Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Characterization of Penicillin-Resistant Streptococcus pneumoniae Isolates from Bulgaria

ABSTRACT As part of an ongoing surveillance program of antibiotic-resistantStreptococcus pneumoniae in Sofia, Bulgaria, 120 penicillin-resistant strains (PRSP) (most of them recovered from children hospitalized with pneumococcal disease) were analyzed by microbiological and molecular methods. Several unique features of this collection are of particular interest. (i) Most isolates (112 of 120) were also resistant to trimethoprim-sulfamethoxazole (SXT) (97 of 120 isolates, or 80%), and over 70% (86 of 120) of the isolates were resistant to at least three antibiotics in addition to penicillin. (ii) Close to 80% of all isolates were represented by large clusters of bacteria, each with a unique serotype, antibiotype, and chromosomal macrorestriction pattern (determined by pulsed-field gel electrophoresis), as well as unique restriction fragmentation length polymorphisms of the penicillin-binding protein genespbp1a, pbp2x, and pbp2b. (iii) A large proportion (45 of 120, or 38%) of the strains belonged to two internationally spread epidemic clones of S. pneumoniae, the first expressing capsular type 23F and the second expressing serotype 9. (iv) A unique Bulgarian cluster composed of eight serotype 19F isolates was resistant to tetracycline, SXT, cefotaxime, and extremely high levels of penicillin and erythromycin. Nevertheless, this clone did not react with either the erm or the mef DNA probes, and thus the mechanism of macrolide resistance in this group of PRSP remains to be elucidated.
Analytical-based approach for capacitor placement with gradient error compensation and device correlation enhancement in analog integrated circuits

Switched capacitors are commonly used in analog design. The circuit performance based on this technique relies on the accuracy of capacitance ratios, which are affected by random and systematic mismatches. To meet the accuracy requirement, designers can increase the layout area of unit capacitors to reduce random mismatch. Since increasing layout area enlarges the distance between unit capacitors, it induces more gradient errors, which results in larger systematic mismatch. Therefore, the better way for reducing the gradient errors is to carefully determine the locations of unit capacitors in a capacitor array. Moreover, the resulting placement must have high capacitance correlation in order to enhance yield. In this paper, we first explore the attributes of a good capacitor placement, which can reduce gradient errors and increase capacitance correlation. Then, an analytical-based approach is proposed to complete capacitor placement considering these issues. Finally, the results are optimized by arbitrarily swapping two unit capacitors. Compared with the simulated annealing based approach, the proposed method not only achieves better placement results but also gets 34x faster for the largest benchmark capacitor array.
Limits to Trophic Levels and Omnivory in Complex Food Webs: Theory and Data

While trophic levels have found broad application throughout ecology, they are also in much contention on analytical and empirical grounds. Here, we use a new generation of data and theory to examine long‐standing questions about trophic‐level limits and degrees of omnivory. The data include food webs of the Chesapeake Bay, U.S.A. , the island of Saint Martin, a U.K. grassland, and a Florida seagrass community, which appear to be the most trophically complete food webs available in the primary literature due to their inclusion of autotrophs and empirically derived estimates of the relative energetic contributions of each trophic link. We show that most (54%) of the 212 species in the four food webs can be unambiguously assigned to a discrete trophic level. Omnivory among the remaining species appears to be quite limited, as judged by the standard deviation of omnivores’ energy‐weighted food‐chain lengths. This allows simple algorithms based on binary food webs without energetic details to yield surprisingly accurate estimates of species’ trophic and omnivory levels. While maximum trophic levels may plausibly exceed historically asserted limits, our analyses contradict both recent empirical claims that these limits are exceeded and recent theoretical claims that rampant omnivory eliminates the scientific utility of the trophic‐level concept.
C-Reactive Protein and Soluble Vascular Cell Adhesion Molecule-1 Are Associated With Elevated Urinary Albumin Excretion but Do Not Explain Its Link With Cardiovascular Risk

