Miracle-dz/UniFAR-FTUs huggingface dataset:
Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

We introduce Dirichlet multinomial mixtures (DMM) for the probabilistic modelling of microbial metagenomics data. This data can be represented as a frequency matrix giving the number of times each taxa is observed in each sample. The samples have different size, and the matrix is sparse, as communities are diverse and skewed to rare taxa. Most methods used previously to classify or cluster samples have ignored these features. We describe each community by a vector of taxa probabilities. These vectors are generated from one of a finite number of Dirichlet mixture components each with different hyperparameters. Observed samples are generated through multinomial sampling. The mixture components cluster communities into distinct ‘metacommunities’, and, hence, determine envirotypes or enterotypes, groups of communities with a similar composition. The model can also deduce the impact of a treatment and be used for classification. We wrote software for the fitting of DMM models using the ‘evidence framework’ (http://code.google.com/p/microbedmm/). This includes the Laplace approximation of the model evidence. We applied the DMM model to human gut microbe genera frequencies from Obese and Lean twins. From the model evidence four clusters fit this data best. Two clusters were dominated by Bacteroides and were homogenous; two had a more variable community composition. We could not find a significant impact of body mass on community structure. However, Obese twins were more likely to derive from the high variance clusters. We propose that obesity is not associated with a distinct microbiota but increases the chance that an individual derives from a disturbed enterotype. This is an example of the ‘Anna Karenina principle (AKP)’ applied to microbial communities: disturbed states having many more configurations than undisturbed. We verify this by showing that in a study of inflammatory bowel disease (IBD) phenotypes, ileal Crohn's disease (ICD) is associated with a more variable community.
Learning Accurate and Concise Näıve Bayes Classifiers from Attribute Value Taxonomies and Data 1

In many application domains, there is a need for learning algorithms that can effectively exploit attribute value taxonomies (AVT) hierarchical groupings of attribute values to learn compact, comprehensible, and accurate classifiers from data including data that are partially specified. This paper describes AVT-NBL, a natural generalization of the Näıve Bayes learner (NBL), for learning classifiers from AVT and data. Our experimental results show that AVT-NBL is able to generate classifiers that are substantially more compact and more accurate than those produced by NBL on a broad range of data sets with different percentages of partially specified values. We also show that AVT-NBL is more efficient in its use of training data: AVT-NBL produces classifiers that outperform those produced by NBL using substantially fewer training examples.
A Regularity Lemma, and Low-Weight Approximators, for Low-Degree Polynomial Threshold Functions

We give a "regularity lemma" for degree-d polynomial threshold functions (PTFs) over the Boolean cube {−1,1}^n. Roughly speaking, this result shows that every degree-d PTF can be decomposed into a constant number of subfunctions such that almost all of the subfunctions are close to being regular PTFs. Here a "regular" PTF is a PTF sign(p(x)) where the influence of each variable on the polynomial p(x) is a small fraction of the total influence of p. As an application of this regularity lemma, we prove that for any constants d >= 1, eps > 0, every degree-d PTF over n variables can be approximated to accuracy eps by a constant degree PTF that has integer weights of total magnitude O(n^d). This weight bound is shown to be optimal up to logarithmic factors.
Identiﬁcation and Characterization of Small-Molecule Inhibitors of Yop Translocation in Yersinia pseudotuberculosis (cid:1)

