Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistics-driven datacenter resources provisioning

The virtualization concept along with its underlying technologies has been warmly adopted in many fields of computer science. In modern datacenters, the convergence of communications and computing to a common design and operational entity has proved an inevitable reality, introducing virtual servers as active network elements thus increasing the infrastructure complexity. Effective resource management in such architectures is crucial, impacting both service delivery and the resulting infrastructure operating costs. We propose a novel approach, based on Statistical Process Control (SPC), for the dynamic resource provisioning of datacenter virtualized resources. Our work provides an integrated, platform-independent and technology-neutral, framework consisting of a Common Information Model (CIM) based resource controller which allows for the on-line, adaptive, management of a virtual machine's CPU allocation. The controller can be extended to manage other types of hypervisor-provisioned resources. We provide a successful proof-of-concept of our work, deploying the controller on an IBM pSeries UNIX system running a core banking environment software with actual business data. Given the platform agnostic description of the controller and the managed environment it is, thus, possible to easily provide different operating system and hardware platform ports.
Covenant: An architecture for cooperative scheduling in 802.11 wireless networks

Wireless networks based on 802.11a/b/g protocols have gained wide-spread acceptance in both enterprise as well as home networks. However, these devices lack native support for many advanced features such as service differentiation, etc., that are required in specific application domains. In this paper, we propose Covenant, a software based cooperative scheduling framework to provide a rich set of features for applications that require nodes to cooperate with each other to satisfy system-wide objectives. We propose a novel 2 1/2-stage pipeline architecture as an efficient mechanism to implement cooperative scheduling among multiple nodes. We demonstrate how Covenant can be easily implemented in software, thus requiring absolutely no hardware or firmware changes to the already widely installed base of 802.11a/b/g based wireless devices. We also evaluate, using a real Linux based test-bed with Covenant drivers, the efficacy of the approach on two different scheduling disciplines: proportional priority and strict priority. We demonstrate that these scheduling disciplines are effective in providing service guarantees to multimedia applications even in the presence of other competing traffic.
Experimental transmission of Bartonella henselae by the cat flea

Bartonella henselae is an emerging bacterial pathogen, causing cat scratch disease and bacillary angiomatosis. Cats bacteremic with B. henselae constitute a large reservoir from which humans become infected. Prevention of human infection depends on elucidation of the natural history and means of feline infection. We studied 47 cattery cats in a private home for 12 months to determine the longitudinal prevalence of B. henselae bacteremia, the prevalence of B. henselae in the fleas infesting these cats, and whether B. henselae is transmitted experimentally to cats via fleas. Vector-mediated transmission of B.henselae isolates was evaluated by removing fleas from the naturally bacteremic, flea-infested cattery cats and transferring these fleas to specific-pathogen-free (SPF) kittens housed in a controlled, arthropod-free University Animal Facility. B. henselae bacteremia was detected in 89% of the 47 naturally infected cattery cats. A total of 132 fleas were removed from cats whose blood was simultaneously cultured during different seasons and were tested individually for the presence of B. henselae DNA by PCR. B. henselae DNA was detected in 34% of 132 fleas, with seasonal variation, but without an association between the presence or the level of bacteremia in the corresponding cat. Cat fleas removed from bacteremic cattery cats transmitted B. henselae to five SPF kittens in two separate experiments; however, control SPF kittens housed with highly bacteremic kittens in the absence of fleas did not become infected. These data demonstrate that the cat flea readily transmits B. henselae to cats. Control of feline infestation with this arthropod vector may provide an important strategy for the prevention of infection of both humans and cats.
Human Immunodeficiency Virus Type 1 Nef: Adapting to Intracellular Trafficking Pathways

