Miracle-dz/UniFAR-FTUs huggingface dataset:
Refactoring is a necessary and ongoing process in both the development and maintenance of any codebase

Source Code Replacements. The basic model we implement is that of refactorings as sets of textual replacement operations on source code. Thus, a replacement can be characterised by a location range in a source file and a ‘payload’ string which replaces the existing code within that range. This abstraction is flexible since it can express both the insertion of new code (using a zero-length range) and the deletion of existing code (using a zero-length payload). The Replacement module implements an abstract datatype for the source code replacement operations, and has the basic signature shown in Listing 2. type t (* The abstract type of replacements *) type payload = string module Set : Set.S with type elt = t val mk : Location.t -> payload -> t val apply : t -> Sourcefile.t -> string val apply_all : Set.t -> Sourcefile.t -> string Listing 2. The basic signature of the Replacement abstract datatype. We use the compiler’s Location.t type to represent location ranges in source code. The apply function takes a single replacement and a source file representation, and returns the result of applying the replacement to the source code in the file. The apply_all function applies a set of replacements to the contents of a source file. An Interface for Refactorings. We define a common interface Refactoring.S for refactorings, shown in Listing 3, so that any module implementing this interface may be used by Rotor as a refactoring. A refactoring must be able to carry out four basic operations: 1) return a runtime representation of itself; 2) return the set of refactoring dependencies that are directly induced by the refactoring with respect to a given source file; 3) return the set of replacements that must be applied to the given source file in order to effect the refactoring; and Proceedings of the ACM on Programming Languages, Vol. 1, No. 1, Article . Publication date: March 2018. Towards Large-scale Refactoring for OCaml :15 module Set : Set.S with type elt = Refactoring_repr. t module type S = sig val repr : Repr.t val get_deps : Sourcefile.t -> Set.t val process_file : Sourcefile.t -> Replacement.Set.t val kernel : Codebase.t -> Fileinfos.t list
Pathogens associated with impounded Pacific herring Clupea harengus pallasi, with emphasis on viral erythrocytic necrosis (VEN) and atypical Aeromonas salmonicida.

Maturing Pacific herring (Clupea harengus paUasi Valenciennes) were captured and held in net pens at Departure Bay, British Columbia (Canada), to test the quality and timing of roe production. The health status of the impounded herring was regularly monitored during the 5 mo holding period. Viral erythrocytic necrosis (VEN) increased in the captive herring from an initial prevalence of 3 % to 70 % near the termination of holding. Bacteria isolated from kidneys of randomly sampled herring were tested for pathogenicity in juvenile herring. Significantly, 4 particularly virulent isolates were characterized as atypical Aeromonas salmonicida. Related experiments with herring in the laboratory indicated that they were capable of harbouring the important salmonid ludney disease pathogen Renibacterium salmoninarum for extended periods. In addition, 2 yr old herring (vaccinated parenterally with formalin-lulled Vibrio anguillarurn in adjuvant) failed to produce homologous serum agglutinins in 6 wk although chinook salmon (Oncorl~ynchus tshawytscha) similarly vaccinated developed high agglutinin titres.
Customized Behavioral Normalcy Profiles for Critical Infrastructure Protection

— Targeted cyber-attacks present significant threats to modern computing systems. Industrial Control Systems (ICS), Supervisory Control and Data Acquisition (SCADA) systems, and military networks are examples of high value targets with severe consequences of a successful attack. Anomaly based detection can address targeted attacks against critical infrastructure systems as attacks are likely to distort observable system activity. Typically, anomaly detection is performed on the level of system calls and is known to have shortcomings. Much better results have been obtained by performing behavioral analysis on the highest level of behavioral semantics, and are presented herein. Most critical computer systems serve a specific purpose and are expected to run strictly limited sets of software. Modeling their behavior by customized normalcy profiles facilitates a dependable anomaly based IDS. This technology could be further enhanced by the utilization of behavioral misuse detection performed in the similar fashion. An experimental IDS implementing the above approach is demonstrated.
Earthquake Damage Detection in Urban Areas Using Curvilinear Features

Bright curvilinear features arising from the geometry of man-made structures are characteristic of synthetic aperture radar (SAR) images of urban areas, particularly due to double-reflection mechanisms. An approach to urban earthquake damage detection using double-reflection line amplitude change in single-look images has been established in previous literature. Based on this method, this paper introduces an automated tool for fast, unsupervised damage detection in urban areas. Ridge-based curvilinear features are extracted from a preevent SAR image, and double-reflection candidates are selected using prior probability distributions derived from a simple geometrical building model. The candidate features are then used with the ratio of a pair of single preevent and postevent SAR single-look amplitude images to estimate damage levels. The algorithm is very efficient, with overall computational complexity of O(Nlogk) for an N-pixel image containing features of mean length k. The technique is demonstrated using COSMO-SkyMed data covering L'Aquila, Italy, and Port-au-Prince, Haiti.
Progesterone receptor isoforms A and B: new insights into the mechanism of progesterone resistance for the treatment of endometrial carcinoma

