bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal and spatial distribution of functional nitrogen genes associated with thermal stratification in the subtropical reservoir
Authors: Yang Zhihong , Yang Ming , Bai Chuanzhu , Rong Huanan , Yue Yihong
Published: September 2022

Seasonal thermal stratification is an important hydrological feature of subtropical reservoirs and affects the biogeochemical cycle of nitrogen, which is highly dependent on microbial processes. However, the influence of seasonal thermal stratification on the temporal and spatial distribution of nitrification and denitrification microorganisms is still not clear. This study conducted a detailed survey of a large subtropical reservoir (Xin'anjiang reservoir, XAJR) in eastern China across time (April, July, October 2021, and January 2022) and space (four sampling points with different water depths, covering the epilimnion, thermocline, and isothermal). The research showed that XAJR was a typical subtropical monomer model. Thermal stratification had spatiotemporal heterogeneity, and the DO and pH in water also showed a similar stratification phenomenon. We investigated the temporal and spatial distribution of gene abundance of bacteria and archaea (16S rRNA), ammonia-oxidizing archaea (amoA-AOA), ammonia-oxidizing bacteria (amoA-AOB), and denitrifying bacteria (nirS) by quantitative PCR. We found that the abundance of nitrogen functional genes also showed seasonal stratification in the vertical profile, and the vertical changes of the relative abundance of amoA-AOA / archaea, amoA-AOB / bacteria, and nirS / bacteria genes were highly similar to the corresponding changes of single functional genes. The quantitative distribution of amoA and nirS genes had seasonal differences. The copies number of amoA gene in the stratified stage were greater than that in the mixed stage, while the copies number of the nirS gene in the early and mixed stages of thermal stratification were greater than that in the stratified mature stage. RDA and correlation analysis showed that a variety of environmental factors affected the seasonal distribution of amoA and nirS gene abundance, which may be due to environmental changes caused by thermal stratification. Our results emphasized the importance of seasonal thermal stratification in the reservoir and expanded the understanding of the temporal and spatial distribution patterns of nitrifying and denitrifying microorganisms in the ecosystem of subtropical reservoirs.
Quantization Methods Based on Norms for Complex Gaussian-Like Signals in SDR Applications
Authors: Savaux Vincent , Delacourt Christophe
Published: September 2022

This paper deals with quantization and clipping methods for complex Gaussian-like signal such as multicarrier waveforms in an software define radio (SDR) context. The process involving the quantization of the real and imaginary parts of any signal independently is a basic of digital signal processing, therefore plenty of papers about these techniques are available in the literature. In this paper, we rather consider the quantization of Gaussian complex signals as a whole. To this end, we base our quantization and clipping methods on norms such as Euclidean or infinity norms, allowing the quantized signal to keep the complex argument of the clipped signal samples unchanged and to reduce the peak to average power ratio (PAPR). Furthermore, we derive the corresponding performance analysis in terms of error vector magnitude (EVM), bit error rate (BER), and complexity. We show that simulations match the theoretical results, and that the suggested quantization methods outperform the usual one and reduces the PAPR of the signal, to the cost of an increase of complexity. Furthermore, we discuss the extension of the principle to any norm, as well as practical signals taken from standards such as 5G for instance.
Seasonal Fluctuation of Water Quality and Ecogenomic Phylogeny of Novel Potentional Microbial Pollution Indicators of Veshaw River-Western Himalaya
Authors: Rather Rauoof Ahmad , Ara Shoukat , Padder Shahid Ahmad , Sharma Sanjeev , Mir Shakeel Ahmad , Lone Farooq Ahmad , Mubarak Nabisab Mujawar , Baba Tawseef Rehman
Published: September 2022

Almost a billion people, especially in developing countries, need safe water. Several studies in India show that most drinking water sources have high coliform counts. Standard quality control is needed. This study was conducted in rural parts of South Kashmir in the Western Himalaya from February to January, 2020–2022. Water samples were taken from the river from upstream to downstream using standard water sampling techniques. The purpose of this study was to investigate the detection and molecular identification of coliforms in drinking water and the chemical water quality associated with coliform-contaminated drinking water, which summarises river water pollution. The results showed significant variation in water quality measures, indicating increased pollution levels downstream. In all seasons, the highest coliform count was recorded at Sangam (downstream) of the river. In the summer season at Sangam it was recorded (72.2600 cfu 106/l) and no coliform count was found at Kongwaton (upper stream) during the winter season near the source of the Veshaw river. In all seasons, the highest values of water quality parameters (pH 6.847, EC 71.620 dS/m, BOD 1.120 mg/l, and COD 24.637 mg/l) were recorded at Sangam (downstream) of the river during the summer season. In the winter season at Kongwaton, the lowest values of water quality parameters were pH 8.947, EC 253.680 dS/m, BOD 4.963 mg/l, and COD 51.440 mg/l. The existence of coliforms in water indicates current faecal contamination and determines the presence of disease-causing pathogens. The goal of this work is to examine the level of total coliform contamination, coliform species identification, and chemical water quality properties of drinking water and its associated factors, which implies the pollution level in the river. Total DNA was collected and sequenced for 16S rDNA and metagenomics. Universal primers were used to amplify the bacterial 16S rRNA. Using BLAST, the amplified 16S rRNA gene sequence was matched to the NCBI database. A metagenomic study found 27 species that had different relative abundances. These species include E. coli, Escherichia fergusonii, Escherichia albertii, Klebsiella grimontii, and Shigella dysenteriae. This study is thought to be the first to discriminate against E. fergusonii, Escherichia albertii, Klebsiella grimontii, and Shigella dysenteriae from E. coli and to report on E. fergusonii and E. albertii, Klebsiella grimontii, and Shigella dysenteriae in the river Veshaw water sources in Kulgam, Western Himalaya.
Transmon qubit readout fidelity at the threshold for quantum error correction
without a quantum-limited amplifier
Authors: Chen Liangyu , Li Hang-Xi , Lu Yong , Warren Christopher , Križan Christian , Kosen Sandoko , Rommel Marcus , Ahmed Shahnawaz , Osman Amr , Biznárová Janka , Roudsari Anita Fadavi , Lienhard Benjamin , Caputo Marco , Grigoras Kestutis , Grönberg Leif , Govenius Joonas , Kockum Anton , Delsing Per , Bylander Jonas , Tancredi Giovanna
Published: September 2022

