Miracle-dz/UniFAR-FTUs huggingface dataset:
EXPSOL: Recommending Online Threads for Exception-Related Bug Reports

An exception-related bug is a kind of program bug which causes exceptions. During software maintenance, when programmers repair exception-related bugs, they typically analyze thrown exceptions to understand the root causes of such bugs. When encountering unfamiliar thrown exceptions, programmers often refer to online forum threads (e.g. StackOverflow) to understand how to fix them. Although some general search engines are available and some research tools are proposed, they are insufficient to recommend threads for exception-related bugs from large-scale online resources. In this paper, we propose an approach, named EXPSOL, which recommends online threads as solutions for a newly reported exception-related bug with a model trained by support vector machines. We conduct two evaluations on thousands of threads from StackOverflow and fixed issues from GitHub. The results of our first evaluation show the significance of our internal features and highlight the importance of integrating different features. The results of our second evaluation show that, EXPSOL performs better in mean average precision, mean reciprocal rank and recall than those of the Google search engine, the internal search engine of StackOverflow, and other existing approaches.
Spatial Baseline Optimization for Spaceborne Multistatic SAR Tomography Systems

Spaceborne multistatic synthetic aperture radar (SAR) tomography (SMS-TomoSAR) systems take full advantage of the flexible configuration of multistatic SAR in the space, time, phase, and frequency dimensions, and simultaneously achieve high-precision height resolution and low-deformation measurement of three-dimensional ground scenes. SMS-TomoSAR currently poses a series of key issues to solve, such as baseline optimization, spatial transmission error estimation and compensation, and the choice of imaging algorithm, which directly affects the performance of height-dimensional imaging and surface deformation measurement. This paper explores the impact of baseline distribution on height-dimensional imaging performance for the baseline optimization issue, and proposes a feasible baseline optimization method. Firstly, the multi-base multi-pass baselines of an SMS-TomoSAR system are considered equivalent to a group of multi-pass baselines from monostatic SAR. Secondly, we establish the equivalent baselines as a symmetric-geometric model to characterize the non-uniform characteristic of baseline distribution. Through experimental simulation and model analysis, an approximately uniform baseline distribution is shown to have better SMS-TomoSAR imaging performance in the height direction. Further, a baseline design method under uniform-perturbation sampling with Gaussian distribution error is proposed. Finally, the imaging performance of different levels of perturbation is compared, and the maximum baseline perturbation allowed by the system is given.
Medicaid Expansion and Breast Cancer Screening in Appalachia and Non-Appalachia, United States, BRFSS 2003 to 2015

Background: Prior data suggests that breast cancer screening rates are lower among women in the Appalachian region of the United States. This study examined the changes in breast cancer screening before and after the implementation of the Affordable Care Act Medicaid expansion, in Appalachia and non-Appalachia states. Methods: Data from the Behavioral Risk Factor Surveillance System between 2003 and 2015 were analyzed to evaluate changes in breast cancer screening in the past 2 years among US women aged 50-74 years. Multivariable adjusted logistic regression and generalized estimating equation models were utilized, adjusting for sociodemographic, socioeconomic, and health-care characteristics. Data were analyzed for 2 periods: 2003 to 2009 (pre-expansion) and 2011 to 2015 (post-expansion) comparing Appalachia and non-Appalachia states. Results: The prevalence for of self-reported breast cancer screening in Appalachia and non-Appalachia states were 83% and 82% (P < .001), respectively. In Appalachian states, breast cancer screening was marginally higher in non-expanded versus expanded states in both the pre-expansion (relative risk [RR]: 1.002, 95% confidence interval [CI]: 1.002-1.003) and post-expansion period (RR: 1.001, 95% CI: 1.001-1.002). In non-Appalachian states, screening was lower in non-expanded states versus expanded states in both the pre-expansion (RR: 0.98, 95% CI: 0.97-0.98) and post-expansion period (RR: 0.95, 95% CI: 0.95-0.96). There were modest 3% to 4% declines in breast cancer screening rates in the pos-texpansion period regardless of expansion and Appalachia status. Conclusions: Breast cancer screening rates were higher in Appalachia versus non-Appalachia US states and higher in expanded versus nonexpanded non-Appalachia states. There were modest declines in breast cancer screening rates in the post-expansion period regardless of expansion and Appalachia status, suggesting that more work may be needed to reduce administrative, logistical, and structural barriers to breast cancer screening services.
IL-3 Triggers Chronic Rejection of Cardiac Allografts by Activation of Infiltrating Basophils

