Miracle-dz/UniFAR-FTUs huggingface dataset:
Sources of primary production to Arctic bivalves identified using amino acid stable carbon isotope fingerprinting*

ABSTRACT Benthic invertebrates are a crucial trophic link in Arctic marine food webs. However, estimates of the contribution of different primary production sources sustaining these organisms are not well characterised. We measured the stable carbon isotope values (δ13C) of essential amino acids (EAAs) in muscle tissue from two common bivalve genera (Macoma spp. and Astarte spp.) collected in Hanna Shoal in the northeastern Chukchi Sea. Mixing models comparing the δ13CEAA fingerprints of the bivalves to a suite of primary production endmembers revealed relatively high contributions of EAAs from phytoplankton and bacteria in both species. We also examined whether δ13CEAA fingerprints could be produced from the EAAs preserved in bivalve shells, which could allow primary production sources to be estimated from ancient bivalve shells. The δ13CEAA fingerprints from a suite of paired modern bivalve shells and muscle from Macoma calcarea from across the Chukchi Sea revealed a correspondence between the estimates of the dominant primary production source of EAAs derived from analyses of these two tissue types. Our findings indicate that δ13CEAA fingerprinting of marine bivalves can be used to examine dominant organic matter sources in the Arctic marine benthos in recent years as well as in deeper time.
Forensic analysis reveals fraud in fillets from the “Gurijuba” Sciades parkeri (Ariidae – Siluriformes): a vulnerable fish in Brazilian Coastal Amazon

Abstract The utilization of molecular tools for the certification of fishery products has been increasing over the last years. In general, economically important species are replaced by less valuable species, characterizing a commercial fraud. We evaluated the authenticity of 107 frozen fillets tagged as Gurijuba (Sciades parkeri) and Uritinga (Sciades proops) from local markets in northern amazon coast by sequencing two mitochondrial genes: Cytochrome oxidase subunit I and cytochrome b (Cyt b). About 16% of fillets putatively related to S. parkeri were replaced by S. proops. The Gurijuba faces high fishing pressure, being currently listed by the International Union for Conservation of Nature as vulnerable. Forensic analysis with DNA markers, proved to be highly efficient in the discrimination of the processed seafood products, providing unequivocal identification of species, revealing commercial fraud in the fillets of the Gurijuba, and revealing the utility of Cytb sequences as barcode in fishes.
Reversible Diffusive Mixing by Thermal Velocity FluctuationsThe importance of hydrodynamic fluctuations to diffusion in liquids

[We need to rewrite abstract so it is different from PRL] We study diffusive mixing in the presence of thermal fluctuations under the assumption of large Schmidt number. In this regime we obtain a limiting equation that contains a diffusive thermal drift term with diffusion coefficient obeying a Stokes-Einstein relation, in addition to the expected advection by a random velocity. The overdamped limit correctly reproduces both the enhanced diffusion in the ensemble-averaged mean and the longrange correlated giant fluctuations in individual realizations of the mixing process, and is amenable to efficient numerical solution. Through a combination of Eulerian and Lagrangian numerical methods we demonstrate that diffusion in liquids is not described by Fick’s irreversible law; rather, diffusion is better modeled as reversible random advection by thermal velocity fluctuations. We find that the diffusion coefficient is effectively renormalized to a value that depends on the scale of observation. Our work reveals somewhat unexpected connections between flows at small scales, dominated by thermal fluctuations, and flows at large scales, dominated by turbulent fluctuations.
Molecular engineering strategies for visualizing low-affinity protein complexes

The growing availability of complex structures in the Protein Data Bank has provided key insight into the molecular architecture of protein–protein interfaces. The remarkable diversity observed in protein binding modes is paralleled by a tremendous variation in binding affinities, with interaction half-lives ranging from days to milliseconds. Within the protein interactome, low-affinity binding events have been particularly difficult to visualize by traditional structural methods, which has spurred the development of innovative strategies for reconstituting these short-lived yet biologically essential assemblies. An important takeaway from structural studies of low-affinity systems is that there is no universal solution for stabilizing protein complexes, and approaches such as single-chain fusions, biochemical linkages, and affinity-maturation have each been successful in certain contexts. In this article, we review how advances in molecular engineering have been used to capture weakly associated complexes for structure determination, and we provide perspectives on how the continued application of these methods can shed new light on the “hidden world” of low-affinity interactions. Impact statement Low-affinity protein interactions, while biologically essential, have been difficult to visualize by traditional methods in structural biology. In this review, we describe a series of innovative molecular engineering strategies that have been used to stabilize weakly bound protein complexes for structure determination. By highlighting several examples from the literature along with potential advantages and disadvantages of the individual approaches, we hope to provide an introductory resource for structural biologists studying low-affinity systems.
Renal Iron Accelerates the Progression of Diabetic Nephropathy in HFE (High Fe-iron) Gene Knockout Mouse Model of Iron Overload.

