Miracle-dz/UniFAR-FTUs huggingface dataset:
Supporting Merge Conflict Resolution by Using Fine-Grained Code Change History

Modern version control systems facilitate concurrent work in software development by providing a mechanism to merge revisions that are independently modified by multiple programmers. However, merge conflicts might emerge due to concurrent modifications, and their resolution might require the programmers to scrutinize every modification in the revisions. This paper presents a tool that can alleviate this cumbersome task of merging conflicting revisions. Our tool exploits the fine-grained edit operation history of Java source code and extracts only the edit operations that affect the revision of a particular class member. By just replaying the extracted edit operations, it helps programmers detect merge conflicts between class members within the two revisions and understand the modifications of the conflicting class members. Moreover, it can artificially merge two snapshots that appear during the evolution of the two revisions and show the programmers a unique artificial snapshot that is consistent with both the merged snapshots. By replaying the fine-grained edits that cause merge conflicts and showing the apparent snapshots with no conflicts as hints of the merged revision, the tool reduces the burden of inspecting the code changes behind the conflicts and reconciling the conflicting revisions.
Anti–DNA B Cells in MRL/lpr Mice Show Altered Differentiation and Editing Pattern

We have studied the regulation of anti–DNA B cells in transgenic mice with a heavy chain transgene (3H9H/56R). This transgene codes for a heavy chain that forms anti–double-stranded DNA (dsDNA) antibody when paired with most members of the endogenous Vκ repertoire, but certain L chains, referred to as Vκ editors, do not sustain dsDNA binding in combination with 3H9H/56R. In the nonautoimmune 3H9H/56R BALB/c, most B cells generated do not bind DNA because the transgene itself is edited or is associated with a Vκ editor. A minor population of B cells (30%) bind dsDNA and express the λ1 light chain (known to sustain 3H9H/56R DNA binding). These 3H9/56R/λ1 B cells coexpress a κ editor, and we propose that the down-regulation of the anti-DNA BCR caused by the dual L chain expression may prevent activation of this κ/λ population. These κ/λ B cells are sequestered in the marginal zone. Here, we studied the influence of autoimmunity on expression and regulation of 3H9H/56R. In 3H9H/56R MRL/lpr mice, the expression of anti-dsDNA is vastly accelerated. Anti–dsDNA B cells use noneditor κs but, in addition, most anti–dsDNA B cells have edited the heavy chain transgene. λ1 B cells (without the coexpression of a κ editor) are found and the κ/λ1 MZ population is absent. Our results suggest that improper editing and failure to sequester autoreactive B cells may contribute to the breakdown of tolerance in MRL/lpr mice.
NF-κB Signaling, Elastase Localization, and Phagocytosis Differ in HIV-1 Permissive and Nonpermissive U937 Clones1

To identify positive or negative factors for HIV-1 infectivity, clones from the U937 promonocytic cell line that express similar levels of CD4 and CXCR4, but differ in HIV-1 susceptibility, were compared. In contrast to HIV-1 permissive clone 10 (plus), nonpermissive clone 17 (minus) was adherent to coverslips coated with chemokines, was phagocytic, killed bacteria, and expressed human leukocyte elastase (HLE) in a granule-like compartment (HLEG) that was never detected at the cell surface (HLECS). In contrast to the minus clone, the plus clone expressed HLE on the cell surface and was adherent to coverslips coated with the HLECS ligands α1proteinase inhibitor (α1PI, α1antitrypsin) and the HIV-1 fusion peptide. The phosphorylation status of several important signaling proteins was studied at the single cell level. Tumor suppressor p53, NF-κB p65, and Akt were constitutively phosphorylated in the plus clone, but not in the minus clone. Surprisingly, both α1PI and LPS induced phosphorylation of NF-κB p65 Ser-536 in both clones, but induced dephosphorylation of Ser-529 in the plus clone only. HIV-1 permissivity was conferred to the minus clone in a manner that required stimulation by both α1PI and LPS and was coincident to NF-κB p65 phosphorylation/dephosphorylation events as well as translocation of HLE to the cell surface. Even when stimulated, the minus clone exhibited greater reverse transcriptase activity, but less p24, than the plus clone. Results presented suggest that HIV-1 uptake and production efficiency are influenced by signaling profiles, receptor distribution, and the phagocytic capacity specific to the stage of differentiation of the CD4+ target cell.
ART-GAS: an adaptive and real-time GTS allocation scheme for IEEE 802.15.4