High-fidelity and rapid readout of a qubit state is key to quantum computing and communication,
and it is a prerequisite for quantum error correction. We present a readout scheme for superconducting
qubits that combines two microwave techniques: applying a shelving technique to the qubit
that effectively increases the energy-relaxation time, and a two-tone excitation of the readout resonator
to distinguish among qubit populations in higher energy levels. Using a machine-learning
algorithm to post-process the two-tone measurement results further improves the qubit-state assignment
fidelity. We perform single-shot frequency-multiplexed qubit readout, with a 140 ns readout
time, and demonstrate 99.5% assignment fidelity for two-state readout and 96.9% for three-state
readout—without using a quantum-limited amplifier.
Trivalent Inactivated Influenza Vaccine Response and Immunogenicity Assessment after One Week and Three Months in Repeatedly Vaccinated Adults
Authors: Tawfik Ahmed , Kawaguchi Takahisa , Takahashi Meiko , Setoh Kazuya , Yamaguchi Izumi , Tabara Yasuharu , Steen Kristel Van , Sakuntabhai Anavaj , Matsuda Fumihiko
Published: September 2022

The authors have requested that this preprint be removed from Research Square.
Growth rate and efficiency-related traits in Kermani lambs: estimations of (co)variance components and genetic parameters
Authors: Ehsaninia Jamshid
Published: September 2022

Using Kermani sheep, the current study estimated (co)variance components and genetic parameters for average daily gain, Kleiber ratio, growth efficiency and relative growth rate. Data were analyzed by the average information restricted maximum likelihood (AI-REML) method using six animal models with different combinations of direct and maternal effects. The best-fitting model was determined after testing for improvement in log-likelihood values. The estimates of h2 for average daily gain (ADG), Klieber ratio (KR), growth efficiency (GE) and relative growth rate (RGR) in pre- and post-weaning phases were 0.13 ± 0.6 and 0.17 ± 0.02, 0.12 ± 0.04, and 0.16 ± 0.03; 0.05 ± 0.05 and 0.07 ± 0.03 and 0.06 ± 0.02 and 0.07 ± 0.01, respectively. Maternal heritabilities (m2) ranged from 0.03 ± 0.01 for relative growth rate in pre-weaning phase to 0.11 ± 0.04 for average daily gain in post-weaning period. The maternal permanent environmental component (Pe2) accounted for 3–13% to the phenotypic variance for all the studied traits. Estimated values of additive coefficient of variations (CVA) ranged from 2.79% for relative growth rate at six months of age to 23.74% for growth efficiency at yearling age. Genetic and phenotypic correlations among traits were ranged from − 0.687 to 0.946 and − 0.648 to 0.918, respectively. The result indicated that selection for growth rate and efficiency-related traits would also be less effective in achieving genetic change, because there was little additive genetic variation among Kermani lambs.
Bayesian Shrinkage Estimation for the Erlang Distribution using Type-II Progressive Censored Data
Authors: Kazmi Syed Mohsin Ali , Aslam Muhammad
Published: September 2022

The Bayesian shrinkage estimation using progressive censoring sampling has acquired significant consideration among researchers in the recent decade. In this paper, we have introduced the Bayesian shrinkage estimation for the Erlang distribution by using Type-II progressive censored data. It is observed that the results of Bayesian shrinkage estimation are more tractable than Bayesian estimation and maximum likelihood estimation especially when prior information about the parameter is known in the form of point guess value. For comparison purposes, we have obtained Bayes estimate, Bayes shrinkage estimate, and maximum likelihood estimate along with their associated risks using generalized entropy loss function. The method of elicitation is also employed by using prior predictive distribution to calculate the values of hyperparameters. Some simulated comparisons of the estimates are presented here. Real-life data and rigorous simulation schemes are used to calculate Bayes estimates.
Mathematics Subject Classification: 62F10; 62F15; 62N02; 62N05
Cellulose Derivatives Functionalized with Multidentate N‑Donor Atoms: Comparative Adsorption of Cadmium(II) and Lead(II) Ions from Water
Authors: Ding Baohong , Yang Lu , Fan Hongtao , You Nan
Published: September 2022

