Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating parsimonious models of longitudinal causal effects using regressions on propensity scores

Parsimony is important for the interpretation of causal effect estimates of longitudinal treatments on subsequent outcomes. One method for parsimonious estimates fits marginal structural models by using inverse propensity scores as weights. This method leads to generally large variability that is uncommon in more likelihood‐based approaches. A more recent method fits these models by using simulations from a fitted g‐computation, but requires the modeling of high‐dimensional longitudinal relations that are highly susceptible to misspecification. We propose a new method that, first, uses longitudinal propensity scores as regressors to reduce the dimension of the problem and then uses the approximate likelihood for the first estimates to fit parsimonious models. We demonstrate the methods by estimating the effect of anticoagulant therapy on survival for cancer and non‐cancer patients who have inferior vena cava filters. Copyright © 2013 John Wiley & Sons, Ltd.
Efficacy of Chemicals for the Potential Management of the Queensland Fruit Fly Bactrocera tryoni (Froggatt) (Diptera: Tephritidae)

This study investigated alternative in-field chemical controls against Bactrocera tryoni (Froggatt). Bioassay 1 tested the mortality of adults exposed to fruit and filter paper dipped in insecticide, and the topical application of insecticide to adults/fruit. Bioassay 2 measured the mortality of adults permitted to oviposit on fruit dipped in insecticide and aged 0, 1, 3, or 5 days, plus the production of offspring. Bioassay 3 tested infested fruit sprayed with insecticide. The field bioassay trialed the mortality of adults exposed to one- and five-day insecticide residues on peaches, and subsequent offspring. Abamectin, alpha-cypermethrin, clothianidin, dimethoate (half-label rate), emamectin benzoate, fenthion (half- and full-label rate), and trichlorfon were the most efficacious in bioassay 1, across 18 tested insecticide treatments. Overall, the LT50 value was lowest for fenthion (full-label rate), clothianidin, and alpha-cypermethrin. Fenthion, emamectin benzoate, and abamectin had the greatest effect on adult mortality and offspring production. Infested fruit treated with acetamiprid, fenthion, and thiacloprid produced no/very few offspring. Alpha-cypermethrin demonstrated good field efficacy against adults (one day post treatment: 97.2% mortality, five day post treatment: 98.8% mortality) and subsequent offspring (100% across one and five day post treatments), comparable to that of fenthion (full-label rate) (100% mortality for offspring and adults across both post treatments). Alpha-cypermethrin is a possible alternative to fenthion against B. tryoni; as a pyrethroid, it may not be desirable if adjunct biological control is imperative. Thiacloprid and Acetamiprid may be useful as a post-harvest treatment.
Estimating Differences in Growth and Metabolism in Two Spatially Segregated Groups of Columbia River White Sturgeon Using a Field-Based Bioenergetics Model~!2009-09-05~!2009-09-25~!2010-06-03~!

Recovery of white sturgeon in the Upper Columbia River continues to be limited by our understanding of the species’ biology, including factors which influence growth, habitat selection and their interaction. Sampling challenges in large rivers coupled with limitations to invasive research on endangered species also create specific challenges to the detailed understanding of growth and metabolism. A new bioenergetics modelling approach which estimates basic parameters from field data, specifically length-increment and length-at-age data was therefore applied in order to provide novel insights into white sturgeon growth and metabolism. A large existing capture database was used to examine two groups of white sturgeon which preferentially occupy habitats in the transboundary section of the Upper Columbia River downstream of Keenleyside Dam (HLK group) or further downstream near Waneta (WAN group). Successful application of the model showed differences in both growth and metabolism. Mean annual food intake appears similar for the two groups; however growth was more rapid for the HLK group. This resulted from a higher metabolic rate for the WAN group coupled with contrasts in seasonal food intake. Growth differences between groups lead to slower growth and later maturity for the WAN group. In aggregate, results suggest that the WAN group may be food limited and ultimately may have lower lifetime fecundity due its apparently later maturity and the possibility that lower energy intake might increase the interspawning interval. Finally, the functional structure of the model leads to concerns that both groups are approaching the thermal maxima for consumption, which may lead to reductions in body growth if increases in water temperature continue. Overall, application of this bioenergetics model identified new avenues for study which should assist conservation efforts in this species.
An Improved 3D Human Face Reconstruction Approach Based on Cubic Splines Models

