Miracle-dz/UniFAR-FTUs huggingface dataset:
Compiler Optimization of C++ Virtual Function Calls

We describe two generic optimization techniques to improve run-time performance of C++ virtual function calls: type specification and type prediction. Both involve program analysis that results in a set of call sites to be optimized, and code transformations that replace the original dispatching mechanism in these sites by more efficient call expressions. We implement two special cases. The first is a type-specification optimization, called unique name, that requires static global view of the whole program in order to substitute indirect virtual function call sites by direct calls. The other is a type-prediction kind of optimization, referred to as single type prediction, that uses type-profiling information to replace virtual function calls by conditional expressions which involve direct function calls. These optimizations were implemented in IBM's compiler, the C Set ++ for AIX/6000, and evaluated on a set of C++ standard benchmarks. We received encouraging run-time results with improvements in order of 20% that demonstrate the vitality of these techniques.
Boosting compound-protein interaction prediction by deep learning

The identification of interactions between compounds and proteins plays an important role in network pharmacology and drug discovery. However, experimentally identifying compound-protein interactions (CPIs) is generally expensive and time-consuming, computational approaches are thus introduced. Among these, machine-learning based methods have achieved a considerable success. However, due to the nonlinear and imbalanced nature of biological data, many machine learning approaches have their own limitations. Recently, deep learning techniques show advantages over many state-of-the-art machine learning methods in many applications. In this study, we aim at improving the performance of CPI prediction based on deep learning, and propose a method called DL-CPI (the abbreviation of Deep Learning for Compound-Protein Interactions prediction), which employs deep neural network (DNN) to effectively learn the representations of compound-protein pairs. Extensive experiments show that DL-CPI can learn useful features of compound-protein pairs by a layerwise abstraction, and thus achieves better prediction performance than existing methods on both balanced and imbalanced datasets.
Pituitary Adenoma Pathogenesis: The Presence Of E-Cadherin and Its Influence on Tumor Invasiveness

ECAD has extracellular, transmembrane and cytoplasmic domain Several transcription factors are involved in epithelial-mesenchymal transition via E-cadherin repression, including SLUG, TWIST and SNAIL Epithelial-mesenchymal transition is an important process for embryonic development, in which cells lose their epithelial characteristics and gain mesenchymal properties. Such process is associated with cancer progression, with E-cadherin loss as the initial step of epithelial cell trans differ-entiation to the mesenchymal phenotype Pituitary Adenoma Pathogenesis: The Presence Of E-Cad-herin and Its Influence on Tumor In -vasiveness. abstract E-cadherin (ECAD) loss on cell surface is related to invasiveness, metastases and bad prognosis in several malignant tumors of epithelial origin. Pituitary adenomas are common and benign tumors; however, they can become aggressive and invade other tissues. The herein assessed research describe ECAD positivity in most pituitary adenomas, but the relation between ECAD and tumor invasiveness led to different results. Further research is needed in order to better understand the ECAD impact on tumor development.
HIV-1 Nef Sequence and Functional Compartmentalization in the Gut Is Not Due to Differential Cytotoxic T Lymphocyte Selective Pressure

