Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust estimation using the Robbins-Monro stochastic approximation algorithm

The problem of minmax estimation of a location parameter introduced by Huber is considered. It is shown that under general conditions there exists a solution which is a form of the Robbins-Monro stochastic approximation algorithm. This generalizes earlier work by Martin and Masreliez who have given stochastic approximation (SA)-estimate solutions for two particular cases. As with the M -estimate solutions given by Huber, the SA solutions are completely determined by the probability distribution function with least Fisher information in the distribution set used to model the observation errors.
Asymptotic performance of a modified Schalkwijk-Barron scheme for channels with noiseless feedback (Corresp.)

A modified Schalkwijk-Barron transmission scheme is presented for channels with noiseless feedback. The modified scheme employs blockwise decision and a fixed length transmission in place of Viterbi's sequential decision feedback. The reliability functions of the modified scheme are derived for the additive white Gaussian noise (AWGN) channel and discrete memoryless channels (DMC's). For the AWGN channel the result obtained is asymptotically the same as in the case of the Schalkwijk-Barron scheme. On the other hand, the new result obtained for DMC's shows that the modified scheme also attains high reliability functions for DMC's.
Important Metabolic Pathways and Biological Processes Expressed by Chicken Cecal Microbiota

ABSTRACT The gut microbiota plays important roles in its host. However, how each microbiota member contributes to the behavior of the whole population is not known. In this study, we therefore determined protein expression in the cecal microbiota in chickens of selected ages and in 7-day-old chickens inoculated with different cecal extracts on the day of hatching. Campylobacter, Helicobacter, Mucispirillum, and Megamonas overgrew in the ceca of 7-day-old chickens inoculated with cecal extracts from donor hens. Firmicutes were characterized by ABC and phosphotransferase system (PTS) transporters, extensive acyl coenzyme A (acyl-CoA) metabolism, and expression of l-fucose isomerase. Anaerostipes, Anaerotruncus, Pseudoflavonifractor, Dorea, Blautia, and Subdoligranulum expressed spore proteins. Firmicutes (Faecalibacterium, Butyrivibrio, Megasphaera, Subdoligranulum, Oscillibacter, Anaerostipes, and Anaerotruncus) expressed enzymes required for butyrate production. Megamonas, Phascolarctobacterium, and Blautia (exceptions from the phylum Firmicutes) and all Bacteroidetes expressed enzymes for propionate production pathways. Representatives of Bacteroidetes also expressed xylose isomerase, enzymes required for polysaccharide degradation, and ExbBD, TonB, and outer membrane receptors likely to be involved in oligosaccharide transport. Based on our data, Anaerostipes, Anaerotruncus, and Subdoligranulum might be optimal probiotic strains, since these represent spore-forming butyrate producers. However, certain care should be taken during microbiota transplantation because the microbiota may behave differently in the intestinal tract of a recipient depending on how well the existing communities are established.
Cardiovascular disease prevention via a nurse-facilitated intervention clinic in a regional setting: The Protecting Healthy Hearts Program

Background: Regional-dwelling adults have higher levels of cardiovascular disease (CVD) risk. Aims: To determine the potential benefits of a nurse-led, self-management intervention program to reduce CVD and diabetes risk. Methods and results: A six-month pre/post observational study was conducted in a high risk, under-serviced regional community. A nurse-led heart health clinic was established and 530 self-selected adult individuals (mean age 54±14 years, 62% female) were subject to standardized screening. Individual targets and multidisciplinary strategies to reduce risk factors were individually tailored according to the Green Amber Red Delineation of rIsk And Need (GARDIAN) system. Changes in participants’ CVD risk factors and lifestyle behaviors were compared and independent correlates of improvements in blood pressure (BP), total cholesterol, weight and absolute CVD risk were evaluated. Baseline risk factors for CVD were highly prevalent. Participants required low (43%), moderate (34%) or high (23%) levels of surveillance and management according to GARDIAN criteria. Clinically significant changes in 326 (76%) participants were observed. Average BP decreased by 4 mmHg (systolic) and 1 mmHg (diastolic), weight by almost 1 kg, total cholesterol by 0.6 mmol/l and body mass index (BMI) by 0.3 kg/m2. A change in absolute CVD risk scores of −0.4% was observed. Primary physician attendance independently predicted improvements in BP (odds ratio (OR) 1.67; 95% confidence interval (CI) 1.08–2.58, p=0.022) whereas GARDIAN status, age, physical activity and nurse guidance positively influenced cholesterol, absolute CVD risk and weight outcomes. Conclusions: The feasibility and short-term benefits of a dedicated “heart health” service for high risk regional-dwelling individuals was shown.
A geometrical interpretation of signal detection and estimation (Corresp.)

