Miracle-dz/UniFAR-FTUs huggingface dataset:
An executable formal semantics of PHP with applications to program analysis

Nowadays, many important activities in our lives involve the web. However, the software and protocols on which web applications are based were not designed with the appropriate level of security in mind. Many web applications have reached a level of complexity for which testing, code reviews and human inspection are no longer sufficient quality-assurance guarantees. Tools that employ static analysis techniques are needed in order to explore all possible execution paths through an application and guarantee the absence of undesirable behaviours. To make sure that an analysis captures the properties of interest, and to navigate the trade-offs between efficiency and precision, it is necessary to base the design and the development of static analysis tools on a firm understanding of the language to be analysed. When this underlying knowledge is missing or erroneous, tools can’t be trusted no matter what advanced techniques they use to perform their task. In this Thesis, we introduce KPHP, the first executable formal semantics of PHP, one of the most popular languages for server-side web programming. Then, we demonstrate its practical relevance by developing two verification tools, of increasing complexity, on top of it a simple verifier based on symbolic execution and LTL model checking and a general purpose, fully configurable and extensible static analyser based on Abstract Interpretation. Our LTL-based tool leverages the existing symbolic execution and model checking support offered by K, our semantics framework of choice, and constitutes a first proof-of-concept of the usefulness of our semantics. Our abstract interpreter, on the other hand, represents a more significant and novel contribution to the field of static analysis of dynamic scripting languages (PHP in particular). Although our tool is still a prototype and therefore not well suited for handling large real-world codebases, we demonstrate how our semantics-based, principled approach to the development of verification tools has lead to the design of static analyses that outperform existing tools and approaches, both in terms of supported language features, precision, and breadth of possible applications.
Indentation and Wear Damage Assessment of TiC-Stainless Steel Cermets

Titanium carbide (TiC) based cermets are commonly used in wear and corrosion resistance applications. The microstructural evolution, and related compositional instability, of TiC-based cermets prepared with a 316-L stainless steel binder is described in the present work. Samples were fabricated using a simple vacuum melt-infiltration procedure, with 5 to 30 vol.% binder. Infiltration temperatures ranged from 1475°C to 1550°C, held for up to 240 minutes, typically resulting in sintered samples with densities in excess of 99 % of theoretical. It is demonstrated that irregularly shaped grains (concave/hollow) can arise after sintering, especially at 1475°C, which is discussed in terms of the ‘instability of the solid-liquid interface’ theory. It is demonstrated that a complex, multi-layer core-rim structure arose for the cermets, with accommodation of selected steel constituents into the rim of the TiC grains. In particular, it is shown that the Mo in the original 316-L stainless steel is essentially fully depleted from the metallic binder phase, forming a Mo-rich inner-rim layer on the TiC grain cores.
“In Principle We Have Agreement, But in Practice It Is a Bit More Difficult”: Obtaining Organizational Buy-In to Patient-Centered Medical Home Transformation

The patient-centered medical home (PCMH) is a model of care that emphasizes the coordination of patient treatment among health care providers. Practice transformation to this model, however, presents a number of challenges. One of these challenges is getting the buy-in of all personnel to commit to making organizational changes in the journey to becoming a nationally recognized medical home. This study investigated internal messages of buy-in as communicated by practices transitioning to this type of care. Grounding itself in stakeholder theory, this study analyzed interviews with staff, administration, and practitioners from 20 medical practices in a mid-Atlantic state. The analysis revealed three overarching themes: (a) communication among staff that is open, consistent; (b) implementation of reinforcement techniques; and (c) access to a change implementer who encourages successful evolution. Discussion of these themes provides recommendations for communication approaches to organizational buy-in for medical practices hoping to become a PCMH.
Biotransformation of Aflatoxin B1 and Its Relationship with the Differential Toxicological Response to Aflatoxin in Commercial Poultry Species