Cellulose derivatives functionalized with multidentate N‑donor atoms containing two, three and four amino functional groups (as marked N2-CL, N3-CL and N4-CL) have been prepared by grafting of linear aliphatic polyamines into the cellulose backbone through the Schiff base reaction. Adsorption performances of these cellulose derivatives have been compared. An increase in the adsorptive amounts of Cd2+ and Pb2+ ions with increasing N‑donor atoms of the grafted polyamines onto the cellulose backbone is found to give the maximum capacity N4-CL > N3-CL > N2-CL for both the ions. The N4-CL with high N content (up to 5.2 mmol N g− 1) exhibits higher adsorptive capacities of 249.7 mg g− 1 for Cd2+ and 401.2 mg g− 1 for Pb2+. The adsorption of both the ions by the three cellulose derivatives is achieved within 30 min, is independent of pH in the range of 4.5-6 for Cd2+ and 4–6 for Pb2+, and can be satisfactorily fitted by Langmuir and pseudo-second-order equations. Thermodynamic parameters for the adsorption of both the ions suggest an endothermic and endothermic nature and favorable interactions between N‑donor atoms and the ions. The developed cellulose derivatives are promising for the enhanced removal of Cd2+ and Pb2+ from water.
Prevalence and predictors of unrecognized low sexual desire/interest in men with new onset erectile dysfunction: findings from a cross-sectional, real-life study
Authors: Salonia Andrea , Cilio Simone , Boeri Luca , Pozzi Edoardo , Fallara Giuseppe , Belladelli Federico , Corsini Christian , Capogrosso Paolo , d'Arma Alessia , Imbimbo Ciro , Palmieri Alessandro , Mirone Vincenzo , Montorsi Francesco
Published: September 2022

The interrelationship between male sexual desire and erectile dysfunction (ED) has been scantly investigated. Thus, we aimed at investigating the prevalence of and the predictors of unrecognized low sexual desire/interest (uLSD/I) in a cohort of men with new onset ED. Complete data from 1509 men seeking for first medical help for ED between 2010 and 2021 were analysed. Comorbidities were scored with the Charlson Comorbidity Index (CCI). At entrance, all patients were asked to self-report LSD/I and completed the International Index of Erectile Function (IIEF) and the Beck Depression Inventory (BDI) (depressive symptoms scored as BDI ≥ 11). The IIEF-erectile function (IIEF-EF) domain was categorized according to Cappelleri’s criteria. The median value of the IIEF-sexual desire domain (IIEF-SD) was used to dichotomize men with uLSD/I along with ED (IIEF-SD < 7) vs. ED-only (IIEF-SD ≥ 7). Circulating hormones were measured in every patient. Hypogonadism was defined as total testosterone (tT) < 3.0 ng/mL. Descriptive statistics and logistic regression models tested the association between clinical variables and uLSD/I. Of 1197 patients not self-reporting LSD/I, 369 (30.8%) had IIEF-SD < 7. Patients with ED + uLSD/I were older [median (IQR) 54(41–63) vs. 49(36–59) years], had lower IIEF-EF [10.5(5-21.8) vs. 22(11–28)] but higher BDI [6(3–12) vs. 4(1–8)] and lower tT [4.3(3.2–5.7) vs. 4.8(3.2–6.8) ng/mL] compared to ED-only men (all p < 0.05). Overall, ED + uLSD/I men had higher rate of severe ED (49.9% vs. 23.1%), and of BDI ≥ 11 (30.6% vs. 18.2%) (all p < 0.05). At multivariable logistic regression analysis, lower tT (OR: 0.82), lower IIEF-EF scores (OR:0.95) and BDI ≥ 11 (OR:2.51) were independently associated with ED + uLSD/I, after accounting for age (all p < 0.05). Almost 30% of men seeking first medical help for ED-only had also uLSD/I. Men with both conditions were older, had higher rates of severe ED and more depressive symptoms. A detailed investigation of sexual desire should be always included in men self-complaining only of ED.
Staphylococcus Aureus coverage in acute bacterial sialadenitis in xerostomia patients; Cephalosporins or Beta-lactamase Penicillins?
Authors: Zokaee Haleh , Ahadian Hakimeh , Zandi Hengameh , karbasi Mohammad Hassan Akhavan , Samadaei Mahdis , Owlia Mohammad Bagher
Published: September 2022

Background: Severe dry mouth can be the leading cause of bacterial sialadenitis by Staphylococcus Aureus (SA) as the most causing bacterial agent. Both of the Beta-lactamase Penicillins and the first-generation of Cephalosporins have been suggested as a treatment of the choice in such these conditions. The purpose of this study was to compare the minimum inhibitory concentration of Cephalothin and Oxacillin against the SA by E-Test method.
Methods: In 62 Sjogren's patients, Sampling was done from the right parotid gland and the samples were sent to the lab within two hours. After certain microbial lab procedures (culture, SA identification and isolation), Positive samples for SA were collected and Minimum Inhibitory Concentration (MIC) was measured in each sample for both Cephalothin and Oxacillin by
detecting eclipse around E-Test strips. Also MIC50 and MIC90 of these two antibiotics were recorded. The data were coded by SPSS16 and statistical analysis between two groups was done by Paired T-Test.
Results: SA was isolated from 30 patients (48%). The difference between the average MIC of these two antibiotics was significant (P=0.001). The correlation coefficient between variables was 0.821, which was significant (P<0.0001). MIC 50 of Oxacillin was less than Cephalothin. It was the same for MIC 90. Antibiotic resistance was found in 3% of the patients.
Conclusions: The average MIC in Oxacillin was less than Cephalothin. In other words, Oxacillin was more effective than Cephalothin.
Analysis of the HIV Elimination of Mother-to-Child transmission policy Cascade in Suriname
Authors: Stijnberg Deborah , Holband Suze , Ulenaers Dorien , Schrooten Ward , Adhin Malti R.
Published: September 2022

