Miracle-dz/UniFAR-FTUs huggingface dataset:
Intervention evaluation using gllamm

The gllamm procedure provides a framework in which to undertake many of the more difficult analyses required for trials and intervention studies. Treatment effect estimation in the presence of noncompliance can be undertaken using instrumental variable (IV) methods. I illustrate how gllamm can be used for IV estimation for the full range of types of treatment and outcome measures and describe how missing data may be tackled on an assumption of latent ignorability. I will describe other approaches to account for clustering and the analysis of cluster-randomized studies. Examples from studies of alcohol consumption of primary-care patients, cognitive behavior therapy of depression patients, and a school based smoking intervention are discussed.
Identifying and Managing Threatened Invertebrates through Assessment of Coextinction Risk

Abstract: Invertebrates with specific host species may have a high probability of extinction when their hosts have a high probability of extinction. Some of these invertebrates are more likely to go extinct than their hosts, and under some circumstances, specific actions to conserve the host may be detrimental to the invertebrate. A critical constraint to identifying such invertebrates is uncertainty about their level of host specificity. We used two host‐breadth models that explicitly incorporated uncertainty in the host specificity of an invertebrate species. We devised a decision protocol to identify actions that may increase the probability of persistence of a given dependent species. The protocol included estimates from the host‐breadth models and decision nodes to identify cothreatened species. We applied the models and protocol to data on 1055 insects (186 species) associated with 2 threatened (as designated by the Australian Government) plant species and 19 plant species that are not threatened to determine whether any insect herbivores have the potential to become extinct if the plant becomes extinct. According to the host‐breadth models, 18 species of insect had high host specificity to the threatened plant species. From these 18 insects, the decision protocol highlighted 6 species that had a high probability of extinction if their hosts were to become extinct (3% of all insects examined). The models and decision protocol have added objectivity and rigor to the process of deciding which dependent invertebrates require conservation action, particularly when dealing with largely unknown and speciose faunas.
A Herceptin-Based Chimeric Antigen Receptor with Modified Signaling Domains Leads to Enhanced Survival of Transduced T Lymphocytes and Antitumor Activity1

To generate chimeric Ag receptors (CARs) for the adoptive immunotherapy of cancer patients with ErbB2-expressing tumors, a single-chain Ab derived from the humanized mAb 4D5 Herceptin (trastuzumab) was initially linked to T cell signaling domains derived from CD28 and the CD3ζ to generate a CAR against ErbB2. Human PBLs expressing the 4D5 CAR demonstrated Ag-specific activities against ErbB2+ tumors. However, a gradual loss of transgene expression was noted for PBLs transduced with this 4D5 CAR. When the CD3ζ signaling domain of the CAR was truncated or mutated, loss of CAR expression was not observed, suggesting that the CD3ζ signaling caused the transgene decrease, which was supported by the finding that T cells expressing 4D5 CARs with CD3ζ ITAM mutations were less prone to apoptosis. By adding 4-1BB cytoplasmic domains to the CD28-CD3ζ signaling moieties, we found increased transgene persistence in 4D5 CAR-transduced PBLs. Furthermore, constructs with 4-1BB sequences demonstrated increased cytokine secretion and lytic activity in 4D5 CAR-transduced T cells. More importantly, PBLs expressing this new version of the 4D5 CAR could not only efficiently lyse the autologous fresh tumor digests, but they could strongly suppress tumor growth in a xenogenic mouse model.
Online, interactive user guidance for high-dimensional, constrained motion planning

We consider the problem of planning a collision-free path for a high-dimensional robot. Specifically, we suggest a planning framework where a motion-planning algorithm can obtain guidance from a user. In contrast to existing approaches that try to speed up planning by incorporating experiences or demonstrations ahead of planning, we suggest to seek user guidance only when the planner identifies that it ceases to make significant progress towards the goal. Guidance is provided in the form of an intermediate configuration q^, which is used to bias the planner to go through q^. We demonstrate our approach for the case where the planning algorithm is Multi-Heuristic A* (MHA*) and the robot is a 34-DOF humanoid. We show that our approach allows to compute highly-constrained paths with little domain knowledge. Without our approach, solving such problems requires carefully-crafted domain-dependent heuristics.
Harmonic elimination using Independent Component Analysis

In the field of analysis and processing of weak signals, harmonics always disturb the weak signals and pose a serious problem for the amplitudes of the interferences are comparable to those of the signals. In this paper, independent component analysis (ICA) is used to remove harmonic interferences under the consideration that the original signals and the harmonic interferences are mutually independent. We introduced two additional channels of orthogonal zero-phase harmonic signals to instead of one unknown phase harmonic as two reference resources and combined the artificial signals with the measured signals to form a new data set as the input of ICA. After excluding those independent components related to harmonic interferences, the original signals were reconstructed. Experiment results for practical electroencephalographic (EEG) data show that ICA is a quite effective method for simultaneous elimination of multiple harmonic interferences.
Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster

