Miracle-dz/UniFAR-FTUs huggingface dataset:
SLC30A3 (ZnT3) Oligomerization by Dityrosine Bonds Regulates Its Subcellular Localization and Metal Transport Capacity

Non-covalent and covalent homo-oligomerization of membrane proteins regulates their subcellular localization and function. Here, we described a novel oligomerization mechanism affecting solute carrier family 30 member 3/zinc transporter 3 (SLC30A3/ZnT3). Oligomerization was mediated by intermolecular covalent dityrosine bonds. Using mutagenized ZnT3 expressed in PC12 cells, we identified two critical tyrosine residues necessary for dityrosine-mediated ZnT3 oligomerization. ZnT3 carrying the Y372F mutation prevented ZnT3 oligomerization, decreased ZnT3 targeting to synaptic-like microvesicles (SLMVs), and decreased resistance to zinc toxicity. Strikingly, ZnT3 harboring the Y357F mutation behaved as a “gain-of-function” mutant as it displayed increased ZnT3 oligomerization, targeting to SLMVs, and increased resistance to zinc toxicity. Single and double tyrosine ZnT3 mutants indicate that the predominant dimeric species is formed between tyrosine 357 and 372. ZnT3 tyrosine dimerization was detected under normal conditions and it was enhanced by oxidative stress. Covalent species were also detected in other SLC30A zinc transporters localized in different subcellular compartments. These results indicate that covalent tyrosine dimerization of a SLC30A family member modulates its subcellular localization and zinc transport capacity. We propose that dityrosine-dependent membrane protein oligomerization may regulate the function of diverse membrane protein in normal and disease states.
Document Score Distribution Models for Query Performance Inference and Prediction

Modelling the distribution of document scores returned from an information retrieval (IR) system in response to a query is of both theoretical and practical importance. One of the goals of modelling document scores in this manner is the inference of document relevance. There has been renewed interest of late in modelling document scores using parameterised distributions. Consequently, a number of hypotheses have been proposed to constrain the mixture distribution from which document scores could be drawn. In this article, we show how a standard performance measure (i.e., average precision) can be inferred from a document score distribution using labelled data. We use the accuracy of the inference of average precision as a measure for determining the usefulness of a particular model of document scores. We provide a comprehensive study which shows that certain mixtures of distributions are able to infer average precision more accurately than others. Furthermore, we analyse a number of mixture distributions with regard to the recall-fallout convexity hypothesis and show that the convexity hypothesis is practically useful. Consequently, based on one of the best-performing score-distribution models, we develop some techniques for query-performance prediction (QPP) by automatically estimating the parameters of the document score-distribution model when relevance information is unknown. We present experimental results that outline the benefits of this approach to query-performance prediction.
A clinical perspective of obesity, metabolic syndrome and cardiovascular disease

The metabolic syndrome is a condition characterized by a special constellation of reversible major risk factors for cardiovascular disease and type 2 diabetes. The main, diagnostic, components are reduced HDL-cholesterol, raised triglycerides, blood pressure and fasting plasma glucose, all of which are related to weight gain, specifically intra-abdominal/ectopic fat accumulation and a large waist circumference. Using internationally adopted arbitrary cut-off values for waist circumference, having metabolic syndrome doubles the risk of cardiovascular disease, but offers an effective treatment approach through weight management. Metabolic syndrome now affects 30–40% of people by age 65, driven mainly by adult weight gain, and by a genetic or epigenetic predisposition to intra-abdominal/ectopic fat accumulation related to poor intra-uterine growth. Metabolic syndrome is also promoted by a lack of subcutaneous adipose tissue, low skeletal muscle mass and anti-retroviral drugs. Reducing weight by 5–10%, by diet and exercise, with or without, anti-obesity drugs, substantially lowers all metabolic syndrome components, and risk of type 2 diabetes and cardiovascular disease. Other cardiovascular disease risk factors such as smoking should be corrected as a priority. Anti-diabetic agents which improve insulin resistance and reduce blood pressure, lipids and weight should be preferred for diabetic patients with metabolic syndrome. Bariatric surgery offers an alternative treatment for those with BMI ≥ 40 or 35–40 kg/m2 with other significant co-morbidity. The prevalence of the metabolic syndrome and cardiovascular disease is expected to rise along with the global obesity epidemic: greater emphasis should be given to effective early weight-management to reduce risk in pre-symptomatic individuals with large waists.
Compensatory Functions of Two Alkyl Hydroperoxide Reductases in the Oxidative Defense System of Legionella pneumophila

