Miracle-dz/UniFAR-FTUs huggingface dataset:
Compositional safety verification with Max-SMT

We present an automated compositional program verification technique for safety properties based on conditional inductive invariants. For a given program part (e.g., a single loop) and a postcondition φ, we show how to, using a Max-SMT solver, an inductive invariant together with a precondition can be synthesized so that the precondition ensures the validity of the invariant and that the invariant implies φ. From this, we build a bottom-up program verification framework that propagates preconditions of small program parts as postconditions for preceding program parts. The method recovers from failures to prove the validity of a precondition, using the obtained intermediate results to restrict the search space for further proof attempts. As only small program parts need to be handled at a time, our method is scalable and distributable. The derived conditions can be viewed as implicit contracts between different parts of the program, and thus enable an incremental program analysis.
PET scanning used for monitoring treatment response in Mycobacterium avium complex infection mimicking malignancy.

Abstract:F-18 fluoro-deoxy-glucose- positron emission tomography (FDG-PET) scanning is commonly used for the diagnosis and staging of lung cancer. PET scanning has proved to be useful in differentiating between benign and malignant pulmonary nodules. In oncology, PET scanning is also widely used in
Cooperation of nectin‐1 and nectin‐3 is required for normal ameloblast function and crown shape development in mouse teeth

Nectins are immunoglobulin‐like cell adhesion proteins and their interactions recruit various cell–cell junctions. Mutations in human NECTIN‐1 cause an ectodermal dysplasia syndrome, but Nectin‐1 null mice have only slight defects in teeth, suggesting compensation by other nectin(s). We observed overlapping expression of nectin‐3 with nectin‐1 and enamel abnormality in the nectin‐3 mutant. We, therefore, generated nectin‐1;nectin‐3 compound mutants. However, all teeth developed and no significant dental abnormalities were observed before birth. At postnatal day 10, the upper molars of compound mutants exhibited conical crown shape and retarded enamel maturation. Nectin‐1 was expressed in ameloblasts whereas nectin‐3 was expressed in neighboring stratum intermedium cells at this stage. The immunohistochemical localization and electron microscopical observations indicated that the desmosomal junctions between stratum intermedium and ameloblasts were significantly reduced. These results suggest that heterophilic interaction between nectin‐1 and nectin‐3 recruits desmosomal junctions, and that these are required for proper enamel formation. Developmental Dynamics 239:2558–2569, 2010. © 2010 Wiley‐Liss, Inc.
Mechanochemical switching between growth and differentiation during fibroblast growth factor-stimulated angiogenesis in vitro: role of extracellular matrix

The angiogenic factor, basic fibroblast growth factor (FGF), either stimulates endothelial cell growth or promotes capillary differentiation depending upon the microenvironment in which it acts. Analysis of various in vitro models of spontaneous angiogenesis, in combination with time-lapse cinematography, demonstrated that capillary tube formation was greatly facilitated by promoting multicellular retraction and cell elevation above the surface of the rigid culture dish or by culturing endothelial cells on malleable extracellular matrix (ECM) substrata. These observations suggested to us that mechanical (i.e., tension-dependent) interactions between endothelial cells and ECM may serve to regulate capillary development. To test this hypothesis, FGF-stimulated endothelial cells were grown in chemically defined medium on bacteriological (nonadhesive) dishes that were precoated with different densities of fibronectin. Extensive cell spreading and growth were promoted by fibronectin coating densities that were highly adhesive (greater than 500 ng/cm2), whereas cell rounding, detachment, and loss of viability were observed on dishes coated with low fibronectin concentrations (less than 100 ng/cm2). Intermediate fibronectin coating densities (100-500 ng/cm2) promoted cell extension, but they could not completely resist cell tractional forces. Partial retraction of multicellular aggregates resulted in cell shortening, cessation of growth, and formation of branching tubular networks within 24-48 h. Multicellular retraction and subsequent tube formation also could be elicited on highly adhesive dishes by overcoming the mechanical resistance of the substratum using higher cell plating numbers. Dishes coated with varying concentrations of type IV collagen or gelatin produced similar results. These results suggest that ECM components may act locally to regulate the growth and pattern- regulating actions of soluble FGF based upon their ability to resist cell-generated mechanical loads. Thus, we propose that FGF-stimulated endothelial cells may be "switched" between growth, differentiation, and involution modes during angiogenesis by altering the adhesivity or mechanical integrity of their ECM.
Acquisition of an immunosuppressive protumorigenic macrophage phenotype depending on c-Jun phosphorylation

