The diagnostic performance of serum αvß6 autoantibodies for ulcerative colitis: A systematic review and meta-analysis.

BACKGROUND AND OBJECTIVE: Currently, there is no single golden standard for diagnosing ulcerative colitis (UC). Now serum αvß6 autoantibodies have shown promise as a diagnostic tool for UC. Here the aim was to determine the diagnostic performance of serum αvß6 autoantibodies for UC. METHODS: PubMed, the Cochrane Library, the Embase, and the Web of Science were searched comprehensively. STATA software was utilized to analyze the relevant data. RESULTS: 9 studies from 6 articles with 1827 subjects were eligible. The summary sensitivity and specificity of serum αvß6 autoantibodies to diagnose UC were 0.82 (95 % confidence interval (CI): 0.65-0.92) and 0.94 (95 % CI: 0.90-0.97) with an area under the summary receiver operating characteristic curve of 0.96 (95 % CI: 0.94-0.97). Subgroup analysis was conducted owning to substantial heterogeneity between studies (I2 = 97 % and P < 0.001). The aggregate sensitivity and specificity to diagnose UC in adults were 0.75 (95 % CI: 0.61-0.86) and 0.95 (95 % CI: 0.90-0.97), and when using a threshold of mean control+3SD, 0.80 (95 % CI: 0.60-0.91) and 0.96 (95 % CI: 0.90-0.99), respectively. Additionally, to differentiate UC from healthy participants, non-inflammatory bowel disease, and Crohn's disease, the overall specificity was 0.96, 0.88, and 0.80, respectively. CONCLUSIONS: serum αvß6 autoantibodies, as a non-invasive tool, demonstrated good diagnostic accuracy for UC. However, their application may be limited in some immune-related disorders, and further studies are needed for validation.

Comparison of efficacy and safety of flexible ureteroscopy and mini-percutaneous nephrolithotomy for 2-3 cm renal calculi in women: a single-center study.

OBJECTIVE: This study aimed to compare the efficacy and safety of flexible ureteroscopic lithotripsy (FURSL) and mini-percutaneous nephrolithotomy (mPCNL) in the treatment of 2-3 cm renal calculi in women. PATIENTS AND METHODS: Clinical data of 186 patients who underwent mPCNL (n=96) and FURSL (n=90) surgery in our hospital from June 2018 to February 2023 were collected. Several parameters were assessed and compared between the two groups, including operation duration, length of hospital stay, cost of hospitalization, pain intensity measured by the visual analogue scale (VAS), patient comfort assessed using the Bruggrmann Comfort Scale (BCS), decrease in hemoglobin levels, changes in blood urea nitrogen (BUN), fluctuations in serum creatinine (Scr), hypersensitive C-reactive protein (hs-CRP) levels, complication rates, immediate post-operative stone-free rate (RSFR), and long-term stone-free rate (LSFR). RESULTS: The comparative analysis of patient age, body mass index (BMI), stone size, computed X-ray tomography (CT) value of stones, number of stones, and comorbidities revealed no statistically significant differences between the mPCNL and FURSL groups (p>0.05). The mPCNL cohort exhibited a markedly lower duration of operation (p<0.001) and BCS score (p<0.001) compared to the FURSL cohort. Nonetheless, the mPCNL cohort demonstrated significantly higher hospitalization expenses (p<0.001), length of hospital stay (p<0.001), VAS score for pain (p<0.001), and level of hemoglobin decrease (p<0.001) in comparison to the FURSL cohort. Moreover, the immediate post-operative stone-free rate (RSFR) was significantly higher in the mPCNL group (p=0.007). The long-term stone-free rate (LSFR), however, showed no significant difference between the two groups (p=0.160). Furthermore, the FURSL group exhibited significantly fewer overall complications in contrast to the mPCNL group (p=0.006). CONCLUSIONS: mPCNL and FURSL are both safe and effective surgical methods for treating 2-3 cm renal calculi in women. However, FURSL holds distinct advantages, including minimally invasive procedure, accelerated recovery, reduced cost, and lower incidence of complications.

Hair Zinc and Chromium Levels Were Associated with a Reduced Likelihood of Age Related Cognitive Decline in Centenarians and Oldest-Old Adults.

