Proteome Landscapes of Human Hepatocellular Carcinoma and Intrahepatic Cholangiocarcinoma.

Liver cancer is among the top leading causes of cancer mortality worldwide. Particularly, hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (CCA) have been extensively investigated from the aspect of tumor biology. However, a comprehensive and systematic understanding of the molecular characteristics of HCC and CCA remains absent. Here, we characterized the proteome landscapes of HCC and CCA using the data-independent acquisition (DIA) mass spectrometry (MS) method. By comparing the quantitative proteomes of HCC and CCA, we found several differences between the two cancer types. In particular, we found an abnormal lipid metabolism in HCC and activated extracellular matrix-related pathways in CCA. We next developed a three-protein classifier to distinguish CCA from HCC, achieving an area under the curve (AUC) of 0.92, and an accuracy of 90% in an independent validation cohort of 51 patients. The distinct molecular characteristics of HCC and CCA presented in this study provide new insights into the tumor biology of these two major important primary liver cancers. Our findings may help develop more efficient diagnostic approaches and new targeted drug treatments.

Pulmonary rehabilitation improves exercise capacity, health-related quality of life, and cardiopulmonary function in patients with non-small cell lung cancer.

BACKGROUND: Lung cancer significantly impairs exercise capacity and health-related quality of life (HRQL). Pulmonary rehabilitation (PR) has demonstrated positive effects on exercise capacity and HRQL in lung cancer patients. However, its impact on cardiopulmonary function needs further exploration. The aim of this study was to explore the effects of PR on cardiopulmonary function, exercise capacity and HRQL in patients with lung cancer. METHODS: Patients with lung cancer were enrolled in a 12-week PR program. Each participant underwent a thorough evaluation, which included spirometry, cardiopulmonary exercise testing, respiratory muscle strength test, and evaluation of HRQL using the Chronic Obstructive Pulmonary Disease Assessment Test (CAT). RESULTS: Fifty-six patients completed the PR program. Following PR, exercise capacity significantly improved, as evidenced by increased peak oxygen uptake and work rate (both p < 0.05). Exertional symptoms were notably reduced, including leg soreness and dyspnea at peak exercise, accompanied by a decrease in the CAT score (all p < 0.05). Furthermore, improvements in cardiopulmonary function were observed, encompassing respiratory muscle strength, ventilatory equivalent, tidal volume, stroke volume index, and cardiac index at peak exercise (all p < 0.05). CONCLUSIONS: PR demonstrated notable enhancements in cardiopulmonary function, exertional symptoms, exercise capacity, and HRQL in patients with lung cancer.

Prophylactic Versus Reactive Megestrol Acetate Use for Critical Body Weight Loss in Patients with Pharyngeal and Laryngeal Squamous Cell Carcinoma Undergoing Concurrent Chemoradiotherapy.

This study compared the effects of megestrol acetate (MA) prophylactic (p-MA) versus reactive (r-MA) use for critical body-weight loss (>5% from baseline) during concurrent chemoradiotherapy (CCRT) in patients with advanced pharyngolaryngeal squamous cell carcinoma (PLSCC).Patients receiving CCRT alone in two phase-II trials were included for analyses. Both the p-MA and r-MA cohorts received the same treatment protocol at the same institution, and the critical body-weight loss, survival, and adverse event profiles were compared.The mean (SD) weight loss was 5.1% (4.7%) in the p-MA cohort (n = 54) vs. 8.1% (4.6%) in the r-MA cohort (n = 50) (p = .001). The percentage of subjects with body-weight loss >5% was 42.6% in the p-MA cohort vs. 68.0% in the r-MA cohort (p = .011). Tube feeding was needed in 22.2% of p-MA vs. 62.0% of r-MA patients (p < .001). Less neutropenia (26.0% vs. 70.0% [p < .001]) and a shorter duration of grade 3-4 mucositis (2.4 ± 1.4 vs. 3.6 ± 2.0 wk [p = .009]) were observed with p-MA treatment. Disease-specific survival, locoregional control, or distant metastasis-free survival did not differ. Less competing mortality from secondary primary cancer resulted in a better overall survival trend in the p-MA cohort.p-MA may reduce body-weight loss and improve adverse event profiles during CCRT for patients with PLSCC.

Early relapse is an adverse prognostic factor for survival outcomes in patients with oral cavity squamous cell carcinoma: results from a nationwide registry study.

