MMBench: Is Your Multi-modal Model an All-around Player?

Large vision-language models have recently achieved remarkable progress, exhibiting great perception and reasoning abilities concerning visual information. However, how to effectively evaluate these large vision-language models remains a major obstacle, hindering future model development. Traditional benchmarks like VQAv2 or COCO Caption provide quantitative performance measurements but suffer from a lack of fine-grained ability assessment and non-robust evaluation metrics. Recent subjective benchmarks, such as OwlEval, offer comprehensive evaluations of a model's abilities by incorporating human labor, but they are not scalable and display significant bias. In response to these challenges, we propose MMBench, a novel multi-modality benchmark. MMBench methodically develops a comprehensive evaluation pipeline, primarily comprised of two elements. The first element is a meticulously curated dataset that surpasses existing similar benchmarks in terms of the number and variety of evaluation questions and abilities. The second element introduces a novel CircularEval strategy and incorporates the use of ChatGPT. This implementation is designed to convert free-form predictions into pre-defined choices, thereby facilitating a more robust evaluation of the model's predictions. MMBench is a systematically-designed objective benchmark for robustly evaluating the various abilities of vision-language models. We hope MMBench will assist the research community in better evaluating their models and encourage future advancements in this domain. Project page: https://opencompass.org.cn/mmbench

Utility of clinical metagenomics in diagnosing malignancies in a cohort of patients with Epstein-Barr virus positivity

BackgroundsDifferentiation between benign and malignant diseases in EBV-positive patients poses a significant challenge due to the lack of efficient diagnostic tools. Metagenomic Next-Generation Sequencing (mNGS) is commonly used to identify pathogens of patients with fevers of unknown-origin (FUO). Recent studies have extended the application of Next-Generation Sequencing (NGS) in identifying tumors in body fluids and cerebrospinal fluids. In light of these, we conducted this study to develop and apply metagenomic methods to validate their role in identifying EBV-associated malignant disease.MethodsWe enrolled 29 patients with positive EBV results in the cohort of FUO in the Department of Infectious Diseases of Huashan Hospital affiliated with Fudan University from 2018 to 2019. Upon enrollment, these patients were grouped for benign diseases, CAEBV, and malignant diseases according to their final diagnosis, and CNV analysis was retrospectively performed in 2022 using samples from 2018 to 2019.ResultsAmong the 29 patients. 16 of them were diagnosed with benign diseases, 3 patients were diagnosed with CAEBV and 10 patients were with malignant diseases. 29 blood samples from 29 patients were tested for mNGS. Among all 10 patients with malignant diagnosis, CNV analysis suggested neoplasms in 9 patients. Of all 19 patients with benign or CAEBV diagnosis, 2 patients showed abnormal CNV results. The sensitivity and specificity of CNV analysis for the identification for tumors were 90% and 89.5%, separately.ConclusionsThe application of mNGS could assist in the identification of microbial infection and malignancies in EBV-related diseases. Our results demonstrate that CNV detection through mNGS is faster compared to conventional oncology tests. Moreover, the convenient collection of peripheral blood samples adds to the advantages of this approach

Application of Angiotensin Receptor–Neprilysin Inhibitor in Chronic Kidney Disease Patients: Chinese Expert Consensus

Chronic kidney disease (CKD) is a global public health problem, and cardiovascular disease is the most common cause of death in patients with CKD. The incidence and prevalence of cardiovascular events during the early stages of CKD increases significantly with a decline in renal function. More than 50% of dialysis patients die from cardiovascular disease, including coronary heart disease, heart failure, arrhythmia, and sudden cardiac death. Therefore, developing effective methods to control risk factors and improve prognosis is the primary focus during the diagnosis and treatment of CKD. For example, the SPRINT study demonstrated that CKD drugs are effective in reducing cardiovascular and cerebrovascular events by controlling blood pressure. Uncontrolled blood pressure not only increases the risk of these events but also accelerates the progression of CKD. A co-crystal complex of sacubitril, which is a neprilysin inhibitor, and valsartan, which is an angiotensin receptor blockade, has the potential to be widely used against CKD. Sacubitril inhibits neprilysin, which further reduces the degradation of natriuretic peptides and enhances the beneficial effects of the natriuretic peptide system. In contrast, valsartan alone can block the angiotensin II-1 (AT1) receptor and therefore inhibit the renin–angiotensin–aldosterone system. These two components can act synergistically to relax blood vessels, prevent and reverse cardiovascular remodeling, and promote natriuresis. Recent studies have repeatedly confirmed that the first and so far the only angiotensin receptor–neprilysin inhibitor (ARNI) sacubitril/valsartan can reduce blood pressure more effectively than renin–angiotensin system inhibitors and improve the prognosis of heart failure in patients with CKD. Here, we propose clinical recommendations based on an expert consensus to guide ARNI-based therapeutics and reduce the occurrence of cardiovascular events in patients with CKD

