Biomechanical evaluation of ortho-bridge system and proximal femoral nail antirotation in intertrochanteric fractures with lateral wall fracture based on finite element analysis.

Background: The integrity of the lateral wall in femoral intertrochanteric fractures significantly impacts fracture stability and internal fixation. In this study, we compared the outcomes of treating intertrochanteric fractures with lateral wall involvement using the ortho-bridge system (OBS) combined with proximal femoral nail antirotation (PFNA) versus simple PFNA from a biomechanical perspective. Methods: Finite-element models of femoral intertrochanteric fractures with lateral wall involvement were subjected to fixation with OBS combined with PFNA and simple PFNA. Von Mises stress measurements and corresponding displacement assessments for each component of the model, including the proximal femur and lateral wall, were used to evaluate the biomechanical effects of OBS fixation on bone and intramedullary nail stability. Results: Using PFNA alone to fix intertrochanteric fractures with lateral wall involvement resulted in von Mises stress levels on the lateral wall exceeding safe stress tolerances for bone growth. OBS fixation significantly reduced stress on the lateral wall of the femur and minimized the stress on each part of the intramedullary nail, reducing the overall displacement. Conclusion: In cases of intertrochanteric fractures with lateral wall involvement, PFNA fixation alone may compromise the biomechanical integrity of the lateral femoral wall, increasing the risk of postoperative complications. The addition of OBS to PFNA significantly reduces stress on the lateral femoral wall. Consequently, OBS should be considered for lateral wall fixation when managing intertrochanteric fractures combined with lateral wall fractures.

Active surveillance of hepatitis E: a 10-year epidemiological analysis in a city in eastern China.

Hepatitis E virus (HEV) is an important cause of acute hepatitis, however, is highly neglected and largely underreported. This study aimed to describe the detailed epidemiology of hepatitis E (HE) through a 10-year surveillance. A community-based active hepatitis surveillance was conducted between November 2007 and October 2017 in 11 townships of Dongtai City in China, involving 355,673 residents. Serum samples were obtained from patients presenting with hepatitis symptoms for more than 3 days. Serum alanine aminotransferase (ALT) levels greater than 2.5 times the upper limit of normal (ULN) were considered acute hepatitis. Samples were subsequently tested for IgG and IgM anti-HEV antibodies, HEV RNA, and hepatitis B surface antigen (HBsAg). The data indicated the incidence of HE fluctuated downward from 2007 to 2017, with an average annual age-standardized incidence of 17.50 per 100,000, exceeding the 10.26 per 100,000 in the National Notifiable Disease Report System (NNDRS). The incidence was notably higher among males (20.95 per 100,000) and individuals aged 50-69 years (37.47 per 100,000). Genotype 4 (HEV-4) was the predominantly circulating genotype during the study period. Furthermore, the study revealed the incidence of hepatitis with HEV and hepatitis B virus (HBV) co-infection was 4.99 per 100,000. The active surveillance system identified a higher incidence of HE compared to NNDRS, with a decreased prevalence over a 10-year period. While efforts are still needed to prevent HE in high-risk populations, including individuals with hepatitis B and the elderly.

Nucleoporin 93 Regulates Cancer Cell Growth and Stemness in Bladder Cancer via Wnt/ß-Catenin Signaling.

Bladder cancer (BLCA) is a prevalent cancer type with an unmet need for new therapeutic strategies. Nucleoporin 93 (Nup93) is implicated in the pathophysiology of several cancers, but its relationship with bladder cancer remains unclear. Nup93 expression was analyzed in TCGA datasets and 88 BLCA patient samples. Survival analysis and Cox regression models evaluated the association between Nup93 levels and patient prognosis. BLCA cells were used to investigate the effects of Nup93 overexpression or knockdown on cell growth, invasion, stemness (sphere formation and ALDH2 + cancer stem cell marker), and Wnt/ß-catenin signaling in vitro. The Wnt activator BML-284 was used to confirm the involvement of Wnt/ß-catenin signaling pathway. A xenograft mouse model validated the in vitro findings. Nup93 was highly expressed in BLCA tissues and cell lines, and high Nup93 expression correlated with poor prognosis in BLCA patients. Nup93 silencing inhibited BLCA cell proliferation, Wnt/ß-catenin activation, and cancer cell stemness. Conversely, Nup93 overexpression promoted these effects. BML-284 partially rescued the reduction in cell growth and stemness markers caused by Nup93 knockdown. Nup93 knockdown also suppressed the tumor formation of BLCA cells in vivo. Nup93 regulates BLCA cell growth and stemness via the Wnt/ß-catenin pathway, suggesting its potential as a prognostic marker and therapeutic target in BLCA.

