Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrating observability don't cares in all-solution SAT solvers

All-solution Boolean satisfiability (SAT) solvers are engines employed to find all the possible solutions to a SAT problem. Their applications are found throughout the EDA industry in fields such as formal verification, circuit synthesis and automatic test pattern generation. Typically, these engines iteratively find each solution by calling a standard SAT solving procedure. Each solution is minimized using different post processing techniques and the problem is constrained to prevent recurring solutions. In this work, instead of applying post processing techniques, the objective is to minimize the size of the solution "on the fly" during the all-solution SAT solving process. This is achieved by allowing the solver to exploit the structural circuit observability don't cares (ODC) arising from the problem. The solver makes decisions such that the number of ODCs is maximized in each solution thus leading to an overall smaller number of iterations. Through extensive experiments, it is demonstrated that integrating ODC techniques within an all-solution SAT solver results in increased performance and more compact solutions
Implementing software product lines using traits

A software product line (SPL) is a set of software systems with well-defined commonalities and variabilities that are developed by managed reuse of common artifacts. In this paper, we present a novel approach to implement SPL by fine-grained reuse mechanisms which are orthogonal to class-based inheritance. We introduce the Featherweight Record-Trait Java (FRTJ) calculus where units of product functionality are modeled by traits, a construct that was already shown useful with respect to code reuse, and by records, a construct that complements traits to model the variability of the state part of products explicitly. Records and traits are assembled in classes that are used to build products. This composition of product functionalities is realized by explicit operators of the calculus, allowing code manipulations for modeling product variability. The FRTJ type system ensures that the products in the SPL are type-safe by type-checking only once the records, traits and classes shared by different products. Moreover, type-safety of an extension of a (type-safe) SPL can be guaranteed by checking only the newly added parts.
Continuous trajectory estimation for 3D SLAM from actuated lidar

We extend the Iterative Closest Point (ICP) algorithm to obtain a method for continuous-time trajectory estimation (CICP) suitable for SLAM from actuated lidar. Traditional solutions to SLAM from actuated lidar rely heavily on the accuracy of an auxiliary pose sensor to form rigid frames. These frames are then used with ICP to obtain accurate pose estimates. However, since lidar records a single range sample at time, any error in inter-sample sensor motion must be accounted for. This is not possible if the frame is treated as a rigid point cloud. In this work, instead of ICP we estimate a continuous-time trajectory that takes into account inter-sample pose errors. The trajectory is represented as a linear combination of basis functions and formulated as a solution to a (sparse) linear system without restrictive assumptions on sensor motion. We evaluate the algorithm on synthetic and real data and show improved accuracy in open-loop SLAM in comparison to state-of-the-art rigid registration methods.
Fitness and energy expenditure after strength training in obese prepubertal girls.

PURPOSE The purpose of this study was to determine the effects of a school-based, low-volume strength training program on energy expenditure, strength, and physical fitness in obese prepubertal girls. METHODS A longitudinal, 5-month strength training exercise program was undertaken by healthy, obese (> 95th percentile weight-for-height, N = 11) girls age 7-10 yr. The following were measured: strength by the one-repetition maximum test; fitness (VO2peak) by a treadmill exercise test; resting metabolic rate (RMR), 24-h sedentary energy expenditure (SEE), and sleeping metabolic rate (SMR) by room respiration calorimetry; and total energy expenditure (TEE) by the doubly labeled water method. Physical activity energy expenditure (AEE) was calculated as TEE-(RMR + 0.1.TEE) and physical activity level (PAL) as TEE/RMR. An age-matched, nonoverweight control group was measured for (VO2peak) and RMR over the same time period. RESULTS Strength increased by 19.6 and 20.0% in the upper and lower body (P < 0.01), respectively. (VO2peak) (mL.min-1) increased in both groups over time (P < 0.05), but not when covaried for fat-free mass (FFM) or weight. After adjusting for FFM or weight, RMR did not change, but SMR and 24-h SEE decreased significantly in the exercise group. There were no changes in nonprotein respiratory quotient or substrate oxidation. No changes in TEE, AEE, and PAL occurred, either unadjusted or adjusted for FFM or weight. CONCLUSION This long-term, school-based, low-volume strength training program favorably increases strength in obese prepubertal girls but does not increase their daily energy expenditure.
Enterococcal Rgg-Like Regulator ElrR Activates Expression of the elrA Operon