Significance Tumor-associated macrophages are often associated with poor prognosis, but the molecular cues that impart the change in macrophage phenotypes are mostly unclear. Our findings identify c-Jun N-terminal phosphorylation as a key mediator of macrophage education and point to a recruitment of immunosuppressive regulatory T cells as a possible effector protumorigenic mechanism. This cross-talk between adaptive and innate immune responses occurs before overt tumorigenesis, reversing the classic paradigm of initiation and promotion. Our findings raise the possibility that targeting immune checkpoints could be effective for tumor prevention in chronic inflammatory diseases. The inflamed tumor microenvironment plays a critical role in tumorigenesis. However, the mechanisms through which immune cells, particularly macrophages, promote tumorigenesis have only been partially elucidated, and the full scope of signaling pathways supplying macrophages with protumorigenic phenotypes still remain largely unknown. Here we report that germ-line absence of c-Jun N-terminal phosphorylation at serines 63 and 73 impedes inflammation-associated hepatocarcinogenesis, yet deleting c-Jun only in hepatocytes does not inhibit hepatocellular carcinoma (HCC) formation. Moreover, in human HCC-bearing livers, c-Jun phosphorylation is found in inflammatory cells, whereas it is mostly absent from malignant hepatocytes. Interestingly, macrophages in livers of mice with chronic hepatitis gradually switch their phenotype along the course of disease. Macrophage phenotype and density are dictated by c-Jun phosphorylation, in vitro and in vivo. Transition of macrophage phenotype, from antitumorigenic to protumorigenic, occurs before tumorigenesis, resulting in the production of various chemokines, including chemokine (C-C motif) ligand 17 (CCL17) and CCL22. Such signals, emanating from the liver microenvironment, direct the recruitment of regulatory T cells, which are known to facilitate HCC growth. Our findings identify c-Jun phosphorylation as a key mediator of macrophage education and point to the recruitment of immunosuppressive regulatory T cells as a possible protumorigenic mechanism.
Circulating mitochondrial DNA increases with age and is a familiar trait: Implications for “inflamm‐aging”

Mitochondrial components, including mitochondrial DNA (mtDNA), when released extracellularly, can act as “damage‐associated molecular pattern” (DAMP) agents and cause inflammation. As many elderly people are characterized by a low‐grade, chronic inflammatory status defined “inflamm‐aging,” we evaluated if circulating mtDNA can contribute to this phenomenon. Eight hundred and thirty‐one Caucasian subjects were enrolled in the study, including 429 siblings aged 90–104 (90+ siblings). mtDNA plasma levels increased gradually after the fifth decade of life. In 90+ subjects, mtDNA values of two members of the same sibling relationship were directly correlated, suggesting a role for familiar/genetic background in controlling the levels of circulating mtDNA. The subjects with the highest mtDNA plasma levels had the highest amounts of TNF‐α, IL‐6, RANTES, and IL‐1ra; the subjects with the lowest mtDNA levels had the lowest levels of the same cytokines. In vitro stimulation of monocytes with mtDNA concentrations similar to the highest levels observed in vivo resulted in an increased production of TNF‐α, suggesting that mtDNA can modulate the production of proinflammatory cytokines. Our findings therefore show that circulating mtDNA increases with age, and can significantly contribute to the maintenance of the low‐grade, chronic inflammation observed in elderly people.
Avoiding and Escaping Depressions in Real-Time Heuristic Search