Aflatoxin B1 (AFB1) is a highly toxic compound (LD50 = 1-50 mg/kg) for most animal species, although it is extremely toxic (LD50 turkey poults > goslings > pheasant chicks > quail chicks > chicks (Leeson et al., 1995). Even though there is still no clear explanation for this differential sensitivity, differences in susceptibility could be due to differences in AFB1 biotransformation pathways among species. The aim of the present chapter is to review the current knowledge on AFB1 biotransformation, with emphasis on
Walking while Talking and Falls in Aging

Background: While divided attention tasks are recognized as predictors of falls in older adults, a comprehensive examination of this association is lacking. Objective: We examined the validity of a ‘walking while talking' (WWT) task for predicting falls. Methods: We studied the associations of 8 selected gait markers measured during WWT (individually as well as domains derived by factor analysis) with incident falls in 646 adults (mean age 79.9 years; 61% women) enrolled in an aging study who received quantitative gait assessments. Cox regressions adjusted for multiple potential confounders and normal-pace walking were used to examine the associations. Results: Over a mean follow-up of 2.6 years, 337 participants (52%) fell. Step length was the only individual WWT parameter that predicted falls [hazard ratio (HR) 0.98; p = 0.034]. Factor analysis identified 3 gait domains, of which only the pace factor predicted falls (HR 1.31; p = 0.002). Results remained robust after adjusting for multiple potential confounders and accounting for normal-pace walking. Conclusions: WWT performance was a significant predictor of falls. Gait domains in WWT should be further studied to improve current fall risk assessments and to develop new interventions.
Tumour Control Probability in Cancer Stem Cells Hypothesis

The tumour control probability (TCP) is a formalism derived to compare various treatment regimens of radiation therapy, defined as the probability that given a prescribed dose of radiation, a tumour has been eradicated or controlled. In the traditional view of cancer, all cells share the ability to divide without limit and thus have the potential to generate a malignant tumour. However, an emerging notion is that only a sub-population of cells, the so-called cancer stem cells (CSCs), are responsible for the initiation and maintenance of the tumour. A key implication of the CSC hypothesis is that these cells must be eradicated to achieve cures, thus we define TCPS as the probability of eradicating CSCs for a given dose of radiation. A cell surface protein expression profile, such as CD44high/CD24low for breast cancer or CD133 for glioma, is often used as a biomarker to monitor CSCs enrichment. However, it is increasingly recognized that not all cells bearing this expression profile are necessarily CSCs, and in particular early generations of progenitor cells may share the same phenotype. Thus, due to the lack of a perfect biomarker for CSCs, we also define a novel measurable TCPCD+, that is the probability of eliminating or controlling biomarker positive cells. Based on these definitions, we use stochastic methods and numerical simulations parameterized for the case of gliomas, to compare the theoretical TCPS and the measurable TCPCD+. We also use the measurable TCP to compare the effect of various radiation protocols.
A Cooperative Communication Scheme Based on Coalition Formation Game in Clustered Wireless Sensor Networks

In this work, we study the problem of how to strike a balance between the QoS provisioning and the energy efficiency when a cooperative communication scheme is applied to a clustered wireless sensor network. Specifically, we first characterize the tradeoff by a multi-variable optimization problem, with the goal of balancing the outage performance and the network lifetime. Then, we horizontally decompose the problem into the concatenation of two subproblems: i) the long-haul transmit power per sensor node, and ii) the set of assisting cluster nodes. For the former one, an optimal long-haul transmit power solution is proposed based on the Lambert W function. The latter one is modeled as a coalition formation game, where the characteristic function is designed based on the combination of the former subproblem's results. Furthermore, an optimal algorithm is proposed by using a dynamic coalition formation process based on the best-reply process with trial opportunity. Extensive simulation results are presented to demonstrate the effectiveness of our proposed scheme.
Layer-Specific Organization of Local Excitatory and Inhibitory Synaptic Connectivity in the Rat Presubiculum