Background
The calculation of the cascade for the Elimination Mother-to-Child-Transmission of HIV (EMTCT) enables the systematic evaluation of different steps in the health care system towards not transmitting HIV to the exposed infant. This study aims to calculate the EMTCT cascade and identify influencing sociodemographic and clinical factors for Suriname.
Methods
Descriptive analytical study using data regarding prenatal care for women 15–49 year collected in the Multi Indicator Cluster Survey (MICS) 2018. Furthermore, national data from infants and their HIV infected mothers born 2016 to 2018 were used. Multiple regression looking into sociodemographic and clinical factors effecting the transmission of HIV from mother-to-child was executed.
Results
In 89% (95%CI 85–92%) of the cases there was no transmission of HIV from mother-to-child. Earlier cascade steps show 38% unmet family planning needs and evaluating pregnant women 15% with no prenatal visit, 8% deliveries outside a health facility and 72% HIV test coverage during prenatal care. Of the 0.9% (95%CI 0.8-1.0) of pregnant women with HIV, the ART coverage was 84% (95%CI 80–88%). Their infants received HIV prophylactic treatment in 96% (95%CI 93–98%) and a PCR test after birth in 94% (95%CI 90–96%) of the cases. Increased odd of having a negative PCR result was linked with HIV treatment for mother (aOR 26.8, 95% CI 4.1–173.7) and child (aOR 33.9, 95% CI 2.7–419.7). This while living in the interior compared to urban living decreased the odds (aOR 0.8, 95% CI 0.6-1.0).
Conclusions
HIV medication for both HIV infected mothers and their infants remain key in the prevention of HIV mother-to-child-transmission. Prenatal care for pregnant women in general shows gaps reaching those important steps. Interventions with a particular focus on mothers living in the interior, guaranteeing the continuity of care are needed.
Teaching Medical Students How to Break Bad News Using a Students' Activity: The Role of Mentored Peer Experience
Authors: Ali Eithar M. , Kheiralla Tibyan A. F. , Nasrallah Eman A. , Mohammed Walaa A. , Abdelfatah Duaa S. , Elfadul Khansaa M. , Khair Randa Zaki A. M. , Elkhidir Ibrahim H. , Elhassan Ahmed E. , Abdalrahman Ihab B. , Muneer Mohamed S.
Published: September 2022

Objectives: Peer learning is a well-known teaching approach that involves students learning from one another. It might be done in a variety of settings, including a student activity (SA). SA is carried out under the guidance of supportive supervisors. It enhances students' confidence and inventiveness as well as achieving learning goals. This study used a structured questionnaire to evaluate the use of the SA as a teaching/learning tool for breaking bad news (BBN) among medical students.Results: Fourth-year medical students were surveyed pre-and post- BBN SA. A total of 132 and 101 students completed the pre- and post-SA questionnaires, respectively. In the pre-SA and post-SA groups, the average age of the respondents was 21.1±1.6 and 21.1±1.7 years, respectively. Females made up 72.7 % of the pre-SA group and 82.7 % of the post-SA group, respectively. With comparing students’ responses post-SA to the pre-SA ones, there was a statistically significant difference in students' perceptions of their competence to break bad news and the perceived requirement to be well trained on BBN. In a post-SA survey, 28.6 % and 27.3 %, respectively, found SA beneficial and pleasant.
Stability of vertical dimension following total arch intrusion
Authors: Kang Dong-Ok , Yu Hyung-Seog , Choi Sung-Hwan , Kim Seong-Taek , Jung Hwi-Dong , Lee Kee-Joon
Published: September 2022

Background
The purpose of this study is to evaluate stability of vertical dimension following total arch intrusion using miniscrews by measuring the change during treatment and relapse amount after more than one year of retention.
Methods
Thirty patients (6 men, 24 women) were included in this study. Lateral cephalographs were taken with conventional radiography at the start of treatment (T0), after treatment (T1), and at least one year after treatment (T2). The evaluation was performed by measuring changes of selected parameters during treatment and the extent of relapse after more than one year.
Results
During total arch intrusion treatment, anterior and posterior teeth intruded significantly. The mean vertical distance between the maxillary posterior teeth and palatal plane was reduced by 2.30mm(P < 0.001). The mean vertical distance between the maxillary anterior teeth and palatal plane was reduced by 2.04mm(P < 0.001). During retention periods, the FMA angle increased by 0.70°(P < 0.05), the SN-GoMe angle by 0.73°(P < 0.01), and the anterior facial height by 0.81mm(P < 0.01). Among the dental changes during this period, the vertical distance between the maxillary anterior teeth and the palatal plane significantly increased by 0.92mm (P < 0.001).
Conclusions
Skeletally, counterclockwise rotation of the mandible occurs after treatment and, in turn, improves skeletal long face. Anterior and posterior tooth significantly intruded during treatment. Anterior facial height significantly decreases after treatment. During retention period, relapse of AFH and maxillary anterior teeth observed. There was no correlation between initial amount of AFH, mandibular plane angle, or SNPog and posttreatment AFH relapse. However, there was a significant correlation between the amount of intrusion of anterior and posterior teeth achieved by the treatment and the extent of relapse.
Tolerance of repeated toxic injuries of murine livers is associated with steatosis and inflammation
Authors: Hammad Seddik , Ogris Christoph , Othman Amnah , Erdoesi Pia , Schmidt-Heck Wolfgang , Biermayer Ina , Helm Barbara , Piorońska Weronika , Gao Yan , D'Alessandro Lorenza , Theis Fabian , Ebert Matthias , Klingmüller Ursula , Hengstler Jan , Dooley Steven , Mueller Nikola
Published: September 2022

