Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecological niche differentiation of ammonia-oxidising archaea and bacteria in acidic soils due to land use change

Nitrification can be driven by either ammonia-oxidising bacteria (AOB) or ammonia-oxidising archaea (AOA) and is a central process in the nitrogen cycle. However, to date, it is not clear how the ecological niche differentiation of AOB and AOA are affected by land use and management changes in strongly acidic soils in subtropical China. In this study, three different land-use acidic soils – forest, upland, and paddy soils – were collected and a DNA Stable-Isotope Probing experiment performed to determine the relative contributions of AOA and AOB to ammonia oxidation in these soils. The results showed that AOA, but not AOB, amoA genes were detected in 13C-labelled DNA in the forest and paddy soils; however, only AOB amoA genes were detected in 13C-labelled DNA in the upland agricultural soils. The growth and activity of AOA and AOB in the different land-use soils provided direct evidence for the shift in roles for AOA and AOB in ammonia oxidation. AOA played the predominant role in ammonia oxidation in acidic forest and paddy soils. However, AOB, not AOA, mainly regulated the ammonia oxidation in acidic upland agricultural soils. Phylogenetic analysis indicated that AOA members within the marine Group1.1a-associated lineage dominated nitrification in the forest and paddy soils. Ammonia oxidation in the upland soil was catalysed by Nitrosospira cluster 3-like AOB. The moisture condition was likely the main reason inducing the ecological niche differentiation between upland and paddy soils; and AOA was more suitable for growth in the flooded, low oxygen conditions.
Sexual Minority Health Disparities in Adult Men and Women in the United States: National Health and Nutrition Examination Survey, 2001-2010.

OBJECTIVES We used nationally representative data to investigate health disparities associated with sexual minority status among adults in the United States. METHODS We analyzed data from 11,114 adults who participated in the 2001 to 2010 waves of the National Health and Nutrition Examination Survey. Using multiple logistic regressions, we examined the prevalence of HIV, sexually transmitted infections, mental health problems, cigarette smoking, and alcohol and illicit drug use in sexual minorities and heterosexual adults. RESULTS After adjusting for sociodemographic characteristics, sexual minority men had greater odds of mental health problems, testing positive for HIV and herpes simplex virus type 2 and self-reported gonorrhea and chlamydia. Sexual minority women had greater odds of mental health problems, testing positive for hepatitis C, smoking, heavy drinking, and illicit drug use. CONCLUSIONS Numerous health disparities continue to face sexual minority men and women in the United States. Notably, health disparities persisted beyond the role of sociodemographic factors, including access to insurance and primary care, suggesting that further research is warranted to identify the determinants of health inequity for sexual minorities.
Biomass burning aerosol transport and vertical distribution over the South African‐Atlantic region

Optically thick smoke aerosol plumes originating from biomass burning (BB) in the southwestern African Savanna during the austral spring are transported westward by the free tropospheric winds to primarily overlie vast stretches of stratocumulus cloud decks in the southeast Atlantic. We evaluated the simulations of long‐range transport of BB aerosol by the Goddard Earth Observing System (GEOS‐5) and four other global aerosol models over the complete South African‐Atlantic region using Cloud‐Aerosol Lidar with Orthogonal Polarization (CALIOP) observations to find any distinguishing or common model biases. Models, in general, captured the vertical distribution of aerosol over land but exhibited some common features after long‐range transport of smoke plumes that were distinct from that of CALIOP. Most importantly, the model‐simulated BB aerosol plumes quickly descend to lower levels just off the western coast of the continent, while CALIOP data suggest that smoke plumes continue their horizontal transport at elevated levels above the marine boundary layer. This is crucial because the sign of simulated aerosol semidirect effect can change depending on whether the bulk of the absorbing aerosols is present within or above the cloud levels in a model. The levels to which the aerosol plumes get subsided and the steepness of their descent vary amongst the models and amongst the different subregions of the domain. Investigations into possible causes of differences between GEOS‐5 and CALIOP aerosol transport over the ocean revealed a minimal role of aerosol removal process representation in the model as opposed to model dynamics.
0 N ov 1 99 7 Quantum Theory of Geometry II : Volume operators

