Search

Abstract Background Gastrointestinal stromal tumours (GISTs) represent a heterogeneous group of tumours of mesenchymal origin characterized by gain-of-function mutations in KIT or PDGFRA of the type III receptor tyrosine kinase family. Although mutations in either receptor are thought to drive an early oncogenic event through similar pathways, two previous studies reported the mutation-specific gene expression profiles. However, their further conclusions were rather discordant. To clarify the molecular characteristics of differentially expressed genes according to GIST receptor mutations, we combined microarray-based analysis with detailed functional annotations. Methods Total RNA was isolated from 29 frozen gastric GISTs and processed for hybridization on GENECHIP® HG-U133 Plus 2.0 microarrays (Affymetrix). KIT and PDGFRA were analyzed by sequencing, while related mRNA levels were analyzed by quantitative RT-PCR. Results Fifteen and eleven tumours possessed mutations in KIT and PDGFRA, respectively; no mutation was found in three tumours. Gene expression analysis identified no discriminative profiles associated with clinical or pathological parameters, even though expression of hundreds of genes differentiated tumour receptor mutation and expression status. Functional features of genes differentially expressed between the two groups of GISTs suggested alterations in angiogenesis and G-protein-related and calcium signalling. Conclusion Our study has identified novel molecular elements likely to be involved in receptor-dependent GIST development and allowed confirmation of previously published results. These elements may be potential therapeutic targets and novel markers of KIT mutation status.

Background: Gastrointestinal stromal tumours (GISTs) represent a heterogeneous group of tumours of mesenchymal origin characterized by gain-of-function mutations in KIT or PDGFRA of the type III receptor tyrosine kinase family. Although mutations in either receptor are thought to drive an early oncogenic event through similar pathways, two previous studies reported the mutation-specific gene expression profiles. However, their further conclusions were rather discordant. To clarify the molecular characteristics of differentially expressed genes according to GIST receptor mutations, we combined microarray-based analysis with detailed functional annotations.Methods: Total RNA was isolated from 29 frozen gastric GISTs and processed for hybridization on GENECHIP HG-U133 Plus 2.0 microarrays (Affymetrix). KIT and PDGFRA were analyzed by sequencing, while related mRNA levels were analyzed by quantitative RT-PCR.Results: Fifteen and eleven tumours possessed mutations in KIT and PDGFRA, respectively; no mutation was found in three tumours. Gene expression analysis identified no discriminative profiles associated with clinical or pathological parameters, even though expression of hundreds of genes differentiated tumour receptor mutation and expression status. Functional features of genes differentially expressed between the two groups of GISTs suggested alterations in angiogenesis and G-protein-related and calcium signalling.Conclusion: Our study has identified novel molecular elements likely to be involved in receptor-dependent GIST development and allowed confirmation of previously published results. These elements may be potential therapeutic targets and novel markers of KIT mutation status. [ABSTRACT FROM AUTHOR]

The molecular beam epitaxy (MBE) technique is renowned as the most suitable for the growth of high-quality crystalline materials and nanostructures such as GaAs. However, once established, optimal growth parameters required for repeatability of top-quality structures may be easily lost as MBE is highly sensitive to any changes in the system. Especially, routine servicing procedures, which include any activity which requires unsealing of the growth chamber, are devastating for developed growth parameters and force the necessity of recalibration. In this work, we present the process of growth parameter pre-optimization for obtaining homoepitaxial GaAs layers after servicing and restarting the MBE system. Namely, we present how each step of reestablishing optimal growth condition influences various characteristics of obtained GaAs layers. Those include in situ, structural, and spectral measurement techniques. An additional aspect was to compare the optimal conditions for the growth of homoepitaxial GaAs layers from two growth campaigns in which the main difference is the addition of an ion pump and increasing the temperature gradient on the Ga cell., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

We demonstrate strain-balanced InAs/AlSb type-II superlattices (T2SL) grown on GaSb substrates employing two kinds of interfaces (IFs): AlAs-like IF and InSb-like IF. The structures are obtained by molecular beam epitaxy (MBE) for effective strain management, simplified growth scheme, improved material crystalline quality, and improved surface quality. The minimal strain T2SL versus GaSb substrate can be achieved by a special shutters sequence during MBE growth that leads to the formation of both interfaces. The obtained minimal mismatches of the lattice constants is smaller than that reported in the literature. The in-plane compressive strain of 60-period InAs/AlSb T2SL 7ML/6ML and 6ML/5ML was completely balanced by the applied IFs, which is confirmed by the HRXRD measurements. The results of the Raman spectroscopy (measured along the direction of growth) and surface analyses (AFM and Nomarski microscopy) of the investigated structures are also presented. Such InAs/AlSb T2SL can be used as material for a detector in the MIR range and, e.g., as a bottom n-contact layer as a relaxation region for a tuned interband cascade infrared photodetector.

