Miracle-dz/UniFAR-FTUs huggingface dataset:
Linkages between Plant Community Composition and Soil Microbial Diversity in Masson Pine Forests

Plant species identity influences soil microbial communities directly by host specificity and root exudates, and indirectly by changing soil properties. As a native pioneer species common in early successional communities, Masson pine (Pinus massoniana) forests are widely distributed in subtropical China, and play a key role in improving ecosystem productivity. However, how pine forest composition, especially the dominance of plant functional groups, affects soil microbial diversity remains unclear. Here, we investigated linkages among woody plant composition, soil physicochemical properties, and microbial diversity in forests along a dominance gradient of Masson pine. Soil bacterial and fungal communities were mainly explained by woody plant community composition rather than by woody species alpha diversity, with the dominance of tree (without including shrub) species and ectomycorrhizal woody plant species accounting for more of the variation among microbial communities than pine dominance alone. Structural equation modeling revealed that bacterial diversity was associated with woody plant compositional variation via altered soil physicochemical properties, whereas fungal diversity was directly driven by woody plant composition. Bacterial functional groups involved in carbohydrate and amino acid metabolism were negatively correlated with the availability of soil nitrogen and phosphorus, whereas saprotrophic and pathogenic fungal groups showed negative correlations with the dominance of tree species. These findings indicate strong linkages between woody plant composition than soil microbial diversity; meanwhile, the high proportion of unexplained variability indicates great necessity of further definitive demonstration for better understanding of forest–microbe interactions and associated ecosystem processes.
Aflatoxin B1 Detoxification Potentials of Garlic, Ginger, Cardamom, Black Cumin, and Sautéing in Ground Spice Mix Red Pepper Products

The uses of natural plant origin bioactive compounds are emerging as a promising strategy to detoxify aflatoxin B1 (AFB1). This study aimed to explore the potential of cooking, phytochemicals content, and antioxidant activities derived from garlic, ginger, cardamom, and black cumin to detoxify AFB1 on spice mix red pepper powder (berbere) and sauté. The effectiveness of the samples was analyzed for AFB1 detoxification potential through standard methods for the examination of food and food additives. These major spices showed an AFB1 level below the detection limit. After cooking in hot water for 7 min at 85 ℃, the experimental and commercial spice mix red pepper showed the maximum AFB1 detoxification (62.13% and 65.95%, respectively). Thus, mixing major spices to produce a spice mix red pepper powder had a positive effect on AFB1 detoxification in raw and cooked spice mix red pepper samples. Total phenolic content, total flavonoid content, 2,2-diphenyl-1-picrylhydrazyl, ferric ion reducing antioxidant power, and ferrous ion chelating activity revealed good positive correlation with AFB1 detoxification at p < 0.05. The findings of this study could contribute to mitigation plans of AFB1 in spice-processing enterprises. Further study is required on the mechanism of AFB1 detoxification and safety of the detoxified products.
Pharmacological Evidence Suggests That Slo3 Channel Is the Principal K+ Channel in Boar Spermatozoa

Sperm ion channels are associated with the quality and type of flagellar movement, and their differential regulation is crucial for sperm function during specific phases. The principal potassium ion channel is responsible for the majority of K+ ion flux, resulting in membrane hyperpolarization, and is essential for sperm capacitation-related signaling pathways. The molecular identity of the principal K+ channel varies greatly between different species, and there is a lack of information about boar K+ channels. We aimed to determine the channel identity of boar sperm contributing to the primary K+ current using pharmacological dissection. A series of Slo1 and Slo3 channel modulators were used for treatment. Sperm motility and related kinematic parameters were monitored using a computer-assisted sperm analysis system under non-capacitated conditions. Time-lapse flow cytometry with fluorochromes was used to measure changes in different intracellular ionic concentrations, and conventional flow cytometry was used to determine the acrosome reaction. Membrane depolarization, reduction in acrosome reaction, and motility parameters were observed upon the inhibition of the Slo3 channel, suggesting that the Slo3 gene encodes the main K+ channel in boar spermatozoa. The Slo3 channel was localized on the sperm flagellum, and the inhibition of Slo3 did not reduce sperm viability. These results may aid potential animal-model-based extrapolations and help to ameliorate motility and related parameters, leading to improved assisted reproductive methods in industrial livestock production.
Low-Frequency and Random Telegraph Noise in 14-nm Bulk Si Charge-Trap Transistors