Heuristics used for solving hard real-time search problems have regions with depressions. Such regions are bounded areas of the search space in which the heuristic function is inaccurate compared to the actual cost to reach a solution. Early real-time search algorithms, like LRTA*, easily become trapped in those regions since the heuristic values of their states may need to be updated multiple times, which results in costly solutions. State-of-the-art real-time search algorithms, like LSS-LRTA* or LRTA*(k), improve LRTA*'s mechanism to update the heuristic, resulting in improved performance. Those algorithms, however, do not guide search towards avoiding depressed regions. This paper presents depression avoidance, a simple real-time search principle to guide search towards avoiding states that have been marked as part of a heuristic depression. We propose two ways in which depression avoidance can be implemented: mark-and-avoid and move-to-border. We implement these strategies on top of LSS-LRTA* and RTAA*, producing 4 new real-time heuristic search algorithms: aLSS-LRTA*, daLSS-LRTA*, aRTAA*, and daRTAA*. When the objective is to find a single solution by running the real-time search algorithm once, we show that daLSS-LRTA* and daRTAA* outperform their predecessors sometimes by one order of magnitude. Of the four new algorithms, daRTAA* produces the best solutions given a fixed deadline on the average time allowed per planning episode. We prove all our algorithms have good theoretical properties: in finite search spaces, they find a solution if one exists, and converge to an optimal after a number of trials.
Eastchester clapping sign: A novel test of parietal neglect

Hand clapping is a motor program mastered in infancy. Inspired by a question posed by an Eastchester High School AP Psychology class, we present a case series of 14 patients with hemispatial neglect who, when asked to clap, repeatedly performed one‐handed motions stopping abruptly at the midline of the visual hemispace, as if pantomiming slapping an invisible board. In contrast, hemiplegic patients without neglect will reach across and clap against their plegic hands. This phenomenon provides an easy, rapid, and unambiguous test for neglect, applicable to patients of any ethnicity or age. Ann Neurol 2009;66:114–117
On the V-Line Radon Transform and Its Imaging Applications

Radon transforms defined on smooth curves are well known and extensively studied in the literature. In this paper, we consider a Radon transform defined on a discontinuous curve formed by a pair of half-lines forming the vertical letter V. If the classical two-dimensional Radon transform has served as a work horse for tomographic transmission and/or emission imaging, we show that this V-line Radon transform is the backbone of scattered radiation imaging in two dimensions. We establish its analytic inverse formula as well as a corresponding filtered back projection reconstruction procedure. These theoretical results allow the reconstruction of two-dimensional images from Compton scattered radiation collected on a one-dimensional collimated camera. We illustrate the working principles of this imaging modality by presenting numerical simulation results.
Content based image retrieval using curvelet transform

Feature extraction is a key issue in content-based image retrieval (CBIR). In the past, a number of texture features have been proposed in literature, including statistic methods and spectral methods. However, most of them are not able to accurately capture the edge information which is the most important texture feature in an image. Recent researches on multi-scale analysis, especially the curvelet research, provide good opportunity to extract more accurate texture feature for image retrieval. Curvelet was originally proposed for image denoising and has shown promising performance. In this paper, a new image feature based on curvelet transform has been proposed. We apply discrete curvelet transform on texture images and compute the low order statistics from the transformed images. Images are then represented using the extracted texture features. Retrieval results show, it significantly outperforms the widely used Gabor texture feature.
Exploiting a corpus of business letters from a phraseological, functional perspective*

Abstract This paper illustrates how a freely available online corpus has been exploited in a module on teaching business letters covering the following four speech acts (functions) commonly found in business letters: invitations, requests, complaints and refusals. It is proposed that different strategies are required for teaching potentially non-face-threatening (invitations, requests) and face-threatening (complaints, refusals) speech acts. The hands-on pedagogic activities follow the ‘guided inductive approach’ advocated by Johansson (2009) and draw on practices and strategies covered in the literature on using corpora in language learning and teaching, viz. the need for ‘pedagogic mediation’, and the ‘noticing’ hypothesis from second language acquisition studies.
Effects of pH on CdO films deposited onto ITO coated glass substrates by electrodeposition

