Miracle-dz/UniFAR-FTUs huggingface dataset:
Incremental whole-program analysis in Datalog with lattices

Incremental static analyses provide up-to-date analysis results in time proportional to the size of a code change, not the entire code base. This promises fast feedback to programmers in IDEs and when checking in commits. However, existing incremental analysis frameworks fail to deliver on this promise for whole-program lattice-based data-flow analyses. In particular, prior Datalog-based frameworks yield good incremental performance only for intra-procedural analyses. In this paper, we first present a methodology to empirically test if a computation is amenable to incrementalization. Using this methodology, we find that incremental whole-program analysis may be possible. Second, we present a new incremental Datalog solver called LADDDER to eliminate the shortcomings of prior Datalog-based analysis frameworks. Our Datalog solver uses a non-standard aggregation semantics which allows us to loosen monotonicity requirements on analyses and to improve the performance of lattice aggregators considerably. Our evaluation on real-world Java code confirms that LADDDER provides up-to-date points-to, constant propagation, and interval information in milliseconds.
Pool of Experts: Realtime Querying Specialized Knowledge in Massive Neural Networks

In spite of the great success of deep learning technologies, training and delivery of a practically serviceable model is still a highly time-consuming process. Furthermore, a resulting model is usually too generic and heavyweight, and hence essentially goes through another expensive model compression phase to fit in a resource-limited device like embedded systems. Inspired by the fact that a machine learning task specifically requested by mobile users is often much simpler than it is supported by a massive generic model, this paper proposes a framework, called Pool of Experts (PoE), that instantly builds a lightweight and task-specific model without any training process. For a realtime model querying service, PoE first extracts a pool of primitive components, called experts, from a well-trained and sufficiently generic network by exploiting a novel conditional knowledge distillation method, and then performs our train-free knowledge consolidation to quickly combine necessary experts into a lightweight network for a target task. Thanks to this train-free property, in our thorough empirical study, PoE can build a fairly accurate yet compact model in a realtime manner, whereas it takes a few minutes per query for the other training methods to achieve a similar level of the accuracy.
Conceptualising sound-driven design: an exploratory discourse analysis

Sound-driven design is an emerging, human-centered design practice informed by technology and listening in the multisensory dimension of interaction. In this paper we present a discourse analysis approach aimed at qualitatively understanding the constituent concepts of such a practice, by means of semi-structured interviews with sound designers, design researchers, engineers and expert users in the context of critical care. Preliminary results show that sound-driven design is inherently embodied, situated, and participatory, that the four categories of interviewees equally contribute to the definition of the design problem, and yet that a clear, shared arena is still missing.
Does the Early Bird Catch the Worm? Earliness of Students' Work and its Relationship with Course Outcomes

Intuitively, it seems plausible that students who start their work earlier and work on more days than their peers should perform better in any course. But does the early bird really catch the worm? In this article, we examine introductory programming students' time management behavior as evidenced by data collected from a programming environment. We analyze: 1) the earliness of students' work, i.e. when they start working on their course assignments, 2) the number of days students work on course assignments, and 3) the relationship between earliness, the number of days worked, and course outcomes. Our results provide further support for the notion that, on average, students who start working on course assignments early perform slightly better in the course. At the same time, we found that starting early does not necessarily mean that students work on more days, and that starting early and working on many days does not necessarily mean that students get better grades. In addition, some students who start working early on the assignments in the first weeks of the course seem to start delaying when they begin working on assignments as the course progresses, while other students seem to be able to continue starting early throughout the course.
Shedding Light on Opaque Application Queries