An elevated urinary albumin excretion rate (UAER) is associated with an increased risk of cardiovascular mortality, but the pathophysiological mechanism underlying this association is poorly understood. To investigate the role of endothelial dysfunction, leukocyte adhesion, and low-grade inflammation (1) in the development of elevated UAER (study I) and (2) in linking elevated UAER with risk of cardiovascular mortality (study II), we performed a prospective study in an age–, sex–, and glucose tolerance– stratified sample of a population-based cohort aged 50 to 75 years. High levels of von Willebrand factor, soluble vascular cell adhesion molecule-1 (sVCAM-1), and C-reactive protein (CRP) were used as markers of endothelial dysfunction, leukocyte adhesion, and low-grade inflammation, respectively. For study I, subjects who had normal UAER at baseline (n=316 subjects, 66 with type 2 diabetes) were reexamined after a mean follow-up of 6.1 years. The development of elevated UAER was defined as a mean albumin-to-creatinine ratio >2.0 mg/mmol at follow-up. Age–, sex–, and glucose tolerance– adjusted logistic regression analyses showed the development of elevated UAER to be significantly associated with levels of sVCAM-1 and CRP (odds ratio 1.14 [95% CI 1.02 to 1.27] per 10% increase of sVCAM-1 and odds ratio 1.17 [95% CI 1.04 to 1.32] per 50% increase of CRP). The results were not materially different after additional adjustment for hypertension, body mass index, cardiovascular disease, and creatinine clearance or stratification by the presence of diabetes. For study II, the vital status of all subjects (n= 575) was determined after a mean follow-up of 6.6 years. Eighty-one of 575 subjects died (30 died of cardiovascular disease). The presence of elevated UAER at baseline was associated with a 4.1-fold (1.94 to 8.73) increased risk of cardiovascular death after adjustment for age, sex, and glucose tolerance status. Adjustment for levels of von Willebrand factor, sVCAM-1, or CRP did not materially affect the results, nor did additional adjustment for the presence of hypertension, retinopathy, and cardiovascular disease and for levels of homocysteine, triglycerides, and high density lipoprotein cholesterol. Leukocyte adhesion (sVCAM-1) and low-grade inflammation (CRP) are determinants of the development of elevated UAER. However, these determinants do not explain the association between elevated UAER and cardiovascular mortality.
Use of EBV-based Vector/HVJ-liposome complex vector for targeted gene therapy of EBV-associated neoplasms.

Targeted suicide gene therapy for Epstein-Barr virus (EBV)-associated neoplasms was attempted by using EBV-based plasmid vectors coupled with hemagglutinating virus of Japan (HVJ)-liposome in vitro. Expression of EBV nuclear antigen (EBNA)1 is a common feature of the neoplasms associated with EBV. When various leukemic cell lines were transduced with a vector carrying a marker gene and EBV replication origin of plasmid (oriP), the marker gene product was exclusively detected in cells expressing EBNA1. Transduction of herpes simplex virus (HSV)-1 thymidine kinase (Tk) gene resulted in a marked reduction in viable cell number by ganciclovir (GCV) specifically in EBNA1 positive cells. The results demonstrate that this virus-free system may be applicable to gene therapy of EBV-associated neoplasms.
Jaw Osteonecrosis Associated with Use of Bisphosphonates and Chemotherapy: Paradoxical Complication of Treatment of Bone Lesions in Multiple Myeloma Patients

It has been demonstrated that bisphosphonate-based supportive therapy (pamidronate or zoledronate) reduces skeletal events (onset or progression of osteolytic lesions) both in patients with multiple myeloma (MM) and in cancer patients with bone metastasis. Bisphosphonates (eg, alendronate) are also indicated in the treatment of osteoporosis. Nevertheless, osteonecrosis of the jaw (ONJ) has been reported in some patients being treated with bisphosphonates. We present a series of 9 MM patients who developed ONJ after treatment with bisphosphonates and chemotherapy. All the patients in this case series had undergone tooth extraction for recurrent dental abscesses while taking bisphosphonates. We also review the diagnostic and therapeutic implications of this paradoxical complication associated with treatment of bone lesions in MM.
Pulmonary Physiology and Pathophysiology in Obesity Obesity and lung inflammation

