Towards Understanding What Code Language Models Learned

Pre-trained language models are effective in a variety of natural language tasks, but it has been argued their capabilities fall short of fully learning meaning or understanding language. To understand the extent to which language models can learn some form of meaning, we investigate their ability to capture semantics of code beyond superficial frequency and co-occurrence. In contrast to previous research on probing models for linguistic features, we study pre-trained models in a setting that allows for objective and straightforward evaluation of a model's ability to learn semantics. In this paper, we examine whether such models capture the semantics of code, which is precisely and formally defined. Through experiments involving the manipulation of code fragments, we show that code pre-trained models of code learn a robust representation of the computational semantics of code that goes beyond superficial features of form alon

Construction of a cross-species cell landscape at single-cell level.

Individual cells are basic units of life. Despite extensive efforts to characterize the cellular heterogeneity of different organisms, cross-species comparisons of landscape dynamics have not been achieved. Here, we applied single-cell RNA sequencing (scRNA-seq) to map organism-level cell landscapes at multiple life stages for mice, zebrafish and Drosophila. By integrating the comprehensive dataset of > 2.6 million single cells, we constructed a cross-species cell landscape and identified signatures and common pathways that changed throughout the life span. We identified structural inflammation and mitochondrial dysfunction as the most common hallmarks of organism aging, and found that pharmacological activation of mitochondrial metabolism alleviated aging phenotypes in mice. The cross-species cell landscape with other published datasets were stored in an integrated online portal-Cell Landscape. Our work provides a valuable resource for studying lineage development, maturation and aging

Formation and Evolution of Cellular Structures in Wedge-Induced Oblique Detonations

Numerical simulation of an oblique detonation induced by a wedge is performed to investigate the formation and evolution of the oblique cellular detonation structure and the quantitative comparison of the cellular structure of a normal and an oblique detonation. The compressible reactive Euler equations are solved using the seventh-order WENO scheme on an adaptive mesh based on the open source program Adaptive Mesh Refinement in Object-oriented C++ (AMROC). The numerical results show that there are two sets of transverse waves, the left-running transverse waves (LRTW) and the right-running transverse waves (RRTW), which form the oblique cellular detonation structure. Although both sets of transverse waves are convected downstream, they propagate at almost the same relative velocity in the opposite direction. The LRTWs start in the transition zone because of the detonation instability. However, the RRTWs form due to the interaction between the deformed detonation front and the reflected shock wave from the wedge. For the same degree of overdrive, numerical simulations reveal that the characteristic cell size of an oblique detonation is almost the same as that of a normal detonation

Clinical Characteristics of Hospitalized Patients with Drug-Induced Acute Kidney Injury and Associated Risk Factors: A Case-Control Study

Background. Drug-induced acute kidney injury (D-AKI) is increasingly common and can extend the hospital length of stay and increase mortality. This study is aimed at analyzing the clinical characteristics of hospitalized patients with D-AKI and the associated risk factors in a multidrug environment. Methods. A retrospective study among hospitalized patients was conducted in July 2019 based on the Adverse Drug Events Active Surveillance and Assessment System-2 developed by the authors. Four controls were matched with each case according to the matching criteria. The risk factors for D-AKI were identified by binary multivariate logistic regression. Results. A total of 23,073 patients were hospitalized in July 2019, 21,131 of whom satisfied the inclusion criteria. The independent risk factors for D-AKI consisted of alcohol abuse (odds ratio (OR), 2.05; 95% confidence interval (CI), 1.04-4.07), nonsteroidal anti-inflammatory drug (NSAID) use (OR, 2.39; 95% CI, 1.25-4.58), diuretic use (OR, 2.64; 95% CI, 1.42-4.92), prior anemia (OR, 4.10; 95% CI, 1.94-8.67), and prior chronic kidney disease (OR, 2.33; 95% CI, 1.07-5.08). Conclusions. The occurrence of D-AKI in hospitalized patients had significant associations with alcohol abuse, combination therapy with NSAIDs or diuretics, and prior anemia or chronic kidney disease. Clinicians should meticulously follow patients with the above characteristics