Abhay Ashtekar, Jerzy Lewandowski 1 Center for Gravitational Physics and Geometry Department of Physics, Penn State, University Park, PA 16802-6300, USA 2 Instytut Fizyki Teoretycznej, Uniwersytet Warszawski ul. Hoza 69, 00-681 Warszawa, Poland 3 Max-Planck-Institut für Gravitationsphysik, Albert Einstein Institut, Schlaatzweg 1, D-14473 Potsdam, Germany 4 Erwin Schrödinger International Institute for Mathematical Sciences Boltzmanngasse 9, A-1090 Vienna, Austria
Longitudinal analyses of the surgical outcomes of pediatric epilepsy patients with focal cortical dysplasia.

OBJECT The long-term surgical outcome of pediatric patients with epilepsy accompanied by focal cortical dysplasia (FCD) is not clear. The authors report on the long-term surgical outcomes of children with FCD, based on longitudinal analyses. METHODS The authors retrospectively analyzed the records of 41 children who underwent epilepsy surgery for pathologically proven FCD. Twenty of these patients were male and 21 were female. The median age at surgery was 9 years (range 1-17 years). RESULTS The actuarial seizure-free rates were 49, 44, and 33% in the 1st, 2nd, and 5th years after surgery, respectively. There was no seizure recurrence after 3 years. Three patients with initial failure of seizure control experienced late remission of seizures (the so-called running-down phenomenon). Eventually, 19 patients (46%) were seizure free at their last follow-up visit. Absence of a lesion on MR imaging and incomplete resection were significantly associated with seizure-control failure. Concordance of presurgical evaluation data was a marginally significant variable for seizure control in patients with lesional epilepsy. Three patients with seizure-control failure became seizure free as a result of the running-down phenomenon. The actuarial rate of antiepileptic drug discontinuation was 91% in the 5th year in the seizure-free patients. CONCLUSIONS The seizure-free rate after surgery in children with FCD was 49% in the 1st year; however, it declined thereafter. The running-down phenomenon could be an important mechanism of seizure alleviation for patients with FCD during long-term follow-up. Because a complete resection of FCD has a strong prognostic implication for seizure control, a better method to define the extent of FCD is required to assist with resection, especially in nonlesional epilepsy.
Prefrontal Hypometabolism in Alzheimer Disease Is Related to Longitudinal Amyloid Accumulation in Remote Brain Regions

In PET studies of patients with Alzheimer disease (AD), prominent hypometabolism can occur in brain regions without major amyloid load. These hypometabolism-only (HO) areas may not be explained easily as a consequence of local amyloid toxicity. The aim of this longitudinal multimodal imaging study was the investigation of locoregional and remote relationships between metabolism in HO areas and longitudinal amyloid increase in functionally connected brain areas, with a particular focus on intrinsic functional connectivity as a relevant linking mechanism between pathology and dysfunction. Methods: Fifteen AD patients underwent longitudinal examinations with 11C-Pittsburgh compound B (11C-PiB) and 18F-FDG PET (mean follow-up period, 2 y). The peak HO region was identified by the subtraction of equally thresholded statistical T maps (hypometabolism minus amyloid burden), resulting from voxel-based statistical parametric mapping group comparisons between the AD patients and 15 healthy controls. Then functionally connected and nonconnected brain networks were identified by means of seed-based intrinsic functional connectivity analysis of the resting-state functional MRI data of healthy controls. Finally, network-based, region-of-interest–based, and voxel-based correlations were calculated between longitudinal changes of normalized 11C-PiB binding and 18F-FDG metabolism. Results: Positive voxel-based and region-of-interest–based correlations were demonstrated between longitudinal 11C-PiB increases in the HO-connected network, encompassing bilateral temporoparietal and frontal brain regions, and metabolic changes in the peak HO region as well as locoregionally within several AD-typical brain regions. Conclusion: Our results indicate that in AD amyloid accumulation in remote but functionally connected brain regions may significantly contribute to longitudinally evolving hypometabolism in brain regions not strongly affected by local amyloid pathology, supporting the amyloid- and network-degeneration hypothesis.
Non-uniform Sampling in Clustering and Streaming