IEEE 802.15. 4 supports a Guaranteed Time Slot (GTS) allocation mechanism for time-critical and delay-sensitive data transmissions in Wireless Personal Area Networks (WPANs). However, the inflexible first-come-first-served GTS allocation policy and the passive deallocation mechanism significantly reduce network efficiency. In this paper, we propose an Adaptive and Real-Time GTS Allocation Scheme (ART-GAS) to provide differentiated services for devices with different priorities, which guarantees data transmissions for time-sensitive and high-traffic devices. The bandwidth utilization in IEEE 802.15. 4-based PAN is improved. Simulation results show that our ART-GAS algorithm significantly outperforms the existing GTS mechanism specified in IEEE 802.15. 4.
Performance evaluation of a voice call handover scheme between LTE and UMTS

In this paper we analyze the performance of a voice handover scheme for Long Term Evolution (LTE) and Universal Mobile Telecommunications System (UMTS) networks. Single Radio Voice Call Continuity (SRVCC) is deemed to be the long-term solution for LTE and UMTS voice handover. The scheme is modeled on handover signal flows. The analysis is done using a Radio Link Control (RLC) Protocol model, a network node queuing model and a remote network model. The simulation of the handover performance was on these three models. The simulation results were analyzed and compared with Third Generation Partnership Project (3GPP) specifications.
Program Slicing Based Web-Service Generation and Composition

As the development of web services, much attention has been drawn to web service because of its convenience and platform-independence. However, how to discover, generate and compose services has become an open issue recently. This paper proposes a method based on program slicing to realize the generation and composition of web services. It gives the method about how to generate a WSDL file and a SOAP message from source codes as well as a theory of function dependence graph. The results of experiments show that our methods of web service generation and composition are feasible and effective.
Metabolic model for diversity-generating biosynthesis

Significance How is chemical diversity generated by biological systems? Some biosynthetic pathways are constrained to produce one metabolite, but others are relatively relaxed and can produce a set of diverse compounds. Using the example of the tru pathway to cyanobactins, we propose a model of diversity-generating metabolism in which pathway flux and properties are strikingly different from the canonical design of conventional metabolic pathways. A conventional metabolic pathway leads to a specific product. In stark contrast, there are diversity-generating metabolic pathways that naturally produce different chemicals, sometimes of great diversity. We demonstrate that for one such pathway, tru, each ensuing metabolic step is slower, in parallel with the increasing potential chemical divergence generated as the pathway proceeds. Intermediates are long lived and accumulate progressively, in contrast with conventional metabolic pathways, in which the first step is rate-limiting and metabolic intermediates are short-lived. Understanding these fundamental differences enables several different practical applications, such as combinatorial biosynthesis, some of which we demonstrate here. We propose that these principles may provide a unifying framework underlying diversity-generating metabolism in many different biosynthetic pathways.
Computation of Stirling Numbers and Generalizations

We consider the computation of Stirling numbers and generalizations for positive and negative arguments. We describe computational schemes for Stirling Partition and Stirling Cycle numbers, and for their generalizations to associated Stirling numbers. The schemes use recurrence relations and are more efficient than the current method used in Maple for cycle numbers, which is based on an algebraic expansion.
High Capacity and Statistical Attacks Resistant Reversible Image Data Hiding Scheme using LSB Substitution

Reversible data hiding technique is advancing with each passing day. It is a form of steganography in which the hidden data can be recovered or extracted by the authorized user. In this paper, we have proposed the variable least significant bit based digital image hiding system based on LSB substitution. The proposed scheme has high security, better embedding capacity and increased imperceptibility. Also, the proposed scheme successfully resists the stastical attacks like Rs analysis, histogram analysis and chi-square analysis which adds to the efficiency of the proposed scheme. General Terms Steganography, Cryptography, Steganalysis.
Prioritizing consumers in smart grid: Energy management using game theory