BACKGROUND: Cognitive function has inevitable decline with advancing age in nature, and age-related cognitive decline (ARCD) is of increasing concern to aging population. Scarce study has involved the associations between hair trace elements and ARCD in older adults, especially in centenarians and oldest-old adults. This study was to investigate the associations between hair trace elements and ARCD in centenarians and oldest-old adults. METHODS: Based on the household registration information of centenarians and oldest-old adults provided by the Civil Affairs Department of Hainan Province, China, the investigators conducted a one-to-one household survey among centenarians (≥100 years old) and oldest-old adults (80-99 years old). All 50 centenarians had a median age of 103 years and females accounted for 68.0%. All 73 oldest-old adults aged 80-99 years had a median age of 90 years and females accounted for 82.2%. Basic information were obtained with questionnaire interview, physical examination, biological test and hair collection by pre-trained local doctors and nurses. An inductively coupled plasma mass spectrometer was used to measure hair trace elements. All data in this study comes from China. Age, sex, body mass index, systolic blood pressure, diastolic blood pressure, smoking, drinking, hemoglobin, albumin, fasting blood pressure, zinc, chromium, copper, selenium, iron, manganese, strontium, lead, magnesium, potassium, and barium were simultaneously included in multivariate Logistic regression analysis. One adjusted model was done with all hair trace elements together. RESULTS: Zinc and chromium levels were significantly lower in participants with ARCD than those without ARCD (P < 0.05 for all). Multivariate Logistic regression analysis indicated that zinc [odds ratio (OR): 0.988, 95%confidence interval (95%CI): 0.977-0.999] and chromium (OR: 0.051, 95%CI: 0.004-0.705) were associated with a reduced likelihood of ARCD (P < 0.05 for all). CONCLUSIONS: Hair zinc and chromium levels were associated with a reduced likelihood of ARCD in centenarians and oldest-old adults. Further studies are necessary to verify if zinc and chromium supplementation has the potential to improve cognitive function and prevent ARCD development.

Learning few-shot imitation as cultural transmission.

Cultural transmission is the domain-general social skill that allows agents to acquire and use information from each other in real-time with high fidelity and recall. It can be thought of as the process that perpetuates fit variants in cultural evolution. In humans, cultural evolution has led to the accumulation and refinement of skills, tools and knowledge across generations. We provide a method for generating cultural transmission in artificially intelligent agents, in the form of few-shot imitation. Our agents succeed at real-time imitation of a human in novel contexts without using any pre-collected human data. We identify a surprisingly simple set of ingredients sufficient for generating cultural transmission and develop an evaluation methodology for rigorously assessing it. This paves the way for cultural evolution to play an algorithmic role in the development of artificial general intelligence.

A data integration approach unveils a transcriptional signature of type 2 diabetes progression in rat and human islets.

Pancreatic islet failure is a key characteristic of type 2 diabetes besides insulin resistance. To get molecular insights into the pathology of islets in type 2 diabetes, we developed a computational approach to integrating expression profiles of Goto-Kakizaki and Wistar rat islets from a designed experiment with those of the human islets from an observational study. A principal gene-eigenvector in the expression profiles characterized by up-regulated angiogenesis and down-regulated oxidative phosphorylation was identified conserved across the two species. In the case of Goto-Kakizaki versus Wistar islets, such alteration in gene expression can be verified directly by the treatment-control tests over time, and corresponds to the alteration of α/ß-cell distribution obtained by quantifying the islet micrographs. Furthermore, the correspondence between the dual sample- and gene-eigenvectors unveils more delicate structures. In the case of rats, the up- and down-trend of insulin mRNA levels before and after week 8 correspond respectively to the top two principal eigenvectors. In the case of human, the top two principal eigenvectors correspond respectively to the late and early stages of diabetes. According to the aggregated expression signature, a large portion of genes involved in the hypoxia-inducible factor signaling pathway, which activates transcription of angiogenesis, were significantly up-regulated. Furthermore, top-ranked anti-angiogenic genes THBS1 and PEDF indicate the existence of a counteractive mechanism that is in line with thickened and fragmented capillaries found in the deteriorated islets. Overall, the integrative analysis unravels the principal transcriptional alterations underlying the islet deterioration of morphology and insulin secretion along type 2 diabetes progression.

Reconstructing COVID-19 incidences from positive RT-PCR tests by deconvolution.

