Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of absolute peptide quantitation strategies using selected reaction monitoring

The use of internal peptide standards in selected reaction monitoring experiments enables absolute quantitation. Here, we describe three approaches addressing calibration of peptide concentrations in complex matrices and assess their performance in terms of trueness and precision. The simplest approach described is single reference point quantitation where a heavy peptide is spiked into test samples and the endogenous analyte quantified relative to the heavy peptide internal standard. We refer to the second approach as normal curve quantitation. Here, a constant amount of heavy peptide and a varying amount of light peptide are spiked into matrix to construct a calibration curve. This accounts for matrix effects but due to the presence of endogenous analyte, it is usually not possible to determine the lower LOQ. We refer to the third method as reverse curve quantitation. Here, a constant amount of light peptide and a varying amount of heavy peptide are spiked into matrix to construct a calibration curve. Because there is no contribution to the heavy peptide signal from endogenous analyte, it is possible to measure the equivalent of a blank sample and determine LOQ. These approaches are applied to human plasma samples and used to assay peptides of a set of apolipoproteins.
Current estimates of blindness in India

Background: Evidence based planning has been the hallmark of the blindness control programme in India. A nationwide survey was undertaken in 1999–2001 to document the magnitude and causes of blindness. Methods: One district each in 15 populous states was covered. 25 clusters were randomly selected in each district and all individuals aged 50 years and above were enumerated. Presenting and best corrected vision was recorded using retroilluminated logMAR tumbling E charts and detailed eye examination was offered. Results: The response rate was 89.3%. Presenting vision <6/60, in the better eye, was observed in 8.5% (95% CI: 8.1 to 8.9). Age, sex, residence, literacy, and working status were associated with blindness. The highest risk was among those aged 70+ and the illiterate. Cataract was responsible for 62.4% of bilateral blindness. Prevalence of cataract blindness was 5.3% (95% CI: 4.97 to 5.62). Reduction in blindness prevalence among people aged 50 years and above was observed compared to earlier studies. Conclusion: Blindness control efforts seem to have played a part in arresting the increasing prevalence of blindness in India and there is hope that the goals of the “Vision 2020—right to sight” initiative can be achieved if there is strong political will and prioritised action.
FIXATION OF DELETERIOUS MUTATIONS IN CLONAL LINEAGES: EVIDENCE FROM HYBRIDOGENETIC FROGS

Abstract The hemiclonal waterfrog Rana esculenta (RL genotype), a bisexual hybrid between R. ridibunda (RR) and R. lessonae (LL), eliminates the L genome from its germline and clonally transmits the R genome (hybridogenesis). Matings between hybrids produce R. ridibunda offspring, but they generally die at an early larval stage. Mortality may be due to fixed recessive deleterious mutations in the clonally inherited R genomes that were either acquired through the advance of Muller's ratchet or else frozen in these genomes at hemiclone formation. From this hypothesis results a straightforward prediction: Matings between different hemiclones, that is, between R. esculenta possessing different R genomes of independent origin, should produce viable R. ridibunda offspring because it is unlikely that different clonal lineages have become fixed for the same mutations. I tested this prediction by comparing survival and larval performance of tadpoles from within- and between-population crossings using R. esculenta from Seseglio (Se) in southern, Alpnach (Al) in central, and Elliker Auen (El) in northern Switzerland, respectively. Se is isolated from the other populations by the Alps. Enzyme electrophoresis revealed that parents from Se belonged to a single hemiclone that was different from all hemiclones found north of the Alps. Parents from Al also belonged to one hemiclone, but parents from El belonged to three hemiclones, one of which was indistinguishable from the one in Al. Rana esculenta from Se produced inviable tadpoles when crossed with other hybrids of their own population, but when crossed with R. esculenta from Al and El, tadpoles successfully completed metamorphosis, supporting the hypothesis I tested. Within-population crosses from Al were also inviable, but some within-population crosses from El, where three hemiclones were present, produced viable offspring. Only part of the crosses between Al and El were viable, but there was no consistent relationship between hemiclone combination and tadpole survival. When backcrossed with the parental species R. ridibunda, hybrids from all source populations produced viable offspring. Performance of these tadpoles with a sexual and a clonal genome was comparable to that of normal, sexually produced R. ridibunda tadpoles. Thus, in the heterozygous state, the deleterious mutations on the clonal R genomes did not appear to reduce tadpole fitness. Corresponding Editor: J. Merilä
On homogeneous skewness of unimodal distributions