ABSTRACT The Enterococcus faecalis leucine-rich protein ElrA promotes virulence by stimulating bacterial persistence in macrophages and production of the interleukin-6 (IL-6) cytokine. The ElrA protein is encoded within an operon that is poorly expressed under laboratory conditions but induced in vivo. In this study, we identify ef2687 (renamed elrR), which encodes a member of the Rgg (regulator gene for glucosyltransferase) family of putative regulatory proteins. Using quantitative reverse transcription-PCR, translational lacZ fusions, and electrophoretic mobility shift assays, we demonstrate that ElrR positively regulates expression of elrA. These results correlate with the attenuated virulence of the ΔelrR strain in a mouse peritonitis model. Virulence of simple and double elrR and elrA deletion mutants also suggests a remaining ElrR-independent expression of elrA in vivo and additional virulence-related genes controlled by ElrR.
Intra-Arterial Chemotherapy for Muscle-Invasive Bladder Cancer Following Transurethral Resection

Purpose: To assess the efficacy of intra-arterial chemotherapy as a bladder-preservation treatment in patients with muscle-invasive bladder cancer (MIBC) following transurethral resection of bladder tumors (TURBT). Materials and Methods: From 2005 June to 2012 November, 46 patients diagnosed with MIBC (clinical stage T2-T3N0M0) underwent three courses of cisplatin-based intra-arterial chemotherapy as a remedial approach for bladder preservation after TURBT. All patients also received intravesical instillation of chemotherapy as a maintenance strategy. Results: All 46 patients completed the treatment with minor complications. The median follow-up time was 34.5 months (range, 8-87 months). Thirty-two patients (69.6%) demonstrated complete response. The three-year and five-year overall survival was 70.65 and 61.23%, and the disease-specific survival over the same periods was 78.03 and 67.62%, respectively. During the entire follow-up period, more than 80% preserved their bladder. Conclusions: Intra-arterial chemotherapy can be performed as a remedial treatment for MIBC patient following TURBT. Combined with TURBT, it offers an option for bladder preservation therapy on patients who are unable or unwilling to undergo radical cystectomy.
Simple on-line algorithms for the maximum disjoint paths problem

In this paper we study the problem of finding disjoint paths in graphs. Whereas for specific graphs many (almost) matching upper and lower bounds are known for the competitiveness of on-line path selection algorithms, much less is known about how well on-line algorithms can perform in the general setting. In several papers the expansion has been used to measure the performance of off-line and on-line algorithms in this field. We study a class of simple deterministic on-line algorithms and show that they achieve a competitive ratio that is asymptotically equal to the best possible competitive ratio that can be achieved by any deterministic on-line algorithm. For this we use a parameter caled routing number which allows more precise results than the expansion. Interestingly, our upper bound on the competitive ratio is even better than the best approximation ratio known for off-line algorithms. Furthermore, we show that a refined variant of the routing number allows to construct on-line algorithms with a competitive ratio that is for many graphs significantly below the best possible upper bound for deterministic on-line algorithms if only the routing number or expansion of a graph is known. We also show that our algorithms can be transformed into efficient algorithms for the related unsplittable flow problem.
HER4 expression status correlates with improved outcome in both neoadjuvant and adjuvant Trastuzumab treated invasive breast carcinoma

Prognostic and predictive markers utilized in invasive breast carcinoma are limited and include ER, PR, Ki67, and ERBB2 (HER2). In the case of HER2, over-expression or amplification serves as eligibility for anti-HER2 based therapy, including trastuzumab (Herceptin®, Genentech). While clinical trials have shown trastuzumab improves overall survival and time to progression, an individual's response to anti-HER2 based therapy is highly variable. This suggests that, in a “uniform” HER2 positive population, additional markers could help in predicting patient outcome to therapy. Here we utilized a recently validated high-specificity HER4 antibody (E200) and generated a standard clinical HER4 scoring algorithm (HER4 H-Score) utilizing two breast carcinoma cohorts: 1) patients receiving neoadjuvant trastuzumab (n=47) and 2) patients receiving trastuzumab for metastatic disease (n=33). Our HER4 H-Score showed significant correlation with high sensitivity RT-qPCR performed on matched patients (p=<0.0001). In addition, patients with HER2/HER4 co-over-expression status showed a significant delay in development of metastasis after neo-adjuvant trastuzumab therapy (p= 0.04) and showed a significant improvement in progression free survival after adjuvant trastuzumab therapy (p=0.03). These findings suggest HER4 IHC, used in conjunction with a standard HER2 testing algorithm, could aid in predicting clinical outcome and help identify patients likely to show improved response to trastuzumab therapy.
Interactive visualization of unstructured grids using hierarchical 3D textures

We present a system for interactively rendering large, unstructured grids. Our approach is to voxelize the grid into a 3D voxel octree, and then to render the data using hierarchical, 3D texture mapping. This approach leverages the Current 3D texture mapping PC hardware for the problem of unstructured grid rendering. We specialize the 3D texture octree to the task of rendering unstructured grids through a novel pad and stencil algorithm, which distinguishes between data and non-data voxels. Both the voxelization and rendering processes efficiently manage large, out-of-core datasets. The system manages cache usage in main memory and texture memory, as well as bandwidths among disk, main memory, and texture memory. It also manages rendering load to achieve interactivity at all times. It maximizes a quality metric for a desired level of interactivity. It has been applied to a number of large data and produces high quality images at interactive, user-selectable frame rates using standard PC hardware.
Evaluating the Good Ontology Design Guideline (GoodOD) with the Ontology Quality Requirements and Evaluation Method and Metrics (OQuaRE)