BACKGROUND: The emergency of new COVID-19 variants over the past three years posed a serious challenge to the public health. Cities in China implemented mass daily RT-PCR tests by pooling strategies. However, a random delay exists between an infection and its first positive RT-PCR test. It is valuable for disease control to know the delay pattern and daily infection incidences reconstructed from RT-PCR test observations. METHODS: We formulated the convolution model between daily incidences and positive RT-PCR test counts as a linear inverse problem with positivity restrictions. Consequently, the Richard-Lucy deconvolution algorithm was used to reconstruct COVID-19 incidences from daily PCR tests. A real-time deconvolution was further developed based on the same mathematical principle. The method was applied to an Omicron epidemic data set of a bar outbreak in Beijing and another in Wuxi in June 2022. We estimated the delay function by maximizing likelihood via an E-M algorithm. RESULTS: The delay function of the bar-outbreak in 2022 differs from that reported in 2020. Its mode was shortened to 4 days by one day. A 95% confidence interval of the mean delay is [4.43,5.55] as evaluated by bootstrap. In addition, the deconvolved infection incidences successfully detected two associated infection events after the bar was closed. The application of the real-time deconvolution to the Wuxi data identified all explosive incidence increases. The results revealed the progression of the two COVID-19 outbreaks and provided new insights for prevention and control strategies, especially for the role of mass daily RT-PCR testing. CONCLUSIONS: The proposed deconvolution method is generally applicable to other infectious diseases if the delay model can be assumed to be approximately valid. To ensure a fair reconstruction of daily infection incidences, the delay function should be estimated in a similar context in terms of virus variant and test protocol. Both the delay estimate from the E-M algorithm and the incidences resulted from deconvolution are valuable for epidemic prevention and control. The real-time feedback is particularly useful during the epidemic's acute phase because it can help the local disease control authorities modify the control measures more promptly and precisely.

RegCloser: a robust regression approach to closing genome gaps.

BACKGROUND: Closing gaps in draft genomes leads to more complete and continuous genome assemblies. The ubiquitous genomic repeats are challenges to the existing gap-closing methods, based on either the k-mer representation by the de Bruijn graph or the overlap-layout-consensus paradigm. Besides, chimeric reads will cause erroneous k-mers in the former and false overlaps of reads in the latter. RESULTS: We propose a novel local assembly approach to gap closing, called RegCloser. It represents read coordinates and their overlaps respectively by parameters and observations in a linear regression model. The optimal overlap is searched only in the restricted range consistent with insert sizes. Under this linear regression framework, the local DNA assembly becomes a robust parameter estimation problem. We solved the problem by a customized robust regression procedure that resists the influence of false overlaps by optimizing a convex global Huber loss function. The global optimum is obtained by iteratively solving the sparse system of linear equations. On both simulated and real datasets, RegCloser outperformed other popular methods in accurately resolving the copy number of tandem repeats, and achieved superior completeness and contiguity. Applying RegCloser to a plateau zokor draft genome that had been improved by long reads further increased contig N50 to 3-fold long. We also tested the robust regression approach on layout generation of long reads. CONCLUSIONS: RegCloser is a competitive gap-closing tool. The software is available at https://github.com/csh3/RegCloser . The robust regression approach has a prospect to be incorporated into the layout module of long read assemblers.

The Impact of Interactive MRI-Based Radiologist Review on Radiotherapy Target Volume Delineation in Head and Neck Cancer.