We introduce a new concept of skewness for unimodal continuous distributions which is built on the asymmetry of the density function around its mode. The asymmetry is captured through a skewness function. We call a distribution homogeneously skewed if this skewness function is consistently positive or negative throughout its domain, and partially homogeneously skewed if the skewness function changes its sign at most once. This type of skewness is shown to exist in many popular continuous distributions such as Triangular, Gamma, Beta, Lognormal and Weibull. Two alternative ways of partial ordering among the partially homogeneously skewed distributions are described. Extensions of the notion to broader classes of distributions including discrete distributions have also been discussed.
Doubly Fed Induction Generator Controller Design for the Stable Operation in Weak Grids

With the increasing integration of doubly fed induction generator (DFIG)-based large wind power plants, their impacts on power system static and dynamic behavior must be analyzed. Especially, large wind power plants are always connected to grids with relatively long transmission lines or cables (weak grids). Therefore, the wind power plants stable operation in these weak grids must be considered. This paper provides a method for designing an adaptive DFIG line side converter (LSC) control for enhancing the controller stability and reinforcing the power system stability. SENVION wind turbine and its wind power plant voltage control strategy are applied as an example of the LSC control strategy. Simulation results show the efficiency of the proposed approach.
Phenazine-1-Carboxylic Acid Promotes Bacterial Biofilm Development via Ferrous Iron Acquisition

ABSTRACT The opportunistic pathogen Pseudomonas aeruginosa forms biofilms, which render it more resistant to antimicrobial agents. Levels of iron in excess of what is required for planktonic growth have been shown to promote biofilm formation, and therapies that interfere with ferric iron [Fe(III)] uptake combined with antibiotics may help treat P. aeruginosa infections. However, use of these therapies presumes that iron is in the Fe(III) state in the context of infection. Here we report the ability of phenazine-1-carboxylic acid (PCA), a common phenazine made by all phenazine-producing pseudomonads, to help P. aeruginosa alleviate Fe(III) limitation by reducing Fe(III) to ferrous iron [Fe(II)]. In the presence of PCA, a P. aeruginosa mutant lacking the ability to produce the siderophores pyoverdine and pyochelin can still develop into a biofilm. As has been previously reported (P. K. Singh, M. R. Parsek, E. P. Greenberg, and M. J. Welsh, Nature 417:552-555, 2002), biofilm formation by the wild type is blocked by subinhibitory concentrations of the Fe(III)-binding innate-immunity protein conalbumin, but here we show that this blockage can be rescued by PCA. FeoB, an Fe(II) uptake protein, is required for PCA to enable this rescue. Unlike PCA, the phenazine pyocyanin (PYO) can facilitate biofilm formation via an iron-independent pathway. While siderophore-mediated Fe(III) uptake is undoubtedly important at early stages of infection, these results suggest that at later stages of infection, PCA present in infected tissues may shift the redox equilibrium between Fe(III) and Fe(II), thereby making iron more bioavailable.
Oligomerization of the Mitochondrial Protein Voltage-Dependent Anion Channel Is Coupled to the Induction of Apoptosis

ABSTRACT Accumulating evidence implicates that the voltage-dependent anion channel (VDAC) functions in mitochondrion-mediated apoptosis and as a critical player in the release of apoptogenic proteins, such as cytochrome c, triggering caspase activation and apoptosis. The mechanisms regulating cytochrome c release and the molecular architecture of the cytochrome c-conducting channel remain unknown. Here the relationship between VDAC oligomerization and the induction of apoptosis was examined. We demonstrated that apoptosis induction by various stimuli was accompanied by highly increased VDAC oligomerization, as revealed by cross-linking and directly monitored in living cells using bioluminescence resonance energy transfer technology. VDAC oligomerization was induced in all cell types and with all apoptosis inducers used, including staurosporine, curcumin, As2O3, etoposide, cisplatin, selenite, tumor necrosis factor alpha (TNF-α), H2O2, and UV irradiation, all acting through different mechanisms yet all involving mitochondria. Moreover, correlation between the levels of VDAC oligomerization and apoptosis was observed. Furthermore, the apoptosis inhibitor 4,4′-diisothiocyanostilbene-2,2′-disulfonic acid (DIDS) inhibited VDAC oligomerization. Finally, a caspase inhibitor had no effect on VDAC oligomerization and cytochrome c release. We propose that VDAC oligomerization is involved in mitochondrion-mediated apoptosis and may represent a general mechanism common to numerous apoptogens acting via different initiating cascades. Thus, targeting the oligomeric status of VDAC, and hence apoptosis, offers a therapeutic strategy for combating cancers and neurodegenerative diseases.
Geophysical applications of electrokinetic conversion