Mancuso P. Obesity and lung inflammation. J Appl Physiol 108: 722–728, 2010. First published October 29, 2009; doi:10.1152/japplphysiol.00781. 2009. —The prevalence of obesity has increased dramatically worldwide, predisposing individuals to an increased risk of morbidity and mortality due to cardiovascular disease and type 2 diabetes. Less recognized is the fact that obesity may play a significant role in the pathogenesis of pulmonary diseases through mechanisms that may involve proinflammatory mediators produced in adipose tissue that contribute to a low-grade state of systemic inflammation. In animal models, inflammatory responses in the lung have been shown to influence the production of the adipocytokines, leptin and adiponectin, cytokines, acute phase proteins, and other mediators produced by adipose tissue that may participate in immune responses of the lung. An increased adipose tissue mass may also influence susceptibility to pulmonary infections, enhance pulmonary inflammation associated with environmental exposures, and exacerbate airway obstruction in preexisting lung disease. An increased understanding of the mechanisms by which obesity influences pulmonary inflammation may facilitate the development of novel therapeutic interventions for the treatment of lung disease.
Using a genetic algorithm to optimize problems with feasibility constraints

G.E. Liepins et al. (1990) have shown that genetic algorithm optimization of certain combinatorial optimization problems can be more effective when the genetic algorithm evaluates "repaired" versions of the chromosomes. In this sense "repairing" a chromosome means to take an illegal chromosome and force it to be legal through some repair function, Liepens does not however, advocate returning this "repaired" version of the chromosome to the population. Other researchers also advocate "repairing" illegal chromosomes, but they claim that returning the "repaired" version of the chromosome to the population "improves the convergence rates and solution quality". In this paper we show that a combination of these strategies supports another performance enhancing technique, a variety of Lamarckian evolution in which, with a small probability, original chromosomes are replaced in the population by their "repaired" counterparts. Using this strategy, replacing original chromosomes with a 5% probability, on three different combinatorial optimization problems, performance was better than either never replacing or always replacing. <<ETX>>
Avoiding performance fluctuation in cloud storage

Cloud computing is an elastic computing model whereby users can lease computing and storage resources on demand from a remote infrastructure. Cloud computing is gaining popularity due to its low cost, high reliability and wide availability. However, a serious impediment to its wider deployment is the relative lack of effective data management services. The relatively slow access to persistent data and large variability in cloud storage I/O performance, can significantly degrade the performance of data-intensive applications. This paper addresses the problem of I/O performance fluctuation and proposes an automatic optimization schema for cloud storage called AOSC, which utilizes data chunking, placement, and replication to achieve more stable and predictable performance. Our experimental results based on Amazon Elastic Cloud Computing (EC2) data center show that AOSC can improve the stability and help provide better performance guarantees for cloud computing.
Voted Spheres: An Online, Fast Approach to Large Scale Learning

In this paper, we introduce a novel, non-linear, fast, online algorithm for learning on large data sets. This algorithm, which we call Voted Spheres (VS) is a combination of hypersphere-fitting, and the idea of voting. The algorithm builds hyperspheres around points, with different hyperspheres belonging to different classes allowed to overlap. The advantages of the algorithm are that it is simple to implement, very efficient, and generalises well while being able to handle millions of data points. For the KDD intrusion detection data set consisting of 494,020 data points, the linear version of the algorithm requires under a minute on a standard desktop PC and achieves state of the art performance.
Waste minimization of fishery industry in Muara Angke, Jakarta: a comparison of chemical and biological silage processes

Rising environmental concerns on climate changes are causing an increasing attention on reducing wastes dumped to the landfills. As Indonesia’s marine fishery industry is in developing stage in its capacity and production systems which consequently increases generation of wastes. Approximately 25-35% of fish production will ultimately become residue or waste due to the unsophisticated technology of fish storage and processing facilities. Most of their wastes dumped in landfills which subsequently impact the environment. Waste minimization program like upcycling waste into the more useful product can be an option for not only dumping wastes dumped into the landfill but also subsequently reducing greenhouse gas emissions such as CO2 and methane. This study evaluated the biological and chemical processes of fish silage production using various additives, including molasses as a carbon source and formic acid. Experiments were conducted in five anaerobic reactors containing 10 kg of fish waste each; the observation period was 40 days. The results indicated that adding molasses (10%, 15%, and 20% in volume) and Lactobacillus plantarum to fish waste significantly influenced pH and water/ash content. On average, the silage process reduced around 38% of fish wastes dumped in a landfill.
Fucoxanthin and Its Metabolite Fucoxanthinol in Cancer Prevention and Treatment

