BioCoder: a benchmark for bioinformatics code generation with large language models.

SUMMARY: Pretrained large language models (LLMs) have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks and to be appropriately specialized to particular domains. Here, we target bioinformatics due to the amount of domain knowledge, algorithms, and data operations this discipline requires. We present BioCoder, a benchmark developed to evaluate LLMs in generating bioinformatics-specific code. BioCoder spans much of the field, covering cross-file dependencies, class declarations, and global variables. It incorporates 1026 Python functions and 1243 Java methods extracted from GitHub, along with 253 examples from the Rosalind Project, all pertaining to bioinformatics. Using topic modeling, we show that the overall coverage of the included code is representative of the full spectrum of bioinformatics calculations. BioCoder incorporates a fuzz-testing framework for evaluation. We have applied it to evaluate various models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, GPT-3.5, and GPT-4. Furthermore, we fine-tuned one model (StarCoder), demonstrating that our training dataset can enhance the performance on our testing benchmark (by >15% in terms of Pass@K under certain prompt configurations and always >3%). The results highlight two key aspects of successful models: (i) Successful models accommodate a long prompt (>2600 tokens) with full context, including functional dependencies. (ii) They contain domain-specific knowledge of bioinformatics, beyond just general coding capability. This is evident from the performance gain of GPT-3.5/4 compared to the smaller models on our benchmark (50% versus up to 25%). AVAILABILITY AND IMPLEMENTATION: All datasets, benchmark, Docker images, and scripts required for testing are available at: https://github.com/gersteinlab/biocoder and https://biocoder-benchmark.github.io/.

Revealing the role of necroptosis microenvironment: FCGBP + tumor-associated macrophages drive primary liver cancer differentiation towards cHCC-CCA or iCCA.

Previous research has demonstrated that the conversion of hepatocellular carcinoma (HCC) to intrahepatic cholangiocarcinoma (iCCA) can be stimulated by manipulating the tumor microenvironment linked with necroptosis. However, the specific cells regulating the necroptosis microenvironment have not yet been identified. Additionally, further inquiry into the mechanism of how the tumor microenvironment regulates necroptosis and its impact on primary liver cancer(PLC) progression may be beneficial for precision therapy. We recruited a single-cell RNA sequencing dataset (scRNA-seq) with 34 samples from 4 HCC patients and 3 iCCA patients, and a Spatial Transcriptomic (ST) dataset including one each of HCC, iCCA, and combined hepatocellular-cholangiocarcinoma (cHCC-CCA). Quality control, dimensionality reduction and clustering were based on Seurat software (v4.2.2) process and batch effects were removed by harmony (v0.1.1) software. The pseudotime analysis (also known as cell trajectory) in the single cell dataset was performed by monocle2 software (v2.24.0). Calculation of necroptosis fraction was performed by AUCell (v1.16.0) software. Switch gene analysis was performed by geneSwitches(v0.1.0) software. Dimensionality reduction, clustering, and spatial image in ST dataset were performed by Seurat (v4.0.2). Tumor cell identification, tumor subtype characterization, and cell type deconvolution in spot were performed by SpaCET (v1.0.0) software. Immunofluorescence and immunohistochemistry experiments were used to prove our conclusions. Analysis of intercellular communication was performed using CellChat software (v1.4.0). ScRNA-seq analysis of HCC and iCCA revealed that necroptosis predominantly occurred in the myeloid cell subset, particularly in FCGBP + SPP1 + tumor-associated macrophages (TAMs), which had the highest likelihood of undergoing necroptosis. The existence of macrophages undergoing necroptosis cell death was further confirmed by immunofluorescence. Regions of HCC with poor differentiation, cHCC-CCA with more cholangiocarcinoma features, and the tumor region of iCCA shared spatial colocalization with FCGBP + macrophages, as confirmed by spatial transcriptomics, immunohistochemistry and immunofluorescence. Pseudotime analysis showed that premalignant cells could progress into two directions, one towards HCC and the other towards iCCA and cHCC-CCA. Immunofluorescence and immunohistochemistry experiments demonstrated that the number of macrophages undergoing necroptosis in cHCC-CCA was higher than in iCCA and HCC, the number of macrophages undergoing necroptosis in cHCC-CCA with cholangiocarcinoma features was more than in cHCC-CCA with hepatocellular carcinoma features. Further investigation showed that myeloid cells with the highest necroptosis score were derived from the HCC_4 case, which had a severe inflammatory background on pathological histology and was likely to progress towards iCCA and cHCC-CCA. Switchgene analysis indicated that S100A6 may play a significant role in the progression of premalignant cells towards iCCA and cHCC-CCA. Immunohistochemistry confirmed the expression of S100A6 in PLC, the more severe inflammatory background of the tumor area, the more cholangiocellular carcinoma features of the tumor area, S100A6 expression was higher. The emergence of necroptosis microenvironment was found to be significantly associated with FCGBP + SPP1 + TAMs in PLC. In the presence of necroptosis microenvironment, premalignant cells appeared to transform into iCCA or cHCC-CCA. In contrast, without a necroptosis microenvironment, premalignant cells tended to develop into HCC, exhibiting amplified stemness-related genes (SRGs) and heightened malignancy.

