Contrasting response of comammox Nitrospira, ammonia oxidising bacteria, and archaea to soil pH and nitrogen inputs

This study aimed to investigate the effect of soil pH change, and nitrogen amendment on ammonia oxidiser abundance and comammox Nitrospira community composition. The experimental design used soil mesocosms placed in a temperature-controlled incubator for 90 days. A Templeton silt loam was used as its physiochemical properties are typical of the region's dairy farms. The results showed that comammox Nitrospira clade B preferred the natural (pH 6.1-6.2) soil pH with no applied nitrogen. Furthermore, synthetic urine (N700) decreased the abundance of comammox Nitrospira clade B. This may have been because the large amounts of available ammonia in the N700 treatments inhibited the growth of comammox Nitrospira. These results suggest that while comammox Nitrospira clade B are present in New Zealand dairy farm soils, but their role in nitrification in the very high nitrogen environment under a urine patch in grazed pastures may be limited. Further research is needed to confirm this. In contrast to comammox, the AOB community (dominated by Nitrosospira) responded positively to the application of synthetic urine. The response was greatest in the high pH soil (7.1), followed by the natural and then the low pH (4.9) soils. This may be due to the difference in ammonia availability. At high pH, the ammonia/ammonium equilibrium favours ammonia production. Calculated ammonia availability in the N700 treatments accurately predicted the AOB amoA gene abundance. Interestingly, the AOA community abundance (which was predominantly made up of Thaumarchaeota group I.1b clade E) seemed to prefer the natural and high pH soils over the low pH. This may be due to the specific lineage of AOA present. AOA did not respond to the application of nitrogen.

Site-Specific Analysis of Core and Antenna Fucosylation on Serum Glycoproteins

Fucosylation is an important structural feature of glycans and plays an essential role in the regulation of glycoprotein functions. Fucosylation can be classified into core- (CF) and antenna-fucosylation (AF, also known as (sialyl-) Lewis) based on the location on N-glycans, and they perform distinct biological functions. In this study, core- and antenna-fucosylated N-glycans on human serum glycoproteins that hold great clinical application values were systematically characterized at the site-specific level using StrucGP combined with the recently developed fucosylation assignment method. The results showed that fucosylation was widely distributed on serum glycoproteins, with 50% of fucosylated glycopeptides modified by AF N-glycans, 37% by CF N-glycans, and 13% by dual-fucosylated N-glycans. Interestingly, CF and AF N-glycans preferred to modify different groups of serum glycoproteins with different tissue origins and were involved in distinctive biological processes. Specifically, AF N-glycoproteins are mainly from the liver and participated in complement activation, blood coagulation, and endopeptidase activities, while CF N-glycoproteins originate from diverse tissues and are mainly involved in cell adhesion and signaling transduction. These data further enhanced our understanding of fucosylation on circulation glycoproteins.

Interaction between handgrip strength and vitamin D deficiency on all-cause mortality in community-dwelling older adults: a prospective cohort study

OBJECTIVE

Muscle strength decline and vitamin D deficiency are coexisting conditions associated with multiple adverse health outcomes. This prospective study aimed to investigate the multiplicative and additive interactions between handgrip strength (HS) and serum 25-hydroxyvitamin D [25(OH)D] on all-cause mortality in Chinese community-dwelling older adults.

STUDY DESIGN

This is a population-based cohort study.

METHODS

2635 older adults (85.15 ± 12.01 years) were recruited from the Chinese Longitudinal Healthy Longevity Survey (2012-2018). Low HS was defined according to the Asian Working Group for Sarcopenia 2019 updated consensus (<28 kg for men and <18 kg for women). Serum 25(OH)D < 50 nmol/L were defined as vitamin D deficiency. Cox proportional hazard models were used to examine the association of HS and 25(OH)D with all-cause mortality. Socio-demographics, health status, and clinical characteristics were included as covariates.

RESULTS

1715 (65.09 %) and 1885 (71.54 %) participants had low HS and vitamin D deficiency, respectively. During a median follow-up of 3.52 years, 1107 older people died. After multivariable adjustment, both HS and 25(OH)D levels were inversely associated with all-cause mortality risk (Ps < 0.001). The hazard ratios (HRs) of low HS and vitamin D deficiency for all-cause mortality were 1.73 (95 % CI: 1.41-2.13) and 1.61 (95 % CI: 1.32-1.93), respectively. Although significant multiplicative interactions were not found, the association between low HS and all-cause mortality was attenuated in the higher 25(OH)D subgroup than in the lower 25(OH)D subgroup (stratified by 50 nmol/L). The multiple-adjusted HR of mortality for combined low HS and vitamin D deficiency was 2.18 (95 % CI: 1.73-2.56), which was higher than that for these two conditions alone. Significant additive interactions between low HS and vitamin D deficiency on mortality were observed (relative excess risk due to interaction: 0.71, 95 % CI: 0.37-1.05).

CONCLUSIONS

Low HS and low 25(OH)D levels synergistically increased the risk of all-cause mortality. Our results added new insights to the priority of early detection for older adults with comorbid muscle strength decline and vitamin D deficiency.

Clinically Oriented CBCT Periapical Lesion Evaluation via 3D CNN Algorithm

Apical periodontitis (AP) is one of the most prevalent disorders in dentistry. However, it can be underdiagnosed in asymptomatic patients. In addition, the perioperative evaluation of 3-dimensional (3D) lesion volume is of great clinical relevance, but the required slice-by-slice manual delineation method is time- and labor-intensive. Here, for quickly and accurately detecting and segmenting periapical lesions (PALs) associated with AP on cone beam computed tomography (CBCT) images, we proposed and geographically validated a novel 3D deep convolutional neural network algorithm, named PAL-Net. On the internal 5-fold cross-validation set, our PAL-Net achieved an area under the receiver operating characteristic curve (AUC) of 0.98. The algorithm also improved the diagnostic performance of dentists with varying levels of experience, as evidenced by their enhanced average AUC values (junior dentists: 0.89-0.94; senior dentists: 0.91-0.93), and significantly reduced the diagnostic time (junior dentists: 69.3 min faster; senior dentists: 32.4 min faster). Moreover, our PAL-Net achieved an average Dice similarity coefficient over 0.87 (0.85-0.88), which is superior or comparable to that of other existing state-of-the-art PAL segmentation algorithms. Furthermore, we validated the generalizability of the PAL-Net system using multiple external data sets from Central, East, and North China, showing that our PAL-Net has strong robustness. Our PAL-Net can help improve the diagnostic performance and speed of dentists working from CBCT images, provide clinically relevant volume information to dentists, and can potentially be applied in dental clinics, especially without expert-level dentists or radiologists.

Q-TWiST analysis of survival benefits with brigatinib versus crizotinib in patients with anaplastic lymphoma kinase-positive non-small cell lung cancer based on results of the ALTA-1L trial

OBJECTIVES

The ALTA-1L phase 3 open-label trial demonstrated increased progression-free survival (PFS) with brigatinib versus crizotinib in patients with anaplastic lymphoma kinase-positive (ALK-positive) locally advanced or metastatic non-small cell lung cancer (NSCLC) previously untreated with ALK-targeted therapy. This post-hoc analysis of data from the ALTA-1L trial used the quality-adjusted (QA) time without symptoms of disease or toxicity (Q-TWiST) methodology to compare the QA survival benefit of brigatinib versus crizotinib in this patient population.

PATIENTS AND METHODS

The Q-TWiST analysis was performed using final (January 29, 2021) individual patient-level blinded independent review committee (BIRC)- and investigator-assessed survival data for brigatinib (n = 137) and crizotinib (n = 138) in adult patients (N = 275) with ALK-positive locally advanced or metastatic NSCLC previously untreated with ALK-targeted therapy. Q-TWiST was compared between the two treatments. Subgroup analyses were performed in patients stratified by various clinicopathological characteristics, including presence or absence of brain metastases at baseline.