We investigate a new query reverse-engineering problem of unmasking SQL queries hidden within database applications. The diverse use-cases for this problem range from resurrecting legacy code to query rewriting. As a first step in addressing the unmasking challenge, we present UNMASQUE, an active-learning extraction algorithm that can expose a basal class of hidden warehouse queries. A special feature of our design is that the extraction is non-invasive wrt the application, examining only the results obtained from repeated executions on databases derived with a combination of data mutation and data generation techniques. Further, potent optimizations are incorporated to minimize the extraction overheads. A detailed evaluation over applications hosting hidden SQL queries, or their imperative versions, demonstrates that UNMASQUE correctly and efficiently extracts these queries.
The genomic origin of Zana of Abkhazia

Enigmatic phenomena have sparked the imagination of people around the globe into creating folkloric creatures. One prime example is Zana of Abkhazia (South Caucasus), a well‐documented 19th century female who was captured living wild in the forest. Zana's appearance was sufficiently unusual, that she was referred to by locals as an Almasty—the analog of Bigfoot in the Caucasus. Although the exact location of Zana's burial site was unknown, the grave of her son, Khwit, was identified in 1971. The genomes of Khwit and the alleged Zana skeleton were sequenced to an average depth of ca. 3× using ancient DNA techniques. The identical mtDNA and parent‐offspring relationship between the two indicated that the unknown woman was indeed Zana. Population genomic analyses demonstrated that Zana's immediate genetic ancestry can likely be traced to present‐day East‐African populations. We speculate that Zana might have had a genetic disorder such as congenital generalized hypertrichosis which could partially explain her strange behavior, lack of speech, and long body hair. Our findings elucidate Zana's unfortunate story and provide a clear example of how prejudices of the time led to notions of cryptic hominids that are still held and transmitted by some today.
Outcomes of Burkitt lymphoma with bone marrow involvement or Burkitt leukemia in Chinese children

Burkitt lymphoma with bone marrow involvement and Burkitt leukemia behave aggressively. Thus far, there are limited data concerning survival and toxicity in Chinese children with Burkitt lymphoma or Burkitt leukemia who have undergone treatment with the non‐Hodgkin’s lymphoma Berlin‐Frankfurt‐Münster‐90/95 (NHL‐BFM‐90/95) protocol.
Influence of Onset to Imaging Time on Radiological Thrombus Characteristics in Acute Ischemic Stroke

Introduction: Radiological thrombus characteristics are associated with patient outcomes and treatment success after acute ischemic stroke. These characteristics could be expected to undergo time-dependent changes due to factors influencing thrombus architecture like blood stasis, clot contraction, and natural thrombolysis. We investigated whether stroke onset-to-imaging time was associated with thrombus length, perviousness, and density in the MR CLEAN Registry population. Methods: We included 245 patients with M1-segment occlusions and thin-slice baseline CT imaging from the MR CLEAN Registry, a nation-wide multicenter registry of patients who underwent endovascular treatment for acute ischemic stroke within 6.5 h of onset in the Netherlands. We used multivariable linear regression to investigate the effect of stroke onset-to-imaging time (per 5 min) on thrombus length (in mm), perviousness and density (both in Hounsfield Units). In the first model, we adjusted for age, sex, intravenous thrombolysis, antiplatelet use, and history of atrial fibrillation. In a second model, we additionally adjusted for observed vs. non-observed stroke onset, CT-angiography collateral score, direct presentation at a thrombectomy-capable center vs. transfer, and stroke etiology. We performed exploratory subgroup analyses for intravenous thrombolysis administration, observed vs. non-observed stroke onset, direct presentation vs. transfer, and stroke etiology. Results: Median stroke onset-to-imaging time was 83 (interquartile range 53–141) min. Onset to imaging time was not associated with thrombus length nor perviousness (β 0.002; 95% CI −0.004 to 0.007 and β −0.002; 95% CI −0.015 to 0.011 per 5 min, respectively) and was weakly associated with thrombus density in the fully adjusted model (adjusted β 0.100; 95% CI 0.005–0.196 HU per 5 min). The subgroup analyses showed no heterogeneity of these findings in any of the subgroups, except for a significantly positive relation between onset-to-imaging time and thrombus density in patients transferred from a primary stroke center (adjusted β 0.18; 95% CI 0.022–0.35). Conclusion: In our population of acute ischemic stroke patients, we found no clear association between onset-to-imaging time and radiological thrombus characteristics. This suggests that elapsed time from stroke onset plays a limited role in the interpretation of radiological thrombus characteristics and their effect on treatment results, at least in the early time window.
The Effects of Cardiometabolic Factors on the Association Between Serum Uric Acid and Chronic Kidney Disease in Chinese Middle-Aged and Older Population: A Mediation Analysis

