Miracle-dz/UniFAR-FTUs huggingface dataset:
The Relevance of Application Domain Knowledge: Characterizing the Computer Program Comprehension Process

Recent research using professional programmers suggests that knowledge of the application domain plays a major role in the cognitive processes they use to understand computer programs. In general, programmers use a more top-down comprehension process when working in familiar application domains, and a more bottom-up process in unfamiliar domains. The present study builds on that research by further characterizing comprehension processes. The findings show that: (1) certain programmers use different types of comprehension processes depending on their familiarity with the application domain (flexible approach), while others do not (top-down and bottom-up approaches); (2) familiarity with the application domain and the use of a particular comprehension process have marked effects on references programmers make to both application and programming domain knowledge; and (3) programmers who use a flexible comprehension process achieved the highest levels of comprehension. The present research also examines some cognitive determinants of the comprehension process. The findings highlight the need to consider application, as well as programming, domain knowledge as areas of computer programming expertise, to investigate factors influencing use of specific comprehension processes, and to develop tools to support flexible comprehension processes.
Impact of Stewardship Intervention on Improving Antibiotic Prescribing Practices

Background: Antimicrobial stewardship programs (ASPs) have been found to be an effective method for minimizing antibiotic misuse. Method: A study comparing the quality of antibiotic prescriptions between a one-year period before ASP implementation and a one-year period after its implementation. For each period, antimicrobial prescriptions were evaluated by an antimicrobial stewardship team and classified as appropriate or inappropriate. Results: An improvement between Phase I and Phase II was found in all antibiotic therapies. Discussion: The overall antibiotic inappropriate rate was 45.8% before implemented the stewardship program, which is relatively high and consistent with the findings of other studies mentioned in the literature. Conclusion: Applying the stewardship program led to a significant decrease of the inappropriate use of antibiotics at the hospital.
Yale-CMU-Berkeley dataset for robotic manipulation research

In this paper, we present an image and model dataset of the real-life objects from the Yale-CMU-Berkeley Object Set, which is specifically designed for benchmarking in manipulation research. For each object, the dataset presents 600 high-resolution RGB images, 600 RGB-D images and five sets of textured three-dimensional geometric models. Segmentation masks and calibration information for each image are also provided. These data are acquired using the BigBIRD Object Scanning Rig and Google Scanners. Together with the dataset, Python scripts and a Robot Operating System node are provided to download the data, generate point clouds and create Unified Robot Description Files. The dataset is also supported by our website, www.ycbbenchmarks. org, which serves as a portal for publishing and discussing test results along with proposing task protocols and benchmarks.
Taxonomic isolation and the accumulation of herbivorous insects: a comparison of introduced and native trees

Abstract. 1 Evidence from leaf‐mining insects on Fagaceous hosts suggests that range expansions of insects onto introduced trees often involve species that feed on native hosts closely related to the introduced host. 2 An examination of the herbivorous entomofauna of British trees illustrates that the size of the entomofauna is partially determined by the taxonomic isolation of the host tree.
Interpreting Questions with a Log-Linear Ranking Model in a Virtual Patient Dialogue System

We present a log-linear ranking model for interpreting questions in a virtual patient dialogue system and demonstrate that it substantially outperforms a more typical multiclass classifier model using the same information. The full model makes use of weighted and concept-based matching features that together yield a 15% error reduction over a strong lexical overlap baseline. The accuracy of the ranking model approaches that of an extensively handcrafted pattern matching system, promising to reduce the authoring burden and make it possible to use confidence estimation in choosing dialogue acts; at the same time, the effectiveness of the concept-based features indicates that manual development resources can be productively employed with the approach in developing concept hierarchies.
Identification of Critical Elements for Regulation of Inorganic Pyrophosphatase (PPA1) in MCF7 Breast Cancer Cells

