Miracle-dz/UniFAR-FTUs huggingface dataset:
Crowdsolving Program Verification

In this effort, we consider the verification of properties in C (subset) programs. That is, we prove the validity of a pre/postcondition pair for a program, or demonstrate invalidity via an error trace. This is undecidable in general, and modern static analysis tech- niques struggle to reason about non-linear programs and programs with loops. To that end, we use abstraction for defining results of looping and non-linear computations. Furthermore, existing techniques do not take advantage of programmer's insight, since the programmer receives little feedback from failed proof attempts. To that end, we ask user for facts that are relevant to the proof. Our technique is sound, modulo the correctness of verification tools we rely on. As a first step, existing static analysis and invariant generation techniques are deployed on the program. We try to prove the postcondition using these facts. If that fails, we compute an abstraction of the original program, and query user for facts about the abstract program. We check the validity of each user fact given the set of known proven facts. We again try to prove the postcondition using this new fact. This process iterates until we either discharge the proof, or demonstrate a bug. In summary, we hope to involve a crowd of semi-expert users in solving a verification problem. With game mechanics and proper incentive mechanisms in place, crowdsolving can help scale program verification.
Shape in computing

Values associated with a data type usually have a shape, too. For example, the shape of a matrix is its size. Shape [Jay 1995] refers to data structures into which data can be inserted at various positions, or “holes. ” For example, the shape of a labeled graph is its underlying unlabeled graph; that of a record is its set of field names. Shapes, like types, are important in the specification and semantics of programs, and should support tools for static error detection and improved compilation techniques. This position article outlines the semantic underpinnings of shape theory and suggests how it might be exploited in a variety of computational settings. Currently, shape is clearest in those object-oriented languages that support a container class, where attributes of the container are clearly separated from those of its data. However, the container class plays no special role, and so the full benefits of shape go unrealized. Other computing paradigms fare less well. In database theory, subtyping is used to capture shape restrictions, for example, the addition of field names, but it is also used to capture restrictions on the values that the fields can take. In most imperative and functional languages the shapes are either fixed in advance, leading to rigidity and code duplication, or computed and checked at run-time (as in array-bound checking), which significantly increases overheads. In parallel computing it is typical to focus on the data, stored in arrays, making it difficult to generalize to more irregular shapes. The exploitation of shape requires a calculus in which values can be decomposed into their shape and data, which are manipulated separately and recombined. The semantic foundation for this calculus has already been built [Jay 1995] using a categorical pullback to capture the decomposition. The mere existence of the decomposition may sometimes be of use: graph types are fundamental, but are typically hidden by encodings, for example, as sparse arrays, when they should be manipulated directly, by both the programmer and the compiler. Another example arises when communicating a value along a channel. By sending the shape first, the receiver can fix the data structure, including pointers and the like before handling a uniform data stream, free of shape information. Most transmission errors will then appear as a shape-data mismatch. Now let us consider programming with shapes. When interactions between shape and data are rare, then the decomposition can lead to significant computational gains. For example, the fundamental operation of mapping a function across all the data in a shape is actually independent of the shape, that is, is shape-polymorphic. Similarly, a function that uses only some fields in a record is shape-polymorphic, though this is typically expressed using subtyping. Another variation is adaptive polymorphism in object-oriented programming [Lieberherr 1996], where the variable shape is given by variations in
Patch-based Texture Synthesis for Image Inpainting

Image inpaiting is an important task in image processing and vision. In this paper, we develop a general method for patch-based image inpainting by synthesizing new textures from existing one. A novel framework is introduced to find several optimal candidate patches and generate a new texture patch in the process. We form it as an optimization problem that identifies the potential patches for synthesis from an coarse-to-fine manner. We use the texture descriptor as a clue in searching for matching patches from the known region. To ensure the structure faithful to the original image, a geometric constraint metric is formally defined that is applied directly to the patch synthesis procedure. We extensively conducted our experiments on a wide range of testing images on various scenarios and contents by arbitrarily specifying the target the regions for inference followed by using existing evaluation metrics to verify its texture coherency and structural consistency. Our results demonstrate the high accuracy and desirable output that can be potentially used for numerous applications: object removal, background subtraction, and image retrieval.
Factors influencing receipt of adjuvant chemotherapy after surgery for pancreatic cancer: a two-center retrospective cohort study

