Miracle-dz/UniFAR-FTUs huggingface dataset:
Green mining: A methodology of relating software change to power consumption

Power consumption is becoming more and more important with the increased popularity of smart-phones, tablets and laptops. The threat of reducing a customer's battery-life now hangs over the software developer who asks, “will this next change be the one that causes my software to drain a customer's battery? ” One solution is to detect power consumption regressions by measuring the power usage of tests, but this is time-consuming and often noisy. An alternative is to rely on software metrics that allow us to estimate the impact that a change might have on power consumption thus relieving the developer from expensive testing. This paper presents a general methodology for investigating the impact of software change on power consumption, we relate power consumption to software changes, and then investigate the impact of static OO software metrics on power consumption. We demonstrated that software change can effect power consumption using the Firefox web-browser and the Azureus/Vuze BitTorrent client. We found evidence of a potential relationship between some software metrics and power consumption. In conclusion, we explored the effect of software change on power consumption on two projects; and we provide an initial investigation on the impact of software metrics on power consumption.
External Memory Geometric Data Structures

Many modern applications store and process datasets much larger than the main memory of even state-of-the-art high-end machines. Thus massive and dynamically changing datasets often need to be stored in space efficient data structures on external storage devices such as disks. In such cases the Input/Output (or I/O) communication between internal and external memory can become a major performance bottleneck. Many massive dataset applications involve geometric data (for example points, lines, and polygons) or data that can be interpreted geometrically. Such applications often perform queries that correspond to searching in massive multidimensional geometric databases for objects that satisfy certain spatial constraints. Typical queries include reporting the objects intersecting a query region, reporting the objects containing a query point, and reporting objects near a query point. While development of practically efficient (and ideally also multi-purpose) external memory data structures (or indexes) has always been a main concern in the database community, most data structure research in the algorithms community has focused on worst-case efficient internal memory data structures. Recently however, there has been some cross-fertilization between the two areas. In these lecture notes we discuss some of the recent advances in the development of worstcase efficient external memory geometric data structures. We will focus on fundamental dynamic structures for oneand two-dimensional orthogonal range searching, and try to highlight some of the fundamental techniques used to develop such structures. Accurately modeling memory and disk systems is a complex task. The primary feature of disks we want to model is their extremely long access time relative to that of internal memory. In order to amortize the access time over a large amount of data, typical disks read or write large blocks of contiguous data at once and therefore the standard two-level disk model has the following parameters:
Two-step state transition minimization for lifetime and performance improvement on MLC STT-RAM

Spin-transfer torque random access memory (STT-RAM) is considered as a promising candidate to replace SRAM as the next generation cache memory since it has better scalability and lower leakage power. Recently, 2-bit multi-level cell (MLC) STT-RAM has been proposed to further increase data density. However, a key drawback for MLC STT-RAM is that the magnetization directions of its hard and soft domains cannot be flipped to two opposite directions simultaneously, which leads to the two-step problem in state transitions. Two-step state transitions would significantly impact the lifetime of MLC STT-RAM due to the wasted flips in the soft domains. To solve the problem, this paper proposes a novel two-step state transition minimization (TSTM) scheme, to improve the lifetime of MLC STT-RAM when it is employed in cache design. The basic idea is by sacrificing certain cells as auxiliary flags, the two-step state transitions in STT-RAM can be well eliminated. Experimental results show that the proposed scheme can improve the lifetime of MLC STT-RAM to 318.5%.
Identification of voice pathology using automated speech analysis

The classification performance of an automatic classifier of voice pathology for the detection of normal and pathologic voice types is presented. The proposed classification system is non-intrusive and fully automated. Speech files of sustained phonation of the vowel sound /a/ in the 'Disordered Voice Database Model 4337' provided 631 subjects of both genders (58 normal, 573 pathologic). This database includes features extracted by the Multi Dimensional Voice Program (MDVP). Mel frequency cepstral coefficients (MFCC) were extracted for all of the speech files. Discrete Fourier transform (DFT) features, Log DFT and Cepstral features were also extracted. Cross-fold validation was used to measure the classifier performance. Linear discriminant analysis was employed as the classifier model. The MDVP feature set of shimmer and signal-to-noise ratios are shown to have similar classification performance to the Log DFT and the MFCC features.
IdWristbands: IR-based user identification on multi-touch surfaces

Multi-touch surfaces are predestined to be used by many users at the same time. However, most systems are not able to distinguish touches of different users. This paper presents ongoing work on using wristbands, equipped with infrared LEDs, to provide touches with identities. The LEDs transmit coded light pulses as an identifier. We are using a specific blinking-pattern to determine the orientation of the wristband in order to reliably associate corresponding touches.
One-Time Signatures Revisited: Have They Become Practical?