Flood-Landscape Ecological Risk Assessment under the Background of Urbanization

The Hydrologic Modeling System (HEC-HMS) and statistical analysis method were used to analyze the relationship between flood eigenvalues (i.e., flood volume and peak flow) and landscape pattern metrics. Then, the flood-landscape ecological risk index (ERI_FL) was proposed and constructed to quantitatively assess the flood-landscape ecological risk (FLER). The semivariogram method was used to spatialize the ERI_FL values. Lastly, this study analyzed the spatial–temporal change of FLER at watershed scale and at sub-basin scale, respectively. Two historical landscape distributions (i.e., 2003 and 2017) of Qinhuai River basin were used to perform this study. The results showed that there were certain relationships between landscape pattern and flood eigenvalues, and for different landscapes, the response metrics and degrees were different. FLER increased as urbanization increased. FLER change magnitude had a positive relationship with urban land percentage change magnitude. The distribution of FLER and the distribution of FLER change both showed spatial differences at watershed scale. The structural features of landscape pattern had significant effects on regional floods. In the urbanization process, avoiding forming large-scale landscape patches, improving landscape abundance, and increasing contact area between different types of landscape patches were helpful to reduce the negative effects caused by the increase of urban landscape area on flood.ISSN:2073-444

The Potential of circRNA as a Novel Diagnostic Biomarker in Cervical Cancer

Cervical cancer is the fourth most common cancer among females worldwide. In spite of advances in detection and treatment, it is still one of the most dangerous gynecological malignancies in the world, especially in developing countries, and seriously threatens human health. Circular RNA (circRNA) is a special new type of endogenous noncoding RNA discovered recently. They form a covalently closed continuous loop and are specifically expressed in the eukaryotic transcriptome. With further understanding of circular RNA, a large number of studies have determined the key regulatory role of circRNA in a variety of diseases, especially cancer (including cervical cancer, liver cancer, and lung cancer). In addition, it has also been found that the abnormal expression of circRNA is related to its pathological characteristics in cervical cancer tissue, which can be used as a potential indicator for early screening and diagnosis of cervical cancer, targeted therapy, and prognosis prediction. This article summarizes the recent research achievements of circRNAs in cervical cancer. We briefly described the abnormal expression of circRNA in cervical cancer and discussed the involvement of circRNA in the occurrence process of cervical cancer by regulating cell proliferation, migration, invasion, and apoptosis. We believe that circRNA has potential value as a biomarker in the diagnosis and prognosis of cervical cancer

Trends in the prevalence of cognitive impairment at old age in China, 2002-2018

INTRODUCTION: China has the world's largest number of older adults with cognitive impairment (CI). We aimed to examine secular trends in the prevalence of CI in China from 2002 to 2018.METHODS: Generalized estimating equations (GEE) was used to assess changes in CI trend in 44,154 individuals (72,027 observations) aged 65 to 105 years old.RESULTS: The prevalence of CI increased from 2002 to 2008 and then decreased until 2018. The age-standardized prevalence increased from 25.7% in 2002, 26.1% in 2005, to 28.2% in 2008, then decreased to 26.0% in 2011, 25.3% in 2014, and 24.9% in 2018. Females and those ≥ 80 years old had greater CI prevalence.DISCUSSION: The prevalence of CI showed an inverted U shape from early 2000s to late 2010s with a peak in 2008. Follow-up studies are needed to confirm the decreasing trend after 2008 and examine the contributing factors and underlying mechanisms of this trend.HIGHLIGHTS: Generalized estimating equations (GEE) were used to assess trends of changes in cognitive impairment (CI). CI prevalence in China increased from 2002 to 2008 and then decreased until 2018. Females and those ≥ 80 years old had greater CI prevalence. Stroke, diabetes, and cigarette smoking were risk factors for CI.</p

Comparative Transcriptome Analysis of Two Sweet Sorghum Genotypes with Different Salt Tolerance Abilities to Reveal the Mechanism of Salt Tolerance