Aproximating a sum without computing the summands is a classic problem in statistics and machine learning. The problem is defined as follows: Assume Z is the sum of n numbers, Z1, · · · , Zn i.e., Z = Z1 + · · ·+ Zn. The goal is to estimate Z without computing all the n summands but few. According to the uniform sampling we choose a number Zi with probability 1 n and assign the weight n to Zi. The number nZi will be our estimation for Z. We see that the expectation of the random variable nZi is Z but the variance of nZi can be large. The reason is if the number of large numbers is few, then the probability that the random sample does not take one of them will be high and if this happens the variance of nZi will be large. Using non-uniform sampling we can bound the variance in terms of the expectation and therefore estimate Z within factor (1± ) as follows: Having n probabilities ri ≥ 1 γ Zi Z for 1 ≤ i ≤ n corresponding to the numbers Z1, · · · , Zn we take a sample set A = {a1, · · · , aj, · · · , as} ⊆ [n] of indices according to the probabilities ri and assign a weight of w(Zaj) = 1 s·raj to a sampled number Zaj for 1 ≤ j ≤ s. We then use the concentration bounds to show that for s = O(γ −2 log(1/δ)) the probability that the estimator X = ∑ aj∈Aw(Zaj) · Zaj deviates from Z by more than Z is at most δ. In this thesis we study applications of this estimator in high dimensional clustering and streaming. In particular, for the k-means and the j-subspace problems we get unbiased estimators that can (1± )approximate the cost of the point set to an arbitrary center set. We then use these estimators to get coresets, linear time (1+ )-approximation and insertion only streaming algorithms. In the turnstile streaming model we are given a vector a of length n where the i-th coordinate is represented by ai and a stream S as m = poly(n,M) updates of the form (i, x), where i ∈ [n] and x ∈ {−M,−M + 1, . ,M − 1,M}, indicating that the i-th coordinate ai of a should be incremented by x. Let Zi = |ai| for p ∈ [0, 2], 1 ≤ i ≤ n and Z = Fp(a) = ∑n i=1 |ai| . In this model finding n probabilities ri ≥ 1 γ Zi Z using one pass and polylog space was known to be an open problem in the streaming community [CMI05]. We give a 1-pass poly( −1 logn)-space algorithm called Lp-sampler that samples according to probabilities ri for γ = (1± ), p ∈ [0, 2]. We show that the Lp-sampler leads to many improvements and a unification of well-studied streaming problems, including cascaded norms, heavy hitters, and moment estimation. In particular, as for the moment estimation using O(n1−2/k −2) L2-samplers in parallel for k > 2 we can (1 ± )-estimate Fk(a) = ∑n i=1 |ai| k using optimal space n1−2/k · poly( −1 logn). This algorithm is the first that does not use Nisan’s pseudorandom generator as a subroutine, potentially making it more practical.
Training Ghanaian frontline healthcare workers in public health surveillance and disease outbreak investigation and response

Introduction Beyond initial formal academic education, the need for continuous professional development through in-service workforce capacity improvement programs that are aimed at enhancing knowledge and skills of public healthcare workers has assumed immense priority worldwide. This has been heightened by the on-going Ebola Virus Disease outbreak, which is exposing the weak public health systems in West Africa. In response to this need, the Ghana Field Epidemiology and Laboratory Program organized a short-course for frontline health workers in the Greater Accra region of Ghana in order to augment their surveillance and outbreak response capacity. Methods Human and veterinary health workers were trained using Field Epidemiology and Laboratory Training Program short course model. A two-week didactic course was conducted with a 10-week field placement. Evaluation of the course was done by assessment of participants’ outputs during the training as well as pretest and posttest methods. Results A total of 32 frontline health workers from both the human and veterinary health services benefited from the two-week initial training of the 12-week course. There was a significant gain in knowledge by the participants after the training course. Participants developed concept papers and implemented their fieldwork projects. Overall assessment of the workshop by the participants was very good. Conclusion Capacity of the health workers has been improved in the area of public health surveillance, outbreak investigation and response. We recommend a scale-up of this training course to other regions.
Expression of ephrinB1 and its receptor in glaucomatous optic neuropathy