Abstract The presubiculum is part of the parahippocampal spatial navigation system and contains head direction and grid cells upstream of the medial entorhinal cortex. This position within the parahippocampal cortex renders the presubiculum uniquely suited for analyzing the circuit requirements underlying the emergence of spatially tuned neuronal activity. To identify the local circuit properties, we analyzed the topology of synaptic connections between pyramidal cells and interneurons in all layers of the presubiculum by testing 4250 potential synaptic connections using multiple whole‐cell recordings of up to 8 cells simultaneously. Network topology showed layer‐specific organization of microcircuits consistent with the prevailing distinction of superficial and deep layers. While connections among pyramidal cells were almost absent in superficial layers, deep layers exhibited an excitatory connectivity of 3.9%. In contrast, synaptic connectivity for inhibition was higher in superficial layers though markedly lower than in other cortical areas. Finally, synaptic amplitudes of both excitatory and inhibitory connections showed log‐normal distributions suggesting a nonrandom functional connectivity. In summary, our study provides new insights into the microcircuit organization of the presubiculum by revealing area‐ and layer‐specific connectivity rules and sets new constraints for future models of the parahippocampal navigation system.
A Dual Infection/Competition Assay Shows a Correlation between Ex Vivo Human Immunodeficiency Virus Type 1 Fitness and Disease Progression

ABSTRACT This study was designed to examine the impact of human immunodeficiency virus type 1 (HIV-1) fitness on disease progression through the use of a dual competition/heteroduplex tracking assay (HTA). Despite numerous studies on the impact of HIV-1 diversity and HIV-specific immune response on disease progression, we still do not have a firm understanding of the long-term pathogenesis of this virus. Strong and early CD8-positive cytotoxic T-cell and CD4-positive T-helper cell responses directed toward HIV-infected cells appear to curb HIV pathogenesis. However, the rate at which the virus infects the CD4+ T-cell population and possibly destroys the HIV-specific immune response may also alter the rate of disease progression. For HIV-1 fitness studies, we established conditions for dual HIV-1 infections of peripheral blood mononuclear cells (PBMC) and a sensitive HTA to measure relative virus production. A pairwise comparison was then performed to estimate the relative fitness of various non-syncytium-inducing/CCR5-tropic (NSI/R5) and syncytium-inducing/CXCR4-tropic (SI/X4) HIV-1 isolates. Four HIV-1 strains (two NSI/R5 and two SI/X4) with moderate ex vivo fitness were then selected as controls and competed against primary HIV-1 isolates from an HIV-infected Belgian cohort. HIV-1 isolates from long-term survivors (LTS) were outcompeted by control strains and were significantly less fit than HIV-1 isolates from patients with accelerated progression to AIDS (PRO). In addition, NSI/R5 HIV-1 isolates from PRO overgrew control SI/X4 strains, suggesting that not all SI/X4 HIV-1 isolates replicate more efficiently than all NSI/R5 isolates. Finally, there were strong, independent correlations between viral load and the total relative fitness values of HIV-1 isolates from PRO (r = 0.84, P = 0.033) and LTS (r = 0.86, P = 0.028). Separation of the PRO and LTS plots suggest that HIV-1 fitness together with viral load may be a strong predictor for the rate of disease progression.
Decomposing Large-Scale Capacitated Arc Routing Problems using a random route grouping method

In this paper, a simple but effective Random Route Grouping (RRG) scheme is developed to decompose the LargeScale Capacitated Arc Routing Problem (LSCARP). A theoretical analysis is given to show that the decomposition is guaranteed to be improved by RRG along with the improvement of the best-sofar solution during the search process. Then, RRG is combined with a cooperative co-evolution model to solve LSCARP. The experimental results on the EGL-G LSCARP set showed that given the same computational budget, the proposed approach obtained much better results than its counterpart without using decomposition.
Progress in the Preclinical Discovery and Clinical Development of Class I and Dual Class I/IV Phosphoinositide 3-Kinase (PI3K) Inhibitors