BACKGROUND AND PURPOSE: Peer review of head and neck cancer radiation therapy target volumes by radiologists was introduced in our center to optimize target volume delineation. Our aim was to assess the impact of MR imaging-based radiologist peer review of head and neck radiation therapy gross tumor and nodal volumes, through qualitative and quantitative analysis. MATERIALS AND METHODS: Cases undergoing radical radiation therapy with a coregistered MR imaging, between April 2019 and March 2020, were reviewed. The frequency and nature of volume changes were documented, with major changes classified as per the guidance of The Royal College of Radiologists. Volumetric alignment was assessed using the Dice similarity coefficient, Jaccard index, and Hausdorff distance. RESULTS: Fifty cases were reviewed between April 2019 and March 2020. The median age was 59 years (range, 29-83 years), and 72% were men. Seventy-six percent of gross tumor volumes and 41.5% of gross nodal volumes were altered, with 54.8% of gross tumor volume and 66.6% of gross nodal volume alterations classified as "major." Undercontouring of soft-tissue involvement and unidentified lymph nodes were predominant reasons for change. Radiologist review significantly altered the size of both the gross tumor volume (P = .034) and clinical target tumor volume (P = .003), but not gross nodal volume or clinical target nodal volume. The median conformity and surface distance metrics were the following: gross tumor volume Dice similarity coefficient = 0.93 (range, 0.82-0.96), Jaccard index = 0.87 (range, 0.7-0.94), Hausdorff distance = 7.45 mm (range, 5.6-11.7 mm); and gross nodular tumor volume Dice similarity coefficient = 0.95 (0.91-0.97), Jaccard index = 0.91 (0.83-0.95), and Hausdorff distance = 20.7 mm (range, 12.6-41.6). Conformity improved on gross tumor volume-to-clinical target tumor volume expansion (Dice similarity coefficient = 0.93 versus 0.95, P = .003). CONCLUSIONS: MR imaging-based radiologist review resulted in major changes to most radiotherapy target volumes and significant changes in volume size of both gross tumor volume and clinical target tumor volume, suggesting that this is a fundamental step in the radiotherapy workflow of patients with head and neck cancer.

Dynamic nomogram for long-term survival in patients with locally advanced oropharyngeal cancer after (chemo)radiotherapy.

PURPOSE: This study aimed to establish a nomogram for predicting overall survival (OS) in oropharyngeal cancer patients treated with curative (chemo)radiotherapy. MATERIALS AND METHODS: The dynamic nomogram was constructed on 273 patients with oropharyngeal squamous cell carcinoma treated in a Tertiary Head and Neck Cancer Unit. The clinical features that were previously reported to be associated with OS were analyzed. The performance of the nomogram was assessed using concordance index (C-index) and calibration curves. RESULTS: The nomogram incorporated three explanatory variables derived from a decision tree approach including HPV status, N classification according to 8th edition TNM and early response to (chemo)radiotherapy. The nomogram was capable to predict OS with a validation C-index of 0.768. The proposed stratification in risk groups allowed significant distinction between Kaplan-Meier curves for OS outcome (p < 0.0001). CONCLUSIONS: The nomogram provided an accurate evaluation of OS for oropharyngeal cancer patients treated with curative (chemo)radiotherapy.

Comparative Proteome and Cis-Regulatory Element Analysis Reveals Specific Molecular Pathways Conserved in Dog and Human Brains.

Brain development and function are governed by precisely regulated protein expressions in different regions. To date, multiregional brain proteomes have been systematically analyzed only for adult human and mouse brains. To understand the underpinnings of brain development and function, we generated proteomes from six regions of the postnatal brain at three developmental stages of domestic dogs (Canis familiaris), which are special among animals in terms of their remarkable human-like social cognitive abilities. Quantitative analysis of the spatiotemporal proteomes identified region-enriched synapse types at different developmental stages and differential myelination progression in different brain regions. Through integrative analysis of inter-regional expression patterns of orthologous proteins and genome-wide cis-regulatory element frequencies, we found that proteins related with myelination and hippocampus were highly correlated between dog and human but not between mouse and human, although mouse is phylogenetically closer to human. Moreover, the global expression patterns of neurodegenerative disease and autism spectrum disorder-associated proteins in dog brain more resemble human brain than in mouse brain. The high similarity of myelination and hippocampus-related pathways in dog and human at both proteomic and genetic levels may contribute to their shared social cognitive abilities. The inter-regional expression patterns of disease-associated proteins in the brain of different species provide important information to guide mechanistic and translational study using appropriate animal models.

Nivolumab plus low-dose ipilimumab in previously treated patients with microsatellite instability-high/mismatch repair-deficient metastatic colorectal cancer: 4-year follow-up from CheckMate 142.