RESULTS

Brigatinib was associated with significantly longer time without symptoms of disease or toxicity (P < 0.001) than crizotinib, with significantly greater Q-TWiST (mean [SE] months: BIRC-assessed, 28.2 [1.2] versus 25.1 [1.1], P = 0.045; investigator-assessed, 28.5 [1.2] versus 24.8 [1.1], P = 0.018). Relative gains in Q-TWiST with brigatinib compared to crizotinib were clinically meaningful (BIRC-assessed, 10.4%; investigator-assessed, 12.3%). Patients with brain metastases at baseline receiving brigatinib had significantly greater Q-TWiST (mean [SE] months: BIRC-assessed, 29.0 [1.9] versus 19.0 [1.9], P = 0.0001) than those receiving crizotinib.

CONCLUSION

First-line brigatinib treatment was associated with significant and clinically meaningful gains in Q-TWiST compared to crizotinib in patients with ALK-positive locally advanced or metastatic NSCLC, supporting the results of the ALTA-1L trial and brigatinib as a safe and effective first-line treatment for ALK-positive NSCLC.

Maximal performance of intact N-glycopeptide enrichment using sequential HILIC and MAX columns

Low abundance and heterogeneity of N-glycosylation at the peptide level poses a great challenge to the structural and functional analysis of glycosylation in the field of glycobiology. Solving this conundrum requires a sufficient and specific method for intact N-glycopeptide enrichment. Using the C18 or HLB desalting column followed by the mixed-mode strong anion exchange (MAX) or hydrophilic interaction chromatography (HILIC) glycopeptide enrichment column are commonly applied approaches for sample preparation of intact N-glycopeptides from complex samples. Herein, we compared the effects of different combinations of two desalting columns and two enrichment columns using equal amounts of mouse brain tissues from the same source. The results revealed the C18 column was a bit superior to the HLB column, and the MAX and HILIC columns were complementary on intact N-glycopeptides enrichment. Additionally, the results also demonstrated that enriching glycopeptides using a HILIC column followed by a MAX column from the flow-through solution got a better enrichment performance than the reversed order. Based on these results, the sequential enrichment of glycopeptides using HILIC and then MAX columns could maximize the enrichment performance of intact N-glycopeptides, and therefore is an option for in-depth analysis of site-specific glycoproteome.

PSMA PET Guided Salvage Radiotherapy Among Prostate Cancer Patients in the Post-Prostatectomy Setting: A Single Center Post-Hoc Analysis

PURPOSE/OBJECTIVE(S)

Prostate-specific membrane antigen (PSMA) positron emission tomography (PET) shows improved sensitivity and specificity for detection of locoregional and distant metastatic prostate cancer (PCa) compared to conventional imaging, especially at lower PSA levels as is often the case in the biochemically recurrent (BCR), post radical prostatectomy (RP) setting. Providers are now utilizing PSMA PET findings to guide their salvage radiotherapy (sRT) treatment fields and doses, although it is not well understood how PSMA PET guided sRT impacts patient outcomes.

MATERIALS/METHODS

This was a post-hoc analysis of 5 prospective studies of PSMA PET conducted at UCLA from 2016 to 2021 that included patients with recurrent PCa following RP. Patients were included in this retrospective study if they initiated sRT within 3 months of PSMA PET, had at least 12 months of follow up after sRT completion, had available sRT treatment details, and did not have distant metastases (DM) by conventional imaging on upfront staging. Patients treated with palliative RT were excluded. BCR following sRT was defined as an increase in PSA of 0.2 ng/ml above the post sRT nadir. Metastasis directed therapy (MDT) was defined as sRT to all PSMA+ N1 and M1 lesions. Baseline patient demographics, PSMA PET findings, sRT & ADT treatment details, and patient outcome data were collected.

RESULTS

A total of 176 patients were included in this study. Median time between RP and PSMA PET was 38 months (range 1-329). Median PSA at the time of the PSMA PET was 0.625 ng/mL (range 0.063-35). PSMA PET was positive in 128 patients (73%): 21 (12%) miT+N0M0, 55 (31%) miTxN1M0 and 52 (30%) miTxNxM1 with 19 (11%) miTxNxM1a, 31 (18%) miTxNxM1b, and 2 (1%) miTxNxM1c. Median number of lesions seen on positive PSMA scans was 1 (range 1-8). 39 (22%) patients were subsequently treated with sRT to the prostate bed (PB) only, 59 (34%) to PB + pelvic lymph nodes (PLNs), 33 (19%) to PLNs only, 7 (4%) to PB + PLNs + DM, 7 (4%) to PLNs + DM, and 31 (18%) to DM only. 59 (34%) patients were treated with concurrent ADT at a median duration of 6 months (range 1-39). At a median follow-up of 32 months (range 12-70) after sRT, 80 patients (45%) did not develop BCR or imaging relapse (IR) following sRT, 24 patients (14%) developed BCR but not IR, 1 patient (<1%) developed IR only, and 70 patients (40%) developed both BCR and IR. The median time to BCR and IR following sRT was 15 months (range 1-48) and 19 months (range 6-61), respectively. 1 year post sRT biochemical recurrence free survival was 77%. Of the 83 patients treated with MDT, 32 (39%) did not develop subsequent disease relapse.

CONCLUSION

This post hoc analysis assessed the outcomes of 176 patients treated with PSMA PET guided salvage RT, proving it to be an effective method for treating both pelvic and extrapelvic recurrent PCa. Further investigation is needed to assess the full extent of patient outcomes in this population.

Dose DIBH Really Reduce the Subclinical Cardiac Acute Injury? Analysis of Clinical Real World from Our Institute

PURPOSE/OBJECTIVE(S)

The study is aim to investigate whether Deep-inspirational breath-hold (DIBH), compared with free breathing (FB), could provide a short-term cardiac benefit in patients with early left breast cancer after breast-conserving surgery combined whole breast radiotherapy.

MATERIALS/METHODS

A total of 78 patients with early stage left breast cancer treated with radiotherapy between 2021-2022 after breast-conserving surgery were enrolled. Among them, 32 cases were treated with DIBH technique and 46 cases were treated with free breathing. Patients with previous cardiac disease such as coronary artery disease were excluded. We performed myocardial enzymes, ECG, and ECHO in all patients within 2 weeks before, during, and 6 months after radiotherapy. The results of the two groups were compared using nonparametric tests and chi-square tests, and P < 0.05 indicated statistical significance. Where subclinical acute cardiac injury was defined as new above-normal myocardial enzymes and/or electrocardiographic ST-T or T-wave changes and/or ECHO abnormalities after the start of radiotherapy.

RESULTS

The median follow-up of patients was 6 months and the mean age of patients was 52.3 years for FB and 44.9 years for DIBH. There were no significant differences in staging, molecular subtype, chemotherapy and endocrine therapy history. The proportion of subclinical acute cardiac injury was smaller in the DIBH group compared to the FB group (DIBH = 31/46 and FB = 28/32, p = 0.042). The most sensitive of the subclinical acute cardiac injury events were detected by myocardial enzymes rising, with cTnI (p = 0.034) and NT-proBNP (p = 0.023) appearing significantly lower in the DIBH patients during radiotherapy. The difference of cTnI between 2 groups at 6 months after radiotherapy became non-significant. In contrast, CK-MB was higher in DIBH compared with FB only 6 months after radiotherapy (p = 0.006). The differences in ECG and ECHO were not significant between the two groups.

CONCLUSION

After breast-conserving surgery combined with radiotherapy for left early breast cancer, DIBH compared to FB reduces the proportion of acute subclinical cardiac injury that occurs with the most sensitive changes in myocardial enzymes. Subsequent studies will explore the relationship between the short-term subclinical injury and irradiated dose, as well as long term cardiac injury.

Tolerability of Metastasis-Directed Stereotactic Body Radiotherapy with Short-Course Triple-Agent Androgen Annihilation Therapy in Recurrent Oligometastatic Prostate Cancer: Secondary Analysis of a Phase II Study

PURPOSE/OBJECTIVE(S)

A majority of patients with oligometastatic prostate cancer experience relapse within 12 months of metastasis-directed therapy. Intense, triple-agent androgen annihilation therapy (AAT) with leuprolide, abiraterone acetate plus prednisone (AAP), and apalutamide may improve efficacy, but long courses of AAT have been shown to be associated with increased rates of grade≥3 toxicity. The purpose of this secondary analysis of this study is to characterize the tolerability of a short, six-month course of AAT added to metastasis-directed therapy.