Abstract Objective: The addition of adjuvant chemotherapy after surgical resection has improved survival rates for patients with pancreatic ductal adenocarcinoma (PDAC). However, outside clinical trials, many operated patients still do not receive adjuvant chemotherapy due to clinical and tumor-related factors. The aim of this study was to investigate factors that may influence the receipt of adjuvant chemotherapy and the effect on long-term survival. Materials and methods: Patients undergoing macroscopically curative resection for PDAC at the University Hospitals in Lund and Linköping, Sweden, between 1 January 2007 and 31 December 2015, were retrospectively reviewed. Clinical and pathological data were compared between adjuvant and non-adjuvant chemotherapy groups and factors affecting chemotherapy receipt were analyzed by multiple logistic regression. Multivariable Cox regression analysis was performed to select predictive variables for survival. Results: A total of 233 patients were analyzed. Adjuvant chemotherapy was administered to 167 patients (71.7%). The likelihood of receiving adjuvant chemotherapy decreased with age, OR 0.91, 95% CI 0.86–0.95, p < . 001. Moreover, patients with severe postoperative complications (Clavien–Dindo grade ≥ III) were less likely to receive adjuvant chemotherapy, OR 0.31, 95% CI 0.14–0.71, p = . 005. The presence of lymph node metastases on histopathological reporting was associated with increased likelihood of initiating adjuvant chemotherapy, OR 2.19, 95% CI 1.09–4.40, p = . 028. Adjuvant chemotherapy was an independent factor for prolonged survival on multivariable Cox regression analysis, HR 0.45 (95% CI 0.31–0.65), p < . 001. Conclusions: Age, postoperative complications and the presence of lymph node metastases affect the likelihood of receiving adjuvant chemotherapy after PDAC surgery.
A Novel Protein Isoform of the Multicopy Human NAIP Gene Derives from Intragenic Alu SINE Promoters

The human neuronal apoptosis inhibitory protein (NAIP) gene is no longer principally considered a member of the Inhibitor of Apoptosis Protein (IAP) family, as its domain structure and functions in innate immunity also warrant inclusion in the Nod-Like Receptor (NLR) superfamily. NAIP is located in a region of copy number variation, with one full length and four partly deleted copies in the reference human genome. We demonstrate that several of the NAIP paralogues are expressed, and that novel transcripts arise from both internal and upstream transcription start sites. Remarkably, two internal start sites initiate within Alu short interspersed element (SINE) retrotransposons, and a third novel transcription start site exists within the final intron of the GUSBP1 gene, upstream of only two NAIP copies. One Alu functions alone as a promoter in transient assays, while the other likely combines with upstream L1 sequences to form a composite promoter. The novel transcripts encode shortened open reading frames and we show that corresponding proteins are translated in a number of cell lines and primary tissues, in some cases above the level of full length NAIP. Interestingly, some NAIP isoforms lack their caspase-sequestering motifs, suggesting that they have novel functions. Moreover, given that human and mouse NAIP have previously been shown to employ endogenous retroviral long terminal repeats as promoters, exaptation of Alu repeats as additional promoters provides a fascinating illustration of regulatory innovations adopted by a single gene.
BOLA: Near-optimal bitrate adaptation for online videos

Modern video players employ complex algorithms to adapt the bitrate of the video that is shown to the user. Bitrate adaptation requires a tradeoff between reducing the probability that the video freezes and enhancing the quality of the video shown to the user. A bitrate that is too high leads to frequent video freezes (i.e., rebuffering), while a bitrate that is too low leads to poor video quality. Video providers segment the video into short chunks and encode each chunk at multiple bitrates. The video player adaptively chooses the bitrate of each chunk that is downloaded, possibly choosing different bitrates for successive chunks. While bitrate adaptation holds the key to a good quality of experience for the user, current video players use ad-hoc algorithms that are poorly understood. We formulate bitrate adaptation as a utility maximization problem and devise an online control algorithm called BOLA that uses Lyapunov optimization techniques to minimize rebuffering and maximize video quality. We prove that BOLA achieves a time-average utility that is within an additive term O(1/V) of the optimal value, for a control parameter V related to the video buffer size. Further, unlike prior work, our algorithm does not require any prediction of available network bandwidth. We empirically validate our algorithm in a simulated network environment using an extensive collection of network traces. We show that our algorithm achieves near-optimal utility and in many cases significantly higher utility than current state-of-the-art algorithms. Our work has immediate impact on real-world video players and BOLA is part of the reference player implementation for the evolving DASH standard for video transmission.
The Effects of Truth–Lie Base Rate on Interactive Deception Detection Accuracy

Consistent with the Park and Levine’s (PL) probability model of deception detection accuracy, previous research has shown that as the proportion of honest messages increases, there is a corresponding linear increase in correct truth–lie discrimination. Three experiments (N = 120, 205, and 243, respectively) varied the truth–lie base rate in an interactive deception detection task. Linear base-rate effects were observed in all 3 experiments (average effect r = .61) regardless of whether the judges were interactive participants or passive observers, previously acquainted or strangers, or previously exposed to truths or lies. The predictive power of the PL probability model appears robust and extends to interactive deception despite PL’s logical incompatibility with interpersonal deception theory.
Developing Postmitotic Mammalian Neurons In Vivo Lacking Apaf-1 Undergo Programmed Cell Death by a Caspase-Independent, Nonapoptotic Pathway Involving Autophagy

