Search

Abstract This study investigates how dynamic fluctuations in matrix stiffness affect the behavior of cardiac fibroblasts (CFs) within a three-dimensional (3D) hydrogel environment. Using hybrid hydrogels with tunable stiffness, we created an in vitro model to mimic the varying stiffness of the cardiac microenvironment. By manipulating hydrogel stiffness, we examined CF responses, particularly the expression of α-smooth muscle actin (α-SMA), a marker of myofibroblast differentiation. Our findings reveal that increased matrix stiffness promotes the differentiation of CFs into myofibroblasts, while matrix softening reverses this process. Additionally, we identified the role of focal adhesions and integrin β1 in mediating stiffness-induced phenotypic switching. This study provides significant insights into the mechanobiology of cardiac fibrosis and suggests that modulating matrix stiffness could be a potential therapeutic strategy for treating cardiovascular diseases.

The global temperature is continuously rising, and the impacts of nighttime warming (NW) and daytime warming (DW) on ecosystems have drawn widespread attention. However, most studies on the effects of daytime and nighttime warming on ecosystems have focused primarily on aboveground processes, but little is known about how they affect underground processes, particularly soil microorganisms. Therefore, we examined the effects of daytime and nighttime experimental warming (CK: control, DW: daytime warming, NW: nighttime warming, DW + NW: daily warming) on soil bacterial and fungal diversities at the Experimental Station of Zengcheng Forestry Science Research Institute in Guangdong, China. The results showed that, compared with the CK treatment, the NW rather than DW treatment significantly increased the abundance-based coverage estimator (ACE) diversity index of bacteria and fungi. Fungal beta diversity significantly differed between the DW and NW treatments, while there was no significant difference in bacterial beta diversity. Our research indicated that the NW treatment creates a more favourable microenvironment than the DW treatment, accelerating the mineralization of soil carbon, nitrogen, and phosphorus nutrients, which may be the reason for changes in microbial diversity. Our study provides important theoretical support and practical guidance for predicting the impact of global climate change on the diversity of microbial ecosystems.

In this study, we investigate the enhancement of effective transconductance and gain linearity in submicrometer gate AlGaN-barrier-based transistors utilizing ScAlN/GaN coupling-channel structures. A novel asymmetric gate design, incorporating an AlGaN cap on ScAlN/GaN HEMT, is proposed. This configuration demonstrates a flat transconductance profile and significantly reduced transconductance derivative, thereby improving the linearity of GaN-based transistors. For transistors with a gate length of 0.5 μm, both the current gain cut-off frequency and power gain cut-off frequency are measured at 53.52 GHz and 72.98 GHz, respectively. These values represent a more than threefold increase from the corresponding frequencies of conventional devices. Moreover, the theoretical Output Third-Order Intercept value of the proposed structure has increased by 7.5 dBm compared to conventional HEMTs. This superior linear performance can be attributed to the combined effect of AlGaN cap layer and air cavity. Furthermore, the introduction of the ScAlN layer results in a substantial impact, including a decrease in electron concentration from 4.96 × 1019/cm3 to 1.98 × 1019/cm3 and an increase in electron velocity from 4.5 × 107 to 7.6 × 108 cm/s. These findings underscore the potential of the proposed device for high-frequency applications requiring superior linearity.

Abstract Power battery is one of the core components of electric vehicles (EVs) and a major contributor to the environmental impact of EVs, and reducing their environmental emissions can help enhance the sustainability of electric vehicles. Based on the principle of stiffness equivalence, the steel case of the power cell is replaced with lightweight materials, a life cycle model is established with the help of GaBi software, and its environmental impact is evaluated using the CML2001 method. The results can be summarized as follows: (1) Based on the four environmental impact categories of GWP, AP, ADP (f), and HTP, which are the global warming potential (GWP), acidification potential (AP), abiotic depletion potential (ADP (f)) and human toxicity potential (HTP), the environmental impact of lightweight materials is lower than that of the steel box. Among them, the aluminum alloy box has the largest reduction, and the Carbon Fiber Sheet Molding Compound (CF-SMC) box is the second. (2) In the sensitivity analysis of electric structure, an aluminum alloy box is still the most preferable choice for environmental impact. (3) In the sensitivity analysis of driving mileage, the aluminum alloy box body is also the best choice for vehicle life. (4) Quantitative assessment using substitution factors measures the decrease in greenhouse gas emissions following the substitution of steel battery box with lightweight materials. The adoption of aluminum alloy battery box can lead to a reduction of 1.55 tons of greenhouse gas emissions, with a substitution factor of 1.55 tC sb−1. In the case that composite materials have not been recycled commercially on a large scale, aluminum alloy is still one of the best materials for the integrated environmental impact of the whole life cycle of the battery boxes.