Highly repetitive satellite DNA (satDNA) repeats are found in most eukaryotic genomes. SatDNAs are rapidly evolving and have roles in genome stability and chromosome segregation. Their repetitive nature poses a challenge for genome assembly and makes progress on the detailed study of satDNA structure difficult. Here, we use single-molecule sequencing long reads from Pacific Biosciences (PacBio) to determine the detailed structure of all major autosomal complex satDNA loci in Drosophila melanogaster, with a particular focus on the 260-bp and Responder satellites. We determine the optimal de novo assembly methods and parameter combinations required to produce a high-quality assembly of these previously unassembled satDNA loci and validate this assembly using molecular and computational approaches. We determined that the computationally intensive PBcR-BLASR assembly pipeline yielded better assemblies than the faster and more efficient pipelines based on the MHAP hashing algorithm, and it is essential to validate assemblies of repetitive loci. The assemblies reveal that satDNA repeats are organized into large arrays interrupted by transposable elements. The repeats in the center of the array tend to be homogenized in sequence, suggesting that gene conversion and unequal crossovers lead to repeat homogenization through concerted evolution, although the degree of unequal crossing over may differ among complex satellite loci. We find evidence for higher-order structure within satDNA arrays that suggest recent structural rearrangements. These assemblies provide a platform for the evolutionary and functional genomics of satDNAs in pericentric heterochromatin.
Avaliação de estímulos emocionais em Ex-Combatentes de Guerra com e sem PTSD

O presente estudo teve por objectivo averiguar a forma como sao avaliadas imagens emocionais por Ex-Combatentes de Guerra. O estudo foi realizado com uma amostra de 72 sujeitos que foram submetidos a duas escalas de avaliacao de PTSD, e a visualizacao e categorizacao das imagens atraves do Self-Assessement Manikin (SAM; Lang, Bradley & Cuthbert, 1997). Foram comparados tres grupos, um com diagnostico de PTSD (Grupo PTSD) e dois sem diagnostico de PTSD, constituidos com base nas escalas de auto-avaliacao: um com valores baixos (Grupo Nao-Clinico Baixo – NCB) e outro com valores mais elevados (Grupo Nao-Clinico Alto – NCA). Verificou-se que tanto o grupo com PTSD como o grupo NCA avaliam mais negativamente as imagens desagradaveis (imagens de guerra e “caras zangadas”) em comparacao com o grupo NCB. Alem disso, globalmente, os mesmos grupos tambem avaliam as imagens desagradaveis como mais activadoras e dominantes que o grupo NCB. Em relacao as imagens agradaveis, a diferenciacao entre os tres grupos nao foi significativa.
Robust-SL0 for stable sparse representation in noisy settings

In the last few years, we have witnessed an explosion in applications of sparse representation, the majority of which share the need for finding sparse solutions of underdetermined systems of linear equations (USLE's). Based on recently proposed smoothed ℓ0-norm (SL0), we develop a noise-tolerant algorithm for sparse representation, namely Robust-SL0, enjoying the same computational advantages of SL0, while demonstrating remarkable robustness against noise. The proposed algorithm is developed by adopting the corresponding optimization problem for noisy settings, followed by theoretically-justified approximation to reduce the complexity. Stability properties of Robust-SL0 are rigorously analyzed, both analytically and experimentally, revealing a remarkable improvement in performance over SL0 and other competing algorithms, in the presence of noise.
[Matrikines: a new anticancer therapeutic strategy].

Tumor microenvironment is a complex system composed of a largely altered extracellular matrix (ECM) with different cell types that determine the angiogenic response. Upon the influence of hypoxia, tumor cells secrete cytokines that activate stromal cells to produce proteases and angiogenic factors. The proteases degrade the stromal ECM and participate in the release of various ECM fragments, named matrikines or matricryptins, capable to control tumor invasion and metastasis dissemination. We will focus on the matrikines derived from the NC1 domains of the different constitutive chains of basement membrane-associated collagens and mainly collagen IV. The putative targets of the matrikine action are the proliferation and invasive properties of tumor or inflammatory cells, and the angiogenic and lymphangiogenic responses. For example, canstatin, tumstatin and tetrastatin, respectively derived from the NC1 domains of α2, α3 and α4 chains of collagen IV, inhibit in vivo tumor growth in various experimental cancer models. Their anti-cancer activity comprises an anti-proliferative effect on tumor cells and on endothelial cells by induction of cell apoptosis or cell cycle blockade and the induction of a loss of their migratory phenotype. Matrikines constitute a new family of potent anticancer agents that could be used under various therapeutic strategies: i) induction of their overexpression by cancer cells or by the host cells, ii) use of recombinant proteins or synthetic peptides or structural analogues designed from the structure of the active sequences. These matrikines could be used in combination with conventional chemotherapy or radiotherapy to limit tumor progression.
Does anticipated aid create the need it wants to avoid? An experimental investigation