Fucoxanthin is a carotenoid present in the chloroplasts of brown seaweeds. When ingested, it is metabolized mainly to fucoxanthinol by digestive enzymes of the gastrointestinal tract. These compounds have been shown to have many beneficial health effects, including anti-mutagenic, anti-diabetic, anti-obesity, anti-inflammatory and anti-neoplastic actions. In every cancer tested, modulatory actions of fucoxanthinol on viability, cell-cycle arrest, apoptosis and members of the NF-κB pathway were more pronounced than that of fucoxanthin. Anti-proliferative and cancer preventing influences of fucoxanthin and fucoxanthinol are mediated through different signalling pathways, including the caspases, Bcl-2 proteins, MAPK, PI3K/Akt, JAK/STAT, AP-1, GADD45, and several other molecules that are involved in cell cycle arrest, apoptosis, anti-angiogenesis or inhibition of metastasis. In this review, we address the mechanisms of action of fucoxanthin and fucoxanthinol according to different types of cancers. Current findings suggest that these compounds could be effective for treatment and/or prevention of cancer development and aggressiveness.
An Autoregressive Model-Based Particle Filtering Algorithms for Extraction of Respiratory Rates as High as 90 Breaths Per Minute From Pulse Oximeter

We present particle filtering (PF) algorithms for an accurate respiratory rate extraction from pulse oximeter recordings over a broad range: 12-90 breaths/min. These methods are based on an autoregressive (AR) model, where the aim is to find the pole angle with the highest magnitude as it corresponds to the respiratory rate. However, when SNR is low, the pole angle with the highest magnitude may not always lead to accurate estimation of the respiratory rate. To circumvent this limitation, we propose a probabilistic approach, using a sequential Monte Carlo method, named PF, which is combined with the optimal parameter search (OPS) criterion for an accurate AR model-based respiratory rate extraction. The PF technique has been widely adopted in many tracking applications, especially for nonlinear and/or non-Gaussian problems. We examine the performances of five different likelihood functions of the PF algorithm: the strongest neighbor, nearest neighbor (NN), weighted nearest neighbor (WNN), probability data association (PDA), and weighted probability data association (WPDA). The performance of these five combined OPS-PF algorithms was measured against a solely OPS-based AR algorithm for respiratory rate extraction from pulse oximeter recordings. The pulse oximeter data were collected from 33 healthy subjects with breathing rates ranging from 12 to 90 breaths/ min. It was found that significant improvement in accuracy can be achieved by employing particle filters, and that the combined OPS-PF employing either the NN or WNN likelihood function achieved the best results for all respiratory rates considered in this paper. The main advantage of the combined OPS-PF with either the NN or WNN likelihood function is that for the first time, respiratory rates as high as 90 breaths/min can be accurately extracted from pulse oximeter recordings.
Imaging Subduction Beneath Mount St. Helens: Implications for Slab Dehydration and Magma Transport

Mount St. Helens (MSH) is anomalously 35–50 km trenchward of the main Cascade arc. To elucidate the source of this anomalous forearc volcanism, the teleseismic‐scattered wavefield is used to image beneath MSH with a dense broadband seismic array. Two‐dimensional migration shows the subducting Juan de Fuca crust to at least 80‐km depth, with its surface only 68 ± 2 km deep beneath MSH. Migration and three‐dimensional stacking reveal a clear upper‐plate Moho east of MSH that disappears west of it. This disappearance is a result of both hydration of the mantle wedge and a westward change in overlying crust. Migration images also show that the subducting plate continues without break along strike. Combined with low temperatures inferred for the mantle wedge, this geometry greatly limits possible source regions for mantle melts that contribute to MSH magmas and requires lateral migration over large distances.
Red giant branch in near-infrared colour–magnitude diagrams – II. The luminosity of the bump and the tip