This article demonstrates the effect of reverse gradient barrier layer and floating gate structure on DC and RF performance of GaN-based HEMTs. In terms of power characteristics, using reverse gradient barrier and floating gate, the GaN-HEMTs with Lg of 240 nm and S-D spacing of 8.4 μm demonstrated the maximum drain current and peak transconductance are increased by 70 % and 15 % respectively, and the linearity of GaN based HEMT is greatly improved. Meanwhile, using the reverse gradient barrier layer, the gate leakage current is significantly reduced by nearly 1 to 5 orders of magnitude, and it is proved that the negative polarization effect has a certain effect on increasing the threshold voltage and breakdown voltage. In terms of RF characteristics, due to the existence of the floating gate, the parasitic capacitance is reduced and the frequency performance is improved. In addition, for both conventional and proposed HEMTs, this article proposes two equivalent capacitance models to optimize RF performance. As a result, the optimal structure offers approximately 10 and 7 times improvement in the current gain cutoff frequency (ft) and unilateral power gain cutoff frequency (fmax) (from 5.3 and 9.8 to 52 and 73.8 GHz, respectively). Additionally, the optimal structure exhibits outstanding scaling factors of 12.48 GHz·μm.

Abstract Objective Develop and evaluate an ensemble clinical machine learning–deep learning (CML-DL) model integrating deep visual features and clinical data to improve the prediction of supraspinatus/infraspinatus tendon complex (SITC) injuries. Methods Patients with suspected SITC injuries were retrospectively recruited from two hospitals, with clinical data and shoulder x-ray radiographs collected. An ensemble CML-DL model was developed for diagnosing normal or insignificant rotator cuff abnormality (NIRCA) and significant rotator cuff tear (SRCT). All patients suspected with SRCT were confirmed by arthroscopy examination. The model’s performance was evaluated using sensitivity, specificity, accuracy, and area under the curve (AUC) metrics, and a two-round assessment was conducted to authenticate its clinical applicability. Results A total of 974 patients were divided into three cohorts: the training cohort (n = 828), the internal validation cohort (n = 89), and the external validation cohort (n = 57). The CML-DL model, which integrates clinical and deep visual features, demonstrated superior performance compared to individual models of either type. The model’s sensitivity, specificity, accuracy, and area under curve (95% confidence interval) were 0.880, 0.812, 0.836, and 0.902 (0.858–0.947), respectively. The CML-DL model exhibited higher sensitivity and specificity compared to or on par with the physicians in all validation cohorts. Furthermore, the assistance of the ensemble CML-DL model resulted in a significant improvement in sensitivity for junior physicians in all validation cohorts, without any reduction in specificity. Conclusions The ensembled CML-DL model provides a solution to help physicians improve the diagnosis performance of SITC injury, especially for junior physicians with limited expertise. Critical relevance statement The ensembled clinical machine learning–deep learning (CML-DL) model integrating deep visual features and clinical data provides a superior performance in the diagnosis of supraspinatus/infraspinatus tendon complex (SITC) injuries, particularly for junior physicians with limited expertise. Key points 1. Integrating clinical and deep visual features improves diagnosing SITC injuries. 2. Ensemble CML-DL model validated for clinical use in two-round assessment. 3. Ensemble model boosts sensitivity in SITC injury diagnosis for junior physicians. Graphical Abstract