Convergence in simulating global soil organic carbon by structurally different models after data assimilation.

Current biogeochemical models produce carbon-climate feedback projections with large uncertainties, often attributed to their structural differences when simulating soil organic carbon (SOC) dynamics worldwide. However, choices of model parameter values that quantify the strength and represent properties of different soil carbon cycle processes could also contribute to model simulation uncertainties. Here, we demonstrate the critical role of using common observational data in reducing model uncertainty in estimates of global SOC storage. Two structurally different models featuring distinctive carbon pools, decomposition kinetics, and carbon transfer pathways simulate opposite global SOC distributions with their customary parameter values yet converge to similar results after being informed by the same global SOC database using a data assimilation approach. The converged spatial SOC simulations result from similar simulations in key model components such as carbon transfer efficiency, baseline decomposition rate, and environmental effects on carbon fluxes by these two models after data assimilation. Moreover, data assimilation results suggest equally effective simulations of SOC using models following either first-order or Michaelis-Menten kinetics at the global scale. Nevertheless, a wider range of data with high-quality control and assurance are needed to further constrain SOC dynamics simulations and reduce unconstrained parameters. New sets of data, such as microbial genomics-function relationships, may also suggest novel structures to account for in future model development. Overall, our results highlight the importance of observational data in informing model development and constraining model predictions.

A facile and smart strategy to enhance bone regeneration with efficient vitamin D3 delivery through sterosome technology.

The spontaneous healing of critical-sized bone defects is often limited, posing an increased risk of complications and suboptimal outcomes. Osteogenesis, a complex process central to bone formation, relies significantly on the pivotal role of osteoblasts. Despite the well-established osteogenic properties of vitamin D3 (VD3), its lipophilic nature confines administration to oral or muscle injection routes. Therefore, a strategic therapeutic approach involves designing a multifunctional carrier to enhance efficacy, potentially incorporating it into the delivery system. Here, we introduce an innovative sterosome-based delivery system, utilizing palmitic acid (PA) and VD3, aimed at promoting osteogenic differentiation and facilitating post-defect bone regeneration. The delivery system exhibited robust physical characteristics, including excellent stability, loading efficiency, sustained drug release and high cellular uptake efficiency. Furthermore, comprehensive investigations demonstrated outstanding biocompatibility and osteogenic potential in both 2D and 3D in vitro settings. A critical-sized calvarial defect model in mice recapitulated the notable osteogenic effects of the sterosomes in vivo. Collectively, our research proposes a clinically applicable strategy for bone healing, leveraging PA/VD3 sterosomes as an efficient carrier to deliver VD3 and enhance bone regenerative effects.

Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotype and phenotype in chronic lymphocytic leukemia.