Cytosolic inorganic pyrophosphatase plays an important role in the cellular metabolism by hydrolyzing inorganic pyrophosphate (PPi) formed as a by-product of various metabolic reactions. Inorganic pyrophosphatases are known to be associated with important functions related to the growth and development of various organisms. In humans, the expression of inorganic pyrophosphatase (PPA1) is deregulated in different types of cancer and is involved in the migration and invasion of gastric cancer cells and proliferation of ovarian cancer cells. However, the transcriptional regulation of the gene encoding PPA1 is poorly understood. To gain insights into PPA1 gene regulation, a 1217 bp of its 5’-flanking region was cloned and analyzed. The 5’-deletion analysis of the promoter revealed a 266 bp proximal promoter region exhibit most of the transcriptional activity and upon sequence analysis, three putative Sp1 binding sites were found to be present in this region. Binding of Sp1 to the PPA1 promoter was confirmed by Electrophoretic mobility shift assay (EMSA) and Chromatin immunoprecipitation (ChIP) assay. Importance of these binding sites was verified by site-directed mutagenesis and overexpression of Sp1 transactivates PPA1 promoter activity, upregulates protein expression and increases chromatin accessibility. p300 binds to the PPA1 promoter and stimulates Sp1 induced promoter activity. Trichostatin A (TSA), a histone deacetylase (HDAC) inhibitor induces PPA1 promoter activity and protein expression and HAT activity of p300 was important in regulation of PPA1 expression. These results demonstrated that PPA1 is positively regulated by Sp1 and p300 coactivates Sp1 induced PPA1 promoter activity and histone acetylation/deacetylation may contribute to a local chromatin remodeling across the PPA1 promoter. Further, knockdown of PPA1 decreased colony formation and viability of MCF7 cells.
Learning in Time Ordered Domains with Hidden Changes in Context

Concept drift due to hidden changes in context complicates learning in many real world domains including nancial prediction, medical diagnosis, and communication network performance. Machine learning systems addressing this problem generally use an incremental learning, on-line paradigm. An o-line, meta-learning approach to the identication of hidden context is presented. This approach uses an existing batch learner and the process of contextual clustering to identify stable hidden contexts, and the associated, context specic, locally stable concepts. The approach is broadly applicable to a range of domains and learning methods. We describe several evaluation domains and report current progress on these domains.
Preliminary Screening of Glycoprotein Profiles in Human Normal and Lung Cancer Sera by Different Staining Methods

In this study, the purposes were to compare the staining methods for detection of glycoprotein profiles in normal and lung cancer serum samples and to preliminary screen the carbohydrate specificity of glycoproteins in both serum samples. Using the sequential staining methods of Pro-Q Emerald 488 glycoprotein gel staining, SYPRO® Ruby staining and silver staining revealed that the Emerald 488 glycoprotein gel staining has the specific detection of glycoproteins compared with SYPRO® Ruby and silver staining and provided the differential glycoprotein profiles between normal and lung cancer serum samples. In addition, seven FITC-labeled lectins; Con A, PNA, ECL, WGA, MAL 1, AAL and UEA, were used to detect the differentially expressed glycoproteins and the carbohydrate specificity of glycoproteins in both samples. The results of lectin staining showed that Con A, WGA and AAL lectins have the strong reactivity to the glycoproteins in both samples compared with other lectins and gave the differentially expressed glycoproteins in lung cancer sera. It indicated that the serum glycoproteins in both samples contain the high contents of mannose, GlcNAc, sialic acid and fucose (α1-3/4, a1-6) residues, in which their expression levels may be correlated to the lung cancer development. Therefore, this preliminary detection method was not only used to screen the altered glycoproteins in human normal and lung cancer sera, but also provided the different carbohydrate specificities of glycoproteins that are very useful for further selective glycoprotein purification and analysis.
On the Lattice Isomorphism Problem