BACKGROUND: The prognostic significance of the relapse interval in patients with resected oral cavity squamous cell carcinoma (OCSCC) is a matter of ongoing debate. In this large-scale, registry-based, nationwide study, we examined whether the time interval between surgery and the first disease relapse may affect survival outcomes in Taiwanese patients with OCSCC. METHODS: Data made available by the Taiwan Health Promotion Administration as of 2004 were obtained. The study cohort consisted of patients who were included in the registry between 2011 and 2017. Disease staging was performed according to the American Joint Committee on Cancer (AJCC) Staging Manual, Eight Edition. We retrospectively reviewed the clinical records of 13,789 patients with OCSCC who received surgical treatment. A total of 2327 (16.9%) patients experienced a first disease relapse. The optimal cutoff value for the relapse interval was 330 days when both 5-year disease-specific survival (DSS) and overall survival (OS) (≤ 330/>330 days, n = 1630/697) were taken into account. In addition, we undertook a propensity score (PS)-matched analysis of patients (n = 654 each) with early (≤ 330 days) versus late (> 330 days) relapse. RESULTS: The median follow-up time in the entire study cohort was 702 days (433 and 2001 days in the early and late relapse groups, respectively). Compared with patients who experienced late relapse, those with early relapse showed a higher prevalence of the following adverse prognostic factors: pT4, pN3, pStage IV, poor differentiation, depth of invasion ≥ 10 mm, and extra-nodal extension. Multivariable analysis revealed that early relapse was an independent adverse prognostic factor for both 5-year DSS and OS (average hazard ratios [AHRs]: 3.24 and 3.91, respectively). In the PS-matched cohort, patients who experienced early relapse showed less favorable 5-year DSS: 58% versus 30%, p < 0.0001 (AHR: 3.10 [2.69 - 3.57]) and OS: 49% versus 22%, p < 0.0001 (AHR: 3.32 [2.89 - 3.81]). CONCLUSION: After adjustment for potential confounders and PS matching, early relapse was an adverse prognostic factor for survival outcomes in patients with OCSCC. Our findings may have significant implications for risk stratification.

Preservation of vascular endothelial glycocalyx and barrier by activation of adenosine A2A receptor (A2AR) improved renal dysfunction in cirrhotic rats.

Cirrhosis-related hepatic and renal endothelial dysfunction is characterized by macrophage-endothelium adhesion-mediated inflammation, glycocalyx/barrier damage, and impaired vasodilation. Activation of adenosine A2A receptor (A2AR) protects cirrhotic rats from impairment of hepatic microcirculation post hepatectomy. This study evaluates the effects of A2AR activation on the cirrhosis-related hepatic and renal endothelial dysfunction in biliary cirrhotic rats receiving two weeks of A2AR agonist PSB0777 [bile duct ligated (BDL)+PSB0777] treatment. Endothelial dysfunction in cirrhotic liver, renal vessels, and kidney is characterized by downregulation of the A2AR expressions, decreased vascular endothelial vasodilatory (p-eNOS)/anti-inflammatory (IL-10/IL-10R)/barrier [VE-cadherin (CDH5) and ß-catenin (CTNNB1)]/glycocalyx [syndecan-1 (SDC1) and hyaluronan synthase-2 (HAS2)] markers, and increased leukocyte-endothelium adhesion molecules (F4/80, CD68, ICAM-1, and VCAM-1). In BDL rats, PSB0777 treatment improves hepatic and renal endothelial dysfunction, ameliorates portal hypertension, and attenuates renal hypoperfusion by restoring of the vascular endothelial anti-inflammatory, barrier, glycocalyx markers and vasodilatory response as well as inhibiting the leukocyte-endothelium adhesion. In an in vitro study, conditioned medium (CM) of bone marrow-derived macrophage (BMDM) of BDL rats [BMDM-CM (BDL)] induced barrier/glycocalyx damage, which was reversed by the PSB0777 pre-treatment. The A2AR agonist is a potential agent that can simultaneously correct cirrhosis-related hepatic and renal endothelial dysfunction, portal hypertension, renal hypoperfusion, and renal dysfunction.

A Comparison Study of Outcomes and Complications Between Marginal Mandibulectomy With or Without Additional Mandibulotomy in Tongue Cancers.

