CodePlan: Repository-level Coding using LLMs and Planning

Software engineering activities such as package migration, fixing errors reports from static analysis or testing, and adding type annotations or other specifications to a codebase, involve pervasively editing the entire repository of code. We formulate these activities as repository-level coding tasks. Recent tools like GitHub Copilot, which are powered by Large Language Models (LLMs), have succeeded in offering high-quality solutions to localized coding problems. Repository-level coding tasks are more involved and cannot be solved directly using LLMs, since code within a repository is inter-dependent and the entire repository may be too large to fit into the prompt. We frame repository-level coding as a planning problem and present a task-agnostic framework, called CodePlan to solve it. CodePlan synthesizes a multi-step chain of edits (plan), where each step results in a call to an LLM on a code location with context derived from the entire repository, previous code changes and task-specific instructions. CodePlan is based on a novel combination of an incremental dependency analysis, a change may-impact analysis and an adaptive planning algorithm. We evaluate the effectiveness of CodePlan on two repository-level tasks: package migration (C#) and temporal code edits (Python). Each task is evaluated on multiple code repositories, each of which requires inter-dependent changes to many files (between 2-97 files). Coding tasks of this level of complexity have not been automated using LLMs before. Our results show that CodePlan has better match with the ground truth compared to baselines. CodePlan is able to get 5/6 repositories to pass the validity checks (e.g., to build without errors and make correct code edits) whereas the baselines (without planning but with the same type of contextual information as CodePlan) cannot get any of the repositories to pass them

Causal and associational language in observational health research: a systematic evaluation

We estimated the degree to which language used in the high profile medical/public health/epidemiology literature implied causality using language linking exposures to outcomes and action recommendations; examined disconnects between language and recommendations; identified the most common linking phrases; and estimated how strongly linking phrases imply causality. We searched and screened for 1,170 articles from 18 high-profile journals (65 per journal) published from 2010-2019. Based on written framing and systematic guidance, three reviewers rated the degree of causality implied in abstracts and full text for exposure/outcome linking language and action recommendations. Reviewers rated the causal implication of exposure/outcome linking language as None (no causal implication) in 13.8%, Weak 34.2%, Moderate 33.2%, and Strong 18.7% of abstracts. The implied causality of action recommendations was higher than the implied causality of linking sentences for 44.5% or commensurate for 40.3% of articles. The most common linking word in abstracts was “associate” (45.7%). Reviewer’s ratings of linking word roots were highly heterogeneous; over half of reviewers rated “association” as having at least some causal implication. This research undercuts the assumption that avoiding “causal” words leads to clarity of interpretation in medical research

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

FPGA and ASIC Square Root Designs for High Performance and Power Efficiency

Abstract- Floating-point square root is a fundamental operation in signal processing and various HPC applications. Since this is an expensive operation in resource and energy consumption, its efficient implementation should be of priority in future multicores that will face dark silicon issues. This paper presents a low-cost, low-power consumption design to calculate the square root using the IEEE754 single-precision floating-point format. Two versions of the design are investigated with and without clock gating (CG), respectively. Evaluation involves FPGA and ASIC technologies at 40 and 65 nm. Substantial performance growth and reduced power consumption are gained as compared to a popular iterative solution. The ASIC design demonstrates much lower power consumption, which at 40 nm is lower than that at 65 nm by about a threefold. At 40 nm, CG for the ASIC realization is justified primarily for low activity rates. Keywords—FPGA, ASIC, floating-point square root, energy consumption, multicore processors. I

Cutaneous metastasis: An unusual presenting feature of urologic malignancies

Urological malignancies are well known for their ability to metastasize widely. The incidence of cutaneous metastasis from all urologic malignancies has been reported to be 0.73–1.3% with the primary most commonly being renal cell carcinoma followed by carcinoma bladder, adenocarcinoma prostate, and testicular germ cell tumor in decreasing order of frequency. Metastasis to the skin is unusual and has been predominantly reported as a late manifestation of the disease. We describe two patients with urologic malignancies who had cutaneous metastasis as their initial presenting feature

Numerical Simulations of a Postulated Methanol Pool Fire Scenario in a Ventilated Enclosure Using a Coupled FVM-FEM Approach

Numerical investigations have been carried out for a postulated enclosure fire scenario instigated due to methanol pool ignition in a chemical cleaning facility. The pool fire under consideration is radiation-dominated and poses a risk to the nearby objects if appropriate safety requirements are not met. The objective of the current study was to numerically evaluate the postulated fire scenario and provide safety recommendations to prevent/minimize the hazard. To do this, the fire scenario was first modeled using the finite volume method (FVM) based solver to predict the fire characteristics and the resulting changes inside the enclosure. The FDS predicted temperatures were then used as input boundary conditions to conduct a three-dimensional heat transfer analysis using the finite element method (FEM). The coupled FVM&ndash;FEM simulation approach enabled detailed three-dimensional conjugate heat transfer analysis. The proposed FVM&ndash;FEM coupled approach to analyze the fire dynamics and heat transfer will be helpful to safety engineers in carrying out a more robust and reliable fire risk assessment