Miracle-dz/UniFAR-FTUs huggingface dataset:
Autofolding for Source Code Summarization

Developers spend much of their time reading and browsing source code, raising new opportunities for summarization methods. Indeed, modern code editors provide code folding, which allows one to selectively hide blocks of code. However this is impractical to use as folding decisions must be made manually or based on simple rules. We introduce the autofolding problem, which is to automatically create a code summary by folding less informative code regions. We present a novel solution by formulating the problem as a sequence of AST folding decisions, leveraging a scoped topic model for code tokens. On an annotated set of popular open source projects, we show that our summarizer outperforms simpler baselines, yielding a 28 percent error reduction. Furthermore, we find through a case study that our summarizer is strongly preferred by experienced developers. More broadly, we hope this work will aid program comprehension by turning code folding into a usable and valuable tool.
On the Effective Energy Consumption in Wireless Sensor Networks

We analytically characterize the energy consumption per successfully transmitted packet in end-to-end packet transmissions in a wireless sensor network where nodes are identically and independently distributed in a square area following a homogeneous Poisson process. It is assumed that a greedy forwarding protocol is used for routing. We obtain analytical results on the average number of hops between any two nodes if the transmission is successful and the average number of hops traversed by packets before being dropped if the transmission is unsuccessful. A transmission is unsuccessful if the packet sent from a source to a destination has to be dropped at an intermediate node because the greedy forwarding routing protocol is unable to find a next-hop node that is closer to the destination. Based on the above analysis, we derive the effective energy consumption per successfully transmitted packet. We show that there exists an optimum transmission range which minimizes the effective energy consumption and such optimum transmission range can be computed based on our analysis.
The tidal disruption of protoplanetary accretion discs

In this paper we revisit the problem of the tidal interaction occurring between a protostellar accretion disc and a secondary point mass following a parabolic trajectory. We model the disc response analytically and we compare our results with three-dimensional SPH simulations. Inviscid as well as viscous hydrodynamics is considered. We show that in a viscous system the response derived from inviscid considerations is predominant even for the highest estimates of an anomalous disc shear viscosity. The angular momentum lost from the disc during the encounter is derived from linear theory for distant fty-bys. It is shown that the target discs can become warped and precess by a small amount during non-coplanar encounters. This small precession is shown to give rise to a relative tilt of the disc which is always more important for determining its final orientation than is the change to the orbital inclination. We discuss the implications of our results for protostellar accretion discs and planetary systems.
Making a Science of Model Search

Many computer vision algorithms depend on a variety of parameter choices and settings that are typically hand-tuned in the course of evaluating the algorithm. While such parameter tuning is often presented as being incidental to the algorithm, correctly setting these parameter choices is frequently critical to evaluating a method's full potential. Compounding matters, these parameters often must be re-tuned when the algorithm is applied to a new problem domain, and the tuning process itself often depends on personal experience and intuition in ways that are hard to describe. Since the performance of a given technique depends on both the fundamental quality of the algorithm and the details of its tuning, it can be difficult to determine whether a given technique is genuinely better, or simply better tuned. In this work, we propose a meta-modeling approach to support automated hyper parameter optimization, with the goal of providing practical tools to replace hand-tuning with a reproducible and unbiased optimization process. Our approach is to expose the underlying expression graph of how a performance metric (e.g. classification accuracy on validation examples) is computed from parameters that govern not only how individual processing steps are applied, but even which processing steps are included. A hyper parameter optimization algorithm transforms this graph into a program for optimizing that performance metric. Our approach yields state of the art results on three disparate computer vision problems: a face-matching verification task (LFW), a face identification task (PubFig83) and an object recognition task (CIFAR-10), using a single algorithm. More broadly, we argue that the formalization of a meta-model supports more objective, reproducible, and quantitative evaluation of computer vision algorithms, and that it can serve as a valuable tool for guiding algorithm development.
NLM NIH at TREC 2016 Clinical Decision Support Track