Elevated Levels of Interleukin-18 are Associated with Lymph Node Metastasis in Papillary Thyroid Carcinoma.

Interleukin-18 (IL-18) is a proinflammatory cytokine that primarily stimulates the Th1 immune response. IL-18 exhibits anticancer activity and has been evaluated in clinical trials as a potential cancer treatment. However, evidence suggests that it may also facilitate the development and progression of some cancers. So far, the impact of IL-18 on papillary thyroid cancer (PTC) has not been investigated. In this study, we found that the expression of IL-18 was significantly increased in PTC compared to normal thyroid tissue. Elevated IL-18 expression was closely associated with lymphovascular invasion and lymph node metastases. Furthermore, compared to PTC patients with no nodal metastasis, serum IL-18 levels were slightly increased in patients with 1-4 nodal metastases and significantly elevated in patients with 5 or more nodal metastases. The pro-metastatic effect of IL-18 may be attributed to the simultaneous increase in the expression of S100A10, a known factor that is linked to nodal metastasis in PTC. In addition, the activation of several pathways, such as the intestinal immune network for lgA production and Staphylococcus aureus infection, may be involved in the metastasis process. Taken together, IL-18 may trigger pro-metastatic activity in PTC. Therefore, suppressing the function of IL-18 rather than enhancing it appears to be a reasonable strategy for treating aggressive PTC.

Comprehensive single-cell transcriptomic and proteomic analysis reveals NK cell exhaustion and unique tumor cell evolutionary trajectory in non-keratinizing nasopharyngeal carcinoma.

BACKGROUND: Nonkeratinizing nasopharyngeal carcinoma (NK-NPC) has a strong association with Epstein-Barr virus (EBV) infection. The role of NK cells and the tumor cell evolutionary trajectory in NK-NPC remain unclear. In this study, we aim to investigate the function of NK cell and the evolutionary trajectory of tumor cells in NK-NPC by single-cell transcriptomic analysis, proteomics and immunohistochemistry. METHODS: NK-NPC (n = 3) and normal nasopharyngeal mucosa cases (n = 3) were collected for proteomic analysis. Single-cell transcriptomic data of NK-NPC (n = 10) and nasopharyngeal lymphatic hyperplasia (NLH, n = 3) were obtained from Gene Expression Omnibus (GSE162025 and GSE150825). Quality control, dimension reduction and clustering were based on Seurat software (v4.0.2) process and batch effects were removed by harmony (v0.1.1) software. Normal cells of nasopharyngeal mucosa and tumor cells of NK-NPC were identified using copykat software (v1.0.8). Cell-cell interactions were explored using CellChat software (v1.4.0). Tumor cell evolutionary trajectory analysis was performed using SCORPIUS software (v1.0.8). Protein and gene function enrichment analyses were performed using clusterProfiler software (v4.2.2). RESULTS: A total of 161 differentially expressed proteins were obtained between NK-NPC (n = 3) and normal nasopharyngeal mucosa (n = 3) by proteomics (log2 fold change > 0.5 and P value < 0.05). Most of proteins associated with the nature killer cell mediated cytotoxicity pathway were downregulated in the NK-NPC group. In single cell transcriptomics, we identified three NK cell subsets (NK1-3), among which NK cell exhaustion was identified in the NK3 subset with high ZNF683 expression (a signature of tissue-resident NK cell) in NK-NPC. We demonstrated the presence of this ZNF683 + NK cell subset in NK-NPC but not in NLH. We also performed immunohistochemical experiments with TIGIT and LAG3 to confirm NK cell exhaustion in NK-NPC. Moreover, the trajectory analysis revealed that the evolutionary trajectory of NK-NPC tumor cells was associated with the status of EBV infection (active or latent). The analysis of cell-cell interactions uncovered a complex network of cellular interactions in NK-NPC. CONCLUSIONS: This study revealed that the NK cell exhaustion might be induced by upregulation of inhibitory receptors on the surface of NK cells in NK-NPC. Treatments for the reversal of NK cell exhaustion may be a promising strategy for NK-NPC. Meanwhile, we identified a unique evolutionary trajectory of tumor cells with active status of EBV-infection in NK-NPC for the first time. Our study may provide new immunotherapeutic targets and new sight of evolutionary trajectory involving tumor genesis, development and metastasis in NK-NPC.

