Miracle-dz/UniFAR-FTUs huggingface dataset:
Empirical vs. light-use efficiency modelling for estimating carbon fluxes in a mid-succession ecosystem developed on abandoned karst grassland

Karst systems represent an important carbon sink worldwide. However, several phenomena such as the CO2 degassing and the exchange of cave air return a considerable amount of CO2 to the atmosphere. It is therefore of paramount importance to understand the contribution of the ecosystem to the carbon budget of karst areas. In this study conducted in a mid-succession ecosystem developed on abandoned karst grassland, two types of model were assessed, estimating the gross primary production (GPP) or the net ecosystem exchange (NEE) based on seven years of eddy covariance data (2013–2019): (1) a quadratic vegetation index-based empirical model with five alternative vegetation indices as proxies of GPP and NEE, and (2) the vegetation photosynthesis model (VPM) which is a light use efficiency model to estimate only GPP. The Enhanced Vegetation Index (EVI) was the best proxy for NEE whereas SAVI performed very similarly to EVI in the case of GPP in the empirical model setting. The empirical model performed better than the VPM model which tended to underestimate GPP. Therefore, for this ecosystem, we suggest the use of the empirical model provided that the quadratic relationship observed persists. However, the VPM model would be a good alternative under a changing climate, as it is rooted in the understanding of the photosynthesis process, if the scalars it involves could be improved to better estimate GPP.
Characterization of gamma irradiation-induced mutations in Arabidopsis mutants deficient in non-homologous end joining

Abstract To investigate the involvement of the non-homologous end joining (NHEJ) pathway in plant mutagenesis by ionizing radiation, we conducted a genome-wide characterization of the mutations induced by gamma rays in NHEJ-deficient Arabidopsis mutants (AtKu70−/− and AtLig4−/−). Although both mutants were more sensitive to gamma rays than the wild-type control, the AtKu70−/− mutant was slightly more sensitive than the AtLig4−/− mutant. Single-base substitutions (SBSs) were the predominant mutations in the wild-type control, whereas deletions (≥2 bp) and complex-type mutations [i.e. more than two SBSs or short insertion and deletions (InDels) separated by fewer than 10 bp] were frequently induced in the mutants. Single-base deletions were the most frequent deletions in the wild-type control, whereas the most common deletions in the mutants were 11–30 bp. The apparent microhomology at the rejoined sites of deletions peaked at 2 bp in the wild-type control, but was 3–4 bp in the mutants. This suggests the involvement of alternative end joining and single-strand annealing pathways involving increased microhomology for rejoining DNA ends. Complex-type mutations comprising short InDels were frequently detected in the mutants, but not in the wild-type control. Accordingly, NHEJ is more precise than the backup pathways, and is the main pathway for rejoining the broken DNA ends induced by ionizing radiation in plants.
Vaccination of Mice with a Novel Trypsin from Trichinella spiralis Elicits the Immune Protection against Larval Challenge

Trichinella spiralis is a major foodborne parasite and has a serious threat to meat safety. Development of anti-Trichinella vaccines is prospective to eliminate Trichinella infection in food animal. The aim of this study was to assess the biological properties of a novel T. spiralis trypsin (TsT) and its elicited immune protection against larval challenge. The cDNA sequence of TsT gene was cloned and expressed. Western blotting showed rTsT was identified by infection serum and anti-TsT serum. RT-PCR results revealed that TsT gene was transcribed at diverse T. spiralis lifecycle stages. The IIFT results showed that natural TsT was principally expressed at epicuticle of 5-6 day adult worms, indicating that TsT is a worm somatic antigen and adult-stage specific surface antigen. Vaccination of mice with rTsT triggered an evident humoral immune response (high levels of serum IgG, IgG1/IgG2a, and enteral sIgA), and it also induced the systemic and enteral local cellular immune response, demonstrated by an significantly elevation of cytokines IFN-γ and IL-4. The mice vaccinated with rTsT exhibited a 33.17% reduction of enteral adult worms and a 37.80% reduction of muscle larvae after larval challenge. The results showed that TsT might be considered as a candidate target antigen for anti-T. spiralis vaccines.
Maternal biomarker patterns for metabolism and inflammation in pregnancy are influenced by multiple micronutrient supplementation and associated with child biomarker patterns and nutritional status at 9-12 years of age