Objective Patch technology has been the new technique in the treatment of partial thickness of the rotator cuff tear (PTRCTs) to address the limitation of traditional techniques. Compared with allogeneic patches and artificial materials, coracoacromial ligament is obviously closer to their own biology. The purpose of the study was to evaluate the functional and radiographic outcomes following arthroscopic autologous coracoacromial ligament augment technique for treatment of PTRCTs. Method This study included three female patients with PTRCTs who underwent arthroscopy operation in 2017 with an average age of 51 years (range from 50 to 52 years). The coracoacromial ligament implant was attached to the bursal side surface of the tendon. The clinical results were evaluated by American Shoulder and Elbow Surgeons (ASES) score, Simple Shoulder Test (SST), acromiohumeral distance (AHD) and muscle strength before and 12 months after operation. Magnetic resonance imaging (MRI) was performed 24 months after operation to assess the integrity of the anatomical structure of the original tear site. Result The average ASES score improved significantly from 57.3 preoperatively to 95.0 at 1‐year follow‐up. The strength improved significantly from grade 3 preoperatively to grade 5 at 1 year. Two of three patients underwent the MRI at 2‐year follow‐up. Radiographic released the complete healing of rotator cuff tear. No implant‐related serious adverse events were reported. Conclusion The new technique of using autogenous coracoacromial ligament patch augment provides good clinical results on patients with PTRCTs.

Abstract Since its inception, the frequency diverse array (FDA) has attracted extensive attention and research because of its unique properties. However, most of the research primarily focuses on linear geometry FDA, with fewer studies on planar FDA. This letter proposes a design method based on planar rectangular FDA (PRFDA), which adjusts the frequency of each array element nonlinearly so that the beam direction of planar rectangular FDA can change linearly or nonlinearly with time, forming the desired transmit beampattern. Theoretical analysis and simulation results verify the effectiveness of the proposed method.

This paper presents a GaN-based High Electron Mobility Transistor (HEMT) with a connected dual-channel structure (CDC-HEMT). Specifically, the Al0.05Ga0.95N layer beneath the first channel enables the second channel to be in a non-conducting state while simultaneously increasing the number of electrons available in the conducting state. In contrast to conventional normally-off devices, the CDC-HEMT exhibits excellent DC performance, with a saturation current density increase from 0.67 A/mm to 1.52 A/mm at Vds = 10 V and a maximum transconductance increase from 0.30 S to 0.62 S, which is twice as much. Furthermore, the optimal transconductance interval is widened by 1 V. The RF performance of the devices also demonstrates remarkable performance, with a current gain cut-off frequency of 31.8 GHz and a maximum oscillation frequency of 77 GHz. Under square wave testing, the transistors exhibit extremely low delay. The exceptional findings showcased in this study provide compelling evidence that the CDC-HEMT structure is a highly promising technique for utilizing GaN-based HEMTs with superior performance in power switching and microwave applications.

Abstract Background Evidence from previous studies has suggested that ginger extract exhibits the potential as an alternative treatment for Coronavirus disease 2019 (COVID-19). Here, we want to investigate whether ginger supplement improves the clinical manifestation of hospitalized COVID-19 individuals. Methods A total of 227 hospitalized individuals with COVID-19 were randomized to either the control (n = 132) or intervention group (n = 95). The intervention group took ginger supplement orally at the dosage of 1.5 g twice daily, until they were discharged from the hospital. Both groups received the same standard of general medical care during hospitalization, and the length of stay was recorded and compared between groups. Results Among all participants, a significant reduction in hospitalization time (the difference between the treatment and control groups was 2.4 d, 95% CI 1.6–3.2) was detected in response to the ginger supplement. This effect was more pronounced in men, participants aged 60 years or older, and participants with pre-existing medical conditions, relative to their counterparts (P-interactions