Type three secretion systems (TTSSs) are virulence factors found in many pathogenic Gram-negative species, including the family of pathogenic Yersinia spp. Yersinia pseudotuberculosis requires the translocation of a group of effector molecules, called Yops, to subvert the innate immune response and establish infection. Polarized transfer of Yops from bacteria to immune cells depends on several factors, including the presence of a functional TTSS, the successful attachment of Yersinia to the target cell, and translocon insertion into the target cell membrane. Here we employed a high-throughput screen to identify small molecules that block translocation of Yops into mammalian cells. We identiﬁed 6 compounds that inhibited translocation of effectors without affecting synthesis of TTSS components and secreted effectors, assembly of the TTSS, or secretion of effectors. One compound, C20, reduced adherence of Y. pseudotuberculosis to target cells. Addi-tionally, the compounds caused leakage of Yops into the supernatant during infection and thus reduced polarized translocation. Furthermore, several molecules, namely, C20, C22, C24, C34, and C38, also inhibited ExoS-mediated cell rounding, suggesting that the compounds target factors that are conserved between Pseudomonas aeruginosa and Y. pseudotuberculosis . In summary, we have identiﬁed 6 compounds that speciﬁcally inhibit translocation of Yops into mammalian cells but
Overlay Optimization for Mesh-based Peer-to-peer Streaming Applications

Mesh-based peer-to-peer (P2P) streaming has proven to be a robust and scalable way for delivering live video streams over the Internet. In this paper, we investigate the overlay optimization problem for mesh-based peer-to-peer streaming. By modeling the peer-to-peer overlay as a directed graph, we propose a new overlay optimization method that imposes a strict partial order on the P2P overlay. The partial order can be defined according to different capability metrics of the heterogeneous peers. We have also designed overlay construction and optimization protocols that can promote large capability nodes to higher levels while keeping the overlay robust and efficient. Experimental results show that our optimization method can efficiently promote the high performance peers and improve efficiency in the P2P overlays. Compared with the non-optimized case, the P2P streaming applications that use our method have reduced average latency by 25-40% and increased acceptance rate up to 125%.
Finite-difference Modeling of High-frequency Rayleigh Waves

The finite-difference (FD) method described here is specially developed to model high-frequency Rayleigh-wave propagation in near-surface mediums. Although many FD programs existed for earthquake research and oil exploration, none has been developed to model high-frequency Rayleigh-wave propagation in near-surface elastic mediums when the source and all receivers are on the free-surface. The scheme described here uses the second-order staggered grid, based on a set of first-order differential equations. Special implementations of combined elastic and acoustic free-surface conditions were developed, which were originally derived from surface wave propagation in a transversely isotropic medium. A combination of one-way sponge filtering and anisotropic filtering methods was used to minimize Rayleigh-wave reflections from artificial boundaries. Numerical stability was achieved by using a small spatial grid size and time step. This new FD method was tested and proved satisfactory using dispersion analysis of Rayleigh waves in a homogenous and layered half-space. The present study provides a practical tool for improving the confidence and uniqueness of deriving 2D interpretation of high-frequency Rayleigh-wave data, and makes successful in the first phase to 2D inversion.
An investigation into stress factors and levels of stress as perceived by regular classroom teachers of Newfoundland and Labrador

This study was designed to: (1) identify elements in the teaching environment which regular classroom teachers in Newfoundland and Labrador perceive as being stressful; (2) determine to what degree stress is being experienced by teachers; (3) compare the findings in (1) and (2) for teachers of the three teaching levels, primary, elementary, and high school; (4) examine the different biographical subgroups. -- A review of the literature revealed the current theories of stress and the approaches used to measure stress as experienced by individuals of the teaching profession. -- The instrument used in this study was the Wilson Stress Profile for Teachers, published in 1979, by Dr. Christopher Wilson. To supplement this scale, an additional section, consisting of items relating to unique provincial concerns, titled the Local Scale, was included, as was a biographical information sheet. -- The sample consisted of 582 teachers from all school boards in the province, comprised of representative numbers of primary, elementary and secondary teachers. -- Issues of Time Management, Parent/Teacher Relations and Intrapersonal Conflicts, in that order, were perceived as being the most stressful by teachers of all categories. The teachers reported difficulties in the preparation, delivery, and evaluation of classroom work; also, parental attitudes and pressures were cited as major sources of concern. -- The stress levels reported represented a high moderate degree of stress. The degree to which regular classroom teachers experienced stress, as measured by the WSPT and the Local Scale, revealed no significant differences between the teacher categories of primary, elementary, and secondary. It has been concluded, based upon the results of this study, that, regardless of teaching level, teachers are perceiving and experiencing the same amount of stress. -- The biographical variables studied did not vary in their contribution to the total level of stress; however, variations were revealed upon analysis of the components of each variable with regards to the sample population and teacher category. The results also revealed that perceived stress was related to physiological and psychological well-being. -- As a result of these findings, recommendations were made for further study and for action to be taken, in order to better understand, cope with and utilize the phenomenon of stress.
Examining Hacker Participation Length in Cybercriminal Internet-Relay-Chat Communities