SUMMARY The Nef protein of primate lentiviruses is a unique protein that has evolved in several ways to manipulate the biology of an infected cell to support viral replication, immune evasion, pathogenesis, and viral spread. Nef is a small (25- to 34-kDa), myristoylated protein that binds to a collection of cellular factors and acts as an adaptor to generate novel protein interactions to accomplish specific functions. Of the many biological activities attributed to Nef, the reduction of surface levels of the viral receptor (CD4) and antigen-presenting molecules (major histocompatibility complex class I) has been intensely examined; recent evidence demonstrates that Nef utilizes multiple, distinct pathways to affect these proteins. To accomplish this, Nef promotes the formation of multiprotein complexes, recruiting host adaptor proteins to commandeer intracellular vesicular trafficking routes. The altered trafficking of several other host molecules has also been reported, and an emerging theory suggests that Nef generates pleiotrophic effects in the secretory and endocytic pathways that reprogram intracellular protein trafficking and may ultimately provide an efficient platform for viral assembly. This review critically discusses some of the major findings regarding the impact of human immunodeficiency virus type 1 Nef on host protein transport and addresses some emerging directions in this area of human immunodeficiency virus biology.
Studies on the Development and Behavior of the Dystrophic Growth Cone, the Hallmark of Regeneration Failure, in an In Vitro Model of the Glial Scar and after Spinal Cord Injury

We have developed a novel in vitro model of the glial scar that mimics the gradient of proteoglycan found in vivo after spinal cord injury. In this model, regenerated axons from adult sensory neurons that extended deeply into the gradient developed bulbous, vacuolated endings that looked remarkably similar to dystrophic endings formed in vivo. We demonstrate that despite their highly abnormal appearance and stalled forward progress, dystrophic endings are extremely dynamic both in vitro and in vivo after spinal cord injury. Time-lapse movies demonstrated that dystrophic endings continually send out membrane veils and endocytose large membrane vesicles at the leading edge, which were then retrogradely transported to the rear of the “growth cone. ” This direction of movement is contrary to membrane dynamics that occur during normal neurite outgrowth. As further evidence of this motility, dystrophic endings endocytosed large amounts of dextran both in vitro and in vivo. We now have an in vitro model of the glial scar that may serve as a potent tool for developing and screening potential treatments to help promote regeneration past the lesion in vivo.
An LLC-OCV Methodology for Statistic Timing Analysis

With further increase in chip size and shrink in device dimension, the influence of on chip semiconductor process variation can no longer be ignored in design phase such as STA sign-off. This paper presents the LLC-OCV methodology, which adopts the Monte Carlo analysis to enhance the location-based OCV (LOCV) with gate-level and cell-based perspectives, to be used as a reasonable and complete intra-die process model for STA (statistic timing analysis) sign-off. This new approach shows good prediction for STA sign-off. With LLC-OCV methodology, this paper has correctly identified timing problems in real silicon projects of 0.13 mum process in STA sign-off stage. Comparing the STA results of LOCV and LLC-OCV methodology, our experiment shows that LLC-OCV approach can avoid pessimistic analysis and save chip area.
On Changing Behaviour in Fixed Psychologies: An Integrated, Holistic, Systematic Approach

We develop an integrated, holistic and systematic model of behavioural change in fixed psychologies by making use of a model of the psychology of behaviour. We identify and explain three simple and comprehensive means by which behavioural change is affected by the interaction of the individual's psychology with their environment. This has value for the pure theory of human behaviour, for applied theory (making hypotheses to appraise and to be tested by datasets), and for the practice of policy by demonstrating a fairly simple causal structure underlying the seemingly highly individuated and complex psychological processes which support behavioural change.
Haptic Interface for Finger Exercise and Virtual Rehabilitation

A haptic device with two active degrees of freedom and a tendon driven transmission system was designed, built and tested. It was constructed as a lightweight mechanism with a small workspace that wraps a finger workspace and can generate forces up to 10 N suitable for finger exercise. The control loop and user application were implemented on a personal computer within the MS Windowsreg environment. Together with the device an application including several different experiment types has been developed. The system has been evaluated in group of stroke patients during a one month therapy. The results for two experiment types are presented. The progression of the affected hand side for patients is observed to be higher than for nonaffected side but on the contrary the mean values of the relevant parameters at nonaffected side for patients are higher than for affected side
Improved lumped charge model for high voltage power diode and automated extraction procedure

The “lumped charge” power diode compact model [1] is extended including impact ionization while maintaining the low computational cost. The new model can better reproduce the shape of the current peak during reverse recovery, allowing for more predictive EMI/EMC simulations. The parameter extraction procedure is also improved and automated through multi-objective genetic algorithms, resulting in very good agreement between model and measurements. Finally, calibrated TCAD simulations are used to understand the limitations of the compact model.
Combination gemcitabine and cisplatin chemotherapy for metastatic or recurrent nasopharyngeal carcinoma: report of a phase II study.

