Log10 Values Research Articles

Turbidity assessment in coastal regions combining machine learning, numerical modeling, and remote sensing

ABSTRACT Machine learning models for water quality prediction often face challenges due to insufficient data and uneven spatial-temporal distributions. To address these issues, we introduce a framework combining machine learning, numerical modeling, and remote sensing imagery to predict coastal water turbidity, a key water quality proxy. This approach was tested in the Great Lakes region, specifically Cleveland Harbor, Lake Erie. We trained models using observed data and synthetic data from 3D numerical models and tested them against in situ and remote sensing data from PlanetLabs' Dove satellites. High-resolution (HR) data improved prediction accuracy, with RMSE values of 0.154 and 0.146 log10(FNU) and R2 values of 0.92 and 0.93 for validation and test datasets, respectively. Our study highlights the importance of unified turbidity measures for data comparability. The machine learning model demonstrated skill in predicting turbidity through transfer learning, indicating applicability in diverse, data-scarce regions. This approach can enhance decision support systems for coastal environments by providing accurate, timely predictions of water quality variables. Our methodology offers robust strategies for turbidity and water quality monitoring and has potential for improving input data quality for numerical models and developing predictive models from remote sensing data.

Binocular Visual Deficits at Low to High Spatial Frequency in Intermittent Exotropia After Surgery.

To investigate binocular visual deficits at low to high spatial frequencies in patients with intermittent exotropia (IXT) after surgical correction, using the binocular orientation combination task. Thirteen patients whose IXT has been aligned surgically (17 ± 4.8 years old; 7 females) and 13 normal individuals (21.8 ± 2.5 years old; 6 females) were recruited. All participants had normal or corrected-to-normal visual acuity. The IXT patients had undergone surgery at least one month prior to the study and achieved successful eye alignment post-surgery. We measured participants' balance points (BPs), defined as the interocular contrast ratio (nondominant eye/dominant eye) when both eyes contributed equally to binocular combination, using the binocular orientation combination task at three spatial frequencies (0.5, 4.0, and 8.0 cycles/degree). The absolute values of log10(BP) (i.e., |logBP|) and the area under of the |logBP| versus spatial frequency curve were used to quantify the extent of binocular imbalance. Surgery aligned the eye position of patients with IXT, with a postoperative exodeviation of -4.92 ± 4.29 prism diopters at distance. Participants' |logBP| values showed significant differences between groups, F(1,24) = 9.175, P = 0.006, and across spatial frequencies, F(2,48) = 7.127, P = 0.002. However, the interaction between group and spatial frequency was not significant, F(2,48) = 0.379, P = 0.687. Patients whose IXT has been alighted surgically experience binocular imbalance across a wide range of spatial frequencies, with greater binocular imbalance occurring at high spatial frequencies than low spatial frequencies.

Factors associated with pre-treatment hyperferritinemia in patients with chronic hepatitis C virus infection

Pre-treatment host and viral factors may affect serum ferritin levels in patients with hepatitis C virus (HCV) infection. We delineated pre-treatment factors associated with hyperferritinemia in these patients. 1682 eligible patients underwent pre-treatment assessment for serum ferritin and various host/viral factors. Univariate and multivariate logistic regression analyses were conducted to evaluate factors associated with hyperferritinemia. Multivariate logistic regression analyses revealed that age > 50 years (adjusted odds ratio [OR]: 1.38 (95% confidence interval [CI] 1.09–1.74), p = 0.008), fibrosis stage ≥ F3 (adjusted OR: 1.36 (95% CI 1.04–1.77), p = 0.02), fibrosis index based on four parameters (FIB-4) > 3.25 (adjusted OR: 1.46 (95% CI 1.11–1.92), p = 0.01), presence of metabolic dysfunction-associated steatotic liver disease (MASLD) (adjusted OR: 1.43 (95% CI 1.21–1.76), p = 0.001), and alanine transaminase (ALT) > 2 folds upper limit of normal (ULN) (adjusted OR: 2.87 (95% CI 2.20–3.75), p < 0.001) were associated hyperferritinemia. The log10 value of HBV or HCV viral load was not associated with the log10 value of ferritin level (Spearman’s rank correlation coefficient: − 0.025, p = 0.81 and 0.002, p = 0.92). In conclusion, host factors, rather than viral factors, are associated with hyperferritinemia in patients with HCV.