Abstract To further cybersecurity, there is interest in studying online cybercriminal communities to learn more about emerging cyber threats. Literature documents the existence of many online Internet Relay Chat (IRC) cybercriminal communities where cybercriminals congregate and share hacking tools, malware, and more. However, many cybercriminal community participants appear unskilled and have fleeting interests, making it difficult to detect potential long-term or key participants. This is a challenge for researchers and practitioners to quickly identify cybercriminals that may provide credible threat intelligence. Thus, we propose a computational approach to analyze cybercriminals IRC communities in order to identify potential long-term and key participants. We use the extended Cox model to scrutinize cybercriminal IRC participation for better understanding of behaviors exhibited by cybercriminals of importance. Results indicate that key cybercriminals may be quickly identifiable by assessing the scale of their interaction and networks with other participants.
Why Parents Worry: Initiation into Cannabis Use by Youth and Their Educational Attainment

In this paper we use individual level data from the Australian National Drug Strategy Household Survey to study the relationship between initiation into cannabis use and educational attainment. Using bivariate duration analysis we find that those initiating into cannabis use are much more likely to dropout of school, and that the reduction in years of education depends on the age at which initiation into cannabis occurs. We also find that the impact of cannabis uptake is larger for females than males.
Health status and clinical practice: when will they meet?

In Crossing the Quality Chasm: A New Health System for the 21st Century , the Institute of Medicine proposes 6 specific aims to improve the quality of care in the United States.1 These specific aims are to provide care that is safe, effective, timely, efficient, equitable, and patient centered. Of these goals, patient-centered care has received the least attention from both the scientific community and practicing clinicians. Patient-centered care gives patients opportunities to be “involved in medical decision making,” and guides care providers “in attending to their patients’ physical and emotional needs, and maintaining or improving their quality of life. ”1 See p 43 To promote patient-centered care, clinicians should measure the health status of their patients with the use of standardized surveys, and then use this information to assist in clinical decision-making. There have been significant advances in health status surveys, and these measures are increasingly being used as primary outcomes in clinical trials. Yet formal health status measures are rarely, if ever, used in clinical practice. The reasons for this apparent gap between research and clinical practice are complex but likely include a lack of understanding of the definition of health status, a lack of familiarity with health status surveys, a perception that these measures are “soft,” and most importantly, a lack of acceptance that health status measures may be useful in clinical practice. Health status is the impact of disease on patient function as reported by the patient. More specifically, health status can be defined as the range of manifestation of disease in a given patient including symptoms, functional limitation, and quality of life, in which quality of life is the discrepancy between actual and desired function (Figure 1). An important point here is that clinicians are traditionally focused on the diagnosis of disease and evaluation …
Serological study of a population of alpine chamois (Rupkapra rrupkapra) affected by an outbreak of respiratory disease

A serological survey of respiratory virus infections was carried out from 1998 to 2001 in Lecco province, Italy, as part of a health monitoring programme in a population of alpine chamois, many of which died of pneumonia in autumn and winter 2000 to 2001; 194 carcases of all age classes were found over a short period and in a small area. Eighteen of them, which were examined postmortem, consistently showed signs of severe fibrinous lobar pneumonia or catarrhal bronchopneumonia. Samples of serum from 145 chamois collected from hunted animals and carcases were tested by a virus neutralisation test against bovine respiratory syncytial virus (BRsv), bovine viral diarrhoea virus, bovine herpesvirus type 1 and parainfluenzavirus type 3. Positive results were detected only for BRSV. The area was divided into two subunits on the basis of the distribution of deaths; in the areas where fatalities were observed there was a significant increase of BRSV titres at the beginning of the outbreal. Furthermore, during the 2000 and 2001 hunting seasons antibody titres to BRSV were significantly higher in the areas where mortality occurred. The roe deer living in the same area were not affected by pneumonia and had a low prevalence of titres to BRSV which did not vary during the period of the study.
Deoxypodophyllotoxin Induces G2/M Cell Cycle Arrest and Apoptosis in SGC-7901 Cells and Inhibits Tumor Growth in Vivo