The human liver has a remarkable capacity to regenerate and thus compensate over decades for fibrosis caused by toxic chemicals, drugs, alcohol, or malnutrition. To date, no protective mechanisms have been identified that help the liver tolerate these repeated injuries. In this study, we revealed dysregulation of lipid metabolism and mild inflammation as protective mechanisms by studying longitudinal multi-omic measurements of liver fibrosis-induced by repeated CCl4 injections in mice (n = 45). Based on comprehensive proteomics, transcriptomics, blood- and tissue-level profiling, we uncovered three phases of early disease development - Initiation, Progression, and Tolerance. Using a novel multi-omic network analysis, we identified multi-level mechanisms that are significantly dysregulated in the injury-tolerant response. A public data analysis and shows that these profiles are altered in human liver diseases, including fibrosis and early cirrhosis stages. Our findings mark the beginning of the Tolerance phase as the critical switching point in liver response to repetitive toxic doses. After fostering extracellular matrix accumulation as an acute response, we observe a deposition of tiny lipid droplets in hepatocytes only in the Tolerant phase. Our comprehensive study shows that lipid metabolism and mild inflammation may serve as biomarkers and are putative functional requirements to resist further disease progression.
Determination of 5-Fluorouracil and Doxorubicin Concentrations Required for Effective Induction of Cytotoxicity and Morphological Responses in 3D Tumor Spheroids
Authors: Mutahar Adel Zaid I. , SALIMATH BHARATHI P
Published: September 2022

Introduction:
2-dimensional (2D) cell culture is commonly used for the evaluation of anticancer drugs, which is incapable of simulating the three dimensions (3D) microenvironment of the original tumors, therefore, a new pre-clinical platform for drug screening is urgently needed.
Material and Methods
MDA-MB231 cells were grown either as 2D- monolayers or 3-dimensional (3D) spheroids and treated with 5-FU or doxorubicin. Cytotoxicity assays were performed using trypan blue exclusion dye for 2D- monolayers and 3D spheroids. We have evaluated the efficacy of 5-fluorouracil (5-FU) and doxorubicin at different concentrations on the growth, size of the spheroids, induction of cytotoxicity and cell death over 10 days. Shapiro-Wilk test was used for normal distribution and two-way ANOVA for multiple group comparisons.
Results
2D- and 3D cultures responded with significant sensitivity toward the cytotoxic effect of 5-FU and doxorubicin. However, 3D spheroids were less sensitive to either of these drugs. The 3D spheroids exhibited significant variations in morphometric parameters in response to either 5-FU or doxorubicin treatment. The efficacy of doxorubicin was 1000-fold more effective than 5-FU over 10 days growth period of tumor spheroids. When compared to control spheroids both 5-FU and doxorubicin showed the presence of dead cells in the core of the spheroids as measured by live/dead assay.
Discussion and Conclusion:
Results indicated that 3D spheroid culture recapitulates in vivo tumor microenvironment and reflects the concentration of chemotherapeutic drugs required for effective treatment in cancer patients. Spheroid analysis using AnaSP/ReViSP could be further upgraded to include fluorescent stains within the workflow.
Intrahost variation in early monkeypox virus cases introduced to Finland, 2022
Authors: Vauhkonen Hanna , Kallio-Kokko Hannimari , Hiltunen-Back Eija , Lönnqvist Lasse , Leppäaho-Lakka Jaana , Mannonen Laura , Kant Ravi , Sironen Tarja , Kurkela Satu , Lappalainen Maija , Zorec Tomaž Mark , Zakotnik Samo , Vlaj Doroteja , Korva Miša , Avšič-Županc Tatjana , Poljak Mario , Smura Teemu , Vapalahti Olli
Published: September 2022

We report early importations of monkeypox virus to Finland during late May - early June 2022. Intrahost viral genome variation in one sample comprised a major variant with three lineage B.1.3-specific mutations and a minor variant with ancestral B.1 nucleotides, suggesting either ongoing APOBEC3-mediated evolution or coinfection.
Genetic Diversity and Runs of homozygosity analysis of Hetian Sheep Populations Revealed by Illumina OvineSNP50 BeadChip
Authors: Han Zhipeng , Zhou Wen , Zhang Lulu , Wang Ruotong , Liu Chunjie , Bai Xinyu , Liu Shudong
Published: September 2022

Background
Hetian sheep have a long history, a wide production area and rich genetic resources. Due to the different growing environment and feeding methods, wool, body shape and other traits also have some differences. Hetian sheep can be roughly divided into three groups, but the classification at the genome level is not clear.
Results
We randomly selected 84 healthy, adult ewes were randomly selected from three different ecological regions in Hetian area of Xinjiang, China. DNA was extracted from Ear tissues using phenol chloroform method to produce Illumina OvineSNP50 BeadChip. The SNP chip data were analyzed by Principal component analysis (PCA), neighbor-joining (NJ) phylogenetic and admixture for the population genetic structure of Hetian sheep, and the degree of population linkage was analyzed based on linkage disequilibrium (LD). Finally, the genetic region selection of Hetian sheep genetic germplasm resource populations in three different ecological environments was obtained by runs of homozygosity (ROH) analysis. The obtained candidate genes were annotated with Oar_v4.0 and enriched by GO and KEGG for analysis.Main screened 31 candidate genes adapting to high altitude environment were obtained in the Mountain type. Among them, Genes related to bone cell generation, differentiation and maintenance of bone homeostasis WNT6, WNT10A, CHSY1, etc. Genes related to tooth and tongue development LEF1, TP63, PRDM16, etc. Hearing and vision-related genes RBP4, ATF6, JAG1, etc. Main screened 22 candidate genes related to economic traits were obtained in the Grass type. Among them, Reproduction-related genes PLA2G4F, ACVR1, ADCY2, etc. Growth-related genes CAPN3, YAP1, FGF9, etc.
Conclusions
Hetian sheep can be classified into three subtypes at the genomic level: Mountain, Mountain-Grass and Grass types. The Grass type evolved from the Mountain type, and some of the Grass type further evolved into the Mountain-Grass type, and the genetic relationship between the Mountain-Grass type and Grass type was closest. Genetic structure and ROH analysis of Hetian sheep based on genomic microarray technology revealed the Mountain-Grass type strain. We enriched the genetic diversity of Hetian sheep germplasm resources, provided directions for Hetian sheep breed conservation, and found that genes related to multiparous trait exist in Mountain-Grass and Grass types Hetian sheep, which provides ideas for the selection and breeding of multiparous Hetian sheep.
The Causal Relationship Between Rheumatoid Arthritis and Pneumonia: A Mendelian Randomization Study
Authors: Luo Pan , Hou Weikun , Xu Ke , Liu Lin , Xu Peng
Published: September 2022