BACKGROUND To evaluate the efficacy and toxicity of combination gemcitabine plus cisplatin (GC) chemotherapy in metastatic or recurrent nasopharyngeal carcinoma (NPC). PATIENTS AND METHODS Forty-four patients of Chinese ethnicity with metastatic or recurrent NPC received ambulatory GC chemotherapy every 28 days (gemcitabine 1000 mg/m(2) days 1, 8 and 15; cisplatin 50 mg/m(2) days 1 and 8). There were 40 male and four female patients with a mean age of 47.4 years. More than half (54.5%) of the patients had received either prior platinum-based chemotherapy and/or radiotherapy to target lesions. RESULTS There were nine complete responses and 23 partial responses in the 44 patients, achieving an overall response rate of 73% (78% for the 41 assessable patients). The mean duration of response was 5.3 months. Improved subjective symptom-control scores were found in 78% of patients with pre-existing symptoms, while 64% of patients experienced improved general well-being scores. Toxicity was mainly hematological: grade III/IV anemia, granulocytopenia and thrombocytopenia were found in 11, 37 and 16% of cycles, respectively. With a median follow-up of 17.2 months, 62% survived 1 year while 36% were alive and progression free. CONCLUSIONS Gemcitabine plus cisplatin chemotherapy offers a satisfactory overall response rate, subjective patient improvement and safety profile for metastatic and recurrent NPC.
The Non-Canonical CTD of RNAP-II Is Essential for Productive RNA Synthesis in Trypanosoma brucei

The carboxy-terminal domain (CTD) of the largest subunit (RPB1) of RNA polymerase II (RNAP-II) is essential for gene expression in metazoa and yeast. The canonical CTD is characterized by heptapeptide repeats. Differential phosphorylation of canonical CTD orchestrates transcriptional and co-transcriptional maturation of mRNA and snRNA. Many organisms, including trypanosomes, lack a canonical CTD. In these organisms, the CTD is called a non-canonical CTD or pseudo-CTD (ΨCTD. In the African trypanosome, Trypanosoma brucei, the ΨCTD is ∼285 amino acids long, rich in serines and prolines, and phosphorylated. We report that T. brucei RNAP-II lacking the entire ΨCTD or containing only a 95-amino-acid-long ΨCTD failed to support cell viability. In contrast, RNAP-II with a 186-amino-acid-long ΨCTD maintained cellular growth. RNAP-II with ΨCTD truncations resulted in abortive initiation of transcription. These data establish that non-canonical CTDs play an important role in gene expression.
New Steady-State Analysis Results of Variable Step-Size LMS Algorithm With Different Noise Distributions

The step-size in well-known variable step-size least mean square (VSSLMS) is updated as μ<sub>n+1</sub> = αμ<sub>n</sub> + γe<sub>n</sub><sup>2</sup> with , γ > 0, and μ<sub>n+1</sub> is set to μ<sub>min</sub> or μ<sub>max</sub> when it falls below or above these lower and upper bounds, respectively. It provides fast convergence at early stages of adaptation while ensuring small steady-state misalignment. This paper considers the steady-state performance of the VSSLMS in non-Gaussian noise environments. The contribution of the paper to the VSSLMS is threefold; (1) when γ ≪ 1 - α, the VSSLMS has low steady-state misalignment. (2) when α ≪ 1, the VSSLMS achieves different steady-state misalignments for different noise distributions. (3) In theory, there are different optimal values α for different noise distributions, i.e., 0.17 (Gaussian distribution), 0.21 (Student distribution), 0.38 (Laplace distribution), 0 (Binary and Uniform distributions). Analytical results are compared with simulations and are shown to agree well.
Genu Recurvatum versus Fixed Flexion after Total Knee Arthroplasty

