Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Soil on Fecal Indicator Organisms in a Tidally Influenced Subtropical Environment

ABSTRACT The potential regrowth of fecal indicator bacteria released into coastal environments in recreational water bodies has been of concern, especially in tropical and subtropical areas where the number of these bacteria can be artificially elevated beyond that from fecal impacts alone. The task of determining the factors that influence indicator bacterial regrowth was addressed though a series of field sampling and laboratory experiments using in situ densities of Escherichia coli, enterococci, and Clostridium perfringens in river water, sediment, and soil. Field sampling efforts included the collection of surface sediments along the cross section of a riverbank, a 20-cm-deep soil core, and additional surface soils from remote locations. In addition to field sampling, two types of laboratory experiments were conducted. The first experiment investigated the survival of bacteria already present in river water with the addition of sterile and unsterile sediment. The second experiment was designed to simulate the wetting and drying effects due to tidal cycles. The results from the sampling study found elevated numbers of E. coli and C. perfringens in surficial sediments along the riverbank near the edge of the water. C. perfringens was found in high numbers in the subsurface samples obtained from the soil core. Results from laboratory experiments revealed a significant amount of regrowth for enterococci and E. coli with the simulation of tides and addition of sterile sediment. Regrowth was not observed for C. perfringens. This study demonstrates the need to further evaluate the characteristics of indicator microbes within tropical and subtropical water systems where natural vegetation, soil embankments, and long-term sediment accumulation are present. In such areas, the use of traditional indicator microbes to regulate recreational uses of a water body may not be appropriate.
Setting and within-class ability grouping

Within the United Kingdom and internationally, the practice of separating pupils by ability endures as a characteristic feature of mathematics and science classrooms. Although there is extensive international research literature on ability grouping within classroom-based subjects, limited research exists in the context of physical education (PE). The purpose of this paper is to explore ability grouping in PE in North East of England schools. Specifically, the paper examined the prevalence of setting and within-class ability grouping in PE, the contexts of its use, how sets and within-class ability grouping were established, and the rationales used to justify decisions about setting and within-class ability grouping in the subject. Data were collected via a web-based survey. The electronic survey was sent to 194 PE Heads of Department from North East of England schools catering for pupils in Key Stage 3 (ages 11–14) and/or Key Stage 4 (ages 14–16). The results indicated that setting is embedded in the organisational and pedagogical practices of PE in many secondary schools. Ability also served as a basis upon which to organise pupils within mixed-ability and setted PE lessons. A variety of other factors, including friendship and behaviour, were also reported as factors influencing grouping of pupils in PE lessons. Our discussion directs attention to issues arising for policy and practice in PE and points to the merits of further exploration and analysis of between-class and within-class grouping practices in the subject.
The Adaptive Lasso and Its Oracle Properties

The lasso is a popular technique for simultaneous estimation and variable selection. Lasso variable selection has been shown to be consistent under certain conditions. In this work we derive a necessary condition for the lasso variable selection to be consistent. Consequently, there exist certain scenarios where the lasso is inconsistent for variable selection. We then propose a new version of the lasso, called the adaptive lasso, where adaptive weights are used for penalizing different coefficients in the ℓ1 penalty. We show that the adaptive lasso enjoys the oracle properties; namely, it performs as well as if the true underlying model were given in advance. Similar to the lasso, the adaptive lasso is shown to be near-minimax optimal. Furthermore, the adaptive lasso can be solved by the same efficient algorithm for solving the lasso. We also discuss the extension of the adaptive lasso in generalized linear models and show that the oracle properties still hold under mild regularity conditions. As a byproduct of our theory, the nonnegative garotte is shown to be consistent for variable selection.
Horizontal transfer of chloroplast genomes between plant species

The genomes of DNA-containing cell organelles (mitochondria, chloroplasts) can be laterally transmitted between organisms, a process known as organelle capture. Organelle capture often occurs in the absence of detectable nuclear introgression, and the capture mechanism is unknown. Here, we have considered horizontal genome transfer across natural grafts as a mechanism underlying chloroplast capture in plants. By grafting sexually incompatible species, we show that complete chloroplast genomes can travel across the graft junction from one species into another. We demonstrate that, consistent with reported phylogenetic evidence, replacement of the resident plastid genome by the alien genome occurs in the absence of intergenomic recombination. Our results provide a plausible mechanism for organelle capture in plants and suggest natural grafting as a path for horizontal gene and genome transfer between sexually incompatible species.
Oxidized LDL and the risk of coronary heart disease: results from the MONICA/KORA Augsburg Study.