ABSTRACT Legionella pneumophila expresses two catalase-peroxidase enzymes that exhibit strong peroxidatic but weak catalatic activities, suggesting that other enzymes participate in decomposition of hydrogen peroxide (H2O2). Comparative genomics revealed that L. pneumophila and its close relative Coxiella burnetii each contain two peroxide-scavenging alkyl hydroperoxide reductase (AhpC) systems: AhpC1, which is similar to the Helicobacter pylori AhpC system, and AhpC2 AhpD (AhpC2D), which is similar to the AhpC AhpD system of Mycobacterium tuberculosis. To establish a catalatic function for these two systems, we expressed L. pneumophila ahpC1 or ahpC2 in a catalase/peroxidase mutant of Escherichia coli and demonstrated restoration of H2O2 resistance by a disk diffusion assay. ahpC1::Km and ahpC2D::Km chromosomal deletion mutants were two- to eightfold more sensitive to H2O2, tert-butyl hydroperoxide, cumene hydroperoxide, and paraquat than the wild-type L. pneumophila, a phenotype that could be restored by trans-complementation. Reciprocal strategies to construct double mutants were unsuccessful. Mutant strains were not enfeebled for growth in vitro or in a U937 cell infection model. Green fluorescence protein reporter assays revealed expression to be dependent on the stage of growth, with ahpC1 appearing after the exponential phase and ahpC2 appearing during early exponential phase. Quantitative real-time PCR showed that ahpC1 mRNA levels were ∼7- to 10-fold higher than ahpC2D mRNA levels. However, expression of ahpC2D was significantly increased in the ahpC1 mutant, whereas ahpC1 expression was unchanged in the ahpC2D mutant. These results indicate that AhpC1 or AhpC2D (or both) provide an essential hydrogen peroxide-scavenging function to L. pneumophila and that the compensatory activity of the ahpC2D system is most likely induced in response to oxidative stress.
Synthesis and surface chemistry of Zn3P2

Zinc phosphide (Zn3P2) is a promising alternative to traditional materials (e.g. CIGS, CdTe, a-Si) for thin film photovoltaics. Open circuit voltage in Zn3P2 cells has been limited by Fermi-level pinning due to surfaces states and heterojunction interdiffusion, motivating the need to prepare interfaces that are electrically passive and chemically inert. We investigated the surface chemistry of Zn3P2 via etching with bromine in methanol and passivation with ammonium sulfide in t-butanol. The treatment decreases surface oxidation as determined by x-ray photoelectron spectroscopy and provides a stable, low-defect interface as monitored by steady-state photoluminescence. Magnesium Schottky diodes fabricated with sulfur-passivated interfaces show evidence of enhanced barrier heights in comparison to control devices.
Ex Vivo Assessment of Carbon Tetrachloride (CCl4)-Induced Chronic Injury Using Polarized Light Spectroscopy

The liver performs various functions, such as the production and detoxification of chemicals; therefore, it is susceptible to hepatotoxins such as carbon tetrachloride (CCl4), which causes chronic injury. Thus, assessment of injury and its status of severity are of prime importance. Current work reports an ex vivo study for probing the severance of hepatic injury induced by CCl4 with polarized light over the spectral range 400–800 nm. Different concentrations of CCl4 were used to induce varying severity of hepatic injury in a rat model. Linear retardance, depolarization rates, and diagonal Mueller matrix elements (m22, m33, and m44), were successfully used as the distinguishing criterion for normal and different liver injuries. Our results show that linear retardance for injured liver samples with lower doses of CCl4 tends to increase when compared with normal liver samples, while samples injured at higher doses of CCl4 offer almost no retardance. Total, linear, and circular depolarizations follow decreasing trends with increased liver injury severity over the entire investigated wavelength range. Linear polarization states were observed to be better maintained as compared to circular polarization states for all samples. Furthermore, numerical values of diagonal elements of the experimentally measured Mueller matrix also increase with increasing doses of CCl4. Liver fibroses, change in transport albedo, and the relative refractive index of the extracellular matrix caused by CCl4 are responsible for the observed differences. These results will provide a pathway to gauge the severity of injury caused by toxic chemicals.
Issues in rock physics and implications for DHI interpretation

Seismic techniques for direct hydrocarbon indication rely on the changes in seismic character which accompany changes in pore fluid content. Interpretation and modeling of direct hydrocarbon indicators (DHIs) require an understanding of the factors affecting seismic velocities and reflection coefficients which are, in turn, dependent on pore fluid properties, rock frame properties, and fluid substitution within a given rock frame. Recent developments in rock physics have greatly increased our general understanding in these areas but have also revealed complications that require further research.
Regulation of UCP1, UCP2, and UCP3 mRNA expression in brown adipose tissue, white adipose tissue, and skeletal muscle in rats by estrogen.