In this paper, we develop a new hybrid active vision/geometric modeling approach dedicated to 3D human face recovery. Initially, a 3D coarse reconstruction is obtained via a structured-light assisted stereo sensor. Here, the stereo matching problem is resolved through two main stages: (a) sub-pixel stripe edge localization of projected patterns of light, and (b) correspondences establishing based on adaptive dynamic programming optimization technique. Next, the introduction of smooth interpolation models achieves the fine reconstruction. Here, cubic spline curves are employed in order to improve the quality of the reconstructed models. Indeed, they allow us to produce dense and details preserving reconstructions by following the control points from the coarse reconstruction stage. Furthermore, we present some reconstruction results and discuss both qualitative and quantitative evaluations of the proposed reconstruction scheme.
Live-cell imaging of cyclopropene tags with fluorogenic tetrazine cycloadditions.

There is growing interest in the use of inverse Diels–Alder tetrazine cycloadditions as rapid catalyst-free bioorthogonal reactions. [1–3] Fluorogenic tetrazines that increase in fluorescence after reaction with dienophiles are particularly useful for live-cell imaging applications. [4] Fluorogenic tetrazines have been recently used for live-cell imaging of small molecules, biomolecules tagged enzymatically with dienophiles, and proteins modified by reactive unnatural amino acids. [4,5] Although fluorogenic tetrazine probes hold great potential for intracellular imaging of small molecules, previous approaches are limited by requiring a large strained dienophile, such as trans-cyclooctene, cyclooctyne, or norbornene. [1,6] This situation is in contrast to Staudinger ligations or strain-promoted azide–cycloalkyne cycloadditions that utilize a small azide functional group. [7,8] This requirement has limited the use of tetrazine reactions in methods that require tags with minimal steric impact or nominal effect on the partition ratio. [2] The development of smaller dienophile partners capable of reacting rapidly with tetrazines would therefore represent a major advance. However, it has been unclear whether small dienophiles could be developed that react rapidly with tetrazines while maintaining their stability. Herein, we demonstrate the applicability of methylcyclopropene tags as dienophiles for reaction with fluorogenic tetrazines. Through systematic synthetic modifications we have optimized the stability, size, and reactivity of the cyclopropene scaffold. We have developed methylcyclopropene derivatives that react rapidly with tetrazines while retaining their aqueous stability and small size. These cyclopropene handles elicit fluorescent responses from quenched tetrazine dyes and are suitable for cellular imaging applications, which we demonstrate by imaging cyclopropene phospholipids distributed in live human breast cancer cells.
"Mathematics for All": How Do We Get There?