Phenyldivinylsulfonamides for the construction of antibody-drug conjugates with controlled four payloads.

Phenyldivinylsulfonamides emerged from a series of divinylsulfonamides, demonstrating their ability to effectively re-bridge disulfide bonds. This kind of linkers was attached to monomethyl auristatin E (MMAE) and further conjugated with a model antibody, trastuzumab. After optimization, the linker 20 can deliver stable and highly homogenous DAR (Drug-to-Antibody Ratio) four antibody-drug conjugates (ADCs). The method was also applicable for other IgG1 antibodies to obtain ADCs with controlled four payloads. Moreover, the MMAE-bearing ADC is potent, selective and efficacious against target cell lines.

Site-specific construction of triptolide-based antibody-drug conjugates.

Antibody-drug conjugates (ADCs) have emerging as efficient agents to target deliver cytotoxic drugs and reduce their off-target side effects. Triptolide has attracted attention to be used in ADC development. Herein, three rationally designed triptolide drug-linkers have been synthesized for use in site-specific construction of ADCs. Carbamates that were supposed to be more stable than carbonates were introduced to attach triptolide to the linkers. PEG and discrete PEG chains were incorporated to improve the hydrophilicity of drug-linkers. The ADCs were finally site-specifically prepared by conjugation of the drug-linkers to trastuzumab through disulfide re-bridging approach. The preliminary anti-tumor activities of these ADCs were evaluated and they displayed high potencies against HER2-targeted cancer in vitro and in vivo.

The role of UhpA in regulating the virulence gene expression in Edwardsiella piscicida.

Edwardsiella piscicida (E. piscicida) is an important fish pathogen. However, the mechanism of Glu6P transport regulatory protein UhpA how to affect the virulence gene expression in E. piscicida is still unclear. The results in this study showed that the metabolism-related gene expression of cysteine synthase (orf 1134) and sulphate transporter (ychM) in the uhpA mutant strain ΔuhpA was 0.76-fold and 0.68-fold lower than the ones in the wild strains (p < .05). The gene expression of ethA and ethB in the ΔuhpA strain was 0.80-fold and 0.72-fold lower than the ones in the wild strains (p < .05). However, the gene expression of fliC and flgN in the ΔuhpA was 1.51-fold and 1.21-fold higher than the ones in the wild strains (p < .05). The gene expression of T3SS (esrB and esrC) and T6SS (evpB and evpC) in the ΔuhpA was 1.27-fold, 1.13-fold, 1.28-fold and 1.23-fold higher than the ones in the wild strains (p < .05). This suggested that the uhpA gene could regulate the key virulence gene expression, and the uhpA gene was associated with the pathogenicity of E. piscicida in fish.

LuxS/AI-2 Quorum Sensing System in Edwardsiella piscicida Promotes Biofilm Formation and Pathogenicity.

LuxS/AI-2 is an important quorum sensing system which affects the growth, biofilm formation, virulence, and metabolism of bacteria. LuxS is encoded by the luxS gene, but how this gene is associated with a diverse array of physiological activities in Edwardsiella piscicida (E. piscicida) is not known. Here, we constructed an luxS gene mutant strain, the △luxS strain, to identify how LuxS/AI-2 affects pathogenicity. The results showed that LuxS was not found in the luxS gene mutant strain, and this gene deletion decreased E. piscicida growth compared to that of the wild-type strain. Meanwhile, the wild-type strain significantly increased penetration and motility in mucin compared to levels with the △luxS strain. The 50% lethal dose (LD50) of the E. piscicida △luxS strain for zebrafish was significantly higher than that of the wild-type strain, which suggested that the luxS gene deletion could attenuate the strain's virulence. The AI-2 activities of EIB202 were 56-fold higher than those in the △luxS strain, suggesting that the luxS gene promotes AI-2 production. Transcriptome results demonstrated that between cells infected with the △luxS strain and those infected with the wild-type strain 46 genes were significantly differentially regulated, which included 34 upregulated genes and 12 downregulated genes. Among these genes, the largest number were closely related to cell immunity and signaling systems. In addition, the biofilm formation ability of EIB202 was significantly higher than that of the △luxS strain. The supernatant of EIB202 increased the biofilm formation ability of the △luxS strain, which suggested that the luxS gene and its product LuxS enhanced biofilm formation in E. piscicida All results indicate that the LuxS/AI-2 quorum sensing system in E. piscicida promotes its pathogenicity through increasing a diverse array of physiological activities.