BACKGROUND: In the phase II multicohort CheckMate 142 study, nivolumab plus low-dose (1 mg/kg) ipilimumab provided robust and durable clinical benefit with a manageable safety profile in previously treated patients with microsatellite instability-high/mismatch repair-deficient (MSI-H/dMMR) metastatic colorectal cancer (mCRC) at 13.4- and 25.4-month median follow-up (Overman MJ, Lonardi S, Wong KYM et al. Durable clinical benefit with nivolumab plus ipilimumab in DNA mismatch repair-deficient/microsatellite instability-high metastatic colorectal cancer. J Clin Oncol. 2018;36:773-779. Overman MJ, Lonardi S, Wong KYM, et al. Nivolumab plus low-dose ipilimumab in previously treated patients with microsatellite instability-high/mismatch repair deficient metastatic colorectal cancer: long-term follow-up. J Clin Oncol. 2019;37:635). Here, we present results from the 4-year follow-up of these patients. PATIENTS AND METHODS: Patients received nivolumab (3 mg/kg) plus low-dose (1 mg/kg) ipilimumab every 3 weeks (four doses) followed by nivolumab (3 mg/kg) every 2 weeks until disease progression. Primary endpoint was investigator-assessed objective response rate (ORR; as per RECIST version 1.1). RESULTS: A total of 119 patients were treated; 76% had ≥2 prior lines of therapy. Median follow-up was 50.9 months (range 46.9-62.7 months). Median duration of therapy was 24.9 months [95% confidence interval (CI) 15.8-33.2 months]. Investigator-assessed ORR increased from 55% (95% CI 45% to 64%) at 13.4 months to 65% (95% CI 55% to 73%) at 50.9 months with a disease control rate of 81% (95% CI 72% to 87%). The complete response rate increased from 3% at 13.4 months to 13% at 50.9 months. Partial responses were observed in 52% of patients; 21% had stable disease, and 12% had progressive disease. Median time to response was 2.8 months (range 1.1-37.1 months), and median duration of response was not reached (range 1.4+ to 58.0+ months). At data cut-off, 37 (48%) patients had ongoing responses. Median progression-free survival was not reached [95% CI 38.4 months-not estimable (NE)], and median overall survival was not reached (95% CI NE). Grade 3-4 treatment-related adverse events (TRAEs) were observed in 32% of patients; 13% of patients had any-grade TRAEs leading to discontinuation. CONCLUSIONS: The results confirm long-term benefit of nivolumab plus low-dose ipilimumab for previously treated patients with MSI-H/dMMR mCRC. The safety profile was manageable with no new safety signals.

RegScaf: a regression approach to scaffolding.

MOTIVATION: Crucial to the correctness of a genome assembly is the accuracy of the underlying scaffolds that specify the orders and orientations of contigs together with the gap distances between contigs. The current methods construct scaffolds based on the alignments of 'linking' reads against contigs. We found that some 'optimal' alignments are mistaken due to factors such as the contig boundary effect, particularly in the presence of repeats. Occasionally, the incorrect alignments can even overwhelm the correct ones. The detection of the incorrect linking information is challenging in any existing methods. RESULTS: In this study, we present a novel scaffolding method RegScaf. It first examines the distribution of distances between contigs from read alignment by the kernel density. When multiple modes are shown in a density, orientation-supported links are grouped into clusters, each of which defines a linking distance corresponding to a mode. The linear model parameterizes contigs by their positions on the genome; then each linking distance between a pair of contigs is taken as an observation on the difference of their positions. The parameters are estimated by minimizing a global loss function, which is a version of trimmed sum of squares. The least trimmed squares estimate has such a high breakdown value that it can automatically remove the mistaken linking distances. The results on both synthetic and real datasets demonstrate that RegScaf outperforms some popular scaffolders, especially in the accuracy of gap estimates by substantially reducing extremely abnormal errors. Its strength in resolving repeat regions is exemplified by a real case. Its adaptability to large genomes and TGS long reads is validated as well. AVAILABILITY AND IMPLEMENTATION: RegScaf is publicly available at https://github.com/lemontealala/RegScaf.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Effects of weight loss on bone turnover, inflammatory cytokines, and adipokines in Chinese overweight and obese adults.