Bruton's tyrosine kinase (BTK) inhibitors are effective for the treatment of chronic lymphocytic leukemia (CLL) due to BTK's role in B cell survival and proliferation. Treatment resistance is most commonly caused by the emergence of the hallmark BTKC481S mutation that inhibits drug binding. In this study, we aimed to investigate whether the presence of additional CLL driver mutations in cancer subclones harboring a BTKC481S mutation accelerates subclone expansion. In addition, we sought to determine whether BTK-mutated subclones exhibit distinct transcriptomic behavior when compared to other cancer subclones. To achieve these goals, we employ our recently published method (Qiao et al. 2024) that combines bulk DNA sequencing and single-cell RNA sequencing (scRNA-seq) data to genotype individual cells for the presence or absence of subclone-defining mutations. While the most common approach for scRNA-seq includes short-read sequencing, transcript coverage is limited due to the vast majority of the reads being concentrated at the priming end of the transcript. Here, we utilized MAS-seq, a long-read scRNAseq technology, to substantially increase transcript coverage across the entire length of the transcripts and expand the set of informative mutations to link cells to cancer subclones in six CLL patients who acquired BTKC481S mutations during BTK inhibitor treatment. We found that BTK-mutated subclones often acquire additional mutations in CLL driver genes, leading to faster subclone proliferation. When examining subclone-specific gene expression, we found that in one patient, BTK-mutated subclones are transcriptionally distinct from the rest of the malignant B cell population with an overexpression of CLL-relevant genes.

Efficacy of growth factor gene-modified stem cells for motor function after spinal cord injury in rodents: a systematic review and meta­analysis.

The efficacy of growth factor gene-modified stem cells in treating spinal cord injury (SCI) remains unclear. This study aims to evaluate the effectiveness of growth factor gene-modified stem cells in restoring motor function after SCI. Two reviewers searched four databases, including PubMed, Embase, Web of Science, and Scopus, to identify relevant records. Studies on rodents assessing the efficacy of transplanting growth factor gene-modified stem cells in restoring motor function after SCI were included. The results were reported using the standardized mean difference (SMD) with a 95% confidence interval (95% CI). Analyses showed that growth factor gene-modified stem cell transplantation improved motor function recovery in rodents with SCI compared to the untreated (SMD = 3.98, 95% CI 3.26-4.70, I2 = 86.8%, P < 0.0001) and stem cell (SMD = 2.53, 95% CI 1.93-3.13, I2 = 86.9%, P < 0.0001) groups. Using growth factor gene-modified neural stem/histone cells enhanced treatment efficacy. In addition, the effectiveness increased when viral vectors were employed for gene modification and high transplantation doses were administered during the subacute phase. Stem cells derived from the human umbilical cord exhibited an advantage in motor function recovery. However, the transplantation of growth factor gene-modified stem cells did not significantly improve motor function in male rodents (P = 0.136). Transplantation of growth factor gene-modified stem cells improved motor function in rodents after SCI, but claims of enhanced efficacy should be approached with caution. The safety of gene modification remains a significant concern, requiring additional efforts to enhance its clinical translatability.

The impact of chatbots based on large language models on second language vocabulary acquisition.

In recent years, the integration of artificial intelligence (AI) and machine learning (ML) into education, particularly for Personalized Language Learning (PLL), has garnered significant attention. This approach tailors interventions to address the unique challenges faced by individual learners. Large Language Models (LLMs), including Chatbots, have demonstrated a substantial potential in automating and enhancing educational tasks, effectively capturing the complexity and diversity of human language. In this study, 52 foreign language students were randomly divided into two groups: one with the assistance of a Chatbot based on LLMs and one without. Both groups learned the same series of target words over eight weeks. Post-treatment assessments, including systematic observation and quantitative tests assessing both receptive and productive vocabulary knowledge, were conducted immediately after the study and again two weeks later. The findings demonstrate that employing an AI Chatbot based on LLMs significantly aids students in acquiring both receptive and productive vocabulary knowledge during their second language learning journey. Notably, Chatbots contribute to the long-term retention of productive vocabulary and facilitate incidental vocabulary learning. This study offers valuable insights into the practical benefits of LLM-based tools in language learning, with a specific emphasis on vocabulary development. Chatbots utilizing LLMs emerge as effective language learning aids. It emphasizes the importance of educators understanding the potential of these technologies in L2 vocabulary instruction and encourages the adoption of strategic teaching methods incorporating such tools.

A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data.

