Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating Large Language Models Trained on Code

We introduce Codex, a GPT language model fine-tuned on publicly available code from GitHub, and study its Python code-writing capabilities. A distinct production version of Codex powers GitHub Copilot. On HumanEval, a new evaluation set we release to measure functional correctness for synthesizing programs from docstrings, our model solves 28.8% of the problems, while GPT-3 solves 0% and GPT-J solves 11.4%. Furthermore, we find that repeated sampling from the model is a surprisingly effective strategy for producing working solutions to difficult prompts. Using this method, we solve 70.2% of our problems with 100 samples per problem. Careful investigation of our model reveals its limitations, including difficulty with docstrings describing long chains of operations and with binding operations to variables. Finally, we discuss the potential broader impacts of deploying powerful code generation technologies, covering safety, security, and economics.
MedGPT: Medical Concept Prediction from Clinical Narratives

The data available in Electronic Health Records (EHRs) provides the opportunity to transform care, and the best way to provide better care for one patient is through learning from the data available on all other patients. Temporal modelling of a patient's medical history, which takes into account the sequence of past events, can be used to predict future events such as a diagnosis of a new disorder or complication of a previous or existing disorder. While most prediction approaches use mostly the structured data in EHRs or a subset of single-domain predictions and outcomes, we present MedGPT a novel transformer-based pipeline that uses Named Entity Recognition and Linking tools (i.e. MedCAT) to structure and organize the free text portion of EHRs and anticipate a range of future medical events (initially disorders). Since a large portion of EHR data is in text form, such an approach benefits from a granular and detailed view of a patient while introducing modest additional noise. MedGPT effectively deals with the noise and the added granularity, and achieves a precision of 0.344, 0.552 and 0.640 (vs LSTM 0.329, 0.538 and 0.633) when predicting the top 1, 3 and 5 candidate future disorders on real world hospital data from King's College Hospital, London, UK (\textasciitilde600k patients). We also show that our model captures medical knowledge by testing it on an experimental medical multiple choice question answering task, and by examining the attentional focus of the model using gradient-based saliency methods.
A Survey on Data Augmentation for Text Classification

Data augmentation, the artificial creation of training data for machine learning by transformations, is a widely studied research field across machine learning disciplines. While it is useful for increasing a model's generalization capabilities, it can also address many other challenges and problems, from overcoming a limited amount of training data to regularizing the objective, to limiting the amount of data used to protect privacy. Based on a precise description of the goals and applications of data augmentation and a taxonomy for existing works, this survey is concerned with data augmentation methods for textual classification and aims at providing a concise and comprehensive overview for researchers and practitioners. Derived from the taxonomy, we divide more than 100 methods into 12 different groupings and give state-of-the-art references expounding which methods are highly promising by relating them to each other. Finally, research perspectives that may constitute a building block for future work are provided.
MPLP: Massively Parallelized Lazy Planning

Lazy search algorithms have been developed to efficiently solve planning problems in domains where the computational effort is dominated by the cost of edge evaluation. The existing algorithms operate by intelligently balancing computational effort between searching the graph and evaluating edges. However, they are designed to run as a single process and do not leverage the multithreading capability of modern processors. In this work, we propose a massively parallelized, bounded suboptimal, lazy search algorithm (MPLP) that harnesses modern multi-core processors. In MPLP, searching of the graph and edge evaluations are performed completely asynchronously in parallel, leading to a drastic improvement in planning time. We validate the proposed algorithm in two different planning domains: 1) motion planning for 3D humanoid navigation and 2) task and motion planning for a robotic assembly task. We show that MPLP outperforms the state-of-the-art lazy search as well as parallel search algorithms.
Android Security using NLP Techniques: A Review

Android is among the most targeted platform by attackers. While attackers are improving their techniques, traditional solutions based on static and dynamic analysis have been also evolving. In addition to the application code, Android applications have some metadata that could be useful for security analysis of applications. Unlike traditional application distribution mechanisms, Android applications are distributed centrally in mobile markets. Therefore, beside application packages, such markets contain app information provided by app developers and app users. The availability of such useful textual data together with the advancement in Natural Language Processing (NLP) that is used to process and understand textual data has encouraged researchers to investigate the use of NLP techniques in Android security. Especially, security solutions based on NLP have accelerated in the last 5 years and proven to be useful. This study reviews these proposals and aim to explore possible research directions for future studies by presenting state-of-the-art in this domain. We mainly focus on NLP-based solutions under four categories: description-to-behaviour fidelity, description generation, privacy and malware detection.
Few-body nature of Kondo correlated ground states

