Miracle-dz/UniFAR-FTUs huggingface dataset:
Allometry and Distribution of Nitrogen in Natural Plant Communities of the Tibetan Plateau

Nitrogen (N) is an important element for most terrestrial ecosystems; its variation among different plant organs, and allocation mechanisms are the basis for the structural stability and functional optimization of natural plant communities. The nature of spatial variations of N and its allocation mechanisms in plants in the Tibetan Plateau—known as the world’s third pole—have not been reported on a large scale. In this study, we consistently investigated the N content in different organs of plants in 1564 natural community plots in Tibet Plateau, using a standard spatial-grid sampling setup. On average, the N content was estimated to be 19.21, 4.12, 1.14, and 10.86 mg g–1 in the leaf, branch, trunk, and root, respectively, with small spatial variations. Among organs in communities, leaves were the most active, and had the highest N content, independent of the spatial location; as for vegetation type, communities dominated by herbaceous plants had higher N content than those dominated by woody plants. Furthermore, the allocation of N among different plant organs was allometric, and not significantly influenced by vegetation types and environmental factors; the homeostasis of N was also not affected much by the environment, and varied among the plant organs. In addition, the N allocation strategy within Tibet Plateau for different plant organs was observed to be consistent with that in China. Our findings systematically explore for the first time, the spatial variations in N and allometric mechanisms in natural plant communities in Tibet Plateau and establish a spatial-parameters database to optimize N cycle models.
Analysis of Genetic Alterations in Ocular Adnexal Mucosa-Associated Lymphoid Tissue Lymphoma With Whole-Exome Sequencing

Next-generation sequencing studies on ocular adnexal marginal zone lymphoma of mucosa-associated lymphoid tissue (OAML) have to date revealed several targets of genetic aberrations. However, most of our current understanding of the pathogenesis and prognosis of OAML is primarily based on studies conducted in populations from Europe and the US. Furthermore, the majority were based on formalin-fixed paraffin-embedded (FFPE) tissue, which generally has poor integrity and creates many sequencing artifacts. To better investigate the coding genome landscapes of OAML, especially in the Chinese population, we performed whole-exome sequencing of 21 OAML cases with fresh frozen tumor tissue and matched peripheral blood samples. IGLL5, as a novel recurrently mutated gene, was found in 24% (5/21) of patients, with a higher relapse rate (P=0.032). In addition, mutations of MSH6, DIS3, FAT1, and TMEM127 were found in 10% of cases. These novel somatic mutations indicate the existence of additional/alternative lymphomagenesis pathways in OAML. Moreover, the difference between our and previous studies suggests genetic heterogeneity of OAML between Asian and Western individuals.
Comparing Revision Total Knee Arthroplasty Stems at a High-Volume Revision Center

Introduction Hybrid fixation and fully cemented fixation are commonly used in revision total knee arthroplasty (rTKA). These two techniques are typically done based on surgeon preference and one has not demonstrated superiority over the other. The purpose of this study was to examine if there was a difference in survivorship between the two different techniques. Methods A retrospective cohort study of all consecutive patients undergoing rTKA (CPT 27487) from January 1, 2011 to January 1, 2018 at a single academic center was performed. Patients were divided into cemented and hybrid rTKA groups with comparison of patient demographic, clinical and radiological outcomes, reoperation, change in post-operative hemoglobin (HgB), and length of stay (LOS). Results A total of 133 rTKA for 122 patients were identified: 30.1% in the cemented and 69.9% in the hybrid groups. There was no significant difference in age (p = 0.491), sex (p = 0.250), laterality (p = 0.421), or body mass index (BMI) (p = 0.609) between the two groups. Mean LOS (hybrid 4.13 days, cemented 3.65 days; p = 0.356) and change in Hgb (hybrid 2.95 mg/dL, cemented 2.62mg/dL; p = 0.181) were not statistically different between the groups. Mean follow up for the hybrid (25.4 months, range 2–114 months) and cemented (24.6 months, range 3–75.5 months) rTKA was not statistically significant (p = 0.825). Overall survival rates were 80.9% in the hybrid and 84.6% in the cemented groups (p = 0.642). Conclusions Hybrid and fully cemented rTKA techniques have similar survival rates at a minimum followup of 2 years. Additionally, in our cohort, age, gender, and BMI were not associated with failure in either group. Furthermore, we did not observe differences in LOS or change in hemoglobin suggesting early postoperative complications may not differ between cemented and hybrid stemmed groups. Continued long-term research is required for defining the best rTKA technique.
Keystone Institutions of Democratic Governance Across Indigenous North America