The role of uhpA in Edwardsiella piscicida and the inflammatory cytokine response in tilapia.

Edwardsiella piscicida (E. piscicida) is an important zoonotic pathogen that infects fish by colonizing the intestines. The intestine provides nutrition including Glucose 6-phosphate (Glu6P) and a competitive environment for the microbiota. Although the transport system regulatory protein gene uhpA has been reported in E. piscicida genomes, whether the uhpA gene is involved in the pathogenicity of E. piscicida remains largely unknown. Therefore, the uhpA gene mutants strain E. piscicida ΔuhpA was constructed to elucidate the functions of Glu6P and the uhpA gene in E. piscicida. The results demonstrated that Glu6P significantly increased the gene expression of uhpC/uhpB/uhpA than without adding Glu6P in the culture. The gene expression of uhpC and uhpB was down regulated in the mutant strain than that of in the wild type strain. E. piscicida ΔuhpA exhibited an increase in virulence compared to that of E. piscicida EIB202 [LD50 value: (3.98 × 106 CFU/fish) and LD50 value: (1.45 × 107 CFU/fish) respectively]. Besides, although TNF-α did not show significant differences (p > 0.05) in the spleen of tilapia infected with ΔuhpA and EIB202 in the whole observed period, the gene expression of IL-1ß and TGF-ß in the spleen of tilapia infected with ΔuhpA showed significantly higher (p < 0.05) than that of in tilapia infected with EIB202. Meanwhile, the gene expression of IL-1ß and TGF-ß in spleen of tilapia infected with ΔuhpA showed significantly higher (p < 0.05) than that of in fish infected with EIB202 when zebrafish used as the control in the whole observed period. All these results suggested that Glu6P up-regulated the gene expression of uhpC/uhpB/uhpA; most important, the uhpA gene deletion in E. piscicida down-regulated the gene expression of uhpC and uhpB, enhanced its pathogenicity and its role in inducing the inflammatory cytokine responses in tilapia.

The UhpA mutant of Edwardsiella piscicida enhanced its motility and the colonization in the intestine of tilapia.

Edwardsiella piscicida (E. piscicida) is a significant bacterial pathogen of cultured fish, which infected fish meanly through the intestine. Glucose 6-phosphate (Glu6P) in the intestine is nutritious to the pathogen, Meanwhile, Glu6P was found using as a virulent regulating signal for bacteria. The UhpA, one of the Glu6P transport system regulatory proteins could down-regulate the uhpC/uhpB/uhpA system and decrease its pathogenicity. However, the motility and the colonization of E. piscicida affected by UhpA were still unclear. In this study, the motility and the colonization of E. piscicida were monitored. The result demonstrated that the motility of EIB202 was significantly stronger than that of in ΔuhpA according to fractions 4, 8 and 9. However, the motility of ΔuhpA was significantly stronger than that of EIB202 according to the total number at the whole experiment. Although, there was no difference in the number of bacteria in the posterior intestine of tilapia after infected with E. piscicida EIB202 and ΔuhpA. The number of bacteria in the anterior and the middle intestine of fish infected with ΔuhpA were significantly higher than that of in fish infected with EIB202 at the whole experiment (P < 0.05). Interestingly, both E. piscicida strains colonized in the anterior intestine than that of in the middle and posterior intestines of tilapia. Besides, the gene expression of IL-1ß and TNF-α in the head-kidney of fish infected with ΔuhpA showed significantly higher (p < 0.05) than fish infected with EIB202 during the whole experimental period. Most importantly, the survival rate of E. piscicida EIB202 and ΔuhpA were 57% and 37% respectively. All results indicate that the uhpA gene mutant in E. piscicida could enhance its motility and the colonization in the intestine of tilapia, this illustrates the mechanism of UhpA decreases the pathogenesis of E. piscicida in fish.