The effects of ovariectomy (OVX) and estrogen substitution on body weight, body composition, food intake, weight gain, and expression of uncoupling proteins (UCPs) in brown adipose tissue (BAT), white adipose tissue (WAT), and skeletal muscle were studied in four groups of rats: (1) Sham-operated rats (N = 8), (2) ovariectomized rats (OVX - E) (N = 8), (3) estrogen-treated OVX rats (OVX + E) (N = 8), and (4) OVX rats on energy restriction (OVX - E + D) (N = 8). OVX was associated with an increase in food intake and body weight gain during a 5-week study period compared to sham-operated rats. The estrogen-substituted rats had a significantly lower food intake and weight gain during the 5 weeks compared to the sham-operated group. However, we also included a nontreated OVX group that was allowed to eat only enough chow to match the weight gain of the sham-operated group. To match the weight gain in the two groups, the OVX group had to consume 16% less chow than the sham-operated group. In BAT, the UCP1 expression was significantly lower in estrogen-deficient rats compared to either intact rats or estrogen-substituted rats, whereas UCP2 and UCP3 mRNA expression was similar in BAT from all four groups. In WAT, both estrogen-deficient groups had significantly lower UCP2 mRNA expression compared to the control rats and estrogen-treated rats; In contrast, the UCP3 mRNA expression in WAT was similar in all four groups. Finally, in skeletal muscle the OVX group on mild energy restriction had reduced UCP3 mRNA expression compared to control, OVX, and estrogen-treated rats. In contrast, the UCP2 mRNA expression in skeletal muscle was similar in all four groups. Thus, the findings that estrogen deficiency is followed by reduced UCP1 expression in BAT and reduced UCP2 expression in WAT in association with weight gain probably caused by a decrease in energy expenditure might indicate that UCPs play a role for the estrogen-mediated changes in body weight and energy expenditure.
Dual H-and E-field tunable multiferroic bandpass filters with yttrium iron garnet film

A new type of dual magnetically (H-field) and electrically (E-field) tunable bandpass filters (BPF) with an yttrium iron garnet (YIG) film and with a YIG/ PZN-PT (lead zinc niobate-lead titanate) multiferroic heterostructure have been designed, fabricated and characterized. Single-crystal YIG films at their ferromagnetic resonance were adopted as the resonator which was coupled to a T-shaped microstrip coupling structure to form a new bandpass filter design. The operating frequency of the BPF can be tuned via a bias magnetic field, and a large tunability of the operation frequency of 190 MHz ∼ 840 MHz with relatively small bias field of 50 ∼ 250 Oe, together with a low insertion loss of &#60; 2 dB. This is equivalent to 12% ∼ 54% of the center frequency of the bandpass filter. A clear E-field induced operation frequency shift of 200 MHz, or ∼10% was demonstrated on the multiferroics based bandpass filter having a YIG/PZN-PT heterostructure. These demonstrated new multiferroic tunable bandpass filters with dual H- and E-field tunability are very compact and energy efficient, which could have many applications in RF front and other microwave circuits.
Assessment of the white blood cell subtypes ratio in patients with supraventricular tachycardia: Retrospective cohort study