Maternal nutritional status influences fetal development and long-term risk for adult non-communicable diseases. However, the underlying mechanisms remain poorly understood. We examined whether biomarkers for metabolism and inflammation during pregnancy were associated with maternal health and with child biomarkers and health at 9–12 years of age in 44 maternal-child dyads from the Supplementation with Multiple Micronutrients Intervention Trial (SUMMIT, ISRCTN34151616) in Lombok, Indonesia. Archived blood for each dyad from maternal enrollment, later in pregnancy, postpartum, and from children at 9–12 years comprised 132 specimens. Multiplex microbead immunoassays were used to quantify vitamin D-binding protein (D), adiponectin (A), retinol-binding protein 4 (R), C-reactive protein (C), and leptin (L). Principal component analysis (PCA) revealed distinct variance patterns, i.e. principal components (PC), for baseline pregnancy, bp.pc1. D↓A↓R↓ and bp.pc2. C↓L↑; combined follow-up during pregnancy and postpartum, dp-pp.pc1. D↑↓A↑R↑↓L↓ and dp-pp.pc2. A↑C↑L↑; and children, ch.pc1. D↑R↑C↑ and ch.pc2. D↓A↑L↑. Maternal multiple micronutrient (MMN) supplementation led to an association of baseline maternal bp.pc2. C↓L↑ with decreased post-supplementation maternal dp-pp.pc2. A↑C↑L↑ (p = 0.022), which was in turn associated with both increased child ch.pc1. D↑R↑C↑ (p = 0.036) and decreased child BMI z-score (BMIZ) (p = 0.022). Further analyses revealed an association between maternal dp-pp.pc1. D↑↓A↑R↑↓L↓ and increased child BMIZ (p = 0.036). Child ch.pc1. D↑R↑C↑ was associated with decreased birth weight (p = 0.036) and increased child BMIZ (p = 0.002). Child ch.pc2. D↓A↑L↑ was associated with increased child BMIZ (p = 0.005), decreased maternal height (p = 0.030) and girls (p = 0.002). A pattern of elevated maternal adiponectin and leptin in pregnancy was associated with increased C-reactive protein, vitamin A, and D binding proteins pattern in children, suggesting biomarkers acting in concert may have qualitative as well as quantitative influence beyond single biomarker effects. Patterns in pregnancy proximal to birth were more associated with child status. In addition, child patterns were more associated with child status, particularly child BMI. MMN supplementation affects maternal biomarker patterns of metabolism and inflammation in pregnancy, and potentially in the child. However, child nutrition conditions after birth may have a greater impact on metabolism and inflammation.
Using Genetics in Periodontal Disease to Justify Implant Failure in Down Syndrome Patients

Peri-implant bone loss leading to dental implant failure does not develop in the same way across subjects who apparently present the same condition—specifically, in the case of Down syndrome patients with the same genetic disorder—given that they do not necessarily develop immune–inflammatory disorders to the same extent. Methods: This retrospective case-control study was aimed at identifying the possible genes involved in implant failure in Down syndrome patients by matching the periodontal disease variable by means of a retrospective case-control study. This process involved using the functional analysis of gene expression software Transcriptome Analysis Console (TAC, Affymetrix, Thermo Fisher Scientific, Waltham, MA, USA) and a search for the possible candidate genes involved. Focus was placed on the 92 genes related to the inflammation identified from the TaqMan™ Array Plate Human Inflammation Kit (Thermo Fisher Scientific, Waltham, MA, USA). Results: Six genes showed statistically significant results (p < 0.05) in our comparison. Three of them—PLCG2 (p = 0.0333), ALOX5 (p = 0.03) and LTAH4 (p = 0.0081)—were overexpressed in the implant reject group, and the following three were down-regulated: VCAM1 (p = 0.0182), PLA2G2A (p = 0.0034) and PLA2G10 (p = 0.047). Conclusion: Statistically significant differences exist in the gene expression involved in osteoclastogenesis, inflammatory response and host defensive response.
Effect of bunches spraying with some macro and micronutrients on fruit retention and physical characteristics of “ Deglet Nour ” date palm cultivar during Kimiri stage