Background
At present, it is not clear whether there is a causal relationship between rheumatoid arthritis (RA) and pneumonia.
Method
Single-nucleotide polymorphisms (SNPs), obtained from a genome-wide association study (GWAS) of RA, were used as instrumental variables. Inverse-variance weighted (IVW), weighted median, MR-Egger, simple mode and weighted mode methods were used to investigate causal effects. We applied MR-PRESSO methods and MR–Egger methods to investigate sensitivity. The heterogeneity of individual genetic variants was evaluated by Cochran's Q test and a leave-one-out analysis.
Results
Forty-two SNPs were selected as instrumental variables. The results of the IVW method were very significant (OR, 1.056 for pneumonia per log-odds increment in RA risk, 95% CI 1.034–1.077; p = 1.87E-07), and other methods were also statistically significant. The results of the IVW method showed a causal effect of genetically determined RA on pneumonia (critical care) (OR, 1.053, 95% CI 1.001–1.106; p = 0.044) but no causal effect of genetically determined RA on pneumonia (death) or pneumonia (28-day death in critical care)
Conclusions
The study showed that RA was associated with an increased risk of pneumonia, but it did not cause death or a need for critical care.
Subtype Classification based on Ferroptosis-related Genes and Signature for Predicting Outcomes in Cervical Cancer
Authors: Li Xinrong , Gong Han , Wang Pan , He Ling , Wang Jingjing , Feng Yeqian , Liu Jing , Zou Wen
Published: September 2022

BACKGROUND: Cervical cancer (CC) mainly relies on tumor stage to determine patient prognosis and guide treatment, but the prognosis of patients with the same stage still varies greatly. Ferroptosis, a novel iron-dependent programmed cell death, has been reported in a variety of tumors, but its impact on CC prognosis is currently uncertain. Herein, the express situation and prognostic value of ferroptosis-related genes (FRGs) in CC are explored by collecting public database and constructing a corresponding prognostic signature.
METHODS: Molecular data and corresponding clinicopathological data from the Cancer Genome Atlas-Cervical squamous cell carcinoma and endocervical adenocarcinoma (TCGA-CESC) cohort and the corresponding 10 Normal tissue samples of cervical canal from the Genotype-Tissue Expression (GTEx) database were collected. Applying univariate logistic regression analysis to identify prognostic FRGs. Subsequently, genes were further screened using differentially expressed genes (DEGs) and a prognostic model was constructed using the least absolute shrinkage and selection operator (LASSO)-COX stepwise regression. Finally, Validation of the risk model is achieved by using the corresponding data in the Gene Expression Omnibus (GEO) database of CC patients and clinical specimens from CC patients were collected for Quantitative reverse transcription PCR (qRT-PCR) validation.
RESULTS: Stepwise regression analysis identified five FRG features used to predict outcomes in patients with CC, and further divided patients into two subgroups. KM survival analysis showed that the prognosis of the two subgroups of patients was significantly different, and the Receiver operating characteristic (ROC) curve analysis verified the good specificity and accuracy of the signature. The model was externally validated with the GEO44001 cohort, and the results show that the model has good prognostic power. Finally, detection of clinical specimens by qRT-PCR demonstrated that five FRGs were significantly highly expressed in tumor samples than in normal samples.
CONCLUSION: A risk signature based on five FRGs validated to have excellent prognostic ability for CC patients. Our signature predicting outcomes in CC patients can contribute to targeted and personalized therapy for CC patients.
Vigna Legumes: Exploring Some Biochemical Constituents of the Wild Species for Potential Neo-Domestication Candidates
Authors: Harouna Difo Voukang , Ndakidemi Patrick Alois , Venkataramana Pavithravani B. , Matemu Athanasia O.
Published: September 2022