Effects of programming/erasing (P/E) and total-ionizing dose (TID) are investigated on 2- and 40-fin charge-trap transistors (CTTs) fabricated in a 14-nm bulk-Si CMOS technology. Significant random telegraph noise (RTN) is observed in as-processed CTTs, especially for 2-fin devices. Trapped charge in programed devices does not significantly affect 1/<inline-formula> <tex-math notation="LaTeX">${f}$ </tex-math></inline-formula> noise magnitudes, but P/E leads to trap activation/deactivation, causing changes in border-trap energy and spatial distributions. TID irradiation activates a large number of stable radiation-induced traps.
Mesenchymal Stem Cells in Nerve Tissue Engineering: Bridging Nerve Gap Injuries in Large Animals

Cell-therapy-based nerve repair strategies hold great promise. In the field, there is an extensive amount of evidence for better regenerative outcomes when using tissue-engineered nerve grafts for bridging severe gap injuries. Although a massive number of studies have been performed using rodents, only a limited number involving nerve injury models of large animals were reported. Nerve injury models mirroring the human nerve size and injury complexity are crucial to direct the further clinical development of advanced therapeutic interventions. Thus, there is a great need for the advancement of research using large animals, which will closely reflect human nerve repair outcomes. Within this context, this review highlights various stem cell-based nerve repair strategies involving large animal models such as pigs, rabbits, dogs, and monkeys, with an emphasis on the limitations and strengths of therapeutic strategy and outcome measurements. Finally, future directions in the field of nerve repair are discussed. Thus, the present review provides valuable knowledge, as well as the current state of information and insights into nerve repair strategies using cell therapies in large animals.
Riemannian geometry with skew torsion

• Title: Riemannian geometry with skew torsion • Candidate: Ana Cristina Castro Ferreira • College: St Cross • Degree: Doctor of Philosophy in Mathematics • Term: Hilary 2010 This thesis is concerned with the study of metric connections with skew torsion on the tangent bundle of a Riemannian manifold. We mainly work on compact, orientable Riemannian manifolds of dimension four where we develop the notion of Einstein metrics with skew torsion. Given a three-form on a four-manifold, we define an associated threeform on the moduli space of irreducible self-dual connections. We exhibit explicit formulas for the case of the 4-sphere with a round metric. We also consider the moduli space of 1-instantons on S4 for a family of Einstein metrics with skew torsion defined by Bonneau.
Synthesis of Adaptive Gain Controllers with Adjustable Parameters for a Class of Uncertain Linear Systems via Piecewise Lyapunov Functions

This paper discusses a design problem of robust control systems with adaptive gain controllers for a class of uncertain linear systems. The uncertainties under consideration which are composed of matched part and unmatched one are bounded, but its upper bounds are unknown, and the proposed controller consists of a fixed gain controller and a variable gain controller. In this paper, on the basis of piecewise Lyapunov functions, we show sufficient conditions for the existence of the proposed robust control system with the adaptive gain controller. Finally, numerical examples are presented to demonstrate the effectiveness of the proposed controller.
Composite Likelihood Function in State Space Models.

In general state space models, where the computational effort required in the evaluation of the full likelihood function is infeasible, we ana- lyze the problem of static parameter estimation based on composite likelihood functions, in particular pairwise likelihood functions. We discuss consistency and efficiency properties of the estimators obtained by maximizing these func- tions in state space scenario, linking these properties to the characteristics of the model. We empirically compare the efficiency between maximum pairwise likelihood and maximum full likelihood estimators. We suggest the existence of a 'best' distance between pairs of observations, in terms of variance of the maximum pairwise likelihood estimator.
Persistently Elevated HBV Viral-Host Junction DNA in Urine as a Biomarker for Hepatocellular Carcinoma Minimum Residual Disease and Recurrence: A Pilot Study