PURPOSE: Plenty of studies have examined the long term effect of weight loss on bone mineral density. This study aimed to explore the effects of 10% weight loss on early changes in bone metabolism as well as the possible influencing factors. METHODS: Overweight and obese outpatients (BMI > 24.0 kg/m2) were recruited from the nutrition clinic and followed a calorie-restricted, high-protein, low-carbohydrate diet program. Dietary intake, body composition, serum procollagen type I N-propeptide (PINP), ß-Crosslaps, PTH, 25(OH) VitD, a series of inflammatory cytokines and adipokines were measured for the participants before starting to lose weight and after 10% weight loss (NCT04207879). RESULTS: A total of 75 participants were enrolled and 37 participants achieved a weight loss of at least 10%. It was found that PINP decreased (p = 0.000) and the ß-Crosslaps increased (p = 0.035) in female participants. Decreases in PTH (p = 0.001), serum IL-2 (p = 0.013), leptin (p = 0.001) and increases in 25(OH) VitD (p = 0.001), serum ghrelin (p = 0.033) were found in 37 participants after 10% of their weight had been lost. Change in PINP was detected to be significantly associated with change in lean body mass (r = 0.418, p = 0.012) and change in serum ghrelin(r = - 0.374, p = 0.023). CONCLUSIONS: Bone formation was suppressed and bone absorption was increased in female subjects after a 10% weight loss. Bone turnover was found to be associated with lean body mass and affected by the circulating ghrelin level.

Research Note: Development of a sandwich ELISA for determining plasma growth hormone concentrations in goose.

Growth hormone (GH) is required for normal postnatal development in poultry; however, no immunoassay exists to assess its levels in geese plasma, hindering the study of endocrine regulation in this species. We developed a sandwich ELISA to determine the GH concentrations in the plasma of geese. Recombinant goose GH was produced using a eukaryotic expression system and purified for use as the reference standard in ELISA and the antigen for producing the polyclonal antibodies in rabbits. Rabbit anti-goose GH polyclonal antibody was used to coat the wells of the ELISA plate, and its biotinylated form served as the detection antibody. An avidin-conjugated horseradish peroxidase was used to bind the detection antibody and catalyze the chromogenic reaction of 3,3,5,5-tetramethylbenzidine and H2O2. A sigmoidal curve was fitted to the optical density and the log of the standard GH concentration using the four-parameter logistic model. The sensitivity of the assay was less than 0.156 ng/mL. The intra- and interassay coefficients of variation were less than 9 and 13%, respectively. The response curve of the serially diluted plasma samples from geese exhibited a good parallel relationship with that observed for the reference standards. The assay effectively detected differences in GH concentrations in plasma samples from geese at various physiological stages; thus, it will be useful for future study of their growth and metabolism.

The effect of monomeric and oligomeric FLAVAnols in patients with type 2 diabetes and microalbuminuria (FLAVA-trial): A double-blind randomized controlled trial.

BACKGROUND & AIMS: Microalbuminuria is an early sign of vascular complications of type 2 diabetes and predicts cardiovascular disease and mortality. Monomeric and oligomeric flavanols (MOFs) are linked to improved vascular health. The aim of this study was to assess the effect of 3 months MOFs on albuminuria and endothelial function markers in patients with type 2 diabetes and microalbuminuria. METHODS: We conducted a double-blind, placebo-controlled trial among patients with type 2 diabetes and microalbuminuria. Patients with type 2 diabetes received either 200 mg MOFs or placebo daily on top of their habitual diet and medication. The primary endpoint was the between-group difference of the change in 24-h Albumin Excretion Rate (AER) over three months. Secondary endpoints were the between-group differences of the change in plasma levels of different markers of endothelial dysfunction. Mixed-modelling was applied for the longitudinal analyses. RESULTS: Participants (n = 97) were 63.0 ± 9.5 years old; diabetes-duration was 15.7 ± 8.5 years. Median baseline AER was 60 (IQR 20-120) mg/24 h. There was no within-group difference in median change of AER from baseline to 3 months in the intervention (0 (-35-21) mg/24 h, p = 0.41) or the control group (0 (-20-10) mg/24 h, p = 0.91). There was no between-group difference in the course of AER over three months (log-transformed data: ß = -0.02 (95%CI -0.23-0.20), p = 0.88), nor in the plasma levels of the endothelial dysfunction markers. CONCLUSION: Daily 200 mg MOFs for three months on top of habitual diet and usual care did not reduce AER and plasma markers of endothelial dysfunction compared to placebo, in patients with long-term type 2 diabetes and microalbuminuria. CLINICAL TRIALS REGISTRATION: NTR4669, www.trialregister.nl.

MUREN: a robust and multi-reference approach of RNA-seq transcript normalization.