The gut is the largest lymphoid organ in the body and a site of active HIV-1 replication and immune surveillance. The gut is a reservoir of persistent infection in some individuals with fully suppressed plasma viremia on combination antiretroviral therapy (cART) although the cause of this persistence is unknown. The HIV-1 accessory protein Nef contributes to persistence through multiple functions including immune evasion and increasing infectivity. Previous studies showed that Nef’s function is shaped by cytotoxic T lymphocyte (CTL) responses and that there are distinct populations of Nef within tissue compartments. We asked whether Nef’s sequence and/or function are compartmentalized in the gut and how compartmentalization relates to local CTL immune responses. Primary nef quasispecies from paired plasma and sigmoid colon biopsies from chronically infected subjects not on therapy were sequenced and cloned into Env− Vpu− pseudotyped reporter viruses. CTL responses were mapped by IFN-γ ELISpot using expanded CD8+ cells from blood and gut with pools of overlapping peptides covering the entire HIV proteome. CD4 and MHC Class I Nef-mediated downregulation was measured by flow cytometry. Multiple tests indicated compartmentalization of nef sequences in 5 of 8 subjects. There was also compartmentalization of function with MHC Class I downregulation relatively well preserved, but significant loss of CD4 downregulation specifically by gut quasispecies in 5 of 7 subjects. There was no compartmentalization of CTL responses in 6 of 8 subjects, and the selective pressure on quasispecies correlated with the magnitude CTL response regardless of location. These results demonstrate that Nef adapts via diverse pathways to local selective pressures within gut mucosa, which may be predominated by factors other than CTL responses such as target cell availability. The finding of a functionally distinct population within gut mucosa offers some insight into how HIV-1 may persist in the gut despite fully suppressed plasma viremia on cART.
Factors predicting concurrent cholangiocarcinomas associated with hepatolithiasis.

BACKGROUND/AIMS Hepatolithiasis is a risk factor for cholangiocarcinoma. However, it is difficult to detect early cholangiocarcinoma that occurs as a complication of hepatolithiasis. To identify the factors, which can be used for predicting cholangiocarcinomas in patients with hepatolithiasis, we compared the clinical characteristics of patients who had cholangiocarcinoma associated with hepatolithiasis with those of patients with hepatolithiasis only. METHODOLOGY Forty patients with cholangiocarcinoma associated with hepatolithiasis (group HC) and 73 patients with hepatolithiasis only (group H) were randomly selected for this study. Mean tumor size was 6.1 +/- 2.4 cm in diameter. RESULTS Patients of group HC were older (56.7 +/- 8.9 yr) than those of group H (49.2 +/- 12.9 yr) (p < 0.001). Weight loss was more frequent in group HC (51.5%) than in group H (5.5%) (p < 0.001) and serum alkaline phosphatase levels were higher in group HC (181 +/- 184 IU/L) than in group H (426 +/- 385 IU/L) (p < 0.001). The proportion of the patients who had hepatolithiasis in the right or both lobes of the liver was higher in group HC (72.5%) than in group H (50.6%) (p = 0.024). The optimal cutoff value of serum CEA level for cholangiocarcinoma detection was set at 4.2 ng/mL using ROC cure to give a sensitivity of 67.6% and a specificity of 90.5%. Group HC differed from group H because of its lower rates of both abdominal pain and cholangitis, longer duration of stone history, and lower serum albumin level. Factors that did not predict cholangiocarcinoma included sex ratio, white blood cell count, serum bilirubin level, and hepatic atrophy. CONCLUSIONS Cholangiocarcinoma should be suspected in patients with hepatolithiasis, especially when, the patient is over 40 years old, has a long history of hepatolithiasis with weight loss, a higher level of serum alkaline phosphatase, a lower level of serum albumin, a serum carcinoembryonic antigen level exceeding 4.2 ng/mL, and hepatolithiasis that is located either in the right or both lobes of the liver.
Weighted Round Robin Configuration for Worst-Case Delay Optimization in Network-on-Chip

We propose an approach for computing the end-to-end delay bound of individual variable bit-rate flows in an First Input First Output multiplexer with aggregate scheduling under weighted round robin (WRR) policy. To this end, we use a network calculus to derive per-flow end-to-end equivalent service curves employed for computing least upper delay bounds (LUDBs) of the individual flows. Since the real-time applications are going to meet guaranteed services with lower delay bounds, we optimize the weights in WRR policy to minimize the LUDBs while satisfying the performance constraints. We formulate two constrained delay optimization problems, namely, minimize-delay and multiobjective optimization. Multiobjective optimization has both the total delay bounds and their variance as the minimization objectives. The proposed optimizations are solved using a genetic algorithm. A video object plane decoder case study exhibits a 15.4% reduction of the total worst case delays and a 40.3% reduction on the variance of delays when compared with round robin policy. The optimization algorithm has low run-time complexity, enabling quick exploration of the large design spaces. We conclude that an appropriate weight allocation can be a valuable instrument for the delay optimization in on-chip network designs.
Phosphorylation of Tyr245 in the open‐inhibited state of Abelson kinase does not induce downstream signaling