This paper explores an idea of demand-supply balance for smart grids in which consumers are expected to play a significant role. The main objective is to motivate the consumer, by maximizing their benefit both as a seller and a buyer, to trade their surplus energy with the grid so as to balance the demand at the peak hour. To that end, a Stackelberg game is proposed to capture the interactions between the grid and consumers, and it is shown analytically that optimal energy trading parameters that maximize customers' utilities are obtained at the solution of the game. A novel distributed algorithm is proposed to reach the optimal solution of the game, and numerical examples are used to assess the properties and effectiveness of the proposed approach.
Synthesis and consolidation of boron carbide: a review

Boron carbide is a strategic material, finding applications in nuclear industry, armour for personnel and vehicle safety, rocket propellant, etc. Its high hardness makes it suitable for grinding and cutting tools, ceramic bearing, wire drawing dies, etc. Boron carbide is commercially produced either by carbothermic reduction of boric acid in electric furnaces or by magnesiothermy in presence of carbon. Since many specialty applications of boron carbide require dense bodies, its densification is of great importance. Hot pressing and hot isostatic pressing are the main processes employed for densification. In the recent past, various researchers have made attempts to improve the existing methods and also invent new processes for synthesis and consolidation of boron carbide. All the techniques on synthesis and consolidation of boron carbide are discussed in detail and critically reviewed.
Genetic Systems to Investigate Regulation of Oncogenes and Tumour Suppressor Genes in Drosophila

Animal growth requires coordination of cell growth and cell cycle progression with developmental signaling. Loss of cell cycle control is extremely detrimental, with reduced cycles leading to impaired organ growth and excessive proliferation, potentially resulting in tissue overgrowth and driving tumour initiation. Due to the high level of conservation between the cell cycle machinery of Drosophila and humans, the appeal of the fly model continues to be the means with which we can use sophisticated genetics to provide novel insights into mammalian growth and cell cycle control. Over the last decade, there have been major additions to the genetic toolbox to study development in Drosophila. Here we discuss some of the approaches available to investigate the potent growth and cell cycle properties of the Drosophila counterparts of prominent cancer genes, with a focus on the c-Myc oncoprotein and the tumour suppressor protein FIR (Hfp in flies), which behaves as a transcriptional repressor of c-Myc.
Micro Process Technology, 3. Applications

The article contains sections titled: 1. Introduction 2. Liquid-Phase Reactions 2.1. The Importance of Homogeneity—Fast Mixing on the Microscale 2.2. Performing Hazardous Homogeneous Reactions on a Microscale 2.3. High-Temperature Processing 2.4 High-Pressure Processing 2.5. Solvent Effects 3. Liquid–Solid Flow 3.1. Synthesis of Micro- and Nanostructured Materials in Microfluidic Devices 3.1. 1. Metal Nanoparticles 3.1. 2. Polymer Particles 3.1. 3. Protein Crystallization 3.2. Overcoming Clogging Issues in Microstructured Devices 3.3. Immobilized Catalysts and Reagents in Microflow 3.3.1. Immobilized Metal Catalysts 3.3.2. Immobilized Enzymatic Catalysts 3.3.3. Immobilized Reagents and Scavengers 4. Biphasic Liquid-Liquid Flow 4.1. Reactions in Segmented Flow 4.2. Reactions in (Re)dispersed Flow 4.3. Reactions in Micro Packed-Bed Reactors 5. Gas–Liquid Reactions 5.1. Reactions in Single-Channel Microreactors 5.1. 1. Segmented Flow 5.1. 2. Annular Flow 5.2. Reactions in a Falling-Film Microreactor 5.3. Reactions in a Mesh Microreactor 5.4. Reactions in a Membrane Microreactor 6. Gas-Phase Reactions 6.1. Reactions in Micro Packed-Bed Reactors 6.2. Reactions in Catalytic-Wall Microreactors
BOND STRESS MODEL FOR DESIGN OF ADHESIVE ANCHORS