Picosecond mid-infrared optical parametric amplifier based on LiInSe2 with tenability extending from 3.6 to 4.8 µm.

A picosecond (ps) mid-infrared (MIR) optical parametric amplifier (OPA) with LiInSe2 crystal was demonstrated for the first time. The MIR OPA was pumped by a 30 ps 1064 nm Nd:YAG laser and injected by a barium boron oxide (BBO)-based widely tunable near-infrared seed. A maximum idler pulse energy of 433 µJ at 4 µm has been obtained under a pump energy of 17 mJ, and the corresponding pulse duration was estimated to be ~13 ps. To our knowledge, this is the highest single pulse energy generated by LiInSe2 crystal. Furthermore, an idler spectrum tuning from 3.6 to 4.8 µm was investigated at fixed pump energy of 15 mJ.

Selective lysine modification of native peptides via aza-Michael addition.

A series of vinylsulfonamides were synthesized and screened for site-selective modification of the ε-amino group of lysine-bearing free α-amine residues. N-Methyl-N-phenylethenesulfonamide has emerged as an applicable reagent and has been developed for efficient and highly selective modification of the lysine residue of native peptides in the presence of a free N-terminus via aza-Michael addition. We demonstrated that functional N-phenylvinylsulfonamide derivatives with a fluorescent moiety or drug could also be conjugated to the lysine residue of octreotide and insulin with high specificity, without modifying the N-terminus. Our method provides a promising strategy for site-selective lysine functionalization in native peptides with a free N-terminus.

Withaferin A protects against spinal cord injury by inhibiting apoptosis and inflammation in mice.

CONTEXT: Withaferin A (WFA) exhibits diverse pharmaceutical applications on human diseases, including rheumatoid arthritis, cancers and microbial infection. OBJECTIVE: We evaluated the neuroprotective role of WFA using a mouse model of spinal cord injury (SCI). MATERIALS AND METHODS: BALB/c mice were administrated 10 mg/kg of WFA. Gene expression was measured by real-time PCR, western blot and immunohistochemistry. Cell morphology and apoptosis were determined by H&E staining and TUNEL assay. Motor function was evaluated by the BBB functional scale for continuous 7 weeks. RESULTS: WFA significantly improved neurobehavioural function and alleviated histological alteration of spinal cord tissues in traumatized mice. Brain-derived neurotrophic factor (BDNF) and glial cell line-derived neurotrophic factor (GDNF) significantly increased in WFA-treated mice. Meanwhile, the expression of Nogo-A and RhoA remarkably decreased in the presence of WFA. Furthermore, the apoptotic cell death was attenuated in mice treated with WFA (31.48 ± 2.50% vs. 50.08 ± 2.08%) accompanied by decreased bax and increased bcl-2. In addition, WFA decreased the expression of pro-inflammatory mediators such as IL-1ß (11.20 ± 1.96 ng/mL vs. 17.59 ± 1.42 ng/mL) and TNF-α (57.38 ± 3.57 pg/mL vs. 95.06 ± 9.13 pg/mL). The anti-inflammatory cytokines including TGF-ß1 (14.32 ± 1.04 pg/mL vs. 9.37 ± 1.17 pg/mL) and IL-10 (116.80 ± 6.91 pg/mL vs. 72.33 ± 9.35 pg/mL) were elevated after WFA administration. DISCUSSION AND CONCLUSION: This study demonstrated that WFA has a neuroprotective role by inhibition of apoptosis and inflammation after SCI in mice.

Performances of a diode end-pumped GYSGG/Er,Pr:GYSGG composite laser crystal operated at 2.79 µm.

We demonstrate a comparative investigation on Er,Pr:GYSGG and GYSGG/Er,Pr:GYSGG composite crystals at 2.79 µm. Simulating results show the highest temperatures are 369 K and 318 K, respectively. A maximum output power of 825 mW with slope efficiency of 19.2% and maximum laser energy of 3.65 mJ with slope efficiency of 22.7% are obtained in the GYSGG/Er,Pr:GYSGG composite crystal, which have an obvious improvement than those of Er,Pr:GYSGG crystal. The thermal focal lengths are respectively 41 and 62 mm when the pump power is 2.5 W. All these results indicate that the GYSGG/Er,Pr:GYSGG composite crystal has great advantages in reducing the influence of thermal effects and improving laser performances.