Objective To (1) evaluate the GoodOD guideline for ontology development by applying the OQuaRE evaluation method and metrics to the ontology artefacts that were produced by students in a randomized controlled trial, and (2) informally compare the OQuaRE evaluation method with gold standard and competency questions based evaluation methods, respectively. Background In the last decades many methods for ontology construction and ontology evaluation have been proposed. However, none of them has become a standard and there is no empirical evidence of comparative evaluation of such methods. This paper brings together GoodOD and OQuaRE. GoodOD is a guideline for developing robust ontologies. It was previously evaluated in a randomized controlled trial employing metrics based on gold standard ontologies and competency questions as outcome parameters. OQuaRE is a method for ontology quality evaluation which adapts the SQuaRE standard for software product quality to ontologies and has been successfully used for evaluating the quality of ontologies. Methods In this paper, we evaluate the effect of training in ontology construction based on the GoodOD guideline within the OQuaRE quality evaluation framework and compare the results with those obtained for the previous studies based on the same data. Results Our results show a significant effect of the GoodOD training over developed ontologies by topics: (a) a highly significant effect was detected in three topics from the analysis of the ontologies of untrained and trained students; (b) both positive and negative training effects with respect to the gold standard were found for five topics. Conclusion The GoodOD guideline had a significant effect over the quality of the ontologies developed. Our results show that GoodOD ontologies can be effectively evaluated using OQuaRE and that OQuaRE is able to provide additional useful information about the quality of the GoodOD ontologies.
Teacher Quality in Educational Production: Tracking, Decay, and Student Achievement

Growing concerns over the achievement of U.S. students have led to proposals to reward good teachers and penalize (or fire) bad ones. The leading method for assessing teacher quality is "value added" modeling (VAM), which decomposes students' test scores into components attributed to student heterogeneity and to teacher quality. Implicit in the VAM approach are strong assumptions about the nature of the educational production function and the assignment of students to classrooms. In this paper, I develop falsification tests for three widely used VAM specifications, based on the idea that future teachers cannot influence students' past achievement. In data from North Carolina, each of the VAMs' exclusion restrictions are dramatically violated. In particular, these models indicate large "effects" of 5th grade teachers on 4th grade test score gains. I also find that conventional measures of individual teachers' value added fade out very quickly and are at best weakly related to long-run effects.
Male Homosexuality in Modern Japan: Cultural Myths and Social Realities

This book is the first to look at the wide range of contrasting images of the gay male body in Japanese popular culture, both mainstream and gay, and relate these images to the experience of an interview sample of Japanese gay men. In so doing, it touches on a number of important issues, including whether there can be a universal 'gay identity' and whether or not strategies developed for increasing gay and lesbian visibility in western countries are appropriate to the social situation in Japan
A Before-School Counselor Intervention that Promotes Peer Relational Skills and Influences Prosocial Behavior

The purpose of this dissertation was to understand the student experience and perception of change after participating in a before-school counselor intervention focused on learning prosocial behaviors and developing peer relational skills. This evaluation included both how students experienced the program and if they perceived any change in themselves after participating in the program. Qualitative methods are often used in evaluations because they tell the program’s story by capturing and communicating the participant’s stories (Patton, 2003, p. 2). The purpose of this type of method was to illuminate the process and outcomes of a program. The intent of qualitative findings was to deepen understanding through the eyes of the participants or to “put faces on the statistics to deepen understanding” (Patton, 2003, p. 2). In order to understand the student experience and perception of change, the researcher interviewed eight students who participated in a 12-week before-school program. The interviews were recorded, transcribed, and analyzed. Analysis of the data
Restricted Substrate Specificity for the Geranylgeranyltransferase-I Enzyme in Cryptococcus neoformans: Implications for Virulence