BACKGROUND: Marginal mandibulectomy with or without additional mandibulotomy could represent the alternatives to avoid segmental mandibulectomy in carefully selected tongue cancers. AIM AND OBJECTIVES: This study investigated a subgroup of tongue cancers with suspected involvement to the alveolar bone because of the shallow and deformed mouth floor. We aimed to compare the functional outcomes, postoperative complications, and disease control efficacy between the 2 different marginal mandibulectomy approaches, with or without additional mandibulotomy. MATERIALS AND METHODS: A retrospective study of 29 marginal mandibulectomies and 26 combined mandibulotomies for tongue cancer wide excisions and flap reconstruction at Chang Gung Memorial Hospital Linkou Branch during 2014 to 2019 was performed. RESULTS: The combined mandibulotomy group had more advanced T-status ( P < 0.001) and greater tumor diameters ( P < 0.001) but not increased preexisting trismus, bone invasions, or positive margins. The additional mandibulotomy increased flap necrosis ( P = 0.044), late infections ( P = 0.004), and tongue movement limitations ( P = 0.044) but not osteoradionecrosis. Osteoradionecrosis was unrelated to the resected mandibular length or the mandibulotomy sites. Feeding tube dependence was greater in the combined group at discharge ( P = 0.014), but no long-term differences were noted. Kaplan-Meier overall survival ( P = 0.052) and disease-free survival ( P = 0.670) were both comparable between the 2 groups. CONCLUSIONS: The combined procedure of mandibulotomy and marginal mandibulectomy in large tongue cancers without bone invasions is associated with increased soft tissue-related complications but not bone-related complications. However, comparable disease control, survival, and long-term tube feeding outcomes were noted.

Dunaliella salina Alga Protects against Myocardial Ischemia/Reperfusion Injury by Attenuating TLR4 Signaling.

Myocardial ischemia/reperfusion (I/R) injury is marked by rapid increase in inflammation and not only results in myocardial apoptosis but also compromises the myocardial function. Dunaliella salina (D. salina), a halophilic unicellular microalga, has been used as a provitamin A carotenoid supplement and color additive. Several studies have reported that D. salina extract could attenuate lipopolysaccharides-induced inflammatory effects and regulate the virus-induced inflammatory response in macrophages. However, the effects of D. salina on myocardial I/R injury remain unknown. Therefore, we aimed to investigate the cardioprotection of D. salina extract in rats subjected to myocardial I/R injury that was induced by occlusion of the left anterior descending coronary artery for 1 h followed by 3 h of reperfusion. Compared with the vehicle group, the myocardial infarct size significantly decreased in rats that were pre-treated with D. salina. D. salina significantly attenuated the expressions of TLR4, COX-2 and the activity of STAT1, JAK2, IκB, NF-κB. Furthermore, D. salina significantly inhibited the activation of caspase-3 and the levels of Beclin-1, p62, LC3-I/II. This study is the first to report that the cardioprotective effects of D. salina may mediate anti-inflammatory and anti-apoptotic activities and decrease autophagy through the TLR4-mediated signaling pathway to antagonize myocardial I/R injury.

Activation of peripheral TRPM8 mitigates ischemic stroke by topically applied menthol.

BACKGROUND: No reports exist as to neuroprotective effects associated with topical activation of transient receptor potential melastatin 8 (TRPM8), a noted cold receptor. In the present study, we identified whether activating peripheral TRPM8 can be an adjuvant therapy for ischemic stroke. METHODS: Menthol, an agonist of TRPM8, was applied orally or topically to all paws or back of the mouse after middle cerebral artery occlusion (MCAO). We used Trpm8 gene knockout (Trpm8-/-) mice or TRPM8 antagonist and lidocaine to validate the roles of TRPM8 and peripheral nerve conduction in menthol against ischemic stroke. RESULTS: Application of menthol 16% to paw derma attenuated infarct volumes and ameliorated sensorimotor deficits in stroke mice induced by MCAO. The benefits of topically applied menthol were associated with reductions in oxidative stress, neuroinflammation and infiltration of monocytes and macrophages in ischemic brains. Antagonizing TRPM8 or Trpm8 knockout dulls the neuroprotective effects of topically application of menthol against MCAO. Immunohistochemistry analyses revealed significantly higher TRPM8 expression in skin tissue samples obtained from the paws compared with skin from the backs, which was reflected by significantly smaller infarct lesion volumes and better sensorimotor function in mice treated with menthol on the paws compared with the back. Blocking conduction of peripheral nerve in the four paws reversed the neuroprotective effects of topical menthol administrated to paws. On the other hand, oral menthol dosing did not assist with recovery from MCAO in our study. CONCLUSION: Our results suggested that activation of peripheral TRPM8 expressed in the derma tissue of limbs with sufficient concentration of menthol is beneficial to stroke recovery. Topical application of menthol on hands and feet could be a novel and simple-to-use therapeutic strategy for stroke patients.