Adhesive (chemical) anchors are used frequently in both new construction and repair/retrofit projects. Current design codes do not contain rational design procedures for these anchors. An experimental program was undertaken to determine the behavior of these anchors and to develop a rational procedure for their design. The experimental program described in this study involved 97 tensile tests of 6 adhesive products on the following types of 5/8-in. diameter threaded anchors; fully bonded single anchors; partially bonded single anchors; and fully bonded anchor pairs. A behavioral model based on an elastic formulation is developed and assessed. Design recommendations for single and multiple adhesive anchors are presented in the paper.
Neisseria gonorrhoeae Type IV Pili Undergo Multisite, Hierarchical Modifications with Phosphoethanolamine and Phosphocholine Requiring an Enzyme Structurally Related to Lipopolysaccharide Phosphoethanolamine Transferases*

The zwitterionic phospho-forms phosphoethanolamine and phosphocholine are recognized as influential and important substituents of pathogen cell surfaces. PilE, the major pilin subunit protein of the type IV pilus (Tfp) colonization factor of Neisseria gonorrhoeae undergoes unique, post-translational modifications with these moieties. These phospho-form modifications have been shown to be O-linked alternately to a specific, conserved serine residue of PilE. However, the enzymes and precursors involved in their addition are unknown, and the full spectrum of PilE post-translational modifications has yet to be defined. Here, an intact protein-based mass spectrometric approach was integrated with bioinformatics and reverse genetics to address these matters. Specifically we show that a protein limited in its distribution to pathogenic Neisseria species and structurally related to enzymes implicated in phosphoethanolamine modification of lipopolysaccharide is necessary for PilE covalent modification with phosphoethanolamine and phosphocholine. These findings strongly suggest that protein phospho-form modification is mechanistically similar to processes underlying analogous modifications of prokaryotic saccharolipid glycans. We also show that PilE undergoes multisite and hierarchical phospho-form modifications and that the stoichiometries of site occupancy can be influenced by PilE primary structure and the abundance of the pilin-like protein PilV. Together, these findings have important implications for the structure and antigenicity of PilE.
Structured Pseudospectra for Polynomial Eigenvalue Problems, with Applications

Pseudospectra associated with the standard and generalized eigenvalue problems have been widely investigated in recent years. We extend the usual definitions in two respects, by treating the polynomial eigenvalue problem and by allowing structured perturbations of a type arising in control theory. We explore connections between structured pseudospectra, structured backward errors, and structured stability radii. Two main approaches for computing pseudospectra are described. One is based on a transfer function and employs a generalized Schur decomposition of the companion form pencil. The other, specific to quadratic polynomials, finds a solvent of the associated quadratic matrix equation and thereby factorizes the quadratic $\lambda$-matrix. Possible approaches for large, sparse problems are also outlined. A collection of examples from vibrating systems, control theory, acoustics, and fluid mechanics is given to illustrate the techniques.
Investigating the Effects of Selective Sampling on the Annotation Task

We report on an active learning experiment for named entity recognition in the astronomy domain. Active learning has been shown to reduce the amount of labelled data required to train a supervised learner by selectively sampling more informative data points for human annotation. We inspect double annotation data from the same domain and quantify potential problems concerning annotators' performance. For data selectively sampled according to different selection metrics, we find lower inter-annotator agreement and higher per token annotation times. However, overall results confirm the utility of active learning.
Transmembrane allosteric energetics characterization for strong coupling between proton and potassium ion binding in the KcsA channel