MATERIALS/METHODS

All 28 patients enrolled on this phase II study were included in this analysis. All patients had oligometastatic prostate cancer after initial radical prostatectomy, defined by the presence of 1-5 extrapelvic metastases on prostate-specific membrane antigen (PSMA) PET/CT. Patients were started on six months of AAT. After the first month, patients received stereotactic body radiotherapy (SBRT) in 1, 3, or 5 fractions to metastases with or without radiotherapy to the prostate bed and pelvic lymph nodes. Physician-scored toxicities were graded according to Common Terminology Criteria for Adverse Events (CTCAE), Version 5.0.

RESULTS

Median follow-up time was 11.4 months. Twenty patients (71.4%) completed AAT with all three agents. Six patients (21.4%) completed six months of therapy but discontinued at least one agent [4 patients (14.3%) discontinued apalutamide, 1 patient (3.6%) discontinued AAP, and 1 patient (3.6%) discontinued both apalutamide and AAP]. Two patients (7.1%) withdrew from the trial due to adverse events and did not complete therapy. Grade 2 and grade 3 toxicity rates from AAT were each 21.4%. Of the 6 cases of grade 3 toxicity, 3 were skin rashes, 2 were hypertension, and 1 was hepatic toxicity. At the time of SBRT, 1 patient had withdrawn from the study and 1 patient declined radiation therapy. All 26 remaining patients completed SBRT. Grade 2 and grade 3 toxicity rates from SBRT were 7.7% and 0%, respectively.

CONCLUSION

A majority of patients were able to tolerate and complete AAT in combination with metastasis-directed SBRT. Some patients experienced acute grade 3 toxicities, the most common being drug-related skin rashes and hypertension. While efficacy data are needed to evaluate the oncologic benefit, these data suggest a short course of AAT is considerably better tolerated than longer courses of AAT, with grade 3 toxicity rates similar to long courses of single-agent androgen deprivation therapy alone.

The Role of Radiotherapy in Patients with Refractory Hodgkin Lymphoma after Brentuximab Vedotin and -/or Immune Checkpoint Inhibitors

PURPOSE/OBJECTIVE(S)

Brentuximab vedotin (BV) and immune checkpoint inhibitors (ICIs) had important roles in the treatment of relapse or refractory (R/R) Hodgkin lymphoma (HL). Treatment of refractory disease after BV and -/or ICIs remains a challenge. This study was conducted to evaluate the efficacy and safety of radiotherapy for R/R HL after failure to BV or ICIs.

MATERIALS/METHODS

We retrospectively analyzed patients in two institutions with R/R HL who had failed after first-line therapy, and were refractory to BV or ICIs, and received radiotherapy (RT) thereafter. The overall response rate (ORR), duration of response (DOR), progression-free survival (PFS) and overall survival (OS) were analyzed.

RESULTS

A total of 19 patients were enrolled. First-line systemic therapy consisted of ABVD (84.2%), AVD + ICIs (10.5%) and BEACOPP (5.3%), respectively. After first-line therapy, 15 patients (78.9%) were refractory, and 4 patients (21.1%) relapsed. After diagnosis of R/R HL, 8 patients (42.1%) received BV, and 17 patients (89.5%) received ICIs. RT was delivered in all 19 patients who failed after BV or ICIs. In 16 efficacy-evaluable patients, the ORR and CR rate were 100% and 100%. The median DOR was 17.2 months (range, 7.9 to 46.7 months). 3 patients progressed at outside of the radiation field. The in-field-response rate was 100%. The 12-month PFS and OS were 84.4% and 100%, respectively. No patients were reported with sever adverse events.

CONCLUSION

This study concluded that radiotherapy was effective and safe for refractory HL after BV or ICIs. Further prospective studies were warranted.

Postoperative Radiotherapy to Abdominal and Pelvic Lymphatic Drainage Area for Stage III Epithelial Ovarian Cancer: A Sharp Tool to Prolong Disease-Free Survival Time

PURPOSE/OBJECTIVE(S)

For patients with stage III epithelial ovarian cancer, there are limited studies on the effects of postoperative adjuvant radiotherapy (RT) after standard cytoreductive surgery (CRS) and full treatment of first-line adjuvant chemotherapy (CT). The aims of our study were to assess the therapeutic efficacy and toxicity of our special postoperative radiotherapy to abdominal and pelvic lymphatic drainage area for stage III epithelial ovarian cancer patients.

MATERIALS/METHODS

We retrospectively collected patients with stage III epithelial ovarian cancer after CRS and full-course adjuvant chemotherapy. The CT+RT group patients were treated with intensity modulated radiotherapy (IMRT) to abdominal and pelvic lymphatic drainage area (which has been shown to be an alternative to whole abdominal radiotherapy (WART) both on the basis of clinical result and dosimetric verification from our prior study). The CT group data was obtained from the PUMCH's electronic medical record analytical database between 2010 and 2020. A propensity score matching analysis was performed 1:2 between CT+RT group and CT group.

RESULTS

A total of 132 patients with median follow-up of 73.9 months (9.1-137.7 months) were included (44 and 88 for the CT+RT and CT groups, retrospectively). The baseline characteristics of age, histology, level of CA12-5, surgical staging, residual tumor, courses of adjuvant CT, and courses to reduce CA12-5 to normal were all balanced. The median disease-free survival (DFS) time, 5-year overall survival (OS), and local recurrence free survival (LRFS) of CT+RT group and CT group were 100.0 months versus 25.9 months (p = 0.020), 69.2% versus 49.9% (p = 0.002), 85.9% versus 50.5% (p = 0.020), respectively. Distant metastasis was still the primary reason (57.6%), and local failure rate was 42.3%, the local recurrence rate was significantly lower in CT+RT group, compared with CT group (13.6% versus 45.5%, p = 0.016). In terms of toxicity, CT+RT group mainly presented with acute hematological toxicities, with no statistically significant difference with CT group when compared with grade III intestinal adverse effects (3/44 versus 6/88, p = 0.480).

CONCLUSION

This report demonstrates that long-term disease-free survival could be achieved in stage III epithelial ovarian cancer patients treated with IMRT preventive radiation to abdominal and pelvic lymphatic area. Compared with CT group, DFS and OS were significantly prolonged and adverse effects were acceptable.

Randomized evaluation of an online single-session intervention for minority stress in LGBTQ+ adolescents

Background

LGBTQ+ youth face myriad adverse health outcomes due to minority stress, creating a need for accessible, mechanism-targeted interventions to mitigate these minority stress-related risk factors. We tested the effectiveness and acceptability of Project RISE, an online single-session intervention designed to ameliorate internalized stigma and improve other outcomes among LGBTQ+ youth. We hypothesized that youth assigned to RISE (versus a control) would report significantly reduced internalized stigma and increased identity pride at post-intervention and at two-week follow-up and would find RISE acceptable.

Methods

We recruited adolescents nationally through Instagram advertisements in May 2022 (N = 538; M age = 15.06, SD age = 0.97). Participants were randomly assigned to RISE or an information-only control and completed questionnaires pre-intervention, immediately post-intervention, and two weeks post-intervention. Inclusion criteria included endorsing: (1) LGBTQ+ identity, (2) age 13-16, (3) English fluency (4) Internet access, and (5) subjective negative impact of LGBTQ+ stigma.

Results

Relative to participants in the control condition, participants who completed RISE reported significant decreases in internalized stigma (d = -0.49) and increases in identity pride (d = 0.25) from pre- to immediately post-intervention, along with decreased internalized stigma (d = -0.26) from baseline to two-week follow-up. Participants rated both RISE and the information-only control as highly, equivalently acceptable.

Conclusions

RISE appears to be an acceptable and useful online SSI for LGBTQ+ adolescents, with potential to reduce internalized stigma in both the short- and longer-term. Future directions include evaluating effects of Project RISE over longer follow-ups and in conjunction with other mental health supports.