By introducing an appropriate representation of the observation, detection problems may be interpreted in terms of estimation. The case of the detection of a deterministic signal in Gaussian noise is associated with two orthogonal subspaces: the first is the signal subspace which is generally one dimensional and the second is called a reference noise alone (RNA) space because it contains only the noise component and no signal. The detection problem can then be solved in the signal subspace, while the use of the RNA space is reduced to the estimation of the noise in the signal subspace. This decomposition leads to a very simple interpretation of singular detection, even in the non-Gaussian case, in terms of perfect estimation. The method is also extended to multiple signal detection problems and to some special cases of detection of random signals.
POSTMENOPAUSAL OSTEOPOROSIS: ITS CLINICAL FEATURES

Our object in this paper is to point out the existence of postmenopausal osteoporosis and to describe its clinical features. Some metabolic data showing the effects of therapy with estrogens and other agents are incorporated in other papers.1 It will probably be well to start by explaining and defining the term "osteoporosis. " Adult bone is normally subject to two continuous processes—formation and resorption. The mass of bone may be deficient either because resorption is too great (hyperparathyroidism with osteitis fibrosa generalisata) or because formation is too little (osteoporosis or osteomalacia). Formation of bone may be too little, furthermore, either because the osteoblasts do not lay down sufficient osseous matrix or because the matrix, once laid down, is not calcified. The former condition is osteoporosis; the latter, osteomalacia or rickets (fig. 1). It is thought that stresses and strains are an important stimulus to osteoblastic activity and that the atrophy
Part II: Multisystemic Therapy: Addressing Racial Disparity and Its Effectiveness With Families From Diverse Racial and Ethnic Backgrounds

Disparities in health and mental health care delivered to racial and ethnic minorities became a focus of national policy following reports of the Institute of Medicine (IOM, 2002) and the Surgeon General (USDHHS, 2001). The Surgeon General (USDHHS, 2001) reported racial and ethnic minorities experience disparities in availability and quality of mental health services compared to whites. Two challenges that intersect and compound each other are the disproportionately high numbers of African American children in child welfare with unmet mental health needs remaining in their homes or placed in relative's homes after a substantiation of child maltreatment (USDHHS, 2002) and the lack of culturally appropriate, effective home-based treatments available to them. This study compared outcomes for the youth who received Multisystemic Therapy (MST) controlling for the impact of race and ethnicity. The findings provide further evidence for child welfare practitioners to consider when working with children and families from diverse populations in decision-making.
Coexistence of Microaerophilic, Nitrate-Reducing, and Phototrophic Fe(II) Oxidizers and Fe(III) Reducers in Coastal Marine Sediment