Oxygen vacancy-rich β-Bi2O3/Bi2O2SiO3 Z-Scheme heterojunction: A strategy to enhance visible light-driven photocatalytic removal of ARB and ARGs

Oxygen vacancy-rich β-Bi2O3/Bi2O2SiO3 (BO/BOS) Z-Scheme heterojunction was prepared by hydrothermal method-assisted calcination. Under visible light, β-Bi2O3/Bi2O2SiO3 photocatalyst demonstrated superior photocatalytic efficacy in degrading antibiotics and antibiotic-resistant Escherichia coli (AR E. coli) compared to individual β-Bi2O3 and Bi2O2SiO3. The experimental results showed that BO/BOS-450 sample possessed the best photocatalytic activity against tetracycline (2 h, 80.8%), amoxicillin (4 h, 57.9%) and AR E. coli (3 h, 107.43 CFU·mL−1). BO/BOS-450 sample showed 91.8% electrostatic capture of AR E. coli in the bacterial capture experiment. In the antibiotic-resistant genes (ARGs) degradation experiment, BO/BOS-450 sample was able to bring the log10 (Ct/C0) value of tetA to -3.49 after 2 h. Oxygen vacancies (OVs) were verified through HR-TEM, XPS and EPR analyses. ESR experiments aligned with the quenching experiment results, confirming that the crucial active species were ‧O2- and h+ during photocatalytic sterilization. A small-scale sewage treatment equipment was designed for the effective removal of ARB from real water samples.

Genes putatively involved in Phaseolus vulgaris resistance against Xanthomonas phaseoli pv. phaseoli revealed by a genome‐wide association study

AbstractCarioca and black bean groups play a significant role in Latin American common bean (Phaseolus vulgaris) consumption, serving as excellent sources of nutrients. One of the most significant threats for common bean production is common bacterial blight (CBB), a disease caused by the gram‐negative bacteria Xanthomonas phaseoli pv. phaseoli (Xpp) and Xanthomonas citri pv. fuscans (Xcf). An effective method for managing this disease is the use of plant genetic resistance. However, it is not known whether the same or overlapping sets of genes are associated with resistance to both pathogens. This study aimed to identify a repertoire of genes potentially associated with resistance to Xpp and compare it with that previously reported for Xcf. Eighty carioca and black common bean cultivars that had previously been challenged with Xcf were inoculated with a strain of Xpp, and a genome‐wide association study (GWAS) using single‐nucleotide polymorphisms (SNPs) and disease severity data was conducted. Three carioca and three black bean cultivars exhibited high levels of resistance to Xpp. Five SNPs with the highest −log10(p) values unveiled genes coding for diverse putative biochemical functions, including a light‐regulated Lir1 protein, a proton‐dependent oligopeptide transporter family protein, a metallo‐dependent phosphatase‐like protein, a WPP domain‐interacting tail‐anchored protein 2 and a pectin lyase‐like superfamily protein. No overlap between this repertoire of genes with that reported for Xcf was found. These findings provide important insights into genes potentially involved in the P. vulgaris resistance to Xpp and the complexity of the resistance response to CBB.

The Photodynamic Antibacterial Activity Properties of a Series of Indium(III) Porphyrins and their Gold and Silver Nanoparticle Conjugates

AbstractIn(III) tetraarylporphyrin complexes with 4‐thiomethylphenyl (1‐InPor), thien‐3‐yl (2‐InPor), thien‐2‐yl (3‐InPor) and 5‐bromothien‐2‐yl (4‐InPor) meso‐aryl rings have been synthesized and characterized. The complexes have been conjugated to gold and silver nanoparticles (AuNPs and AgNPs). The photodynamic antimicrobial chemotherapy (PACT) activities of 1–4‐InPor and their AuNP and AgNP conjugates have been investigated against both planktonic bacteria and biofilms of Gram‐(+) S. aureus and Gram‐(−) E. coli. 2.5 μg.mL−1 solutions of 1–4‐InPor exhibited favorable PACT activities against planktonic S. aureus with high Log10 reduction values in the 4.28–7.69 range upon 75 min photoirradiation with a Thorlabs M625L3 LED (240 mW.cm−2) mounted onto the illumination chamber of a Modulight 7710 medical laser system to provide a dose at the well‐plate of 86 mJ.cm−2.min−1. In contrast, low values in the 1.4–1.9 range were obtained against E. coli with 10 μg.mL−1 solutions. 1–4‐InPor exhibited relatively low PACT activity against the biofilm cells of S. aureus and E. coli. Conjugation of 1–4‐InPor to AgNPs and AuNPs significantly enhanced the PACT activities. This is demonstrated by the complete eradication of planktonic S. aureus at shorter irradiation times with high Log10 values&gt;7.69 and moderate Log10 values&gt;2 against planktonic E. coli for the meso‐thienylporphyrin conjugates.