Objective: To determine ephrinB1, ephrinB2 and EphB1 expression in the optic nerve head (ONH) and retina of monkeys with glaucoma and in human ONH astrocytes. Methods: Using immunohistochemistry, the localisation of ephrinB1, ephrinB2 and EphB1 was determined in the ONH and retina bilaterally in monkeys with monocular laser-induced glaucoma. RT-PCR, western blot and immunocytochemistry were used to study ephrinB1, ephrinB2 and EphB1 expression in cultured human ONH astrocytes from donors with and without glaucoma. Results: There was an increase in ephrinB1 and EphB1 expression in mild to moderate glaucoma. In the ONH, both ephrinB1 and EphB1 were localised to astrocytes and EphB1 was also localised to lamina cribrosa cells and perivascular cells. In the retina, ephrinB1 localised to Muller cells and astrocytes, and EphB1 was found in retinal ganglion cells. In ONH astrocytes in humans with glaucoma, ephrinB1 and EphB1 were up-regulated but barely present in donors without glaucoma. Conclusions: Ephrins are activated in early and moderate glaucoma in the ONH and retina. We postulate that the up-regulation of Eph/ephrin pathway may play a protective role by limiting axonal damage and inflammatory cell invasion. Loss of ephrin signalling in advanced glaucoma may explain macrophage activation.
Beta-adrenergic receptor antagonists and chronic heart failure in children

Chronic congestive heart failure (HF) occurs in infants and children as a result of systemic ventricle incompetence. Neurohormonal activation is thought to be the main consequence of cardiac pump failure and cause of further worsening. Several large multicenter randomized trials have demonstrated that beta-adrenergic blocking agents can improve ventricular ejection fraction, symptoms, and survival in adults with chronic congestive HF. Current literature about pediatric HF is very scarce. The only large, multicenter, randomized, placebo-controlled pediatric trial failed to demonstrate any beneficial effect of beta-blockers in infants and children with chronic HF. Other small-size reports showed significant improvement in ejection fraction and/or clinical outcomes. The HF pediatric population is characterized by wide heterogeneicity regarding causes, underlying cardiac disease, drug pharmacokinetics, and interactions, which may account for divergences. Further large-scale studies are needed to elucidate the optimal use (indications and dosages) of beta-blockers in the management of HF in children, with particular attention to the underlying cardiac disease.
Modelling acoustic feature dependencies with artificial neural networks: Trajectory-RNADE

Given a transcription, sampling from a good model of acoustic feature trajectories should result in plausible realizations of an utterance. However, samples from current probabilistic speech synthesis systems result in low quality synthetic speech. Henter et al. have demonstrated the need to capture the dependencies between acoustic features conditioned on the phonetic labels in order to obtain high quality synthetic speech. These dependencies are often ignored in neural network based acoustic models. We tackle this deficiency by introducing a probabilistic neural network model of acoustic trajectories, trajectory RNADE, able to capture these dependencies.
Candida albicans binding to the oral bacterium Streptococcus gordonii involves multiple adhesin-receptor interactions

Candida albicans binds to several species of oral streptococci, in particular Streptococcus gordonii, through recognition of a streptococcal cell wall polysaccharide receptor (A. R. Holmes, P. K. Gopal, and H. F. Jenkinson, Infect. Immun. 63:1827-1834, 1995). We now show that isogenic cell surface protein mutants of S. gordonii DL1, unaltered in expression of cell wall polysaccharide, are reduced in ability to support adherence of C. albicans cells in a solid-phase assay. Inactivation of the S. gordonii cshA and cshB genes, encoding high-molecular-mass cell surface polypeptides, and inactivation of the sspA and sspB genes, encoding antigen I/II salivary adhesins, resulted in 40 and 79% reductions, respectively, in adherence of C. albicans cells. Inactivation of the S. gordonii scaA gene encoding a cell surface lipoprotein had no effect on C. albicans adherence. Polyclonal antiserum to streptococcal antigen I/II protein SpaP and antibodies specific to the amino-terminal nonrepetitive (NR) domain of CshA both inhibited adherence of C. albicans to S. gordonii cells. Conversely antibodies to the amino acid repeat block repetitive (R) domain of CshA, or to ScaA, did not inhibit C. albicans adherence. Immobilized recombinant polypeptide fragments of CshA comprising NR domain or R domain sequences both supported adherence of C. albicans cells. Expression of S. gordonii SspB protein on the surface of Enterococcus faecalis conferred on the enterococcal cells the ability to bind C. albicans, and this was ablated by antigen I/II antiserum. Collectively the results suggest that interaction of C. albicans with S. gordonii is mediated by a complement of adhesin-receptor interactions that involves two families of streptococcal multifunctional polypeptide adhesins, bacterial cell wall polysaccharide, and as yet unidentified yeast cell surface components.
Need to test the arterial inflammation hypothesis.