Background To date, there is no study comparing outcomes between post-total knee replacement genu recurvatum and fixed flexion. This study aims to provide data that will help in deciding which side to err on when neutral extension is not achieved. Methods A prospective cohort study of primary total knee arthroplasties was performed, which compared the 6-month and 2-year clinical outcomes between fixed flexion and genu recurvatum deformities at 6 months. Results At 6 months, knees in genu recurvatum did better than knees in fixed flexion deformity in terms of knee flexion. However, at 2 years, knees in fixed flexion deformity did better in terms of knee scores and showed better improvement in the degree of deformity. Conclusions We conclude that it is better to err on the side of fixed flexion deformity if neutral alignment cannot be achieved.
PaCK: Scalable parameter-free clustering on K-partite graphs

Given an author-paper-conference graph, how can we automatically find groups for author, paper and conference respectively. Existing work either (1) requires fine tuning of several parameters, or (2) can only be applied to bipartite graphs (e.g., author-paper graph, or paper-conference graph). To address this problem, in this paper, we propose PaCK for clustering such k-partite graphs. By optimizing an information-theoretic criterion, PaCK searches for the best number of clusters for each type of object and generates the corresponding clustering. The unique feature of PaCK over existing methods for clustering k-partite graphs lies in its parameter-free nature. Furthermore, it can be easily generalized to the cases where certain connectivity relations are expressed as tensors, e.g., time-evolving data. The proposed algorithm is scalable in the sense that it is linear with respect to the total number of edges in the graphs. We present the theoretical analysis as well as the experimental evaluations to demonstrate both its effectiveness and efficiency.
Bring Into Play the Software Metrics in SAAS - A Cloud Computing Prospective

This paper deals with a kind of distributed computing over the internet known as cloud computing, which can run a program or application on more than one computer at the same time. It is divided further into three categories namely: (i) Infrastructure as a service (IaaS), (ii) Platform as a service (PaaS), and (iii) Software as a service (SaaS). Software as a service is a kind of service which provides much remuneration to the service consumers. What brings Cloud computing in the field of software is a complex issue. Software metrics as a subject area is over 30 years old, but it has barely penetrated into mainstream software Engineering. Software measurement is very important and delicate issue, especially when dealing applications into the practice. Software metrics provide a basis for planning and predicting software development. Quality in fact aids higher productivity, which has brought software metrics to the limelight.
An Empirical Study of QBF Encodings: from Treewidth Estimation to Useful Preprocessing

From an empirical point of view, the hardness of quantified Boolean formulas (QBFs), can be characterized by the (in)ability of current state-of-the-art QBF solvers to decide about the truth of formulas given limited computational resources. In this paper, we start from the problem of computing empirical hardness markers, i.e., features that can discriminate between hard and easy QBFs, and we end up showing that such markers can be useful to improve our understanding of QBF preprocessors. In particular, considering the connection between classes of tractable QBFs and the treewidth of associated graphs, we show that (an approximation of) treewidth is indeed a marker of empirical hardness and it is the only parameter which succeeds consistently in being so, even considering several other purely syntactic candidates which have been successfully employed to characterize QBFs in other contexts. We also show that treewidth approximations can be useful to describe the effect of QBF preprocessors, in that some QBF solvers benefit from a preprocessing phase when it reduces the treewidth of their input. Our experiments suggest that structural simplifications reducing treewidth are a potential enabler for the solution of hard QBF encodings.
Tyrosine phosphorylation is required for Fc receptor-mediated phagocytosis in mouse macrophages

