Observation of Interatomic Coulombic Decay Induced by Double Excitation of Helium in Nanodroplets.

Interatomic Coulombic decay (ICD) plays a crucial role in weakly bound complexes exposed to intense or high-energy radiation. So far, neutral or ionic atoms or molecules have been prepared in singly excited electron or hole states that can transfer energy to neighboring centers and cause ionization and radiation damage. Here we demonstrate that a doubly excited atom, despite its extremely short lifetime, can decay by ICD; evidenced by high-resolution photoelectron spectra of He nanodroplets excited to the 2s2p+ state. We find that ICD proceeds by relaxation into excited He^{*}He^{+} atom-pair states, in agreement with calculations. The ability of inducing ICD by resonant excitation far above the single-ionization threshold opens opportunities for controlling radiation damage to a high degree of element specificity and spectral selectivity.

Efficient Indirect Interatomic Coulombic Decay Induced by Photoelectron Impact Excitation in Large Pure Helium Nanodroplets.

Ionization of matter by energetic radiation generally causes complex secondary reactions that are hard to decipher. Using large helium nanodroplets irradiated by extreme ultraviolet (XUV) photons, we show that the full chain of processes ensuing primary photoionization can be tracked in detail by means of high-resolution electron spectroscopy. We find that elastic and inelastic scattering of photoelectrons efficiently induces interatomic Coulombic decay (ICD) in the droplets. This type of indirect ICD even becomes the dominant process of electron emission in nearly the entire XUV range in large droplets with radius ≳40 nm. Indirect ICD processes induced by electron scattering likely play an important role in other condensed-phase systems exposed to ionizing radiation as well, including biological matter.

Effectiveness of PD-(L)1 inhibitors alone or in combination with platinum-doublet chemotherapy in first-line (1L) non-squamous non-small-cell lung cancer (Nsq-NSCLC) with PD-L1-high expression using real-world data.

BACKGROUND: Anti-programmed cell death protein (death-ligand) 1 [PD-(L)1] therapy alone [cancer immunotherapy (CIT)-mono] or combined with platinum-based chemotherapy (CIT-chemo) is used as the first-line treatment for patients with metastatic non-small-cell lung cancer (NSCLC). Our study compared clinical outcomes with CIT-mono versus CIT-chemo in the specific clinical scenario of non-squamous (Nsq)-NSCLC with a high PD-L1 expression of ≥50% [tumor proportion score (TPS) or tumor cells (TC)]. METHODS: This was a retrospective cohort study using a real-world de-identified database. Patients with metastatic Nsq-NSCLC with high PD-L1 expression initiating first-line CIT-mono or CIT-chemo between 24 October 2016 and 28 February 2019 were followed up until 28 February 2020. We compared overall survival (OS) and real-world progression-free survival (rwPFS) using the Kaplan-Meier methodology. Hazard ratios (HRs) were adjusted (aHR) for differences in baseline key prognostic characteristics using the inverse probability of treatment weighting methodology. RESULTS: Patients with PD-L1-high Nsq-NSCLC treated with CIT-mono (n = 351) were older and less often presented with de novo stage IV disease than patients treated with CIT-chemo (n = 169). With a median follow-up of 19.9 months for CIT-chemo versus 23.5 months for CIT-mono, median OS and rwPFS did not differ between the two groups [median OS: CIT-chemo, 21.0 months versus CIT-mono, 22.1 months, aHR = 1.03, 95% confidence interval (CI) 0.77-1.39, P = 0.83; median rwPFS: CIT-chemo, 10.8 months versus CIT-mono, 11.5 months, aHR = 1.04, 95% CI 0.78-1.37, P = 0.81]. CIT-chemo showed significant and meaningful improvement in OS and rwPFS versus CIT-mono only in the never-smoker subgroup, albeit among a small sample of patients (n = 50; OS HR = 0.25, 95% CI 0.07-0.83, interaction P = 0.02; rwPFS HR = 0.40, 95% CI 0.17-0.95, interaction P = 0.04). CONCLUSION: Except in the subgroup of never-smoker patients, sparing the chemotherapy in first-line CIT treatment does not appear to impact survival outcomes in Nsq-NSCLC patients with high PD-L1 expression.

Relaxation dynamics in excited helium nanodroplets probed with high resolution, time-resolved photoelectron spectroscopy.

Superfluid helium nanodroplets are often considered as transparent and chemically inert nanometer-sized cryo-matrices for high-resolution or time-resolved spectroscopy of embedded molecules and clusters. On the other hand, when the helium nanodroplets are resonantly excited with XUV radiation, a multitude of ultrafast processes are initiated, such as relaxation into metastable states, formation of nanoscopic bubbles or excimers, and autoionization channels generating low-energy free electrons. Here, we discuss the full spectrum of ultrafast relaxation processes observed when helium nanodroplets are electronically excited. In particular, we perform an in-depth study of the relaxation dynamics occurring in the lowest 1s2s and 1s2p droplet bands using high resolution, time-resolved photoelectron spectroscopy. The simplified excitation scheme and improved resolution allow us to identify the relaxation into metastable triplet and excimer states even when exciting below the droplets' autoionization threshold, unobserved in previous studies.

Teachers' mindsets in medical education: A pilot survey of clinical supervisors.

