inhibited the migration of THP‐1 cells, promoted M2‐like macrophage polarization in vitro, and increased the proportion of M2‐like macrophages in a xenograft mouse model. Moreover, both M1‐ and M2‐like macrophage polarization‐associated proteins were induced in macrophages cocultured with RACK1‐silenced cell supernatant. A mechanistic study revealed that the expression and secretion of C‐C motif chemokine 2 (CCL2), C‐C motif chemokine 5 (CCL5), interleukin‐6 (IL‐6), and interleukin‐1 (IL‐1) are closely related to RACK1 expression. In addition, blocking nuclear factor‐kappa B (NF‐κB) could promote M2‐like macrophage polarization. These results indicate that RACK1 and the M2/M1 ratio are predictors of a poor prognosis in OSCC. RACK1 promotes M2‐like polarization by regulating NF‐κB and could be used as a potential therapeutic target for antitumor immunity.
Colistin-resistance gene mcr in clinical carbapenem-resistant Enterobacteriaceae strains in China, 2014–2019

ABSTRACT To investigate whether introduction of colistin into the clinical settings selected colistin-resistant CRE, we performed molecular epidemiological study of 1868 CRE strains collected from different geographical locales in China during the period 2014–2019. 1755 (96.18%) isolates carried the carbapenemase genes bla KPC and bla NDM; 14 Escherichia coli isolates (0.75%) carrying mcr-1 and bla NDM (MCR-CREC) were also identified. Importantly, the number and relative prevalence of MCR-CREC isolates increased from 5 (0.41%) to 9 (1.38%) after introduction of polymyxin into clinical practice. Consistently, results of genetic analysis indicated that MCR-CREC strains collected before December 2017 were genetically diverse, yet those collected after that date exhibited more closely related genetic profiles, indicating that specific MCR-CREC strains were rapidly selected as a result of increased usage of colistin in clinical settings. The resistance level of MCR-CREC isolates to colistin increased after the introduction of polymyxin into clinical use with the MIC to colistin from <2 mg/L in 80% strains to 2 mg/L in 100% strains. Further dissemination of MCR-CREC strains, which exhibit resistance to the last-line drugs of carbapenems and colistin, is expected to pose a severe threat to human health.
Real-Time Quality Assessment of Long-Term ECG Signals Recorded by Wearables in Free-Living Conditions

Objective: Nowadays, methods for ECG quality assessment are mostly designed to binary distinguish between good/bad quality of the whole signal. Such classification is not suitable to long-term data collected by wearable devices. In this paper, a novel approach to estimate long-term ECG signal quality is proposed. Methods: The real-time quality estimation is performed in a local time window by calculation of continuous signal-to-noise ratio (SNR) curve. The layout of the data quality segments is determined by analysis of SNR waveform. It is distinguished between three levels of ECG signal quality: signal suitable for full wave ECG analysis, signal suitable only for QRS detection, and signal unsuitable for further processing. Results: The SNR limits for reliable QRS detection and full ECG waveform analysis are 5 and 18 dB respectively. The method was developed and tested using synthetic data and validated on real data from wearable device. Conclusion: The proposed solution is a robust, accurate and computationally efficient algorithm for annotation of ECG signal quality that will facilitate the subsequent tailored analysis of ECG signals recorded in free-living conditions. Significance: The field of long-term ECG signals self-monitoring by wearable devices is swiftly developing. The analysis of massive amount of collected data is time consuming. It is advantageous to characterize data quality in advance and thereby limit consequent analysis to useable signals.
At least three days of adaptation are required before indigestible markers (chromium, titanium, and acid insoluble ash) are stabilized in the ileal digesta of 60-kg pigs, but values for amino acid digestibility are affected by the marker.

An experiment was conducted to 1) test the hypothesis that a minimum adaptation period to diets used in ileal AA digestibility experiments with pigs is needed, and 2) to test the null-hypothesis that ileal digestibility and basal endogenous losses of AA are not affected by the indigestible marker used. Eight ileal-cannulated barrows with an initial BW of 58.1 ± 4.3 kg were randomly allotted to a 2-period crossover design with 2 diets and 4 pigs per diet in each period. A soybean meal-based diet and an N-free diet were prepared. Both diets contained 0.4% chromium oxide, 0.4% titanium dioxide, and 0.4% Celite (a source of acid insoluble ash; AIA). Pigs were provided feed in a daily amount of 3 times the maintenance requirement for ME, and 2 equal meals were provided each day. Ileal digesta samples were collected from 0800 to 2000 h on each day during the two 9-d collection periods. There were no period by diet interactions observed. Marker concentrations in ileal digesta were analyzed separately for each day, and the point where the concentration of each marker was stabilized in the digesta was determined using a linear broken-line analysis. For pigs fed the soybean meal diet, the breakpoints for Cr, Ti, and AIA in ileal digesta were 2.70, 2.45, and 3.77 d, respectively. In pigs fed the N-free diet, the breakpoints for Cr, Ti, and AIA in ileal digesta were 2.52, 2.39, and 2.29 d, respectively. Based on the pooled data, the basal endogenous losses of most AA calculated using Cr as an indigestible marker were less (P < 0.05) than the values calculated using Ti, but greater (P < 0.05) compared with values calculated based on AIA. The standardized ileal digestibility of most AA in soybean meal calculated using Cr or Ti as a digestibility marker were greater (P < 0.05) than the digestibility values calculated using AIA. In conclusion, 3 d of adaptation is required before markers are stabilized in the ileal outflow if Cr or Ti is used as an indigestible marker and 4 d of adaptation is required if AIA is the marker. Values for AA digestibility calculated using Cr or Ti as the marker are not different, but greater compared with values calculated using AIA as the marker.
Inhibition of the type III secretion system of Pseudomonas syringae pv. tomato DC3000 by resveratrol oligomers identified in Vitis vinifera L.

BACKGROUND The bacterial type III secretion system (T3SS) is one of the virulence determinants of Gram-negative bacteria through which various effector and virulence proteins are translocated into host cells. RESULTS We constructed an assay system to screen inhibitors of hrpA gene expression (a structural gene of Hrp pili) in Pseudomonas syringae pv. tomato DC3000. In a plant extract library screening, the root extract of Vitis vinifera L. displayed the most prominent activity. Three resveratrol oligomers, hopeaphenol, isohopeaphenol and ampelopsin A, were identified in grapevine root extract, which significantly reduced the transcription levels of the hrpA, hrpL and hopP1 genes without growth retardation. Additional resveratrol derivatives identified in other plant extracts were also examined for their inhibitory effect on hrpA expression. Another resveratrol oligomer, kobophenol A, also inhibited the transcription of the hrpA gene and other T3SS-related genes, while resveratrol monomers (resveratrol and piceatannol) were not effective. The severity of bacterial specks was reduced by each hopeaphenol, isohopeaphenol and ampelopsin A treatment. CONCLUSION These results show the potential of resveratrol derivatives as anti-virulence agents for the control of plant diseases. This article is protected by copyright. All rights reserved.
Arthropod Venom Components and Their Potential Usage

Arthropods comprise a predominant and well-succeeded phylum of the animal kingdom that evolved and diversified in millions of species grouped in four subphyla, namely, Chelicerata (arachnids), Crustacea, Myriapoda (centipedes), and Hexapoda (insects) [. ].