Abstract Objective The absence of patellar ligament will bring about a severe negative impact on daily life. Many reconstruction techniques have been described in adults. However, there is a lack of technical introduction regarding the reconstruction of the patellar ligament in children. The purpose of this study was to report a surgical technique for reconstructing the patellar ligament in children. Method A retrospective analysis of the clinical data on a patellar ligament (tendon sheath fibroma) patient with allogeneic tendon reconstruction. An 8‐year‐old child with postoperative recurrence of left patellar ligament tumor was enrolled in our study. Anterior tibialis tendon allograft was used to reconstruct the patellar ligament after complete resection of the patellar ligament for the tumor. The tunnels were constructed on the deep surface of the tibial tubercle and the root of the quadriceps tendon (to decrease the harmful impact on patella development), respectively. The allogeneic tendon was passed through the tunnels above in the shape of “8,” and the two ends of the tendon were attached to the bleeding bone bed at the inferior edge of the patella with suture anchors to achieve better bone‐tendon healing. During the follow‐up, the knee's range of motion and imaging manifestations were recorded. Result Postoperative pathology suggests chondromesenchymal hamartoma, a rare benign soft tissue tumor different from the previous operation (tendon sheath fibroma). During the 4‐year follow‐up, the patient's active range of motion of the knee achieved 0° to 120°; and the patient could walk normally without any external help. Physical examinations (the apprehension sign and J sign) showed no ligamentous instability or patellar ligament tenderness. Imaging analysis showed that the ratio length of the patellar ligament to the patella was almost normal. The integrity, continuity, and shape of the allogeneic ligament showed excellent results in MRI. Combined with clinical and imaging findings, allogeneic tendon patellar ligament reconstruction was deemed successful. Conclusion Allogeneic ligament reconstruction technique can provide a treatment option by reconstructing the extensor mechanism, minimizing the impact on patellar development, and augmenting biological healing for children with the absence of the patellar ligament.

Objective To investigate the Young's modulus value of infraspinatus tendons using shear wave elastography (SWE) technique in normal adults, and to analyze the influence of gender, postures, exercise, and dominant side on Young's modulus of infraspinatus tendons. Methods This is a prospective cross‐sectional study. From January 2019 to July 2020, 14 healthy subjects were identified, including seven males and seven females aged between 24 to 34, with a mean age of 27.67 ± 3.08 years. The Young's modulus of their infraspinatus tendons was measured by two operators using SWE in neutral and maximum external rotation positions of both sides before exercise and the dominant side after exercise. The Young's modulus values in different sexes, different postures, before vs after exercise, and dominant vs non‐dominant side were statistically analyzed. Results All 14 subjects completed the data collection process. The mean Young's modulus values of infraspinatus tendon for dominant sides in neutral position were 33.04 ± 3.01 kPa for males and 28.76 ± 3.09 kPa for females. And for non‐dominant sides in the neutral position, the values were 33.02 ± 2.38 kPa for males and 28.86 ± 2.47 kPa for females. In the maximum external rotation position, the values for dominant sides were 50.19 ± 4.86 kPa for males and 42.79 ± 4.44 kPa for females, and for non‐dominant sides were 50.95 ± 3.24 kPa for males and 42.42 ± 3.66 kPa for females. After exercise, the mean Young's modulus values of infraspinatus tendon for dominant sides in neutral position were 54.56 ± 3.76 kPa for males and 46.66 ± 5.99 kPa for females. And for the maximum external rotation position, the values were 59.13 ± 3.78 kPa for males and 54.49 ± 5.67 kPa for females. The Young's modulus of infraspinatus tendon in the neutral and maximum external rotation positions showed statistically significant differences in males and females, as well as before and after exercise (P 0.05). Intergroup reliability between both operators was excellent (ICC > 0.85). Conclusion There are gender‐related differences and post‐exercise increase in Young's modulus, yet such a difference cannot be witnessed between the dominant and non‐dominant sides.

The Jurassic shale in the northeastern Sichuan Basin is one of the main target intervals for continental shale gas exploitation. Research on the pore structure and gas-bearing properties of shales is the key issue in target interval optimization. Through core observation, geochemistry, bulk minerals, scanning electron microscopy, nitrogen adsorption, and isothermal adsorption experiments, various lithofacies with different pore structure characteristics were clarified. In addition, the factors that control gas-bearing properties were discussed, and a continental shale gas enrichment model was finally established. The results show that the Jurassic continental shale in the northeastern Sichuan Basin can be classified into six lithofacies. Organic pores, intergranular pores, interlayer pores in clay minerals, intercrystalline pores in pyrite framboids, and dissolution pores can be observed in shale samples. Pore structures varied in different shale lithofacies. The contact angle of shales is commonly less than 45°, leading to complex wettability of pores in the shales. Free gas content is mainly controlled by the organic matter (OM) content and the brittleness in the Jurassic shale. The adsorbed gas content is mainly controlled by the OM content, clay mineral type, and water saturation of the shales. The enrichment mode of the Lower Jurassic continental shale gas in the northeastern Sichuan Basin is established. Paleoenvironments control the formation of organic-rich shales in the center part of lakes. The “baffle” layer helps the confinement and high pressure, and the complex syncline controls the preservation, forming the enrichment pattern of the complex syncline-central baffle layer.