In this paper, we present our approach for TREC 2016 Clinical Decision Support (CDS) track. We combined methods for question analysis, query expansion, document retrieval and result fusion to ﬁnd relevant documents to a given clinical question. We submitted three automatic runs using the summaries and two automatic runs using the notes, provided for the ﬁrst time at the CDS track. Our experiments showed that query expansion and rank-based result fusion led to the best performance. Our runs exploring the clinical notes used MeSH for topic analysis and achieved our best P10 score of 0.2533. Using the summaries, we obtained an infNDCG score of 0.1872 and a R-prec score of 0.1465 (score in the top 10 of 107 automatic runs submitted to the 2016 CDS track).
Synthesis of Common Arabic Handwritings to Aid Optical Character Recognition Research

Document analysis tasks such as pattern recognition, word spotting or segmentation, require comprehensive databases for training and validation. Not only variations in writing style but also the used list of words is of importance in the case that training samples should reflect the input of a specific area of application. However, generation of training samples is expensive in the sense of manpower and time, particularly if complete text pages including complex ground truth are required. This is why there is a lack of such databases, especially for Arabic, the second most popular language. However, Arabic handwriting recognition involves different preprocessing, segmentation and recognition methods. Each requires particular ground truth or samples to enable optimal training and validation, which are often not covered by the currently available databases. To overcome this issue, we propose a system that synthesizes Arabic handwritten words and text pages and generates corresponding detailed ground truth. We use these syntheses to validate a new, segmentation based system that recognizes handwritten Arabic words. We found that a modification of an Active Shape Model based character classifiers—that we proposed earlier—improves the word recognition accuracy. Further improvements are achieved, by using a vocabulary of the 50,000 most common Arabic words for error correction.
Crystal Structure of Yeast DNA Polymerase ε Catalytic Domain

DNA polymerase ε (Polε) is a multi-subunit polymerase that contributes to genomic stability via its roles in leading strand replication and the repair of damaged DNA. Here we report the ternary structure of the Polε catalytic subunit (Pol2) bound to a nascent G:C base pair (Pol2G:C). Pol2G:C has a typical B-family polymerase fold and embraces the template-primer duplex with the palm, fingers, thumb and exonuclease domains. The overall arrangement of domains is similar to the structure of Pol2T:A reported recently, but there are notable differences in their polymerase and exonuclease active sites. In particular, we observe Ca2+ ions at both positions A and B in the polymerase active site and also observe a Ca2+ at position B of the exonuclease site. We find that the contacts to the nascent G:C base pair in the Pol2G:C structure are maintained in the Pol2T:A structure and reflect the comparable fidelity of Pol2 for nascent purine-pyrimidine and pyrimidine-purine base pairs. We note that unlike that of Pol3, the shape of the nascent base pair binding pocket in Pol2 is modulated from the major grove side by the presence of Tyr431. Together with Pol2T:A, our results provide a framework for understanding the structural basis of high fidelity DNA synthesis by Pol2.
Anti-snow performance of snow shields designed for brake calipers of a high-speed train

When high-speed trains run on a snowy railway line in cold weather, a large amount of snow and ice will accumulate on the brake calipers, which can lead to huge safety problems. In this paper, to solve this issue, a numerical method based on the detached eddy simulation was used to explore the flow features of a high-speed train running in cold weather. The accuracy of mesh resolution and methodology of Computational Fluid Dynamics (CFD) was validated against the wind tunnel tests. A discrete phase model was used to investigate the process of snow accumulation on the brake calipers by analysing the movement characteristics of snow particles. Based on this analysis, three kinds of anti-snow packing shields for the brake calipers were designed, and the shielding effects were compared via numerical simulations. The results show that a large amount of snow particles below the bogie directly impact the brake calipers causing massive snow packing on the bottom surfaces; some snow particles reflected from the rear equipment cabin cover return to the bogie region and accumulates on the upper surfaces. With the application of anti-snow packing shields with trapezoidal-, triangular- and cambered-shaped openings, the rates of snow accumulation on the brake calipers were reduced by 18.53, 26.68 and 38.81%, respectively. The cambered type provides the best anti-snow packing performance for the brake calipers.
Baseline Immunoglobulin E Levels as a Marker of Doxorubicin- and Trastuzumab-Associated Cardiac Dysfunction.