Deoxypodophyllotoxin (DPT), a natural microtubule destabilizer, was isolated from Anthriscus sylvestris, and a few studies have reported its anti-cancer effect. However, the in vivo antitumor efficacy of DPT is currently indeterminate. In this study, we investigated the anti-gastric cancer effects of DPT both in vitro and in vivo. Our data showed that DPT inhibited cancer cell proliferation and induced G2/M cell cycle arrest accompanied by an increase in apoptotic cell death in SGC-7901 cancer cells. In addition, DPT caused cyclin B1, Cdc2 and Cdc25C to accumulate, decreased the expression of Bcl-2 and activated caspase-3 and PARP, suggesting that caspase-mediated pathways were involved in DPT-induced apoptosis. Animal studies revealed that DPT significantly inhibited tumor growth and decreased microvessel density (MVD) in a xenograft model of gastric cancer. Taken together, our findings provide a framework for further exploration of DPT as a novel chemotherapeutic for human gastric cancer.
Cocaine- and Amphetamine-regulated Transcript (CART) Is Expressed in Several Islet Cell Types During Rat Development

Cocaine- and amphetamine-regulated transcript (CART) is an anorexigenic peptide widely expressed in the central and peripheral, including the enteric, nervous systems. CART is also expressed in pituitary endocrine cells, adrenomedullary cells, islet somatostatin cells, and in rat antral gastrin cells. We used immunocytochemistry (IHC) and in situ hybridization (ISH) to study CART expression in developing rat pancreas. We also examined co-expression of CART and islet hormones and developmental markers and the effect of CART on proliferation using clonal insulin cells (INS-1 832/13). A major portion of each of the islet cell types, except the ghrelin cells, expressed CART during a period before and around birth. Two weeks postnatally, CART expression was restricted to somatostatin cells. Pre- and early postnatally, many of the CART-expressing cells co-expressed cytokeratin 20 (CK20), a marker of duct cells and islet precursor cells, the trophic hormone gastrin, and a smaller subpopulation also harbored the proliferation marker Ki67. CART was also expressed in pancreatic nerve fibers, both sensory and autonomic, and in ganglion nerve cell bodies. Although highly expressed in the developing islets, CART did not affect proliferation of INS-1 cells. We have demonstrated that CART is expressed in several islet cell types during rat development but is restricted to somatostatin cells and neurons in the adult rat.
Physicians' Colorectal Cancer Screening Discussion and Recommendation Patterns

Background: Primary care physician (PCP) actions are pivotal to colorectal cancer (CRC) screening performance, and guidelines recommend discussion with patients about test options and potential benefits and harms. This article profiles patterns of discussion about and recommendations for screening and explores potential associations with multilevel factors (patient, clinician, practice, and environment). Methods: In 2009, we analyzed data from 1,266 physicians responding to the 2006–2007 National Survey of Primary Care Physicians' Recommendations and Practices for Breast, Cervical, Colorectal, and Lung Cancer Screening (absolute response rate = 69.3%; cooperation rate = 75.0%). Descriptive statistics examined physicians' reports of discussion and recommendations. Multivariate analyses assessed the associations of these practices with multilevel factors. Results: Although few respondents reported discussion of all options, 46% usually discuss more than one option; the vast majority of these respondents discuss fecal occult blood testing (FOBT) and colonoscopy (49%) or FOBT, sigmoidoscopy, and colonoscopy (32%). Of physicians who discuss more than one option, a majority reported usually recommending one or more test options, most commonly colonoscopy alone (43%) and FOBT and colonoscopy (43%). Several personal characteristics (specialty), perceived patient characteristics (prefer physician to decide), practice characteristics (geographic location), and community barriers (specialist availability) were independently associated with discussion and/or recommendation patterns. Conclusions: PCPs do not discuss the full menu of test options, but many report selecting one or two options for discussion and recommendation. To ensure that patients' perspectives and concerns are elicited and considered, patient decision-making approaches should be considered. Impact: Attention to informed decision making in CRC screening will be important for enhancing patient-centered quality care. Cancer Epidemiol Biomarkers Prev; 20(3); 509–21. ©2011 AACR.
Induction machine speed control using fuzzy adaptive controller

