Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating the Use of Linear Mixed-Effect Models for Inference of the Concentration-QTc Slope Estimate as a Surrogate for a Biological QTc Model

In concentration‐QTc modeling, oscillatory functions have been used to characterize biological rhythms in QTc profiles. Fitting such functions is not always feasible because it requires sufficient electrocardiograph sampling. In this study, drug concentration and QTc data were simulated using a published biological QTc model (oscillatory functions). Then, linear mixed‐effect models and the biological model were fitted and evaluated in terms of biases, precisions, and qualities of inferences. The simpler linear mixed‐effect model with day and time as a factor variables provided similar accuracy of the concentration‐QTc slope estimates to the complex biological model and was able to accurately predict the drug‐induced QTc prolongation with less than 1 ms bias, despite its empirical nature to account for biological rhythm. The current study may guide a concentration‐QTc modeling strategy that can be easily prespecified, does not suffer from poor convergence, and achieves little bias in drug‐induced QTc estimates.
PI3K Pathway Dependencies in Endometrioid Endometrial Cancer Cell Lines

Purpose: Endometrioid endometrial cancers (EEC) frequently harbor coexisting mutations in phosphoinositide 3-kinase (PI3K) pathway genes, including PTEN, PIK3CA, PIK3R1, and KRAS. We sought to define the genetic determinants of PI3K pathway inhibitor response in EEC cells, and whether PTEN-mutant EEC cell lines rely on p110β signaling for survival. Experimental Design: Twenty-four human EEC cell lines were characterized for their mutation profile and activation state of PI3K and mitogen-activated protein kinase (MAPK) signaling pathway proteins. Cells were treated with pan-class I PI3K, p110α, and p110β isoform-specific, allosteric mTOR, mTOR kinase, dual PI3K/mTOR, mitogen-activated protein/extracellular signal–regulated kinase (MEK), and RAF inhibitors. RNA interference (RNAi) was used to assess effects of KRAS silencing in EEC cells. Results: EEC cell lines harboring PIK3CA and PTEN mutations were selectively sensitive to the pan-class I PI3K inhibitor GDC-0941 and allosteric mTOR inhibitor temsirolimus, respectively. Subsets of EEC cells with concurrent PIK3CA and/or PTEN and KRAS mutations were sensitive to PI3K pathway inhibition, and only 2 of 6 KRAS-mutant cell lines showed response to MEK inhibition. KRAS RNAi silencing did not induce apoptosis in KRAS-mutant EEC cells. PTEN-mutant EEC cell lines were resistant to the p110β inhibitors GSK2636771 and AZD6482, and only in combination with the p110α selective inhibitor A66 was a decrease in cell viability observed. Conclusions: Targeted pan-PI3K and mTOR inhibition in EEC cells may be most effective in PIK3CA- and PTEN-mutant tumors, respectively, even in a subset of EECs concurrently harboring KRAS mutations. Inhibition of p110β alone may not be sufficient to sensitize PTEN-mutant EEC cells and combination with other targeted agents may be required. Clin Cancer Res; 19(13); 3533–44. ©2013 AACR.
Extended contact through cross-group romantic relationships

Cross-group romantic relationships are an extremely intimate and often maligned form of intergroup contact. Yet, according to intergroup contact theory, these relationships have the potential to improve the intergroup attitudes of others via extended contact. This study combines the interpersonal and intergroup literatures to examine the outcomes associated with knowing a partner in a cross-group romantic relationship. Results suggest that cross-group romantic partners encounter greater disapproval toward their relationships than same-group partners and, as a result, their relationships are perceived more negatively. Nevertheless, extended contact with cross-group partners, controlling for participants' cross-group friendships and romantic relationships, predicts more positive attitudes toward cross-group dating and positive intergroup attitudes in general, mediated by perceived ingroup norms toward cross-group relationships.
"Not another Z piece!": Adaptive Difficulty in TETRIS

Difficulty in TETRIS is adjusted by adapting the speed with which blocks fall. In this contribution, we describe results of an exploratory study in which we investigated relationships between players' performance and their subjective assessment of difficulty and fun. We tested five different algorithms that, instead of adjusting game speed, adjust difficulty by choosing blocks based on the current game state. With our results, we establish pile height and bumpiness as parameters that indicate the performance of a player during a live game, discuss the inherent difficulty of different block choosing algorithms and show how the relationship between fun and perceived difficulty varies for distinct player groups. With regard to adapting difficulty, we argue that one can still teach an old dog such a TETRIS a lot of new tricks.
Public and Private Schools: Do Classroom Processes Vary by School Type?