Introduction To explore whether dyslipidemia, hyperglycemia or hypertension has mediating effect on the association between serum uric acid (SUA) and the development of chronic kidney disease (CKD). Methods We conducted a mediation analysis to explore the potential mediating effects of systolic blood pressure (SBP), diastolic blood pressure (DBP), blood glucose, triglyceride (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) on the association between SUA and estimated glomerular filtration rate (eGFR). The data were obtained from China Health and Retirement Longitudinal Study (CHARLS), covering 5,762 individuals. Results SUA had a negative dose-response total effect on eGFR (β -3.11, 95% CI -3.40 to -2.82, P-value<0.001). The linear regression between SUA and seven potential mediators indicated that blood glucose (β 0.80, 95% CI 0.18 to 1.42, P-value=0.012), TG (β 10.01, 95% CI 8.22 to 11.79, P-value<0.001), TC (β 2.64, 95% CI 1.83 to 3.45, P-value<0.001), HDL-C (β -0.27, 95% CI -0.52 to -0.02, P-value=0.034) and LDL-C (β 1.15, 95% CI 0.49 to 1.80, P-value=0.001) all had significant dose-response association with SUA, but SBP and DBP showed no significant association with SUA. In terms of the association between potential mediators and eGFR, only TG (β 0.003, 95% CI -0.001 to 0.01, P-value=0.117) and HDL-C (β 0.01, 95% CI -0.02 to 0.04, P-value=0.444) did not have significant linear association with eGFR. The linear regression showed that SUA was directly associated with eGFR (P-value<0.001). Conclusions This study supported that the association between SUA and the risk of CKD was not mediated by hypertension, hyperglycemia or dyslipidemia.
Expression Characterization of Flavonoid Biosynthetic Pathway Genes and Transcription Factors in Peanut Under Water Deficit Conditions

Drought is one of the hostile environmental stresses that limit the yield production of crop plants by modulating their growth and development. Peanut (Arachis hypogaea) has a wide range of adaptations to arid and semi-arid climates, but its yield is prone to loss due to drought. Other than beneficial fatty acids and micronutrients, peanut harbors various bioactive compounds including flavonoids that hold a prominent position as antioxidants in plants and protect them from oxidative stress. In this study, understanding of the biosynthesis of flavonoids in peanut under water deficit conditions was developed through expression analysis and correlational analysis and determining the accumulation pattern of phenols, flavonols, and anthocyanins. Six peanut varieties (BARD479, BARI2011, BARI2000, GOLDEN, PG1102, and PG1265) having variable responses against drought stress have been selected. Higher water retention and flavonoid accumulation have been observed in BARI2011 but downregulation has been observed in the expression of genes and transcription factors (TFs) which indicated the maintenance of normal homeostasis. ANOVA revealed that the expression of flavonoid genes and TFs is highly dependent upon the genotype of peanut in a spatiotemporal manner. Correlation analysis between expression of flavonoid biosynthetic genes and TFs indicated the role of AhMYB111 and AhMYB7 as an inhibitor for AhF3H and AhFLS, respectively, and AhMYB7, AhTTG1, and AhCSU2 as a positive regulator for the expression of Ah4CL, AhCHS, and AhF3H, respectively. However, AhbHLH and AhGL3 revealed nil-to-little relation with the expression of flavonoid biosynthetic pathway genes. Correlational analysis between the expression of TFs related to the biosynthesis of flavonoids and the accumulation of phenolics, flavonols, and anthocyanins indicated coregulation of flavonoid synthesis by TFs under water deficit conditions in peanut. This study would provide insight into the role of flavonoid biosynthetic pathway in drought response in peanut and would aid to develop drought-tolerant varieties of peanut.
A Comparison of Ex Vivo Expanded Human Regulatory T Cells Using Allogeneic Stimulated B Cells or Monocyte-Derived Dendritic Cells