Prevalence, drivers and surveillance of antibiotic resistance and antibiotic use in rural China: Interdisciplinary study

This study aimed to characterise antibiotic prescribing and dispensing patterns in rural health facilities in China and determine the community prevalence of antibiotic resistance. We investigated patterns and drivers of antibiotic use for common respiratory and urinary tract infections (RTI/UTI) in community settings, examined relationships between presenting symptoms, clinical diagnosis and microbiological results in rural outpatient clinics, and assessed potential for using patient records to monitor antibiotic use. This interdisciplinary mixed methods study included: (i) Observations and exit interviews in eight village clinics and township health centres and 15 retail pharmacies; (ii) Urine, throat swab and sputum samples from patients to identify potential pathogens and test susceptibility; (iii) 103 semi-structured interviews with doctors, patients, pharmacy workers and antibiotic-purchasing customers; (iv) Assessment of completeness and accuracy of electronic patient records through comparison with observational data. 87.9% of 1123 recruited clinic patients were prescribed antibiotics (of which 35.5% contained antibiotic combinations and >40% were for intravenous administration), most of whom had RTIs. Antibiotic prescribing for RTIs was not associated with presence of bacterial pathogens but was correlated with longer duration of infection (OR = 3.33) and presence of sore throat (OR = 1.64). Fever strongly predicted prescription of intravenous antibiotics (OR = 2.87). Resistance rates in bacterial pathogens isolated were low compared with national data. 25.8% of patients reported antibiotics use prior to their clinic visit, but only 56.2% of clinic patients and 53% of pharmacy customers could confirm their prescription or purchase included antibiotics. Diagnostic uncertainty, financial incentives, understanding of antibiotics as anti-inflammatory and limited doctor-patient communication were identified as key drivers of antibiotic use. Completion and accuracy of electronic patient records were highly variable. Prevalence of antibiotic resistance in this rural population is relatively low despite high levels of antibiotic prescribing and self-medication. More systematic use of e-records and in-service training could improve antibiotic surveillance and stewardship in rural facilities. Combining qualitative and observational anthropological methods and concepts with microbiological and epidemiological investigation of antibiotic resistance at both research design and analytic synthesis stages substantially increases the validity of research findings and their utility in informing future intervention development.

[Membrane anatomy-based splenic hilar lymph node dissection for gastric cancer]

There is a consensus that selectively perform splenic lymph node dissection is necessary for high-risk patients with proximal gastric cancer to achieve radical treatment. However, there are still some outstanding issues that need to be solved during the practice of splenic lymph node dissection. These include poorly defined boundaries, technical difficulties, and blurred boundaries in No. 10 and No. 11 lymph nodes, etc. Membrane anatomy has achieved successful applications in the field of gastric and colorectal surgery in recent years. The study of membrane anatomy in the splenic hilum region is controversial due to the special location of the splenic hilum, which involves multiple organs and affiliated mesentery undergoing complex rotation, folding, and fusion during embryonic development. In this manuscript, we summarize the following points based on existing research and personal experience regarding membrane anatomy. 1. There is a membrane anatomical structure that can be used for lymph node dissection in the splenic hilum region. 2. The membrane structure in the splenic hilum region can be divided into two layers: the superficial layer is composed of the dorsal mesogastrium, and the deep layer is composed of Gerota fascia, the tail of the pancreas, and the mesentery of the transverse colon (from head to tail). 3. There is a loose space between the two layers that can be used for separation during surgery. The resection of the dorsal mesogastrium belongs to D2 dissection. The No. 10 lymph node in the deeper layer belongs to the duodenal mesentery, and the resection of the No.10 lymph node exceeds D2 dissection. The complete excision of the gastric dorsal mesentery is consistent with the D2+CME surgical mode proposed by Gong Jianping's group.

[Development of membrane anatomy theory in gastric cancer surgery]

In the past decade, the concept of membrane anatomy has been gradually applied in gastric cancer surgery. Based on this theory, D2 lymphadenectomy plus complete mesogastric excision (D2+CME) has been proposed, which has been demonstrated to significantly reduce intraoperative bleeding and intraperitoneal free cancer cells during surgery, decrease surgical complications, and improve survival. These results indicate that membrane anatomy is feasible and efficacious in gastric cancer surgery. In this review, we will describe the important contents of membrane anatomy, including "Metastasis V"(2013, 2015), proximal segmentation of dorsal mesogastrium (2015), D2+CME procedure (2016), "cancer leak"(2018), and surgical outcomes of D2+CME (2022).

Glycoproteomic analysis of regulatory effects of bisecting N-glycans on N-glycan biosynthesis and protein expressions in human HK-2 cells

Bisecting N-glycan is known to be a metastasis suppressor and plays a regulatory role in the biosynthesis of N-glycans. Previous studies have shown that bisecting N-glycans are capable of modulating both the branching and terminal modifications of glycans. However, these effects have been investigated mainly by glycomic approaches and it remains unclear how they alter when glycans are attached to different glycosites of proteins. Here, we systematically investigated the regulatory roles of bisecting N-glycans in human HK-2 cells using StrucGP, a strategy we developed for structural interpretation of site-specific N-glycans on glycoproteins. The glycoproteomics analysis showed that most of bisecting N-glycans are complex type and often occur in company with core fucosylation. With the overexpression and knockdown of MGAT3, the only enzyme responsible for bisecting N-glycan synthesis, we found that bisecting N-glycans can impact the biosynthesis of N-glycans from multiple aspects, including glycan types, branching, sialylation, fucosylation (different effects for core and terminal fucosylation) as well as the presence of terminal N-acetylglucosamine. Furthermore, gene ontology analysis suggested that most proteins with bisecting N-glycans located in the extracellular region or membrane, where they function mostly in cell adhesion, extracellular matrix regulation and cell signaling. Finally, we showed that overexpression of bisecting N-glycans had a broad impact on the protein expressions of HK-2 cells, involving multiple biological processes. Taken together, our work systematically demonstrated the expression profiles of bisecting N-glycans, and their regulatory effects on the biosynthesis of N-glycans and protein expressions, which provide valuable information for the functional elucidation of bisecting N-glycans.

Independent and combined associations of upper and lower limb strength with all-cause mortality in community-based older adults: findings from the Chinese Longitudinal Healthy Longevity Survey

OBJECTIVE

With the acceleration of aging progress, China is projected to have the largest older population globally. This study aimed to examine the association of upper limb strength (ULS) and lower limb strength (LLS) with all-cause mortality based on the Chinese Longitudinal Healthy Longevity Survey (2012-2018).

STUDY DESIGN

This is a prospective cohort study.

METHODS

Participants were 2442 older adults (aged 84.98 ± 11.94 years) recruited from eight longevity areas in China. Limb muscle strength was evaluated using handgrip strength and objective physical examinations. Cox proportional hazards regression was used to analyze the association of limb muscle strength with all-cause mortality. Demographic characteristics, health status, and biological markers were included as confounders.

RESULTS

Over a median follow-up period of 42.2 months, 993 older people died. After adjusting for all covariates, low ULS was associated with higher mortality risk (hazard ratio [HR] = 1.51, 95% confidence interval [CI] = 1.25-1.84), and the association of low LLS with all-cause mortality was only significant in women (HR = 1.36, 95% CI = 1.04-1.79). Participants with combined low ULS and low LLS had the highest risk of mortality than those with normal limb muscle strength (hazard ratio = 2.06, 95% confidence interval = 1.61-2.63). The combined association of ULS and LLS with mortality was robust in subgroup and sensitivity analyses.

CONCLUSION

Low ULS and low LLS were independently and synergistically associated with higher all-cause mortality risk. Considering the high prevalence of limb muscle weakness among Chinese older adults, especially the oldest-old, limb strength could be considered as a potential doable mortality predictor for community health care.