One-time signatures have been known for more than two decades, and have been studied mainly due to their theoretical value. Recent works motivated us to examine the practical use of one-time signatures in high-performance applications. In this paper we describe FMTseq — a signature scheme that merges recent improvements in hash tree traversal into Merkle’s one-time signature scheme. Implementation results show that the scheme provides a signature speed of up to 35 times faster than a 2048-bit RSA signature scheme, for about one million signatures, and a signature size of only a few kilobytes. We provide an analysis of practical parameter selection for the scheme, and improvements that can be applied in more specific scenarios.
3D reconstruction of urban environments using in-vehicle fisheye camera

This paper proposes a 3D reconstruction algorithm for urban environments from video sequences taken by an in-vehicle fisheye camera. The proposed algorithm employs (i) fisheye camera calibration to apply the general Structure from Motion to video sequences taken by the fisheye camera and (ii) accurate, dense and robust feature point tracking using phase-based correspondence matching. Experimental evaluation using the video sequence taken by the in-vehicle fisheye camera demonstrates that the proposed algorithm exhibits efficient performance of 3D reconstruction compared with the laser measurement system.
Real-time Face Detection from One Camera 1

Nowadays, the importance of the automatic face detection and tracking system has increased as it is needed for video surveillance and new user interfaces [1]. The goal of this research effort is to construct an automatic face detection system using a standard PC camera in real-time. The proposed system is composed of several modules: background subtraction using Gaussian modeling and face detection using machine learning techniques [2]. IMSC has developed several techniques on facial modeling and rendering, for example, facial expression cloning [3] and facial expression analysis [4]. The proposed real-time face detection system easily interacts with these developed methods. The interaction with head pose estimation means that we automatically obtain orientation of head pose from detected regions of the face. The detected face regions are also utilized as input to a face expression analysis system to realize online face expression recognition. A good example for describing the scenario of the system is the one of an ATM machine that can interact with users by recognizing the users' facial expression in real-time. In this report, we describe a method of face detection using the statistical learning method. Whenever people are within the field of view of the camera, the system recognizes the existence of the face and obtains the location among segmented regions. In order to recognize and localize the face simultaneously, we adopt a face detection framework to decide whether the region of image is a face or a non-face. For improving the performances of the system, background regions (i.e. stationary part of the scene) are discarded by focusing on the segmented moving objects. We also use a pyramid approach allowing us to automatically detect faces of various sizes in the image.
A Short Note on Proximity-based Scoring of Documents with Multiple Fields

The BM25 ranking function is one of the most well known query relevance document scoring functions and many variations of it are proposed. The BM25F function is one of its adaptations designed for modeling documents with multiple fields. The Expanded Span method extends a BM25-like function by taking into considerations of the proximity between term occurrences. In this note, we combine these two variations into one scoring method in view of proximity-based scoring of documents with multiple fields.
Social Hash Partitioner: A Scalable Distributed Hypergraph Partitioner

We design and implement a distributed algorithm for balanced k-way hypergraph partitioning that minimizes fanout, a fundamental hypergraph quantity also known as the communication volume and (k - 1)-cut metric, by optimizing a novel objective called probabilistic fanout. This choice allows a simple local search heuristic to achieve comparable solution quality to the best existing hypergraph partitioners. Our algorithm is arbitrarily scalable due to a careful design that controls computational complexity, space complexity, and communication. In practice, we commonly process hypergraphs with billions of vertices and hyperedges in a few hours. We explain how the algorithm's scalability, both in terms of hypergraph size and bucket count, is limited only by the number of machines available. We perform an extensive comparison to existing distributed hypergraph partitioners and find that our approach is able to optimize hypergraphs roughly 100 times bigger on the same set of machines. We call the resulting tool Social Hash Partitioner, and accompanying this paper, we open-source the most scalable version based on recursive bisection.
Self-Association of the Gal4 Inhibitor Protein Gal80 Is Impaired by Gal3: Evidence for a New Mechanism in the GAL Gene Switch