We study the Lattice Isomorphism Problem (LIP), in which given two lattices L_1 and L_2 the goal is to decide whether there exists an orthogonal linear transformation mapping L_1 to L_2. Our main result is an algorithm for this problem running in time n^{O(n)} times a polynomial in the input size, where n is the rank of the input lattices. A crucial component is a new generalized isolation lemma, which can isolate n linearly independent vectors in a given subset of Z^n and might be useful elsewhere. We also prove that LIP lies in the complexity class SZK.
Involvement of phosphatidylinositol 4,5-bisphosphate in RNA polymerase I transcription

Summary RNA polymerase I (Pol I) transcription is essential for the cell cycle, growth and protein synthesis in eukaryotes. In the present study, we found that phosphatidylinositol 4,5-bisphosphate (PIP2) is a part of the protein complex on the active ribosomal promoter during transcription. PIP2 makes a complex with Pol I and the Pol I transcription factor UBF in the nucleolus. PIP2 depletion reduces Pol I transcription, which can be rescued by the addition of exogenous PIP2. In addition, PIP2 also binds directly to the pre-rRNA processing factor fibrillarin (Fib), and co-localizes with nascent transcripts in the nucleolus. PIP2 binding to UBF and Fib modulates their binding to DNA and RNA, respectively. In conclusion, PIP2 interacts with a subset of Pol I transcription machinery, and promotes Pol I transcription.
Optimizing principles underlying the shape of trajectories in goal oriented locomotion for humans

This paper addresses the problem of understanding the shape of the locomotor trajectories for a human being walking in an empty space to reach a goal defined both in position and in direction. Among all the possible trajectories reaching a given goal what are the fundamental reasons to chose one trajectory instead of another? The underlying idea to attack this question has been to relate this problem to an optimal control problem: the trajectory is chosen according to some optimization principle. This is our basic starting assumption. The subject being viewed as a controlled system, the question becomes what criteria is optimized? Is it the time to perform the trajectory? the length of the path? the minimum jerk along the path? In this study we show that the human locomotor trajectories are well approximated by the geodesics of a differential system minimizing the L2 norm of the control. Such geodesics are made of arcs of clothoids. The clothoid or Cornu spiral is a curve, whose curvature grows with the distance from the origin. The study is based on an experimental protocol involving 7 subjects. They had to walk within a motion capture room from a fixed starting point, and to cross over distant porches from which both position in the room and orientation were changing over trials.
A Multi-camera, Multi-projector Super-Resolution Framework for Structured Light

In this work, we present a framework for multi-camera, multi-projector object acquisition based on structured light. This approach allows the reconstruction of an object without moving either the object or the acquisition setup, avoiding any registration of independent measurements. To overcome the resolution limitations of the individual projectors, we introduce a novel super-resolution scheme. By exploiting high dynamic range imaging, we are able to handle even complicated objects, exhibiting strong specularities. We show that, combined with an iterated bundle adjustment, these improvements increase the accuracy of the obtained point cloud.
A 17-nW, 0.5V, 500S/s, rail-to-rail SAR ADC with 8.1 effective number of bits

This paper presents a successive approximation register (SAR) analog-to-digital converter (ADC) in 0. 18μm CMOS for low-power applications. The SAR ADC achieves a wide effective resolution bandwidth (ERBW) and a rail-to-rail signal swing by applying a limited number of bootstrapped switches. A robust low-voltage amplifier is proposed as the building block of the comparator. Measurement results show that at a supply voltage of 0.5-V and an output rate of 500S/s, the SAR ADC achieves a peak signal-to-noise-and-distortion ratio of 50.4 dB and an ERBW up to the Nyquist bandwidth (250 Hz). It consumes only 17 nW.
Clustering-Based Collaborative Filtering for Link Prediction