Using the National Institute of Child Health and Human Development Study of Early Child Care and Youth Development dataset, we examined classroom processes (e.g., time spent on language instruction, overall emotional quality of the classroom) and characteristics (e.g., class size) by school type (public or private). Results indicate that classroom processes do not vary significantly by school type. Based on our results, we conjecture that if private schools are, in fact, superior to public schools, it is likely because of some factor(s) not accounted for by our classroom variables.
Immunosuppression: towards a logical approach in liver transplantation

Over the last two decades there has been a significant increase in the number and types of immunosuppressive agents that have been available to clinicians. The protocols for immunosuppression used in liver transplantation have been derived historically from those in renal transplantation. During the last decade there has been a shift in the use of immunosuppression, with the introduction of interleukin (IL)‐2 receptor antagonists in place of anti‐lymphocyte preparations, substitution of tacrolimus for cyclosporin and mycophenolate for azathioprine. The use of corticosteroids has been reduced. For a variety of reasons, these changes have not always been made on the basis of properly randomized studies. The place of newer agents, such as sirolimus and leflunomide derivatives and of the microbiological agents, is unclear. In this review, we outline briefly the mechanism of action of drugs and suggest possible approaches to the management of the liver allograft recipient, suggesting how treatment could be adjusted according to the indication for transplantation as well as the individual's comorbidities.
Object subsampling strategies to improve computational performance

We investigate object simplification methods based on Centroidal Voronoi Tesselation (CVT) that share the possibility of great speed-ups in various scenarios. We propose Constrained CVT to sample points from the object boundary and the Region-based CVT to be able to subsample lower dimensional objects, as well. Moreover we introduce custom weight functions based on object properties. Thus, we can be more specific on what are the important parts of the subsampled object. We also list several novel applications corresponding to the theoretical achievements presented. The advantages of applying the subsampling strategies are presented for registration, human detection, and the segmentation of the retinal vascular system, respectively. Quantitative results are shown to check the deterioration of the accuracy with the level of subsampling, and the computational gain. We also make comparisons with other naive (e.g. random) subsampling methods.
Generating Vocabulary Knowledge for At-Risk Middle School Readers: Contrasting Program Effects and Growth Trajectories

We tested whether urban middle-school students from mostly low-income homes had improved academic vocabulary when they participated in a freely available vocabulary program, Word Generation (WG). To understand how this program may support students at risk for long-term reading difficulty, we examined treatment interactions with baseline achievement on a state standardized test and also differential effects for students with (n = 398) and without (n = 1,395) individualized education plans (IEPs). Students in this unmatched quasi-experiment (5 WG and 4 comparison schools) completed pre- and postvocabulary assessments during the intervention year. We also retested student vocabulary knowledge after summer vacation and the following spring on 11 target words to construct a longitudinally consistent scaled score across 4 waves of data. Growth models show that students experienced summer setback. Although there were no average underlying differences in growth or differences in summer setback for students by baseline achievement, better readers improved more from program participation. IEP status did not predict differential benefits of program participation, and students with IEPs maintained gains associated with participation in WG; however, participation in the program did not change underlying growth trajectories favoring students who did not have IEPs.
A genome-wide identification and analysis of the DYW-deaminase genes in the pentatricopeptide repeat gene family in cotton (Gossypium spp.)

The RNA editing occurring in plant organellar genomes mainly involves the change of cytidine to uridine. This process involves a deamination reaction, with cytidine deaminase as the catalyst. Pentatricopeptide repeat (PPR) proteins with a C-terminal DYW domain are reportedly associated with cytidine deamination, similar to members of the deaminase superfamily. PPR genes are involved in many cellular functions and biological processes including fertility restoration to cytoplasmic male sterility (CMS) in plants. In this study, we identified 227 and 211 DYW deaminase-coding PPR genes for the cultivated tetraploid cotton species G. hirsutum and G. barbadense (2n = 4x = 52), respectively, as well as 126 and 97 DYW deaminase-coding PPR genes in the ancestral diploid species G. raimondii and G. arboreum (2n = 26), respectively. The 227 G. hirsutum PPR genes were predicted to encode 52–2016 amino acids, 203 of which were mapped onto 26 chromosomes. Most DYW deaminase genes lacked introns, and their proteins were predicted to target the mitochondria or chloroplasts. Additionally, the DYW domain differed from the complete DYW deaminase domain, which contained part of the E domain and the entire E+ domain. The types and number of DYW tripeptides may have been influenced by evolutionary processes, with some tripeptides being lost. Furthermore, a gene ontology analysis revealed that DYW deaminase functions were mainly related to binding as well as hydrolase and transferase activities. The G. hirsutum DYW deaminase expression profiles varied among different cotton tissues and developmental stages, and no differentially expressed DYW deaminase-coding PPRs were directly associated with the male sterility and restoration in the CMS-D2 system. Our current study provides an important piece of information regarding the structural and evolutionary characteristics of Gossypium DYW-containing PPR genes coding for deaminases and will be useful for characterizing the DYW deaminase gene family in cotton biology and breeding.
QueryViz: helping users understand SQL queries and their patterns