ABSTRACT The DNA-binding transcriptional activator Gal4 and its regulators Gal80 and Gal3 constitute a galactose-responsive switch for the GAL genes of Saccharomyces cerevisiae. Gal4 binds to GAL gene UASGAL (upstream activation sequence in GAL gene promoter) sites as a dimer via its N-terminal domain and activates transcription via a C-terminal transcription activation domain (AD). In the absence of galactose, a Gal80 dimer binds to a dimer of Gal4, masking the Gal4AD. Galactose triggers Gal3-Gal80 interaction to rapidly initiate Gal4-mediated transcription activation. Just how Gal3 alters Gal80 to relieve Gal80 inhibition of Gal4 has been unknown, but previous analyses of Gal80 mutants suggested a possible competition between Gal3-Gal80 and Gal80 self-association interactions. Here we assayed Gal80-Gal80 interactions and tested for effects of Gal3. Immunoprecipitation, cross-linking, and denaturing and native PAGE analyses of Gal80 in vitro and fluorescence imaging of Gal80 in live cells show that Gal3-Gal80 interaction occurs concomitantly with a decrease in Gal80 multimers. Consistent with this, we find that newly discovered nuclear clusters of Gal80 dissipate in response to galactose-triggered Gal3-Gal80 interaction. We discuss the effect of Gal3 on the quaternary structure of Gal80 in light of the evidence pointing to multimeric Gal80 as the form required to inhibit Gal4.
Time of symptom onset and value of myocardial blush and infarct size on prognosis in patients with ST-elevation myocardial infarction

In patients with ST-segment elevation myocardial infarction (STEMI), the time of onset of ischemia has been associated with myocardial infarction (MI) size. Myocardial blush grade (MBG) reflects myocardial response to ischemia/reperfusion injury, which may differ according to time of the day. The aim of our study was to explore the 24-hour variation in MBG and MI size in relation to outcomes in STEMI patients. A retrospective multicenter analysis of 6970 STEMI patients was performed. Time of onset of STEMI was divided into four 6-hour periods. STEMI patients have a significant 24-hour pattern in onset of symptoms, with peak onset around 09:00 hour. Ischemic time was longest and MI size, estimated by peak creatine kinase concentration, was largest in patients with STEMI onset between 00:00 and 06:00 hours. Both MBG and MI size were independently associated with mortality. Time of onset of STEMI was not independently associated with mortality when corrected for baseline and procedural factors. Interestingly, patients presenting with low MBG between 00:00 and 06:00 hours had a better prognosis compared to other groups. In conclusion, patients with symptom onset between 00:00 and 06:00 hours have longer ischemic time and consequently larger MI size. However, this does not translate into a higher mortality in this group. In addition, patients with failed reperfusion presenting in the early morning hours have better prognosis, suggesting a 24-hour pattern in myocardial protection.
Post-Silicon Validation and Calibration of Hardware Security Primitives

Physical Unclonable Functions (PUFs) and True Random Number Generators (TRNGs) are gaining significant importance in the field of hardware security. These crypto-graphic primitives harness randomness from IC fabrication process and on-chip noise respectively, necessitating unconventional post-Silicon (Si) validation techniques. In this work, we present a brief survey of post-Si validation techniques for PUFs and TRNGs, highlighting the importance of testing PUFs resilience against novel attacks and monitoring bias in TRNGs. We also propose novel techniques for monitoring PUFs reliability and measuring bias in TRNGs. The proposed techniques do not only facilitate on-chip calibration for hardware security systems, but can also be used as a countermeasure against fault-attacks.
Biological Activities Encoded by the Murine Mesenchymal Stem Cell Transcriptome Provide a Basis for Their Developmental Potential and Broad Therapeutic Efficacy