The article presents a systematic study of Sb-doped Zn 1-x Mg x O layers, with various concentrations of Mg, that were successfully grown by plasma-assisted MBE on polar a - and c -oriented and non-polar r -oriented sapphire substrates. X-ray diffraction confirmed the polar c -orientation of alloys grown on c -and a -oriented sapphire and non-polar structures grown on r -oriented substrates. A uniform depth distribution of the Sb dopant at level of 2 × 10 20 cm -3 was determined by SIMS measurements. Raman spectroscopy revealed the presence of Sb-related modes in all samples. It also showed that Mg alloying reduces the compressive strain associated with Sb doping in ZnO. XPS analysis indicates that the chemical state of Sb atoms in ZnMgO is 3+, suggesting a substitutional position of Sb Zn , probably associated with two V Zn vacancies. Luminescence and transmission spectra were measured to determine the band gaps of the Zn 1-x Mg x O layers. The band gap energies extracted from the transmittance measurements differ slightly for the a , c , and r substrate orientations, and the differences increase with increasing Mg content, despite identical growth conditions. The differences between the energy gaps, determined from transmission and PL peaks, are closely correlated with the Stokes shift and increase with the Mg content in the analyzed series of ZnMgO layers.

Background: Cerebral blood flow (CBF) can be related to the risk of occurrence of neurological symptoms. Well-developed collateral circulation is a good prognostic factor in patients with cerebrovascular disease. Understanding the mechanisms of collateral circulation may be important in the diagnosis, treatment, and monitoring in this group of patients. The aim of this study covered the assessment of CBF in patients with 70−99% Internal carotid artery (ICA) stenosis, focusing on the circulation pathways and flow volume in extracranial arteries. Materials and methods: 53 patients with 70−99% ICA stenosis (mean age 73.4 ± 7 years old; 17 female, mean age 73.9 ± 7.5 years old; 36 male, mean age 73.2 ± 6.8 years old) were included in the study. In all patients a Doppler ultrasound (DUS) examination, measuring blood flow volume in the internal carotid artery (ICA), external carotid artery (ECA), and vertebral artery (VA), was performed. The cerebral blood flow (CBF) was compared to the previously reported CBF values in the healthy population > 65 years old. Results: Among the study groups three subgroups with flow differences were identified: patients with elevated CBF (significant volumetric flow compensation—26/53, 49%), patients with CBF similar to (mild compensation—17/53, 32%), and patients with CBF lower than (no compensation—10/53, 19%) the healthy, equally aged population. The percentage of patients with significant volumetric flow compensation was the highest in age groups 65−69 years old (62.5%) and >80 years old (60%). In the oldest age group (>80 years old) no patients without flow compensation (0%) were observed. The level of compensation depends on the number of the arteries with compensatory increased flow. In patients with significant volumetric flow compensation, the compensatory increased flow was observed, on average, in 3.31 arteries, in the mild compensation group—in 2.18 arteries, and in the no compensation group only in 1 artery. ICA plays the most important role in the volumetric flow compensation—the increase in the flow volume, in comparison to the reference values, was between 116.7 mL/min and 251.9 mL/min (in the ECA 57.6 mL/min−110.4 mL/min; in the VA 73.9 mL/min−104.9 mL/min). The relative flow increase was highest in the VA: 215−246%, then in the ECA: 163−206%, and finally in the ICA: 148.6−192%. The increased flow was most commonly observed in the VA—57 arteries, in second place in the ECA—42 arteries, and ICA—31 arteries. In patients with unilateral ICA stenosis, the volumetric flow increase was stated more frequently in the ipsilateral ECAs then in the contralateral ones (23 vs. 14). In the VA the opposite tendency was observed (29 contralateral vs. 23 ipsilateral). The ability of volumetric flow compensation decreased significantly with increasing age. Conclusions: Understanding the mechanisms of collateral circulation and their assessment in Doppler ultrasonography may provide a novel and easily accessible tool of identifying and monitoring patients with cerebrovascular disease., Competing Interests: The authors declare no conflict of interest.