Hepatitis B virus (HBV)-host junction sequences (HBV-JSs) has been detected in the urine of patients with HBV infection. This study evaluated HBV-JSs as a marker of minimum residual disease (MRD) and tumor recurrence after treatment in HBV-hepatocellular carcinoma (HCC) patients. Archived serial urine DNA from two HBV–HCC with recurrence as confirmed by MRI and four HBV-related cirrhosis (LC) patients were used. Urinary HBV-JSs were identified by an HBV-targeted NGS assay. Quantitative junction-specific PCR assays were developed to investigate dynamic changes of the most abundant urinary HBV-JS. Abundant urinary HBV-JSs were identified in two cases of tumor recurrence. In case 1, a 78-year-old female with HBV- HCC underwent a follow-up MRI following microwave ablation. While MRI results were variable, the unique HBV-JS DNA, HBV-Chr17, steadily increased from initial diagnosis to HCC recurrence. In case 2, a 74-year-old male with HBV–HCC contained two HBV-JS DNA, HBV-Chr11 and HBV-TERT, that steadily increased after initial HCC diagnosis till recurrence. One LC examined had HBV-TERT DNA detected, but transiently in 3.5 years during HCC surveillance. HBV-JS DNA was persistently elevated prior to the diagnosis of recurrent HCC, suggesting the potential of urinary HBV-JS DNA to detect MRD and HCC recurrence after treatment.
Laparoscopic Restorative Total Proctocolectomy with Ileal Pouch-Anal Anastomosis for Familial Adenomatous Polyposis and Ulcerative Colitis

Background: Although laparoscopic total proctocolectomy with ileal pouch-anal anastomosis has recently been used for this group of patients, there are rare reports of its treatment outcomes and postoperative complications. For this purpose, the very aim of the present study was to evaluate the complications of this surgery after 6 months in patients with familial adenomatous polyposis (FAP) and ulcerative colitis (UC). Materials and Methods: The present cross-sectional study was performed on 20 patients undergoing restorative proctocolectomy with ileal pouch-anal anastomosis (RPC-IPAA) for FAP or UC during 2009–2014. Outcomes of patients were recorded 6 months after surgery for complications and satisfaction. Results: There were 11 (60%) males and 9 (40%) females with a mean age of 30.65 ± 9.59 years. There were 12 patients (60%) with FAP and eight patients (40%) with UC. The length of stay (LOS) ranged from 4 days to 10 days with the mean of 6.40 ± 1.76 days. The incidence of complications including leak, urinary retention, and wound infection were 10%, 5%, and 10%, respectively. Moreover, no postoperative mortalities occurred. Male patients had no problems during sexual activity or micturition. All patients were highly satisfied with the outcome of the surgery. Conclusion: According to the results of the present study, laparoscopic RPC-IPAA was a surgery with the least complications and the highest level of satisfaction for young patients with FAP and UC. Therefore, it seems that this surgery can be a suitable surgical method for the mentioned patients.
Immune Cell Response during COVID-19 Infection and following SARS-CoV-2 Vaccination in Patients Admitted to Intensive Care Unit

Background Immune response plays a crucial role in virus clearance during COVID-19 infection and underpins vaccine efficacy. Herein, we aimed to assess the immune response during COVID-19 infection and following SARS-CoV-2 vaccination. Methods In this retrospective study, 94 confirmed COVID-19 patients admitted to the intensive care unit were categorized into unvaccinated patients (n = 50), including 33 deceased and 17 discharged patients, and vaccinated group (n = 44) with 26 deceased and 18 discharged patients. Records of patients with severe COVID-19 admitted to the ICU between March, 2021 and March, 2022 were gathered and analyzed. Result The assessment of immune cell counts revealed a large rise of neutrophils associated to decrease number of lymphocytes in patients with COVID-19 infection. In dead patients, we detected a significant correlation between neutrophils and inflammatory parameters such as IL-6 and CRP. Moreover, analysis of immune cell count following vaccination did not reveal any significant difference. However, the most substantial result, herein, detected is the decrease level of IL-6 in vaccinated patients as compared to unvaccinated. The reduce level of IL-6 following vaccination is observed in discharged patients as compared to deceased. Regarding the level of mortality after vaccination, we showed that all patients who received the first dose were died (46.1%, n = 12) as compared to those who have received two doses (34.6%, n = 9) and the third dose of vaccine (19.23%, n = 3) (p=0.0018). Strikingly, studying the inflammatory parameters after each vaccine dose, we revealed a significant decrease of IL-6 level after the booster dose (third dose), especially in vaccinated discharged patients. Conclusions Neutrophils combined with IL-6 and CRP can be very useful markers to predict disease severity in patients admitted to ICU. The decrease level of IL-6 in vaccinated group pointed out the impact of vaccination to prevent inflammatory cytokine release.
THE EFFECT OF BASKETBALL SPORT ON SOME POSTURAL PARAMETERS