Angular momentum transport via gravitational instability in the Elias 2–27 disc

Gravitational instability is thought to be one of the main drivers of angular momentum transport in young protoplanetary discs. The disc around Elias 2−27 offers a unique example of gravitational instability at work. It is young and massive, displaying two prominent spiral arms in dust continuum emission and global non-axisymmetric kinematic signatures in molecular line data. In this work, we used archival ALMA observations of 13CO line emission to measure the efficiency of angular momentum transport in the Elias 2−27 system through the kinematic signatures generated by gravitational instability, known as “GI wiggles”. Assuming the angular momentum is transported by the observed spiral structure and leveraging previously-derived dynamical disc mass measurements, the amount of angular momentum transport we found corresponds to an α-viscosity of α = 0.038 ± 0.018. This value implies an accretion rate onto the central star of log10 Ṁ⋆ = −6.99 ± 0.17 M⊙ yr−1, which reproduces the one observed value of log10 Ṁ⋆,obs = −7.2 ± 0.5 M⊙ yr−1 very well. The excellent agreement we have found serves as further proof that gravitational instability is the main driver of angular momentum transport acting in this system.

Combined serum CTRP7 and CTRP15 levels as a novel biomarker for insulin resistance and type 2 diabetes mellitus

AimsThis study aimed to examine the alterations in the serum CTRP7 and CTRP15 concentrations in patients newly diagnosed with type 2 diabetes mellitus (T2DM) and to assess the diagnostic potential of the log10 (CTRP7+CTRP15) for insulin resistance (IR) and T2DM. MethodsSerum CTRP7, CTRP15, and adiponectin levels were measured using an enzyme-linked immunosorbent assay (ELISA). Bioinformatics analysis was conducted to investigate CTRP7 and CTRP15-related genes and metabolic signaling pathways. ResultsLog10 (CTRP7+CTRP15) levels were notably elevated in the impaired glucose tolerance (IGT) and T2DM cohorts compared with those in the normal control (NGT) cohort. Log10(CTRP7+CTRP15) exhibited positive correlations with HOMA-IR, area under the glucose curve (AUCg), HbA1c%, triglyceride (TG), visceral adiposity index (VAI), body mass index (BMI), and free fatty acid (FFA), levels but negative correlations with adiponectin. Multivariate stepwise regression analysis revealed that HOMA-IR, BMI, HbA1c and FFA levels were independent factors affecting the log10 (CTRP7+CTRP15). Logistic regression analysis revealed that log10 (CTRP7+CTRP15) was independently associated with T2DM and significantly associated with increased risk. Receiver operating characteristic (ROC) curve analysis indicated that the predictive value of log10 (CTRP7+CTRP15) for T2DM and IR was superior to that of CTRP7 or CTRP15 alone. Intervention studies demonstrated that insulin, FFAs and acute exercise contribute to the elevation of serum CTRP7 levels, while hyperglycemia inhibited CTRP7 secretion. Short-term changes in blood glucose, insulin, FFA and acute exercise had minimal effects on serum CTRP15 levels. Bioinformatics analysis revealed that CTRP7 and CTRP15 interact with multiple metabolism-related genes and are enriched in glucose and lipid metabolism-related pathways. ConclusionLog10 (CTRP7+CTRP15) may serve as a valuable diagnostic marker for the management of metabolic-related diseases, particularly T2DM and IR.

Genome wide association study and genomic prediction for stripe rust resistance at the seedling stage in advanced spring bread wheat genotypes of ICARDA Morocco