In this paper, we propose a novel collaborative filtering approach for predicting the unobserved links in a network (or graph) with both topological and node features. Our approach improves the well-known compressed sensing based matrix completion method by introducing a new multiple-independent-Bernoulli-distribution model as the data sampling mask. It makes better link predictions since the model is more general and better matches the data distributions in many real-world networks, such as social networks like Facebook. As a result, a satisfying stability of the prediction can be guaranteed. To obtain an accurate multiple-independent-Bernoulli-distribution model of the topological feature space, our approach adjusts the sampling of the adjacency matrix of the network (or graph) using the clustering information in the node feature space. This yields a better performance than those methods which simply combine the two types of features. Experimental results on several benchmark datasets suggest that our approach outperforms the best existing link prediction methods.
Fluorescent Voltage‐Sensitive Dyes: Applications for Neurophysiology

Voltage-sensitive dyes are a means to optically monitor changes in membrane potential. Their application in research has grown steadily over the last two decades as better dyes have been developed. The techniques presently in use are providing unique information about biologic systems from bacteria to the functional organization of primate occipital cortex. This review provides a history of the dyes, the data supporting their voltage sensitivity, and the techniques required for their use. The limitations in using and interpreting the voltage-sensitive dyes, as well as their diverse applications in all areas of research, especially neurophysiology, are comprehensively presented.
Moderating Effects of Climate and External Support on Transformational Leadership and Technological Innovation: An Investigation in Creative Ventures in Turkey

The purpose of this study was to investigate the influence of transformational leadership on technological innovation at the organizational level. Specifically, it was proposed that transformational leadership would have a positive effect on organizational innovation. Furthermore, this effect was proposed to be moderated by an innovation-supporting climate and support received from external organizations. These relationships were tested on 163 R&D personnel and managers of 43 micro- and small-sized Turkish entrepreneurial software development companies. The results confirmed the positive impact of transformational leadership on organizational innovation, which was measured with a market-oriented criterion developed specifically for developing countries and newly developing industries. Furthermore, the relationship between transformational leadership and organizational innovation was stronger when external support was at high levels than when there was no external support. The moderating effect of an innovation-supporting climate was not significant. Managerial implications as well as policy recommendations are provided, for micro and small-sized enterprises in particular
Effect of processing techniques on the contents of flatulence factors and emulsion properties of cowpea ( Vigna unguiculata )

The effect of some processing techniques (germination boiling and dehulling) on the soluble sugar contents and the emulsion property of processed flour were studied. Results show that germination significantly reduced the raffinose level from the third to the fifth day sprouting period (P 0.05). The contents of other soluble sugars-galactose, glucose and sucrose were increased by germination (P 0.05) but reduced by dehulling (P>0.05). Germination, dehulling and boiling lowered the emulsion stability property of cowpea flour. Even though, it is not conventional to either malt or dehull cowpea seeds before cooking, individuals should be advised to do so, in order to minimize the flatus potential and the accompanied discomfort associated with beans consumption. However, such processing techniques would not be appropriate for foods that need good emulsion. Journal of Applied Sciences and Environmental Management Vol. 9(2) 2005: 65-72
Gait-based recognition of humans using continuous HMMs

Gait is a spatio-temporal phenomenon that typifies the motion characteristics of an individual. In this paper, we propose a view-based approach to recognize humans through gait. The width of the outer contour of the binarized silhouette of a walking person is chosen as the image feature. A set of stances or key frames that occur during the walk cycle of an individual is chosen. Euclidean distances of a given image from this stance set are computed and a lower-dimensional observation vector is generated. A continuous hidden Markov model (HMM) is trained using several such lower-dimensional vector sequences extracted from the video. This methodology serves to compactly capture structural and transitional features that are unique to an individual. The statistical nature of the HMM renders overall robustness to gait representation and recognition. The human identification performance of the proposed scheme is found to be quite good when tested in natural walking conditions.
Properties and roles of an intramembranous charge mobilized at high voltages in frog skeletal muscle.