D ISPARITIES IN MATHEMATICS ACHIEVEMENT and enrollment in higher level mathematics between White middle class males and other groups of students such as African Americans, Latinos, Native Americans, and poor students have concerned educators at all levels for many years. Mathematics achievement data indicate that White students outperform African American and Hispanic students on tests of basic skills, problem solving, and applications, and on college entrance examinations (Secada, 1992; Tate, 1997). During the 1980s and 1990s there was evidence that the gaps in mathematics achievement had grown smaller. However, Michael Nettles, of the National Assessment Governing Board, recently reported new evidence again showing significant disparities in mathematics achievement between African American and White students (“Lagging Behind,” 2000). Policymakers and researchers have acknowledged these achievement differences in their calls for improving mathematics learning for all students. What has not been clear is how teachers and administrators in individual schools and districts throughout the country might accomplish equity in mathematics with their students. Teachers’ work with students in individual classrooms is at the heart of any program designed to attain equity for all students. However, teachers do not and cannot work in isolation to accomplish broadly conceived goals for equity in mathematics education. Administrators, teacher educators, researchers, and policymakers must all understand the issues, take initiative, and commit to supporting students and teachers in a collaborative effort to address the complex issues involved in achieving mathematics for all. A definition of equity is an essential starting point. Our definition begins with the premise that all students, regardless of their race, ethnicity, class, gender, or language proficiency, will learn and use mathematics. A second premise is that all of the people who are involved with and interested in the education of children must become aware of the social, economic, and political contexts of schooling that can either hinder or facilitate mathematics learning for underrepresented students (Apple, 1992). Equity in mathematics education requires: (a) equitable distribution of resources to schools, students, and teachers, (b) equitable quality of instruction, and (c) equitable outcomes for students. Equity is achieved when differences among subgroups of students in these three areas are decreasing or disappearing (Hewson & Kahle, 1998). Teachers’ knowledge of mathematics, their preparation to teach mathematics, and their beliefs Martha Allexsaht-Snider Laurie E. Hart
An Intramolecular Upstream Helix Ensures the Stability of a Toxin-Encoding RNA in Enterococcus faecalis

ABSTRACT The par stability determinant is required for the stable inheritance of the plasmid pAD1 in its native host, Enterococcus faecalis. It is the only antisense RNA-regulated addiction module identified to date in gram-positive bacteria. It encodes two small, convergently transcribed RNAs, RNA I and RNA II. RNA I encodes the Fst toxin and RNA II acts as the antitoxin by interacting with RNA I posttranscriptionally. As the toxin-encoding component of the system, it is important that RNA I is more stable than RNA II. This study reveals that a helix sequestering the 5′ end of RNA I plays a crucial role in maintaining the stability of the RNA I. An adjacent structure previously determined to regulate Fst translation was not required to enhance stability. Results indicated that endoribonuclease J2 contributes significantly to the degradation of a mutant disrupting the upstream helix (UH) of RNA I in Bacillus subtilis. Finally, it was shown that interaction with RNA II stabilized the UH mutant of RNA I.
The contemplative organization

As part of a qualitative research project to map the use of contemplative practices in secular settings, in‐depth interviews were conducted with 79 people who have founded or lead organizations where contemplative practices play a key role. In a number of interviews, contemplative practices were introduced into the workplace not only as ancillary stress‐reduction techniques for individuals, but as a core part of the organization's structure. As interviewees described how their organizations function, a number of characteristics pointed toward “the contemplative organization” as an emerging model of an organization that infuses a contemplative approach into the workplace. Such an organization strives to incorporate contemplative practices into all aspects of work; embody and explore organizational mission and values; move between cycles of action and reflection; balance product with process; and have an organizational structure that reflects a contemplative philosophy. Interviewees also reported the impact.
Optimization of the MIMO Compound Capacity

In this paper, we consider the optimization of the compound capacity in a rank one Ricean multiple input multiple output channel using partial channel state information at the transmitter side. We model the channel as a deterministic matrix within a known ellipsoid, and address the compound capacity defined as the maximum worst case mutual information in the set. We find that the optimal transmit strategy is always beamforming, and can be found using a simple one dimensional search. Similar results are derived for the worst case sum-rate of a multiple access channel with individual power constraints and a total power constraint. In this multiuser setting we assume equal array response at the receiver for all users. These results motivate the growing use of systems using simple beamforming transmit strategies
Intracellular calibration of a pH-sensitive dye in isolated, perfused salamander proximal tubules