Defining and examining democracy in non-Western contexts is a conceptual challenge. This is largely because scholars of contemporary political systems outside of anthropology can envision no alternative pathways other than Western expressions of democracy. Such thinking inhibits our understanding of past, and indeed future, democratic systems. In this paper, we argue that there is no such thing as a “democracy, ” but rather there are institutions that facilitate democratic governance. More specifically, we argue that in Indigenous North America “keystone institutions” facilitated complex institutional arrangements and broad participation by a citizenry in the distribution of power and authority. While these characteristics define such Western democratic institutions as the Athenian assembly, the Icelandic Althing, or the U.S. Congress, we argue that comparable keystone institutions of governance can be identified across Indigenous North America. To illustrate these points, we provide a series of cases that demonstrate the variability in the forms that democratic keystone institutions might take. We specifically focus on axes of variability related to the scale and scope of participation facilitated by each institution, the degree to which the institutions distribute power equitably, and the complexity and formality of the institutional arrangements held together by the keystone institution. Importantly, we argue that the concept of the keystone institution as an analytical tool for seeking out the emergence and role of democratic forms of governance transcends the utility of dichotomous categories such as Western/non-Western or state/non-state that limit productive comparative frameworks and the inclusion of non-traditional case studies of democracy in global conversations.
Exploring New Characteristics: Using Deep Learning and 3D Reconstruction to Compare the Original COVID-19 and Its Delta Variant Based on Chest CT

Purpose: Computer-aided diagnostic methods were used to compare the characteristics of the Original COVID-19 and its Delta Variant. Methods: This was a retrospective study. A deep learning segmentation model was applied to segment lungs and infections in CT. Three-dimensional (3D) reconstruction was used to create 3D models of the patient’s lungs and infections. A stereoscopic segmentation method was proposed, which can subdivide the 3D lung into five lobes and 18 segments. An expert-based CT scoring system was improved and artificial intelligence was used to automatically score instead of visual score. Non-linear regression and quantitative analysis were used to analyze the dynamic changes in the percentages of infection (POI). Results: The POI in the five lung lobes of all patients were calculated and converted into CT scores. The CT scores of Original COVID-19 patients and Delta Variant patients since the onset of initial symptoms were fitted over time, respectively. The peak was found to occur on day 11 in Original COVID-19 patients and on day 15 in Delta Variant patients. The time course of lung changes in CT of Delta Variant patients was redetermined as early stage (0–3 days), progressive and peak stage (4–16 days), and absorption stage (17–42 days). The first RT-PCR negative time in Original COVID-19 patients appeared earlier than in Delta Variant patients (22 [17–30] vs. 39 [31–44], p < 0.001). Delta Variant patients had more re-detectable positive RT-PCR test results than Original COVID-19 patients after the first negative RT-PCR time (30.5% vs. 17.1%). In the early stage, CT scores in the right lower lobe were significantly different (Delta Variant vs. Original COVID-19, 0.8 ± 0.6 vs. 1.3 ± 0.6, p = 0.039). In the absorption stage, CT scores of the right middle lobes were significantly different (Delta Variant vs. Original COVID-19, 0.6 ± 0.7 vs. 0.3 ± 0.4, p = 0.012). The left and the right lower lobes contributed most to lung involvement at any given time. Conclusion: Compared with the Original COVID-19, the Delta Variant has a longer lung change duration, more re-detectable positive RT-PCR test results, different locations of pneumonia, and more lesions in the early stage, and the peak of infection occurred later.
The Prediction and Influential Factors of Violence in Male Schizophrenia Patients With Machine Learning Algorithms