Progesterone therapy is an effective treatment for atypical endometrial hyperplasia and early endometrial carcinoma (EC). However, progesterone resistance is the main obstacle to the success of conservative treatment in women with type I EC and remains a major clinical challenge. Studies indicate that progesterone and progesterone receptors (PRs) play a significant role in both normal and neoplastic endometria. Most EC arises in the epithelial cells of the endometrial glands, and a large body of in vitro evidence suggests that the absence or reduced expression of PR isoform B might result in the failure of progesterone treatment and lead to aberrant PRB-mediated signalling in EC cells. A recently developed in vivo knockout mouse model suggests that enhanced DNA methylation decreases the level of stromal PR isoform A and that this is also a main contributor to progesterone resistance in EC cells. The endometrial stroma within the EC might create a microenvironment that determines how epithelial-derived cancer cells respond to progesterone. This novel study opened a new avenue for research seeking to clarify the mechanisms that regulate the specific PR isoforms that are associated with the stromal cell responses to progesterone and has led to new understanding of both endometrial cell-specific and mechanical contributions of the stroma to EC development.
NetPIPE: A Network Protocol Independent Performance Evaluator

This paper presents the design of NetPIPE, a new Network Protocol Independent Performance Evaluator. NetPIPE maps the performance of a network across a wide range and presents the data in a new manner. Its protocol independence allows for visualization of the overhead associated with a protocol layer. Using Net-PIPE has led to the discovery of a deep plunge in ATM performance for certain transfer block sizes, which is examined in detail. The performance drop is also shown to exist at certain block sizes for FDDI. Both aberrations are not detected by other benchmarks.
Fast Abductive Reasoning over Ontologies

In this paper we present a new method for reasoning abductively over instances of a triples ontology. We compute the usefulness of evidence toward making an inference rather than its truth value, probabilistic or otherwise. This allows us to process ambiguous, incomplete, and inconsistent information effectively while remaining faithful to the ontology. The method is fast, scalable, and robust. We first motivate the method with a simple cognitive model and then present details of the algorithms. Finally, we present results from experiments that indicate that the method scales well in space and time complexity and promises to be highly effective.
The discourse functions of sentence-initial adverbials: studies in comprehension

In the last thirty years, numerous linguists have stressed the discourse functions of adverbials. More specifically, sentence-initial temporal and spatial adverbials are often seen as "grammatical signals" that highlight the beginning of a new discourse unit for which they provide the setting (Brown & Yule, 1983; Chafe, 1984; Charolles, 1997; Longacre, 1979; van Dijk, 1982; Virtanen, 1992). These expressions are thus supposed to affect the cognitive processes during the reading of a text.
Race , Cognitive Ability , and Rising Wage Inequality : 1968-1991

Race, Cognitive Ability, and Rising Wage Inequality: 1968-1991 Patrick L. Mason January 16, 1998 Both interracial and intraracial wage inequalities have increased substantially during the 1980s and 1990s. For example, after adjusting differences in experience, length of time on the job, and other relevant factors, a college graduate’s weekly earnings were 31 percent greater than the weekly earnings of a high school graduate in 1979 (Gottschalk,1997). By the early 1990s, the college weekly earnings premium was 53 percent. Wage data from the Current Population Survey, a widely used US government database, show that African American progress came to a sudden halt in 1975, with whites maintaining at least a 15 percent wage premium from the mid1970s onward. Worst, all men at or below the 77 th percentile saw their weekly wages decline between 1973 and 1994 (after adjusting for inflation), while the wages of the highest earners increased. Women at the 30 th percentile or lower did not lose ground during this period, but they did not make much progress either. On the other hand, women at the 95 th p rcent saw their wages increase by 40 percent. Comparing the mid-1970s to the mid-1990s: those who had, got more; those who had not, were blessed if they lost no more than 10 percent. Is the increase in intraracial inequality causally related to the increase in interracial inequality? What is the relationship between both increases in inequality and other factors, for example, technological change, increased globalization and competitiveness, decrease in worker bargaining power, changes in family structure, macroeconomic policy, and racial discrimination? Let me state my conclusions in advance. Examining data from the Panel Study on Income Dynamics for the years 1968 to 1991, I find that an increase in the rate of return to cognitive ability (a proxy for skill) has been a contributory factor to the post-1979 increase in intraracial
Fluorescence lifetime excitation cytometry by kinetic dithering