BACKGROUND Oxidative stress plays a critical role in the initiation and progression of atherosclerosis. Oxidized LDL (oxLDL) is a marker of oxidative stress. We prospectively investigated whether increased serum oxLDL concentrations are associated with incident coronary heart disease (CHD). METHODS We conducted a prospective population-based case-cohort study within the MONICA/KORA Augsburg studies. Serum oxLDL concentrations were measured in 333 case individuals with incident CHD and in 1727 noncase individuals selected from a source population of 9300 middle-aged, healthy men and women. The mean (SD) follow-up time was 10.8 (4.6) years. RESULTS Baseline oxLDL concentrations were higher in case individuals than in noncase individuals (P < 0.001). After adjustment for age, sex, survey, smoking status, systolic blood pressure, physical activity, diabetes, body mass index, parental history of myocardial infarction, and alcohol consumption, the hazard ratio (HR) for comparing the first and third tertiles was 1.87 (95% CI, 1.33-2.64; P < 0.001). Additional adjustment for lipid parameters, inflammatory markers, and markers of endothelial dysfunction attenuated the association (HR, 1.29; 95% CI, 0.88-1.89; P = 0.087). We observed no significant interactions between oxLDL and sex or being overweight. CONCLUSIONS Increased oxLDL concentrations were associated with an increased risk for incident CHD. Nevertheless, because this effect became nonsignificant after adjustment for covariates, particularly the ratio of total cholesterol to HDL cholesterol, it may be mediated primarily by lipid parameters. Further studies are warranted to clarify this issue.
Enhancing Tumor Targeting and Apoptosis Using Noncovalent Antibody Homodimers

A rare type of antibody that spontaneously binds to each self (homodimerizes) has been described. This self-binding (autophilic) antibody provides stronger protection against bacterial infection than a non self-binding antibody with identical specificity and affinity due to increase of polymeric avidity. A peptide derived from the self-binding domain of the autophilic antibody was crosslinked to the Fc carbohydrate of two monoclonal antibodies specific for the B-cell receptor (BCR) of a murine and a human B-cell tumor. Peptide-crosslinked antibodies bind to themselves on solid phase ELISA as homodimer and establish in solution a monomer-dimer equilibrium. Autophilic antibodies bind to their respective tumor target cells with increased efficiency as determined by FACS analysis. They also induce twice the amount of apoptosis of target tumor cells than the control antibodies. Furthermore, the modified antibodies inhibit tumor growth in culture more efficiently than the control antibodies. Criss-cross protocols in FACS, apoptosis, and growth inhibition indicate the specificity of targeting the BCR with autophilic antitumor antibodies. The chemical approach of increasing the binding of antibodies without creating chemically crosslinked dimers mimics naturally occurring autophilic antibodies and represents a simple and attractive alternative to chemical dimerizing and antibody engineering techniques for improving their antitumor effect. Furthermore, these results provide a guide to incorporate the self-binding peptide into the structure of antibodies using modeling and molecular crafting techniques.
Development of octreotide-conjugated polymeric prodrug of bufalin for targeted delivery to somatostatin receptor 2 overexpressing breast cancer in vitro and in vivo

Background Development of polymeric prodrugs of small molecular anticancer drugs has become one of the most promising strategies to overcome the intrinsic shortcomings of small molecular anticancer drugs and improve their anticancer performance. Materials and methods In the current work, we fabricated a novel octreotide (Oct)-modified esterase-sensitive tumor-targeting polymeric prodrug of bufalin (BUF) and explored its anticancer performance against somatostatin receptor 2 overexpressing breast cancer. Results The obtained tumor-targeting polymeric prodrug of BUF, P(oligo[ethylene glycol] monomethyl ether methacrylate [OEGMA]-co-BUF-co-Oct), showed a nanosize dimension and controlled drug release features in the presence of esterase. It was demonstrated by in vitro experiment that P(OEGMA-co-BUF-co-Oct) showed enhanced cytotoxicity, cellular uptake, and apoptosis in comparison with those of free BUF. In vivo experiment further revealed the improved accumulation of drugs in tumor tissues and enhanced anticancer performance of P(OEGMA-co-BUF-co-Oct). Conclusion Taken together, this study indicated that polymeric prodrug of BUF holds promising potential toward the treatment of somatostatin receptor 2 overexpressing breast cancer.
Br Ief Definitive Repor T