The present study was carried out on Phoenix dactylifera L. cv. Deglet Nour to investigate the effect of boron, zinc and potassium on percentage of fruit retention and fruit physical characteristics. Bunches were sprayed with boric acid (1000,1500 and 2000 ppm), zinc sulfate (250, 500 and 750 ppm), potassium nitrate (1 and 2%) and potassium sulfate (1 and 2%). Results proved that all the studied treatments resulted in a significant increase in the percentage of retained fruits compared with the control in both studied seasons. Higher percentage of retained fruits was resulted from KNO3 and K2SO4 at (1&2%) and H3BO3 at 2000 ppm in both studied seasons. All the studied parameters were increased significantly from the first date 75 days after pollination (DAP) to the last one (115 DAP) which has the highest values in both seasons. Boron spraying at 1000 and 1500 ppm and zinc sulfate at 250 and 500 ppm significantly increased fruit weight, fruit size, fruit Length, and fruit Diameter, flesh weight and seed weight at different sampling dates compared to other the treatments including the control . In general, the highest values of fruit weight, fruit size, fruit Length, and fruit Diameter, flesh weight were resulted from zinc sulfate at 250 ppm in both seasons. There were no significant differences among treatments in total soluble solids. The results of this study showed that mineral nutrients increased fruit retention percentage and fruit physical properties of date palm. Therefore, it is concluded that the foliar application of zinc, boron and potassium may be applied in order to increase the production and to control the fruit drop of date palm.
A Multivariate Study of Human Mate Preferences: Findings from the California Twin Registry

Abstract Much research examining the biological and social-cultural underpinnings of human mate preferences has focused on univariate or bivariate analyses of demographic variables and personality constructs. In this paper, we argue that a multivariate approach more effectively highlights the multifaceted structure and correlates of human mate preferences. To support this claim, we applied several multivariate techniques to data from a large adult sample to (1) examine the major dimensions underlying individual differences in mate preferences, and (2) elucidate how these preferences relate to individual differences in personality. An exploratory factor analysis of an omnibus mate preference questionnaire yielded a 14-factor solution with dimensions mirroring trends in evolutionary psychology and the Big Five personality framework. An inter-battery factor analysis of these dimensions paired with higher-order personality factors provided strong support for the “likes attract” model of partner preferences. Bootstrap confidence intervals for all factor loadings highlighted the robustness of our results.
The role of molecular modelling and simulation in the discovery and deployment of metal-organic frameworks for gas storage and separation*

ABSTRACT Metal-organic frameworks (MOFs) are highly tuneable, extended-network, crystalline, nanoporous materials with applications in gas storage, separations, and sensing. We review how molecular models and simulations of gas adsorption in MOFs have informed the discovery of performant MOFs for methane, hydrogen, and oxygen storage, xenon, carbon dioxide, and chemical warfare agent capture, and xylene enrichment. Particularly, we highlight how large, open databases of MOF crystal structures, post-processed to enable molecular simulations, are a platform for computational materials discovery. We discuss how to orient research efforts to routinise the computational discovery of MOFs for adsorption-based engineering applications.
Simultaneous Determination of Docetaxel and Celecoxib in Porous Microparticles and Rat Plasma by Liquid-Liquid Extraction and HPLC with UV Detection: in vitro and in vivo Validation and Application.

PURPOSE A simple, rapid, sensitive, and reliable HPLC method with UV detection was developed and validated for simultaneous quantitation of docetaxel and celecoxib and paclitaxel for dissolution characterization and pharmacokinetic studies. METHODS The HPLC assay was performed isocratically on a reversed-phase C18 μ-Bondapack column using a mobile phase of acetonitrile:water (45:55, v/v) at a flow rate of 1.2 mL/min, and the analytes were detected at 230 nm. Paclitaxel was used as an internal standard for analysis of plasma samples following simple liquid-liquid extraction with n-hexane:isoamyl alcohol (97:3). The method was validated for specificity, linearity, sensitivity, precision, accuracy, robustness, and in vitro-in vivo application. RESULTS The retention times for docetaxel, paclitaxel, and celecoxib were 10.94, 12.4, and 16.81 min, respectively. The standard curves covering 0.1-1 μg/mL and 0.05-4 μg/mL were linear using dissolution medium and rat plasma, respectively. The limit of quantitation of the method was 50 ng/mL using 100 μL of rat plasma sample and injection of 50 μL of the residue. Within- and between-day precision and accuracy did not exceed 16.86% and 12.10%, respectively. This validated method was successfully used to quantify docetaxel and celecoxib simultaneously in the release study of docetaxel- celecoxib -loaded porous microparticles and pharmacokinetics studies. The methods were found to be simple, specific, precise, accurate, and reproducible. In this study, paclitaxel was used as the internal standard while dexamethasone, flutamide, and budesonide proved suitable alternative as an internal standard. CONCLUSION Since docetaxel and celecoxib could be co-administered for the treatment of a wide range of cancers such as non-small cell lung carcinoma, the developed method is particularly advantageous for routine therapeutic drug monitoring and pharmacokinetic studies of these drugs.
The Sphingosine Kinase 1 Inhibitor, PF543, Mitigates Pulmonary Fibrosis by Reducing Lung Epithelial Cell mtDNA Damage and Recruitment of Fibrogenic Monocytes