Previous studies have shown that caspases and Apaf-1 are required for the normal programmed cell death (PCD) in vivo of immature postmitotic neurons and mitotically active neuronal precursor cells. In contrast, caspase activity is not necessary for the normal PCD of more mature postmitotic neurons that are establishing synaptic connections. Although normally these cells use caspases for PCD, in the absence of caspase activity these neurons undergo a distinct nonapoptotic type of degeneration. We examined the survival of these more mature postmitotic neuronal populations in mice in which Apaf-1 has been genetically deleted and find that they exhibit quantitatively normal PCD of developing postmitotic neurons. We next characterized the morphological mode of PCD in these mice and show that the neurons degenerate by a caspase-independent, nonapoptotic pathway that involves autophagy. However, autophagy does not appear to be involved in the normal PCD of postmitotic neurons in which caspases and Apaf-1 are present and functional because quantitatively normal neuronal PCD occurred in the absence of a key gene required for autophagy (ATG7). Finally, we examined the possible role of another caspase-independent type of neuronal PCD involving the apoptosis-inducing factor (AIF). Mice deficient in AIF also exhibit quantitatively normal PCD of postmitotic neurons after caspase inhibition. Together, these data indicate that, when key components of the type 1 apoptotic pathway (i.e., caspases and Apaf-1) are perturbed in vivo, developing postmitotic neurons nonetheless undergo quantitatively normal PCD by a caspase-independent pathway involving autophagy and not requiring AIF.
High-Order Staggered Finite Difference Methods for Maxwell's Equations in Dispersive Media

We study the stability properties of, and the phase error present in, several higher order (in space) staggered finite difference schemes for Maxwell’s equations coupled with a Debye or Lorentz polarization model. We present a novel expansion of the symbol of finite difference approximations, of arbitrary (even) order, of the first order spatial derivative operator. This alternative representation allows the derivation of a concise formula for the numerical dispersion relation for all (even) order schemes applied to each model, including the limiting (infinite order) case. We further derive a closed-form analytical stability condition for these schemes as a function of the order of the method. Using representative numerical values for the physical parameters, we validate the stability criterion while quantifying numerical dissipation. Lastly, we demonstrate the effect that the spatial discretization order, and the corresponding stability constraint, has on the dispersion error.
Novel Peptide Ligands of RGS4 from a Focused One‐Bead, One‐Compound Library

Regulators of G protein signaling accelerate GTP hydrolysis by Gα subunits and profoundly inhibit signaling by G protein‐coupled receptors. The distinct expression patterns and pathophysiologic regulation of regulators of G protein signaling proteins suggest that inhibitors may have therapeutic potential. We previously reported the design, mechanistic evaluation, and structure–activity relationships of a disulfide‐containing cyclic peptide inhibitor of RGS4, YJ34 (Ac‐Val‐Lys‐c[Cys‐Thr‐Gly‐Ile‐Cys]‐Glu‐NH2, S‐S) (Roof et al., Chem Biol Drug Des, 67, 2006, 266). Using a focused one‐bead, one‐compound peptide library that contains features known to be necessary for the activity of YJ34, we now identify peptides that bind to RGS4. Six peptides showed confirmed binding to RGS4 by flow cytometry. Two analogs of peptide 2 (Gly‐Thr‐c[Cys‐Phe‐Gly‐Thr‐Cys]‐Trp‐NH2, S‐S with a free or acetylated N‐terminus) inhibited RGS4‐stimulated Gαo GTPase activity at 25–50 μm. They selectively inhibit RGS4 but not RGS7, RGS16, and RGS19. Their inhibition of RGS4 does not depend on cysteine‐modification of RGS4, as they do not lose activity when all cysteines are removed from RGS4. Peptide 2 has been modeled to fit in the same binding pocket predicted for YJ34 but in the reverse orientation.
New Old Things: Fabrication, Physical Computing, and Experiment in Historical Practice

ABSTRACT Matter is a new medium for historical research, providing the opportunity to explore physical and experiential questions while working with digitized and materialized forms. RESUME La matiere est un nouveau sujet pour la recherche historique, donnant l’occasion aux chercheurs d’explorer des questions physiques et experientielles tout en leur permettant de travailler avec des formes numerisees et materialisees.
Renal tubular dysfunction in patients with inflammatory bowel disease treated with aminosalicylate.