Enhanced CO2 Adsorption and Selectivity of CO2/N2 on Amine@ZIF-8 Materials

The ZIF-8 crystals were successfully postsynthetically modified using methylamine (MA), ethylenediamine (ED), and N, N′-dimethylethylenediamine (MMEN) to improve their adsorption performance toward CO2. Results showed that, compared with the original ZIF-8, the BET specific surface area of MA-ZIF-8, MMEN-ZIF-8, and ED-ZIF-8 has increased by 118.2%, 92.0%, and 29.8%, respectively. In addition, their total pore volume increased separately by 130.8%, 100%, and 48.7%. The adsorption capacities of CO2 on the amine-modified ZIF-8 samples followed the order MA−ZIF−8>MMEN−ZIF−8>ED−ZIF−8>ZIF−8. The CO2 adsorption capacities at 298 K on MA-ZIF-8, MMEN-ZIF-8, and ED-ZIF-8 were increased by 118.2%, 90.2%, and 29.8%, respectively. What is more, the CO2/N2 selectivities calculated using an IAST model of the amine@ZIF-8 samples at 0.01 bar and 298 K were also significantly improved and followed the order MA−ZIF−8 31.4>ED−ZIF−8 25.1>MMEN−ZIF−8 14.1>ZIF−8 11.5, which increased by 173.0%, 121.4%, and 22.6%, respectively. The isosteric heat of CO2 adsorption (Qst) on the MA-ZIF-8, MMEN-ZIF-8, and ED-ZIF-8 all becomes higher, while Qst of N2 on these samples was slightly lower in comparison with that on the ZIF-8. Furthermore, after six recycle runs of gravimetric CO2 adsorption-desorption on MA-ZIF-8, the adsorption performance of CO2 is still very good, indicating that the MA-ZIF-8 sample has good regeneration performance and can be applied into industrial CO2 adsorption and separation

Evaluation of the remaining reserves of shale gas and countermeasures to increase the utilization of reserves: Case study of the Wufeng–Longmaxi formations in Changning area, southern Sichuan Basin, China

The evaluation of remaining reserves is crucial for assessing the developmental effect and further enhancing the recovery of a gas field. In this research, with the Changning shale gas field in the southern Sichuan Basin as the center of study, a comprehensive analysis was conducted on reservoir distribution, remaining reserves, and strategies to enhance recovery through the utilization of diverse methodologies, including organic geochemical testing, triaxial rock mechanics experiments, and numerical simulations. The results show that, in the study area, the recovery percentage of the well-controlled reserves ranges from 45% to 70%, with the average remaining reserves of wells falling within the (50–150) × 106 m3 range, alongside the potential for additional development in specific local areas. The Changning shale gas field exhibits three distinct types of undeveloped reserves, identified in areas where no wells have been drilled, inadequately fractured zones, and vertically undeveloped areas, respectively. In the areas where the average remaining reserves of wells are exceeding 100 × 106 m3, wells for repeated fracturing are selected depending on the coupling of geological, engineering, and development. In the case of well infilling, areas characterized by developed reticular fractures and existing well spacing >500 m are prioritized, taking into account the surface wellsite conditions. Through an extensive analysis, which include reservoir assessments, rock mechanics evaluations, and numerical modeling, sublayer⑤ is identified as the optimal target in the upper gas interval, with a vertical distance of more than 20 m from sublayer① in the lower gas interval. Zones with well-developed reticular natural fractures, a pressure coefficient >1.2, and a continuous thickness of Class I reservoirs in the upper gas interval >10 m, are selected for staggered tridimensional development with an expected increase in the platform-level recovery percent by 30%. These findings can provide valuable references and guidance for the deployment of well patterns in shale gas blocks

RIP3 impedes transcription factor EB to suppress autophagic degradation in septic acute kidney injury