Thin films of CdO were deposited onto indium tin oxide (ITO) coated glass substrates using electrodeposition method. The pH of the final solutions was adjusted from 4 to 8 and effects of pH on the films were investigated. The maximum film thickness was reached at pH 5 and XRD studies showed that this film had relatively high peak intensities. Optical studies showed that band gap varies between 2.04 and 2.41 eV and depend on pH. The surface morphologies were analysed by SEM images and they revealed that films were deposited compact and there were no voids, cracks or pinholes.
AP-1 Is a Component of the Transcriptional Network Regulated by GSK-3 in Quiescent Cells

Background The protein kinase GSK-3 is constitutively active in quiescent cells in the absence of growth factor signaling. Previously, we identified a set of genes that required GSK-3 to maintain their repression during quiescence. Computational analysis of the upstream sequences of these genes predicted transcription factor binding sites for CREB, NFκB and AP-1. In our previous work, contributions of CREB and NFκB were examined. In the current study, the AP-1 component of the signaling network in quiescent cells was explored. Methodology/Principal Findings Using chromatin immunoprecipitation analysis, two AP-1 family members, c-Jun and JunD, bound to predicted upstream regulatory sequences in 8 of the 12 GSK-3-regulated genes. c-Jun was phosphorylated on threonine 239 by GSK-3 in quiescent cells, consistent with previous studies demonstrating inhibition of c-Jun by GSK-3. Inhibition of GSK-3 attenuated this phosphorylation, resulting in the stabilization of c-Jun. The association of c-Jun with its target sequences was increased by growth factor stimulation as well as by direct GSK-3 inhibition. The physiological role for c-Jun was also confirmed by siRNA inhibition of gene induction. Conclusions/Significance These results indicate that inhibition of c-Jun by GSK-3 contributes to the repression of growth factor-inducible genes in quiescent cells. Together, AP-1, CREB and NFκB form an integrated transcriptional network that is largely responsible for maintaining repression of target genes downstream of GSK-3 signaling.
The ganges water machine.

The river Ganges and its tributaries, and the flat and fertile plain through which they flow, are one of earth's great natural resources. For thousands of years abundant water and generous land have provided the foundation for a highly developed civilization based on agriculture and for one of the world's largest concentrations of human populations. But farming is mainly traditional and at a subsistence level, with little surplus, and as a result the population has remained overwhelmingly rural and most people are desperately poor. Although irrigation from canals and wells has been practiced for millennia, chiefly as a protection against the uncertainties of the monsoon rains, the water resources are largely untapped; the small fraction of water used for irrigation is poorly managed and its productivity is low. Deeply embedded cultural, social, and economic problems inhibit modernization of agriculture and fuller utilization of the water resources. Capital investments and technological changes on a large scale are also required. As experience elsewhere shows, the introduction of technological changes on the required scale might break the chains of tradition and injustice that now bind the people in misery and poverty.
Impaired Synaptic Plasticity and cAMP Response Element-Binding Protein Activation in Ca2+/Calmodulin-Dependent Protein Kinase Type IV/Gr-Deficient Mice

The Ca2+/calmodulin-dependent protein kinase type IV/Gr (CaMKIV/Gr) is a key effector of neuronal Ca2+ signaling; its function was analyzed by targeted gene disruption in mice. CaMKIV/Gr-deficient mice exhibited impaired neuronal cAMP-responsive element binding protein (CREB) phosphorylation and Ca2+/CREB-dependent gene expression. They were also deficient in two forms of synaptic plasticity: long-term potentiation (LTP) in hippocampal CA1 neurons and a late phase of long-term depression in cerebellar Purkinje neurons. However, despite impaired LTP and CREB activation, CaMKIV/Gr-deficient mice exhibited no obvious deficits in spatial learning and memory. These results support an important role for CaMKIV/Gr in Ca2+-regulated neuronal gene transcription and synaptic plasticity and suggest that the contribution of other signaling pathways may spare spatial memory of CaMKIV/Gr-deficient mice.
A Simple Microfluidic Platform for Long-Term Analysis and Continuous Dual-Imaging Detection of T-Cell Secreted IFN-γ and IL-2 on Antibody-Based Biochip