Alloreactive regulatory T cells (arTregs) are more potent than polyclonal Tregs at suppressing immune responses to transplant antigens. Human arTregs can be expanded with allogeneic CD40L-stimulated B cells (sBcs) or stimulated-matured monocyte-derived dendritic cells (sDCs). Here, we compared the expansion efficiency and properties of arTregs stimulated ex vivo using these two types of antigen-presenting cells. Compared to sBcs, sDCs stimulated Tregs to expand two times more in number. The superior expansion-inducing capacity of sDCs correlated with their higher expression of CD80, CD86, and T cell-attracting chemokines. sBc- and sDC-arTregs expressed comparable levels of FOXP3, HELIOS, CD25, CD27, and CD62L, demethylated FOXP3 enhancer and in vitro suppressive function. sBc- and sDCs-arTregs had similar gene expression profiles that were distinct from primary Tregs. sBc- and sDC-arTregs exhibited similar low frequencies of IFN-γ, IL-4, and IL-17A-producing cells, and the cytokine-producing arTregs expressed high levels of FOXP3. Almost all sBc- and sDC-arTregs expressed CXCR3, which may enable them traffic to inflammatory sites. Thus, sDCs-arTregs that expand more readily, are phenotypically similar to sBc-arTregs, supporting sDCs as a viable alternative for arTreg production for clinical evaluation.
Reciprocal EGFR signaling in the Anchor Cell ensures precise inter-organ connection during C. elegans vulval morphogenesis

During C. elegans vulval development, the uterine anchor cell (AC) first secretes an epidermal growth factor (EGF) to specify the vulval cell fates and then invades into the underlying vulval epithelium. Thereby, the AC establishes direct contact with the invaginating 1° vulF cells and attaches the developing uterus to the vulva. The signals involved and the exact sequence of events joining these two organs are not fully understood. Using a conditional let-23 egf receptor (EGFR) allele along with novel microfluidic short- and long-term imaging methods, we discovered a specific function of the EGFR in the AC during vulval lumen morphogenesis. Tissue-specific inactivation of let-23 in the AC resulted in imprecise alignment of the AC with the 1° vulval cells, delayed AC invasion and disorganized adherens junctions at the newly forming contact site between the AC and the dorsal vulF toroid. We propose that EGFR signaling, activated by a reciprocal EGF cue from the 1° vulval cells, positions the AC at the vulval midline, guides it during invasion and assembles a cytoskeletal scaffold organizing the adherens junctions that connect the developing uterus to the dorsal vulF toroid. EGFR signaling in the AC thus ensures the precise alignment of the two developing organs.
Prediction of biological age by morphological staging of sarcopenia in Caenorhabditis elegans

Sarcopenia encompasses a progressive decline in allover muscle quantity and quality. Given its close association with aging, it may represent a valuable healthspan marker. Given the strong commonalities with human muscle structure and the facile visualization possibilities, C. elegans represents an attractive model for studying the relationship between sarcopenia and healthspan. However, classical assessment relies on visual scoring of muscle architecture, which is subjective and inaccurate. To resolve this, we have developed an automated image analysis pipeline for the detailed quantification and classification of muscle integrity in confocal microscopy images from a cohort of aging myosin::GFP reporter strains. We then extracted a variety of morphological descriptors and found a subset to scale linearly with age. This allowed us to establish a general linear model that predicts biological age from a morphological muscle signature. To validate the model, we evaluated muscle architecture in long-lived worms that are known to experience delayed sarcopenia by targeted RNAi-mediated knockdown of the daf-2 gene. We conclude that quantitative microscopy allows for staging sarcopenia in C. elegans and will be of use for systematic screening for pharmacological or genetic modulators that mitigate age-related muscle frailty and thus improve healthspan in C. elegans.
Sticking around: plant persistence strategies on edaphic islands