The aim of the study is to investigate the effects of basketball as a hard team sport on players’ postural structure with using computer software. A sedentary group of 23 and elite level of 23 basketball players were involved in the study. The average age of sedentary group is 22.2±2.1/year with the average height of 179.4±2.5 cm; however, the average age of players is 23.6±2.2/year with the average height of 189.45±3.23 cm. Totally three photo shootings were applied to the participants, which are; from anterior perspective for anthropometric measurement, from anterior and lateral perspective for posture analysis. The graphics acquired were digitized via computer software and were analyzed by using SPSS v.19 packaged software. As a result of the analysis done, there are statistically significant differences found in the angle of head lateral deviation (right), in the angle of head front deviation in sagittal plane, in the angles of claviculare anterior (right), in the symmetry between right and left acromion processes, in the angle of sagittal-anterior pelvic tilt, in the distance between acromion process and plumbline anterior (right-left), in the distance between head posture and acromion process sagittal(cm), in the horizontal symmetry distance of plumbline and acromion process (right and left), in the horizontal symmetry of sternal notch and the plumbline (anterior left and right), in the horizontal symmetry between sternal notch and plummet (anterior right-left), in the horizontal symmetry between greater trochanter and the plumbline sagittal(posterior) groups. (p<0.05). As a result, in a long time period, training oneself in a particular sport branch has a significant effect on the development of players’ dynamic and static postures. It can also be stated that the evidence found will be useful for determining the success criteria in basketball, specifying and arranging the training program.
Epigenetic and Tumor Microenvironment for Prognosis of Patients with Gastric Cancer

Background: Epigenetics studies heritable or inheritable mechanisms that regulate gene expression rather than altering the DNA sequence. However, no research has investigated the link between TME-related genes (TRGs) and epigenetic-related genes (ERGs) in GC. Methods: A complete review of genomic data was performed to investigate the relationship between the epigenesis tumor microenvironment (TME) and machine learning algorithms in GC. Results: Firstly, TME-related differential expression of genes (DEGs) performed non-negative matrix factorization (NMF) clustering analysis and determined two clusters (C1 and C2). Then, Kaplan–Meier curves for overall survival (OS) and progression-free survival (PFS) rates suggested that cluster C1 predicted a poorer prognosis. The Cox–LASSO regression analysis identified eight hub genes (SRMS, MET, OLFML2B, KIF24, CLDN9, RNF43, NETO2, and PRSS21) to build the TRG prognostic model and nine hub genes (TMPO, SLC25A15, SCRG1, ISL1, SOD3, GAD1, LOXL4, AKR1C2, and MAGEA3) to build the ERG prognostic model. Additionally, the signature’s area under curve (AUC) values, survival rates, C-index scores, and mean squared error (RMS) curves were evaluated against those of previously published signatures, which revealed that the signature identified in this study performed comparably. Meanwhile, based on the IMvigor210 cohort, a statistically significant difference in OS between immunotherapy and risk scores was observed. It was followed by LASSO regression analysis which identified 17 key DEGs and a support vector machine (SVM) model identified 40 significant DEGs, and based on the Venn diagram, eight co-expression genes (ENPP6, VMP1, LY6E, SHISA6, TMEM158, SYT4, IL11, and KLK8) were discovered. Conclusion: The study identified some hub genes that could be useful in predicting prognosis and management in GC.
Reduced-Order Model for Wind-Solar Multi-Microgrids Considering Time-Scale Coupling