The quenching of degenerate impurity states in metals generally induces a long-range correlated quantum state known as the Kondo screening cloud. While a macroscopic number of particles clearly take part in forming this extended structure, assessing the number of truly entangled degrees of freedom requires a careful analysis of the relevant many-body wavefunction. For this purpose, we examine the natural single-particle orbitals that are eigenstates of the single-particle density (correlation) matrix for the ground state of two quantum impurity problems: the interacting resonant level model (IRLM) and the single impurity Anderson model (SIAM). As a simple and general probe for few-body versus many-body character we consider the rate of exponential decay of the correlation matrix eigenvalues towards inactive (fully empty or filled) orbitals. We find that this rate remains large in the physically most relevant region of parameter space, implying a few-body character. Genuine many-body correlations emerge only when the Kondo temperature becomes exponentially small, for instance near a quantum critical point. In addition, we demonstrate that a simple numerical diagonalization of the few-body problem restricted to the Fock space of the most correlated orbitals converges exponentially fast with respect to the number of orbitals, to the true ground state of the IRLM. We also show that finite size effects drastically affect the correlation spectrum, shedding light on an apparent paradox arising from previous studies on short chains.
New Bounds on the Biplanar and $k$-Planar Crossing Numbers

The biplanar crossing number of a graph $G$ is the minimum number of crossings over all possible drawings of the edges of $G$ in two disjoint planes. We present new bounds on the biplanar crossing number of complete graphs and complete bipartite graphs. In particular, we prove that the biplanar crossing number of complete bipartite graphs can be approximated to within a factor of $3$, improving over the best previously known approximation factor of $4.03$. For complete graphs, we provide a new approximation factor of $3.17$, improving over the best previous factor of $4.34$. We provide similar improved approximation factors for the $k$-planar crossing number of complete graphs and complete bipartite graphs, for any positive integer $k$. We also investigate the relation between (ordinary) crossing number and biplanar crossing number of general graphs in more depth, and prove that any graph with a crossing number of at most $10$ is biplanar.
A Novel Folic Acid Receptor-Targeted Drug Delivery System Based on Curcumin-Loaded β-Cyclodextrin Nanoparticles for Cancer Treatment

Purpose A novel folate receptor-targeted β-cyclodextrin (β-CD) drug delivery vehicle was constructed to improve the bioavailability, biosafety, and drug loading capacity of curcumin. Controlled release and targeted delivery was achieved by modifying the nanoparticles with folic acid (FA). Methods Folate-conjugated β-CD-polycaprolactone block copolymers were synthesized and characterized. Curcumin-loaded nanoparticles (FA-Cur-NPs) were structured by self-assembly. The physicochemical properties, stability, release behavior and tumor-targeting ability of the fabricated nanoparticles were studied. Results The average particle size and drug loading of FA-Cur-NPs was 151.8 nm and 20.27%, respectively. Moreover, the FA-Cur-NPs exhibited good stability in vitro for 72 h. The drug release profiles showed that curcumin from FA-Cur-NPs was released significantly faster in a pH 6.4 phosphate buffered solution (PBS) than in pH 7.4, indicating that curcumin can be enriched around the tumor site compared with normal cells. Additionally, the internalization of FA-Cur-NPs was aided by FA receptor-mediated endocytosis, and its cytotoxicity was proportional to the cellular uptake efficiency. Furthermore, in vivo studies confirmed that FA-Cur-NPs exhibited marked accumulation in the tumor site and excellent antitumor activity. Conclusion These findings suggest that FA-Cur-NPs are a promising approach for improving cancer therapy through active targeting and controllable release.
Lung Abscess in Critically Ill Coronavirus Disease 2019 Patients With Ventilator-Associated Pneumonia: A French Monocenter Retrospective Study

The pulmonary vascular endothelialitis together with the high rate of distal pulmonary embolism or thrombosis extensively reported in critically ill coronavirus disease 2019 patients may impair antibiotic diffusion in the lung parenchyma of coronavirus disease 2019 patients with ventilator-associated pneumonia leading to insufficient antibiotic concentration, thus promoting lung abscess formation. We report that 17 of 119 coronavirus disease 2019 patients (14%) with ventilator-associated pneumonia developed a lung abscess. Proportion of patients receiving corticosteroids did not differ between patients with and without lung abscess. Most of lung abscess were polymicrobial. Enterobacteriaceae, Pseudomonas aeruginosa, and Staphylococcus aureus were the leading causative bacteria. Most of lung abscesses involved the right lower lobe. Three patients had concomitant pulmonary embolism or thrombosis in the territory of lung abscess. Lung abscess was retrospectively visible on chest radiograph in 29% of the patients. As the occurrence of lung abscess impacts the duration of antibiotics therapy, chest CT scan should be easily performed in case of treatment failure of ventilator-associated pneumonia despite adequate antimicrobial therapy.
The Patient's Point of View: Characterizing Patient-Level Factors Associated with Perceptions of Health Care