Species extinction risk at local scales can be partially offset by strategies promoting in-situ persistence. We explored how persistence-related traits of clonal and non-clonal plants in temperate dry grasslands respond intra- and interspecifically to variation in environmental conditions (soil, climate) and insularity. We focused on edaphic island specialist species, hypothesizing that plants experiencing harsh soil environments and strong insularity are distinguished by traits supporting enhanced persistence, such as small stature, long lifespan and resource-conservative strategies. We used linear mixed-effect models and bivariate ordinary least squares linear models to explore the response of species triats to environmental and biogeographic predictors. We found general support for this hypothesis. Soil properties and insularity emerged as the most important drivers of trait patterns. However, clonal species showed more consistent responses to variation in environmental conditions and insularity than non-clonal plants, which were characterized by distinct species-specific responses. Soil properties and insularity confirmed their major role in shaping the persistence strategies of edaphic island plant species. These drivers may exert their effect on specific functions (e.g. belowground resource conservation captured by BDMC). Additionally, we unambiguously identified that clonal species had different persistence strategies than non-clonal ones.
Visualizing looping of two endogenous genomic loci using synthetic zinc‐finger proteins with anti‐FLAG and anti‐HA frankenbodies in living cells

In eukaryotic nuclei, chromatin loops mediated through cohesin are critical structures that regulate gene expression and DNA replication. Here we demonstrate a new method to visualize endogenous genomic loci using synthetic zinc-finger proteins harboring repeat epitope tags (ZF probes) for signal amplification via binding of tag-specific intracellular antibodies, or frankenbodies, fused with fluorescent proteins. We achieve this in two steps. First, we develop an anti-FLAG frankenbody that can bind FLAG-tagged proteins in diverse live-cell environments. The anti-FLAG frankenbody complements the anti-HA frankenbody, enabling two-color signal amplification from FLAG and HA-tagged proteins. Second, we develop a pair of cell-permeable ZF probes that specifically bind two endogenous chromatin loci predicted to be involved in chromatin looping. By coupling our anti-FLAG and anti-HA frankenbodies with FLAG- and HA-tagged ZF probes, we simultaneously visualize the dynamics of the two loci in single living cells. This reveals close association between the two loci in the majority of cells, but the loci markedly separate upon the triggered degradation of the cohesin subunit RAD21. Our ability to image two endogenous genomic loci simultaneously in single living cells provides a proof-of-principle that ZF probes coupled with frankenbodies are useful new tools for exploring genome dynamics in multiple colors.
Lipid nanodiscs facilitate the identification of a fragment compound inhibiting the enzymatic activity of the bacterial membrane protein MsbA

Membrane proteins are critical elements of numerous therapeutic approaches ranging from cancer to bacterial infections. MsbA is a bacterial membrane protein that has received increasing attention as an antibacterial target for its role in the processing of Lipid A, a key precursor of lipopolysaccharide that is essential for bacterial growth. When employing nanodiscs it is possible to stabilize MsbA by providing a membrane-like environment that enhances its enzymatic activity. Taking advantage of this property we have carried out a fragment screening using the biophysical method of surface plasmon resonance. This approach identified several compounds that bind specifically to MsbA. In particular, one of these fragment molecules not only binds to the target, but also inhibits the ATPase activity of the MsbA protein. The similarity of this fragment to the adenine moiety of ATP points at a route to generate stronger and more potent inhibitors for MsbA and even other proteins of its family of ABC transporters. Collectively, our study reveals biophysical approaches that facilitate the identification of fragment candidates inhibiting the activity of membrane proteins.