Idiopathic pulmonary fibrosis (IPF) is a chronic disease for which novel approaches are urgently required. We reported increased sphingosine kinase 1 (SPHK1) in IPF lungs and that SPHK1 inhibition using genetic and pharmacologic approaches reduces murine bleomycin-induced pulmonary fibrosis. We determined whether PF543, a specific SPHK1 inhibitor post bleomycin or asbestos challenge mitigates lung fibrosis by reducing mitochondrial (mt) DNA damage and pro-fibrotic monocyte recruitment—both are implicated in the pathobiology of pulmonary fibrosis. Bleomycin (1.5 U/kg), crocidolite asbestos (100 µg/50 µL) or controls was intratracheally instilled in Wild-Type (C57Bl6) mice. PF543 (1 mg/kg) or vehicle was intraperitoneally injected once every two days from day 7−21 following bleomycin and day 14−21 or day 30−60 following asbestos. PF543 reduced bleomycin- and asbestos-induced pulmonary fibrosis at both time points as well as lung expression of profibrotic markers, lung mtDNA damage, and fibrogenic monocyte recruitment. In contrast to human lung fibroblasts, asbestos augmented lung epithelial cell (MLE) mtDNA damage and PF543 was protective. Post-exposure PF543 mitigates pulmonary fibrosis in part by reducing lung epithelial cell mtDNA damage and monocyte recruitment. We reason that SPHK1 signaling may be an innovative therapeutic target for managing patients with IPF and other forms of lung fibrosis.
Improved Surgical Safety via Intraoperative Navigation for Transnasal Transsphenoidal Resection of Pituitary Adenomas

Abstract Objectives Intraoperative navigation during neurosurgery can aid in the detection of critical structures and target lesions. The safety and efficacy of intraoperative, stereotactic computed tomography (CT) in the transnasal transsphenoidal resection of pituitary adenomas were explored. Design Retrospective chart review Setting Tertiary care hospital Participants Patients who underwent transsphenoidal resection of pituitary adenomas from February 2002 to May 2017. Intraoperative stereotactic CT navigation was used for all patients after mid-October 2013. Main Outcome Measures Operative time, estimated blood loss, gross total resection rate. Results Of 634 patients included, 175 underwent surgery with intraoperative navigation and 444 had no intraoperative navigation during surgery. There was no difference in mean age, sex, tumor type, or tumor size between the two groups. Operative time, endoscope use, cerebrospinal fluid diversion, and estimated blood loss were also similar. Two patients showed intraoperative, iatrogenic misdirection in the absence of stereotactic CT navigation (p = 0.99) but similar numbers of patients having navigated and non-navigated surgery returned to the operating room, underwent gross total resection, and showed endocrinological normalization. Conclusions These results suggest that intraoperative navigation can reduce injury without resulting in increased operative time, estimated blood loss, or reduction in gross total resection.
Violent Inaction: The Necropolitical Experience of Refugees in Europe