Flow cytometers are powerful high‐throughput devices that capture spectroscopic information from individual particles or cells. These instruments provide a means of multi‐parametric analyses for various cellular biomarkers or labeled organelles and cellular proteins. However, the spectral overlap of fluorophores limits the number of fluorophores that can be used simultaneously during experimentation. Time‐resolved parameters enable the quantification of fluorescence decay kinetics, thus circumventing common issues associated with intensity‐based measurements. This contribution introduces fluorescence lifetime excitation cytometry by kinetic dithering (FLECKD) as a method to capture multiple fluorescence lifetimes using a hybrid time‐domain approach. The FLECKD approach excites fluorophores by delivering short pulses of light to cells or particles by rapid dithering and facilitates measurement of complex fluorescence decay kinetics by flow cytometry. Our simulations demonstrated a resolvable fluorescence lifetime value as low as 1.8 ns (±0.3 ns) with less than 20% absolute error. Using the FLECKD instrument, we measured the shortest average fluorescence lifetime value of 2.4 ns and found the system measurement error to be ±0.3 ns (SEM), from hundreds of monodisperse and chemically stable fluorescent microspheres. Additionally, we demonstrate the ability to detect two distinct excited state lifetimes from fluorophores in single cells using FLECKD. This approach presents a new ability to resolve multiple fluorescence lifetimes while retaining the fluidic throughput of a cytometry system. The ability to discriminate more than one average fluorescence lifetime expands the current capabilities of high‐throughput and intensity‐based cytometry assays as the need to tag one single cell with multiple fluorophores is now widespread.
Relating the statistical values of turbulence to the flow induced sound and resulting mechanical vibrations in multi-channel systems

Our multi-channel system consists of two parallel pipes which are joined in to a single, larger pipe and transmits a high speed flow of Reynolds number ranging between 0.7 and 1.8 million. The turbulence, which is amplified by combining the two flows, results in large fluctuations in the fluid pressure. These pressure fluctuations lead to the production of sound, which excites the acoustic resonances of the system and in turn causes mechanical vibrations in the pipe. Using hybrid numerical simulation techniques, the investigations show that the sound pressure level and mechanical displacement magnitudes are interdependent on the Reynolds number of the flow and the frequency of the acoustic resonance. This behavior is linked to the turbulent energy spectrum at the location of the largest sound source for a certain Reynolds number. The frequency content of the turbulent energy is shown to determine the amplitude of the acoustic resonances excited in the system, and thus the mechanical vibration magnitudes in the pipe.
Identification of Key Candidate Genes and Pathways in Endometrial Cancer by Integrated Bioinformatical Analysis

Endometrial Cancer is the most common female genital tract malignancy, its pathogenesis is complex, not yet fully described. To identify key genes of Endometrial Cancer we downloaded the gene chip GSE17025 from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified through the GEO2R analysis tool. Functional and pathway enrichment analysis were performed for DEGs using DAVID database. The network of protein–protein-interaction (PPI) was established by STRING website and visualized by Cytoscape. Then, functional and pathway enrichment analysis of DEGS were performed by DAVID database. A total of 1000 significant differences genes were obtained, contain 362 up-regulated genes and 638 down-regulated genes. PCDH10, SLC6A2, OGN, SFRP4, TRH, ANGPTL, FOSB are down-regulated genes. The gene of IGH, CCL20, ELF5, LTF, ASPM expression level in tumor patients are up-regulated. Biological function of enrichment include metabolism of xenobiotics by cytochrome P450, MAPK signaling pathway, Serotonergic synapse, Protein digestion and absorption, IL-17 signaling pathway, Chemokine signaling pathway, HIF-1 signaling pathway, p53 signaling pathway. All in all, the current study to determine endometrial differentially expressed genes and biological function, comprehensive analysis of intrauterine membrane carcinoma pathogenesis mechanism, and might be used as molecular targets and diagnostic biomarkers for the treatment of endometrial cancer.
Distribution of eigenfrequencies for oscillations of the ground state in the Thomas-Fermi limit

In this work, we present a systematic derivation of the distribution of eigenfrequencies for oscillations of the ground state of a repulsive Bose-Einstein condensate in the semi-classical (Thomas-Fermi) limit. Our calculations are performed in one, two, and three-dimensional settings. Connections with the earlier work of Stringari, with numerical computations, and with theoretical expectations for invariant frequencies based on symmetry principles are also given.
Optical flow for non Lambertian surfaces by cancelling illuminant chromaticity

Optical flow, the pixel level correspondences between a pair of images is an important problem in computer vision. Standard optical flow computation algorithms assume constant brightness and fail on specular surfaces. Earlier work to alleviate problems with specularity evaluate the illuminant chromaticity using a few correspondences in the images and then jointly optimize flow and appearance under the dichromatic model. We argue that the correspondences obtained by these methods are mostly pairs of pixels that are Lambertian thus giving a noisy estimate of the illuminant chromaticity. We suggest a new approach to evaluate the illuminant chromaticity which does not require exact correspondences and gives a better estimate of illuminant chromaticity. We use the evaluated chromaticity to project the input images on to a specular invariant color space and show that standard optical flow algorithms on this color space significantly improves the flow results. The suggested approach is simple, efficient and more importantly can utilize existing algorithms to compute optical flow on non Lambertian surfaces.
Measuring Outcome in an Early Intervention Program for Toddlers with Autism Spectrum Disorder: Use of a Curriculum-Based Assessment