Due to the foresight of food system collapse, the search for alternative food and feed sources for human and animal nutrition becomes a daunting task. In addition, achieving Zero Hunger target by the year 2030 as set by the FAO is challenging. Re-exploring the less explored foods, coupled to refining less refined traits, cultivating the uncultivated, and popularizing the unpopular food crops are steps to achieve the domestication of wild plants for food and nutrition security. In that line of thought, this study explored the proximate composition of 87 accessions of four wild unexplored Vigna species in order to reveal information leading to their future domestication and utilization. Standard procedures and methods approved by AOAC were used in carrying out the proximate composition of the wild Vigna legumes. The study revealed that the wild Vigna species possess a large variation range of nutrient characteristics which could be exploited in the improvement of domesticated species or guide their domestication. It was also found that some individual wild accessions have higher nutrient, content as compared with domesticated ones which could be advantageous for bio-fortification or domestication. Indications relating to the candidate accessions favorable for domestication, based on the nutrient characteristics were revealed.
Ensifer meliloti denitrification is involved in infection effectiveness and N2O emissions by alfalfa root nodules
Authors: DELGADO Maria Jesus , Pacheco Pedro J , Bedmar Eulogio J , Mesa Socorro , Torosa German
Published: September 2022

Purpose: Ensifer meliloti, the endosymbiont of alfalfa, contains all the denitrification genes but the capacity of alfalfa root nodules to produce N2O is not known. In this work, N2O emissions as well as the influence of bacteroidal denitrification on nodulation competitiveness and N2O release from alfalfa nodules has been investigated.
Methods: Medicago sativa cv. Victoria plants were inoculated with E. meliloti 1021 and napA-, nap+ and nosZ- mutants. Plants were grown in the presence of different nitrate and copper treatments and subjected to flooding during one week before harvesting. MV+-NR and MV+-NIR enzymatic activities were measured in isolated bacteroids by analysing the capacity of the cells to produce or consume nitrite, respectively. Bacteroidal nitrous reductase (N2OR) activity was determined by measuring N2O consumption capacity. N2O was analysed by using a gas cromatograph.
Results: Alfalfa root nodules are able to produce N2O in response to nitrate and flooding. Overexpression of the periplasmic nitrate reductase (Nap) improved nodulation competitiveness and induced N2O emissions. The addition of Cu to the plant nutrient is required for an effective symbiosis as well as triggered a reduction of N2O production by alfalfa nodules due to the induction of the N2OR and a reduction of NIR activities in the bacteroids.
Conclusion: Alfalfa root nodules emit N2O. Nap is involved in nodulation competitiveness and in N2O emissions by the nodules. Bacteroidal N2OR and NIR activities are modulated by Cu and may be considered as effective targets for the mitigation strategies of N2O emissions derived from alfalfa crops.
Abnormal variations in expression of LRP5, β-catenin, OPG, RANKL and LGR4 in postmenopausal osteoporotic fractures
Authors: Wang Bin , Mai Caiyuan , Pan Lei
Published: September 2022

Background: The various osteogenesis and osteoclastogenesis factors including LRP5, β-catenin, OPG, RANKL and LGR4 have been associated with osteoporotic incidence, and can be regulated via the activation of diverse signaling pathways including Wnt/β-catenin, OPG/RANKL and LGR4/RANKL/RANK. This study aimed to analyze the expressions of the factors associated with these three pathways in postmenopausal osteoporotic fracture (PMOPF).
Methods: Patientswith proximal tibial fractures were first divided into control group and PMOPF group. Bone samples were obtained from them during surgery and the expressions of RNAs and proteins derived from the bone tissues were analyzed using RT-qPCR and Western Blot. It was observed that as the time of the collected peripheral serum changed, PMOPF group turned into groups A-F, whereas control group were also converted into groups A0-F0. The expression of the selected serum factors was analyzed using ELISA. We then analyzed significant differences in the expression of the factors between groups A-F and groups A0-F0. LRP5, β-catenin, OPG, and LGR4 were found to be underexpressed in PMOPF group, relative to control group, and they were underexpressed in groups A-F, relative to groups A0-F0 respectively. In contrast, RANKL was overexpressed in PMOPF group, and it was overexpressed in groups A-F, relative to groups A0-F0 respectively.
Results:LRP5 was expressed as the lowest level in group B (the third day after racture), whereas β-catenin was expressed as the lowest in group C (the seventh day after racture), on the contrary, RANKL was expressed as the highest level in group C and finally, OPG and LGR4 were expressed as the lowest in group E (the twenty-eighth day after fracture).
Conclusions:The Wnt/β-catenin, OPG/RANKL and LGR4/RANKL/RANK signaling pathways have been reported to be closely associated with the fracture development or repair in PMOPF. The factors changed at different time intervals in PMOPF patients, which could be potentially associated with the bone repair process in osteoporotic fractures.
Comprehensive Analysis of Circular RNAs in Porcine Small Intestine Epithelial Cells Associated with Susceptibility to Escherichia coli F4ac Diarrhea
Authors: Zhao Qingyao , Xu Qinlei , Serafino MA. , Zhang Qin , Wang Chuduan , Yu Ying
Published: September 2022