Although Fc receptor-mediated phagocytosis is accompanied by a variety of transmembrane signaling events, not all signaling events are required for particle ingestion. For example, Fc receptor-mediated phagocytosis in mouse inflammatory macrophages (Di Virgilio, F., B. C. Meyer, S. Greenberg, and S. C. Silverstein. 1988. J. Cell Biol. 106:657; Greenberg, S., J. El Khoury, F. Di Virgilio, and S. C. Silverstein. 1991. J. Cell Biol. 113:757) and neutrophils (Della Bianca, V., M. Grzeskowiak, and F. Rossi. 1990. J. Immunol. 144:1411) occurs in the absence of cytosolic calcium transients. We sought to identify transmembrane signaling events that are essential for phagocytosis. Here we show that tyrosine phosphorylation is an early event after Fc receptor ligation in mouse inflammatory macrophages, and that the formation of tyrosine phosphoproteins coincides temporally with the appearance of F-actin beneath phagocytic cups. The distribution of tyrosine phosphoproteins that accumulated beneath phagocytic cups was punctate and corresponded to areas of high ligand density on the surface of the antibody-coated red blood cells, which provided the phagocytic stimulus. A tyrosine kinase inhibitor, genistein, but not several inhibitors of protein kinase C, blocked the appearance of tyrosine phosphoproteins as assessed by immunofluorescence, the focal accumulation of F-actin beneath immunoglobulin G-opsonized particles, and the ingestion of these particles as well. We suggest that tyrosine phosphorylation is a critical signaling event that underlies Fc receptor-mediated phagocytosis in mouse macrophages, and is necessary for the engulfment per se.
SNP calling using genotype model selection on high-throughput sequencing data

MOTIVATION A review of the available single nucleotide polymorphism (SNP) calling procedures for Illumina high-throughput sequencing (HTS) platform data reveals that most rely mainly on base-calling and mapping qualities as sources of error when calling SNPs. Thus, errors not involved in base-calling or alignment, such as those in genomic sample preparation, are not accounted for. RESULTS A novel method of consensus and SNP calling, Genotype Model Selection (GeMS), is given which accounts for the errors that occur during the preparation of the genomic sample. Simulations and real data analyses indicate that GeMS has the best performance balance of sensitivity and positive predictive value among the tested SNP callers. AVAILABILITY The GeMS package can be downloaded from https://sites.google. com/a/bioinformatics.ucr. edu/xinping-cui/home/software or http://computationalbioenergy.org/software.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
MHCP Model for Quality Evaluation for Software Structure Based on Software Complex Network

Accidents caused by defective software systems have long been a nightmare. Though engineers utilize advanced techniques and rigorous quality control procedures, we still have to admit that the increasing complexity and expanding scale of software systems make it extremely difficult to guarantee high quality deliverables. Since large-scale software systems exhibit the characteristics of complex networks, applying the principles of complex networks to evaluate the quality of software systems has attracted attention from both academia and industry. Unfortunately, most current research studies focus only on one or a limited number of attributes of software structures which makes them ineffective in providing comprehensive and insightful quality evaluation for software structures. To overcome this problem, we propose an approach based on various software structural characteristics to evaluate software structures from modularity, hierarchy, complexity, and fault propagation points of view. A model based on these four aspects is proposed to better understand software structural quality. A prediction model is also proposed to provide insights on the nature of software evolution and its current status. Experiments using two software projects were performed against the thresholds obtained by evaluating more than 5,000 versions of open source projects. Our results suggest that the approach described in this paper can help us analyze real-world software projects for better quality evaluation.
Strategi Mempublikasikan Hasil Penelitian dalam Jurnal Internasional Bereputasi

Dalam perkembangan dunia saat ini, publikasi dalam jurnal internasional bereputasi merupakan salah satu acuan untuk mengukur kemajuan suatu bangsa. Kemampuan untuk menghadirkan karya ilmiah di jurnal internasional dapat meningkatkan kepercayaan masyarakat dunia terhadap kualitas produk dan teknologi yang dihasilkan oleh bangsa tersebut. Saat ini, jumlah publikasi hasil penelitian Indonesia di dunia internasional masih rendah, terutama publikasi jurnal terindeks di pengindeks internasional bereputasi. Salah satu faktor penyebabnya adalah budaya menulis yang belum berkembang dengan baik dalam masyarakat pada umumnya dan perguruan tinggi khususnya. Kemampuan dalam melakukan kegiatan penelitian belum diikuti dengan komitmen moral untuk mempublikasikan hasilnya pada masyarakat luas baik dalam aplikasi praktis maupun pengembangan teroritis. Untuk itu, dalam makalah ini akan disajikan beberapa strategi untuk mempublikasikan hasil-hasil penelitian dalam jurnal internasional bereputas