Despite intensive basic and clinical investigation, coronary artery disease remains the principal cause of death and disability in the United States. In recent years, the appreciation of arterial inflammation as an important risk factor has had considerable implications for changing our approach to managing these patients.1,2⇓ Arterial inflammation has emerged as central to the progression of atherothrombosis.3 Of the markers of inflammation, the high-sensitivity C-reactive protein (CRP) is the most studied, with evidence that it may also play a direct pathogenic role in atherosclerotic lesion formation.4– 11⇓⇓⇓⇓⇓⇓⇓ In the absence of active infection, measurements of CRP are reasonably reproducible, comparable to measurements of total cholesterol.12,13⇓ Additionally, elevated CRP appears to be a more potent risk factor than other mediators of inflammation, such as tumor necrosis factor-α, interleukin-6, or serum amyloid A.4,14⇓ A group of pharmacotherapies that are currently available, such as aspirin, statins, angiotensin converting enzyme inhibitors (ACE-Is), thienopyridines, and peroxisome proliferator-activated receptor (PPAR) agonists have been shown, in addition to their other properties, to reduce CRP and/or arterial inflammation. Although it is clear that elevated CRP denotes increased risk and emerging evidence suggests that there are novel therapies that result in lowering of CRP, the most important unanswered question is whether suppression of inflammation and consequent lowering of CRP will translate into a decrease in clinical events.15 Surprisingly, despite the importance of the question, the “inflammation hypothesis” of intentional CRP suppression as compared with standard care has not yet been tested. Such a prospective study of patients with established cardiovascular disease and elevated baseline CRP in which incremental pharmacotherapy would be guided by reassessments of the CRP marker could allow formulation of a rational therapeutic strategy instead of an approach of “polypharmacy” for …
Aspect oriented GoF design patterns

Design patterns provided experienced solutions to common problems in software development, but recent studies have shown that several design patterns involve crosscutting concerns where object oriented abstractions failed to handle, this led to decreasing system modularity, reusability and maintainability. This encourages investigating the impact of aspect oriented approaches on design patterns not only on the implementation level but also on the design level. In this paper, the effect of applying the aspect oriented concepts on the design and implementation levels of GoF design patterns is examined.
Leakage suppression in the toric code

Quantum codes excel at correcting local noise but fail to correct leakage faults that excite qubits to states outside the computational space. Aliferis and Terhal have shown that an accuracy threshold exists for leakage faults using gadgets called leakage reduction units (LRUs). However, these gadgets reduce the threshold and increase experimental complexity, and the costs have not been thoroughly understood. We explore a variety of techniques for leakage resilience in topological codes. Our contributions are threefold. First, we develop a leakage model that is physically motivated and efficient to simulate. Second, we use Monte-Carlo simulations to survey several syndrome extraction circuits. Third, given the capability to perform 3-outcome measurements, we present a dramatically improved syndrome processing algorithm. Our simulations show that simple circuits with one extra CNOT per qubit reduce the accuracy threshold by less than a factor of 4 when leakage and depolarizing noise rates are comparable compared to a scenario without leakage. This becomes a factor of 2 when the decoder uses 3-outcome measurements. Finally, we make the surprising observation that for physical error rates less than 2 × 10-4, placing LRUs after every gate may achieve the lowest logical error rate. We expect that the ideas may generalize to other topological codes.