Extended-Spectrum ß-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae: Risk Factors and Economic Burden Among Patients with Bloodstream Infections.

Introduction: Although Extended-spectrum ß-lactamase-producing Escherichia coli and Klebsiella pneumoniae (ESBL-EK) significantly contribute to bloodstream infections, their economic repercussions remain largely unquantified. Data Source and Methods: We performed a retrospective analysis of inpatients diagnosed with Escherichia coli or Klebsiella pneumoniae bacteremia in a tertiary hospital from January 2020 to December 2022 in Guangzhou, China. We employed the chi-square test to examine ESBL risk factors and utilized propensity score matching (PSM) to negate baseline confounding factors, assessing economic burden through disability-adjusted life years (DALYs), hospital costs and productivity losses. We employed mediation analysis to eliminate confounding factors and better identify ESBL sources of burden related. Results: We found 166 ESBL-EC/KP BSI patients (52.2% of the total examined 318 patients). Post-PSM analysis revealed that ESBL-producing EC/KP will reduce the effectiveness of empirical medication by 19.8%, extend the total length of hospitalization by an average of 3 days, and increase the patient's financial burden by US$2047. No significant disparity was found in overall mortality and mean DALYs between the groups. Mediation analysis showed that the link between ESBL and hospital costs is predominantly, if not entirely, influenced by the appropriateness of empirical antibiotic treatment and length of hospital stay. Conclusion: Patients with BSI due to ESBL-producing ESBL-EK incur higher costs compared to those with non-ESBL-EK BSI. This cost disparity is rooted in varying rates of effective empirical antimicrobial therapy and differences in hospital stay durations. A nuanced approach, incorporating a thorough understanding of regional epidemiological trends and judicious antibiotic use, is crucial for mitigating the financial impact on patients.

Practice of standardization of CLSI M45 A3 antimicrobial susceptibility testing of Infrequently Isolated or Fastidious Bacteria strains isolated from blood specimens in Guangdong Province 2017-2021.

The concentration of antimicrobial agents in environments like water and food has increased rapidly, which led to a rapid increase in antimicrobial resistance levels in the environment. Monitoring of bacterial resistance levels is considered as a necessary means to control the bacterial resistance. Reference standards are critical for antimicrobial susceptibility testing. CLSI M45 A3 standard defines pathogenic microorganisms that cause infections less frequently than those covered by CLSI M02, M07, and M100 as Infrequently Isolated or Fastidious Bacteria and specifies antimicrobial susceptibility testing methods. Our study investigated the epidemiology and antimicrobial susceptibility testing data of Infrequently Isolated or Fastidious Bacteria strains isolated from blood specimens in 70 hospitals in Guangdong Province between 2017 and 2021. We defined testing methods other than those specified in CLSI M45 A3 as "Non-Standardized." The proportion of standardized antimicrobial susceptibility testing for penicillin increased significantly (Corynebacterium spp. 17.4% vs. 50.0% p < 0.05; Micrococcus spp. 50.0% vs. 77.8% p < 0.05; Abiotrophia spp. and Granulicatella spp. 21.4% vs. 90.9% p < 0.001), while for cefotaxime (Corynebacterium spp. 0.0% vs. 45.2% p < 0.05; Abiotrophia spp. and Granulicatella spp. 0.0% vs. 14.3% p = 0.515) and vancomycin increased finitely. Non-standardized methods were used for all other antimicrobials. Due to limitations in the economic and medical environment, some clinical laboratories are unable to fully comply with CLSI M45 A3 standard. We recommend that CLSI should add breakpoints for disk diffusion method to improve the standardization of antimicrobial susceptibility testing.

Spectroscopic properties and diode end-pumped 2.79 µm laser performance of Er,Pr:GYSGG crystal.

We demonstrate a 968 nm diode end-pumped Er,Pr:GYSGG (Gd1.17Y1.83Sc2Ga3O12) laser at 2.79 µm operated in the pulse and continuous-wave (CW) modes. The lifetimes for the upper laser level 4I11/ 2 and lower level 4I13/2 are 0.52 and 0.60 ms, respectively. The laser produces 284 mW of power in the CW mode, corresponding to the optical-to-optical efficiency of 14.8% and slope efficiency of 17.4%. The maximum laser energy achieved is 2.4 mJ at a repetition rate of 50 Hz and pulse duration of 0.5 ms, corresponding to a peak power of 4.8 W and slope efficiency of 18.3%. These results suggest that doping deactivator Pr3+ ions can effectively decrease the lower-level lifetime and improve the laser efficiency.