Binding of tyrosine kinase inhibitors such as imatinib was shown to induce a novel open‐inhibited conformation of BCR‐ABL, in which Tyr245 is exposed and prone to phosphorylation. To evaluate whether this leads to priming of the kinase in cellular systems, we probed activation of downstream signaling as a result of Tyr245 phosphorylation in a series of cellular washout experiments. While a spike in Tyr245 phosphorylation was observed both in overexpression and endogenous settings, no induction of downstream signaling was detected, showing that the priming hypothesis is not relevant for the therapeutic situation.
Exploiting idle cycles for algorithm level re-computing

Deep sub-micron VLSI circuits are susceptible to permanent and transient faults. Several techniques for concurrent error detection (CED) recovery and correction have been proposed to target permanent and transient faults. We propose a new register transfer (RT) level time redundancy based CED technique that exploits the idle cycles in the data path. Although algorithm level re-computing techniques can trade-off the detection capability of CED vs. time overhead, it results in 100 % time overhead when the strongest CED capability is achieved. Using the idle cycles in the data path to do the re-computation can reduce this time overhead. However dependencies between operations prevent the recomputation from fully utilizing the idle cycles. Deliberately breaking some of these data dependencies can further reduce the time overhead associated with algorithm level re-computing.
Condition-Based Maintenance with both Perfect and Imperfect Maintenance Actions

This paper deals with a condition-based maintenance (CBM) model considering both perfect and imperfect maintenance actions for a deteriorating system whose condition is aperiod- ically monitored according to a remaining useful life (RUL) based-inspection policy. Perfect maintenance actions restore completely the system to the ’as good as new’ state. Their related cost are however often high. Imperfect preventive maintenance restores partially the system with reduced main- tenance cost. Nevertheless, it may however make the system more susceptible to future deterioration. The aim of the pa- per is to propose a CBM model which can help to construct optimal maintenance policies when both perfect and imper- fect maintenance actions are possible. To illustrate the use of the proposed CBM model, a numerical example finally is introduced.
Shared content editing in opportunistic networks

This paper examines shared content editing in opportunistic networks. Instead of immutable messages, such as photos or music files that are often assumed in opportunistic network applications, we focus on mutable content, such as wiki-pages, that can be edited by anyone carrying a copy. We show through simulations that mutable content can be handled by using revision control mechanisms (merging), or by simply adopting/discarding versions wholesale.
Targeted expansion of Protected Areas to maximise the persistence of terrestrial mammals

Over a quarter of species assessed by the IUCN Red List are threatened with extinction. A global commitment to protect 17% of land and 10% of the oceans by 2020 is close to being achieved, but with limited ecological impacts due to its inadequacy and poor enforcement. Here, we reverse-engineer IUCN Red List criteria to generate area-based conservation targets and spatial conservation priorities to minimize the extinction risk of the world terrestrial mammals. We find that approximately 60% of the Earth’s non-Antarctic land surface would require some form of protection. Our results suggest that global conservation priority schemes, among which the Aichi targets, will be inadequate to secure the persistence of terrestrial mammals. To achieve this goal, international cooperation is required to implement a connected and comprehensive conservation area network, guided by high priority regions outlined in this study.
An iterative, non-local approach for restoring depth maps in RGB-D images

In this paper, we present a novel iterative median filter based strategy to improve the quality of the depth maps provided by sensors like Microsoft Kinect. The quality of the depth map is improved in two aspects, by filling holes present in the maps and by addressing the random noise. The holes are filled by iteratively applying a median based filter which takes into account the RGB components as well. The color similarity is measured by finding the absolute difference of the neighbourhood pixels and the median value. The hole filled depth map is further improved by applying a bilateral filter and processing the detail layer separately using Non-Local Denoising. The denoised detail layer is combined with the base layer to obtain a sharp and accurate depth map. We show that the proposed approach is able to generate high quality depth maps which can be quite useful in improving the performance of various applications of Microsoft Kinect such as pose estimation, gesture recognition, skeletal and facial tracking, etc.
Indolent Systemic Mastocytosis as the Cause of a Long History of Unexplained Hypotensive Episodes