The phosphoinositide 3-kinases (PI3Ks) constitute an important family of lipid kinase enzymes that control a range of cellular processes through their regulation of a network of signal transduction pathways, and have emerged as important therapeutic targets in the context of cancer, inflammation and cardiovascular diseases. Since the mid-late 1990s, considerable progress has been made in the discovery and development of small molecule ATP-competitive PI3K inhibitors, a number of which have entered early phase human trials over recent years from which key clinical results are now being disclosed. This review summarizes progress made to date, primarily on the discovery and characterization of class I and dual class I/IV subtype inhibitors, together with advances that have been made in translational and clinical research, notably in cancer.
Long-term adherence of patients with relapsing-remitting multiple sclerosis to subcutaneous self-injections of interferon β-1a using an electronic device: the RIVER study

ABSTRACT Objectives: The BRIDGE study has previously shown a high short-term (12 weeks) adherence rate (>85%) of patients with relapsing-remitting multiple sclerosis (RRMS) to subcutaneous self-injections of interferon β-1a using an electronic auto-injection device (RebiSmart®). The primary goal of the RIVER study was to investigate in a real-life setting the long-term adherence to the use of RebiSmart among patients enrolled in the parent BRIDGE study. Methods: The RIVER study was designed as a real-life extension study of the BRIDGE trial. RRMS patients who completed BRIDGE and still had an indication for treatment were included. Data were collected prospectively through the RebiSmart device, and analyzed retrospectively. Long term adherence (administration of ≥ 80% of injections) to and safety of RebiSmart were assessed. The expected follow-up period ranged from 19 to 26 months. Results: A total of 57 RRMS patients participated in the follow-up study. The mean observation period was 20.5 ± 5.7 months. The overall adherence to the use of RebiSmart in the entire study cohort was 79.8% (median = 85.2%, range = 16–100%). There were 36 patients (63.2%) who completed at least 80% of the scheduled injections. No statistically significant differences were found between adherent and non-adherent patients in terms of age, sex, duration of the observation period, and occurrence of relapses. No serious treatment-related adverse events occurred. Conclusions: This study showed a high level of long-term adherence to the use of RebiSmart, with 63.2% of participants meeting the criterion for adherence to treatment.
Item-method directed forgetting and working memory capacity: A hierarchical multinomial modeling approach

Intentional forgetting of information that has recently been encoded is regarded an active and adaptive process and is widely studied using the item-method or the list-method directed forgetting (DF) paradigm. In the present research, we tested whether inter-individual differences in working-memory capacity (WMC), that have been identified as a relevant predictor of DF within the list method, are also related to stronger DF effects within the item method. Furthermore, we investigated relationships between WMC and item-method DF at different processing stages by applying the multinomial storage–retrieval model hierarchically to our data. Results showed that individuals with high WMC are better able to store to-be-remembered information than individuals with low WMC, whereas WMC was not related to retrieval of to-be-remembered information or to either storage or retrieval of to-be-forgotten information. Implications for theoretical accounts of item-method DF are discussed.
Local Optimization Strategies in Urban Vehicular Mobility

The comprehension of vehicular traffic in urban environments is crucial to achieve a good management of the complex processes arising from people collective motion. Even allowing for the great complexity of human beings, human behavior turns out to be subject to strong constraints—physical, environmental, social, economic—that induce the emergence of common patterns. The observation and understanding of those patterns is key to setup effective strategies to optimize the quality of life in cities while not frustrating the natural need for mobility. In this paper we focus on vehicular mobility with the aim to reveal the underlying patterns and uncover the human strategies determining them. To this end we analyze a large dataset of GPS vehicles tracks collected in the Rome (Italy) district during a month. We demonstrate the existence of a local optimization of travel times that vehicle drivers perform while choosing their journey. This finding is mirrored by two additional important facts, i.e., the observation that the average vehicle velocity increases by increasing the travel length and the emergence of a universal scaling law for the distribution of travel times at fixed traveled length. A simple modeling scheme confirms this scenario opening the way to further predictions.
Metastatic pheochromocytoma : clinical , genetic , and histopathologic characteristics