Myeloid DC subsets play specialized roles in tolerance induction during homeostasis and in protective immunity during infection. Several recent studies have focused on DCs in the dermis, intestines, lung, liver, kidney , and pancreas that express the integrin E7 (CD103; Ginhoux, et al., 2009). In the dermis, lung, liver, and kidney, these cells coexpress the C type lectin langerin, and are CD11b low or negative. Dermal langerin + CD103 + CD11b lo-neg DCs have been implicated in CD4 + and CD8 + T cell priming after epicutaneous immunization (Bursch Pulmonary langerin + CD103 + DCs are required for optimal clearance of influenza virus (GeurtsvanKessel et al., 2008). The recognition that the langerin + CD103 + DC subset might be particularly adept at inducing certain forms of T cell immunity has stimulated interest in its developmental lineage and biological properties. GM-CSF is a growth factor that promotes the differentiation and mobilization of myeloid cells in vivo (Hamilton and Anderson, 2004; King et al., 2009). It is widely used in vitro to stimulate the development of DCs from bone marrow precursors (Inaba et al., 1992). Studies with GM-CSF–deficient mice and WT mice treated with anti–GM-CSF neutralizing antibodies have established a nonredundant role of this cyto-kine in the generation of protective immunity against a range of microbes, as well as pathological immunity against self-antigens. Hence, GM-CSF / mice succumb to infection with Mycobacteria and Streptococcus and are resistant to the induction of experimental autoimmune en-cephalomyelitis (EAE), collagen-induced arthritis , and autoimmune myocarditis (LeVine et al.
The Cramér-Rao Bound for Estimating a Sparse Parameter Vector

The goal of this contribution is to characterize the best achievable mean-squared error (MSE) in estimating a sparse deterministic parameter from measurements corrupted by Gaussian noise. To this end, an appropriate definition of bias in the sparse setting is developed, and the constrained Cramer-Rao bound (CRB) is obtained. This bound is shown to equal the CRB of an estimator with knowledge of the support set, for almost all feasible parameter values. Consequently, in the unbiased case, our bound is identical to the MSE of the oracle estimator. Combined with the fact that the CRB is achieved at high signal-to-noise ratios signal-to-noise ratio (SNRs) by the maximum likelihood technique, our result provides a new interpretation for the common practice of using the oracle estimator as a gold standard against which practical approaches are compared.
Optimal schedules for parallel prefix computation with bounded resources

Given x 1 ; . ; x N , parallel pre x computes x 1 x 2 . x k , for 1 k N , with associative operation . We show optimal schedules for parallel pre x computation with a xed number of resources p 2 for a pre x of size N p(p + 1)=2 . The time of the optimal schedules with p resources is d2N=(p + 1)e for N p(p + 1)=2, which we prove to be the strict lower bound(i.e., which is what can be achieved maximally). We then present a pipelined form of optimal schedules with d2N=(p + 1)e + d(p 1)=2e 1 time, which takes a constant overhead of d(p 1)=2e time more than the optimal schedules. Parallel pre x is an important common operation in many algorithms including the evaluation of polynomials, general Hornor expressions, carry look-ahead circuits and ranking and packing problems. A most important application of parallel pre x is loop parallelizing transformation.
Biosurfactant-and-Bioemulsifier Produced by a Promising Cunninghamella echinulata Isolated from Caatinga Soil in the Northeast of Brazil

A Mucoralean fungus was isolated from Caatinga soil of Pernambuco, Northeast of Brazil, and was identified as Cunninghamella echinulata by morphological, physiological, and biochemical tests. This strain was evaluated for biosurfactant/bioemulsifier production using soybean oil waste (SOW) and corn steep liquor (CSL) as substrates, added to basic saline solution, by measuring surface tension and emulsifier index and activity. The best results showed the surface water tension was reduced from 72 to 36 mN/m, and an emulsification index (E24) of 80% was obtained using engine oil and burnt engine oil, respectively. A new molecule of biosurfactant showed an anionic charge and a polymeric chemical composition consisting of lipids (40.0% w/w), carbohydrates (35.2% w/w) and protein (20.3% w/w). In addition, the biosurfactant solution (1%) demonstrated its ability for an oil displacement area (ODA) of 37.36 cm2, which is quite similar to that for Triton X-100 (38.46 cm2). The stability of the reduction in the surface water tension as well as of the emulsifier index proved to be stable over a wide range of temperatures, in pH, and in salt concentration (4%–6% w/v). The biosurfactant showed an ability to reduce and increase the viscosity of hydrophobic substrates and their molecules, suggesting that it is a suitable candidate for mediated enhanced oil recovery. At the same time, these studies indicate that renewable, relatively inexpensive and easily available resources can be used for important biotechnological processes.
The role of community pharmacists in patient counseling and health education: a survey of their knowledge and level of involvement in relation to type 2 diabetes mellitus