BACKGROUND: Normalization of RNA-seq data aims at identifying biological expression differentiation between samples by removing the effects of unwanted confounding factors. Explicitly or implicitly, the justification of normalization requires a set of housekeeping genes. However, the existence of housekeeping genes common for a very large collection of samples, especially under a wide range of conditions, is questionable. RESULTS: We propose to carry out pairwise normalization with respect to multiple references, selected from representative samples. Then the pairwise intermediates are integrated based on a linear model that adjusts the reference effects. Motivated by the notion of housekeeping genes and their statistical counterparts, we adopt the robust least trimmed squares regression in pairwise normalization. The proposed method (MUREN) is compared with other existing tools on some standard data sets. The goodness of normalization emphasizes on preserving possible asymmetric differentiation, whose biological significance is exemplified by a single cell data of cell cycle. MUREN is implemented as an R package. The code under license GPL-3 is available on the github platform: github.com/hippo-yf/MUREN and on the conda platform: anaconda.org/hippo-yf/r-muren. CONCLUSIONS: MUREN performs the RNA-seq normalization using a two-step statistical regression induced from a general principle. We propose that the densities of pairwise differentiations are used to evaluate the goodness of normalization. MUREN adjusts the mode of differentiation toward zero while preserving the skewness due to biological asymmetric differentiation. Moreover, by robustly integrating pre-normalized counts with respect to multiple references, MUREN is immune to individual outlier samples.

The ability of post-chemoradiotherapy DWI ADCmean and 18F-FDG SUVmax to predict treatment outcomes in head and neck cancer: impact of human papilloma virus oropharyngeal cancer status.

OBJECTIVES: To evaluate the ability of post-chemo-radiotherapy (CRT) diffusion-weighted-MRI apparent diffusion coefficient (ADCmean) and 18F-FDG PET maximum standardized uptake value (SUVmax) to predict disease-free survival (DFS) in head and neck squamous cell carcinoma (HNSCC), and to determine whether this ability is influenced by human papillomavirus oropharyngeal cancer (HPV-OPC) status. METHODS: This prospective cohort observational study included 65 participants (53 male, mean ± SD age 59.9 ± 7.9 years, 46 HPV-OPC) with stage III or IV HNSCC. Primary tumour and nodal ADCmean (pre-treatment, 6- and 12-weeks post-CRT) and SUVmax (12-weeks post-CRT) were measured. Variables were compared with 2-year DFS (independent t-test/Mann-Whitney test) and overall DFS (Cox regression), before and after accounting for HPV-OPC status. Variables were also compared between HPV-OPC and other HNSCC subgroups after stratifying for DFS. RESULTS: Absolute post-CRT ADCmean values predicted 2-year DFS and overall DFS for all participants (p = 0.03/0.03, 6-week node; p = 0.02/0.03 12-week primary tumour) but not in the HPV-OPC subgroup. In participants with DFS, percentage interval changes in primary tumour ADCmean at 6- and 12-weeks were higher in HPV-OPC than other HNSCC (p = 0.01, 6 weeks; p = 0.005, 12 weeks). The 12-week post-CRT SUVmax did not predict DFS. CONCLUSION: Absolute post-CRT ADCmean values predicted DFS in HNSCC but not in the HPV-OPC subgroup. Amongst participants with DFS, post-CRT percentage interval changes in primary tumour ADCmean were significantly higher in HPV-OPC than in other HNSCC. Knowledge of HPV-OPC status is crucial to the clinical utilisation of post-CRT DWI-MRI for the prediction of outcomes.

Impairment of testes development in Yangzhou ganders by augmentation of leptin receptor signaling.

The aim of this study was to determine the cellular and molecular mechanisms of leptin (LEP) and the leptin receptor (LEPR) in testicular development of prepubertal ganders. In an in vivo animal experiment, active immunization against LEPR severely depressed prepubertal testicular development by significantly reducing testicular weights at 200 and 227 days of age. The number of elongated spermatids in the seminiferous tubules was also significantly decreased by immunization with LEPR at ages of 200 and 227 days. Inhibition of testicular development by LEPR immunization was associated with decreases in LHR, StAR, 3ß-HSD, CYP11A1, CYP17A1, and PRLR mRNA expression levels in testicular tissue, which resulted in a significant decrease in testosterone synthesis. In the in vitro experiments, the addition of LEP combined with anti-LEPR antibodies strengthened LEPR signal transduction, and inhibited significantly testosterone production in cultured Leydig cells isolated from prepubertal gander testes. The mRNA expression of LHR, StAR, 3ß-HSD, CYP11A1, CYP17A1 also decreased significantly after treatment with LEP combined with anti-LEPR antibodies in cultured Leydig cells. These results suggest that anti-LEPR antibodies strengthen LEPR signaling transduction in the presence of LEP, and immunization against LEPR inhibited testes development and testosterone secretion in prepubertal ganders.