Genetic and gene expression heterogeneity is an essential hallmark of many tumors, allowing the cancer to evolve and to develop resistance to treatment. Currently, the most commonly used data types for studying such heterogeneity are bulk tumor/normal whole-genome or whole-exome sequencing (WGS, WES); and single-cell RNA sequencing (scRNA-seq), respectively. However, tools are currently lacking to link genomic tumor subclonality with transcriptomic heterogeneity by integrating genomic and single-cell transcriptomic data collected from the same tumor. To address this gap, we developed scBayes, a Bayesian probabilistic framework that uses tumor subclonal structure inferred from bulk DNA sequencing data to determine the subclonal identity of cells from single-cell gene expression (scRNA-seq) measurements. Grouping together cells representing the same genetically defined tumor subclones allows comparison of gene expression across different subclones, or investigation of gene expression changes within the same subclone across time (i.e., progression, treatment response, or relapse) or space (i.e., at multiple metastatic sites and organs). We used simulated data sets, in silico synthetic data sets, as well as biological data sets generated from cancer samples to extensively characterize and validate the performance of our method, as well as to show improvements over existing methods. We show the validity and utility of our approach by applying it to published data sets and recapitulating the findings, as well as arriving at novel insights into cancer subclonal expression behavior in our own data sets. We further show that our method is applicable to a wide range of single-cell sequencing technologies including single-cell DNA sequencing as well as Smart-seq and 10x Genomics scRNA-seq protocols.

Deep Learning-based Prediction of Percutaneous Recanalization in Chronic Total Occlusion Using Coronary CT Angiography.

Background CT is helpful in guiding the revascularization of chronic total occlusion (CTO), but manual prediction scores of percutaneous coronary intervention (PCI) success have challenges. Deep learning (DL) is expected to predict success of PCI for CTO lesions more efficiently. Purpose To develop a DL model to predict guidewire crossing and PCI outcomes for CTO using coronary CT angiography (CCTA) and evaluate its performance compared with manual prediction scores. MATERIALS AND METHODS: Participants with CTO lesions were prospectively identified from one tertiary hospital between January 2018 and December 2021 as the training set to develop the DL prediction model for PCI of CTO, with fivefold cross validation. The algorithm was tested using an external test set prospectively enrolled from three tertiary hospitals between January 2021 and June 2022 with the same eligibility criteria. All participants underwent preprocedural CCTA within 1 month before PCI. The end points were guidewire crossing within 30 minutes and PCI success of CTO.Results A total of 534 participants (mean age, 57.7 years ± 10.8 [SD]; 417 [78.1%] men) with 565 CTO lesions were included. In the external test set (186 participants with 189 CTOs), the DL model saved 85.0% of the reconstruction and analysis time of manual scores (mean, 73.7 seconds vs 418.2-466.9 seconds) and had higher accuracy than manual scores in predicting guidewire crossing within 30 minutes (DL, 91.0%; CT Registry of Chronic Total Occlusion Revascularization, 61.9%; Korean Multicenter CTO CT Registry [KCCT], 68.3%; CCTA-derived Multicenter CTO Registry of Japan (J-CTO), 68.8%; P < .05) and PCI success (DL, 93.7%; KCCT, 74.6%; J-CTO, 75.1%; P < .05). For DL, the area under the receiver operating characteristic curve was 0.97 (95% CI: 0.89, 0.99) for the training test set and 0.96 (95% CI: 0.90, 0.98) for the external test set. Conclusion The DL prediction model accurately predicted the percutaneous recanalization outcomes of CTO lesions and increased the efficiency of noninvasively grading the difficulty of PCI. © RSNA, 2023 Supplemental material is available for this article. See also the editorial by Pundziute-do Prado in this issue.

Effect of Yiyuan moxibustion on urodynamics and TRPV4/ATP/P2X5 signal pathway of bladder tissue in rats with neurogenic bladder after sacral cord injury. / ç›Šå ƒç¸å¯¹éª¶é«“æŸä¼¤åŽç¥žç»æºæ€§è†€èƒ±å¤§é¼ å°¿æµåŠ¨åŠ›å­¦åŠè†€èƒ±ç»„ç»‡TRPV4/ATP/P2X5信号通路的影响.