In this paper, the photoluminescence spectra of excitons in ZnO/ZnMgO/ZnO double asymmetric quantum wells grown on a-plane Al2O3 substrates with internal electric-field bands structures were studied. In these structures, the electron and the hole in the exciton are spatially separated between neighbouring quantum wells, by a ZnMgO barrier with different thickness. The existence of an internal electric field generates a linear potential and, as a result, lowers the energy of quantum states in the well. For the wide wells, the electrons are spatially separated from the holes and can create indirect exciton. To help the understanding of the photoluminescence spectra, for single particle states the 8 k·p for wurtzite structure is employed. Using these states, the exciton in the self-consistent model with 2D hydrogenic 1s-like wave function is calculated.

The fourth EMBO-sponsored conference on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems (https://www.embl.de/training/events/2016/EAE16-01/), was held at the EMBL in Heidelberg, Germany, October 19-23, 2016. The conference was organized by Judith Berman (Tel Aviv University), Maitreya Dunham (University of Washington), Jun-Yi Leu (Academia Sinica), and Lars Steinmetz (EMBL Heidelberg and Stanford University). The meeting attracted ~120 researchers from 28 countries and covered a wide range of topics in the fields of genetics, evolutionary biology, and ecology with a unifying focus on yeast as a model system. Attendees enjoyed the Keith Haring inspired yeast florescence microscopy artwork (Figure 1), a unique feature of the meeting since its inception, and the one-minute flash talks that catalyzed discussions at two vibrant poster sessions. The meeting coincided with the 20th anniversary of the publication describing the sequence of the first eukaryotic genome, Saccharomyces cerevisiae (Goffeau et al. 1996). Many of the conference talks focused on important questions about what is contained in the genome, how genomes evolve, and the architecture and behavior of communities of phenotypically and genotypically diverse microorganisms. Here, we summarize highlights of the research talks around these themes. Nearly all presentations focused on novel findings, and we refer the reader to relevant manuscripts that have subsequently been published., (Copyright © 2017, G3: Genes, Genomes, Genetics.)

A total proctocolectomy with ileal pouch-anal anastomosis (IPAA) is considered the surgery of choice for definitive management of familial adenomatous polyposis (FAP) and some patients with ulcerative colitis (UC). However, this surgical treatment is often associated with pouchitis, a long-term complication that occurs mostly in UC patients. The purpose of this study was to better define the molecular background of pouchitis. A microarray-based survey was performed using pouch mucosal samples collected from 28 and 8 patients undergoing surgery for UC and FAP, respectively. There were 4,770 genes that significantly differentiated uninflamed from inflamed mucosal samples, and their functional features were represented mostly by metabolic and cell proliferation pathways. In contrast, functional analyses of aberrantly expressed genes between UC and FAP samples, irrespective of mucosal inflammation status, revealed multiple pathways and terms that were linked to changes in immune response. Interestingly, the comparison of uninflamed UC and FAP samples identified a set of 29 altered probe sets, including an inflammation-related transcript encoding a Charcot-Leyden crystal (CLC) protein. The most distinct changes in gene expression profiles differentiating uninflamed UC and FAP pouch mucosal samples were attributed to the Gene Ontology category innate immune response. Our study confirmed that alterations in immune responses can be found between patients who underwent surgery for UC and FAP, independent of the pouch inflammation status. This observation may be important when managing IPAA patients.

Up to date several authors discussed interactions between cells forming inflammatory infiltrates in the course of inflammatory bowel disease (IBD), mainly dealing with endoscopic biopsy specimens. These usually contain only mucosa. We have evaluated full bowel wall sections, which seems to be especially important in patients with Crohn's disease (CD). The purpose of our study was to evaluate the relationship between vascular density and expression of thrombospondin-1 (TSP-1) and vascular endothelial growth factor receptor 1 (VEGFR-1) in full-thickness tissue fragments of intestinal wall taken from patients after colectomy, comparing those with IBD to non-IBD control group. Histological sections were immunostained with antibodies against CD-31, TSP-1, and VEGFR-1 and analyzed by pathologists with the use of computer-assisted morphometrics. Our research showed significantly higher vascular density and vascular area percentage in all layers of bowel wall in patients with CD when compared to control. We have also demonstrated differences in vascular density distribution between ulcerative colitis (CU) and CD and between CU and control. However we have not found statistically significant correlation between those findings and VEGFR-1 or TSP-1 expression. Our results might suggest existence of different, TSP-1 independent pathways of antiangiogenesis in IBD.