In recent years, connected automated vehicles (CAVs) have attracted much attention, and the coordination strategy of CAVs in isolated intersections has been widely discussed. However, these algorithms for isolated intersections cannot be directly applied in a multi-intersection road network (MiRN). The coordination strategy in the MiRN requires further investigation. This paper proposes a two-tier strategy for CAV coordination in the MiRN. First, we analyze the coordination problem in isolated intersections and formulate it as a mixed-integer programming problem. Then, for the MiRN, we propose a consensus prediction method to estimate the travel time for CAVs with different paths. Finally, a novel coordination approach is given, showing how to determine the optimal path for CAVs. The experimental results demonstrate the efficiency of the proposed strategy under various traffic flow rates. Compared with the fixed signal time assignment method and the actuated signal time assignment method, our method reduces the average travel time by about 74–83% under different flow rates. We also evaluate the impact of parameters on the strategy’s performance and provide some suggestions for setting these parameters.

Fish can swim in a variety of states. For example, they look flexible and perform low-frequency undulatory locomotion when cruising, but they seem very powerful and stiff and perform high-frequency undulatory when hunting. In the process of changing the motion state, the stiffness of the fish body affects the swimming performance of the fish. In this article, we imitated the change of stiffness by superimposing rubber sheets and used experimental methods to test its swimming performance under different swing frequencies. A series of rubber fish tails were made according to the analysis of the swimming movement of real fish, providing different stiffness values and changing the curves of the body. In the prototype experiments, the base of the fish tail was fixed to a platform via a force sensor, which can oscillate at various speeds, so that the fish tail was able to swing and the thrust could be tested at different frequencies. According to the experimental results, we found that with the change of the swing frequency, there were different optimal stiffnesses that could make the thrust reach the maximum value, and with the increase of stiffness, the envelope interval of the swing curve gradually widened, the amplitude increased, and the hysteresis of the tail fin relative to the end decreased.

For studying the strata behavior due to multi-slicing top coal caving longwall mining along-the-strike direction in steeply dipping extra thick coal seams, the shield support pressures of the upper and lower slices of panel 37220 in Dongxia Coal Mine were monitored using the KJ513 dynamic monitoring system. The set up rooms adopted the “horizontal line-arc segment-inclined line” form and used different types of shield supports. The results show that the strata pressure of upper slice panel 37220-1 changed slightly along the strike direction, while along the dip direction it exhibited strong to weak pressure from bottom to top. The first weighting interval of lower slice panel 37220-2 was about 60.8 m, and the average periodic weighting interval were about 22.6 m. The strata behavior of panel 37220-2 exhibited a spatio-temporal characteristic in that periodic weighting occurred first in the middle-upper part, followed by the middle and upper parts, arc segment, and finally the lower part. During the periodic weighting, the weighting interval and intensity also exhibited strong space characteristics. The average dynamic load coefficient was 1.48 and the maximum lateral load of the side shield was 20–25 MPa. Keywords: Monitoring, Steeply dipping seam, Slicing, Longwall along the strike, Fully mechanized top-caving face, Strata behavior