A computationally efficient and accurate reduced-order model (ROM) that characterizes the time-scale coupling caused by the high penetration of power-electronic converters in microgrids (MGs) is crucial to system stability analysis. When such MGs are interconnected into multi-microgrids (MMGs), the coupling between fast and slow dynamics will be more complicated due to the interactions among each MG. The traditional ROM without concerning dynamic coupling may lead to low accuracy and even misjudgment of system stability. In this paper, by considering primary energy dynamics of renewable energy sources, e.g., doubly-fed induction generator (DFIG) and photovoltaic (PV), a small-signal model that characterizes the practical multi-timescale of MMGs is firstly presented. Then with the division of the entire MMGs into fast and slow dynamic subsystems based on the assumption of time-scale separating, the coupling dynamics are identified via the residues-based method. Finally, a ROM considering coupling dynamics and preserving physical meaning is proposed by reconfiguring the fast and slow dynamic subsystems based on singular perturbation. The accuracy of the proposed ROM is verified by comparing it with the detailed model under different control parameters, wind speeds and irradiance conditions. The time-domain simulation is employed to validate the dynamic response of the proposed ROM.
Insights into the pathogenesis of normal-pressure hydrocephalus

Normal-pressure hydrocephalus (NPH) is a poorly defined clinical syndrome, classically characterized by the phenotypic triad of gait instability, cognitive impairment, and urinary incontinence, accompanied by neuroimaging evidence of ventriculomegaly and disproportionally enlarged subarachnoid space hydrocephalus and normal intracranial pressure.1,2 The diagnosis of this syndrome is complex since the characterizing symptoms are highly nonspecific and occur together in fewer than two thirds of NPH patients. In addition, a growing body of evidence supports the observation that NPH patients often have a coexistent neurodegenerative disorder that may be a concurrent or sole cause of both clinical symptoms and ventriculomegaly. This may be the main cause for the short-lived benefits secondary to an NPH-targeted therapeutic intervention, such as the placement of a ventriculoperitoneal shunt.2
Monge-Ampère measures and Poletsky-Stessin Hardy spaces on bounded hyperconvex domains

In this thesis study, we consider Poletsky-Stessin Hardy (PS-Hardy) spaces that are generated by continuous, plurisubharmonic exhaustion functions on hyperconvex domains. In the first part of this study we examine these spaces on domains in the complex plane that are bounded by an analytic Jordan curve. In this setting we focus on PS-Hardy spaces generated by exhaustion functions that have finite Monge-Ampre mass but are not necessarily maximal outside of a compact set. This choice gives us new Banach spaces strictly contained in classical Hardy spaces. We characterize PS-Hardy spaces through their boundary values and we show factorization results analogous to unit disc case. Using functional analysis techniques we prove that the algebra of holomorphic functions which are continuous on the boundary are dense in PS-Hardy spaces. Moreover, we consider the composition operators with holomorphic symbols acting on PS-Hardy spaces and show that contrary to classical case, not all composition operators are bounded on PS-Hardy spaces. In the second part, we study PS-Hardy spaces on polydisc, complex ellipsoid and on strongly convex domains. On complex ellipsoid case, we prove the existence of radial boundary values and then by applying a classical method given by Stein we show the existence of boundary values along admissible approach regions. As an application of this method , we also obtain that polynomials are dense in PS-Hardy spaces on complex ellipsoids. Lastly, we examine the boundedness of composition operators on PS-Hardy spaces on hyperconvex domains in several variables.
A semiparametric Bayesian approach for joint modeling of longitudinal trait and event time

ABSTRACT Inference on the whole biological system is the recent focus in bioscience. Different biomarkers, although seem to function separately, can actually control some event(s) of interest simultaneously. This fundamental biological principle has motivated the researchers for developing joint models which can explain the biological system efficiently. Because of the advanced biotechnology, huge amount of biological information can be easily obtained in current years. Hence dimension reduction is one of the major issues in current biological research. In this article, we propose a Bayesian semiparametric approach of jointly modeling observed longitudinal trait and event-time data. A sure independence screening procedure based on the distance correlation and a modified version of Bayesian Lasso are used for dimension reduction. Traditional Cox proportional hazards model is used for modeling the event-time. Our proposed model is used for detecting marker genes controlling the biomass and first flowering time of soybean plants. Simulation studies are performed for assessing the practical usefulness of the proposed model. Proposed model can be used for the joint analysis of traits and diseases for humans, animals and plants.