ABSTRACT Iron is abundant in sediments, where it can be biogeochemically cycled between its divalent and trivalent redox states. The neutrophilic microbiological Fe cycle involves Fe(III)-reducing and three different physiological groups of Fe(II)-oxidizing microorganisms, i.e., microaerophilic, anoxygenic phototrophic, and nitrate-reducing Fe(II) oxidizers. However, it is unknown whether all three groups coexist in one habitat and how they are spatially distributed in relation to gradients of O2, light, nitrate, and Fe(II). We examined two coastal marine sediments in Aarhus Bay, Denmark, by cultivation and most probable number (MPN) studies for Fe(II) oxidizers and Fe(III) reducers and by quantitative-PCR (qPCR) assays for microaerophilic Fe(II) oxidizers. Our results demonstrate the coexistence of all three metabolic types of Fe(II) oxidizers and Fe(III) reducers. In qPCR, microaerophilic Fe(II) oxidizers (Zetaproteobacteria) were present with up to 3.2 × 106 cells g dry sediment−1. In MPNs, nitrate-reducing Fe(II) oxidizers, anoxygenic phototrophic Fe(II) oxidizers, and Fe(III) reducers reached cell numbers of up to 3.5 × 104, 3.1 × 102, and 4.4 × 104 g dry sediment−1, respectively. O2 and light penetrated only a few millimeters, but the depth distribution of the different iron metabolizers did not correlate with the profile of O2, Fe(II), or light. Instead, abundances were homogeneous within the upper 3 cm of the sediment, probably due to wave-induced sediment reworking and bioturbation. In microaerophilic Fe(II)-oxidizing enrichment cultures, strains belonging to the Zetaproteobacteria were identified. Photoferrotrophic enrichments contained strains related to Chlorobium and Rhodobacter; the nitrate-reducing Fe(II) enrichments contained strains related to Hoeflea and Denitromonas. This study shows the coexistence of all three types of Fe(II) oxidizers in two near-shore marine environments and the potential for competition and interrelationships between them.
Iron Corrosion Induced by Nonhydrogenotrophic Nitrate-Reducing Prolixibacter sp. Strain MIC1-1

ABSTRACT Microbiologically influenced corrosion (MIC) of metallic materials imposes a heavy economic burden. The mechanism of MIC of metallic iron (Fe0) under anaerobic conditions is usually explained as the consumption of cathodic hydrogen by hydrogenotrophic microorganisms that accelerates anodic Fe0 oxidation. In this study, we describe Fe0 corrosion induced by a nonhydrogenotrophic nitrate-reducing bacterium called MIC1-1, which was isolated from a crude-oil sample collected at an oil well in Akita, Japan. This strain requires specific electron donor-acceptor combinations and an organic carbon source to grow. For example, the strain grew anaerobically on nitrate as a sole electron acceptor with pyruvate as a carbon source and Fe0 as the sole electron donor. In addition, ferrous ion and l-cysteine served as electron donors, whereas molecular hydrogen did not. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MIC1-1 was a member of the genus Prolixibacter in the order Bacteroidales. Thus, Prolixibacter sp. strain MIC1-1 is the first Fe0-corroding representative belonging to the phylum Bacteroidetes. Under anaerobic conditions, Prolixibacter sp. MIC1-1 corroded Fe0 concomitantly with nitrate reduction, and the amount of iron dissolved by the strain was six times higher than that in an aseptic control. Scanning electron microscopy analyses revealed that microscopic crystals of FePO4 developed on the surface of the Fe0 foils, and a layer of FeCO3 covered the FePO4 crystals. We propose that cells of Prolixibacter sp. MIC1-1 accept electrons directly from Fe0 to reduce nitrate.
The Bacillus cereus Group Is an Excellent Reservoir of Novel Lanthipeptides

ABSTRACT Lantibiotics are ribosomally synthesized peptides that contain multiple posttranslational modifications. Research on lantibiotics has increased recently, mainly due to their broad-spectrum antimicrobial activity, especially against some clinical Gram-positive pathogens. Many reports about various bacteriocins in the Bacillus cereus group have been published, but few were about lantibiotics. In this study, we identified 101 putative lanthipeptide gene clusters from 77 out of 223 strains of this group, and these gene clusters were further classified into 20 types according to their gene organization and the homologies of their functional genes. Among them, 18 types were novel and have not yet been experimentally verified. Two novel lantibiotics (thuricin 4A-4 and its derivative, thuricin 4A-4D) were identified in the type I-1 lanthipeptide gene cluster and showed activity against all tested Gram-positive bacteria. The mode of action of thuricin 4A-4 was studied, and we found that it acted as a bactericidal compound. The transcriptional analysis of four structural genes (thiA1, thiA2, thiA3, and thiA4) in the thuricin 4A gene cluster showed that only one structural gene, thiA4, showed efficient transcription in the exponential growth phase; the other three structural genes did not. In addition, the putative transmembrane protein ThiI was responsible for thuricin 4A-4 immunity. Genome analysis and functional verification illustrated that B. cereus group strains were a prolific source of novel lantibiotics.
Phylogenetic Inferences Reveal a Large Extent of Novel Biodiversity in Chemically Rich Tropical Marine Cyanobacteria