[Characteristics of plasma Epstein-Barr virus DNA in children with primary infection]

Objective: To explore the characteristics of plasma Epstein-Barr virus (EBV) DNA in primary infection in pediatric cases. Methods: The laboratory and clinical data of 571 children diagnosed with EBV primary infection in Children's Hospital of Fudan University during September 1^st, 2017 to September 30^th, 2018 were retrospectively analyzed. According to the results of plasma EBV DNA, they were divided into positive group and negative group. According to the EBV DNA, they were devided into high plasma virol load group and low plasma virol load group. The Chi-square test, Wilcoxon rank sum test were used to compare the differences between groups. Results: Among the 571 children with EBV primary infection, 334 were males and 237 were females. The age of first diagnosis was 3.8 (2.2, 5.7) years. There were 255 cases in positive group and 316 cases in negative group. The percentage of cases with fever,hepatomegaly and (or) splenomegaly, elevated transaminase in the positive group were higher than those in the negative group (235 cases (92.2%) vs. 255 cases (80.7%), χ²=15.22, P<0.001; 169 cases (66.3%) vs. 85 cases (26.9%), χ²=96.80, P<0.001; and 144 cases (56.5%) vs. 120 cases (38.0%), χ²=18.27, P<0.001; respectively).In the positive group, 70 cases were followed up for 46 (27, 106) days, 68 cases (97.1%) turned negative within 28 days, with the exception of 2 cases (2.9%) developed chronic active EBV infection by follow-up revision.There were 218 cases in high plasma viral DNA copies group and 37 cases in low copies group. More cases presented with elevated transaminases in the high plasma viral DNA copies group than those in the low group (75.7% (28/37) vs. 56.0%(116/207), χ²=5.00, P=0.025).Both the positive rate of EBV DNA in peripheral blood leukocytes (84.2% (266/316) vs. 44.7% (255/571), χ²=76.26, P<0.001) and the copies of EBV DNA (7.0×10⁷ (1.3×10⁷, 3.0×10⁸) vs. 3.1×10⁶ (1.6×10⁶, 6.1×10⁶) copies /L, Z=15.23, P<0.001) were higher than that of plasma. Conclusions: In immunocompetent pediatric cases diagnosed as EBV primary infection, cases with positive plasma EBV DNA were prone to have fever, hepatomegaly and (or) splenomegaly, and elevated transaminase than those with negative plasma viral DNA. The plasma EBV DNA usually turns negative within 28 days after initial diagnosis.Most cases with high viral load in plasma showed elevated aminotransferase.

[Clinical characteristics of anomalous aortic origin of a coronary artery in children]

Objective: To analyze the clinical characteristics, diagnosis and treatment of anomalous aortic origin of a coronary artery (AAOCA) in children. Methods: There were 17 children diagnosed with AAOCA from January 2013 to January 2022 in Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine.Their clinical manifestations, laboratory and imaging data, treatment and prognosis were retrospectively analyzed. Results: These 17 children included 14 males and 3 females, with the age of (8.7±3.5) years. There were 4 anomalous left coronary artery (ALCA) and 13 anomalous right coronary artery (ARCA). Seven children presented with chest pain or chest pain after exercise, three patients presented with cardiac syncope, one complained chest tightness and weakness, and the other six patients had no specific symptoms. Cardiac syncope and chest tightness occurred in patients with ALCA. Fourteen children had the dangerous anatomical basis of myocardial ischemia caused by coronary artery compression or stenosis on imaging. Seven children had coronary artery repair, of whom two were ALCA and five were ARCA. One patient had received heart transplantation because of heart failure. The incidence of adverse cardiovascular events and poor prognosis in ALCA group was higher than that in ARCA group (4/4 vs. 0/13, P<0.05). They were followed up in the outpatient department regularly for 6 (6, 12) months; except for the one who lost visit, the rest of the patients had a good prognosis. Conclusions: Cardiogenic syncope or cardiac insufficiency usually occurs in ALCA, and adverse cardiovascular events and poor prognosis are more common in ALCA than in ARCA. Early surgical treatment should be considered for children with ALCA and ARCA accompanied by myocardial ischemia.

Incidence of sacroiliac joint pain after lumbosacral spine fusion: A systematic review

OBJECTIVES

To determine the incidence of sacroiliac joint (SIJ) pain after lumbosacral spinal fusion.

BACKGROUND

Persistent low back pain is a potential source of disability and poor outcomes following lumbar spine fusion. The SIJ has been described as a potential source. However, there is a paucity of data concerning its importance.

METHODS

This is a PROSPERO registered systematic review. A systematic search of the English literature was performed in Medline, Embase and Cochrane Library databases. MeSH terms such as Lumbar vertebrae, Sacrum, Spinal Fusion, Pain, Sacrum, Ligaments, Sacroiliac Joint were utilized for the search. Key words such as "sacroiliac dysfunction.mp." and "sacroiliac complex.mp." were utilized for the search. Two independent reviewers reviewed articles to determine eligibility for final review and analysis. The Newcastle-Ottawa Scale was used to appraise the quality of all nonrandomized observational studies. Inverse variance weighting with random effects was used to pool data. The GRADE approach, PRISMA workflow and checklists was performed.

RESULTS

Twelve studies were included. All studies were observational and of moderate to low quality. The pooled incidence of sacroiliac joint pain was 15.8%. The pooled incidence of SIJ pain for patients without fusion extending to the sacrum was 15.8%. The pooled incidence of SIJ pain for patients with fusion extending to the sacrum was 32.9%. There was high heterogeneity.

CONCLUSION

SIJ pain is a potential cause of persistent pain after lumbar spine surgery. The current literature of poor quality. Patients presenting with pain after lumbosacral spine fusion should be evaluated for SIJ related pain.

[Cross-sectional associations between reproductive lifespan duration and urinary albumin-creatinine ratio]

Objective: To investigate the association between reproductive lifespan duration (RLD) and urinary albumin-creatinine ratio (UACR) in a Chinese postmenopausal population. Methods: This cross-sectional study included 11 055 naturally postmenopausal women from seven regions of China from May to December 2011. RLD was divided into four groups. Propensity score matching was performed to reduce bias, and logistic regressions and stratifications were conducted to investigate the association between RLD and increased UACR (≥30 mg/g). Mediation effect analysis was performed to quantify the effect of RLD on cardiovascular disease (CVD) induced by elevated UACR. Results: There were 2 373 participants with a RLD of 18-31 years, 2 888 participants with a RLD of 32-34 years, 2 472 participants with a RLD of 35-36 years, and 3 322 participants with a RLD of 37-50 years. The shortest RLD (18-31 years) group was characterized with older age (P<0.001), a higher incidence of CVD (P=0.025), and the highest level of UACR (P<0.001). After adjusting for confounders, women with a longer RLD (37-50 years group) exhibited a lower risk of UACR elevation compared with those with the shortest RLD (18-31 years group) (OR=0.72, 95%CI 0.64-0.82, P<0.001). Every 1-year extension in RLD was linked to a 2% reduction in the risk of UACR elevation (OR=0.98, 95%CI 0.97-0.99, P<0.001). Stratified analysis revealed a more significant association between RLD and UACR in women who were a normal weight (P=0.003) or overweight (P=0.001), in those without CVD history (P=0.001), and in those with impaired estimated glomerular filtration rate (P=0.004). The mediation casual analysis showed that 3.0% of proteinuria inducing CVD events was mediated by RLD (P=0.048). Conclusion: A longer RLD (37-50 years) is associated with a lower UACR in Chinese postmenopausal women.