We evaluated the dye 4',5'-dimethyl-5-(and -6-) carboxyfluorescein (Me2CF) for determining the intracellular pH(pHi) of isolated, perfused proximal tubules of the salamander. The intracellular absorbance spectrum, corrected for the intrinsic absorbance of the tubule, was obtained once per second. The dye was incorporated into tubule cells by exposing them to the membrane-permeable precursor 4',5'-dimethyl-5- (and -6-) carboxyfluorescein diacetate. The introduction of the dye had no significant effect on either pHi or cell voltage transients. Compared with dye contained in a cuvette, intracellular dye had a peak absorbance that was red-shifted by approximately 5 nm, and an apparent pK that was increased by approximately 0.3. These differences precluded an accurate calculation of pHi by the comparison of intracellular spectra with in vitro calibration spectra. However, when Me2CF was calibrated intracellularly, using the K-H exchanger nigericin to equalize external pH and pHi, the dye-derived, steady state pHi was within approximately 0.1 of the value obtained with pH-sensitive microelectrodes. Furthermore, when pHi was simultaneously measured with dye and microelectrodes during rapid pHi transients, the pHi time courses measured by the two methods were very similar. We conclude that the intracellular absorbance spectrum of Me2CF can be used to measure steady state pHi and rapid pHi transients reliably, provided the dye is calibrated intracellularly.
A Generalized Approach to Portfolio Optimization: Improving Performance by Constraining Portfolio Norms

In this paper, we provide a general nonlinear programming framework for identifying portfolios that have superior out-of-sample performance in the presence of estimation error. This general framework relies on solving the traditional minimum-variance problem but subject to the additional constraint that the norm of the portfolio-weight vector be smaller than a given threshold. We show that our general framework nests as special cases several wellknown (shrinkage and constrained) approaches considered in the literature. We also use our general framework to propose several new portfolio strategies that we term partial minimum-variance portfolios. These portfolios are obtained by applying the classical conjugate-gradient method to solve the minimum-variance problem. We compare empirically (in terms of portfolio variance, Sharpe ratio, and turnover), the out-of-sample performance of the new portfolios to various wellknown strategies across several datasets. We find that the norm-constrained portfolios we propose outperform shortsale-constrained portfolio approaches, shrinkage approaches, the 1/N portfolio, factor portfolios, and also other strategies considered in the literature.
An on-chip-trainable Gaussian-kernel analog support vector machine

We propose an analog circuit architecture of the Gaussian-kernel support vector machine having on-chip training capability. Thanks to the hardware-friendly algorithm, the learning function is realized by attaching a small additional circuitry to the SVM classifying hardware. Though the system works as analog circuits, the input and output signals including training results are all available in digital format. Therefore, the learned parameters are easily stored and reused after training sessions. The Gaussian kernel is realized by a new type of circuits utilizing Gilbert multipliers. The proof-of-concept chip was designed and sent to fabrication. Its successful operation was confirmed by transistor level SPICE simulation.
Insights into novel antimicrobial compounds and antibiotic resistance genes from soil metagenomes

In recent years a major worldwide problem has arisen with regard to infectious diseases caused by resistant bacteria. Resistant pathogens are related to high mortality and also to enormous healthcare costs. In this field, cultured microorganisms have been commonly focused in attempts to isolate antibiotic resistance genes or to identify antimicrobial compounds. Although this strategy has been successful in many cases, most of the microbial diversity and related antimicrobial molecules have been completely lost. As an alternative, metagenomics has been used as a reliable approach to reveal the prospective reservoir of antimicrobial compounds and antibiotic resistance genes in the uncultured microbial community that inhabits a number of environments. In this context, this review will focus on resistance genes as well as on novel antibiotics revealed by a metagenomics approach from the soil environment. Biotechnology prospects are also discussed, opening new frontiers for antibiotic development.
Network Exchange Theory