We have previously identified NOD2 genotype and inflammatory bowel diseases (IBD) phenotype, as associated with shifts in the ileal microbiome ("dysbiosis") in a patient cohort. Here we report an integrative analysis of an expanded number of Crohn's disease (CD) related genetic defects in innate immune function (NOD2, ATG16L1, IRGM, CARD9, XBP1, ORMDL3) and composition of the ileal microbiome by combining the initial patient cohort (Batch 1, 2005-2010, n = 165) with a second consecutive patient cohort (Batch 2, 2010-2012, n = 118). These combined patient cohorts were composed of three non-overlapping phenotypes: 1.) 106 ileal CD subjects undergoing initial ileocolic resection for diseased ileum, 2.) 88 IBD colitis subjects without ileal disease (predominantly ulcerative colitis but also Crohn's colitis and indeterminate colitis, and 3.) 89 non-IBD subjects. Significant differences (FDR < 0.05) in microbiota were observed between macroscopically disease unaffected and affected regions of resected ileum in ileal CD patients. Accordingly, analysis of the effects of genetic and clinical factors were restricted to disease unaffected regions of the ileum. Beta-diversity differed across the three disease categories by PERMANOVA (p < 0.001), whereas no significant differences in alpha diversity were noted. Using negative binomial models, we confirmed significant effects of IBD phenotype, C. difficile infection, and NOD2 genotype on ileal dysbiosis in the expanded analysis. The relative abundance of the Proteobacteria phylum was positively associated with ileal CD and colitis phenotypes, but negatively associated with NOD2R genotype. Additional associations with ORMDL3 and XBP1 were detected at the phylum/subphylum level. IBD medications, such as immunomodulators and anti-TNFα agents, may have a beneficial effect on reversing dysbiosis associated with the IBD phenotype. Exploratory analysis comparing microbial composition of the disease unaffected region of the resected ileum between 27 ileal CD patients who subsequently developed endoscopic recurrence within 6-12 months versus 34 patients who did not, suggested that microbial biomarkers in the resected specimen helped stratify patients with respect to risk of post-surgical recurrence.

[This corrects the article DOI: 10.1371/journal.pone.0153125.].

Incidence and mortality rates of colorectal carcinoma (CRC) are higher in African Americans (AAs) than in Caucasian Americans (CAs). Deficient micronutrient intake due to dietary restrictions in racial/ethnic populations can alter genetic and molecular profiles leading to dysregulated methylation patterns and the inheritance of somatic to germline mutations.Total DNA and RNA samples of paired tumor and adjacent normal colon tissues were prepared from AA and CA CRC specimens. Reduced Representation Bisulfite Sequencing (RRBS) and RNA sequencing were employed to evaluate total genome methylation of 5'-regulatory regions and dysregulation of gene expression, respectively. Robust analysis was conducted using a trimming-and-retrieving scheme for RRBS library mapping in conjunction with the BStool toolkit.DNA from the tumor of AA CRC patients, compared to adjacent normal tissues, contained 1,588 hypermethylated and 100 hypomethylated differentially methylated regions (DMRs). Whereas, 109 hypermethylated and 4 hypomethylated DMRs were observed in DNA from the tumor of CA CRC patients; representing a 14.6-fold and 25-fold change, respectively. Specifically; CHL1, 4 anti-inflammatory genes (i.e., NELL1, GDF1, ARHGEF4, and ITGA4), and 7 miRNAs (of which miR-9-3p and miR-124-3p have been implicated in CRC) were hypermethylated in DNA samples from AA patients with CRC. From the same sample set, RNAseq analysis revealed 108 downregulated genes (including 14 ribosomal proteins) and 34 upregulated genes (including POLR2B and CYP1B1 [targets of miR-124-3p]) in AA patients with CRC versus CA patients.DNA methylation profile and/or products of its downstream targets could serve as biomarker(s) addressing racial health disparity.

Mutation of the adenomatous polyposis coli (APC gene), an early event in the adenoma-carcinoma sequence, is present in 70-80% of sporadic human colorectal adenomas and carcinomas. To test the hypothesis that mutation of the APC gene alters microbial interactions with host intestinal mucosa prior to the development of polyposis, culture-independent methods (targeted qPCR assays and Illumina sequencing of the 16S rRNA gene V1V2 hypervariable region) were used to compare the intestinal microbial composition of 30 six-week old C57BL/6 APCMin/+ and 30 congenic wild type (WT) mice. The results demonstrate that similar to 12-14 week old APCMin/+ mice with intestinal neoplasia, 6 week old APCMin/+ mice with no detectable neoplasia, exhibit an increased relative abundance of Bacteroidetes spp in the colon. Parallel mouse RNA sequence analysis, conducted on a subset of proximal colonic RNA samples (6 APCMin/+, 6 WT) revealed 130 differentially expressed genes (DEGs, fold change ≥ 2, FDR