Amac: Notrofil/lenfosit orani (NLO), monosit/lenfosit orani (MLO) ve lenfosif/monosit orani (LMO) yeni kardiyovaskuler risk belirleyicileri olarak degerlendirilmistir. Inflammation has been demonstrated to be associated with various types of arrhythmia. Bu calismadaki amacimiz geriye donuk olarak supraventrikuler tasikardi (SVT) tanili hastalarda NLO, LMO ve MLO ile iliskisini arastirmayi amacladik. Yontemler: Calismamiz 18 yas ve uzerinde, Aralik 2017- Aralik 2018 tarihleri arasinda klinigimizde takip edilen 59 hastayi icermektedir. Hastalarin 33 tanesi carpinti tanisi konmus ablasyon icin yatis verdigimiz hastalar olup, diger 26 tanesi noninvaziv yontemlerle ritm bozuklugu tanisi konulamayan fakat carpinti sikayetleri devam eden kesin tanisini koyabilmek icin elektrofizyolojik calisma (EPS) yaptigimiz hastalardan olusmaktadir. Tum hastalardan islem oncesi hemogram olcumu icin kan ornegi alindi. NLO degeri notrofil sayisinin lenfosit sayisina orani, MLO degeri monosit sayisinin lenfosit sayisina orani ve LMO degeri lenfosit sayisinin monosit sayisina orani olarak hesaplandi. Ayrica SVT tanisi mevcut hastalarimiza tedavi amacli; hem de noninvaziv yontemlerle tanisi konulamayan carpinti hastalarina tani ve tedavi amacli EPS yapildi. Bulgular: Calismaya SVT'li 33 hasta ve EPS sonucu normal olan 26 tane saglikli kontrol grubu dahil edildi. Hematolojik parametreler karsilastirildiginda NLO (1,96 (0,69) 103/μL karsi 2,17 (1,28) 103/μL, p=0,42) istatiksel olarak anlamli degildi. Bir diger parametrelerde hem MLO iki grup arasinda (0,25 (0,09) 103/μL karsi 0,22 (0,08) 103/μL, p=0,19) hem de LMO iki grup arasinda istatiksel olarak anlamli degildi. (4,38 (1,37) 103/μL karsi 4,64 (1,45) 103/μL, p=0,49). Sonuc: Yaptigimiz calismada NLO, LMO ve MLO degerlerinin SVT’nin varligi icin kullanilabilir gosterge olmadiklarini gostermis olduk.
Effect of Solution Ionic Strength and Iron Coatings on Mineral Grains on the Sorption of Bacterial Cells to Quartz Sand

Understanding the interaction between bacterial cells and solid surfaces is essential to our attempts to quantify and predict the transport of microbes in groundwater aquifers, whether from the point of view of contamination or from that of bioremediation. The sorption of bacterial cells suspended in groundwater to porous medium grains was examined in batch studies. Bacterial sorption to clean quartz sand yielded equilibrium, linear, adsorption isotherms that varied with the bacterial strain used and the ionic strength of the aqueous solution. Values of Kd (the slope of the linear sorption isotherm) ranged from 0.55 to 6.11 ml g-1, with the greatest sorption observed for the highest groundwater ionic strength. These findings are consistent with the interpretation that an increasingly compressed electrical double layer results in stronger adsorption between the like-charged mineral surface and the bacterial cells. When iron-oxyhydroxide-coated sand was used, however, all of the added bacteria were adsorbed up to a threshold of 6.93 × 108 cells g of coated sand-1, beyond which no further adsorption occurred. The irreversible, threshold adsorption is the result of a strong electrostatic attraction between the sesquioxide coating and the bacterial cells. Experimental results of adsorption in mixtures of quartz and Fe(III)-coated sand were successfully predicted by a simple additive model for sorption by the two substrate phases. Even small amounts of Fe(III)-coated sand in a mixture influenced the extent of adsorption of bacterial cells. A quantitative description of adsorption in the mixtures can be realized by using a linear isotherm for reversible adsorption to the quartz grains with a y intercept that represents the number of cells irreversibly adsorbed to the Fe(III)-coated sand.
A Qualitative and Quantitative Study of Grumose Degeneration in Progressive Supranuclear Palsy

Grumose degeneration (GD) of the dentate nucleus is a common feature in progressive supranuclear palsy (PSP), but its pathogenesis has not been well studied, and its clinical significance remains unknown. This report describes a quantitative study of GD in 9 cases of PSP using image analysis with single- and double-immunolabeling, as well as histochemical stains for myelin and axons. GD was associated with demyelination, axonal loss, glial tau pathology, and microgliosis in regions juxtaposed to the dentate nucleus (DN). Specifically, demyelination and microgliosis were prominent in the superior cerebellar peduncle (SCP), dentate hilus, and cerebellar hemispheric white matter. Tau pathology and microgliosis were less prominent in the DN itself. The degree of myelin loss correlated with the tau burden in the SCP. GAP-43, which is a phosphoprotein known to be involved in axonal growth and sprouting, was decreased in the DN of PSP, and the degree of GAP-43 loss correlated with severity of GD. These results suggest that GD may be related to progressive pathology in the dentatorubrothalamic tract as well as the cerebellar hemispheric white matter, and that GD may be a consequence of concurrent degeneration in both output from and input to the DN. The results further suggest a possible role for oligodendroglial and myelin pathology in the pathogenesis of PSP.
Effects of ethanol on hippocampal neurogenesis depend on the conditioned appetitive response