OBJECTIVES: To observe the effect of Yiyuan moxibustion on urodynamics and the expressions of transient receptor potential vanilloid 4 (TRPV4), adenosine triphosphate (ATP), tyrosine protein kinase KIT (C-Kit) and adenosine triphosphate receptor P2X5 in bladder tissue of rats with detrusor reflex-free neurogenic bladder (NB) after sacral cord injury (SCI), so as to explore its mechanism in promoting the recovery of urination function of NB rats. METHODS: Female SD rats were randomly divided into sham operation, model, Yiyuan moxibustion, Yiyuan moxibustion+inhibitor (combination) and inhibitor groups, with 12 rats in each group. The model of detruser reflex-free NB after sacral SCI was established by modified Hassan Shaker spinal cord transection method. The behavioral score of Basso Beasttie Bresnahan (BBB) and urodynamic indexes were used to evaluate the model of rats after operation. Fifteen days after modeling, Yiyuan moxibustion was applied to "Shenque" (CV8) and "Guanyuan" (CV4) for 20 min, once daily for 14 days. Rats of the inhibitor and combination groups were given intravesical instillation of HC067047 (1 mL, 1 µmol/L, 30 min). After the interventions, urodynamics was used to evaluate the bladder function of rats. HE staining was used to observe the morphology of bladder tissue. ATP content in bladder tissue was detected by colorimetric method. The positive expression rates of C-Kit and their receptor P2X5 in bladder tissue were observed by immunofluorescence double labeling method, and TRPV4, C-Kit, and P2X5 protein expression levels in bladder tissue were detected by Western blot. RESULTS: Compared with the sham operation group, the maximum bladder capacity and bladder compliance of rats in the model group were increased (P<0.01), the leak point pressure, ATP content, the possitive expression rates of C-Kit and P2X5, and the protein expression levels of TRPV4, C-Kit, P2X5 in bladder tissue were decreased (P<0.01). In comparison with the model and combination groups, the Yiyuan moxibustion group showed a decrease in maximum bladder capacity and bladder compliance (P<0.01), an increase in leakage point pressure, ATP content, the possitive expression rates of C-Kit and P2X5, and TRPV4, C-Kit, and P2X5 protein expression levels (P<0.01, P<0.05)；However, these indicators showed opposite trends in the inhibitor group (P<0.01, P<0.05). CONCLUSIONS: Yiyuan moxibustion can improve the urodynamics and bladder function in rats with bladder detrusor nonreflective after SCI, which may be related to its effect in activating the TRPV4 channel in bladder tissue, promoting the release of ATP from bladder epithelium, thus increasing the expression of bladder Cajal interstitial cells and their purinergic P2X5 receptors.

Derivation and Validation of a Risk Score for Methicillin-Resistant Staphylococcus aureus Bloodstream Infection.

BACKGROUND: Compared with methicillin sensitive Staphylococcus aureus (MSSA), the prognosis of patients with methicillin resistant Staphylococcus aureus (MRSA) bloodstream infection is poor. Therefore, the construction of MRSA and MSSA identification model has certain value for the selection of antibiotics and treatment outcome control. This study aimed to derive and validate a simple risk prediction model for MRSA bloodstream infection in Chinese patients. METHODS: Three hundred and thirty-five patients with Staphylococcus aureus (S. aureus) bloodstream infection were retrospectively analyzed and divided into three groups. The first group was used for the risk score derivation (n = 163), the second group was used for internal validation (n = 80), and the third group was used for external validation (n = 92). According to the odds ratio (OR) obtained from multivariate logistic regression, the risk prediction model for MRSA bloodstream infection was established, and the prediction efficiency of the model in three cohorts were evaluated. RESULTS: Hospital stay before BSI ≥ 7 days, hospital acquired BSI, infection source ≥ 2 sites, indwelling gastric tube before BSI and carbapenems used before BSI and after admission were independent influencing factors of MRSA in the derivation group, the above influencing factors were scored 3, 5, 4, 3, and 3, respectively. The derivation, internal and external validation groups showed adequate discrimination (the AUCs were 0.788, 0.780, and 0.742, respectively) and good calibration (H-L tests were χ2 = 3.896, p = 0.306; χ2 = 4.221, p = 0.298; and χ2 = 3.974, p = 0.352, respectively). The risk scores were further divided into very low-risk (score 0 - 3), low-risk (score 4 - 7), high-risk (score 8 - 12), and very high-risk (score ≥ 13) layers. CONCLUSIONS: The simple risk score model for predicting MRSA bloodstream infection has good predictive effect, high predictive accuracy, and good clinical applicability, which can help clinicians choose sensitive antibiotics and reduce the adverse prognosis of patients.