ABSTRACT Proper cellular localization is required for the function of many proteins. The CaaX prenyltransferases (where CaaX indicates a cysteine followed by two aliphatic amino acids and a variable amino acid) direct the subcellular localization of a large group of proteins by catalyzing the attachment of hydrophobic isoprenoid moieties onto C-terminal CaaX motifs, thus facilitating membrane association. This group of enzymes includes farnesyltransferase (Ftase) and geranylgeranyltransferase-I (Ggtase-1). Classically, the variable (X) amino acid determines whether a protein will be an Ftase or Ggtase-I substrate, with Ggtase-I substrates often containing CaaL motifs. In this study, we identify the gene encoding the β subunit of Ggtase-I (CDC43) and demonstrate that Ggtase-mediated activity is not essential. However, Cryptococcus neoformans CDC43 is important for thermotolerance, morphogenesis, and virulence. We find that Ggtase-I function is required for full membrane localization of Rho10 and the two Cdc42 paralogs (Cdc42 and Cdc420). Interestingly, the related Rac and Ras proteins are not mislocalized in the cdc43Δ mutant even though they contain similar CaaL motifs. Additionally, the membrane localization of each of these GTPases is dependent on the prenylation of the CaaX cysteine. These results indicate that C. neoformans CaaX prenyltransferases may recognize their substrates in a unique manner from existing models of prenyltransferase specificity. It also suggests that the C. neoformans Ftase, which has been shown to be more important for C. neoformans proliferation and viability, may be the primary prenyltransferase for proteins that are typically geranylgeranylated in other species.
In the twinkling of an eye: Synchronization of EEG and eye tracking based on blink signatures

Achieving robust adaptive synchronization of multimodal biometric inputs: The recent arrival of wireless EEG headsets that enable mobile real-time 3D brain imaging on smartphones, and low cost eye trackers that provide gaze control of tablets, will radically change how biometric sensors might be integrated into next generation user interfaces. In experimental lab settings EEG neuroimaging and eye tracking data are traditionally combined using external triggers to synchronize the signals. However, with biometric sensors increasingly being applied in everyday usage scenarios, there will be a need for solutions providing a continuous alignment of signals. In the present paper we propose using spontaneous eye blinks, as a means to achieve near real-time synchronization of EEG and eye tracking. Analyzing key parameters that define eye blink signatures across the two domains, we outline a probability function based algorithm to correlate the signals. Comparing the accuracy of the method against a state of the art EYE-EEG plug-in for offline analysis of EEG and eye tracking data, we propose our approach could be applied for robust synchronization of biometric sensor data collected in a mobile context.
Mind and brain: Dialogues in cognitive neuroscience

Researchers in both the brain and the cognitive sciences are attempting to understand the mind. They should be natural allies, but neuroscientists and cognitive psychologists tend to work in isolation. Brain and Mind represents a pioneering attempt to bring them together. The editors' objective was to force scientists who are working on the same problem but from different perspectives to address each other. Through a series of written dialogues on four topics - attention, perception, memory, and emotion - leading researchers sought to discover similarities and differences in their varied approaches. The dialogues demonstrate compellingly that workers in neuroscience and cognition have much to gain by increasing their interactions across disciplinary boundaries. The eight main chapters are each detailed, up-to-date, scholarly reviews of the major methodological, theoretical, and empirical issues.
Synthetic Studies of Natural 10-Membered Lactones, Mueggelone, Microcarpalide, and Sch 642305, Which Have Interesting Bioactivities

A number of 10-membered lactones have been isolated as secondary metabolites, and many of them have interesting and potent activities. Because of synthetic and biological interests, many synthetic studies of these compounds have been made. This review summarizes synthetic approaches to three natural 10-membered lactones, mueggelone, microcarpalide, and Sch 642305. Mueggelone is an inhibitor of fish development, microcarpalide is a microfilament disrupting agent, and Sch 642305 is an inhibitor of bacterial DNA primase.
Regulation of Brain-Derived Neurotrophic Factor Exon IV Transcription through Calcium Responsive Elements in Cortical Neurons

Activity-dependent transcription of brain-derived neurotrophic factor (BDNF) has been studied as an important model to elucidate the mechanisms underlying numerous aspects of neuroplasticity. It has been extensively emphasized that Ca2+ influx through different routes may have significantly different effects on BDNF transcription. Here, we examined the regulatory property of the major calcium responsive elements (CaRE) in BDNF promoter IV in cultured rat cortical neurons. BDNF promoter IV, as well as CaRE1 and CaRE3, was significantly activated by Ca2+ influx through L-type voltage-gated calcium channel (L-VGCC) or NMDA receptor (NMDAR). However, the L-VGCC- and NMDAR-mediated activation of CaRE was differentially regulated by different Ca2+-stimulated protein kinases. Specifically, PKA, CaMKI, and CaMKIV activity were required for L-VGCC-, but not NMDAR-mediated CaRE1 activation. CaMKI activity was required for NMDAR- but not L-VGCC-mediated CaRE3 activation. Surprisingly, the activation of CaRF, a previously identified transcription factor for CaRE1, was stimulated via L-VGCC but not NMDAR, and required MEK, PI3K and CaMKII activity. These results suggest a new working model that activity-dependent BDNF IV up-regulation may be coordinately mediated by CaRE1 and CaRE3 activity, which show different responses to Ca2+-stimulated kinases. Our data also explain how the individual cis-element in BDNF promoter is distinctively coupled to different Ca2+ routes.