ABSTRACT Benthic marine cyanobacteria are known for their prolific biosynthetic capacities to produce structurally diverse secondary metabolites with biomedical application and their ability to form cyanobacterial harmful algal blooms. In an effort to provide taxonomic clarity to better guide future natural product drug discovery investigations and harmful algal bloom monitoring, this study investigated the taxonomy of tropical and subtropical natural product-producing marine cyanobacteria on the basis of their evolutionary relatedness. Our phylogenetic inferences of marine cyanobacterial strains responsible for over 100 bioactive secondary metabolites revealed an uneven taxonomic distribution, with a few groups being responsible for the vast majority of these molecules. Our data also suggest a high degree of novel biodiversity among natural product-producing strains that was previously overlooked by traditional morphology-based taxonomic approaches. This unrecognized biodiversity is primarily due to a lack of proper classification systems since the taxonomy of tropical and subtropical, benthic marine cyanobacteria has only recently been analyzed by phylogenetic methods. This evolutionary study provides a framework for a more robust classification system to better understand the taxonomy of tropical and subtropical marine cyanobacteria and the distribution of natural products in marine cyanobacteria.
Multifactorial Effects of Ambient Temperature, Precipitation, Farm Management, and Environmental Factors Determine the Level of Generic Escherichia coli Contamination on Preharvested Spinach

ABSTRACT A repeated cross-sectional study was conducted to identify farm management, environment, weather, and landscape factors that predict the count of generic Escherichia coli on spinach at the preharvest level. E. coli was enumerated for 955 spinach samples collected on 12 farms in Texas and Colorado between 2010 and 2012. Farm management and environmental characteristics were surveyed using a questionnaire. Weather and landscape data were obtained from National Resources Information databases. A two-part mixed-effect negative binomial hurdle model, consisting of a logistic and zero-truncated negative binomial part with farm and date as random effects, was used to identify factors affecting E. coli counts on spinach. Results indicated that the odds of a contamination event (non-zero versus zero counts) vary by state (odds ratio [OR] = 108.1). Odds of contamination decreased with implementation of hygiene practices (OR = 0.06) and increased with an increasing average precipitation amount (mm) in the past 29 days (OR = 3.5) and the application of manure (OR = 52.2). On contaminated spinach, E. coli counts increased with the average precipitation amount over the past 29 days. The relationship between E. coli count and the average maximum daily temperature over the 9 days prior to sampling followed a quadratic function with the highest bacterial count at around 24°C. These findings indicate that the odds of a contamination event in spinach are determined by farm management, environment, and weather factors. However, once the contamination event has occurred, the count of E. coli on spinach is determined by weather only.
Taxonomic Identification of Commensal Bacteria Associated with the Mucosa and Digesta throughout the Gastrointestinal Tracts of Preweaned Calves