Clinical Outcomes of Taiwanese Patients with Resected Oral Cavity Squamous Cell Carcinoma Who Underwent Reconstruction with Free Versus Local Flaps.

BACKGROUND: We sought to compare the clinical outcomes of Taiwanese patients with resected oral cavity squamous cell carcinoma (OCSCC) who underwent reconstruction with free versus local flaps. METHODS: From 2011 to 2017, we examined 8646 patients with first primary OCSCC who received surgery either with or without adjuvant therapy. Of these patients, 7297 and 1349 received free and local flap reconstruction, respectively. Two propensity score-matched groups of patients who underwent free versus local flap (n = 1268 each) reconstructions were examined. Margin status was not included as a propensity score-matched variable. RESULTS: Compared with local flaps, patients who received free flaps had a higher prevalence of the following variables: male sex, age < 65 years, pT3-4, pN1-3, p-Stage III-IV, depth ≥ 10 mm, margin > 4 mm, extranodal extension (ENE), and adjuvant therapy (all p < 0.0001). Multivariable analysis identified the reconstruction method (local vs. free flaps, only overall survival [OS]), age ≥ 65 years, pT3-4, pN1-3, p-Stage III-IV, depth ≥ 10 mm (only OS), margins ≤ 4 mm, and ENE as independent adverse prognosticators for disease-specific survival (DSS) and OS. The results of propensity score-matched analyses revealed that, compared with free flaps, patients who underwent local flap reconstruction showed less favorable 5-year DSS (hazard ratio [HR] 1.26, 82%/77%; p = 0.0100) and OS (HR 1.21, 73%/68%; p = 0.0079). CONCLUSIONS: After adjusting for covariates using multivariate models, and also by propensity score modeling, OCSCC patients who underwent free flap reconstruction showed a higher frequency of clear margins and a significant survival advantage compared with those who received local flaps.

Transcriptome analysis in patients with asthma after inhaled combination therapy with long-acting ß2-agonists and corticosteroids.

Introduction: Asthma is one of the major public health problems that imposes a great burden on societal, financial, and healthcare around the world. Asthma poorly affects the health-related quality of life and daily activities of patients. Treatment of asthma, including inhaled corticosteroids (ICS) and long-acting beta-agonists (LABAs), mainly aims to improve the lung function and reduce symptoms and exacerbations. Current treatment regimens are symptom-based strategies, and the status of airway inflammation after treatment is yet unknown. We conducted this study to understand the comprehensive inflammation or airway remodeling status of patients after ICS-LABA treatment through RNA transcriptome analysis. Materials and methods: Eight newly diagnosed asthmatic patients and two healthy subjects were recruited in this study. Asthmatic patients underwent blood tests, lung function test, and RNA transcriptome analysis before and after ICS-LABA treatment. Results: In comparison with healthy subjects, pretreatment asthmatic patients had higher expression of protein tyrosine kinase and related signaling pathways. After ICS-LABA treatment, the expression of nuclear receptor transcription coactivator, N-acetyltransferase, protein tyrosine kinase, nuclear receptor, and RNA polymerase II-activating transcription factor were downregulated. However, the post-treatment asthmatic patients still had higher expression of cysteine-type endopeptidase, endodeoxyribonuclease, apolipoprotein, and unfolded protein was still upregulated than healthy subjects. Conclusions: The combination of ICS/LABAs decreased airway inflammatory and remodeling pathways. However, allergen stimulation-related pathways were still upregulated in patients after ICS/LABA treatment. The combination of medication and allergen removal is a complete strategy for asthma.

Cytomegalovirus viral interleukin-10 in patients with Aspergillus infection and effects on clinical outcome.