Diabetic Nephropathy (DN) is the most common cause of end-stage renal disease associated with high mortality worldwide. Increase in iron levels have been reported in the diabetic rat kidneys as well as in the human urine of diabetic patients. In addition, low iron diet or iron chelators delay DN progression in diabetic patients and in animal models of diabetes. Possible maladaptive mechanisms of organ damage by tissue iron accumulation have not been well studied. We recently reported that iron induced retinal renin angiotensin system (RAS) and accelerated the progression of diabetic retinopathy. However, whether iron regulates systemic RAS is unknown. To explore if iron alters the expression of intra renal RAS and its role in the progression of DN, we used HFE (High Fe-iron) knockout mouse, a genetic model of systemic iron overload. We found that diabetes upregulated the expression of iron regulatory proteins and augmented tissue iron accumulation in the kidneys of both type-1 and type-2 diabetic mouse models. Iron accumulation in kidneys of HFE knockout mouse was associated with increase in serum and intra renal renin expression. Inducing diabetes in HFE knockout mice using streptozotocin caused much higher accumulation of renal iron and accelerated the nephropathy progression compared to diabetic wildtype mice. Treatment of diabetic mice with iron chelator deferiprone reversed the renin upregulation and reduced kidney injury. Thus, our results establish a new link between renal iron and RAS activity. Exploring the mechanisms of iron-induced RAS activation further may have significant therapeutic impact on hypertension and DN.
An Experimentally Validated Attitude Observer Based on Range and Inertial Measurements

Abstract This paper addresses the problem of attitude and rate gyros bias estimation, based on inertial data and range measurements from beacons installed in inertial frame and acoustic sensors fixed in vehicle frame. A nonlinear observer is proposed and its stability and performance properties are studied resorting to Lyapunov techniques. The estimation error is shown to converge exponentially fast to the desired equilibrium point in any closed neighborhood inside the region of attraction in the presence of bias in the rate gyros. The performance of the proposed nonlinear observer is illustrated in simulation and experimentally validated using a high precision calibration table, which provides ground truth signals for comparison with the resulting estimates.
Comparison of measurement Methods of osmotic adjustment in rice cultivars

Osmotic adjustment (OA) is a major component of drought resistance. Four different methods for measuring OA in plants are in general use, but there is no information on the comparative performance of these methods. Two similar experiments were designed to evaluate the four methods for measuring OA in diverse indica and japonica cultivars of rice (Oryza sativa L) subjected to a drying cycle in large pots in the greenhouse. The four methods were: (i) derivation of OA from regressions of leaf relative water content (RWC) on leaf osmotic potential (OP); (ii) estimation of OA from OP of stressed plants calculated to rehydrated state; (iii) estimation of OA from OP of stressed plants that have been rehydrated; and (iv) estimation (from data used in Method 1) of OA capacity by the sustained RWC at a given OP of -3.5 MPa. Method 1 was a priori considered as the best estimate. Under relatively mild atmospheric conditions and a slow development of water deficit (first experiment), mean OA over 12 cultivars was 0.89, 0.51, and 0.72 MPa by Methods 1, 2, and 3, respectively. Mean RWC at -3.5 MPa was 69.3%. Significant (P < 0.05) variation in OA among cultivars was observed by all methods, up to a four-fold difference in OA among cultivars (0.35-1.51 MPa) by Method L Simple correlation for OA across 12 cultivars with Method 1 was significantly higher for Method 3 (r = 0.76; P = 0.04) and Method 4 (r = 0.87; P < 0.01) than for Method 2 (r = 0.54; P = 0.07). OA by Method 4 was better correlated with Method 3 (r = 0.80; P< 0.01) than with Method 2 (r = 0.67; P = 0.02). The coefficient of variation (CV) as a measure of error was greater for Method 1 (47%) and Method 2 (31%) than for Method 3 (21%) or 4 (24%). Both Methods 2 and 3 were less demanding on labor and plant materials than Methods 1 and 4. The results support the use of Method 3 (the rehydration method) as a faster and an economical replacement for Method 1.
Injection of mRNA isolated from trophozoites of Giardia intestinalis induces expression of three types of chloride currents in Xenopus laevis oocytes.