RATIONALE There is a critical need to develop robust, mechanistic strategies to identify patients at increased risk of cancer therapeutics-related cardiac dysfunction (CTRCD). OBJECTIVE We aimed to discover new biomarkers associated with doxorubicin- and trastuzumab-induced CTRCD using high-throughput proteomic profiling. METHODS AND RESULTS Plasma, echocardiograms, and clinical outcomes were collected at standardized intervals in breast cancer patients undergoing doxorubicin and trastuzumab cancer therapy. Thirty-one longitudinal plasma samples from 3 cases with CTRCD and 4 age- and cancer-matched controls without CTRCD were processed and analyzed using label-free liquid chromatography-mass spectrometry. From these analyses, 862 proteins were identified from case/control pairs 1 and 2 and 1360 proteins from case/control pair 3. Proteins with a >1.5-fold change in cases compared with controls with a P<0.05 either at the time of CTRCD diagnosis or across all time points were considered candidate diagnostic or predictive biomarkers, respectively. The protein that demonstrated the largest differences between cases and controls was immunoglobulin E, with higher levels detected at baseline and across all time points in controls without CTRCD as compared with matched CTRCD cases (P<0.05). Similarly, in a validation study of 35 participants treated with doxorubicin and trastuzumab, high baseline immunoglobulin E levels were associated with a significantly lower risk of CTRCD (P=0.018). CONCLUSIONS In patients receiving doxorubicin and trastuzumab, high baseline immunoglobulin E levels are associated with a lower risk of CTRCD. These novel findings suggest a new paradigm in cardio-oncology, implicating the immune system as a potential mediator of doxorubicin- and trastuzumab-induced cardiac dysfunction.
High-Throughput Screening of Chemical Effects on Steroidogenesis Using H295R Human Adrenocortical Carcinoma Cells

Disruption of steroidogenesis by environmental chemicals can result in altered hormone levels causing adverse reproductive and developmental effects. A high-throughput assay using H295R human adrenocortical carcinoma cells was used to evaluate the effect of 2060 chemical samples on steroidogenesis via high-performance liquid chromatography followed by tandem mass spectrometry quantification of 10 steroid hormones, including progestagens, glucocorticoids, androgens, and estrogens. The study employed a 3 stage screening strategy. The first stage established the maximum tolerated concentration (MTC; ≥ 70% viability) per sample. The second stage quantified changes in hormone levels at the MTC whereas the third stage performed concentration-response (CR) on a subset of samples. At all stages, cells were prestimulated with 10 µM forskolin for 48 h to induce steroidogenesis followed by chemical treatment for 48 h. Of the 2060 chemical samples evaluated, 524 samples were selected for 6-point CR screening, based in part on significantly altering at least 4 hormones at the MTC. CR screening identified 232 chemical samples with concentration-dependent effects on 17β-estradiol and/or testosterone, with 411 chemical samples showing an effect on at least one hormone across the steroidogenesis pathway. Clustering of the concentration-dependent chemical-mediated steroid hormone effects grouped chemical samples into 5 distinct profiles generally representing putative mechanisms of action, including CYP17A1 and HSD3B inhibition. A distinct pattern was observed between imidazole and triazole fungicides suggesting potentially distinct mechanisms of action. From a chemical testing and prioritization perspective, this assay platform provides a robust model for high-throughput screening of chemicals for effects on steroidogenesis.
The effects of sodium-glucose co-transporter 2 inhibitors in patients with type 2 diabetes: protocol for a systematic review with meta-analysis of randomised trials