18F-FDG-PET in guided dose-painting with intensity modulated radiotherapy in oropharyngeal tumours: A phase I study (FiGaRO).

BACKGROUND AND PURPOSE: The FiGaRO trial assessed the feasibility and safety of using an FDG-PET-based dose-painting technique to deliver a radiotherapy (RT) boostto the FDG-avid primary tumour in patients with locally advanced high and intermediate risk oropharyngeal cancer. MATERIALS AND METHOD: Patients underwent a planning 18FDG-PET-CT scan, immobilised in the treatment position, after one cycle of induction chemotherapy. The volume of persistent FDG-avidity in the primary tumour was escalated to 71.5 Gy in30 fractions delivered using a simultaneous integrated boost Intensity Modulated RT (SIB-IMRT) technique. RT was delivered with concomitant Cisplatin following 2 cycles of induction chemotherapy. The primary outcome was the incidence of grade ≥ 3 late mucosal toxicity 12 months post-treatment, with an excess rate of >10% regarded as unacceptable. RESULTS: Twenty-nine patients were included and twenty-four were treated between 2014 and 2018, in two UK centres. Median follow-up was 36 months (range 4-56 months). Pre-defined planning target volume objectives and organ at risk dose constraints were met in all cases. There were no incidents of acute grade 4 toxicity. There were 4 cases of grade ≥ 3 mucosal toxicity at 12 months post-treatment (19.1%). There were no cases of persistent mucosal ulceration at 12 months. Overall survival at 3-years was 87.5%, 92.9% for intermediate and 70.0% for high risk patients. CONCLUSION: Late toxicity rates, although higher than anticipated, are comparable to contemporary published data for standard dose chemo-IMRT. Results suggest improved 3y survival rates for high risk patients. This approach merits further investigation. ClinicalTrials.gov Identifier: NCT02953197.

[Genome-wide analysis of LBD(lateral organ boundaries domain) gene family in Cannabis sativa of traditional Chinese medicine hemp seed].

LBD(lateral organ boundaries)transcription factors play an important role in the regulation of plant growth, development and secondary metabolism. In order to explore the function of LBD genes in cannabis, the Cannabis sativa genome and transcriptome were used to identify the C. sativa LBD gene family, and analyzed their expression patterns. Our results showed that the cannabis LBD contains 32 members, which were divided into two major categories, seven sub-families. Class Ⅰ was divided into 5 sub-families, named Class Ⅰ_a to Class Ⅰ_e, while Class Ⅱ was divided into 2 sub-families, including Class Ⅱ_a and Class Ⅱ_b. Analysis showed that the number of amino acids encoded LBDs was between 172 and 356, and the isoelectric point was between 4.92 and 9.43. The mole-cular weight of LBD was between 18 862.92 Da and 40 081.33 Da, and most members are located in the nucleus. Chromosome positioning of LBD showed that 32 members were unevenly distributed on 10 chromosomes of C. sativa LBD transcription factor domain, gene structure and motifs are relatively conservative, and the characteristics of different class members are similar. The upstream promoter region of the gene contains a variety of cis-acting elements related to plant hormones and environmental factors, C. sativa LBD genes have different expression patterns in the stems, leaves, and flowers of ZYS varieties(low tetrahydrocannabinol, high cannabidiol). The members of the LBD gene family are mainly expressed in the flowers and stems of ZYS varieties, while members expressed in the leaves very few; Class Ⅱ members CsLBD21 and CsLBD23 are expressed in flowers and stems, and CsLBD8 and CsLBD18 are expressed in flowers, stems and leaves. These genes may participate in the growth and development of cannabis and affect the biosynthesis of cannabinoids. This study laid the foundation for the subsequently functional research of the cannabis LBD gene family.