Assessment of patients with unexplained hypotensive episodes in outpatient practice is often challenging, with an extensive differential diagnosis. The prevalence of systemic mast cell disease (MCD) is unknown, and the diagnosis is often elusive because serum and urine markers may become positive only after one of the self-limited, recurrent hypotensive episodes. Nevertheless, MCD is increasingly recognized as a cause of unexplained hypotension, secondary osteoporosis, and anaphylactic reactions to Hymenoptera stings. We describe a 38-year-old man who had a 15-year history of undiagnosed, recurrent hypotensive episodes with stereotypic symptoms. Extensive evaluation during these years was unrevealing. On physical examination, he appeared to be a healthy man with a prominent macular rash. Results of skin biopsy showed tryptase-positive mast cells. He had markedly elevated serum tryptase levels, and results of bone marrow biopsy revealed 10% mast cells; all these findings were consistent with indolent systemic mastocytosis. Key features in his history and physical examination prompted the conclusive testing. The most telling features were hypotension, tachycardia, and the rash (urticaria pigmentosa).
XP and Junior Developers: 7 Mistakes (and how to avoid them)

In two years of leading agile projects at Avanade, an organization heavy in recent college hires, the author learned a number of lessons about how to be successful with junior developers on an agile team. Indeed, my most successful team has been my most junior. The author discovered that my biggest mistakes with junior teams were related to partially adopting XP. Where a senior team, by virtue of its experience, can adapt to replace missing XP practices, a junior team reveals the extent to which the XP practices form a whole and are best adopted together.
Being naturalised, being left b

With around five million people accessing anti-retroviral treatment, which significantly reduces mortality and extends life, the HIV pandemic now exists in a context of treatment possibility, if not access. This paper discusses ways in which the pandemic is becoming naturalised through medicalisation, normalisation and marketisation, and how these processes undermine themselves internally. The paper goes on to examine some further denaturalising discontinuities in how the contemporary HIV era is is lived, which derive from HIV's specific biological, socioeconomic and psychological characteristics, and which leave many at some distance from the relatively hopeful HIV present. The paper argue that naturalisation, and aspects of 'being left behind,' are important elements of HIV experience which require continued attention. Throughout, it examines the significance of naturalising and denaturalising processes for HIV citizenship. The paper draws on narrative data from studies of HIV support in the UK, 1993-present, and in South Africa, 2001-4, to make these arguments.
Prolonged shedding of rotavirus in a geriatric inpatient

This study concerns a nosocomial rotaviral infection of a geriatric patient with clinical symptoms of acute gastroenteritis. The virological diagnosis was based on the detection of rotaviral antigens using a Rota kit, viral genome RNA by reverse transcription‐polymerase chain reaction method, and viral particles by electron microscopy in the stool samples. Prolonged rotaviral shedding was suggested to be due to impaired natural killer cell activity, possibly together with deficiency of specific local immune response of the patient. J. Med. Virol. 67:613–615, 2002. © 2002 Wiley‐Liss, Inc.
System-on-Chip Platform Security Assurance: Architecture and Validation

Modern system-on-chip (SoC) designs include a wide variety of highly sensitive assets which must be protected from unauthorized access. A significant aspect of SoC design involves exploration, analysis, and evaluation of resiliency mechanisms against attacks to such assets. These attacks may arise from a number of sources, including malicious intellectualproperty blocks (IPs) in the hardware, malicious or vulnerable firmware and software, insecure communication of the system with other devices, and side-channel vulnerabilities through power and performance profiles. Countermeasures for these attacks are equally diverse, which include architecture, design, implementation, and validation-based protection. In this paper, we provide a comprehensive overview of the security infrastructure in modern SoC designs, including both resiliency techniques and their validation paradigms at presilicon and postsilicon stages. We identify gaps in current resiliency and analysis architectures and propose design and validation solutions to address them. Finally, we provide industry perspectives on the role and impact of current practices on SoC security, and discuss some emerging trends in this important area.
Robust Guided Image Filtering Using Nonconvex Potentials