Introduction Sodium-glucose co-transporter 2 inhibitors (SGLT-2i) increase urinary glucose excretion through a reduced renal glucose reabsorption. We plan to perform a systematic review of SGLT-2i for treatment of type 2 diabetes. Methods and analysis A systematic review with meta-analyses of randomised clinical trials on SGLT-2i versus placebo, other oral glucose lowering drugs or insulin for patients with type 2 diabetes will be performed. The primary end point will be the glycated haemoglobin. Secondary end points will include changes in body weight, body mass index, fasting plasma glucose, plasma cholesterol, kidney and liver blood tests, blood pressure and adverse events. Electronic (the Cochrane Library, MEDLINE, EMBASE and the Science Citation Index) and manual searches will be performed. Meta-analyses will be performed and the results presented as mean differences for continuous outcomes and risk differences for dichotomous outcomes, both with 95% CIs. Subgroup, sensitivity, regression and sequential analyses will be performed to evaluate intertrial heterogeneity, bias and the robustness of results due to cumulative testing. Ethics and dissemination The study will contribute to the knowledge regarding the beneficial and harmful effects of SGLT-2i in patients with type 2 diabetes. We plan to publish the study irrespective of the results. Results The study will be disseminated by peer-review publication and conference presentation. Trial registration number PROSPERO CRD42014008960
Modeling the seismic response of a two-storey calcium silicate brick masonry structure with nonlinear pushover and time-history analyses

In the recent years, increasing induced seismic activities have been observed in the northern part of the Netherlands due to gas extraction. These seismic events may cause severe damages to the building stock in this area, which is mainly composed of unreinforced masonry (URM) buildings not designed to withstand seismic loads. An extensive experimental campaign has been carried out at the Stevin II laboratory of Delft University of Technology to characterize the seismic responses of these URM structures. In this framework, a quasi-static cyclic pushover test on a full-scale masonry assemblage has been performed. In this treatise, the seismic behavior of the tested masonry assemblage is modeled and analyzed via finite element analyses. The validation against the experimental results is achieved through nonlinear pushover analyses on a well-built model of the assemblage. Moreover, as the pushover method used in the aforementioned studies is based on static loading, its accuracy and applicability on studying the seismic behavior for this type of masonry structure need to be evaluated. The evaluation is achieved by performing a series of nonlinear time-history analyses on the model to obtain accurate seismic response of the structure. The applied horizontal ground motion is representative of the earthquakes in the Groningen province and the incremental dynamic analysis method (IDA) is employed. The nonlinear pushover analyses reproduce the test results properly, showing similar maximum base shear forces and asymmetric capacity curves. In both experimental and numerical analyses, cracks start to form at the top and bottom of the masonry piers due to rocking mechanism and the failure of the structure is governed by damages of the wide piers. Moreover, a sensitivity study based on the monotonic pushover analysis shows that the post-peak behavior of the model is directly related to the masonry compressive strength. The incremental dynamic analysis provides similar base shear capacity and failure mechanisms as the nonlinear pushover analysis. However, the maximum displacement is smaller in both loading directions and a more distributed crack pattern is observed. Overall, for the studied masonry house, the pushover method is capable of properly estimating the base shear capacity but the deformation capacity might be overestimated.
Cross-layering for performance improvement in multi-hop wireless networks

Cross-layering represents a perspective design principle for adapting natively wired protocols to the wireless scenario and for improving their performance. The paper explores the possibilities of cross-layer design as a candidate tool for performance optimization, focusing on problems deriving from the usage of ARQ schemes in today's wireless networks and proposes a novel and general cross-layer interaction scheme between the transport and the link layers. Achieved results in the framework of a IEEE 802.11-based multi-hop wireless network demonstrate the value of the proposed framework, and allow to provide guidelines for future work on the topic.
Enhancing Osteoconduction of PLLA-Based Nanocomposite Scaffolds for Bone Regeneration Using Different Biomimetic Signals to MSCs