Key Points IL-3 induces allograft fibrosis and chronic rejection of heart transplants. IL-3 exerts profibrotic effects by activation of infiltrating basophils. IL-6 is an important basophil-derived mediator of fibrosis. Chronic rejection is a major problem in transplantation medicine, largely resistant to therapy, and poorly understood. We have shown previously that basophil-derived IL-4 contributes to fibrosis and vasculopathy in a model of heart transplantation with depletion of CD4+ T cells. However, it is unknown how basophils are activated in the allografts and whether they play a role when cyclosporin A (CsA) immunosuppression is applied. BALB/c donor hearts were heterotopically transplanted into fully MHC-mismatched C57BL/6 recipients and acute rejection was prevented by depletion of CD4+ T cells or treatment with CsA. We found that IL-3 is significantly upregulated in chronically rejecting allografts and is the major activator of basophils in allografts. Using IL-3–deficient mice and depletion of basophils, we show that IL-3 contributes to allograft fibrosis and organ failure in a basophil-dependent manner. Also, in the model of chronic rejection involving CsA, IL-3 and basophils substantially contribute to organ remodeling, despite the almost complete suppression of IL-4 by CsA. In this study, basophil-derived IL-6 that is resistant to suppression by CsA, was largely responsible for allograft fibrosis and limited transplant survival. Our data show that IL-3 induces allograft fibrosis and chronic rejection of heart transplants, and exerts its profibrotic effects by activation of infiltrating basophils. Blockade of IL-3 or basophil-derived cytokines may provide new strategies to prevent or delay the development of chronic allograft rejection.
Protocadherin17 Promoter Methylation is a Potential Predictive Biomarker in Clear Cell Renal Cell Carcinoma

Background Protocadherin17 (PCDH17) is a tumor suppressor gene, and is frequently silenced by promoter methylation in human cancers, including clear cell renal cell carcinoma (ccRCC). However, the clinical significance of PCDH17 methylation in ccRCC remains largely unclear. The aim of the present study was to investigate the methylation status of PCDH17 in ccRCC and its potential relevance to clinicopathological parameters and prognosis. Material/Methods Methylation-specific PCR was used to examine the methylation status of PCDH17 in 191 ccRCC tumors and matched paired adjacent noncancerous tissues. Subsequently, the associations between PCDH17 methylation and clinicopathological parameters and prognosis of patients with ccRCC were analyzed. Results PCDH17 methylation occurred in 66.5% of ccRCC tumors, but in only 12.1% of adjacent noncancerous tissues. PCDH17 methylation is significantly correlated with advanced stage, higher grade, and lymph node metastasis in ccRCC. Moreover, it is an independent prognostic factor for progression-free survival and overall survival of patients with ccRCC. Conclusions PCDH17 methylation occurred more frequently and was associated with malignant clinicopathological characteristics and poor prognosis in ccRCC patients. Thus, PCDH17 methylation may be used as a novel biomarker to predict the prognosis of patients with ccRCC.
Statistics on the heterotic landscape: Gauge groups and cosmological constants of four-dimensional heterotic strings

Recent developments in string theory have reinforced the notion that the space of stable supersymmetric and nonsupersymmetric string vacua fills out a landscape whose features are largely unknown. It is then hoped that progress in extracting phenomenological predictions from string theory--such as correlations between gauge groups, matter representations, potential values of the cosmological constant, and so forth--can be achieved through statistical studies of these vacua. To date, most of the efforts in these directions have focused on type I vacua. In this note, we present the first results of a statistical study of the heterotic landscape, focusing on more than 10{sup 5} explicit nonsupersymmetric tachyon-free heterotic string vacua and their associated gauge groups and one-loop cosmological constants. Although this study has several important limitations, we find a number of intriguing features which may be relevant for the heterotic landscape as a whole. These features include different probabilities and correlations for different possible gauge groups as functions of the number of orbifold twists. We also find a vast degeneracy amongst nonsupersymmetric string models, leading to a severe reduction in the number of realizable values of the cosmological constant as compared with naieve expectations. Finally, we find strong correlations between cosmological constantsmore » and gauge groups which suggest that heterotic string models with extremely small cosmological constants are overwhelmingly more likely to exhibit the standard model gauge group at the string scale than any of its grand-unified extensions. In all cases, heterotic world sheet symmetries such as modular invariance provide important constraints that do not appear in corresponding studies of type I vacua. « less
Macrophage markers soluble CD163 and soluble mannose receptor are associated with liver injury in patients with paracetamol overdose