Background Early to identify male schizophrenia patients with violence is important for the performance of targeted measures and closer monitoring, but it is difficult to use conventional risk factors. This study is aimed to employ machine learning (ML) algorithms combined with routine data to predict violent behavior among male schizophrenia patients. Moreover, the identified best model might be utilized to calculate the probability of an individual committing violence. Method We enrolled a total of 397 male schizophrenia patients and randomly stratified them into the training set and the testing set, in a 7:3 ratio. We used eight ML algorithms to develop the predictive models. The main variables as input features selected by the least absolute shrinkage and selection operator (LASSO) and logistic regression (LR) were integrated into prediction models for violence among male schizophrenia patients. In the training set, 10 × 10-fold cross-validation was conducted to adjust the parameters. In the testing set, we evaluated and compared the predictive performance of eight ML algorithms in terms of area under the curve (AUC) for the receiver operating characteristic curve. Result Our results showed the prevalence of violence among male schizophrenia patients was 36.8%. The LASSO and LR identified main risk factors for violent behavior in patients with schizophrenia integrated into the predictive models, including lower education level [0.556 (0.378–0.816)], having cigarette smoking [2.121 (1.191–3.779)], higher positive syndrome [1.016 (1.002–1.031)] and higher social disability screening schedule (SDSS) [1.081 (1.026–1.139)]. The Neural Net (nnet) with an AUC of 0.6673 (0.5599–0.7748) had better prediction ability than that of other algorithms. Conclusion ML algorithms are useful in early identifying male schizophrenia patients with violence and helping clinicians take preventive measures.
Comparative Analysis of Codon Bias in the Chloroplast Genomes of Theaceae Species

Theaceae species are dicotyledonous angiosperms with extremely high ornamental and economic value. The chloroplast genome is traditionally used to study species evolution, expression of chloroplast genes and chloroplast transformation. Codon usage bias (CUB) analysis is beneficial for investigations of evolutionary relationships and can be used to improve gene expression efficiency in genetic transformation research. However, there are relatively few systematic studies of the CUB in the chloroplast genomes of Theaceae species. In this study, CUB and nucleotide compositions parameters were determined by the scripts written in the Perl language, CodonW 1.4. 2, CU.Win2000, RStudio and SPSS 23.0. The chloroplast genome data of 40 Theaceae species were obtained to analyse the codon usage (CU) characteristics of the coding regions and the influence of the source of variation on CUB. To explore the relationship between the CUB and gene expression levels in these 40 Theaceae plastomes, the synonymous codon usage order (SCUO) and measure independent of length and composition (MILC) values were determined. Finally, phylogenetic analysis revealed the genetic evolutionary relationships among these Theaceae species. Our results showed that based on the chloroplast genomes of these 40 Theaceae species, the CUB was for codons containing A/T bases and those that ended with A/T bases. Moreover, there was great commonality in the CUB of the Theaceae species according to comparative analysis of relative synonymous codon usage (RSCU) and relative frequency of synonymous codon (RFSC): these species had 29 identical codons with bias (RSCU > 1), and there were 19 identical high-frequency codons. The CUB of Theaceae species is mainly affected by natural selection. The SCUO value of the 40 Theaceae species was 0.23 or 0.24, and the chloroplast gene expression level was moderate, according to MILC values. Additionally, we observed a positive correlation between the SCUO and MILC values, which indicated that CUB might affect gene expression. Furthermore, the phylogenetic analysis showed that the evolutionary relationships in these 40 Theaceae species were relatively conserved. A systematic study on the CUB and expression of Theaceae species provides further evidence for their evolution and phylogeny.
Crossing the Line: Seroprevalence and Risk Factors for Transboundary Animal Diseases Along the Tanzania-Zambia Border