Measuring progress of children with autism spectrum disorder (ASD) during intervention programs is a challenge faced by researchers and clinicians. Typically, standardized assessments of child development are used within research settings to measure the effects of early intervention programs. However, the use of standardized assessments is not without limitations, including lack of sensitivity of some assessments to measure small or slow progress, testing constraints that may affect the child's performance, and the lack of information provided by the assessments that can be used to guide treatment planning. The utility of a curriculum-based assessment is discussed in comparison to the use of standardized assessments to measure child functioning and progress throughout an early intervention program for toddlers with risk for ASD. Scores derived from the curriculum-based assessment were positively correlated with standardized assessments, captured progress masked by standardized assessments, and early scores were predictive of later outcomes. These results support the use of a curriculum-based assessment as an additional and appropriate method for measuring child progress in an early intervention program. Further benefits of the use of curriculum-based measures for use within community settings are discussed.
The effect of atomoxetine on directed and random exploration in humans

The adaptive regulation of the trade-off between pursuing a known reward (exploitation) and sampling lesser-known options in search of something better (exploration) is critical for optimal performance. Theory and recent empirical work suggest that humans use at least two strategies for solving this dilemma: a directed strategy in which choices are explicitly biased toward information seeking, and a random strategy in which decision noise leads to exploration by chance. Here we examined the hypothesis that random exploration is governed by the neuromodulatory locus coeruleus-norepinephrine system. We administered atomoxetine, a norepinephrine transporter blocker that increases extracellular levels of norepinephrine throughout the cortex, to 22 healthy human participants in a double-blind crossover design. We examined the effect of treatment on performance in a gambling task designed to produce distinct measures of directed exploration and random exploration. In line with our hypothesis we found an effect of atomoxetine on random, but not directed exploration. However, contrary to expectation, atomoxetine reduced rather than increased random exploration. We offer three potential explanations of our findings, involving the non-linear relationship between tonic NE and cognitive performance, the interaction of atomoxetine with other neuromodulators, and the possibility that atomoxetine affected phasic norepinephrine activity more so than tonic norepinephrine activity.
Keyword-based search and exploration on databases

Empowering users to access databases using simple keywords can relieve users from the steep learning curve of mastering a structured query language and understanding complex and possibly fast-evolving data schemas. In this tutorial, we give an overview of the state-of-the-art techniques for supporting keyword-based search and exploration on databases. Several topics will be discussed, including query result definition, ranking functions, result generation and top-k query processing, snippet generation, result clustering, result comparison, query cleaning and suggestion, performance optimization, and search quality evaluation. Various data models will be discussed, including relational data, XML data, graph-structured data, data streams, and workflows. Finally we identify the challenges and opportunities for future research to advance the field.
Effects of female reproductive competition on birth rate and reproductive scheduling in a historical human population

Personality affects response to alarm calls. This study reveals that boldness explains how vigilant chipmunks behave in response to alarm calls, and that vigilance diminishes in response to shyer callers. Chipmunks thus evaluate the personality of callers and discount the danger associated with calls from highly risk-sensitive individuals. Adjusting responsiveness relative to caller reliability improves foraging while reducing the risk of predation.
A pedagogical integration of electromagnetic and energy conversion concepts: The synchronous nanomotor and the synchronous reluctance motor

We present an example of integration for subjects of classical electromagnetism and energy conversion included in an undergraduate program in electric engineering. It is shown how to induce by means of light the rotation of a microscopic or nanoscopic particle, making an analogy with the synchronous reluctance motor. The variables for controlling the resulting velocity are identified and in both cases the conditions for obtaining a continuous rotation are studied. We synthesize that the common principle in both cases is the transfer of angular momentum from a rotating electromagnetic field to an electrically or magnetically polarizable system.
Gecko inspired Electrostatic Chuck

We introduce a climbing system, inspired by gecko foot that uses Electrostatic Chuck (ESC) in place of Van der Waals interaction. Electrostatic chucks are currently used in wafer foundries to pick-up and move delicate thin semiconductor wafers. The properties of ESC make it an interesting adhesion force for wall mobility applications. However the great dependency of current ESCs' adhesion force on the surface roughness of the substrate renders them ineffective in "normal-roughness" walls. By combining ESC adhesion with gecko's foot-hair surface-roughness adaptability function we propose a device for wall mobility applications.