We present new empirical calibrations of the red giant branch (RGB) bump and tip based on a homogeneous near-infrared data base of 24 Galactic globular clusters. The luminosities of the RGB bump and tip in the J, H and K bands and their dependence on the cluster metallicity have been studied, yielding empirical relationships. By using recent transformations between the observational and theoretical planes, we also derived similar calibrations in terms of bolometric luminosity. Direct comparisons between updated theoretical models and observations show an excellent agreement. The empirical calibration of the RGB tip luminosity in the near-infrared passbands presented here is a fundamental tool to derive distances to galaxies far beyond the Local Group, in view of using the new ground-based adaptive optics facilities and, in the near future, the James Webb Space Telescope.
On beating the hybrid argument

The hybrid argument allows one to relate the distinguishability of a distribution (from uniform) to the predictability of individual bits given a prefix. The argument incurs a loss of a factor k equal to the bit-length of the distributions: ε-distinguishability implies ε/k-predictability. This paper studies the consequences of avoiding this loss - what we call "beating the hybrid argument" -- and develops new proof techniques that circumvent the loss in certain natural settings. Specifically, we obtain the following results: 1. We give an instantiation of the Nisan-Wigderson generator (JCSS '94) that can be broken by quantum computers, and that is o(1)-unpredictable against AC0. We conjecture that this generator indeed fools AC0. Our conjecture implies the existence of an oracle relative to which BQP is not in the PH, a longstanding open problem. 2. We show that the "INW" generator by Impagliazzo, Nisan, and Wigderson (STOC '94) with seed length O(log n log log n) produces a distribution that is 1/log n-unpredictable against poly-logarithmic width (general) read-once oblivious branching programs. Obtaining such generators where the output is indistinguishable from uniform is a longstanding open problem. 3. We identify a property of functions f, "resamplability," that allows us to beat the hybrid argument when arguing indistinguishability of [EQUATION] from uniform. This gives new pseudorandom generators for classes such as AC0[p] with a stretch that, despite being sub-linear, is the largest known. We view this as a first step towards beating the hybrid argument in the analysis of the Nisan-Wigderson generator (which applies [EQUATION] on correlated x1,.,xk) and proving the conjecture in the first item.
A Rank-Metric Approach to Error Control in Random Network Coding

The problem of error control in random linear network coding is addressed from a matrix perspective that is closely related to the subspace perspective of Rotter and Kschischang. A large class of constant-dimension subspace codes is investigated. It is shown that codes in this class can be easily constructed from rank-metric codes, while preserving their distance properties. Moreover, it is shown that minimum distance decoding of such subspace codes can be reformulated as a generalized decoding problem for rank-metric codes where partial information about the error is available. This partial information may be in the form of erasures (knowledge of an error location but not its value) and deviations (knowledge of an error value but not its location). Taking erasures and deviations into account (when they occur) strictly increases the error correction capability of a code: if mu erasures and delta deviations occur, then errors of rank t can always be corrected provided that 2t les d - 1 + mu + delta, where d is the minimum rank distance of the code. For Gabidulin codes, an important family of maximum rank distance codes, an efficient decoding algorithm is proposed that can properly exploit erasures and deviations. In a network coding application, where n packets of length M over F(q) are transmitted, the complexity of the decoding algorithm is given by O(dM) operations in an extension field F(qn).
An in Vivo Investigation of Brain Inflammation in Gulf War Illness with Integrated PET/MR Imaging

Abstract : This project is aimed at evaluating the contribution of brain glia to the pathophysiology of Gulf War Illness, as well as fibromyalgia (a functional pain disorder characterized by similar symptoms). So far we have completed administrative and regulatory review, and have begun subject enrollment. The first two participants have completed the study. An additional three participants were enrolled and found to be ineligible at the time of screening. Throughout the recruitment process, we have actively modified our inclusion criteria to address concerns of ambiguity as they have arisen. Recruitment has been slower than anticipated, but efforts are well underway to improve recruitment procedures. Additionally, we experienced recent delays as a result of the Martinos Center cyclotron undergoing repair for more than one month. However, the resolution of these hurdles is in sight, and we are confident that well soon be able to increase our recruitment rate and successfully complete the project within the expected timeframe.