BACKGROUND: Human cytomegalovirus (CMV) is associated with aspergillosis, but the simultaneous presence of CMV viral interleukin-10 (cmvIL-10) and aspergillosis has never been investigated. CmvIL-10 is produced by CMV-infected cells and acts as an immune modulator during CMV infection. The aim of this study was to evaluate cmvIL-10 levels in peripheral blood and its influence on the clinical outcomes of Aspergillus infection. METHODS: Patients who visited or were admitted to the hospital with suspected Aspergillus infection, including invasive aspergillosis (IA) and chronic pulmonary aspergillosis (CPA), were prospectively enrolled. The cmvIL-10, human IL-10 (hIL-10), IL-1B, IL-6, IL-8, IFN-γ, and TNF-α levels in peripheral blood were measured. RESULTS: Patients with Aspergillus infection had a higher level of cmvIL-10 than the control group (158 ± 305 vs 27.9 ± 30.4 pg/ml, p < .05). The level of cmvIL-10 was not correlated with CMV viremia or end-organ disease. The cmvIL-10 but not hIL-10 level was positively correlated with the IFN-γ level (p < .05) and marginally negatively correlated with IL-1B and IL-8 levels (p < .1). In patients with CPA, a high level of cmvIL-10 (≥100 pg/ml) was a poor prognostic factor for long-term survival (p < .05). In contrast, CMV viremia or end-organ disease was associated with poor survival in patients with IA (p = .05). CONCLUSIONS: Aspergillus infection was associated with CMV coinfection with cmvIL-10 in blood. A cmvIL-10 concentration ≥100 pg/ml was a predictor for unfavourable outcome in CPA patients.

Postoperative Sore Throat Helps Predict Swallowing Disturbance on Postoperative Day 30 of Anterior Cervical Spine Surgery: A Secondary Exploratory Analysis of a Randomized Clinical Trial of Tracheal Intubation Modes.

Nasotracheal intubation benefits dysphonia recovery after anterior cervical spine surgery (ACSS). The aim of the present study was to investigate the effect of tracheal intubation modes on post-ACSS swallowing function and identify factors associated with deglutition on postoperative day 30 (POD 30). Adult patients were randomized to receive either nasotracheal or orotracheal intubation during surgery. A numerical rating scale (NRS) was used to assess postoperative sore throat, and the Bazaz grading system was used to assess the severity of swallowing disturbance. The primary endpoints were the effect of tracheal intubation modes on postoperative sore throat and deglutition. Thereafter, we further elucidated the predictors of swallowing disturbance on POD 30. Postoperative sore throat and swallowing disturbance did not differ between the nasotracheal and orotracheal intubation groups. A secondary dataset analysis revealed that among 108 patients with complete follow-up until POD 30, 71 (65.7%) presented complete recovery without swallowing disturbance, whereas 37 (34.3%) presented varying degrees of swallowing disturbance. Receiver operating characteristic curve analysis indicated that the NRS score for sore throat predicted a swallowing disturbance-free status on POD 30. The optimal cutoff values were ≤ 4 and ≤ 2 on PODs 1 and 2, respectively. The adjusted odds ratio (OR) for independent predictors was a sore throat NRS score of ≤ 4 on POD 1 (OR 3.2; 95% CI 1.29-7.89; P = 0.012) and score of ≤ 2 on POD 2 (OR 6.67; 95% CI 2.41-18.47; P < 0.001). Therefore, tracheal intubation mode did not affect the incidence of post-ACSS swallowing disturbance, and the severity of sore throat on PODs 1 and 2 could predict a swallowing disturbance-free status on POD 30.The trial was registered at clinicaltrials.gov (Trial No. NCT03240042, date of registration 10/17/2017).

Practice and outcomes of airway management in patients with cervical orthoses.

BACKGROUND/PURPOSE: Increasing evidence indicates an association of video laryngoscopy with the success rate of airway management in patients with neck immobilization. Nevertheless, clinical practice protocols for tracheal intubation in patients immobilized using various types of cervical orthoses and the outcomes remain unclear. METHODS: We retrospectively assessed the tracheal intubation techniques selected for patients immobilized using cervical orthoses from 2015 to 2018. The endpoints were the intubation outcomes of the different techniques and the factors associated with the selection of the technique. RESULTS: We included 218 patients, 118 of whom wore halo vest braces (halo vest group) and 100 wore cervical collars (collar group). GlideScope video laryngoscopy (GVL) and fiberoptic bronchoscopy (FOB) were the initial intubation methods in 98 and 120 patients, respectively. GVL had a higher first-attempt success rate than did FOB in the collar group (p = 0.002) but not in the halo vest group (p = 0.522). GVL was associated with a lower risk of episodes of SaO2< 90% (adjusted relative risk [aRR], 0.11; 95% CI, 0.02-0.67; p = 0.016) and shorter intubation time (aRR, -3.52; 95% CI, -4.79∼-2.25; p < 0.001) in the collar group. However, in the halo vest group, more frequent requirement of a rescue technique (p = 0.002) and necessity of patient awakening (p = 0.001) was noted when GVL was used. Use of the halo vest brace and noting of severe cord compression were independent predictors of the initial selection of FOB. CONCLUSION: Caution should be exercised when using GVL for tracheal intubation in patients immobilized using halo vest braces.