One of the most devastating diseases impacting wheat (Triticum aestivum L.) worldwide is stripe rust, which is propagated by Puccinia striiformis f. Sp. Tritici (Pst). The development and utilization of resistant cultivars offer an effective and eco-friendly approach to manage this disease. However, the emergence of new virulent strains of Pst, driven by continuous mutations within the pathogen, rapidly undermines the effectiveness of existing resistance genes. This necessitates the ongoing identification and incorporation of new resistance genes to breed wheat varieties that can maintain resistance against evolving strains of the pathogen. A genome-wide association study (GWAS) and genomic prediction (GP) were conducted using yellow rust data from the seedling stage under controlled conditions, involving 200 elite bread wheat genotypes and 13,151 SNP markers. GWAS analysis identified fourteen SNP markers significantly associated with yellow rust resistance, using a general linear model (GLM). The markers (wsnp Ex c1085 2078944, wsnp Ku c3682 6,786,230) on chromosome 1D and (wsnp Ex c8240 13,914,674) on chromosome 3A were notably correlated with seedling-level resistance to yellow rust. Additionally, the marker 'AX-94703603′ on chromosome 3A, which recorded the highest -Log10(p) value, was linked to the gene 'TraesCS3A02G335300' encoding the protein kinase domain. These markers, after validation, could be utilized for gene pyramiding in wheat breeding programs to enhance rust resistance through marker-assisted selection.

Future prediction of biogas potential and CH4 emission with boosting algorithms: the case of cattle, small ruminant, and poultry manure from Turkey

Animal waste can be converted into a renewable energy source using biogas technology. This process has an impact on greenhouse gas emissions and is a sustainable source of energy for countries. It can reduce the effects of climate change and protect the planet for future generations. Tier1 and tier2 approaches are commonly used in the literature to calculate emissions factors. With boosting algorithms, this study estimated each animal category’s biogas potential and CH4 emissions (tier1 and tier2 approach) for 2004–2021 in all of Turkey’s provinces. Two different scenarios were created in the study. For scenario-1, the years 2020–2021 were predicted using data from 2004 to 2019, while for scenario-2, the years 2022–2024 were predicted using data from 2004 to 2021. According to the scenario-1 analysis, the eXtreme Gradient Boosting Regressor (XGBR) algorithm was the most successful algorithm with an R2 of 0.9883 for animal-based biogas prediction and 0.9835 and 0.9773 for animal-based CH4 emission predictions (tier1 and tier2 approaches) for the years 2020–2021. When the mean absolute percentage error was evaluated, it was found to be relatively low at 0.46%, 1.07%, and 2.78%, respectively. According to the scenario-2 analysis, the XGBR algorithm predicted the log10 values of the animal-based biogas potential of five major cities in Turkey for the year 2024, with 11.279 for Istanbul, 12.055 for Ankara, 12.309 for Izmir, 11.869 for Bursa, and 12.866 for Antalya. In the estimation of log10 values of CH4 emission, the tier1 approach yielded estimates of 3.080, 3.652, 3.929, 3.411, and 3.321, respectively, while the tier2 approach yielded estimates of 1.810, 2.806, 2.757, 2.552 and 2.122, respectively.Graphical

Serum Soluble Interleukin-2 Receptor Levels in Hairy Cell Leukemia As a Marker of Tumor Burden with Prognostic Value and As a Tool for Disease Monitoring