In Volume 1 of Geophysics (1936), R.R. Thompson of Humble Oil and Refining Company proposed that the coupling of seismic and electrical energy can be used as an exploration tool. Subsequent efforts were directed toward using electric‐field antennas as geophones. Small‐scale studies concluded that antennas are not as sensitive as conventional geophones and their response is highly variable, depending on the local soil conditions. By 1959, Martner and Sparks of Pan American Petroleum reported in Geophysics a systematic study of seismoelectric coupling using explosives at various depths. Their results were the first to show that the conversion of seismic to electromagnetic energy at the water table could be detected using surface antennas. No studies have systematically explored the full potential of electroseismic methods using the same level of experimental sophistication used in seismic exploration.
Pharmacologic Considerations for Therapeutic Success with Antiretroviral Agents

OBJECTIVE: To explore pharmacologic elements that contribute to therapeutic success with agents used for the treatment of HIV infection. DATA SOURCES: Primary articles were identified through MEDLINE (January 1990–January 1999) and secondary sources. Conference abstracts were selected by review of published proceedings. STUDY SELECTION AND DATA EXTRACTION: The author evaluated all articles, and relevant information was selected for incorporation into this review. DATA SYNTHESIS: Heterogeneity in the response to antiretroviral therapy has been attributed to virologic, immunologic, behavioral, and pharmacologic differences among patients. Patients receiving the same dose of an antiretroviral agent will not have the same systemic or intracellular concentration because of interpatient variability in drug absorption, distribution, metabolism, and excretion. Pharmacologic theory and available clinical data support relationships between drug concentration and anti-HIV effect. Thus, variability in drug concentrations contributes to variability in antiviral effect. Desirable pharmacologic characteristics for an antiretroviral drug include high oral bioavailability, a long elimination half-life, low intra- and interpatient pharmacokinetic variability, and a predictable dose–concentration–effect relationship. CONCLUSIONS: Treatment of the individual who is infected with HIV is a challenging long-term undertaking. Optimal management requires synthesis of a rapidly evolving base of basic and clinical knowledge. The selection of an antiretroviral regimen based on an understanding of the degree to which each individual agent possesses the desired pharmacologic characteristics should help the healthcare provider to translate the therapeutic principles of treatment of HIV infection into clinical reality for all patients.
Development of a Summarized Health Index (SHI) for Use in Predicting Survival in Sea Turtles

Veterinary care plays an influential role in sea turtle rehabilitation, especially in endangered species. Physiological characteristics, hematological and plasma biochemistry profiles, are useful references for clinical management in animals, especially when animals are during the convalescence period. In this study, these factors associated with sea turtle surviving were analyzed. The blood samples were collected when sea turtles remained alive, and then animals were followed up for surviving status. The results indicated that significantly negative correlation was found between buoyancy disorders (BD) and sea turtle surviving (p < 0.05). Furthermore, non-surviving sea turtles had significantly higher levels of aspartate aminotranspherase (AST), creatinine kinase (CK), creatinine and uric acid (UA) than surviving sea turtles (all p < 0.05). After further analysis by multiple logistic regression model, only factors of BD, creatinine and UA were included in the equation for calculating summarized health index (SHI) for each individual. Through evaluation by receiver operating characteristic (ROC) curve, the result indicated that the area under curve was 0.920 ± 0.037, and a cut-off SHI value of 2.5244 showed 80.0% sensitivity and 86.7% specificity in predicting survival. Therefore, the developed SHI could be a useful index to evaluate health status of sea turtles and to improve veterinary care at rehabilitation facilities.
On image analysis by the methods of moments