A novel two-person "charity game" is used to experimentally investigate whether anticipation of help crowds out incentives to work, and therefore impulses to help. We distinguish two treatments differing in whether the causes of neediness are verifiable or not. Helping behavior does not vary significantly between treatments, but is positively correlated with dictator giving, suggesting idiosyncratic attitudes to help. Needy subjects are unaffected by anticipated help, but react optimally to chance.
Novel Integrated System of RFID Tag and Self-Powered Oxygen Sensor Indicator

Recently, the combination of passive RFID tags with sensors has been absolutely required in various fields as well as distribution. In this study, we develop a novel sensor-type oxygen indicator based on a battery, which changes both color and electric signals depending on oxygen concentration, and propose the combined system of the self-powered oxygen sensor indicator with a passive UHF band RFID tag. Using this system, we monitored the oxygen concentration in a plastic package with oxygen absorber. The experimental results show that this novel system functions well.
Evaluations Versus Expectations: Children's Divergent Beliefs About Resource Distribution

Past research reveals a tension between children's preferences for egalitarianism and ingroup favoritism when distributing resources to others. Here we investigate how children's evaluations and expectations of others' behaviors compare. Four- to 10-year-old children viewed events where individuals from two different groups distributed resources to their own group, to the other group, or equally across groups. Groups were described within a context of intergroup competition over scarce resources. In the Evaluation condition, children were asked to evaluate which resource distribution actions were nicer. In the Expectation condition, children were asked to predict which events were more likely to occur. With age, children's evaluations and expectations of others' actions diverged: Children evaluated egalitarian actions as nicer yet expected others to behave in ways that benefit their own group. Thus, children's evaluations about the way human social actors should behave do not mirror their expectations concerning those individuals' actions.
A quantized kernel least mean square scheme with entropy-guided learning for intelligent data analysis

Quantized kernel least mean square (QKLMS) algorithm is an effective nonlinear adaptive online learning algorithm with good performance in constraining the growth of network size through the use of quantization for input space. It can serve as a powerful tool to perform complex computing for network service and application. With the purpose of compressing the input to further improve learning performance, this article proposes a novel QKLMS with entropy-guided learning, called EQ-KLMS. Under the consecutive square entropy learning framework, the basic idea of entropy-guided learning technique is to measure the uncertainty of the input vectors used for QKLMS, and delete those data with larger uncertainty, which are insignificant or easy to cause learning errors. Then, the dataset is compressed. Consequently, by using square entropy, the learning performance of proposed EQ-KLMS is improved with high precision and low computational cost. The proposed EQ-KLMS is validated using a weather-related dataset, and the results demonstrate the desirable performance of our scheme.
Tactile discrimination of shape: responses of slowly and rapidly adapting mechanoreceptive afferents to a step indented into the monkey fingerpad

The representation of shape in the responses of monkey cutaneous mechanoreceptive afferents to steps of varying shape vertically indented into the fingerpad was studied. A series of flat plates was used, each with a step change in thickness in the middle so that one- half of the plate was thicker than the other. The cross-sectional shape of the step approximated that of a half-cycle sinusoid, 0.5 mm high, that was varied in half-cycle wavelength (step width) and hence in steepness and curvature. The steps fell into 2 categories, characterized as “steep” and “‘gradual. ” Evoked action potentials were recorded from single, slowly adapting and from rapidly adapting Meissner corpuscle mechanoreceptive afferent fibers (SA and RA, respectively) innervating the fingerpad of the anesthetized monkey while each step was indented at a succession of lateral positions across the fiber's receptive field. The responses of each SA provided a spatial response profile (number of evoked impulses as a function of step position) that was directly related to the variation in curvature across the step. The rate of discharge was greatest under the sharpest (convex) portion of the step, least under the adjacent concave portion, and intermediate under the flat portions of the steps. The results indicated an exquisite sensitivity of the SA, even during the ramp phase of vertical indentation, to the changes in skin curvature. The spatial response profile remained relatively undistorted over time during the ensuing steady phase, while the contrast between the peak and the minimum response improved. RAs responded only during the ramp phase and with fewer responses, and gave rise to a poorly modulated spatial response profile, even though half of the RAs tested showed limited sensitivity to the amount or rate of change of skin curvature. It was hypothesized that RA responses are predominantly influenced by the vertical velocity of the most sensitive spot in the receptive field. When the same step stimuli were applied to the human fingerpad, the capacities of humans to discriminate differences in step shape were found to correlate with the discriminability of SAs, as opposed to the considerably poorer discriminability of RAs. It is concluded that information concerning the local curvature and hence the shape of objects indenting the skin is primarily coded by the SAs. In the 2 preceding papers (LaMotte and Srinivasan, 1987a, b), we investigated the responses of SAs and RAs to the same sinusoidal steps stroked back and forth across the fingerpad under constant compressional force. (ABSTRACT TRUNCATED AT 400 WORDS)
Structure and Function of Cross-class Complexes of G Protein-coupled Secretin and Angiotensin 1a Receptors*