In order to assess potential associations between autism spectrum disorder (ASD) phenotype, functional GI disorders and fecal microbiota, we recruited simplex families, which had only a single ASD proband and neurotypical (NT) siblings, through the Simons Simplex Community at the Interactive Autism Network (SSC@IAN). Fecal samples and metadata related to functional GI disorders and diet were collected from ASD probands and NT siblings of ASD probands (age 7-14). Functional gastrointestinal disorders (FGID) were assessed using the parent-completed ROME III questionnaire for pediatric FGIDs, and problem behaviors were assessed using the Child Behavior Check List (CBCL). Targeted quantitative polymerase chain reaction (qPCR) assays were conducted on selected taxa implicated in ASD, including Sutterella spp., Bacteroidetes spp. and Prevotella spp. Illumina sequencing of the V1V2 and the V1V3 regions of the bacterial 16S rRNA genes from fecal DNA was performed to an average depth of 208,000 and 107,000 high-quality reads respectively. Twenty-five of 59 ASD children and 13 of 44 NT siblings met ROME III criteria for at least one FGID. Functional constipation was more prevalent in ASD (17 of 59) compared to NT siblings (6 of 44, P = 0.035). The mean CBCL scores in NT siblings with FGID, ASD children with FGID and ASD without FGID were comparably higher (58-62 vs. 44, P < 0.0001) when compared to NT children without FGID. There was no significant difference in macronutrient intake between ASD and NT siblings. There was no significant difference in ASD severity scores between ASD children with and without FGID. No significant difference in diversity or overall microbial composition was detected between ASD children with NT siblings. Exploratory analysis of the 16S rRNA sequencing data, however, identified several low abundance taxa binned at the genus level that were associated with ASD and/or first order ASD*FGID interactions (FDR

Adherent-invasive Escherichia coli (AIEC) strains are detected more frequently within mucosal lesions of patients with Crohn's disease (CD). The AIEC phenotype consists of adherence and invasion of intestinal epithelial cells and survival within macrophages of these bacteria in vitro. Our aim was to identify candidate transcripts that distinguish AIEC from non-invasive E. coli (NIEC) strains and might be useful for rapid and accurate identification of AIEC by culture-independent technology. We performed comparative RNA-Sequence (RNASeq) analysis using AIEC strain LF82 and NIEC strain HS during exponential and stationary growth. Differential expression analysis of coding sequences (CDS) homologous to both strains demonstrated 224 and 241 genes with increased and decreased expression, respectively, in LF82 relative to HS. Transition metal transport and siderophore metabolism related pathway genes were up-regulated, while glycogen metabolic and oxidation-reduction related pathway genes were down-regulated, in LF82. Chemotaxis related transcripts were up-regulated in LF82 during the exponential phase, but flagellum-dependent motility pathway genes were down-regulated in LF82 during the stationary phase. CDS that mapped only to the LF82 genome accounted for 747 genes. We applied an in silico subtractive genomics approach to identify CDS specific to AIEC by incorporating the genomes of 10 other previously phenotyped NIEC. From this analysis, 166 CDS mapped to the LF82 genome and lacked homology to any of the 11 human NIEC strains. We compared these CDS across 13 AIEC, but none were homologous in each. Four LF82 gene loci belonging to clustered regularly interspaced short palindromic repeats region (CRISPR)--CRISPR-associated (Cas) genes were identified in 4 to 6 AIEC and absent from all non-pathogenic bacteria. As previously reported, AIEC strains were enriched for pdu operon genes. One CDS, encoding an excisionase, was shared by 9 AIEC strains. Reverse transcription quantitative polymerase chain reaction assays for 6 genes were conducted on fecal and ileal RNA samples from 22 inflammatory bowel disease (IBD), and 32 patients without IBD (non-IBD). The expression of Cas loci was detected in a higher proportion of CD than non-IBD fecal and ileal RNA samples (p