Purpose The present study aimed at evaluating the knowledge and level of involvement of community pharmacists in the provision of patient counseling and health education services for patients with DM and perceived barriers that limit the delivery of such services. Materials and methods A self-administered questionnaire based-survey was undertaken from January to March, 2017 with 412 pharmacists working in community pharmacies in six cities of Amhara regional state of Ethiopia: Debre Markos, Gondar, Dessie, Bahir Dar, Woldya, and Debre Birhan. Descriptive statistics, ANOVA, and Student’s t-test were employed to examine different variables. Results Community pharmacists were found to have poor knowledge and low level of involvement, with an overall mean score of 11.54 and 2.06, respectively. A significant number of community pharmacists never practiced promoting smoking cessation (45.2%), counseling on good foot care techniques (33.7%), and counseling on the potential impact of over–the-counter and herbal drugs on DM management (34%). On the other hand, describing the right time to administer antidiabetic medications (46%) and counseling on suitable administration, handling, and storage of insulin (33.7%) were done more frequently. The main reported barriers to the delivery of these services were lack of knowledge or clinical skills, lack of access to additional training programs, and lack of personnel or resources. Conclusion The present study revealed a poor knowledge and low level of involvement in counseling and health education services for patients with DM. Lack of knowledge or clinical skills was the most commonly reported barrier for providing such services. In order to better integrate community pharmacies into future public health programs and optimize the contribution of pharmacists, interventions should focus on overcoming the identified barriers.
Brain potentials predict substance abuse treatment completion in a prison sample

National estimates suggest that up to 80% of prison inmates meet diagnostic criteria for a substance use disorder. Because more substance abuse treatment while incarcerated is associated with better post‐release outcomes, including a reduced risk of accidental overdose death, the stakes are high in developing novel predictors of substance abuse treatment completion in inmate populations.
Sparse Recovery with Fusion Frames via RIP

—We extend ideas from compressive sensing to a structured sparsity model related to fusion frames. We present theoretical results concerning the recovery of sparse signals in a fusion frame from undersampled measurements. We provide both nonuniform and uniform recovery guarantees. The novelty of our work is to exploit an incoherence property of the fusion frame which allows us to reduce the number of measurements needed for sparse recovery.
The transcription factor PU.1 is critical for viability and function of human brain microglia

Microglia are the predominant resident immune cells of the brain and can assume a range of phenotypes. They are critical for normal brain development and function but can also contribute to many disease processes. Although they are widely studied, the transcriptional control of microglial phenotype and activation requires further research. PU.1 is a key myeloid transcription factor expressed by peripheral macrophages and rodent microglia. In this article, we report the presence of PU.1 specifically in microglia of the adult human brain and we examine its functional role in primary human microglia. Using siRNA, we achieved substantial PU.1 protein knock‐down in vitro. By assessing a range of characteristic microglial proteins we found decreased viability of adult human microglia with reduced PU.1 protein expression. This observation was confirmed with PU.1 antisense DNA oligonucleotides. An important function of microglia is to clear debris by phagocytosis. We assessed the impact of loss of PU.1 on microglial phagocytosis and show that PU.1 siRNA reduces the ability of adult human microglia to phagocytose amyloid‐beta1‐42 peptide. These results show that PU.1 controls human microglial viability and function and suggest PU.1 as a molecular target for manipulation of human microglial phenotype.
Learning Topic Models and Latent Bayesian Networks Under Expansion Constraints

Author(s): Anandkumar, Animashree; Hsu, Daniel; Javanmard, Adel; Kakade, Sham M | Abstract: Unsupervised estimation of latent variable models is a fundamental problem central to numerous applications of machine learning and statistics. This work presents a principled approach for estimating broad classes of such models, including probabilistic topic models and latent linear Bayesian networks, using only second-order observed moments. The sufficient conditions for identifiability of these models are primarily based on weak expansion constraints on the topic-word matrix, for topic models, and on the directed acyclic graph, for Bayesian networks. Because no assumptions are made on the distribution among the latent variables, the approach can handle arbitrary correlations among the topics or latent factors. In addition, a tractable learning method via $\ell_1$ optimization is proposed and studied in numerical experiments.
Quantifying the security of graphical passwords: the case of android unlock patterns

Graphical passwords were proposed as an alternative to overcome the inherent limitations of text-based passwords, inspired by research that shows that the graphical memory of humans is particularly well developed. A graphical password scheme that has been widely adopted is the Android Unlock Pattern, a special case of the Pass-Go scheme with grid size restricted to 3x3 points and restricted stroke count. In this paper, we study the security of Android unlock patterns. By performing a large-scale user study, we measure actual user choices of patterns instead of theoretical considerations on password spaces. From this data we construct a model based on Markov chains that enables us to quantify the strength of Android unlock patterns. We found empirically that there is a high bias in the pattern selection process, e.g., the upper left corner and three-point long straight lines are very typical selection strategies. Consequently, the entropy of patterns is rather low, and our results indicate that the security offered by the scheme is less than the security of only three digit randomly-assigned PINs for guessing 20% of all passwords (i.e., we estimate a partial guessing entropy G_0.2 of 9.10 bit). Based on these insights, we systematically improve the scheme by finding a small, but still effective change in the pattern layout that makes graphical user logins substantially more secure. By means of another user study, we show that some changes improve the security by more than doubling the space of actually used passwords (i.e., increasing the partial guessing entropy G_0.2 to 10.81 bit).