Giardia lamblia is one of the most important worldwide causes of intestinal infections, yet little is known about its cellular physiology, especially the diversity of ionic channels that this parasite expresses. In this work, we show that injection of mRNA isolated from trophozoites of Giardia, into Xenopus laevis oocytes, induces expression of three types of chloride currents (here referred to as ICl‐G1, ICl‐G2, and ICl‐G3), which have different biophysical and pharmacological properties. ICl‐G1 currents show inward rectification and voltage dependence are enhanced by hypotonicity, show a selectivity sequence of (I > Br > Cl > F), and are inhibited by NPPB, DIDS, SITS, 9AC, DPC, and Zinc. These findings suggest that ICl‐G1 is the result of expression of chloride channels related to ClC2. ICl‐G2 currents show outward rectification and are dependent of intracellular calcium, its selectivity sequence is (Cl > Br > I > F) and are inhibited by NPPB, DIDS, SITS, 9AC, DPC, niflumic acid, tannic acid, and benzbromarone. These findings suggest that they are produced by calcium dependent chloride channels (CaCC). The third type of currents (ICl‐G3) appears only after a hypoosmotic challenge, and has similar properties to those described for ICl‐swell, such as outward rectification, instant activation, and slow inactivation at large depolarizing voltages. They were blocked by NPPB, DIDS, 9AC, NIf, DCPIB, and tamoxifen. Our results indicate that Giardia intestinalis has at least three types of anion conductances.
Immediate and Lasting Effects of the d ō TERRA AromaTouch Technique ® , a Topical Essential Oil Application Procedure , on Autonomic Function and Salivary Biomarkers : A Pilot Trial

Objectives: To explore the immediate and lasting benefits of the essential oils used in the dōTERRA AromaTouch Technique®, an essential oil application method similar to a full-body aromatherapy massage, on stress, immune secretions, inflammatory signaling, and anxiety in healthy volunteers. Design: Pilot trial. Location: dōTERRA International corporate campus (Pleasant Grove, UT) Subjects: Healthy volunteers (n=18). Interventions: Half of the subjects (n=9) received the technique twice per week for three weeks. Control groups consisted of the other healthy individuals (n=9) who received the same massage-like technique with fractionated coconut oil instead of the essential oils. Outcome Measures: Salivary levels of cortisol (μg/dL), TNF-α (pg/ mL), IL-6 (pg/mL), IL-1β (pg/mL), IL-8 (ng/mL), and C-reactive protein (ng/mL) as well as the secretory rate of immunoglobulin A (μg/min), heart rate (beats/minute), blood pressure (mm Hg), and Spielberger state anxiety scores. Baseline measurements were taken immediately before the first session. Additional measurements were taken immediately after the first session and after receiving bi-weekly sessions for a 3-week period. Results: Both groups experienced decreases in heart rate, mean arterial pressure, diastolic blood pressure, state anxiety scores, and salivary levels of cortisol immediately after the first session. The essential oil group also showed significantly decreased levels of C-reactive protein in the saliva immediately after the technique. After three weeks of regularly receiving the technique, subjects in the essential oil group had significantly lower salivary levels of C-reactive protein and three of the four inflammatory cytokines tested. Conclusions: Because of the experimental design, many outcomes of the technique can be attributed specifically to the activity of the essential oils. The essential oils used in the AromaTouch Technique may be effective for enhancing the relaxation associated with a massagelike procedure involving physical touch. The oils in the technique may also be solely responsible for a major inhibitory effect on inflammatory signaling. Validation of this result warrants further investigation in a trial with a larger sample size.
A Method for Detecting Significant Places from GPS Trajectory Data