Filtering images using a guidance signal, a process called guided or joint image filtering, has been used in various tasks in computer vision and computational photography, particularly for noise reduction and joint upsampling. This uses an additional guidance signal as a structure prior, and transfers the structure of the guidance signal to an input image, restoring noisy or altered image structure. The main drawbacks of such a data-dependent framework are that it does not consider structural differences between guidance and input images, and that it is not robust to outliers. We propose a novel SD (for static/dynamic) filter to address these problems in a unified framework, and jointly leverage structural information from guidance and input images. Guided image filtering is formulated as a nonconvex optimization problem, which is solved by the majorize-minimization algorithm. The proposed algorithm converges quickly while guaranteeing a local minimum. The SD filter effectively controls the underlying image structure at different scales, and can handle a variety of types of data from different sensors. It is robust to outliers and other artifacts such as gradient reversal and global intensity shift, and has good edge-preserving smoothing properties. We demonstrate the flexibility and effectiveness of the proposed SD filter in a variety of applications, including depth upsampling, scale-space filtering, texture removal, flash/non-flash denoising, and RGB/NIR denoising.
Effects of CD40 binding on ovarian carcinoma cell growth and cytokine production in vitro

The poor prognosis associated with ovarian carcinoma (OVCA) is linked to the high incidence of local recurrence. There is a pressing need to identify factors that can play a role in OVCA growth and spread. Here, we focused on CD40, a member of the tumour necrosis factor (TNF) receptor superfamily with important functions in immune response. The expression of CD40 has been reported on various types of carcinoma cells, but its biological role is still poorly understood. The aim of the present study was to investigate the expression and function of the CD40 in OVCA cell lines. Detectable CD40 levels ranging from low to very high were found on the cell surface of several OVCA cell lines by flow cytometry analysis. Co‐culture with a murine cell line transfected with CD40 ligand (CD40L) inhibited cell growth and up‐regulated the secretion of proinflammatory cytokines interleukin (IL)‐6, IL‐8 and TNF‐α in high‐level CD40‐expressing OVCA cell lines. Similarly, an increase of IL‐6 and IL‐8 release could be obtained by adding a soluble form of CD40L to the OVCA cultures. These results suggest that CD40–CD40L interaction is an important pathway affecting growth regulation and cytokine production in OVCA.
Alterations in Vascular Gene Expression in Invasive Breast Carcinoma

The molecular signature that defines tumor microvasculature will likely provide clues as to how vascular-dependent tumor proliferation is regulated. Using purified endothelial cells, we generated a database of gene expression changes accompanying vascular proliferation in invasive breast cancer. In contrast to normal mammary vasculature, invasive breast cancer vasculature expresses extracellular matrix and surface proteins characteristic of proliferating and migrating endothelial cells. We define and validate the up-regulated expression of VE-cadherin and osteonectin in breast tumor vasculature. In contrast to other tumor types, invasive breast cancer vasculature induced a high expression level of specific transcription factors, including SNAIL1 and HEYL, that may drive gene expression changes necessary for breast tumor neovascularization. We demonstrate the expression of HEYL in tumor endothelial cells and additionally establish the ability of HEYL to both induce proliferation and attenuate programmed cell death of primary endothelial cells in vitro. We also establish that an additional intracellular protein and previously defined metastasis-associated gene, PRL3, appears to be expressed predominately in the vasculature of invasive breast cancers and is able to enhance the migration of endothelial cells in vitro. Together, our results provide unique insights into vascular regulation in breast tumors and suggest specific roles for genes in driving tumor angiogenesis.