Background: Diarrhea is one of the most common diseases in pig industry, which seriously threatens the health of piglets and causes huge economic losses. Enterotoxigenic Escherichia coli (ETEC) F4 is regarded as the most important cause of diarrhea in piglets. Some pigs are naturally resistant to those diarrheas caused by ETEC-F4, because they have no F4 receptors (F4R) on their small intestine epithelial cells that allow F4 fimbriae adhesion. Circular RNA (circRNA) plays an important regulatory role in the pathogenesis of disease. However, the mechanism of circRNAs regulating Enterotoxigenic Escherichia coli F4 fimbriae (ETEC-F4ac) adhesion phenotype in small intestine epithelial cells of Large White piglets is still unclear. Hence, the present study assessed the circRNA expression profiling in small intestine epithelial cells of eight male piglets with different ETEC-F4 adhesion phenotypes and ITGB5genotypes to unravel their regulatory function in susceptibility to ETEC-F4ac diarrhea. Piglets were divided into two groups: non-adhesive group (n= 4) with CC genotype and adhesive group (n = 4) with TT genotype.
Results: The RNA-seq data analysis identified 13,199 circRNAs from eight samples, most of which were exon-derived. In the small intestine epithelial cells, 305 were differentially expressed (DE) circRNAs between the adhesive and non-adhesive groups; of which 46 circRNAs were upregulated, and 259 were downregulated. Gene ontology and KEGG enrichment analysis revealed that most significantly enriched DE circRNAs’ host genes were linked to cytoskeletal components, protein phosphorylation, cell adhesion, ion transport and pathways associated with ETEC diarrhea. The circRNA-miRNA-mRNA interaction network was also constructed to elucidate their underlying regulatory relationships. Our results identified several candidate circRNAs that affects susceptibility to ETEC diarrhea. Among them, circ-SORBS1 can adsorb ssc-miR-345-3p to regulate the expression of its host gene SORBS1, thus improving cell adhesion.
Conclusion: Our results provided insights into the regulation function of circRNAs in susceptibility to ETEC diarrhea of piglets, and enhanced our understanding of the role of circRNAs in regulating ETEC diarrhea, and reveal the great potential of circRNA as a diagnostic marker for susceptibility of ETEC diarrhea in piglets.
Localization-enhanced moiré exciton in twisted transition metal dichalcogenide heterotrilayer superlattices
Authors: LIU Yanping , Zheng Haihong , Wu Biao , Li Shaofei , Ding Junnan , He Jun , Liu Zongwen , Wang Chang-Tian , Wang Jian-Tao , Pan Anlian
Published: September 2022

Moiré superlattice created by the stacking of twisted 2D layered materials have become a new platform for the study of quantum optics. The strong coupling of moiré superlattices can generate flat minibands that enhance electronic interactions and produce a variety of fascinating strongly correlated states such as non-conventional superconductivity, Mott insulating states and moiré excitons. However, the influence between the adjustment and localization of moiré excitons in Van der Waals heterostructures has not been the subject of experimental investigations. Here we report experimental evidence of the localization-enhanced moiré excitons in the twisted WSe2/WS2/WSe2 heterotrilayer with type-II band alignments. At low temperature, we observed multiple excitons splitting phenomena in the twisted WSe2/WS2/WSe2 heterotrilayer, manifesting as multiple sharp emission lines, contrasting strongly with the moiré excitonic behavior of the twisted WSe2/WS2 heterobilayer (the linewidth is 4 times narrower). This is primarily because the enhancement of the two moiré potentials in the twisted heterotrilayer enables the moiré excitons at the highly localized interface. Furthermore, the changes in temperature, laser power and valley polarization further demonstrate the confinement effect of moiré potential on moiré excitons. Our findings provide a new way for the localization of moiré excitons in twist-angle heterostructures, facilitating the development of coherent quantum light emitters.
The Structural Analysis of Driving Forces to Adaptive Capacity with Climate Change in Ahvaz City. Iran
Authors: dehcheshmeh mostafa mohammadi , Ghaedi Sohrab , Shanbehpour Fereshteh
Published: September 2022

Climate change is an increasing concern for national and local governments around the world. The severity of the natural disasters affected by these changes has led to negative impacts on various economic, social and environmental dimensions in cities. One of the important global strategies in responding to the adverse effects of climate change is the adaptation strategy. The aim of this study is to identification and structural modeling of driving forces for adaptation to climate change according to the special geography of Ahvaz city as a strategic city in southwest of Iran. After identifying the factors and indicators through the study of records and a survey of the elite group, analysis and stratification was done using the combined ISM-DEMATEL model and finally the main driving forces of adapting to climate change in Ahvaz were identified by Mic-Mac Structural Model. The research findings have shown: among the five economic, social, institutional, physical and technological factors, the economy has known as the most effective factor in adapting to climate change in Ahvaz. Also, among the 44 selected indicators, 10 important driving forces were selected that 6 driving forces, have the economic and social background. Based on cross-impact analysis by Mic-Mac; the financial support for vulnerable groups, business improvement, alleviation poverty measures, diversification of economic activities, social cohesion and social trust to government were recognized as the main drivers of Ahvaz city's adaptation to climate change.
Characterization of regional CH 4 emanation and total particulate pollution from the underground coal mines
Authors: Ayub Ayesha , Ahmad Sheikh Saeed
Published: September 2022

Emission of methane from the underground coalmine is currently a global concern. The study aims to quantify the emission of potent toxic gases along with atmospheric dust in the suburbs of underground coal mines, in the field of Balochistan Pakistan. Related variables selected for quality check included particulate matter (i.e. PM10), CH4, O2, CO and elemental composition of PM10 (i.e. Cr, Cd, Co, Fe, Cu, Pb, Ni and Mn). A seasonal comparative study was designed. Widely applied GIS tool (i.e.IDW) was incorporated. Strengthening data with correlation matrix analysis apprehended interrelationship among the variables. Air quality variables were found above the safe allowable limits set by various standards (WHO, EPA, NIOSH, U.S National Ambient Air Concentration). No significant seasonal variation was recorded; but the pollutant concentration remained elevated during both seasons. Pearson correlation matrix analysis showed that CH4 had a strong negative correlation with O2. Moreover, air probed inside the underground coalmine showed a deteriorated status. This alarming status is primarily attributed to all the mining activities and secondarily to vehicular emissions, mine fire and poor ventilation system. This study will provide a baseline data for concerned authorities for planning management, pollutant prevention and strategies for environmental monitoring in future.