Purpose: We explored the association between perception of care, as measured by the Interpersonal Processes of Care (IPC) survey, and patient-level factors, including (1) Trust in physicians; (2) Perceived empathy; (3) Stereotype threat; (4) Perceived everyday discrimination; and (5) Self-Reported Health. Methods: Fifty participants from diverse racial backgrounds and education levels were surveyed. We examined the associations between the five patient-level factors and each subdomain of the IPC using multiple linear regression. We added a race interaction term to assess whether associations between IPC subdomains and predictors differed by race. We tested for correlation among factors found to be significantly associated with the IPC. Results: In adjusted analyses, trust in the physician, perceived empathy from the provider, and perceived everyday discrimination were significantly associated with most subdomains of the IPC. There was no significant race interaction. Conclusion: This exploratory study suggests that empathy, trust, and perceived everyday discrimination are significantly linked to patient perception of quality care, which are linked to clinical outcomes. Results present modifiable factors that may potentially improve patient care. Practice Implications: Increased efforts to improve clinician communication of empathy and general communication skill may have a positive effect on quality of care.
The role of bacterial extracellular polymers in cell surface chemistry, metal adsorption and biomineralisation

Bacteria and other microorganisms can significantly influence the biogeochemical cycling of metal ions in many environmental settings. Recent studies have investigated the roles of bacterial cells in proton and metal adsorption, and in biologicallyinduced mineral precipitation This study aimed to characterise the role of bacterial extracellular polymers in surface reactivity, metal adsorption and biomineralisation. This was undertaken using an EPS-producing, thermophilic, bacterial strain, Bacillus lichenformis S-86. Experimental work was undertaken comparing cells with the EPS layer intact (native cells) with cells from which the EPS layer had been extracted (EPSfree cells). The study incorporated surface characterisation by potentiometric titration, infrared analysis and electrophoretic mobility analysis. Investigation of the mechanisms of Zn adsorption to cell surfaces was undertaken by both macroscopic batch adsorption experiments, and spectroscopic (EXAFS) analysis. Mineralisation experiments were carried out in order to investigate the effect of EPS on CaCO3 precipitation. Surface complexation modelling of the potentiometric titration data indicated that the native and EPS-free cells contained four proton-active functional groups, with pK a values of 3.3-3.4, 5.3-5.4, 7.4-7.5 and 9.9-10.1. These were tentatively identified as phosphodiester, carboxyl, phosphoryl and amine groups respectively, and ATR-FTIR analysis supported identification of the PK a 5.3-5.4 site as carboxylic. The site concentrations of the pK a 3.3-3.4 and 9.9-10.1 groups were significantly lower in the EPS-free cells than in the native cells. The macroscopic and EXAFS metal adsorption studies indicated that both the carboxyl and phosphoryl groups are involved in Zn complexation, and a lack of temperature-dependent adsorption provides evidence that Zn binds by an outer-sphere mechanism. Biomineralisation experiments indicated that the presence of EPS affects both CaCO3 morphology and polymorphism. The presence of EPS appears to favour precipitation of the stable polymorph calcite over the metastable polymorph vaterite. The results of this study have shown that EPS, and potentially the associated dissolved organic carbon, can significantly affect the surface reactivity of bacterial cells.
Fatty Acid–Binding Protein 4 (FABP4) Suppresses Proliferation and Migration of Endometrial Cancer Cells via PI3K/Akt Pathway

Purpose Endometrial cancer (EC) is the sixth most common cancer in women and its incidence and mortality have been rising over the last decades. The latest research indicates that FABP4 plays a significant role in multiple types of cancer. But few studies were focused on EC. The aim of this article is to investigate whether FABP4 can suppress tumor growth and metastasis of EC via PI3K/Akt pathway to provide a novel therapeutic target for the treatment of EC. Materials and Methods FABP4 mRNA levels of EC were analysed through The Cancer Genome Atlas database (TCGA), and expression of FABP4 in EC cancer tissues was determined by immunohistochemistry (IHC) assays. Stable overexpressing cell lines were established using lentivirus infection to analyze the biological function of FABP4 in vitro. CCK8 assay and colony formation assay were performed to assess cell proliferation ability. Wound healing assay and transwell were performed to analyse migration and invasion of cells. The subcutaneous xenograft mouse model was used to evaluate tumor growth in vivo. Additionally, all protein levels were detected by Western blotting assay. Results We found that the expression of the FABP4 mRNA was decreased in tumor samples compared to normal tissue according to TCGA database analysis. Subsequent experimental mRNA and protein expression analysis confirmed that FABP4 expression was lower in EC tissue than normal endometrial tissue. In addition, we found overexpression of FABP4 inhibited the proliferation, migration and invasion in vitro and suppressed tumor growth in vivo. Further functional and mechanistic analysis of FABP4 demonstrated that its function is mediated by restraining the phosphorylation of PI3K/Akt signaling pathway. Conclusion Our studies shed light for the first time about the functional role of FABP4 in EC and provide a novel biomarker for EC as well as a therapeutic target for the therapy of EC.
Toward ultrafast magnetic depth profiling using time-resolved x-ray resonant magnetic reflectivity