Various types of moments have been used to recognize image patterns in a number of applications. The authors evaluate a number of moments and addresses some fundamental questions, such as image representation ability, noise sensitivity, and information redundancy. Moments considered include regular moments, Legendre moments, Zernike moments, pseudo-Zernike moments, rotational moments and complex moments. Properties of these moments are examined in detail, and the interrelationships among them are discussed. Both theoretical and experimental results are presented. <<ETX>>
Characterization and quantification of the nickel resistant microbial community in activated sludge using 16S rDNA and nickel resistance genes

The effect of nickel on the microbial community in the activated sludge of a sequencing batch reactor (SBR) reactor was investigated by continuously dosing nickel from 60 to 240 mg Ni(II) L−1. The diversity of the microbial community was investigated by polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis of the variable V3 region of the bacterial 16S rDNA. The experimental results showed that the community structure changed significantly after dosing with nickel with a shift in dominant species, the disappearance of some original species and the emergence of some new species. The existence of a nickel resistant gene was also investigated using PCR. The obtained nickel resistance gene had a maximum homology with the plasmid pMOL30 of Ralstonia metallidurans CH34. The quantitative real‐time PCR results indicated that the quantity of the nickel resistance gene was related to the nickel concentration loaded to the reactor.
Metformin Therapy and Risk of Cancer in Patients with Type 2 Diabetes: Systematic Review

Aims/Hypothesis Diabetes treatments were related with either an increased or reduced risk of cancer. There is ongoing debate about a potential protective action of metformin. To summarize evidence on the association between metformin and risk of cancer and cancer mortality in patients with diabetes. Methods Data source: MEDLINE and EMBASE (January 1966-April 2012). We selected randomized studies comparing metformin and other hypoglycaemic agents and observational studies exploring the association between exposure to metformin and cancer. Outcomes were cancer mortality, all malignancies and site-specific cancers. Results Of 25307 citations identified, 12 randomized controlled trials (21,595 patients) and 41 observational studies (1,029,389 patients) met the inclusion criteria. In observational studies there was a significant association of exposure to metformin with the risk of cancer death [6 studies, 24,410 patients, OR:0.65, 95%CI: 0.53-0.80], all malignancies [18 studies, 561,836 patients, OR:0.73, 95%CI: 0.61-0.88], liver [8 studies, 312,742 patients, OR:0.34; 95%CI: 0.19-0.60] colorectal [12 studies, 871,365 patients, OR:0.83, 95%CI: 0.74–0.92], pancreas [9 studies, 847,248 patients, OR:0.56, 95%CI: 0.36–0.86], stomach [2 studies, 100701 patients, OR:0.83, 95%CI: 0.76–0.91], and esophagus cancer [2 studies, 100694 patients, OR:0.90, 95%CI: 0.83–0.98]. No significant difference of risk was observed in randomized trials. Metformin was not associated with the risk of: breast cancer, lung cancer, ovarian cancer, uterus cancer, prostate cancer, bladder cancer, kidney cancer, and melanoma. Conclusions/Interpretation Results suggest that Metformin might be associated with a significant reduction in the risk of cancer and cancer-related mortality. Randomized trials specifically designed to evaluate the efficacy of metformin as an anticancer agent are warranted.
Embedded in the Shadow of the Separator

Eigenvectors to the second smallest eigenvalue of the Laplace matrix of a graph, also known as Fiedler vectors, are the basic ingredient in spectral graph partitioning heuristics. Maximizing this second smallest eigenvalue over all nonnegative edge weightings with bounded total weight yields the absolute algebraic connectivity introduced by Fiedler, who proved tight connections of this value to the connectivity of the graph. Our objective is to gain a better understanding of the connections between separators and the eigenspace of this eigenvalue by studying the dual semidefinite optimization problem to the absolute algebraic connectivity. By exploiting optimality conditions we show that this problem is equivalent to finding an embedding of the $n$ nodes of the graph in $n$-space so that their barycenter is the origin, the distance between adjacent nodes is bounded by one, and the nodes are spread as much as possible (the sum of the squared norms is maximized). For connected graphs we prove that, for any separator in the graph, at least one of the two separated node sets is embedded in the shadow (with the origin being the light source) of the convex hull of the separator. Furthermore, we show that there always exists an optimal embedding whose dimension is bounded by the tree width of the graph plus one.
Burn depth estimation--man or machine.