Complexes of secretin (SecR) and angiotensin 1a (Atr1a) receptors have been proposed to be functionally important in osmoregulation, providing an explanation for overlapping and interdependent functions of hormones that bind and activate different classes of GPCRs. However, the nature of these cross-class complexes has not been well characterized and their signaling properties have not been systematically explored. We now use competitive inhibition of receptor bioluminescence resonance energy transfer and bimolecular fluorescence complementation to establish the dominant functionally important state as a symmetrical homodimeric form of SecR decorated by monomeric Atr1a, interacting through lipid-exposed faces of Atr1a TM1 and TM4. Conditions increasing prevalence of this complex exhibited negative allosteric modulatory impact on secretin-stimulated cAMP responses at SecR. In contrast, activating Atr1a with full agonist in such a complex exhibited a positive allosteric modulatory impact on the same signaling event. This modulation was functionally biased, with secretin-stimulated calcium responses unaffected, whereas angiotensin-stimulated calcium responses through the complex were reduced or absent. Further supporting this interpretation, Atr1a with mutations of lipid-exposed faces of TM1 and TM4 that did not affect its ability to bind or signal, could be expressed in the same cell as SecR, yet not exhibit either the negative or positive allosteric impact on cAMP observed with the inactive or activated states of wild type Atr1a on function, and not interfere with angiotensin-stimulated calcium responses like complexes with Atr1a. This may provide a more selective means of exploring the physiologic functional impact of this cross-class receptor complex without interfering with the function of either component receptor.
Whole-plant and organ-level nitrogen isotope discrimination indicates modification of partitioning of assimilation, fluxes and allocation of nitrogen in knockout lines of Arabidopsis thaliana.

The nitrogen isotope composition (δ¹⁵N) of plants has potential to provide time-integrated information on nitrogen uptake, assimilation and allocation. Here, we take advantage of existing T-DNA and γ-ray mutant lines of Arabidopsis thaliana to modify whole-plant and organ-level nitrogen isotope composition. Nitrate reductase 2 (nia2), nitrate reductase 1 (nia1) and nitrate transporter (nrt2) mutant lines and the Col-0 wild type were grown hydroponically under steady-state NO₃⁻ conditions at either 100 or 1000 μM NO₃⁻ for 35 days. There were no significant effects on whole-plant discrimination and growth in the assimilatory mutants (nia2 and nia1). Pronounced root vs leaf differences in δ¹⁵N, however, indicated that nia2 had an increased proportion of nitrogen assimilation of NO₃⁻ in leaves while nia1 had an increased proportion of assimilation in roots. These observations are consistent with reported ratios of nia1 and nia2 gene expression levels in leaves and roots. Greater whole-plant discrimination in nrt2 indicated an increase in efflux of unassimilated NO₃⁻ back to the rooting medium. This phenotype was associated with an overall reduction in NO₃⁻ uptake, assimilation and decreased partitioning of NO₃⁻ assimilation to the leaves, presumably because of decreased symplastic intercellular movement of NO₃⁻ in the root. Although the results were more varied than expected, they are interpretable within the context of expected mechanisms of whole-plant and organ-level nitrogen isotope discrimination that indicate variation in nitrogen fluxes, assimilation and allocation between lines.
A Brunswik lens model of consumer health judgments of packaged foods

Consumer health judgments of packaged food were compared with an objective healthfulness criterion using a Brunswik lens model. Consumer judgments were obtained from a representative consumer sample (N=1329) who evaluated the healthfulness of 198 packaged food products. The objective healthfulness criterion was calculated for each product according to its specific nutrition values using a validated nutrition profile. The lens model included explicit cues such as nutrition values, nutrition and health claims, food category, and brand and implicit cues such a packaging design and category representativeness. The study revealed that the objective healthfulness criterion is highly predictable on the basis of cues such as the food category, brand, carbohydrate content, and whether the food is a typical “light” product. However, consumer judgments of food healthfulness are based almost entirely on the food category and to a lesser extent on the brand and consumer familiarity with the product. The results are in conflict with consumers’ self-reported use of nutrition information but are in accordance with findings from studies using implicit methods.