Spectroscopic, diode-pumped laser properties and gamma irradiation effect on Yb, Er, Ho:GYSGG crystals.

We demonstrate a diode end-pumped Yb, Er, Ho:Gd(1.17)Y(1.83)Sc(2)Ga(3)O(12) (GYSGG) laser operated at 2.79 µm in continuous-wave mode. Spectral analysis shows that Yb(3+) and Ho(3+) act as sensitizer and deactivator ions, respectively. Pumping with a 967 nm laser diode produces the maximum output power of 411 mW, corresponding to optical-optical conversion and slope efficiencies of 11.6% and 13.1%, respectively. The minimum laser threshold is only 81 mW because of Ho(3+) doping. The laser properties are only slightly influenced by 100 mrad gamma irradiation. The Yb, Er, Ho:GYSGG crystal possesses excellent radiation resistance and is a potential laser gain medium in radiant environments.

A comprehensive analysis of the potential role of necroptosis in hepatocellular carcinoma using single-cell RNA Seq and bulk RNA Seq.

PURPOSE: Necroptosis plays an essential role in oncogenesis and tumor progression in hepatocellular carcinoma (HCC). This study aimed to investigate the role of necroptosis in the development and progression of HCC. Specifically, we constructed a prognostic prediction model using necroptosis-associated genes (NAGs) to predict patient outcomes. METHODS: Using data from The Cancer Genome Atlas (TCGA) database, we analyzed gene expression and clinical data. We identified a 5-gene model associated with NAGs and explored genetic features and immune cell infiltration using the CIBERSORT algorithm. In addition, we conducted single-cell RNA sequencing to investigate the potential role of necroptosis in HCC. RESULTS: We constructed a 5-gene prognostic model based on NAGs that demonstrated excellent predictive accuracy in both training and validation sets. Using multifactorial cox regression analysis, we confirmed the risk score derived from the model as an independent predictor of prognosis, surpassing other clinical characteristics. Patients with high risk scores had significantly worse prognosis than those with low risk scores. To enhance the clinical utility of the necroptosis score, we constructed an accurate nomogram. Additionally, we compared metabolic pathway and immune microenvironment differences between HCC tumors with high and low risk scores. Our single-cell RNA sequencing analyses revealed that necroptosis in HCC was primarily associated with a specific subset of macrophages. CONCLUSIONS: Our study revealed the presence of two distinct necroptosis subtypes in HCC and developed a robust prognostic model with exceptional predictive accuracy. We observed significantly higher infiltration of M0 macrophages in the high-risk group. We propose that rescuing cytochrome c metabolism in HCC could serve as a potential therapeutic strategy. Furthermore, at a single-cell resolution, our analysis identified myeloid cells as the primary cells exhibiting necroptosis. Specifically, macrophages expressing CD5L, CETP, and MARCO, which may belong to a subset of tissue-resident macrophages, were found to be highly susceptible to necroptosis. These findings suggest the involvement of this specific macrophage subset in potential antitumor therapies. Our study provides novel insights into predicting patient prognosis and developing personalized therapeutic approaches for HCC.

Accurate Retention Time Prediction Based on Monolinked Peptide Information to Confidently Identify Cross-Linked Peptides.

Cross-linking mass spectrometry methods have not been successfully applied to protein-protein interaction discovery at a proteome-wide level mainly due to the computation complexity (O (n2)) issue. In a previous report, we proposed a decision tree searching strategy (DTSS), which can reduce complexity by orders of magnitude. In this study, we further found that the monolinked peptides carry out the information on the retention time of the corresponding cross-linked pairs; therefore, the retention time of cross-linked peptide pairs can be predicted accurately. By utilizing the retention time as an extra filter, the false positive rate can be reduced by around 86% with a sensitivity loss of 10%. The method combined with DTSS (T-DTSS) not only benefits improving identification confidence but also leads to lower cutoff scores and facilitates substantially increasing inter-cross-link identification. T-DTSS was successfully applied to the identification of inter-cross-links obtained from Escherichia coli cell lysate cross-linked by a newly synthesized enrichable cross-linker, pDSBE. The approach can be applicable to both cleavable and noncleavable methods.