Abstract The macrophage activation markers, soluble CD163 (sCD163) and soluble mannose receptor (sMR), are associated with liver disease severity and prognosis. We aimed to investigate macrophage activation reflected by sMR and sCD163 in patients with mild and severe paracetamol (PCM) intoxication and effects of antidote treatment in patients and healthy controls. We measured sMR and sCD163 levels by in-house enzyme-linked immunosorbent assays in two independent prospective cohorts of PCM overdosed patients: 49 patients with early mild PCM overdose from Aarhus University Hospital and 30 patients with severe acute liver injury included at the Royal Infirmary of Edinburgh. Furthermore, we investigated sMR and sCD163 in 14 healthy controls during N-acetylcysteine treatment. Within the mild PCM cohort, patients with elevated alanine transaminase on admission had significantly higher levels of sCD163 compared with patients with normal alanine transaminase (2.92[2.00–5.75] versus 1.29[1.02–1.69] mg/L, p = .009), whereas sMR showed no significant difference. In patients with acute liver injury, both markers were markedly higher compared to the mild PCM cohort (sCD163: 10.73[5.79–14.62] versus 1.34[1.06–1.96], p < .001; sMR: 0.80[0.63–1.14] versus 0.18[0.14–0.25], p < .001). Antidote treatment significantly reduced sCD163 levels in both PCM overdosed patients and healthy controls. In conclusion, macrophage activation assessed by the levels of sMR and sCD163 is associated with the degree of liver injury in patients with PCM intoxication and is ameliorated by antidote treatment, suggesting macrophage involvement in PCM-induced liver injury.
CaCO3 as an Environmentally Friendly Renewable Material for Drug Delivery Systems: Uptake of HSA-CaCO3 Nanocrystals Conjugates in Cancer Cell Lines

Chemical and biochemical functionalization of nanoparticles (NPs) can lead to an active cellular uptake enhancing their efficacy thanks to the targeted localization in tumors. In the present study calcium carbonate nano-crystals (CCNs), stabilized by an alcohol dehydration method, were successfully modified by grafting human serum albumin (HSA) on the surface to obtain a pure protein corona. Two types of CCNs were used: naked CaCO3 and the (3-aminopropyl)triethoxysilane (APTES) modified CaCO3-NH2. The HSA conjugation with naked CCN and amino-functionalized CCN (CCN-NH2) was established through the investigation of modification in size, zeta potential, and morphology by Transmission Electron Microscopy (TEM). The amount of HSA coating on the CCNs surface was assessed by spectrophotometry. Thermogravimetric analysis (TGA) and Differential scanning calorimetry (DSC) confirmed the grafting of APTES to the surface and successive adsorption of HSA. Furthermore, to evaluate the effect of protein complexation of CCNs on cellular behavior, bioavailability, and biological responses, three human model cancer cell lines, breast cancer (MCF7), cervical cancer (HeLa), and colon carcinoma (Caco-2) were selected to characterize the internalization kinetics, localization, and bio-interaction of the protein-enclosed CCNs. To monitor internalization of the various conjugates, chemical modification with fluorescein-isothiocyanate (FITC) was performed, and their stability over time was measured. Confocal microscopy was used to probe the uptake and confirm localization in the perinuclear region of the cancer cells. Flow cytometry assays confirmed that the bio-functionalization influence cellular uptake and the CCNs behavior depends on both cell line and surface features.
miR‐30e‐5p suppresses cell proliferation and migration in bladder cancer through regulating metadherin