Sweet sorghum is a C4 crop that can be grown for silage forage, fiber, syrup and fuel production. It is generally considered a salt-tolerant plant. However, the salt tolerance ability varies among genotypes, and the mechanism is not well known. To further uncover the salt tolerance mechanism, we performed comparative transcriptome analysis with RNA samples in two sweet sorghum genotypes showing different salt tolerance abilities (salt-tolerant line RIO and salt-sensitive line SN005) upon salt treatment. These response processes mainly focused on secondary metabolism, hormone signaling and stress response. The expression pattern cluster analysis showed that RIO-specific response genes were significantly enriched in the categories related to secondary metabolic pathways. GO enrichment analysis indicated that RIO responded earlier than SN005 in the 2 h after treatment. In addition, we identified more transcription factors (TFs) in RIO than SN005 that were specifically expressed differently in the first 2 h of salt treatment, and the pattern of TF change was obviously different. These results indicate that an early response in secondary metabolism might be essential for salt tolerance in sweet sorghum. In conclusion, we found that an early response, especially in secondary metabolism and hormone signaling, might be essential for salt tolerance in sweet sorghum

Immediate Abnormal Intrinsic Brain Activity Patterns in Patients with End-stage Renal Disease During a Single Dialysis Session Resting-state Functional MRI Study

PURPOSE: To investigate cerebral amplitude of low-frequency fluctuations (ALFF) changes during a single hemodialysis (HD) in end-stage renal disease (ESRD) patients who need maintenance HD. MATERIALS AND METHODS: A total of 24 patients and 27 healthy subjects were included. The patients underwent neuropsychological tests and took twice resting-state fMRI (rs-fMRI) (before and after HD). Healthy group had one rs-fMRI. The zALFF based on rs-fMRI was calculated. Paired t and independent t test was applied to compare zALFF among groups. The associations between zALFF and duration of HD, ultrafiltration volume, and neuropsychological tests was calculated by partial correlation. RESULTS: Compared to healthy group, patients before HD showed significant worse performances on digit symbol test (DST) and serial dotting test (SDT). Patients after HD performed DST better than before HD. The patients after HD showed higher zALFF in left putamen than before HD. Multiple regions of both HD groups showed significant lower zALFF than healthy group. The zALFF of left putamen of patients after HD was significant negative correlated with the ultrafiltration volume (R = -0.679). The zALFF in patients before HD exhibited significantly positive or negative correlations with DST and SDT in multiple regions. The zALFF of patients after HD significantly negative correlated with DST in right temporal, positive and negative correlated with ultrafiltration volume in right frontal, left putamen respectively. CONCLUSION: ESRD patients showed changed spontaneous brain activity and cognitive impairments. After a single HD session, patients performed better in neuropsychological test, and spontaneous brain activity changed in left putamen. Ultrafiltration volume might be associated with activity of left putamen.status: publishe

Synchronously in vivo real‐time monitoring bacterial load and temperature with evaluating immune response to decipher bacterial infection

Abstract Determining the precise course of bacterial infection requires abundant in vivo real‐time data. Synchronous monitoring of the bacterial load, temperature, and immune response can satisfy the shortage of real‐time in vivo data. Here, we conducted a study in the joint‐infected mouse model to synchronously monitor the bacterial load, temperature, and immune response using the second near‐infrared (NIR‐II) fluorescence imaging, infrared thermography, and immune response analysis for 2 weeks. Staphylococcus aureus (S. aureus) was proved successfully labeled with glucose‐conjugated quantum dots in vitro and in subcutaneous‐infected model. The bacterial load indicated by NIR‐II fluorescence imaging underwent a sharp drop at 1 day postinfection. At the same time, the temperature gap detected through infrared thermography synchronously brought by infection reached lowest value. Meanwhile, the flow cytometry analysis demonstrated that immune response including macrophage, neutrophil, B lymphocyte, and T lymphocyte increased to the peak at 1 day postinfection. Moreover, both M1 macrophage and M2 macrophage in the blood have an obvious change at ~ 1 day postinfection, and the change was opposite. In summary, this study not only obtained real‐time and long‐time in vivo data on the bacterial load, temperature gap, and immune response in the mice model of S. aureus infection, but also found that 1 day postinfection was the key time point during immune response against S. aureus infection. Our study will contribute to synchronously and precisely studying the complicated complex dynamic relationship after bacterial infection at the animal level