[Outcomes of different types of pulmonary atresia in neonates treated by ductus arteriosus stenting]

Objective: To summarize the outcomes of different types of pulmonary atresia in neonates treated by ductus arteriosus stenting. Methods: This study was a retrospective cohort study. A total of 19 neonates who had pulmonary atresia treated by ductus arteriosus stenting in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine from April 2014 to June 2021 were included. They were divided into the intact ventricular septum (PA-IVS) group and the ventricular septal defect (PA-VSD) group. Ductus arteriosus stents were implanted by different approaches. These children were followed up regularly at the 1, 3, 6, and 12 months after the surgery and annually since then to evaluate the outcome. Independent sample t-test was used for the statistical analysis. Results: There were 12 children in PA-IVS group and 7 in PA-VSD group. All of them were full term in fants. The gestational age of the PA-IVS group and the PA-VSD group was (38.8±1.1) and (37.7±1.8) weeks, the birth weights were (3.2±0.4) and (3.4±1.1) kg, and the age at operation was (10±9) and (12±7) days, respectively, without significant difference (all P>0.05). Among the 12 children with PA-IVS, 9 had stents successfully implanted through the femoral artery and 3 through the femoral vein. Of the 7 children with PA-VSD, 2 had the stents successfully implanted via the femoral artery and 2 failed, and the remaining 3 had stents successfully implanted via the left carotid artery. There was no postoperative thromboembolism, arteriovenous fistula, pseudoaneurysm or other vascular complications. Five children with PA-VSD who had successful operations were followed up at 6 months of age. They all had the operation for pulmonary atresia, repair of the ventricular septal defect, removal of arterial duct stents, and ligation of the arterial duct. All children survived without any stent displacement or stenosis and biventricular circulation was achieved during the follow-up. Conclusions: Ductus arteriosous stenting can be the first-stage treatment for children with PA-IVS and PA-VSD. In addition to the traditional femoral vein and femoral artery approach, the carotid artery can be used as a route for stent placement.

Impact of economic growth on physical activity and sedentary behaviors: a Systematic Review

OBJECTIVES

This study systematically reviewed scientific evidence regarding the impact of economic growth on physical activity (PA) and sedentary behaviors.

METHODS

A keyword and reference search was conducted in PubMed, Web of Science, Cochrane Library, Scopus, and EBSCO from the inception of an electronic bibliographic database to November 2021. Studies that met all of the following criteria were included in the review: (1) study designs: observational studies; (2) study subjects: people of all ages; (3) exposure: macroeconomic growth; (4) outcomes: PA or sedentary behaviors/sitting time.

RESULTS

15 studies were identified. Eight among 12 studies found economic growth positively associated with at least one domain/measure of PA, whereas the remaining four found an inverse relationship. One of two studies examined the association of economic growth and physical inactivity found a positive relationship, while another found no significant relationship. Four studies examined the associations between economic growth and sedentary behaviors, and the results were inconclusive. The impact of economic growth on PA is through three main pathways-(a) building and maintaining parks and green spaces, (b) adoption of the modern workplace and high technology, and (c) motorized transportation.

CONCLUSION

Building and maintaining parks and green spaces can effectively promote leisure time physical activity and active commute in developed countries, whereas promoting workplace and transportation-related PA could be prioritized in developing nations. Future research calls for longitudinal study design and further exploration of macro-environmental factors. Policymakers and stakeholders should be informed about the potential PA reduction resulting from economic growth and develop preventive strategies to alleviate the problem.

Precision Characterization of Site-Specific O-Acetylated Sialic Acids on N-Glycoproteins

O-Acetylation is a common modification of sialic acid, playing a significant role in glycoprotein stability, immune response, and cell development. Due to the lack of efficient methods for direct analysis of O-acetylated sialoglycopeptides (O-AcSGPs), the majority of identified O-acetylated sialic acids (O-AcSia) until now had no glycosite/glycoprotein information. Herein, we introduced a new workflow for precise interpretation of O-AcSGPs with probability estimation by recognizing the characteristic B and Y ions of O-AcSias. With further optimization of mass spectrometry parameters, the method allowed us to identify a total of 171 unique O-AcSGPs in mouse serum. Although the majority of these O-AcSGPs were at a relatively low abundance compared with their non-O-acetylated states, they were mainly involved in peptidase/endopeptidase inhibitor activities. The method paves the way for large-scale structural and functional analyses of site-specific O-AcSias in various complex samples as well as further identification of many other similar chemical modifications on glycoproteins.

Nonfood Probiotic, Prebiotic, and Synbiotic Use Reduces All-Cause and Cardiovascular Mortality Risk in Older Adults: A Population-Based Cohort Study

OBJECTIVES

Pro-, pre-, and synbiotic supplements improve cardiovascular risk factors. However, the association between nonfood pro-, pre-, and synbiotics (NPPS) and long-term all-cause and cardiovascular mortality has not been studied. Thus, our objective was to determine the impact of nonfood pro-, pre-, and synbiotics on all-cause and cardiovascular mortality.

DESIGN, SETTING, AND PARTICIPANTS

This was a retrospective, cohort study of 4837 nationally representative American participants aged 65 years or older with a median follow-up duration of 77 months.

MEASUREMENTS

All-cause and cardiovascular mortality were measured.

RESULTS

A total of 1556 participants died during the median 77-month follow-up, and 517 died from cardiovascular disease. Compared with participants without NPPS use, participants who used NPPS experienced a reduced risk of all-cause mortality by nearly 41% (hazard ratio 0.59, 95% CI 0.43 to 0.79) and cardiovascular mortality by 52% (HR 0.48, 95% CI 0.30 to 0.76). Such an effect persisted in most subgroup analyses and complete-case analyses.

CONCLUSION AND RELEVANCE

In this study, we found a protective effect of NPPS against all-cause and cardiovascular mortality in Americans aged 65 years or older. Nonfood pro-, pre-, and synbiotics can be a novel, inexpensive, low-risk treatment addition for all-cause and cardiovascular mortality for older individuals.

Relationship between Social Support, Sarcopenia, and Cognitive Impairment in Chinese Community-Dwelling Older Adults

BACKGROUND

Cognitive impairment and sarcopenia have become important challenges for the growing aging population. Social support has been shown to protect against cognitive impairment, but its impact on sarcopenia remains unknown. The purpose of this study was to explore the correlation between social support, sarcopenia, and cognitive impairment in Chinese older adults.

METHOD

A multi-stage whole group sampling method was used to conduct a cross-sectional survey of 720 community-dwelling older people in Shanghai. The definition of sarcopenia was in accordance with the criteria of the Asian Working Group for Sarcopenia (AWGS) 2019. Cognitive impairment was evaluated using a computerized neuropsychological assessment device that had been previously validated. Social support was assessed using the Social Support Rate Scale. Logistic regression analyses were conducted to explore the relationship between social support cognitive impairment and sarcopenia, fully adjusting for all potential confounding factors.

RESULTS

Our study found that 230 (31.94%) of the participants had cognitive impairment and 97 (13.47%) of the participants had sarcopenia. The mean social support score was 35.10 ± 7.54. Besides, the results showed that cognitive impairment was associated with sarcopenia (OR:1.650, 95% CI: 1.048, 2.596, P=0.030) after adjusting for confounding factors. Older adults with high level social support had the lowest risk of cognitive impairment (OR: 0.297, 95% CI: 0.115, 0.680, P=0.021) and sarcopenia (OR: 0.113, 95% CI: 0.031, 0.407, P=0.001), respectively.

CONCLUSION

Our analysis revealed that high level social support was negatively associated with sarcopenia and cognitive impairment. These findings provide strong support for the health promotion effect of social networks against sarcopenia and cognitive impairment in Chinese community-dwelling older adults, with important implications for healthcare policy makers.

Identifying intact N-glycopeptides from tandem mass spectrometry data using StrucGP

Protein glycosylation is of great importance in many biological processes. Glycosylation has been increasingly analyzed at the intact glycopeptide level using mass spectrometry to study site-specific glycosylation changes under different physiological and pathological conditions. StrucGP is a glycan database-independent search engine for the structural interpretation of N-glycoproteins at the site-specific level. To ensure the accuracy of results, two collision energies are implemented in instrument settings for each precursor to separate fragments of peptides and glycans. In addition, the false discovery rates (FDR) of peptides and glycans as well as probabilities of detailed structures are estimated. In this protocol, the use of StrucGP is demonstrated, including environment configuration, data preprocessing as well as result inspection and visualization using our in-house software "GlycoVisualTool". The described workflow should be able to be performed by anyone with basic proteomic knowledge.