Recent studies have suggested that miR‐30e‐5p is dysregulated in several human carcinomas; however, the mechanism of miR‐30e‐5p in bladder cancer (BCa) remains unknown. Here, we confirmed that the expression of miR‐30e‐5p was decreased in human BCa specimens and cell lines by quantitative reverse‐transcription polymerase chain reaction (qRT‐PCR). Upregulation of miR‐30e‐5p decreased the proliferation and migration in T24 and UM‐UC‐3 cells. Metadherin (MTDH) was a potential target for miR‐30e‐5p through bioinformatics analysis. Dual‐luciferase assays were conducted to validate the interaction between miR‐30e‐5p and MTDH, which demonstrates that the relative luciferase activity was significantly downregulated after transfected miR‐30e‐5p mimic compared with control mimic in 293T cells. We also detected that whether silencing of MTDH by using small interfering(si)‐MTDH matched effects caused by miR‐30e‐5p overexpression in BCa cells lines by Cell Counting Kit‐8 (CCK‐8), colony formation, and transwell assay, and we found the effects of silencing of MTDH same as miR‐30e‐5p overexpression. Furthermore, we verified that the restoration of MTDH in miR‐30e‐5p‐overexpressed BCa cells rescued the inhibitory effects of miR‐30e‐5p. In conclusion, these results demonstrated that miR‐30e‐5p may inhibit BCa cells growth and invasiveness by targeting MTDH and may be a promising therapeutic agent for treating clinical BCa patients.
Calculating architectural reliability via modeling and analysis

We present a software architecture-based approach to compositional estimation of system's reliability. Our approach is applicable to early stages of development when the implementation artifacts are not yet available, and exact execution profile is unknown. The uncertainty of the execution profile is modeled using stochastic processes with unknown parameters. The compositional approach calculates overall reliability of the system as a function of the reliability of its constituent components and their (complex) interactions. Sensitivity analysis to identify critical components and interactions will be provided.
Traffic profiling for modern enterprise networks: A case study

While Internet traffic has received a lot of attention, little is known about enterprise traffic. In this paper, we shed light on the basic characteristics of modern enterprise networks using a 24-hour long packet trace captured in a mid-size academic network. Our approach is to contrast the external and internal activities of the enterprise network under study. We demonstrate that these two types of traffic differ along several dimensions of our analysis, especially traffic composition, symmetry level or RTT. Overall, such a study provides valuable insights for traffic engineering in enterprise networks and could pave the way towards the design of specific workload models for enterprise networks.
Towards Secure E-Commerce Based on Virtualization and Attestation Techniques

We present a secure e-commerce architecture that is resistant to client compromise and man-in-the-middle attacks on SSL. To this end, we propose several security protocols that use attestation techniques offered by the Trusted Computing Group (TCG). Using these protocols, we can ensure that the client configuration remains untampered and trusted for the duration of the transaction. In addition, confidential data, such as authentication passwords, are only accessible by the electronic commerce server to which the users intend to transfer their data. Since we employ a trusted third party that is responsible for verifying a client's platform configuration, our approach does not depend on trusted computing at the server but instead only requires minor modification to server logic.
UC San Francisco UC San Francisco Previously Published Works Title Compartmentalization of calcium entry pathways in mouse rods

Photoreceptor metabolism, gene expression and synaptic transmission take place in a highly polarized structure consisting of the ellipsoid, subellipsoid, cell body and synaptic terminal regions. Although calcium, a key second messenger, regulates cellular functions throughout the photoreceptor, the molecular mechanisms underlying local region-specific action of Ca in photoreceptors are poorly understood. I have investigated the compartmentalization of voltage-dependent and independent Ca channels in mouse photoreceptors. Transient receptor potential channels isoform 6 (TRPC6), a putative store-operated Ca channel, was selectively localized to the cell body of rods. By contrast, voltage-operated Ca channels were expressed in the synaptic terminal and in the ellipsoid ⁄ subellipsoid regions. Likewise, Ca store transporters and channels were strongly associated with the subellipsoid region. A moderate TRPC6 signal was observed in cell bodies of bipolar, amacrine and ganglion cells, but was absent from both plexiform layers. These results suggest that Ca entry mechanisms in mammalian photoreceptors and bipolar cells are highly compartmentalized, consistent with local, region-specific activation of Ca-dependent processes.
Dynamin-dependent and dynamin-independent processes contribute to the regulation of single vesicle release kinetics and quantal size