Colon anastomosis is therapeutically challenging because multiple, usually undetectable factors influence a spectrum of repair mechanisms. We hypothesized that low molecular weight heparins, routinely administered perioperatively, may differentially affect gene expression related to colon healing. Twenty pairs of untreated and enoxaparin-treated rats underwent left-side hemicolectomy with a primary end-to-end anastomosis. Normal colon and anastomotic bowel segments were resected on day 0 and on days 1, 3, 5, and 7 after surgery, respectively. Serial anastomosis transverse cross-sections were evaluated microscopically and by microarray (Rat Genome 230 2.0, Affymetrix). Differentially expressed probe sets were annotated with Gene Ontology. We also examined the influence of enoxaparin on fibroblast proliferation and viability in vitro. Among the 5476 probe sets, we identified differential expression at each healing time point, yielding 79 subcategories. Most indicated genes were involved in wound healing, including multicellular organismal development, locomotory behavior, immune response, cell adhesion, inflammatory response, cell-cell signaling, blood vessel development, and tissue remodeling. Although we found no intensity differences in histological features of healing between enoxaparin-treated and control rats, treatment did induce significant expression changes during early healing. Of these changes, 83 probe sets exhibited at least twofold changes and represented different functional annotations, including inflammatory response, regulation of transcription, regulation of apoptosis, and angiogenesis. Fibroblast culture confirmed an anti-viability effect of enoxaparin. Enoxaparin affects colon wound-related gene expression profiles, but further studies will resolve whether heparin treatment is a risk factor after intestinal surgery, at least in some patients.

Background: Clinical progression of colorectal cancers (CRC) may occur in parallel with distinctive signaling alterations. We designed multidirectional analyses integrating microarray-based data with biostatistics and bioinformatics to elucidate the signaling and metabolic alterations underlying CRC development in the adenoma-carcinoma sequence., Methodology/principal Findings: Studies were performed on normal mucosa, adenoma, and carcinoma samples obtained during surgery or colonoscopy. Collections of cryostat sections prepared from the tissue samples were evaluated by a pathologist to control the relative cell type content. The measurements were done using Affymetrix GeneChip HG-U133plus2, and probe set data was generated using two normalization algorithms: MAS5.0 and GCRMA with least-variant set (LVS). The data was evaluated using pair-wise comparisons and data decomposition into singular value decomposition (SVD) modes. The method selected for the functional analysis used the Kolmogorov-Smirnov test. Expressional profiles obtained in 105 samples of whole tissue sections were used to establish oncogenic signaling alterations in progression of CRC, while those representing 40 microdissected specimens were used to select differences in KEGG pathways between epithelium and mucosa. Based on a consensus of the results obtained by two normalization algorithms, and two probe set sorting criteria, we identified 14 and 17 KEGG signaling and metabolic pathways that are significantly altered between normal and tumor samples and between benign and malignant tumors, respectively. Several of them were also selected from the raw microarray data of 2 recently published studies (GSE4183 and GSE8671)., Conclusion/significance: Although the proposed strategy is computationally complex and labor-intensive, it may reduce the number of false results.

Barrett's esophagus represents a well-defined precursor lesion of esophageal adenocarcinoma, although only a subset of patients with these lesions advances to invasive cancer. Currently, reliable markers predicting neoplastic progression in Barrett's esophagus are lacking. The only clinically useful risk factor is the presence of dysplasia in Barrett's epithelium, but its use as a prognostic marker of disease progression has several significant limitations. Thus, identification of biomarkers of potential prognostic value in dysplasia development in Barrett's esophagus is highly important. The aim of the study was to determine if expression levels of selected genes support histologic diagnosis of dysplastic changes in Barrett's esophagus. Upon rigorous sampling and independent histopathologic examination of endoscopic specimens by two experienced gastrointestinal pathologists, 56 patients with Barrett's esophagus (16 negative for dysplasia, 15 with indefinite, 21 with low-grade, and 4 with high-grade dysplasia) were selected for molecular analysis. The relative mRNA levels of ten selected genes were estimated by quantitative real-time polymerase chain reaction (PCR) analysis. Although expression of nine genes showed trends toward down- or upregulation during progression from Barrett's esophagus without dysplasia to Barrett's esophagus with high-grade dysplasia, only a decrease in S100A2 mRNA levels was statistically significant (P<0.05). However, there was considerable variation among individuals and significant overlapping of ranges. Furthermore, detailed, comparative analysis of serial samples from Barrett's mucosa and normal squamous epithelium shows large intra-individual variability of gene expression levels. In conclusion, expression of this set of ten genes cannot be used as a molecular marker aiding histological examination of dysplasia in Barrett's esophagus. Significant inter- and intra-patient variations of gene expression levels makes use of the selected genes impractical.