In bone engineering, the adhesion, proliferation and differentiation of mesenchymal stromal cells rely on signaling from chemico-physical structure of the substrate, therefore prompting the design of mimetic “extracellular matrix”-like scaffolds. In this study, three-dimensional porous poly-L-lactic acid (PLLA)-based scaffolds have been mixed with different components, including single walled carbon nanotubes (CNT), micro-hydroxyapatite particles (HA), and BMP2, and treated with plasma (PT), to obtain four different nanocomposites: PLLA + CNT, PLLA + CNTHA, PLLA + CNT + HA + BMP2 and PLLA + CNT + HA + PT. Adult bone marrow mesenchymal stromal cells (MSCs) were derived from the femur of orthopaedic patients, seeded on the scaffolds and cultured under osteogenic induction up to differentiation and mineralization. The release of specific metabolites and temporal gene expression profiles of marrow-derived osteoprogenitors were analyzed at definite time points, relevant to in vitro culture as well as in vivo differentiation. As a result, the role of the different biomimetic components added to the PLLA matrix was deciphered, with BMP2-added scaffolds showing the highest biomimetic activity on cells differentiating to mature osteoblasts. The modification of a polymeric scaffold with reinforcing components which also work as biomimetic cues for cells can effectively direct osteoprogenitor cells differentiation, so as to shorten the time required for mineralization.
Scientific Challenge –

Lack of specific information may be one of the many reasons that make an individual rely on common knowledge, habits, similar previous experiences, religion or stereotypes when faced with a new decision. Culture encodes much of such information. Many differences in behavior are attributed to culture. It is not hard to see the need for a new approach to decision making that takes into account the cultural differences. The importance of taking into account these cultural differences manifests in many dimensions of software development and design. The topic is very novel among computer scientists and there is a rapidly growing body of literature on the cultural issues related to how people interact with computers but few have attempted to computationally model cultural decision making paradigm. Since this project shows such effort, the proposal’s potential contribution is aimed at “Human and Social Dynamics” challenge area but its application can be beneficial for the ongoing research conducted in “Behavioral targeting and social network advertising” and “Computational Advertisement” groups at Yahoo. For example the calculation of the utility based on the culture of the consumers would be a good indicator of the desirability of an option for a consumer.
POWER REDUCTION IN PIPELINE DESIGNS

The realization of fast datapaths in signal processing environments requires fastest logic styles with synchronous behavior. This paper presents a systematic method which efficiently combines improvements on algorithm and logic level. Thus, the design of power efficient, fast and synchronous pipelines is possible. To reduce the power consumption of dynamic logic, we show methods for single-rail structures utilizing redundant number systems. Therefore, we discuss the realization of self-timed structures with single-rail logic and redundant number systems and we present a new scheme which eases the understanding and construction of such self-timed structures. First simulations for a horizontal redundant adder slice show area and power savings of 40% and 30% compared to complementary Domino logic.
Targeting Mnks for Cancer Therapy

Deregulation of protein synthesis is a common event in human cancer and a key player in translational control is eIF4E. Elevated expression levels of eIF4E promote cancer development and progression. Recent findings suggest that eIF4E activity is a key determinant of the PI3K/Akt/mTOR and Ras/Raf/MEK/ERK mediated tumorigenic activity and targeting eIF4E should have a major impact on these pathways in human cancer. The function of eIF4E is modulated through phosphorylation of a conserved serine (Ser209) by Mnk1 and Mnk2 downstream of ERK. While the phosphorylation event is necessary for oncogenic transformation, it seems to be dispensable for normal development. Hence, pharmacologic Mnk inhibitors may provide non-toxic and effective anti-cancer strategy. Strong circumstantial evidence indicates that Mnk inhibition presents attractive therapeutic potential, but the lack of selective Mnk inhibitors has so far confounded pharmacological target validation and clinical development.