Accumulating evidence suggests that the kinetics of release from single secretory vesicles can be regulated and that quantal size can be modified during fast kiss-and-run fusion. Multiple pathways for vesicle retrieval have been identified involving clathrin and dynamin. It has been unclear whether dynamin could participate in a fast kiss-and-run process to reclose a transient fusion pore and thereby limit vesicle release. We have disrupted dynamin function in adrenal chromaffin cells by expression of the amphiphysin Src-homology domain 3 (SH3) or by application of guanosine 5′-[γ-thio]triphosphate (GTPγS), and have monitored single vesicle release events, evoked by digitonin and Ca2+, by using carbon-fiber amperometry. Under both conditions, there was an increase in mean quantal size accompanying an increase in the half-width of amperometric spikes and a slowing of the fall time. These data suggest the existence of a dynamin-dependent process that can terminate vesicle release under basal conditions. Protein kinase C activation changed release kinetics and decreased quantal size by shortening the release period. The effects of phorbol ester treatment were not prevented by expression of the amphiphysin SH3 domain or by GTPγS suggesting the existence of alternative dynamin-independent process underlying fast kiss-and-run exocytosis.
Thinking Like a Wolf, a Sheep, or a Firefly: Learning Biology Through Constructing and Testing Computational Theories—An Embodied Modeling Approach

Biological phenomena can be investigated at multiple levels, from the molecular to the cellular to the organismic to the ecological. In typical biology instruction, these levels have been segregated. Yet, it is by examining the connections between such levels that many phenomena in biology, and complex systems in general, are best explained. We describe a computation-based approach that enables students to investigate the connections between different biological levels. Using agent-based, embodied modeling tools, students model the microrules underlying a biological phenomenon and observe the resultant aggregate dynamics. We describe 2 cases in which this approach was used. In both cases, students framed hypotheses, constructed multiagent models that incorporate these hypotheses, and tested these by running their models and observing the outcomes. Contrasting these cases against traditionally used, classical equation-based approaches, we argue that the embodied modeling approach connects more directly to students' experience, enables extended investigations as well as deeper understanding, and enables "advanced" topics to be productively introduced into the high school curriculum.
Proposed classification of endoleaks after endovascular treatment of Stanford type-B aortic dissections

Objectives Despite two decades of experience, no dedicated classification system exists to document and prognosticate patterns of endoleak encountered after endovascular therapy of type-B aortic dissection. This nomenclature gap has led to inconsistent management and underreporting of significant findings associated with adverse outcomes after endovascular treatment of type-B aortic dissection. Our goal was to propose a reproducible and prognostically relevant classification. Methods A multidisciplinary team of seven experienced open and endovascular aortic surgeons was assembled to provide consensus opinion. Extensive literature review was conducted. Deficiencies in the current classification approach of the various patterns of persistent filling of false lumen after endovascular therapy were identified. Results Our focus was to categorize high-risk and low-risk subgroups within endoleaks after endovascular treatment of type-B aortic dissection. In this classification, type-Ia endoleak refers to persistent filling of the false lumen in an antegrade manner. Causes include failure to cover the primary entry tear and sizing or technical related proximal seal failure. False lumen filling via distal entry tears is classified as type Ib endoleak, which is further sub-classified into b1 (major branch-related tears), and b2 (multiple small branches related tears). Retrograde ascending aortic dissection and stent graft-induced new entry were classified as type-I endoleaks (type-Ir and type-Is, respectively). Another focus was reclassification type-II endoleaks, with type-IIa endoleak referring to conventional retroleak from one or more posterior branches and type-IIx referring to retroleak from major branches (visceral or left subclavian arteries). Conclusions The majority of endoleaks after endovascular treatment of type-B aortic dissection are related to persistent or new filling of the false lumen. We propose a new false lumen-based classification schema for endoleaks occurring after endovascular therapy of type-B aortic dissection.