[Efficacy differences between electroacupuncture and moxibustion for neurogenic bladder after spinal cord injury: a randomized controlled trial].

OBJECTIVE: To compare the clinical efficacy between electroacupuncture(EA) and moxibustion for neurogenic bladder (NB) after spinal cord injury (SCI). METHODS: One hundred and twenty patients with NB after SCI were randomly divided into an EA group, a moxibustion group, and an intermittent catheterization group, with 40 patients in each group. The patients in the intermittent catheterization group were treated with routine treatment and intermittent catheterization, while the patients in the EA group and the moxibustion group were treated with additional treatments of EA (discontinuous wave, with a frequency of 1.3-1.6 Hz, and intensity based on patient tolerance) and moxibustion, respectively. The acupoints used in both groups were Zhongji (CV 3) and Guanyuan (CV 4), bilateral Zusanli (ST 36), Yinlingquan (SP 9), and Baliao points. Each session lasted for 30 min, once daily, six times a week, for a total of six weeks.The maximum bladder capacity (MBC), residual urine vdume (RUV), detrusor pressure (Pdet) during the filling phase, bladder compliance (BC), maximum renal pelvis separation width of both kidneys, urine white blood cell count, TCM syndrome score, and World Health Organization quality of life assessment-BREF (WHOQOL-BREF) score were compared before and after treatment in the 3 groups. The number of patients in each group who achieved bladder functional balance was recorded, and the clinical efficacy was assessed after treatment. RESULTS: After treatment, the MBC, Pdet, BC, and WHOQOL-BREF scores in the EA group and the moxibustion group were increased (P<0.05), while the RUV, maximum renal pelvis separation width of both kidneys, urine white blood cell count, and TCM syndrome scores were decreased (P<0.05, P<0.01). In the intermittent catheterization group, MBC, RUV, maximum renal pelvis separation width of both kidneys, and urine white blood cell count were decreased (P<0.05), while BC and WHOQOL-BREF score were increased (P<0.05) after treatment. After treatment, the MBC, Pdet, BC, and WHOQOL-BREF scores in the EA group and the moxibustion group were higher than those in the intermittent catheterization group (P<0.05), while the RUV and TCM syndrome scores were lower than those in the intermittent catheterization group (P<0.05). Moreover, after treatment, the MBC and Pdet in the moxibustion group were higher than those in the EA group (P<0.05), while the RUV, maximum renal pelvis separation width of both kidneys, and TCM syndrome score in the EA group were lower than those in the moxibustion group (P<0.05). The number of patients who achieved bladder functional balance after treatment in the EA group and the moxibustion group was higher than that in the intermittent catheterization group (P<0.05). The cured and effective rate was 85.0% (34/40) in the EA group and 82.5% (33/40) in the moxibustion group, which were both higher than 65.0% (26/40) in the intermittent catheterization group (P<0.05), there was no significant difference between the EA group and the moxibustion group (P>0.05). CONCLUSION: EA and moxibustion could effectively improve the functional state of bladder in patients with NB after SCI. EA is more effective in reducing residual urine volume and excessive activity of the urethral sphincter, and relieving TCM syndromes, while moxibustion is more effective in increasing the pressure of the detrusor during the filling period and establishing the detrusor reflex.

Increased precipitation over land due to climate feedback of large-scale bioenergy cultivation.