During the last two decades, a variety of models have been developed to explain the ultrafast quenching of magnetization following femtosecond optical excitation. These models can be classified into two broad categories, relying either on a local or a non-local transfer of angular momentum. The acquisition of the magnetic depth profiles with femtosecond resolution, using time-resolved x-ray resonant magnetic reflectivity, can distinguish local and non-local effects. Here, we demonstrate the feasibility of this technique in a pump–probe geometry using a custom-built reflectometer at the FLASH2 free-electron laser (FEL). Although FLASH2 is limited to the production of photons with a fundamental wavelength of 4 nm ( ≃310 eV), we were able to probe close to the Fe L3 edge ( 706.8 eV) of a magnetic thin film employing the third harmonic of the FEL. Our approach allows us to extract structural and magnetic asymmetry signals revealing two dynamics on different time scales which underpin a non-homogeneous loss of magnetization and a significant dilation of 2 Å of the layer thickness followed by oscillations. Future analysis of the data will pave the way to a full quantitative description of the transient magnetic depth profile combining femtosecond with nanometer resolution, which will provide further insight into the microscopic mechanisms underlying ultrafast demagnetization.
Treatment Modality Based Survival in Gastric Carcinoma Patients with Stand-Alone Peritoneal Metastasis: a Case-Control Study

Purpose To date, there are no promising treatments for gastric carcinoma with peritoneal metastasis. Some researchers have suggested a survival benefit of gastrectomy in select patients. This study investigated the survival of gastric carcinoma patients with stand-alone peritoneal metastasis according to the type of treatment modality. Materials and Methods We reviewed the data of 132 patients with gastric carcinoma and stand-alone peritoneal metastasis. We performed gastrectomy when the primary tumor was deemed resectable and systemic chemotherapy was administered. We analyzed patient survival according to the type of treatment, and the prognostic value of gastrectomy was evaluated in univariate and multivariate models. Results Among all patients, 70 underwent gastrectomy plus chemotherapy, 20 underwent gastrectomy alone, 36 underwent chemotherapy alone, and 6 received supportive care. The median patient survival was 13 months. Patients who underwent gastrectomy had significantly longer survival than those who did not undergo gastrectomy (14 vs. 8 months, P<0.001). Patients who received chemotherapy showed significantly longer survival than those who did not (13 vs. 7 months, P=0.032). Patients who underwent gastrectomy plus chemotherapy showed better survival than those who underwent other treatments. In multivariate analysis, gastrectomy was found to be an independent prognostic factor (hazard ratio, 0.52; 95% confidence interval, 0.33–0.82) in addition to chemotherapy. Conclusions Our study showed that patients who underwent gastrectomy plus chemotherapy had the best survival. Although the survival benefit of gastrectomy remains uncertain, it is a favorable prognostic indicator in patients with stand-alone peritoneal metastasis.
Correlation Between 25 Hydroxyvitamin D Levels and Nonalcoholic Fatty Liver Disease in Chinese Patients with Type 2 Diabetes Mellitus: A Cross-Sectional Study

Purpose We aimed to analyze the serum vitamin D level in Chinese patients with type 2 diabetes mellitus (T2DM) and discuss its correlation with nonalcoholic fatty liver disease (NAFLD). Patients and Methods A total of 300 patients with T2DM (92 patients without NAFLD and 208 patients with NAFLD) were enrolled, and 25-hydroxyvitamin D [25-(OH)D] levels were compared between the two groups. Second, the NAFLD fibrosis score (NFS) and fatty liver index (FLI) were used to group patients with T2DM complicated by NAFLD, and the differences in serum 25-(OH)D in patients with different degrees of liver fibrosis were compared. Third, multiple regression analysis was used to analyze the independent predictors of liver fibrosis in patients with T2DM complicated by NAFLD. Results The level of 25-(OH)D in patients with T2DM complicated by NAFLD was significantly lower than that in patients with T2DM alone. Based on the NFS and FLI, the 25-(OH)D level of the hepatic fibrosis subgroup was significantly lower than that of the subgroup without liver fibrosis. 25-(OH)D was found to be an independent predictor of liver fibrosis in patients with T2DM complicated by NAFLD. Conclusion The serum 25-(OH)D level in patients with T2DM complicated by NAFLD was significantly reduced, and the 25-(OH)D level showed a gradual downward trend with the degree of liver fibrosis. Low concentrations of 25-(OH)D may be indicative of the degree of liver fibrosis in diabetic patients.