Background Neoplastic cells in hairy cell leukemia (HCL) express the α chain of the interleukin-2 receptor on their surface, which is secreted in large amounts in the serum in a soluble form (sIL-2R). High serum levels of sIL-2R have previously been reported in HCL. Thus, we assessed whether serum sIL-2R levels correlated with tumor burden, represented a prognostic factor, and if they could be used as a tool for disease monitoring. Methods Serum levels of sIL-2R were measured in 59 patients affected by classical HCL followed at the Hematology Unit of Padova University Hospital. To assess whether sIL-2R levels were representative of tumor burden, we evaluated the relationship of pre-therapy sIL-2R levels with other hematologic features such as leukocyte count, the presence of splenomegaly, β-2 microglobulin levels, lactate dehydrogenase (LDH) levels, CD38 expression, the percentages of circulating hairy cells and bone marrow infiltration. In 50 patients we investigated whether post-therapy sIL-2R levels correlated with clinical response and measurable residual disease (MRD) status evaluated by immunohistochemistry according to consensus guidelines. To determine the usefulness of serum sIL-2R levels for disease monitoring, yearly serial sIL-2R levels were measured in 59 patients, including 5 (8.4%) cases in watch &amp; wait phase and 54 (91.6%) with disease remission after therapy with purine analogues. sIL-2R kinetics were correlated with time to cytopenia (TTC) (hemoglobin &amp;lt;100g/L, neutrophils &amp;lt; 1000/µL or platelets &amp;lt;100.000/µL) and time to next treatment (TTNT). Serum sIL-2R levels were measured by enzyme-linked immunosorbent assay. The correlation of sIL-2R levels with other variables was evaluated by linear or logistic regression as appropriate. Medians were compared using the Mann-Whitney U test. Survival and univariate analyses for TTC and TTFT were conducted according to the Kaplan-Meier method and Cox proportional hazards model. Results The mean age of patients was 60.6 years; 10 were females (17%), and 49 were males (83%). Among treated patients, 47/54 (87%) received cladribine and 7/54 (13%) pentostatin. Pre-therapy sIL-2R levels significantly correlated with leukocyte count (r 2 = 0.13; p = 0.009), β-2 microglobulin levels (r 2 = 0.44; p &amp;lt; 0.001), CD38 expression (p = 0.018), the percentage of circulating hairy cells (r 2 = 0.17; p = 0.017) and the percentage of bone marrow infiltration (r 2 = 0.15; p = 0.009), but not splenomegaly (p = 0.167) or LDH levels (r 2 = 0.02; p = 0.369). We found a significant difference between serum sIL-2R levels measured before and after therapy (median 16.185 vs 599 kU/L respectively; p &amp;lt; 0.001), with a median reduction in sIL-2R levels of 15.628 kU/L after treatment with purine analogues. A similar decrease in sIL-2R levels after therapy was observed in 4 relapsed patients treated with rituximab-vemurafenib (median pre-therapy sIL-2R 11.460 vs. 467 kU/L after treatment, p = 0.03; median reduction 10.848 kU/L). Among responding patients, the absolute value of log10(sIL-2R) levels measured 6 months after therapy was a predictor of shorter TTNT in univariate analysis (HR 15.14; 95% CI 1.3 - 176; p = 0.03). Furthermore, sIL-2R correlated with the depth of response. Post-therapy median sIL-2R levels were significantly lower in patients achieving a complete remission (CR) versus those who did not (median 568 kU/L for CR vs. 3.272 kU/L for partial remission/stable disease; p = 0.002). A statistically significant difference was also observed in post-therapy sIL-2R levels between MRD- and MRD+ patients (median 502 vs 724 kU/L; p = 0.003) (Figure 1A). In the patients that underwent yearly serial sIL-2R measurements during follow-up, a rise from the nadir after therapy in serum sIL-2R levels of ≥ 25% between two samples was associated with both shorter TTC (HR 26.2; 95 % CI 3.44 - 200; p &amp;lt; 0.001) (Figure 1B) and TTNT (HR 8.83; 95 % CI 1.9 - 40.9; p &amp;lt; 0.001). Conclusion The consistent reduction in sIL-2R levels after therapy and their correlation with other standard disease parameters show how serum sIL-2R levels could be an effective marker of tumor burden in HCL. While more data is required to validate its use in clinical routine, sIL-2R could be used as an effective marker for disease monitoring. Moreover, given the prognostic significance of post-therapy levels, sIL-2R may represent a prognostic factor alongside MRD to identify those patients that are more likely to develop early relapse.

Association of multidrug resistant &lt;i&gt;Staphylococcus aureus&lt;/i&gt; and &lt;i&gt;Escherichia coli&lt;/i&gt; with specific naira denominations

Currency serves as a global tool for commerce but is notorious for its association with potentially pathogenic bacteria. This has been further complicated by the growing evolution and emergence of drug resistance among bacteria, with various currencies associated with multidrug resistant (MDR) strains. This could be a silent factor in the current scourge of multidrug resistance. This study therefore set out to explore the presence of multidrug resistance Escherichia coli and Staphylococcus aureus in specific denominations of Naira, the Nigerian currency in Rivers State, Nigeria. A total of 50 naira notes comprised of two commonly used denominations (₦50 and ₦100) made up of two different materials (polymer and paper) were analyzed for microbial load, presence of key bacteria and drug resistance using standard tests. Results of the study revealed high bacterial loads with Log10 values ranging from 4.52 to 5.39 for the ₦100 notes and 4.52 to 5.31 for ₦50 notes. Samples had a higher occurrence of S. aureus (26) than E. coli (8). These isolates were associated with very high rates of resistance though the Gram-positive organisms were more resistant. Both S. aureus and E. coli had high rates of MDR (96.2% and 100% respectively). This study reveals an association of the Nigerian currency, Naira, with a variety of drug resistant bacteria and high levels of multidrug resistance in key pathogens and primarily underscores the need for continuous hand washing as the first key step in disease prevention.

Unravelling the Genetic Basis of Moisture Deficit Stress Tolerance in Wheat for Seedling Vigour-Related Traits and Root Traits Using Genome-Wide Association Study.