Background: Based on recommendations of the Fifth and Sixth Reports of the Joint National Committee (JNC) on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure, Health Care Plan (now Univera Healthcare) Buffalo, NY, developed a clinical guideline to improve the management of patients with hypertension. To increase awareness and utilization, the guideline was distributed as hard copy reports and made available through our electronic information system., Objective: To determine blood pressure (BP) control rates and adherence to guideline recommendations., Study Design: Retrospective chart review., Patients and Methods: We randomly sampled hypertensive patients seen during 1998 to evaluate hypertension management. Computerized medical and pharmacy records were reviewed for patient demographics, antihypertensive medications, comorbid conditions, and BP readings. Patient assessment was based on antihypertensive regimen and achievement of target BP according to the recommendations of the guidelines (< 140/90 mm Hg for the general population and < 130/85 mm Hg for special populations). In addition, we assessed control rates using traditional Health Plan Employer Data and Information Set (HEDIS) measures (< 140/90 mm Hg)., Results: Overall, 35% of patients achieved target BP and 68% were treated with agents recommended by our JNC-based guideline. In contrast, using traditional HEDIS measures, 41% of patients achieved BP control. Of 39 patients with compelling indications (primarily diabetic patients), 13% achieved BP target and 67% were treated with recommended agents., Conclusions: The impact of our clinical guideline is reflected through the relatively high utilization of recommended drugs. However, optimal BP control continues to be problematic. In particular, patients with diabetes warrant focused attention.

Background: The complex between urokinase (uPA) and its type-1 inhibitor (PAI-1) is formed exclusively from the active forms of these components; thus, the complex concentration in a biological sample may reflect the ongoing degree of plasminogen activation. Our aim was to establish an ELISA for specific quantification of the uPA:PAI-1 complex in plasma of healthy donors and breast cancer patients., Methods: A kinetic sandwich format immunoassay was developed, validated, and applied to plasma from 19 advanced-stage breast cancer patients, 39 age-matched healthy women, and 31 men., Results: The assay detection limit was <2 ng/L, and the detection of complex in plasma was validated using immunoabsorption, competition, and recovery tests. Eighteen cancer patients had a measurable complex concentration (median, 68 ng/L; range, <16 to 8700 ng/L), whereas for healthy females and males the median signal values were below the detection limit (median, <16 ng/L; range, <16 to 200 ng/L; P <0.0001). For patient plasma, a comparison with total uPA and PAI-1 showed that the complex represented a variable, minor fraction of the uPA and PAI-1 concentrations of each sample., Conclusion: The reported ELISA enables detection of the uPA:PAI-1 complex in blood and, therefore, the evaluation of the complex as a prognostic marker in cancer.

Spinal cord injuries (SCIs) in the pediatric population present a unique challenge to the caregiver in that both the physical injury and the growth and development issues need to be addressed simultaneously. Different types of injuries are anticipated than those seen in adults because of the developmental phases of the pediatric spinal cord. This article will review the differences between the pediatric and adult spinal cords, growth and development, and the types of injuries incurred by this population, followed by a case presentation.

Mammalian bites account for 1% of all emergency department visits and dogs are common perpetrators. School-aged children are the most vulnerable and experience the majority of this type of trauma. Most of the cases involve a known dog and many of the attacks involve the family pet. When a child presents with a severe dog bite, the injury should be managed using appropriate assessment and intervention techniques. In some cases, conscious sedation can be used to provide amnesia, analgesia and sedation during the surgical repair. Proper preparation of the wound prior to repair will decrease infection rates. The need for tetanus and rabies prophylaxis must be evaluated in all dog bites. Facial injuries may require complex repair and reconstruction with appropriate surgical referral. Thorough discharge instructions are an important aspect of the nursing role.

The tumor-suppressor gene p53 is altered by missense mutation in numerous human malignancies. However, the biochemical properties of p53 and the effect of mutation on these properties are unclear. A human DNA sequence was identified that binds specifically to wild-type human p53 protein in vitro. As few as 33 base pairs were sufficient to confer specific binding. Certain guanines within this 33-base pair region were critical, as methylation of these guanines or their substitution with thymine-abrogated binding. Human p53 proteins containing either of two missense mutations commonly found in human tumors were unable to bind significantly to this sequence. These data suggest that a function of p53 may be mediated by its ability to bind to specific DNA sequences in the human genome, and that this activity is altered by mutations that occur in human tumors.