We present QueryViz, a novel visualization tool for SQL queries that reduces the time needed to read and understand existing queries. It targets two principal audiences: (i) users who often issue the same or similar queries and who need to quickly browse through a repository of existing queries; and (ii) novices that try to familiarize themselves with the logic behind alternative patterns of SQL queries. QueryViz uses as input only two strings: the database schema and the SQL query. It can thus serve as light-weight add-on to existing database systems and is also available via an online interface at http://queryviz.com. In this demonstration, we explain our visual alphabet, walk through the visualization algorithm, and let users experience the difference in understanding SQL queries from text or our graphical representation while browsing through repositories of well-known textbook SQL queries.
A model-based control method applicable to unstable, non-minimum-phase, nonlinear processes

This paper presents a nonlinear control system that is applicable to stable and unstable processes, whether non-minimum- or minimum-phase. The closed-loop stability is ensured by forcing every process state variable to follow a desired linear response. This approach results in a nonlinear state feedback that induces approximately linear responses to the state variables. The control system includes the nonlinear state feedback and a reduced-order nonlinear state observer. The application and performance of the control system are shown by implementing it on a chemical reactor with multiple steady states. The control system is used to operate the reactor at one of the steady states, which is unstable and non-minimum-phase. The simulation results show that the closed-loop system is asymptotically stable for all physically-meaningful initial conditions.
Robust design of in-wheel PM motor by fuzzy-based Taguchi method

In this paper, a novel systematic and efficient approach, using the fuzzy-based Taguchi method with multiple performance characteristics index (MPCI), is employed for obtaining the robust design of an in-wheel permanent-magnet (PM) motor with both lower torque ripple factor and higher efficiency. According to the geometric parameters of the PM motor, we select the controllable factors and their levels, such as the permanent magnet thickness in rotor, air-gap width, opening slot width and slot tooth width at stator. The proposed method first establishes the orthogonal array (OA) that is recommended by the Taguchi method. Then the multiple targets are coordinated by the fuzzy inference mechanism to obtain the better combination of the geometric parameters for achieving multiple quality targets. The finite element method (FEM) is used as the tool for analyzing the torque ripple and performance of PM motor. Results have shown that the proposed method can obtain the suitable motor's geometric parameters for reducing the cogging torque and enhancing the operating efficiency.
Revisiting the prime–probe contextual similarity effect on negative priming: The impact of cue variability

In previous studies on negative priming, the effect of prime–probe contextual similarity was not stable. On occasions, negative priming was greater when similar rather than different contexts were presented in a prime and a probe trial; however, at other times, negative priming was not affected by such manipulation. The current study demonstrates that the effect of contextual similarity can be optimised when cue variability is high. Cue variability was manipulated between-subject across Experiments 1a and 1b and as a within-subject variable in Experiment 2. Symbols were presented as contextual cues. The results indicated that when cue variability was high, the prime–probe contextual similarity effect was observed on negative priming; however, when cue variability was low, the contextual similarity effect and the negative priming effect were absent.
Voice over Wireless Mesh Networks: A Case Study in the Brazilian Amazon Region during the Rainy Season

In this paper we present the results of an experimental analysis of the behavior and performance of VoIP calls using different codecs in a wireless mesh network (WMN) based on the IEEE 802.11g standard. Most measurements were done during the rainy season in a Brazilian Amazon region.We assessed the call quality of codecs using real measurement conditions showing the codecs coding performance over wireless mesh networks.Both between unidirectional and bidirectional transmissions were studied.
A low-power CAM using a 12-transistor design cell

A low-power CAM design using a 12-transistor cell is proposed. The CAM cell is based on the conventional 6T cross- coupled inverters used for storing data with an addition of two NMOS transistors for reading out. In addition, the CAM has another four transistors for mask comparison operation through classical pre-charge operation. The read-out port exploits a pre- charge reading mechanism in order to alleviate the drawback of power consumption generated from sensing amplifiers and all other related synchronization circuits which are structured in every column in the memory. Thus, the read and match features can have concurrent operations. An experimental CAM structure of storage size 64-bit x 128-bit is designed using 0.18- μm CMOS single poly and three layers of metals measuring a cell die area of 24.4375 μm2 and a total silicon area of 0.269192 mm2. The circuit works up to 200 MHz in simulation with total power consumption of 0.016 W at 1.8-V supply voltage
Sentence recognition from articulatory movements for silent speech interfaces