Background—Pheochromocytomas are tumors arising from chromaffin tissue located in the adrenal medulla associated with typical symptoms and signs which may occasionally develop metastases, which are defined as the presence of tumor cells at sites where these cells are not found. This retrospective analysis was focused on clinical, genetic, and histopathologic characteristics of primary metastatic versus primary benign pheochromocytomas. Materials and methods—We identified 41 subjects with metastatic pheochromocytoma and 108 subjects with apparently benign pheochromocytoma. We assessed dimension and biochemical profile of the primary tumor, age at presentation, and time to develop metastases. Results—Subjects with metastatic pheochromocytoma presented at a significantly younger age (41.4±14.7 vs. 50.2±13.7 years; P<0.001), with larger primary tumors (8.38±3.27 cm vs. 6.18±2.75 cm; P<0.001) and secreted more frequently norepinephrine (95.1% vs. 83.3 %; P=0.046) compared to subjects with apparently benign pheochromocytomas. No significant differences were found in the incidence of genetic mutations in both groups of subjects (25.7 % in the metastatic group and 14.7 % in the benign group; P=0.13). From available histopathologic markers of potential malignancy, only necrosis occurred more frequently in subjects with metastatic pheochromocytoma (27.6 % vs. 0 %; P<0.001). The median time to develop metastases was 3.6 years with the longest interval 24 years. Corresponding author: Karel Pacak, M.D., Ph.D., D.Sc., Professor of Medicine, Chief, Section on Medical Neuroendocrinology, Reproductive and Adult Endocrinology Program, NICHD, NIH Building 10, CRC, 1-East, Room 1-3140, 10 Center Drive, MSC-1109, Bethesda, Maryland 20892-1109, karel@mail.nih. gov, Fax: 1-301-402-0884, Phone: 1-301-402-4594. DISCLOSURE STATEMENT: The authors have nothing to disclose. NIH Public Access Author Manuscript Eur J Clin Invest. Author manuscript; available in PMC 2012 October 1. Published in final edited form as: Eur J Clin Invest. 2011 October ; 41(10): 1121–1128. doi:10.1111/j.1365-2362.2011. 02518.x. N IH PA Athor M anscript N IH PA Athor M anscript N IH PA Athor M anscript Conclusions—In conclusion, regardless of a genetic background, the size of a primary pheochromocytoma and age of its first presentation are two independent risk factors associated with the development of metastatic disease.
Prognostic and predictive markers of response to treatment in patients with locally advanced unresectable and metastatic pancreatic adenocarcinoma treated with gemcitabine/nab-paclitaxel: Results of a retrospective analysis

Background: Recent studies support the use of gemcitabine and nab-paclitaxel in adults with locally advanced unresectable or metastatic pancreatic adenocarcinoma although insufficient data are available on prognostic and predictive markers of response to treatment. Objective: The objective of this study is to identify treatment response markers in patients with locally advanced unresectable or metastatic pancreatic adenocarcinoma. Materials and Methods: This is an observational, retrospective, and multicenter study. Sociodemographic, clinical, and therapeutic data were collected. Cox regression models were applied to determine associations. Results: In total, 39 patients were included; 23.1% presented locally advanced pancreatic cancer and 76.9% metastatic disease. They received a mean of 6 ± 3 treatment cycles; 59% required dose reduction, 59% treatment delay, and 20.5% switched to a biweekly regimen. The overall response rate was 23% and the disease control rate was 81%. Median progression-free survival was 9 months and median overall survival (OS) was 15 months. A higher neutrophil/lymphocyte ratio (NLR) was significantly associated with lower OS. We reported Grades 1–4 nonhematological and hematological toxicities. Conclusion: NLR is a useful prognostic factor for OS in patients with locally advanced unresectable or metastatic pancreatic adenocarcinoma treated with gemcitabine and nab-paclitaxel. Moreover, we suggest that a biweekly regimen is an option for certain groups of patients.