We used serial analysis of gene expression to catalog the transcriptome of murine mesenchymal stem cells (MSCs) enriched from bone marrow by immunodepletion. Interrogation of this database, results of which are delineated in the appended databases, revealed that immunodepleted murine MSCs (IDmMSCs) highly express transcripts encoding connective tissue proteins and factors modulating T‐cell proliferation, inflammation, and bone turnover. Categorizing the transcriptome based on gene ontologies revealed the cells also expressed mRNAs encoding proteins that regulate mesoderm development or that are characteristic of determined mesenchymal cell lineages, thereby reflecting both their stem cell nature and differentiation potential. Additionally, IDmMSCs also expressed transcripts encoding proteins regulating angiogenesis, cell motility and communication, hematopoiesis, immunity and defense as well as neural activities. Immunostaining and fluorescence‐activated cell sorting analysis revealed that expression of various regulatory proteins was restricted to distinct subpopulations of IDmMSCs. Moreover, in some cases, these proteins were absent or expressed at reduced levels in other murine MSC preparations or cell lines. Lastly, by comparing their transcriptome to that of 17 other murine cell types, we also identified 43 IDmMSC‐specific transcripts, the nature of which reflects their varied functions in bone and marrow. Collectively, these results demonstrate that IDmMSC express a diverse repertoire of regulatory proteins, which likely accounts for their demonstrated efficacy in treating a wide variety of diseases. The restricted expression pattern of these proteins within populations suggests that the cellular composition of marrow stroma and its associated functions are more complex than previously envisioned.
Design of a Broadband Stacked Rectangular MPA with Shorting Pins for GSM-Family and Other Cellular Applications

This paper presents a design of a single coaxial-feed stacked rectangular microstrip patch antenna (MPA) with shorting pins. The proposed MPA design is based on the multilayer structure technique, and the cellular hand-set plastic cover is put as a one layer of the MPA structure layers. A finite- element based solver has been used to achieve the proposed design. This stacked MPA can cover most of the GSM-family standards including E-GSM 900 (880-960 MHz), GSM 1800/DCS (1710-1880 MHz) , GSM 1900/PCS (1850-1975 MHz), UMTS (1885-2200 MHz), the global new 3-G IMT-2000 (2500-2690 MHz), and WLAN+Bluetooth applications (2400 MHz) with return loss L rem ges 10 dB. A good agreement was obtained between the simulated and measured results.
Fatty acids rather than hormones restore in vitro angiogenesis in human male and female endothelial cells cultured in charcoal-stripped serum

Charcoal-stripped serum (CSS) is a well-accepted method to model effects of sex hormones in cell cultures. We have recently shown that human endothelial cells (ECs) fail to growth and to undergo in vitro angiogenesis when cultured in CSS. However, the mechanism(s) underlying the CSS-induced impairment of in vitro EC properties are still unknown. In addition, whether there is any sexual dimorphism in the CSS-induced EC phenotype remains to be determined. Here, by independently studying human male and female ECs, we found that CSS inhibited both male and female EC growth and in vitro angiogenesis, with a more pronounced effect on male EC sprouting. Reconstitution of CSS with 17-β estradiol, dihydrotestosterone, or the lipophilic thyroid hormone did not restore EC functions in both sexes. On the contrary, supplementation with palmitic acid or the acetyl-CoA precursor acetate significantly rescued the CSS-induced inhibition of growth and sprouting in both male and female ECs. We can conclude that the loss of metabolic precursors (e.g., fatty acids) rather than of hormones is involved in the impairment of in vitro proliferative and angiogenic properties of male and female ECs cultured with CSS.
Stacks: an analysis tool set for population genomics

Massively parallel short‐read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype‐by‐sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP‐by‐SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
Control of twisted and coiled polymer actuator with anti-windup compensator

A twisted and coiled polymer actuator (TCPA) is a novel soft actuator. It is fabricated by twisting nylon thread or fishing line. It can be thermally activated and has remarkable properties such as high power/mass ratio and large deformation. By applying conductive nylon fibers to the actuator, it can be electrically driven by Joule heating. However, if a controller of the actuator is designed without considering an input saturation, the control performance may be descended by windup phenomena. In this paper, to solve this problem, a feedback control with an anti-windup compensator is applied. The validity of the applied method is investigated through numerical simulations and experiments.
The Human Oral Microbiome

ABSTRACT The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org ). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.