1. Membrane Ca2+ currents (ICa), intramembranous charge movement currents and changes in intracellular Ca2+ concentrations were recorded in voltage clamped cut skeletal muscle fibres of the frog. Intra‐ and extracellular solutions, designed to prevent ionic current, and use of the saponin‐permeabilization procedure made possible the measurement of transfer of intramembranous charge up to high positive potentials. 2. Substantial charge moved at positive potentials. This charge was shown to be intramembranous in four tests of charge conservation, demonstrating that the total displacement of charge depended only on the initial and final voltages, and not on the history or pathway of intermediate voltages. 3. On average, in twenty‐three cells, the charge moved at 50 mV was 31 +/‐ 1.9 nC microF‐1 (mean +/‐ S.E.M.), and at 0 mV was 25 +/‐ 1.5 nC microF‐1. Approximately one‐fifth of the total charge moved above 0 mV. 4. The charge that moved at high voltage could be fitted, in most cases, with a Boltzmann distribution function. In twenty of twenty‐three cells, the total charge distribution could be fitted as the sum of two Boltzmann terms; the high voltage term was centred at 11 +/‐ 3.9 mV, with a steepness factor of 12 +/‐ 1.6 mV and a magnitude of 8.6 +/‐ 1.1 nC microF‐1. The low voltage term was centered at ‐43 +/‐ 2.1 mV, with a steepness factor of 7.7 +/‐ 0.6 mV and a magnitude of 22 +/‐ 1.8 nC microF‐1. Thus, the high voltage component comprised about one‐quarter of the mobile charge. In four cells it was possible to fit the sum of three Boltzmann terms to the distribution of mobile charge; the parameters of the high voltage term then were similar to those found by fitting the sum of two Boltzmann terms to the same data. 5. The voltage dependence of activation of ICa was determined in a buffered 2 mM Ca2+ external solution, from the tails of ionic current at ‐30 mV, after activating pulses to various voltages, the duration of which was sufficient to reach the peak of inward current. The voltage dependence was described by a Boltzmann function centred at 2.6 +/‐ 6.9 mV (n = 6), with a steepness factor of 20 +/‐ 1.4 mV. The voltages at which the high voltage charge moved were roughly the same as those at which ICa was activated. 6. Calcium release from the sarcoplasmic reticulum was determined from the Ca2+ transients. Calcium release continued to increase at potentials above 0 mV. (ABSTRACT TRUNCATED AT 400 WORDS)
MDL region-based image registration

We propose a new image registration criterion that uses segmented versions of the images to exploit both the geometric and photometric characteristics of the distinct regions they contain. It is inspired on the minimum description length principle, considering the alignment parameters as side information, in a coding framework. The criterion is robust with respect to unstable segmentation, a frequent problem in close observation of natural scenes. Results on real images illustrate the performance attained.
Dynamic relocalization of hOGG1 during the cell cycle is disrupted in cells harbouring the hOGG1-Cys326 polymorphic variant

Numerous lines of evidence support the role of oxidative stress in different types of cancer. A major DNA lesion, 8-oxo-7,8-dihydroguanine (8-oxoG), is formed by reactive oxygen species in the genome under physiological conditions. 8-OxoG is strongly mutagenic, generating G·C→T·A transversions, a frequent somatic mutation in cancers. hOGG1 was cloned as a gene encoding a DNA glycosylase that specifically recognizes and removes 8-oxoG from 8-oxoG:C base pairs and suppresses G·C→T·A transversions. In this study, we investigated the subcellular localization and expression of hOGG1 during the cell cycle. Northern blots showed cell-cycle-dependent mRNA expression of the two major hOGG1 isoforms. By using a cell line constitutively expressing hOGG1 fused to enhanced green fluorescence protein (EGFP), we observed a dynamic relocalization of EGFP-hOGG1 to the nucleoli during the S-phase of the cell cycle, and this localization was shown to be linked to transcription. A C/G change that results in an amino acid substitution from serine to cysteine in codon 326 has been reported as a genetic polymorphism and a risk allele for a variety of cancers. We investigated the cellular localization of the corresponding protein, hOGG1-Cys326, fused to EGFP and observed a dramatic effect on its localization that is explained by a change in the phosphorylation status of hOGG1.