Tumor Suppressor miRNA-503 Inhibits Cell Invasion in Head and Neck Cancer through the Wnt Signaling Pathway via the WNT3A/MMP Molecular Axis.

Head and neck cancer (HNC) is the fifth most common cancer worldwide, and its incidence and death rates have been consistently high throughout the past decades. MicroRNAs (miRNAs) have recently gained significant attention because of their role in the regulation of a variety of biological processes via post-transcriptional silencing mechanisms. Previously, we determined a specific profile of miRNAs associated with HNC using a miRNA microarray analysis. Of the 23 miRNAs with highly altered expression in HNC cells, miR-503 was the most significantly downregulated miRNA. In this study, we confirmed that miR-503 acts as a tumor suppressor, as our results showed decreased levels of miR-503 in cancer cells and patients with HNC. We further characterized the role of miR-503 in the malignant functions of HNC. Although there was a minimal effect on cell growth, miR-503 was found to inhibit cellular invasion significantly. Algorithm-based studies identified multiple potential target genes and pathways associated with oncogenic mechanisms. The candidate target gene, WNT3A, was confirmed to be downregulated by miR-503 at both the mRNA and protein levels and validated by a reporter assay. Furthermore, miR-503 modulated multiple invasion-associated genes, including matrix metalloproteinases (MMPs), through the Wnt downstream signaling pathway. Overall, this study demonstrates that miR-503 suppresses HNC malignancy by inhibiting cell invasion through the Wnt signaling pathway via the WNT3A/MMP molecular axis. The modulation of miR-503 may be a novel therapeutic approach to intervene in cancer invasion.

Very Low-Efficiency Droop in 293 nm AlGaN-Based Light-Emitting Diodes Featuring a Subtly Designed p-Type Layer.

This paper reports an AlGaN-based ultraviolet-B light-emitting diode (UVB-LED) with a peak wavelength at 293 nm that was almost free of efficiency droop in the temperature range from 298 to 358 K. Its maximum external quantum efficiencies (EQEs), which were measured at a current density of 88.6 A cm-2, when operated at 298, 318, and 338 K were 2.93, 2.84, and 2.76%, respectively; notably, however, the current droop (J-droop) in each of these cases was less than 1%. When the temperature was 358 K, the maximum EQE of 2.61% occurred at a current density of 63.3 A cm-2, and the J-droop was 1.52%. We believe that the main mechanism responsible for overcoming the J-droop was the uniform distribution of the concentrations of injected electrons and holes within the multiple quantum wells. Through the subtle design of the p-type AlGaN layer, with the optimization of the composition and doping level, the hole injection efficiency was enhanced, and the Auger recombination mechanism was inhibited in an experimental setting.

PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation.

The performance of data-independent acquisition (DIA) mass spectrometry (MS) depends on the separation efficiency of peptide precursors. In Orbitrap-based mass spectrometers, separation efficiency of peptide precursors is limited by the relatively slow scanning rate compared to time of flight (TOF)-based MS. Here, we present PulseDIA, a multi-injection gas-phase fractionation (GPF) strategy for enhanced DIA-MS. This is achieved by equally dividing the conventional DIA analysis covering the entire mass range into multiple injections for DIA analyses with complementary windows. Using mouse liver digests, the PulseDIA method identified up to 50% more peptides and 29% more protein groups than that by conventional DIA with the same length of effective gradient time. Compared to conventional multi-injection GPF, PusleDIA exhibited higher flexibility and identified up to 18% more peptides and 8% more protein groups using two injections. The gain of peptides per effective time unit was the highest in PulseDIA compared to conventional DIA and GPF. We further applied the PulseDIA method to profile the proteome of 18 human tissue samples (benign and malignant) from nine cholangiocarcinoma (CCA) patients. PulseDIA identified 7796 protein groups in these CCA samples, with a 14% increase of protein group identification compared to the conventional DIA method. The missing value for protein matrix dropped by 7% using PulseDIA compared to DIA. A total of 681 significantly altered proteins were detected in CCA samples using PulseDIA, including several dysregulated proteins, which were absent in the conventional DIA analysis. Taken together, we present PulseDIA as an enhanced DIA-MS method with improved sensitivity and reproducibility.