Neurogenesis in the subgranular layer of the dentate gyrus (DG) has been suggested to underlie some forms of associative learning. The present study was undertaken to determine whether there was also a role of neurogenesis in the ethanol (EtOH)‐induced conditioned place preference (CPP). Outbreed Swiss mice were conditioned with EtOH (2.0 g/kg) in one compartment of a non‐biased place preference chamber and saline in the other compartment. This procedure produced three groups of mice: some developed a conditioned preference (EtOH_Cpp), others developed a conditioned avoidance (EtOH_Cpa) and still others demonstrated indifference to the context previously paired with ethanol (EtOH_Ind). BrdU (40 mg/kg, i.p.) was administered 4 hours after each session comprising the conditioning phase. When measured 24 hours following the CPP test, there was no effect of EtOH on doublecortin (DCX) expression or Fluoro Jade B staining. However, there were decreases in the number of BrdU+ and Ki‐67+ cells in the EtOH_Cpa and EtOH_Ind groups, but not in the EtOH_Cpp group. Most of BrdU+ cells were co‐labeled with DCX. Similarly, in another experiment, in that the perfusion was done 28 days after CPP test, most BrdU+ cells were co‐localized with NeuN. These results suggest that conditioned appetitive response is able to maintain normal levels of neurogenesis in DG and might counteract ethanol‐produced decreased cell proliferation/survival rate.
Removal of xenoreactive human anti-pig antibodies by absorption on recombinant mucin-containing glycoproteins carrying the Gal alpha1,3Gal epitope.

BACKGROUND The hyperacute rejection caused by preformed natural antibodies in the recipient species reacting with donor species endothelial antigens is one of the major obstacles preventing routine use of clinical xenotransplantation. Based on the known structure and biosynthetic pathway of the major porcine xenoantigen, Gal alpha1,3Gal, we developed a novel strategy aimed at specific removal of human, natural anti-pig antibodies. METHODS Cotransfection of COS cells with expression plasmids encoding a secreted mucin/immunoglobulin chimera and the porcine alpha1,3-galactosyltransferase facilitated simple immunoaffinity purification of a highly Gal alpha1,3Gal-substituted mucin/immunoglobulin fusion protein from transfected cell supernatants. RESULTS Cotransfection of COS cells resulted in a mucin/Ig concentration in the supernatants ranging from 150 to 200 ng/ml. Approximately 300 ng of mucin/Ig chimeras absorbed onto 50 microl of packed anti-mouse IgG agarose beads could completely remove cytotoxic human anti-pig antibodies from 1 ml of human AB serum, as estimated in porcine endothelial cell cytotoxicity assays. Purified human IgG, IgM, and IgA all bound porcine endothelium, but only IgG and IgM were cytotoxic in the presence of rabbit complement. When the cytotoxicity of human IgG at 8 mg/ml and IgM at 1 mg/ml was completely removed by absorption on the mucin/Ig chimera, the binding to porcine endothelium was only partly reduced. Antibodies mediating antibody-dependent cellular cytotoxicity against porcine endothelium were also absorbed, indicating the importance of Gal alpha1,3Gal epitopes for this effect. CONCLUSIONS We describe the construction and production of a new and effective Gal alpha1,3Gal-substituted, mucin domain-containing absorber that can be used in a pretransplant extracorporeal immunoabsorption setting to remove anti-pig antibodies involved in antibody-dependent, complement- and cell-mediated cytotoxicity of pig endothelial cells.
Bacteriophages with Potential for Inactivation of Fish Pathogenic Bacteria: Survival, Host Specificity and Effect on Bacterial Community Structure

Phage therapy may represent a viable alternative to antibiotics to inactivate fish pathogenic bacteria. Its use, however, requires the awareness of novel kinetics phenomena not applied to conventional drug treatments. The main objective of this work was to isolate bacteriophages with potential to inactivate fish pathogenic bacteria, without major effects on the structure of natural bacterial communities of aquaculture waters. The survival was determined in marine water, through quantification by the soft agar overlay technique. The host specificity was evaluated by cross infection. The ecological impact of phage addition on the structure of the bacterial community was evaluated by DGGE of PCR amplified 16S rRNA gene fragments. The survival period varied between 12 and 91 days, with a higher viability for Aeromonas salmonicida phages. The phages of Vibrio parahaemolyticus and of A. salmonicida infected bacteria of different families with a high efficacy of plating. The specific phages of pathogenic bacteria had no detectable impact on the structure of the bacterial community. In conclusion, V. parahaemolyticus and A. salmonicida phages show good survival time in marine water, have only a moderated impact on the overall bacterial community structure and the desired specificity for host pathogenic bacteria, being potential candidates for therapy of fish infectious diseases in marine aquaculture systems.