ABSTRACT Bacterial colonization in the gastrointestinal tracts (GIT) of preweaned calves is very important, since it can influence early development and postweaning performance and health. This study investigated the composition of the bacteria along the GIT (rumen, jejunum, ileum, cecum, and colon) of preweaned bull calves (3 weeks old) using pyrosequencing to understand the segregation of bacteria between the mucosal surface and digesta. Phylogenetic analysis revealed that a total of 83 genera belonging to 13 phyla were distributed throughout the GIT of preweaned calves, with the Firmicutes, Bacteroidetes, and Proteobacteria predominating. Quantitative PCR (qPCR) analysis of selected abundant bacterial genera (Prevotella, Bacteroides, Lactobacillus, and Faecalibacterium) revealed that their prevalence was significantly different among the GIT regions and between mucosa- and digesta-associated communities. Rumens contained the most diverse bacterial population, consisting of 47 genera, including 16 rumen-specific genera, followed by the large intestine and then the small intestine. Bacterial species richness was higher at the mucosal surface than in the local digesta, with the exception of the rumen. The majority of bacteria found on the rumen epithelial surface and within the small intestine could not be identified due to a lack of known genus-level information. Thus, future studies will be required to fully characterize the microbiome during the development of the rumens and the mucosal immune systems of newborn calves. This is the first study to analyze in depth the bacterial composition of the GIT microbiome in preweaned calves, which extends previous findings regarding early rumen colonization and bacterial segregation between mucosa- and digesta-associated microbial communities.
Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Nonheme Iron Oxygenase Carbazole 1,9a-Dioxygenase

ABSTRACT Carbazole 1,9a-dioxygenase (CARDO), a Rieske nonheme iron oxygenase (RO), is a three-component system composed of a terminal oxygenase (Oxy), ferredoxin, and a ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy-encoding gene from Janthinobacterium sp. strain J3 generated the I262V, F275W, Q282N, and Q282Y Oxy derivatives, which showed oxygenation capabilities different from those of the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. The I262V, F275W, and Q282Y derivatives catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15, 25, and 25°, respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and the imino nitrogen of carbazole. In the crystal structure of the F275W derivative complexed with fluorene, C-9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate-binding position that, in turn, favors specific oxygenation reactions toward various substrates.
Statistical modeling of co-articulation in continuous speech based on data driven interpolation

Parsimonious modeling of the context dependency nature of speech due to co-articulation is very important for improving the performance of speech recognition systems. Numerous approaches have been proposed in the literature to address this problem. However, most of the methods are based on the idea of using context-dependent speech units, which inevitably increases the complexity of the model space. This paper presents a new approach of speech co-articulation modeling with complexity only comparable to context-independent models. In this model, the movement of a sequence of speech signals is characterized by a set of anchor points in the feature vector space that correspond to the target phonemic units. The transitions between the phonemic units due to co-articulation are modeled as interpolations between the target vectors. Two types of parameters are involved in the models: the intrinsic parameters in the models of target units and the auxiliary parameters specifying the transitional units. The auxiliary parameters are estimated "online" for a given sequence of speech feature vectors, hence it does not contribute to the complexity of the models. Unlike "triphone"-type context dependent models, the complexity of this approach is comparable to the context independent phoneme models, yet, some phonetic classification experiments showed that the new model can achieve the same performance as the more complex context dependent models.
Early stage detection of conduit artery endothelial dysfunction in patients with type 1 diabetes

Flow-mediated dilatation evaluation using hand skin heating may possibly be more accurate than post-ischaemic hyperaemia to detect conduit artery endothelial dysfunction in type 1 diabetes. We measured in 24 type 1 diabetic patients (n=16 without microangiopathy) and 24 healthy matched subjects radial artery diameter (echotracking), blood flow and mean wall shear stress during heating and post-ischaemic hyperaemia. Compared with controls, flow-mediated dilatation was lower in diabetic patients during post-ischaemic hyperaemia and heating. However, in the subgroup of uncomplicated patients, a decreased flow-mediated dilatation was only apparent during heating (17.1±1.6% vs. 24.3±0.7%, p<0.05) but not during post-ischaemic hyperaemia (10.1±1.1% vs. 10.5±0.6%, NS). This was confirmed by the lower slope of the diameter—mean wall shear stress relationship in these patients in the absence of modification in endothelium-independent dilatation. We conclude that hand skin heating permits the early detection of conduit artery endothelial dysfunction in type 1 diabetic patients with normal response to post-ischaemic hyperaemia. This procedure could be useful to investigate the prognostic role of vascular dysfunction and the impact of vasculoprotective treatments in this patient population.