Transboundary pathogens pose a threat to livelihood security in countries such as Zambia and Tanzania. This study aimed to investigate the seroprevalence of peste des petits ruminants virus (PPRV), foot and mouth disease virus (FMDV), sheep and goat pox virus (SGPV), Rift Valley fever virus (RVFV) and Brucella spp. in sheep and goats along the Tanzania-Zambia border. Another aim was to assess the association between certain predictor variables and seroprevalence, focusing on trade and proximity to an international border, to a town and to the Tanzania-Zambia highway. During September-October 2018, 486 serum samples from small ruminants in Zambia and 491 in Tanzania were collected and analyzed using enzyme-linked immunosorbent assays (ELISA). A questionnaire focused on management strategies was administered to each household. The animal-level seroprevalence in Zambia was 0.21% [95% confidence interval (CI) (0.01–1.14) for PPRV, 1.03% (95% CI 0.33–2.39) for FMDV, 0% (95% CI 0–0.76) for SGPV, 2.26% (95% CI 1.14–4.01) for RVFV and 1.65% (95% CI 0.71–3.22) for Brucella spp. ]. In Tanzania, animal-level seroprevalence was 2.85% (95% CI 1.57–4.74) for PPRV, 16.9% (95% CI 13.7–20.5) for FMDV, 0.20% (95% CI 0.01–1.13) for SGPV, 3.26% (95% CI 1.87–5.24) for RVFV and 20.0% (95% CI 14.5–26.5) for Brucella spp. For PPRV (OR 6.83, 95% CI 1.37–34.0, p = 0.019) and FMDV (OR 5.68, 95% CI 1.58–20.3, p = 0.008), herds situated more than 30 km from an international border were more likely to be seropositive, while being located 10–30 km (OR 4.43, 95% CI 1.22–16.1 p = 0.024) from a border was identified as a risk factor for Brucella spp. For FMDV (OR 79.2, 95% CI 4.52–1388.9, p = 0.003), being situated within 30 km from a town was associated with seropositivity. Furthermore, contact with wild ruminants (OR 18.2, 95% CI 1.36–244), and the presence of sheep in the household (OR 5.20, 95% CI 1.00–26.9, p = 0.049), was associated with seropositivity for PPRV, and FMDV. No significant associations between trade or distance to the Tan-Zam highway and seroprevalence were found. We recommend that the impact of trade and proximity to borders, towns and roads should be further evaluated in larger studies, ideally incorporating aspects such as temporal trade fluctuations.
The Effect of Two Acute Bouts of Exercise on Oxidative Stress, Hematological, and Biochemical Parameters, and Rectal Temperature in Trained Canicross Dogs

Canicross is a sport discipline that connects human and canine athletes in running. Changes in physiological, hematological, and biochemical parameters, and exercise-induced oxidative stress have not been thoroughly characterized in canicross dogs. The aim of our study was the assessment of the health status of trained canicross dogs that were subjected to two acute bouts of exercise with their owners during the training season. Health status was assessed by measuring the rectal temperature, hematological and biochemical parameters, as well as blood oxidative stress parameters (plasma malondialdehyde, lipid peroxidation marker; whole blood glutathione peroxidase and erythrocyte superoxide dismutase1, antioxidant enzymes) before and during a two-day canicross training session and after a 24-h rest period. Seven trained canicross dogs (three females/four males) aged 12–120 months were included in the study. Blood samples were collected before and immediately after the first acute bout of exercise (day 1), after the second acute bout of exercise (day 2), and after 24 h of rest (day 3). Rectal temperature was measured at the same time as blood sample collection. The majority of hematological and biochemical parameters remained within reference ranges at all sampling times. Rectal temperature was significantly higher after training on days 1 and 2 compared to resting temperature on day 3. Hematological parameters did not change significantly; however, there were significant differences in urea, creatinine, creatine kinase, and triglycerides between specific sampling times. Despite significant changes, these biochemical parameters remained within reference ranges. Significant changes in biochemical parameters seem to reflect the dogs' physiological response to each acute bout of exercise, considering all biochemical parameters and rectal temperature returned to pre-exercise values after a 24-h rest period (day 3). No significant differences in oxidative stress parameters were found between any sampling times. Relatively high erythrocyte superoxide dismutase1 activity at all sampling times may indicate that the canicross dogs are adapted to training by an increased expression of antioxidant enzymes. Based on our results, we can conclude that the trained canicross dogs included in our study were healthy, in good physical condition, and fit for the two acute bouts of field exercise.
Natural Human Immunity Against Staphylococcal Protein A Relies on Effector Functions Triggered by IgG3

Staphylococcal protein A (SpA) is a multifunctional, highly conserved virulence factor of Staphylococcus aureus. By binding the Fc portion of all human IgG subclasses apart from IgG3, SpA interferes with antibody and complement deposition on the bacterial surface, impairing staphylococcal clearance by phagocytosis. Because of its anti-opsonic properties, SpA is not investigated as a surface antigen to mediate bacterial phagocytosis. Herein we investigate human sera for the presence of SpA-opsonizing antibodies. The screening revealed that sera containing IgG3 against SpA were able to correctly opsonize the target and drive Fcγ receptor-mediated interactions and phagocytosis. We demonstrated that IgG3 Fc is significantly more efficient in inducing phagocytosis of SpA-expressing S. aureus as compared to IgG1 Fc in an assay resembling physiological conditions. Furthermore, we show that the capacity of SpA antibodies to induce phagocytosis depends on the specific epitope recognized by the IgGs on SpA molecules. Overall, our results suggest that anti-SpA IgG3 antibodies could favor the anti-staphylococcal response in humans, paving the way towards the identification of a correlate of protection against staphylococcal infections.
Natural SARS-CoV-2 Infection Affects Neutralizing Activity in Saliva of Vaccinees