Significance Although C-type inactivation in potassium channels is crucial in many biological signaling processes, its mechanism is debated. We address a hypothesis that K+ affinity reduction and ion loss due to allosterically coupled activation is a major factor in promoting inactivation. We show that in KcsA, activation by proton binding at the intracellular pH sensor can significantly reduce K+ affinity at the extracellular selectivity filter, which would be expected to contribute to current cessation (inactivation). This allosteric coupling is substantially reduced by mutating a residue that connects the inner transmembrane helix hinge (involved in activation) to the base of the selectivity filter, thus providing clear evidence for the allosteric coupling network and explaining why this mutant is inactivationless. The slow spontaneous inactivation of potassium channels exhibits classic signatures of transmembrane allostery. A variety of data support a model in which the loss of K+ ions from the selectivity filter is a major factor in promoting inactivation, which defeats transmission, and is allosterically coupled to protonation of key channel activation residues, more than 30 Å from the K+ ion binding site. We show that proton binding at the intracellular pH sensor perturbs the potassium affinity at the extracellular selectivity filter by more than three orders of magnitude for the full-length wild-type KcsA, a pH-gated bacterial channel, in membrane bilayers. Studies of F103 in the hinge of the inner helix suggest an important role for its bulky sidechain in the allosteric mechanism; we show that the energetic strength of coupling of the gates is strongly altered when this residue is mutated to alanine. These results provide quantitative site-specific measurements of allostery in a bilayer environment, and highlight the power of describing ion channel gating through the lens of allosteric coupling.
Correction of intensity flicker in old film sequences

Temporal intensity flicker is a common artifact in old film sequences. Removing disturbing temporal fluctuations in image intensities is desirable because it increases both the subjective quality and, where image sequences are stored in a compressed format, the coding efficiency. We describe a robust technique that corrects intensity flicker automatically by equalizing local frame means and variances in the temporal sense. The low complexity of our method makes it suitable for hardware implementation. We tested the proposed method on sequences with artificially added intensity flicker and on original film material. The results show a great improvement.
Engineering Optimization for Tar Removal Process in Corn Straw Gasification

The LS-SVM(the least square supporting vector machine) model of tar removal process by catalytic cracking in corn straw gasification was established according to the experimental data in [2]. On this base, a multi-objective optimization function was put forward, by which the Pareto-optimal solutions were gained in a single run. From the perspective of engineering optimization, the efficient solutions that are suitable for power generation and gas supply were selected respectively from the Pareto-optimal solutions by analysising different demands for gas.
Imperfect financial integration, uncovered interest parity and central bank foreign exchange reserves

This paper shows than when there are significant costs for private agents to change their positions in foreign bonds, an incomplete markets two-country general equilibrium monetary model with sticky prices can reproduce a “forward premium anomaly”, an upward sloping term structure of uncovered interest parity (UIP) regression slope coefficients, Sharpe ratios for carry-trade strategies close to the data, and predicts a 2.3 basis-point decrease in the short-term foreign interest rate after an unexpected one standard deviation central bank purchase of foreign bonds. A crucial element of the analysis is the interaction between the central bank balance sheet, the private agents budget constraints, and market clearing conditions in both bond markets.
3D Storyboards for Interactive Visual Search

Interactive image and video search tools typically use a grid-like arrangement of thumbnails for preview purpose. Such a display, which is commonly known as storyboard, provides limited flexibility at interactive search and it does not optimally exploit the available screen estate. In this paper we design and evaluate alternatives to the common two-dimensional storyboard. We take advantage of 3D graphics in order to present image thumbnails in cylindrical arrangements. Through a user study we evaluate the performance of these interfaces in terms of visual search time and subjective performance.
Initial stage of the active mode-locking in semiconductor heterolasers

We make an attempt to develop a novel approach to describing the initial stage of the active mode-locking in semiconductor laser structures based on analyzing the properties of dispersion relations in terms of stability for small initial perturbations. Nonlinear process of shaping optical pulses is interpreted as manifesting instability of diffusion type. For the purposes of experimental investigations, the auto-manual opto-electronic measuring system detecting average time parameters inherent in ultra-short optical pulse trains has been designed. This system is able to register auto-correlation functions of the second order exploiting the interferometric technique as well as to identify a pulsed character of the incoming light radiation. Experimental confirmations of appearing the diffusive instability within the active mode-locking process in semiconductor laser structures operating in the near infrared range are presented.