This paper investigates fuzzy adaptive control of induction machine (IM) speed. The proposed controller consists of two parts: the first is classical fuzzy logic controller (FLC) constituted by fuzzy If-Then rules. The second part is adaptation mechanism, which adjusts the fuzzy controller parameters in order to minimize the error between the reference speed and the machine speed. The fuzzy adaptive controller (FAC) can be started without prior information on the machine, and can learn and tune rapidly the fuzzy controller rules to meet the desired performance, even when the machine parameters change. Simulation studies for various operating conditions show the superior performance of the FAC compared to PI controller.
Why are there virtually no mandatory open access policies at American universities?

Key points U.S. university OA policies are far less mandatory than those in the U.K. The waiver clauses in U.S. university policies make it easy for authors to decline making their articles OA. The relative autonomy – and competitiveness – of U.S. universities may be the reason for weaker OA policies. OA in the U.S. is likely to be driven by government funding agency policies rather than by academia.
Toward a Calculus of Meaning: Studies in markedness, distinctive features and deixis

1. Contributors 2. Introduction 3. I: Theoretical and Methodological Overview 4. 1. Phoneme and Morpheme and the sign Nature of Language (by Schooneveld, Cornelis H. van) 5. 2. Phonological Markedness and a Plea for useful Linguistics (by Liberman, Anatoly) 6. 3. Remarks on the Semantic features of Cases and Prepositions as Related to Syntax (by Sgall, Petr) 7. 4. The Human Factor and the Insufficiency of Invariant Meanings (by Kirsner, Robert S.) 8. II: Studies in Russian and Slavic Languages 9. 1. Gender and Declension Shifts in Contemporary Standard Russian: Markedness as a Semiotic Principle (by Andrews, Edna) 10. 2. Markedness and the Typology of Russian Verb Stems (by Feinberg, Lawrence E.) 11. 3. The Semantic Markings of Russian Verbal Suffixes (by Sperling, Annie Joly) 12. 4. Regular and Deviant Patterns of Russian Nominal Stress and Their relationship to Markedness (by Feldstein, Ronald F.) 13. 5. Deixis in Time and Space: The Fate of the Russian Demonstrativessej (by Dolgova, Irina) 14. 6. A Panchronic Approach to Morphological Competition in the East Slavic Substantive (Plural Paradigms) (by Pugh, Stefan M.) 15. III: Applications to Other Languages, Language Families, and Aphasia 16. 1. "Things" in a Noun Class Language: Semantic Functions of Grammatical Agreement in Swahili (by Contini-Morava, Ellen) 17. 2. Markers of Association and Distance in German Reported Speech (by Fennell, Barbara A.) 18. 3. The Five Deictics of Lak (by Friedman, Victor A.) 19. 4. Typologies of Person Categories in Slavic and Semitic (by Fradkin, Robert) 20. 5. Invariance, Markedness and Distinctive Feature Theory: The Modern Hebrew Verb (by Tobin, Yishai) 21. 6. The Application of Distinctive Semantic Features to the Production abd Comprehension of Locative Prepositions in Different Forms of Aphasia (by Leikin, Mark) 22. Name Index 23. Subject Index