Application of StrucGP in medical immunology: site-specific N-glycoproteomic analysis of macrophages

The structure of N-glycans on specific proteins can regulate innate and adaptive immunity via sensing environmental signals. Meanwhile, the structural diversity of N-glycans poses analytical challenges that limit the exploration of specific glycosylation functions. In this work, we used THP-1-derived macrophages as examples to show the vast potential of a N-glycan structural interpretation tool StrucGP in N-glycoproteomic analysis. The intact glycopeptides of macrophages were enriched and analyzed using mass spectrometry (MS)-based glycoproteomic approaches, followed by the large-scale mapping of site-specific glycan structures via StrucGP. Results revealed that bisected GlcNAc, core fucosylated, and sialylated glycans (e.g., HexNAc₄Hex₅Fuc₁Neu5Ac₁, N₄H₅F₁S₁) were increased in M1 and M2 macrophages, especially in the latter. The findings indicated that these structures may be closely related to macrophage polarization. In addition, a high level of glycosylated PD-L1 was observed in M1 macrophages, and the LacNAc moiety was detected at Asn-192 and Asn-200 of PD-L1, and Asn-200 contained Lewis epitopes. The precision structural interpretation of site-specific glycans and subsequent intervention of target glycoproteins and related glycosyltransferases are of great value for the development of new diagnostic and therapeutic approaches for different diseases.

Recognition of Core-Fucosylated Glycopeptides Based on the Y1+Fuc/Y1 Ratio in Low-Energy HCD Spectra

Accurate identification of core fucosylation on N-glycopeptides remains challenging due to fucose migration during mass spectrometry analysis. Here, we introduce a simple and straightforward method for core-fucosylated glycopeptide recognition based on the relative intensities of Y1+Fuc ions compared with their corresponding Y1 ions (labeled as Y1+Fuc/Y1 or simply Y1F/Y1 ratio > 0.1) in low-energy HCD-based spectra. The method was first developed by systematically evaluating the influence of fucose migration on the Y1F ion from antenna fucoses based on the distribution of the Y1F/Y1 ratios in the MS/MS spectra of antenna-fucosylated glycopeptides from Fut8^-/- mouse brain. The feasibility of the method was then confirmed by using two standard glycoproteins, comparison with glycopeptides in Fut8^+/+ mouse brain with/without in silico core-fucosylation removal, and Y1F/Y1 ratio alterations under a lower HCD energy. This method will be applicable to the manual interpretation and software-based high-throughput analysis of core-fucosylated glycopeptides.

[The clinical value of using a distant-image screen for reading and learning]

Objective: To investigate the effect and comfort of using a distant-image screen for reading and learning. Methods: It was a prospective cross-over study. Thirty-nine volunteers, including 13 males and 26 females, aged (26.4±4.5) years (20 to 37 years), were recruited from Beijing Tongren Hospital Affiliated to Capital Medical University in July 2021. The volunteers read the digital correction table printed on paper and displayed on a distant-image screen in a random order and rest in an interval of 2 hours. Reading speed, efficiency and accuracy of using the two devices were recorded, and the changes of logMAR vision, diopter, flicker fusion frequency and visual fatigue score after reading were calculated. Comparison of the quantitative data was performed using the paired t-test. Results: The speed, accuracy and efficiency were (41.2±11.6) digit groups/min, 80.7%±13.3% and (32.4±7.4) digit groups/min in reading on paper, (41.7±11.1) digit groups/min, 76.4%±12.6% and (31.1±6.4) digit groups/min in reading from screen, respectively. There was no significant difference in reading speed (t=-0.462, P=0.648) and reading efficiency (t=1.954, P=0.058), but there was significant difference in reading accuracy (t= 2.226, P=0.032). The logMAR visual acuity of right eye and left eye decreased by 0.014±0.032 and 0.013±0.050 after reading on paper, but increased by 0.007±0.033 and 0.007±0.036 after reading from screen, respectively. The difference was significant (right eye, t=2.592, P=0.013; left eye, t =2.154, P=0.038). The myopia degree of right eye and left eye increased by (0.07±0.29) D and (0.06±0.24) D after reading on paper, and increased by (0.01±0.29) D and (0.02±0.28) D after reading from screen, respectively. The flicker fusion frequency decreased by (0.1±1.0) Hz after reading on paper, but increased by (0.3±1.2) Hz after reading from screen. There was no significant difference (P>0.05). The subjective scale score of visual fatigue increased in both groups, with no statistically significant difference (t=1.165, P=0.251). Conclusion: The use of a distant-image screen for reading and learning does not affect the reading efficiency or increase the visual fatigue, and can avoid the decline of visual acuity caused by near viewing compared with using the printed matter.

[Parameningeal or non-parameningeal head and neck rhabdomyosarcoma: a study based on propensity score matching and survival analysis]

Objective: To compare the prognoses between parameningeal and non-parameningeal head and neck rhabdomyosarcoma based on propensity score matching and to explore the prognostic factors of overall survival in patients with head and neck rhabdomyosarcoma. Methods: The medical records of 64 patients with pathologically diagnosed as head and neck rhabdomyosarcoma from January 2016 to May 2020 in Peking Union Medical College Hospital were retrospectively retrieved, including 31 males and 33 females, with an average age of (8.0±8.9) years. Kaplan-Meier method was used to draw and compare survival curves in subgroup analysis according to different histopathological characteristics. Patients were divided into non-parameningeal (27 cases) and parameningeal (37 cases) group based on the location of primary lesion. Patients were further selected using 1∶1 propensity score matching method. The basic clinical data and overall survival were compared before and after matching. Prognostic factors were anlysed using Cox's proportional hazards regression model. Results: In 64 patients with head and neck rhabdomyosarcoma, lower risk stratification, and lower TNM stage indicated higher overall survival (all P<0.05). Before matching, patients in parameningeal group presented with higher T stage and IRS (Intergroup Rhabdomyosarcoma Study) staging (all P<0.05). There were no significant differences in basic clinical data and 1-, 2-, and 3-year overall survival rates between two groups after matching(P>0.05). Tumor size smaller than 5 cm, embryonal histology, negative FOXO1 fusion gene, lower risk stratification, and lower TNM stage were associated with higher overall survival (all P<0.05). Among these, tumor size and histology were independent prognostic factors (HR=2.36, 95%CI:1.07-5.20, P=0.033; HR=5.54, 95%CI: 1.18-25.95, P=0.030). Conclusions: There is no significant difference in overall survival between patients with parameningeal and non-parameningeal rhabdomyosarcomas. Tumor size smaller than 5 cm and embryonal histology are two independent prognostic factors.

6-Shogaol protects against isoproterenol-induced cardiac injury in rats through attenutating oxidative stress, inflammation, apoptosis and activating nuclear respiratory factor-2/heme oxygenase-1 signaling pathway

The current study investigated the preventive effect of 6-Shogaol on isoproterenol hydrochloride (ISO)-induced myocardial cardiac injury. 6-Shogaol (50 mg/kg b.w.) was administered for 14 days at pretreatment and ISO-induction (85 mg/kg b.w.) for the last two days (13th and 14th days) by subcutaneous injection. Cardiac markers in serum like creatine kinase (CK), creatine kinase-MB (CK-MB), lactate dehydrogenase (LDH), cardiac troponins T (cTn T) and I (cTn I) increased in ISO-induced rats. Moreover, lipid peroxidative markers like thiobarbituric acid reactive substances (TBARS) and lipid hydroperoxides (LOOH) were raised, and the activities/level of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and reduced glutathione (GSH) were diminished in ISO-treated heart tissue. In addition, inflammatory and nuclear respiratory factor (Nrf)-2 signalling molecules were upregulated in ISO-induced ischemic rats. 6-Shogaol pretreatment decreased the activities of cardiac and lipid peroxidative markers and enhanced the antioxidant status in ISO-induced cardiac injury rats. Further, 6-Shogaol pretreatment inhibited serum inflammatory markers: tumour necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), nuclear factor-kappaB (NF-κB), Nrf-2 molecule and heme oxygenase (HO)-1 in ISO-induced cardial damage rats. We noticed the effect of 6-Shogaol inhibited pro-apoptotic genes like B-cell lymphoma 2 (Bcl-2)-associated X protein (Bax), Fas, caspase-3, -8, -9, cytochrome C, and inflammatory genes and increased Bcl-2 expression in ISO-treated rats. The cardioprotective activity of 6-Shogaol in rats with ISO-induced myocardial damage may be due to its ability to reduce oxidative stress, inflammation, and apoptosis, perhaps via the Nrf-2/HO-1 signalling pathway.