Abstract Autophagy is an important renal-protective mechanism in septic acute kidney injury (AKI). Receptor interacting protein kinase 3 (RIP3) has been implicated in the renal tubular injury and renal dysfunction during septic AKI. Here we investigated the role and mechanism of RIP3 on autophagy in septic AKI. We showed an activation of RIP3, accompanied by an accumulation of the autophagosome marker LC3II and the autophagic substrate p62, in the kidneys of lipopolysaccharide (LPS)-induced septic AKI mice and LPS-treated cultured renal proximal tubular epithelial cells (PTECs). The lysosome inhibitor did not further increase the levels of LCII or p62 in LPS-treated PTECs. Moreover, inhibition of RIP3 attenuated the aberrant accumulation of LC3II and p62 under LPS treatment in vivo and in vitro. By utilizing mCherry-GFP-LC3 autophagy reporter mice in vivo and PTECs overexpression mRFP-GFP-LC3 in vitro, we observed that inhibition of RIP3 restored the formation of autolysosomes and eliminated the accumulated autophagosomes under LPS treatment. These results indicated that RIP3 impaired autophagic degradation, contributing to the accumulation of autophagosomes. Mechanistically, the nuclear translocation of transcription factor EB (TFEB), a master regulator of the lysosome and autophagy pathway, was inhibited in LPS-induced mice and LPS-treated PTECs. Inhibition of RIP3 restored the nuclear translocation of TFEB in vivo and in vitro. Co-immunoprecipitation further showed an interaction of RIP3 and TFEB in LPS-treated PTECs. Also, the expression of LAMP1 and cathepsin B, two potential target genes of TFEB involved in lysosome function, were decreased under LPS treatment in vivo and in vitro, and this decrease was rescued by inhibiting RIP3. Finally, overexpression of TFEB restored the autophagic degradation in LPS-treated PTECs. Together, the present study has identified a pivotal role of RIP3 in suppressing autophagic degradation through impeding the TFEB-lysosome pathway in septic AKI, providing potential therapeutic targets for the prevention and treatment of septic AKI

Early identification and severity prediction of acute respiratory infection (ESAR): a study protocol for a randomized controlled trial

Abstract Background The outbreak of SARS-CoV-2 at the end of 2019 sounded the alarm for early inspection on acute respiratory infection (ARI). However, diagnosis pathway of ARI has still not reached a consensus and its impact on prognosis needs to be further explored. Methods ESAR is a multicenter, open-label, randomized controlled, non-inferiority clinical trial on evaluating the diagnosis performance and its impact on prognosis of ARI between mNGS and multiplex PCR. Enrolled patients will be divided into two groups with a ratio of 1:1. Group I will be directly tested by mNGS. Group II will firstly receive multiplex PCR, then mNGS in patients with severe infection if multiplex PCR is negative or inconsistent with clinical manifestations. All patients will be followed up every 7 days for 28 days. The primary endpoint is time to initiate targeted treatment. Secondary endpoints include incidence of significant events (oxygen inhalation, mechanical ventilation, etc.), clinical remission rate, and hospitalization length. A total of 440 participants will be enrolled in both groups. Discussion ESAR compares the efficacy of different diagnostic strategies and their impact on treatment outcomes in ARI, which is of great significance to make precise diagnosis, balance clinical resources and demands, and ultimately optimize clinical diagnosis pathways and treatment strategies. Trial registration Clinicaltrial.gov, NCT04955756, Registered on July 9th 2021

Evaluation of droplet digital PCR rapid detection method and precise diagnosis and treatment for suspected sepsis (PROGRESS): a study protocol for a multi-center pragmatic randomized controlled trial

Abstract Background Sepsis is still a major public health concern and a medical emergency due to its high morbidity and mortality. Accurate and timely etiology diagnosis is crucial for sepsis management. As an emerging rapid and sensitive pathogen detection tool, digital droplet PCR (ddPCR) has shown promising potential in rapid identification of pathogens and antimicrobial resistance genes. However, the diagnostic value and clinical impact of ddPCR tests remains to be studied in patients with suspected sepsis. PROGRESS trial is aimed to evaluate the clinical effectiveness of a novel ddPCR assay compared with standard practice. Methods PROGRESS is a multicenter, open-label, pragmatic randomized controlled trial (pRCT) set in ten hospitals, including departments of infectious disease and intensive care units. In this study, a total of 2292 patients with suspected sepsis will be randomly assigned to two arms: the ddPCR group and the control group with a ratio of 3:1. The primary outcome is the diagnostic efficacy, that is, the sensitivity and specificity of the ddPCR assay compared with the synchronous blood culture. Secondary outcomes include the mortality rates and the mean Sequential Organ Failure Assessment (SOFA) score at follow-up time points, the length of stay in the hospital, the time to directed antimicrobial therapy, duration of broad-spectrum antibiotic use, and the EQ-5D-5L score on day 90. Discussion It is the first multicenter pragmatic RCT to explore the diagnostic efficacy and clinical impact of the ddPCR assay in patients with suspected sepsis, taking advantage of both RCT’s ability to establish causality and the feasibility of pragmatic approaches in real-world studies (RWS). This trial will help us to get a comprehensive view of the assay’s capacity for precise diagnosis and treatment of sepsis. It has the potential to monitor the pathogen load change and to guide the antimicrobial therapy, making a beneficial impact on the prognosis of sepsis patients. Trial registration: ClinicalTrial.gov, NCT05190861. Registered January 13, 2022—‘Retrospectively registered’, https://clinicaltrials.gov/ct2/show/NCT05190861