Background SARS-CoV-2 transmission mainly occurs through exposure of the upper airway mucosa to infected secretions such as saliva, which are excreted by an infected person. Thus, oral mucosal immunity plays a central role in the prevention of and early defense against SARS-CoV-2 infection. Although virus-specific antibody response has been extensively investigated in blood samples of SARS-CoV-2-infected patients and vaccinees, local humoral immunity in the oral cavity and its relationship to systemic antibody levels needs to be further addressed. Material and Methods We fine-tuned a virus neutralization assay (vNTA) to measure the neutralizing activity (NA) of plasma and saliva samples from 20 SARS-CoV-2-infected (SI), 40 SARS-CoV-2-vaccinated (SV), and 28 SARS-CoV-2-vaccinated subjects with a history of infection (SIV) using the “wild type” SARS-CoV-2 lineage B.1 (EU) and the Delta (B.1.617.2) strains. To validate the vNTA results, the presence of neutralizing antibodies (NAbs) to the spike receptor binding domain (RBD) was evaluated with an ELISA assay. Results NA to SARS-CoV-2 lineage B.1 (EU) was present in plasma samples from all the tested subjects, with higher titers in SIV compared to both SI and SV. Conversely, NA was detected in saliva samples from 10.3% SV, 45% SI, and 92.6% SIV, with significantly lower titers in SV compared to both SI and SIV. The detection of NAbs in saliva reflected its reduced NA in SV. Discussion The difference in NA of plasma vs. saliva was confirmed in a vNTA where the SARS-CoV-2 B.1 and Delta strains were tested head-to-head, which also revealed a reduced NA of both specimens compared to the B.1 variant. Conclusions The administration of SARS-CoV-2 vaccines was associated with limited virus NA in the oral cavity, as measured in saliva and in comparison to plasma. This difference was more evident in vaccinees without a history of SARS-CoV-2 infection, possibly highlighting the importance of local exposure at the site of virus acquisition to effectively prevent the infection and block its spread. Nevertheless, the presence of immune escape mutations as possibly represented by the SARS-CoV-2 Delta variant negatively affects both local and systemic efficacy of NA associated with vaccination.
Comprehensive Assessment of Selected Immune Cell Subpopulations Changes in Chemotherapy-Naïve Germ Cell Tumor Patients

The pattern of immune cell distribution in testicular germ cell tumors (GCT) significantly differs from the immune environment in normal testicular tissues. The present study aimed to evaluate the role of different leukocyte subpopulation in GCTs. A cohort of 84 chemotherapy-naïve GCT patients was analyzed. Immunophenotyping of peripheral blood leukocyte subpopulations was carried out by flow cytometry. In addition, the data assessing the immunophenotypes and the baseline clinicopathological characteristics of the included subjects were statistically evaluated. Their prognostic value for the assessment of progression-free survival (PFS) and overall survival (OS) was estimated. The percentage of different innate/adaptive immune cell subpopulations was significantly associated with poor risk-related clinical features, including the number of metastatic sites, presence of retroperitoneal, mediastinal, lung, brain and non-pulmonary visceral metastases as well as with the S-stage and International Germ Cell Consensus Classification Group (IGCCCG) risk groups. In univariate analysis, the percentages of neutrophils, eosinophils, dendritic cells type 2, lymphocytes and T cytotoxic cells were significantly associated with PFS, while the neutrophil, non-classical monocyte and lymphocyte percentage were associated with OS. However, all these outcome correlations were not independent of IGCCCG in multivariate analysis. The data indicated a link among different innate/adaptive peripheral immune cell subpopulations in GCT patients. In addition, the association between these subpopulations and tumor characteristics was also investigated. The findings of the present study may contribute to a deeper understanding of the interactions between cancer and innate/adaptive immune response in GCT patients.