A significant outcome of the global crisis for refugees has been the abandonment of forced migrants to live in makeshift camps inside the EU. This paper details how state authorities have prevented refugees from surviving with formal provision, leading directly to thousands having to live in hazardous spaces such as the informal camp in Calais, the site of this study. We then explore the violent consequences of this abandonment. By bringing together thus far poorly integrated literatures on bio/necropolitics (Michel Foucault; Achille Mbembe) and structural violence (Johan Galtung), we retheorize the connections between deliberate political indifference towards refugees and the physiological violence they suffer. In framing the management of refugees as a series of violent inactions, we demonstrate how the biopolitics of migrant control has given way to necropolitical brutality. Advancing geographies of violence and migration, the paper argues that political inaction, as well as action, can be used as a means of control.
Singular Vectors and Time-Dependent Normal Modes of a Baroclinic Wave-Mean Oscillation

Abstract Linear disturbance growth is studied in a quasigeostrophic baroclinic channel model with several thousand degrees of freedom. Disturbances to an unstable, nonlinear wave-mean oscillation are analyzed, allowing the comparison of singular vectors and time-dependent normal modes (Floquet vectors). Singular vectors characterize the transient growth of linear disturbances in a specified inner product over a specified time interval and, as such, they complement and are related to Lyapunov vectors, which characterize the asymptotic growth of linear disturbances. The relationship between singular vectors and Floquet vectors (the analog of Lyapunov vectors for time-periodic systems) is analyzed in the context of a nonlinear baroclinic wave-mean oscillation. It is found that the singular vectors divide into two dynamical classes that are related to those of the Floquet vectors. Singular vectors in the “wave dynamical” class are found to asymptotically approach constant linear combinations of Floquet vector.
Dynamic Facility Location with Stochastic Demand and Congestion

In this thesis, we study a multi-periodic facility location problem with stochastic demand to determine the optimal location, capacity selection and demands allocation of facilities within distinct time periods, while, each facility contains a server with a limited capacity. It causes facilities to experience a period of congestion, when not all arriving demands can be served immediately. Customers that arrive in this period might await service in a queue. This thesis perspective incorporates customers waiting costs as part of the objective. In this case, facilities do not utilize whole of the established capacity to ensure a maximum waiting time of the allocated customers. Firstly, a mathematical model is presented for a dynamic facility location problem with stochastic demand and congestion. The problem is setup as a network of spatially distributed queues and formulated as a nonlinear mixed integer program (MINLP). To transform the nonlinear congestion function to a piecewise linear, a linearization method is adapted. This method adds a set of inequalities to the model. We show that lifting this set of inequalities, with keeping generality of the method, reduces CPU times up to 3.5 times, on average. Moreover, a decent heuristic is proposed to solve the problem. Computational experiments indicate that the heuristic results in less costly solutions than them obtained by CPLEX algorithms, in 58% of relatively-difﬁcult test problems.
ProbeGuard: Mitigating Probing Attacks Through Reactive Program Transformations

Many modern defenses against code reuse rely on hiding sensitive data such as shadow stacks in a huge memory address space. While much more efficient than traditional integrity-based defenses, these solutions are vulnerable to probing attacks which quickly locate the hidden data and compromise security. This has led researchers to question the value of information hiding in real-world software security. Instead, we argue that such a limitation is not fundamental and that information hiding and integrity-based defenses are two extremes of a continuous spectrum of solutions. We propose a solution, ProbeGuard, that automatically balances performance and security by deploying an existing information hiding based baseline defense and then incrementally moving to more powerful integrity-based defenses by hotpatching when probing attacks occur. ProbeGuard is efficient, provides strong security, and gracefully trades off performance upon encountering more probing primitives.
Small-scale farming and hunger: the enabling role of social assistance programmes in South Africa’s former homelands

Cash transfers successfully alleviate poverty in many developing countries. South Africa is a case in point, implementing one of the largest unconditional cash transfer programmes internationally, and with substantial benefits to household well-being along multiple dimensions. Yet, grants discourage formal labour market attachment, creating dependencies on the fiscus. This study uses a fuzzy regression discontinuity design to establish that state-funded Old Age Pensions encourage non-market economic activity (in the form of small-scale farming), and improve the self-reported food security of rural households that farm, vis-a-vis those that do not. The role of small-scale farming is of broader interest in rural development, given the context of the 1913 and 1936 Land Acts that constrained this form of livelihood in former apartheid homelands. This paper’s contribution is two-fold: grants are an effective channel to actively promote rural development through small-scale farming, and they improve food security by non-market mechanisms.