A key abiotic stress that negatively affects seed germination, plant development, and crop yield is moisture deficit stress. Achieving higher vigour and uniform germination under stress conditions is essential for crop establishment and productivity and to enhance the yield. Hence, revealing wheat's capacity to withstand moisture deficit stress during seed germination and early growth stages is fundamental in improving its overall performance. However, the genetic regulation of moisture deficit stress tolerance during the seed germination phase remains largely unexplored. In this study, a total of 193 wheat genotypes were subjected to simulated moisture deficit stress using PEG-6000 (-0.4 MPa) during the seed germination stage. The induced moisture deficit stress significantly reduced various seedling-vigour-related traits. The genetic regions linked to these traits were found using a genome-wide association study (GWAS). The analysis identified 235 MTAs with a significance -log10(p) value of >4. After applying the Bonferroni correction, the study identified 47 unique single nucleotide polymorphisms (SNPs) that are linked to candidate genes important for the trait of interest. The current study emphasises the effectiveness of genome-wide association studies (GWAS) in identifying promising candidate genes, improving wheat seedling vigour and root traits, and offering essential information for the development of wheat cultivars tolerant to moisture deficit stress.

Transcriptomic analysis of humic acid in relieving the inhibitory effect of high nitrogen on soybean nodulation.

Nitrogen fertilizer intake promotes soybean growth before the formation of nodules, but excess nitrogen has an inhibitory effect on soybean nodulation. It is important to balance nitrogen levels to meet both growth and nodulation needs. the nitrogen level suitable for soybean growth and nodulation was studied, the role of humic acid (HA) in alleviating the inhibition of high nitrogen on soybean nodulation was analyzed, and transcriptomic analysis was performed to understand its mechanism. The results showed that a lower level of nitrogen with 36.4 mg urea per pot could increase the number of nodules of soybean, and a higher level of nitrogen with 145.9 mg urea per pot (U4 group) had the best growth indicators but inhibited nodulation significantly. HA relieved the inhibitory effect at high nitrogen level, and the number of nodules increased by 122.1% when 1.29 g HA was added (H2 group) compared with the U4 group. The transcriptome analysis was subsequently performed on the H2 and U4 groups, showing that there were 2995 differentially expressed genes (DEGs) on the 25th day, accounting for 6.678% of the total annotated genes (44,848) under the test conditions. These DEGs were enriched in mitogen-activated protein kinase signaling pathway-plant, flavonoid biosynthesis, and plant hormone signal transduction based on the -log10 (P adjusted) value in the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG). HA balanced the nitrogen level through the above pathways in soybean planting to control the number of nodules.

Genome-wide association studies for epistatic genetic effects on fertility and reproduction traits in Holstein cattle.

Non-additive genetic effects are well known to play an important role in the phenotypic expression of complex traits, such as fertility and reproduction. In this study, a genome scan was performed using 41,640 single nucleotide polymorphism (SNP) markers to identify genomic regions associated with epistatic (additive-by-additive) effects in fertility and reproduction traits in Holstein cattle. Nine fertility and reproduction traits were analysed on 5825 and 6090 Holstein heifers and cows with phenotypes and genotypes, respectively. The Marginal Epistasis Test (MAPIT) was used to identify SNPs with significant marginal epistatic effects at a chromosome-wise 5% and 10% false discovery rate (FDR) level. The -log10 (p) values were adjusted by the genomic inflation factor (λ) to correct for the potential bias on the p-values and minimize the possible effects of population stratification. After adjustments, MAPIT enabled the identification of genomic regions with significant marginal epistatic effects for heifers on BTA5 for age at first insemination, BTA3 and BTA24 for non-return rate (NRR); BTA16 and BTA28 for gestation length (GL); BTA1, BTA4 and BTA17 for stillbirth (SB). For the cow traits, MAPIT enabled the identification of regions on BTA11 for GL, BTA11 and BTA16 for SB and BTA19 for calf size (CZ). An additional approach for mapping epistasis in a genome-wide association study was also proposed, in which the genome scan was performed using estimates of epistatic values as the input pseudo-phenotypes, computed using single-trait animal models. Significant SNPs were identified at the chromosome-wise 5% and 10% FDR levels for all traits. For the heifer traits, significant regions were found on BTA7 for AFS; BTA12 for NRR; BTA14 and BTA19 for GL; BTA19 for calving ease (CE); BTA5, BTA24, BTA25 and in the X chromosome for SB; BTA23 and in the X chromosome for CZ and in the X chromosome for the number of services (NS). For the cow traits, significant regions were found on BTA29 and in the X chromosome for NRR, BTA11, BTA16 and in the X chromosome for SB, BTA2 for GL, BTA28 for CZ, BTA19 for calving to first insemination, and in the X chromosome for NS and first insemination to conception. The results suggest that the epistatic genetic effects are likely due to many loci with a small effect rather than few loci with a large effect and/or a single SNP marker alone do not capture the epistatic effects well. The genomic architecture of fertility and reproduction traits is complex, and these results should be validated in independent dairy cattle populations and using alternative statistical models.