Bioenergy with carbon capture and storage (BECCS) is considered to be a key technology for removing carbon dioxide from the atmosphere. However, large-scale bioenergy crop cultivation results in land cover changes and activates biophysical effects on climate, with earth's water recycling altered and energy budget re-adjusted. Here, we use a coupled atmosphere-land model with explicit representations of high-transpiration woody (i.e., eucalypt) and low-transpiration herbaceous (i.e., switchgrass) bioenergy crops to investigate the range of impact of large-scale rainfed bioenergy crop cultivation on the global water cycle and atmospheric water recycling. We find that global land precipitation increases under BECCS scenarios, due to enhanced evapotranspiration and inland moisture advection. Despite enhanced evapotranspiration, soil moisture decreases only slightly, due to increased precipitation and reduced runoff. Our results indicate that, at the global scale, the water consumption by bioenergy crop growth would be partially compensated by atmospheric feedbacks. Thus, to support more effective climate mitigation policies, a more comprehensive assessment, including the biophysical effects of bioenergy cultivation, is highly recommended.

quickBAM: a parallelized BAM file access API for high-throughput sequence analysis informatics.

MOTIVATION: In time-critical clinical settings, such as precision medicine, genomic data needs to be processed as fast as possible to arrive at data-informed treatment decisions in a timely fashion. While sequencing throughput has dramatically increased over the past decade, bioinformatics analysis throughput has not been able to keep up with the pace of computer hardware improvement, and consequently has now turned into the primary bottleneck. Modern computer hardware today is capable of much higher performance than current genomic informatics algorithms can typically utilize, therefore presenting opportunities for significant improvement of performance. Accessing the raw sequencing data from BAM files, e.g. is a necessary and time-consuming step in nearly all sequence analysis tools, however existing programming libraries for BAM access do not take full advantage of the parallel input/output capabilities of storage devices. RESULTS: In an effort to stimulate the development of a new generation of faster sequence analysis tools, we developed quickBAM, a software library to accelerate sequencing data access by exploiting the parallelism in commodity storage hardware currently widely available. We demonstrate that analysis software ported to quickBAM consistently outperforms their current versions, in some cases finishing an analysis in under 3 min while the original version took 1.5 h, using the same storage solution. AVAILABILITY AND IMPLEMENTATION: Open source and freely available at https://gitlab.com/yiq/quickbam/, we envision that quickBAM will enable a new generation of high-performance informatics tools, either directly boosting their performance if they are currently data-access bottlenecked, or allow data-access to keep up with further optimizations in algorithms and compute techniques.

Microbial carbon use efficiency promotes global soil carbon storage.

Soils store more carbon than other terrestrial ecosystems1,2. How soil organic carbon (SOC) forms and persists remains uncertain1,3, which makes it challenging to understand how it will respond to climatic change3,4. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss5-7. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways4,6,8-11, microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes12,13. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved7,14,15. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.

Heteronuclear Trimetallic MFe2 and M2 Fe (M=V, Nb, and Ta) Clusters for Dinitrogen Activation.

Catalysts with heteronuclear metal active sites may have high performance in the nitrogen reduction reaction (NRR), and the in-depth understanding of the reaction mechanisms is crucial for the design of related catalysts. In this work, the dissociative adsorption of N2 on heteronuclear trimetallic MFe2 and M2 Fe (M=V, Nb, and Ta) clusters was studied with density functional theory calculations. For each cluster, two reaction paths were studied with N2 initially on M and Fe atoms, respectively. Mayer bond order analysis provides more information on the activation of N-N bonds. M2 Fe is generally more reactive than MFe2 . The coordination mode of N2 on three metal atoms can be end-on: end-on: side-on (EES) for both MFe2 and M2 Fe. In addition, a unique end-on: side-on: side-on (ESS) coordination mode was found for M2 Fe, which leads to a higher degree of N-N bond activation. Nb2 Fe has the highest reactivity towards N2 when both the transfer of N2 and the dissociation of N-N bonds are taken into account, while Ta-containing clusters have a superior ability to activate the N-N bond. These results indicate that it is possible to improve the performance of iron-based catalysts by doping with vanadium group metals.