Preface Network Exchange Theory: Issues and Directions Actors in Relations Relations in Structures Power Relations Preface Power Relations in Exchange Networks by Markovsky, Willer and Patton The Discovery of Weak Power Exclusion and Power Preface Exclusion and Power: A Test of Four Theories of Power in Exchange Networks by Skvoretz and Willer Negotiated Exchanges Preface Negotiated Exchanges in Social Networks by Lovaglia et al. An Alternative for Predicting Weak Power by Lovaglia and Willer Network Connections Preface Network Connections and Exchange Ratios: Theory, Predictions and Experimental Tests by Willer and Skvoretz Power and Influence Preface Power and Influence: A Theoretical Bridge by Willer, Lovaglia and Markovsky Status Influence and Status Value by Thye Recent Problems and Solutions in Network Exchange Theory Preface An Automated Approach to the Theoretical Analysis of Difficult Problems by Lovaglia et al. A New Method for Finding Power Structures by Simpson and Willer Developing Network Exchange Theory
Using semantic similarity to detect features in yeast protein complexes

Biological data stored in databases can be associated with information (knowledge) such as experiments, properties and functions, response to drugs etc. Such a knowledge is often stored in biological ontologies. Gene Ontology is one of the main resource of biological knowledge providing both a categorization of terms and a source of annotation for genes and proteins. This enables the use of ontology-based methodologies for the analysis of proteins and their functions. One methodology is based on semantic based similarity measures. Recently there is a growing interest in the use of semantic based methodologies to the analysis of protein interaction data such as the prediction of protein complexes based on semantic similarity measures. Despite this interest, there is the need for an assessment of semantic measures as well as a deep study on the impact of the chosen measure in the obtained results. This paper treats the problem of using semantic similarity measure to analyse protein complexes and to improve protein complexes prediction frameworks. Tests have been performed in yeast protein complexes. Results indicate that there exists a bias among measures as well as an higher value of semantic similarity within proteins that participate in the same complex, proving both a possible use of semantic similarity protein complexes prediction and a suggestion in the measure.
Active Evasion of CTL Mediated Killing and Low Quality Responding CD8+ T Cells Contribute to Persistence of Brucellosis

Brucellosis is a common zoonotic disease that remains endemic in many parts of the world. Dissecting the host immune response during this disease provides insight as to why brucellosis is often difficult to resolve. We used a Brucella epitope specific in vivo killing assay to investigate the ability of CD8+ T cells to kill targets treated with purified pathogenic protein. Importantly, we found the pathogenic protein TcpB to be a novel effector of adaptive immune evasion by inhibiting CD8+ T cell killing of Brucella epitope specific target cells in mice. Further, BALB/c mice show active Brucella melitensis infection beyond one year, many with previously unreported focal infection of the urogenital area. A fraction of CD8+ T cells show a CD8+ Tmem phenotype of LFA-1hi, CD127hi, KLRG-1lo during the course of chronic brucellosis, while the CD8+ T cell pool as a whole had a very weak polyfunctional cytokine response with diminished co-expression of IFN-γ with TNFα and/or IL-2, a hallmark of exhaustion. When investigating the expression of these 3 cytokines individually, we observed significant IFN-γ expression at 90 and 180 days post-infection. TNFα expression did not significantly exceed or fall below background levels at any time. IL-2 expression did not significantly exceeded background, but, interestingly, did fall significantly below that of uninfected mice at 180 days post-infection. Brucella melitensis evades and blunts adaptive immunity during acute infection and our findings provide potential mechanisms for the deficit observed in responding CD8+ T cells during chronic brucellosis.
Adopting Open Source Software Engineering (OSSE) Practices by Adopting OSSE Tools

The open source movement has created and uses a set of software engineering tools with features that fit the characteristics of open source development processes. To a large extent, the open source culture and methodology are conveyed to new developers via the toolset itself, and through the demonstrated usage of these tools on existing projects. The rapid and wide adoption of open source tools stands in stark contrast to the difficulties encountered in adopting traditional Computer-Aided Software Engineering (CASE) tools. This chapter explores the characteristics that make these tools adoptable and discusses how adopting them may influence software development processes.