An Unsaturated Hydraulic Conductivity Model Based on the Capillary Bundle Model, the Brooks‐Corey Model and Waxman‐Smits Model

AbstractSoil unsaturated hydraulic conductivity (K), which depends on water content (θ) and matric potential (ψ), exhibits a high degree of variability at the field scale. Here we first develop a theoretical hydraulic‐electrical conductivity (σ) relationship under low and high salinity cases based on the capillary bundle model and Waxman and Smits model which can account for the non‐linear behavior of σ at low salinities. Then the K‐σ relationship is converted into a K(θ, ψ) model using the Brooks‐Corey model. The model includes two parameters c and γ. Parameter c accounts for the variation of the term (λ + 2)/(λ + 4) where λ is the pore size distribution parameter in the Brooks‐Corey model, and the term m‐n where m and n are Archie's saturation and cementation exponents, respectively. Parameter γ is the sum of the tortuosity factor accounting for the differences between hydraulic and electrical tortuosity and Archie's saturation exponent. Based on a calibration data set of 150 soils selected from the UNSODA database, the best fitting log(c) and γ values were determined as −2.53 and 1.92, −4.39 and −0.14, −5.01 and −1.34, and −5.79 and −2.27 for four textural groups. The estimated log10(K) values with the new K(θ, ψ) model compared well to the measured values from an independent data set of 49 soils selected from the UNSODA database, with mean error (ME), relative error (RE), root mean square error (RMSE) and coefficient of determination (R2) values of 0.02, 8.8%, 0.80 and 0.73, respectively. A second test of the new K(θ, ψ) model using a data set representing 23 soils reported in the literature also showed good agreement between estimated and measured log10(K) values with ME of −0.01, RE of 9.5%, RMSE of 0.77 and R2 of 0.85. The new K(θ, ψ) model outperformed the Mualem‐van Genuchten model and two recently published pedo‐transfer functions. The new K(θ, ψ) model can be applied for estimating K under field conditions and for hydrologic modeling without need for soil water retention curve data fitting to derive a K function.

Environmental DNA clarifies impacts of combined sewer overflows on the bacteriology of an urban river and resulting risks to public health

There is no reference of microbiological water quality in the European Union's Water Framework Directive, adapted into English law, and consequently microbial water quality is not routinely monitored in English rivers, except for two recently designated bathing water sites. To address this knowledge gap, we developed an innovative monitoring approach for quantitative assessment of combined sewer overflow (CSO) impacts on the bacteriology of receiving rivers. Our approach combines conventional and environmental DNA (eDNA) based methods to generate multiple lines of evidence for assessing risks to public health. We demonstrated this approach by investigating spatiotemporal variation in the bacteriology of the Ouseburn in northeast England for different weather conditions in the summer and early autumn of the year 2021 across eight sampling locations that comprised rural, urban, and recreational land use settings. We characterized pollution source attributes by collecting sewage from treatment works and CSO discharge at the peak of a storm event. CSO discharge was characterized by log10 values per 100 mL (average ± stdev) of 5.12 ± 0.03 and 4.90 ± 0.03 for faecal coliforms and faecal streptococci, and 6.00 ± 0.11 and 7.78 ± 0.04 for rodA and HF183 genetic markers, for E. coli and human host associated Bacteroides, respectively, indicating about 5 % sewage content. SourceTracker analysis of sequencing data attributed 72–77 % of bacteria in the downstream section of the river during a storm event to CSO discharge sources, versus only 4–6 % to rural upstream sources. Data from sixteen summer sampling events in a public park exceeded various guideline values for recreational water quality. Quantitative microbial risk assessment (QMRA) predicted a median and 95th percentile risk of 0.03 and 0.39, respectively, of contracting a bacterial gastrointestinal disease when wading and splashing around in the Ouseburn. We show clearly why microbial water quality should be monitored where rivers flow through public parks, irrespective of their bathing water designation.