BACKGROUND: An increasing number of case reports indicate potential nephrotoxicity of 5-aminosalicylic acid (5-ASA), which shares similarities with the chemical structures of both phenacetin and acetylsalicylic acid. AIM: In a point prevalence study the occurrence of sensitive indices indicative of early kidney malfunction was assessed in outpatients with inflammatory bowel disease. METHODS: Routine indices of kidney function (creatinine clearance, urinary protein content, pH, electrolytes, and microscopy) were investigated in 223 patients with inflammatory bowel disease as well as sensitive markers of glomerular or tubular dysfunction (microproteinuria by SDS polyacrylamide gel electrophoresis (SDS-PAGE), urinary concentrations of N-acetyl-beta-D-glucosaminidase, alpha 1-microglobulin, gamma-glutamyltransferase (GGT), alkaline phosphatase (AP), and albumin). Histories of exposure to 5-ASA were assessed by questionnaire. RESULTS: Patients receiving high amounts of 5-ASA, both actual as well as on a lifetime basis, showed an increased prevalence of tubular proteinuria by SDS-PAGE. Raised values for urinary AP and GGT indicate proximal tubular epithelial cells as the source. All other kidney function tests were normal. Analysis of covariates indicated strong associations between disease activity and size of 5-ASA doses as well as alterations in kidney tubular function. CONCLUSION: The possibility exists that high doses of 5-ASA may be associated with proximal tubular proteinuria. This point prevalence study cannot dissect the possible impact of chronic inflammation from high dose 5-ASA treatment and further prospective studies are warranted.
Antiplasmodial activity of iron(II) and ruthenium(II) organometallic complexes against Plasmodium falciparum blood parasites

This work reports the in vitro activity against Plasmodium falciparumblood forms (W2 clone, chloroquine-resistant) of tamoxifen-based compounds and their ferrocenyl (ferrocifens) and ruthenocenyl (ruthenocifens) derivatives, as well as their cytotoxicity against HepG2 human hepatoma cells. Surprisingly with these series, results indicate that the biological activity of ruthenocifens is better than that of ferrocifens and other tamoxifen-like compounds. The synthesis of a new metal-based compound is also described. It was shown, for the first time, that ruthenocifens are good antiplasmodial prototypes. Further studies will be conducted aiming at a better understanding of their mechanism of action and at obtaining new compounds with better therapeutic profile.
Association Between Type of Dietary Fish and Seafood Intake and the Risk of Incident Type 2 Diabetes

OBJECTIVE To investigate the association between fish and seafood intake and new-onset type 2 diabetes. RESEARCH DESIGN AND METHODS This was a population-based prospective cohort (European Prospective Investigation of Cancer [EPIC]-Norfolk) study of men and women aged 40–79 years at baseline (1993–1997). Habitual fish and seafood intake (white fish, oily fish, fried fish, and shellfish) was assessed using a semiquantitative food frequency questionnaire and categorized as less than one or one or more portions/week. During a median (interquartile range) follow-up of 10.2 (9.1–11.2) years, there were 725 incident diabetes cases among 21,984 eligible participants. RESULTS Higher total fish intake (one or more versus less than one portions/week) was associated with a significantly lower risk of diabetes (odds ratio [OR] 0.75 [95% CI 0.58–0.96]), in analyses adjusted for age, sex, family history of diabetes, education, smoking, physical activity, dietary factors (total energy intake, alcohol intake, and plasma vitamin C) and obesity (BMI and waist circumference). White fish and oily fish intakes were similarly inversely associated with diabetes risk, but the associations were not significant after adjustment for dietary factors (oily fish) or obesity (white fish). Fried fish was not significantly associated with diabetes risk. Consuming one or more portions/week of shellfish was associated with an increased risk of diabetes (OR 1.36 [1.02–1.81]) in adjusted analyses. CONCLUSIONS Total, white, and oily fish consumption may be beneficial for reducing risk of diabetes, reinforcing the public health message to consume fish regularly. Greater shellfish intake seems to be associated with an increased risk of diabetes, warranting further investigation into cooking methods and mechanisms.
Prioritization of Genetic Variants in the microRNA Regulome as Functional Candidates in Genome-Wide Association Studies

Comprehensive analyses of results from genome‐wide association studies (GWAS) have demonstrated that complex disease/trait‐associated loci are enriched in gene regulatory regions of the genome. The search for causal regulatory variation has focused primarily on transcriptional elements, such as promoters and enhancers. microRNAs (miRNAs) are now widely appreciated as critical posttranscriptional regulators of gene expression and are thought to impart stability to biological systems. Naturally occurring genetic variation in the miRNA regulome is likely an important contributor to phenotypic variation in the human population. However, the extent to which polymorphic miRNA‐mediated gene regulation underlies GWAS signals remains unclear. In this study, we have developed the most comprehensive bioinformatic analysis pipeline to date for cataloging and prioritizing variants in the miRNA regulome as functional candidates in GWAS. We highlight specific findings, including a variant in the promoter of the miRNA let‐7 that may contribute to human height variation. We also provide a discussion of how our approach can be expanded in the future. Overall, we believe that the results of this study will be valuable for researchers interested in determining whether GWAS signals implicate the miRNA regulome in their disease/trait of interest.