—Detecting significant places are necessary for learning patterns of human behavior. Moreover, the Global Positioning System is the high accurate estimation of positioning method for mobile tracking. In this paper, we propose a method for detecting significant places based on GPS data. It is difficult to determine significant places relying on the clusters from using distance and time thresholds because of the difference of noises. Therefore, we introduce a method based on EIDBSCAN algorithm to detect arbitrary shape clusters with different densities, namely MKEIDBSCAN. We also propose the way to estimate input parameters of density-based clustering algorithms including the radius and the minimum number of points. As a result of using our proposal, significant places are detected more accurately and the running time is reduced. 
Dimethylsulfoniopropionate (DMSP) lyase activity in different strains of the symbiotic alga Symbiodinium microadriaticum

Dimethylsulfoniopropionate (DMSP) lyases are responsible for the enzymatic conver- sion of the algal metabolite DMSP into dimethylsulfide (DMS) and other products. DMSP lyase poten- tial activity (DLA) was assayed in 5 cultured strains of Symbiodinium microadriaticum to investigate whether DLA was present and whether variations in DLA occurred among strains. S. microadri- aticum are important primary producers symbiotic with corals and other cnidarians. Four of the 5 tested S. microadriaticum strains were capable of performing enzymatic lysis of DMSP, and the lev- els of DLA varied significantly among the strains. Average DLA normalized to chlorophyll a (chl a) was significantly higher in strain CCMP 829 (5.3 ± 0.9 nmol DMS · min -1 · µg -1 ) compared with all other strains investigated. DLA was not detected in strain CCMP 830, suggesting that DMSP lyase may not be a universal enzyme in S. microadriaticum. DMSP levels also varied between strains, but there was no correlation between cellular DMSP and DLA. Additionally, our data indicate that in non-axenic S. microadriaticum strains, the bacterial contribution to DLA was not substantial in any of the algal cultures investigated. These results are supportive of the idea that S. microadriaticum contain DLA, that DMSP producers are not necessarily capable of DLA, and that, even within a spe- cies, DMSP and DLA levels vary significantly. These findings suggest important differences in the regulation of DMSP and DLA in S. microadriaticum, but the reasons for these differences remain to be elucidated.
Multi Sensor Stockpile Measurement – A system for large heap shaped object reconstruction and volume measurement

Observation and measurement of large scale heap objects, like consumed raw material in iron plants, for deriving volume data from real scale 3D models for automated data processing is done under very special conditions by now. A complete system is presented, starting at the su cient acquisition of raw data, over the description of a computational 3D model up to delivering evaluation results that will eventually support business decisions related on more exact base parameters calculated by our system. The approach presented in this work allows an accurate and automatic extraction of volume measurements for large scale stockpile heap structures by analyzing and evaluating the data of multiple sensor devices.
Pattern of Prevalent Hepatitis B Virus Genotypes in Zaria, Nigeria

Background: Hepatitis B virus (HBV) is hyperendemic in Nigeria. Available literature reveal genotype E as being predominant in West Africa. This study aimed at identifying the current pattern and prevalent genotypes of HBV in Zaria, Nigeria. Materials and Methods: Four millilitre of blood was collected in ethylenediaminetetraacetic acid-container from each of 165 HBV surface antigen-positive participants recruited purposively from the gastroenterology clinic from May to August, 2017. Plasma was separated and frozen at −20°C till analysis. Multiplex-nested polymerase chain reaction using type-specific primers was used to identify the various HBV genotypes. Results: Median (and interquartile range) age of the participants was 31.0 (25.5–39.0) years, with males constituting 107 (64.8%). Majority (83.6%) of the samples analysed were HBV-DNA-positive with 82.6% of the HBV-DNA-positive samples being mixed genotype infections. Irrespective of mode of occurrence, five HBV genotypes were identified with HBV/E (97.1%) being the most predominant, followed by HBV/B (82.6%), HBV/A (24.6%), then HBV/C (17.4%), while HBV/D (0.7%) was the least prevalent. Conclusion: In most (99.1%) of the mixed-infection were a combination of genotype E, the predominant genotype, with other genotypes predominantly genotype B. HBV genotypes E, B, A, C and D are the prevalent genotypes in Zaria, Nigeria, as they occur in single genotype and in mixed-genotypes pattern.
Toxins of Clostridium perfringens as virulence factors in animal diseases