Early gonadal differentiation is associated with the antagonistic action of Foxl2 and Dmrt1l in the Pacific oyster.

As the second largest phylum in the zoological kingdom next to arthropods, the mechanism of gonadal differentiation in mollusca is quite complex. Currently, although much has been carried out on gonadal differentiation in the Pacific oyster, there is still unknown information that needs to be further explored. Here, analysis of the Foxl2 and Dmrt1l expression in samples at different development periods of male and female gonads as well as in annual gonad samples revealed that Log10 (Foxl2/Dmrt1l) values were an effective method for sex identification in oysters. In differentiated gonadal tissue, Log10 (Foxl2/Dmrt1l) values greater than 2 were females and less than 1 for males. Subsequent sequential sampling of the same individuals verified that Log10 (Foxl2/Dmrt1l) values greater than 2 for resting gonads would develop as females and less than 1 would develop as males in the future. Relative expression analysis of Foxl2 and Dmrt1l in the annual samples revealed a negative correlation between Log10 (Foxl2) and Log10 (Dmrt1l). Double fluorescence reporter validation results showed that DMRT1L protein was able to bind the Foxl2 promoter and repress its activity with a weak dosage effect. Antagonism between Dmrt1l and Foxl2 is therefore not restricted to vertebrates, and the competing regulatory networks are of great significance in the maintenance of gonadal sex in oysters after sexual differentiation. This study provides novel ideas and insights into the study of early gonadal differentiation in the adult oyster.

Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice.

Salt stress is a major constraint in rice production worldwide. Salt stress is estimated to cause annual losses of 30-50% in rice production. Discovering and deploying salt-resistance genes are the most effective ways to control salt stress. We performed a genome-wide association study (GWAS) to detect QTLs related to salt tolerance at the seedling stage using the japonica-multiparent advanced generation intercross (MAGIC) population. Four QTLs (qDTS1-1, qDTS1-2, qDTS2, and qDTS9) associated with salt tolerance were identified on chromosomes 1, 2, and 9. Among these QTLs, a novel QTL, qDTS1-2, was located between flanking SNPs (1354576 and id1028360) on chromosome 1, with the largest -log10(P) value of 5.81 and a total phenotypic variance of 15.2%. RNA-seq analysis revealed that among the seven differentially expressed genes (DEGs) commonly identified in both P6 and JM298 showing salt tolerance, two upregulated genes, Os01g0963600 (ASR transcription factor) and Os01g0975300 (OsMYB48), related to salt and drought tolerance, were also involved in the target region of qDTS1-2. The results of this study can provide insights into further understanding of salt tolerance mechanisms and developing DNA markers for marker-assisted selection (MAS) breeding to improve the salt tolerance of cultivars in rice breeding programs.

Attenuated niacin response is associated with a subtype of first-episode drug-naïve psychosis characterized as serious negative symptoms.

Although the phenomenon of attenuated niacin response (ANR) has been widely replicated in some patients with first-episode psychosis (FEP), its relevance to the negative symptoms (NS) of psychosis remains unclear. Total of 240 patients with drug-naïve FEP and 101 healthy controls (HCs) were recruited, and 209 were followed up for 1year. Psychotic symptoms were assessed using the Positive and Negative Syndrome Scale (PANSS), and niacin-induced responses were measured using laser Doppler flowmetry. We calculated the log-transform EC50 [concentration of methyl nicotinate required to elicit a half-maximal blood flow (MBF) response] and MBF values. Core-NS was generated by factor analysis of the PANSS-NS subscale and cluster analysis to produce subtypes. Significant differences were found in the log10 (EC50) values between the FEP and HC groups (p < 0.001), supporting the ANR in patients with FEP. A higher NS severity was found in the ANR subgroup than that in other patients. Factor analysis determined that a two-dimensional model included core NS and rigidity of thinking. The log10 (EC50) value was significantly associated with only the core NS. Cluster analysis revealed three subtypes-36.7% (cluster-1, n = 88), 16.7% (cluster-2, n = 40), and 46.7% (cluster-3, n = 112). Cluster-2 characterized by extensive NS appeared to have a moreremarkable ANR and less symptomatic improvement than those with other clusters during follow-up. No significant changes were found in the niacin response trajectories between the baseline and follow-up. Our findings indicate a significant correlation between ANR and core NS in patients with FEP. ANR may be a potential biomarker for certain subtypes with NS-dominated characteristics and poor symptomatic remission.