Computational Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage and Applications to 15 Tumors.

Efficient peptide and protein identifications from data-independent acquisition mass spectrometric (DIA-MS) data typically rely on a project-specific spectral library with a suitable size. Here, we describe subLib, a computational strategy for optimizing the spectral library for a specific DIA data set based on a comprehensive spectral library, requiring the preliminary analysis of the DIA data set. Compared with the pan-human library strategy, subLib achieved a 41.2% increase in peptide precursor identifications and a 35.6% increase in protein group identifications in a test data set of six colorectal tumor samples. We also applied this strategy to 389 carcinoma samples from 15 tumor data sets: up to a 39.2% increase in peptide precursor identifications and a 19.0% increase in protein group identifications were observed. Our strategy for spectral library size optimization thus successfully proved to deepen the proteome coverages of DIA-MS data.

Signal and noise analysis for chiral structured illumination microscopy.

Recently, chiral structured illumination microscopy has been proposed to image fluorescent chiral domains at sub-wavelength resolution. Chiral structured illumination microscopy is based on the combination of structured illumination microscopy, fluorescence-detected circular dichroism, and optical chirality engineering. Since circular dichroism of natural chiral molecules is typically weak, the differential fluorescence is also weak and can be easily buried by the noise, hampering the fidelity of the reconstructed images. In this work, we systematically study the impact of the noise on the quality and resolution of chiral domain images obtained by chiral SIM. We analytically describe the signal-to-noise ratio of the reconstructed chiral SIM image in the Fourier domain and verify our theoretical calculations with numerical demonstrations. Accordingly, we discuss the feasibility of chiral SIM in different experimental scenarios and propose possible strategies to enhance the signal-to-noise ratio for samples with weak circular dichroism.

Structured illumination microscopy for simultaneous imaging of achiral and chiral domains.

We propose double structured illumination microscopy (SIM) method, which enables simultaneous imaging of achiral and chiral domains at sub-wavelength resolution. In double SIM, the illumination field is spatially structured both in the intensity and optical chirality so that moiré effects can be concurrently generated on the achiral and chiral fluorescent domains of a sample. This allows for down-modulating the high spatial frequency of both domains at the same time and thus provides sub-wavelength details after image reconstruction. We introduce the working principle of double SIM and theoretically demonstrate the feasibility of this method using different kinds of synthetic samples.

Deletion of intestinal SIRT1 exacerbated muscle wasting in cirrhotic mice by decreasing the intestinal concentration of short-chain fatty acids and inflammation.

Systemic sirtuin 1 (SIRT1) activation alleviates muscle wasting and improves muscle function by downregulation of myotropic and proteolytic markers. In this study, we evaluated the effects of the intestinal Sirt1 deletion on the dysregulated gutmuscle axis in cirrhotic mice. Cirrhosis-related muscle wasting was induced by common bile duct ligated (BDL) in either wild-type (WT) or intestine-specific Sirt1-deleted (Sirt1IEC-KO) mice, including WT-BDL, WT-sham, Sirt1IEC-KO-BDL and Sirt1IEC-KO-sham mice. Compared with WT-BDL mice, Sirt1IEC-KO-BDL mice showed worsened low lean mass, exacerbated muscle wasting, increased expression of myotropic markers, increased muscular protein degradation, and decreased expression of myogenic markers through aggravation of intestinal inflammation (as evidenced by increased fecal calprotectin/lipocalin-2 levels, increased intestinal macrophage infiltration, and increased intestinal TNFα/IL-6 levels), decrease in abundance of short-chain fatty acid (SCFA)-producing bacteria, decrease in levels of intestinal SCFAs (with anti-inflammatory effects), and downregulation of SCFA receptor GPR43. In biliary cirrhotic mice, a decrease in the abundance of SCFA-producing bacteria and an increase in the levels of intestinal/muscular inflammatory markers are involved in the pathogenesis of dysregulated gut-muscle axis-related muscle wasting, and intestinal deletion of Sirt1 exacerbated these changes.