Glycoproteomic analysis reveals the effects of bisecting GlcNAc in intrahepatic cholangiocarcinoma

Intrahepatic cholangiocarcinoma (ICC) is the second major subtype of primary liver cancer and has caused more and more attention with increasing incidence and mortality worldwide. Our previous study found that bisecting N-glycans are commonly increased in ICC, while the effects and potential functions of bisecting GlcNAc in ICC are still largely unclear. In this study, we further confirmed that the structures of bisecting GlcNAc were significantly up-regulated in ICC compared with paracancer tissues by glycoproteomic data and lectin histochemistry. The expression of its glycosyltransferase MGAT3 was also up-regulated in ICC tissues at both mRNA and protein levels, and expression of MGAT3 is negatively correlated with overall survival explored by bioinformatic analyses and published datasets from 255 patients. Next, the silencing of MGAT3 could inhibit the growth and invasion of ICC cells, and overexpressing of MGAT3 only promoted ICC cell invasion. Further glycoproteomic analysis showed that the commonly glycoproteins modified by bisecting GlcNAc after MGAT3-overexpression in two ICC cell lines were mainly involved in cell movement-related biological processes, such as cell adhesion, integrin-related and ECM-receptor interaction. This study sheds light on the potential effects of bisecting GlcNAc in ICC cells and suggests that MGAT3 might be used as a potential target in the therapy of ICC.

Commercial ChIP-Seq Library Preparation Kits Performed Differently for Different Classes of Protein Targets

Background

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) is a powerful method commonly used to study global protein-DNA interactions including both transcription factors and histone modifications. We have found that the choice of ChIP-Seq library preparation protocol plays an important role in overall ChIP-Seq data quality. However, very few studies have compared ChIP-Seq libraries prepared by different protocols using multiple targets and a broad range of input DNA levels.

Results

In this study, we evaluated the performance of 4 ChIP-Seq library preparation protocols (New England Biolabs [NEB] NEBNext Ultra II, Roche KAPA HyperPrep, Diagenode MicroPlex, and Bioo [now PerkinElmer] NEXTflex) on 3 target proteins, chosen to represent the 3 typical signal enrichment patterns in ChIP-Seq experiments: sharp peaks (H3K4me3), broad domains (H3K27me3), and punctate peaks with a protein binding motif (CTCF). We also tested a broad range of different input DNA levels from 0.10 to 10 ng for H3K4me3 and H3K27me3 experiments.

Conclusions

Our results suggest that the NEB protocol may be better for preparing H3K4me3 (and potentially other histone modifications with sharp peak enrichment) libraries; the Bioo protocol may be better for preparing H3K27me3 (and potentially other histone modifications with broad domain enrichment) libraries, and the Diagenode protocol may be better for preparing CTCF (and potentially other transcription factors with well-defined binding motifs) libraries.  For ChIP-Seq experiments using novel targets without a known signal enrichment pattern, the NEB protocol might be the best choice, as it performed well for each of the 3 targets we tested across a wide array of input DNA levels.

Evaluation of absorbent cotton for glycopeptide enrichment

Selecting proper and efficient glycopeptide enrichment approaches are essential for mass spectrometry-based glycoproteomics since glycopeptides are usually with microheterogeneity and low abundance in most biological samples. Herein, we introduced a cotton hydrophilic interaction liquid chromatography (HILIC) approach for large-scale glycopeptide enrichment with 80% acetonitrile/1% trifluoroacetic acid as the optimal sample loading buffer. The comparison of cotton HILIC with Venusil HILIC and mixed anion-exchange (MAX) approaches indicated that cotton HILIC was superior in overall glycopeptide enrichment, whereas Venusil HILIC preferred in complex glycan structures and MAX performed better with high mannose glycans. Exploration of capacity and recovery rate of cotton HILIC illustrated that 5mg cotton packed in a 200μL tip achieved a reasonable glycopeptide enrichment performance (~6% recovery) from ~0.5mg peptides. In conclusion, cotton HILIC can be used as an optional glycopeptide enrichment approach in glycosylation analysis with its specific merit.

Structural- and Site-Specific N-Glycosylation Characterization of COVID-19 Virus Spike with StrucGP

The spike (S) protein plays a key role in COVID-19 (SARS-CoV-2) infection and host-cell entry. Previous studies have systematically analyzed site-specific glycan compositions as well as many important structural motifs of the S protein. Here, we further provide structural-clear N-glycosylation of the S protein at a site-specific level by using our recently developed structural- and site-specific N-glycoproteomics sequencing algorithm, StrucGP. In addition to the common N-glycans as detected in previous studies, many uncommon glycosylation structures such as LacdiNAc structures, Lewis structures, Mannose 6-phosphate (M6P) residues, and bisected core structures were unambiguously mapped at a total of 20 glycosites in the S protein trimer and protomer. These data further support the glycosylation structural-functional investigations of the COVID-19 virus spike.

AnFiSA: An open-source computational platform for the analysis of sequencing data for rare genetic disease

Despite genomic sequencing rapidly transforming from being a bench-side tool to a routine procedure in a hospital, there is a noticeable lack of genomic analysis software that supports both clinical and research workflows as well as crowdsourcing. Furthermore, most existing software packages are not forward-compatible in regards to supporting ever-changing diagnostic rules adopted by the genetics community. Regular updates of genomics databases pose challenges for reproducible and traceable automated genetic diagnostics tools. Lastly, most of the software tools score low on explainability amongst clinicians. We have created a fully open-source variant curation tool, AnFiSA, with the intention to invite and accept contributions from clinicians, researchers, and professional software developers. The design of AnFiSA addresses the aforementioned issues via the following architectural principles: using a multidimensional database management system (DBMS) for genomic data to address reproducibility, curated decision trees adaptable to changing clinical rules, and a crowdsourcing-friendly interface to address difficult-to-diagnose cases. We discuss how we have chosen our technology stack and describe the design and implementation of the software. Finally, we show in detail how selected workflows can be implemented using the current version of AnFiSA by a medical geneticist.

De-sialylation of glycopeptides by acid treatment: enhancing sialic acid removal without reducing the identification

Sialic acid, a common terminal monosaccharide on many glycoconjugates, plays essential roles in many biological processes such as immune responses, pathogen recognition, and cancer development. For various purposes, sialic acids may need to be removed from glycopeptides or glycans, mainly using enzymatical or chemical approaches. In this study, we found that most commonly used chemical methods couldn't completely remove sialic acids from glycopeptides. Although the de-sialylation efficiency could be further enhanced by increasing the treatment time or acid concentration, the undesirable side reactions on the peptide portion would decrease glycopeptide identification. By adding the deamidation on carbamidomethyl-cysteine (C), asparagine (N), and glutamine (Q) residues as a variable modification during database search, most of the unidentified spectra could be recovered. This optional acid-treatment and database search method for the complete removal of sialic acids without losing much spectral identification should be quite useful for many glycomic and glycoproteomic studies.

Concrete damage analysis based on higher-order beam theories using fracture energy regularization

This paper presents the numerical damage analysis of concrete structures using higher-order beam theories based on Carrera Unified Formulation (CUF). The concrete constitutive relation is modeled using continuum damage mechanics based on a modified Mazars concrete damage model, in which both the tensile and compressive softening behaviors are regularized with classical fracture energy methodology. An expression is proposed to estimate the characteristic length in higher-order beam theories, to prevent mesh dependency. Both softening constitutive laws and fracture energy calculations are obtained according to Model Code 2010. To assess the efficiency of the proposed model, three classical benchmark quasi-static experiments are taken for validation. From the comparison between numerical and experimental results, the proposed CUF model using continuum damage mechanics can present 3D accuracy with low computational costs and reduce the mesh dependency.