Clostridium perfringens is a Gram-positive, rod shaped, anaerobic, spore forming bacterium and is responsible for various forms of acute enteric diseases called enterotoxemias, in sheep, goats, and other animals. Based on the toxin production, C. perfringens strains are classified into five toxinotypes, namely alpha (CPA), beta (CPB), epsilon (ETX) and iota (ITX). However, this microorganism has the ability to produce more than 16 toxins in various combinations, including lethal toxins such as perfringolysin O (PFO), enterotoxin (CPE), and beta2 toxin (CPB2). C. perfringens produce many toxins with diverse characteristics which imparts a virulence flexibility to it in order to cause an array of diseases. Most diseases caused by this microorganism are mediated by one or more of these toxins. Many animal models experiments have been done for C. perfringens infection and the use of toxin gene knock-out mutants have demonstrated the specific pathogenic role of several toxins of C. perfringens in animal diseases.
Genetic Association of Angiotensin-Converting Enzyme (ACE) Gene I/D Polymorphism with Preterm Birth in Korean Women: Case-Control Study and Meta-Analysis

Background and Objectives: The ACE gene encodes the angiotensin-converting enzyme (ACE), a component of the renin-angiotensin system. Increased ACE activity may cause abnormal regulation of placental circulation and angiogenesis, resulting in adverse pregnancy outcomes. Previous studies have reported that the insertion/deletion (I/D) polymorphism of the ACE gene is associated with the development of preterm birth (PTB). However, results of the association between ACE gene I/D and PTB are inconsistent in various populations. Therefore, we performed a case-control study and a meta-analysis to evaluate the association between ACE I/D polymorphism and PTB. Materials and Methods: We analyzed a total of 254 subjects (111 patients with PTB and 143 women at ≥38 weeks gestation) for the case-control study. For the meta-analysis, we searched Google Scholar, PubMed, and NCBI databases with the terms “ACE,” “angiotensin-converting enzyme,” “preterm birth,” “preterm delivery,” and their combinations. Results: Our results of the case-control study indicated that ACE I/D polymorphism is significantly associated with PTBs in the overdominant genetic model (odds ratio (OR) 0.57, 95% confidence interval (CI) 0.347–0.949, p = 0.029) and that the ID genotype of ACE I/D polymorphism has a protective effect for PTB (OR 0.57, 95% CI 0.333–0.986, p = 0.043). Similarly, the meta-analysis showed that the OR for the ACE gene ID genotype was 0.66 (95% CI 0.490–0.900, p < 0.01). Conclusion: The ACE gene ID genotype has a significant association with PTB and is a protective factor for PTB. A larger sample set and functional studies are required to further elucidate of our findings.
Kidney graft survival of >25 years: a single center report including associated graft biopsy results

Only few centers have reported their observations on patients with very long‐term kidney graft survival of more than 25 years. Eighty‐six subjects were identified in our center with graft survival of >25 years. Donor age was 31.3 ± 18.5 years. Mean duration of transplantation was 30.3 ± 3.6 years. At last follow‐up, the cystatin C clearance was 47 ± 23 ml/min. Transplant biopsies for cause were performed in 30 subjects at a median of 28.4 years (19.1–40.3) after transplantation. Acute or chronic active T cell‐mediated rejection was present in five cases and histological characteristics of acute or chronic active humoral rejection in eight cases. More than 80% of biopsies had inflammatory infiltrates in nonatrophic or atrophic cortical areas. The number of HLA mismatches were higher in biopsied subjects (3.0 ± 1.8 vs. 2.2 ± 1.7 without biopsy). Immunosuppressive therapy was adapted in most biopsied subjects; impaired graft function and proteinuria was unchanged at last follow‐up. Sixty percent of all subjects had hyperparathyroidism (iPTH of the whole group: 132 ± 157 pg/ml), which was predominantly secondary, as judged by serum calcium and graft function. Young donor age was certainly a prerequisite of longterm graft survival. Nonetheless, inflammation or rejection in most biopsied patients suggests an important role of alloreactivity even in this late course.