A Burn Depth Indicator, utilizing reflectance ratios of red, green, and infrared light, has been devised and clinically tested for 18 months at our Burn Center. Using the endpoint of wound healing in less than or more than 3 weeks, clinical assessment by two experienced surgeons of intermediate depth wounds was compared to readings from the BDI . In about one third of cases the surgeons were unwilling to commit themselves to a prediction. In the cases where the surgeons were willing to make a prediction, they were incorrect about 25% of the time. The BDI was significantly more accurate than the clinical assessment in those predicted not to heal by the surgeons and maintained an accuracy of 79% in the wounds where the surgeons would not make a prediction. The BDI is portable, noninvasive, and provides an immediate reading. It may have utility as a triage tool for emergency rooms or combat situations, and has utility at present in our Burn Center as a more accurate tool than our clinical judgment in predicting which wounds should be excised and grafted during the first few days after injury.
Receptor-mediated Immunoglobulin G Transport Across Mucosal Barriers in Adult Life

Mucosal secretions of the human gastrointestinal, respiratory, and genital tracts contain the immunoglobulins (Ig)G and secretory IgA (sIgA) that function together in host defense. Exactly how IgG crosses epithelial barriers to function in mucosal immunity remains unknown. Here, we test the idea that the MHC class I–related Fc-receptor, FcRn, transports IgG across the mucosal surface of the human and mouse lung from lumen to serosa. We find that bronchial epithelial cells of the human, nonhuman primate, and mouse, express FcRn in adult-life, and demonstrate FcRn-dependent absorption of a bioactive Fc-fusion protein across the respiratory epithelium of the mouse in vivo. Thus, IgG, like dimeric IgA, can cross epithelial barriers by receptor-mediated transcytosis in adult animals. These data show that mucosal surfaces that express FcRn reabsorb IgG and explain a mechanism by which IgG may act in immune surveillance to retrieve lumenal antigens for processing in the lamina propria or systemically.
Relationships between extractable Al, selected soil properties, pH buffer capacity and lime requirement in some acidic Queensland soils

The objectives of this study were to examine (1) interrelationships between various forms of extractable A1 and selected soil properties, (2) the contribution of extractable A1 to pH buffer capacity, and (3) investigate the use of extractable A1 to predict lime requirement. Aluminium was extracted from each of 60 Queensland soils with a range of chloride salts: 1 M KCl (AlK), 0.5 M CuCl2 (AlCu), 0.33 M LaCl3 (AlLa) and 0.01 M CaCl2 (AlCa). The amounts of A1 extracted were in the order AlCu > AlLa > Alk > AlCa. Little or no A1 was extracted by KC1 or Lac13 in soils with pHw values greater than 5.5 , whereas CuCl2 extracted some A1 irrespective of soil pH. The greater amounts of A1 extracted by CuCl2 were attributed mainly to A1 from organic matter, even though all of the soils were mineral soils (organic carbon 54.7%). Both AlCu and AlLa, were significantly (P < 0.001) correlated with organic carbon, whereas none of the extractable A1 measures was correlated with clay content. AlK and A~L, were poorly correlated to pH buffer capacity. The linear relationship between AlCu and pH buffer capacity (r2 = 0.49) obtained in this study supports the view of previous researchers that the hydrolysis of A1 adsorbed by organic matter is a source of pH buffering in soils. However, the change in CEC with pH accounted for 76% of the variation in pH buffer capacity, indicating that other mechanisms such as deprotonation of organic groups and variable charge minerals are also involved in pH buffering. The ability of CuCl2 and LaCl3extractable Al to estimate lime requirement depended on the target pH. The results suggest that lime requirements based on neutralization of AlLa would be sufficient to raise pHw to around 5.5, whereas requirements based on neutralization of AlCu substantially overestimated the actual lime requirement to pHw 5.5, but gave a reasonable estimation of the lime requirement to pHw 6 5.