Recent research has demonstrated the potential of using an articulation-based silent speech interface for command-and-control systems. Such an interface converts articulation to words that can then drive a text-to-speech synthesizer. In this paper, we have proposed a novel near-time algorithm to recognize whole-sentences from continuous tongue and lip movements. Our goal is to assist persons who are aphonic or have a severe motor speech impairment to produce functional speech using their tongue and lips. Our algorithm was tested using a functional sentence data set collected from ten speakers (3012 utterances). The average accuracy was 94.89% with an average latency of 3.11 seconds for each sentence prediction. The results indicate the effectiveness of our approach and its potential for building a real-time articulation-based silent speech interface for clinical applications.
Evaluation of the Amount of Therapist Contact in a Smoking Cessation Program

This research tested a multicomponent self-help manual that contained nicotine fading and some behavioral techniques. It also evaluated the incremental effects of using higher amounts of therapist contact on quitting rates. 114 smokers were randomly assigned to one of four treatment groups: (1) A 10-session multicomponent program (n = 25); (2) a 5-session multicomponent program (n = 31); (3) a 5-session multicomponent plus a self-help manual program (n = 25); and (4) a self-help-manual-only program (n = 33). A control group (n = 48) did not receive any treatment. The distinctive characteristic of the treatments was the different amount of therapist contact. Common components of the programs were a refundable deposit, self-monitoring, information on smoking, stimulus control, CO feedback, nicotine fading, and strategies to avoid withdrawal symptoms. End-of- treatment quit rates ranged from 36% (self-help manual) to 68% (10-session multicomponent program). At 12-month follow-up there were significant differences between groups, and the most effective group was the 5-session plus manual group, with an abstinence rate of 48%. En esta investigación se ha evaluado un manual multicomponente de autoayuda para dejar de fumar. Este manual incluye un programa basado en la reducción gradual de nicotina y alquitrán, junto con otras técnicas conductuales. También se ha evaluado el efecto que sobre las tasas de abstinencia tiene incrementar el contacto terapéutico. Se asignaron al azar 114 fumadores a los siguientes grupos de tratamiento: (1) programa multicomponente con 10 sesiones (n = 25); (2) programa multicomponente con 5 sesiones (n = 31); (3) programa multicomponente con 5 sesiones y manual de autoayuda (n = 25); (4) manual de autoayuda (n = 33). Además hubo un grupo control (n = 48) que no recibió ningún tratamiento. Los grupos diferían entre sí en la cantidad de contacto terapéutico. El programa incluía: un depósito recuperable, autorregistros, información sobre el tabaco, control de estímulos, retroalimentación del nivel de monóxido de carbono (CO), reducción gradual de nicotina y estrategias para evitar el síndrome de abstinencia. La tasa de abstinencia al final del tratamiento osciló entre el 36% (grupo sólo con manual) y el 68% (grupo con 10 sesiones). A los 12 meses de seguimiento hubo diferencias estadísticamente significativas entre los grupos, siendo el tratamiento más efectivo el del grupo con 5 sesiones y manual, con un 48% de abstinencia.
OF NITROGEN FATE MODELS APPLICABLE TO FOREST LANDSCAPES IN THE SOUTHERN U .

Assessing the environmental impacts of fertilizer nitrogen (N) used to increase productivity in managed forests is complex due to a wide range of abiotic and biotic factors affecting its forms and movement. Models developed to predict fertilizer N fate (e.g., cycling processes) and water quality impacts vary widely in their design, scope, and potential application. We review the applicability of five commonly used eco-hydrologic models (APEX, MIKESHE-DNDC, DRAINMOD-FOREST, REMM, and SWAT) in assessing N fate and transport in southern forest landscapes (<50 km) because of their comprehensiveness and multi-scale predictions. The field-scale models DRAINMOD-FOREST and REMM contain process-level components characterizing hydrology, forest growth, and N dynamics, but they have limited capability to describe transport processes at the landscape scale. APEX can describe hydrology, forest growth, N fate processes, and plant competition at the landscape and small watershed scales mostly for upland. SWAT is best suited to hydrologic simulations at watershed scale (>50 km), although N routing below the subbasin level does not yet exist. Similarly, the distributed MIKESHE-DNDC model has been used to assess N cycles across different spatial scales, on both uplands and lowlands, but was not intended to model lateral N transport. However, MIKESHE alone is capable of describing the hydrology and N transport. The strengths of each of the models reflect their original design and scope intent. Based on this review, none of the five models that we considered is independently adequate to address the fate of N fertilizers applied to forest stands at both small and large scales, including uplands and lowlands. While efforts are underway to extend these tools’ capabilities and address their various limitations, the models must be validated using experimental data before using their outputs, together with uncertainty analysis, for developing forest fertilization guidelines and the fate and transport of N.