BACKGROUND: Colorectal cancer (CRC) has the third highest mortality rates among the US population. According to the most recent concept of carcinogenesis, human tumors are organized hierarchically, and the top of it is occupied by malignant stem cells (cancer stem cells, CSCs, or cancer-initiating cells, CICs), which possess unlimited self-renewal and tumor-initiating capacities and high resistance to conventional therapies. To reflect the complexity and diversity of human tumors and to provide clinically and physiologically relevant cancer models, large banks of characterized patient-derived low-passage cell lines, and especially CIC-enriched cell lines, are urgently needed. PRINCIPAL FINDINGS: Here we report the establishment of a novel CIC-enriched, highly tumorigenic and clonogenic colon cancer cell line, CR4, derived from liver metastasis. This stable cell line was established by combining 3D culturing and 2D culturing in stem cell media, subcloning of cells with particular morphology, co-culture with carcinoma associated fibroblasts (CAFs) and serial transplantation to NOD/SCID mice. Using RNA-Seq complete transcriptome profiling of the tumorigenic fraction of the CR4 cells in comparison to the bulk tumor cells, we have identified about 360 differentially expressed transcripts, many of which represent stemness, pluripotency and resistance to treatment. Majority of the established CR4 cells express common markers of stemness, including CD133, CD44, CD166, EpCAM, CD24 and Lgr5. Using immunocytochemical, FACS and western blot analyses, we have shown that a significant ratio of the CR4 cells express key markers of pluripotency markers, including Sox-2, Oct3/4 and c-Myc. Constitutive overactivation of ABC transporters and NF-kB and absence of tumor suppressors p53 and p21 may partially explain exceptional drug resistance of the CR4 cells. CONCLUSIONS: The highly tumorigenic and clonogenic CIC-enriched CR4 cell line may provide an important new tool to support the discovery of novel diagnostic and/or prognostic biomarkers as well as the development of more effective therapeutic strategies.

Crohn's disease (CD) is a chronic inflammatory disease of the gastrointestinal tract. Genetic polymorphisms can confer CD risk and influence disease phenotype. Indoleamine 2,3 dioxygenase-1 (IDO1) is one of the most over-expressed genes in CD and mediates potent anti-inflammatory effects via tryptophan metabolism along the kynurenine pathway. We aimed to determine whether non-synonymous polymorphisms in IDO1 or IDO2 (a gene paralog) are important either as CD risk alleles or as modifiers of CD phenotype.Utilizing a prospectively collected database, clinically phenotyped CD patients (n = 734) and non-IBD controls (n = 354) were genotyped for established IDO1 and IDO2 non-synonymous single nucleotide polymorphisms (SNPs) and novel genetic variants elucidated in the literature. Allelic frequencies between CD and non-IBD controls were compared. Genotype-phenotype analysis was conducted. IDO1 enzyme activity was assessed by calculating the serum kynurenine to tryptophan ratio (K/T).IDO1 SNPs were rare (1.7% non-IBD vs 1.1% CD; p = NS) and not linked to Crohn's disease diagnosis in this population. IDO1 SNPs did however associate with a severe clinical course, presence of perianal disease, extraintestinal manifestations and a reduced serum K/T ratio during active disease suggesting lower IDO1 function. IDO2 minor allele variants were common and one of them, rs45003083, associated with reduced risk of Crohn's disease (p = 0.025). No IDO2 SNPs associated with a particular Crohn's disease clinical phenotype.This work highlights the functional importance of IDO enzymes in human Crohn's disease and establishes relative rates of IDO genetic variants in a US population.

The reactive cast-infiltration technique was used to produce an Fe-WC surface composite laer on an iron casting, in which the WC particulates were formed in situ from a reaction of W with C. The structure and phase construction of the surface composite were evaluated by using X-ray diffraction (XRD), scanning electron microscope (SEM), energy-dispersive X-ray (EDS), etc. An Fe-WC surface composite layer witha volume fraction of WC particles up to30% and particle size in the range 10-30 μm was successfully produced. Abrasive resistance test results show that the Fe-WC surface cmposite layer possesses great abrasive resistance.

Next generation sequencing (NGS) is a revolutionary technology for biomedical research. One highly cost-efficient application of NGS is to detect disease association based on pooled DNA samples. However, several key issues need to be addressed for pooled NGS. One of them is the high sequencing error rate and its high variability across genomic positions and experiment runs, which, if not well considered in the experimental design and analysis, could lead to either inflated false positive rates or loss in statistical power. Another important issue is how to test association of a group of rare variants. To address the first issue, we proposed a new blocked pooling design in which multiple pools of DNA samples from cases and controls are sequenced together on same NGS functional units. To address the second issue, we proposed a testing procedure that does not require individual genotypes but by taking advantage of multiple DNA pools. Through a simulation study, we demonstrated that our approach provides a good control of the type I error rate, and yields satisfactory power compared to the test-based on individual genotypes. Our results also provide guidelines for designing an efficient pooled.