The identification and characterization, at the cellular level, of cytokine productions present a high interest for both fundamental research and clinical studies. However, the majority of techniques currently available (ELISA, ELISpot, flow cytometry, etc.) have several shortcomings including, notably, the assessment of several cytokines in relation to individual secreting cells and the monitoring of living cell responses for a long incubation time. In the present work, we describe a system composed of a microfluidic platform coupled with an antibody microarray chip for continuous SPR imaging and immunofluorescence analysis of cytokines (IL-2 and IFN-γ) secreted by T-Lymphocytes, specifically, and stably captured on the biochip under flow upon continued long-term on-chip culture (more than 24 h).
CHOICE OF THE MODEL OF PRESENTING TEMPORAL DATA IN THE SYSTEM OF THE TRAIN TRAFFIC SCHEDULE

The authors have suggested three possible models of presenting temporal data in Information Systems (IS) of the train schedule, differing in the building principles. Choice of the optimal model of data presenting is performed with the account of different indicators characterizing the IS. For evaluating the efficiency of suggested models the Analytic Hierarchy Process (AHP) method is applied. There are developed 13 evaluating criteria, which are distributed in three groups: Hardware, Maintenance and Performance. The research is carried out for four different classes of IS. For user friendliness there have been used different tools of visualization which allowed visual presentation of the most important criteria and of the alternatives’ preference.
Adaptive region matching for region-based image retrieval by constructing region importance index

This study deals with the problem of similarity matching in region-based image retrieval (RBIR). A novel visual similarity measurement called adaptive region matching (ARM) has been developed. For decreasing negative influence of interference regions and important information loss simultaneously, a region importance index is constructed and semantic meaningful region (SMR) is introduced. Moreover, ARM automatically performs SMR-to-image matching or image-to-image matching. Extensive experiments on Corel-1000, Caltech-256 and University of Washington (UW) databases demonstrate the authors proposed ARM is more flexible and more efficient than the existing visual similarity measurements that were originally developed for RBIR.
Trends and Determinants of Rural Poverty: A Logistic Regression Analysis of Selected Districts of Punjab

Poverty is widespread in the rural areas, where the people are in a state of human deprivation with regard to incomes, clothing, housing, health care, education, sanitary facilities and human rights. Nearly 61 percent of the country’s populations live in rural areas. In Pakistan poverty has been increased in rural areas and is higher than urban areas. Of the total rural population 65 percent are directly or indirectly linked with agriculture sector. In Pakistan more than 44.8 percent people generate their income from agriculture sector, and the higher rate of increase in poverty in the rural areas has provoked debate on growth and productivity trends in the agriculture sector. Therefore, it is the need of the hour to determine such factors which affect the poverty status of a rural household. Utilising unique IFPRI (International Food Policy Research Institute) panel data together with sub-sample of PRHS (Pakistan Rural Household Survey) for two districts of Punjab (Attock and Faisalabad) the present study aim at analysing and estimating the rural poverty trends and determinants of rural poverty from the late 1980s to 2002. The data was analysed by using binary logistic model and head count measure. The results show that the chance of a household tripping to poverty increased due to increase in household size, dependency ratio, while, education, value of livestock, remittances and farming decreased the likelihood of being a poor. Moreover, the socio-economic opportunities as represented by the availability of infrastructure in the residential region also play a significant role in the level of poverty faced by a household. This study makes a modest contribution by attempting to analyse the need for focusing on anti-poverty policies, which can nip the evil in the bud.