Purpose: Current medical education models maintain that competencies such as professionalism and communication can be taught; however, some argue that certain attributes that make up these competencies, such as empathy, are fixed. Teachers' implicit theories, or mindsets (beliefs about the fixed versus learnable nature of human attributes) have been shown to impact their teaching and assessment practices; but little work has explored mindsets in medical education. We examined clinical supervisors' mindsets of two cognitive attributes (intelligence and clinical reasoning) and two affective attributes (moral character and empathy).Methods: Clinical supervisors (n = 40) from three specialities completed a survey designed to measure mindsets using two existing instruments for intelligence and moral character and 18 new items for clinical reasoning and empathy. Participants completed the survey twice for test-retest reliability (n = 25).Results: New items had satisfactory psychometric properties. Clinical supervisors' mindsets were mixed. Only 8% of participants saw clinical reasoning as fixed while more saw empathy (45%), intelligence (53%), and moral character (53%) as fixed - running counter to current educational models that characterize these attributes as learnable.Conclusion: This study provides evidence supporting the use of these new tools to measure mindsets that may help to better understand the impact of mindsets on medical education.

Interobserver agreement and diagnostic accuracy of shearwave elastography for the staging of hepatitis C virus-associated liver fibrosis.

PURPOSE: Our study aimed to evaluate the technical success rate, interobserver reproducibility, and accuracy of shearwave elastography (SWE) in the staging of hepatitis C virus (HCV)-associated liver fibrosis. METHODS: A total of 10 healthy controls and 49 patients with chronic liver disease were enrolled prospectively. Two examiners performed point shearwave elastography (pSWE) and two-dimensional shearwave elastography (2D-SWE) measurements with an RS85A ultrasound scanner using the S-Shearwave application (Samsung Medison, Hongcheon, Korea). The performance of S-Shearwave in the staging (METAVIR F0-F4) of liver fibrosis was compared with prior transient elastography (TE) with receiver operating characteristic (ROC) curve analysis. RESULTS: The interobserver reproducibility was excellent with pSWE (ICC = 0.92, 95% CI: 0.86-0.95, P < .001). A very good agreement was found between pSWE and TE measurements (ICC =0.85, 95% CI: 0.78-0.89, P < .001). The ROC analysis determined the optimal cut-off values of pSWE for the staging of chronic hepatitis C-associated fibrosis (F2, 1.46 m/s; F3, 1.63 m/s; F4, 1.95 m/s). Both observers achieved excellent diagnostic accuracy (AUROC: 94% vs 97%) in the detection of significant (≥F2) liver fibrosis. CONCLUSION: The interobserver agreement is excellent with S-Shearwave pSWE, and observers can diagnose significant liver fibrosis with a comparable accuracy to TE.

Interrelationship between iodine nutritional status of lactating mothers and their absolutely breast-fed infants in coastal districts of Gangetic West Bengal in India.

Iodine nutritional status of 128 lactating mothers and their breast-fed infants (1-3 months) from iodine-replete villages during post-salt iodization period was evaluated. Mothers' urine, blood, and breast milk (BM) and infants' urine and blood were collected and analyzed for iodine and serum FT4 and TSH estimation. Mothers' and infants' age, parity, occupation, education, and household income were recorded. Median urinary iodine concentration (UIC) of infants was 250 µg/L, indicating their iodine intake was more than adequate. Mothers' median UIC was 185 µg/L, indicating adequate iodine nutrition; however, 13.28% had mild to severe deficiency. Median breast milk iodine concentration (BMIC) was 230 µg/L, which was more than their median UIC 185 µg/L. In iodine-deficient mothers, positive correlation was found between mothers' and infants' serum FT4 and TSH levels, and negative correlation was found between mothers' and infants' serum FT4 and TSH levels in excessive iodine nutrition group. CONCLUSION: Iodine intake of breast-fed infants was at the limit of above requirement, and they are possibly at the risk of excess iodine intake. In iodine deficient and excessive iodine intake mothers, their infants' serum FT4 and TSH are independent on their iodine nutritional status but dependent on thyroid hormone profile of their mothers but differently. What is Known: • A median urinary iodine of 100 µg/L is used to define adequate iodine intake of lactating mothers and children < 2 years. However, adequate iodine intake in terms of urinary iodine of infants of age 1-3 months is not known. What is New: • Iodine intake of absolutely breast-fed infants (1-3 months) was more than adequate, though their mother's intake was adequate as breast milk contains more iodine than urine. The infants of iodine deficient and excessive iodine intake mothers, infants' hormonal profile is independent of their iodine nutritional status but dependent on their mothers thyroid hormone profile.

Evaluation of junctional zone differential and ratio as possible markers of clinical efficacy in uterine artery embolisation of adenomyosis.

BACKGROUND: Uterine artery embolisation is a recommended method of adenomyosis treatment with good clinical results. Changes in uterine volume and maximal junctional zone thickness (JZmax) after embolisation are thoroughly analyzed in the literature. In contrast changes in other suggested morphological diagnostic markers of adenomyosis (junctional zone differential / JZdiff-and junctional zone ratio / JZratio) are rarely evaluated. This single-centre retrospective study aimed to analyse the changes in morphological parameters used for the MR imaging diagnosis of adenomyosis (including JZdiff and JZratio) after UAE. Clinical effectiveness and safety were also analysed. MATERIALS AND METHODS: Patients who underwent UAE for pure adenomyosis from Jan 2008 to Dec 2021 were evaluated. Adenomyosis was diagnosed based on JZmax, JZdiff, and JZratio measured on MR imaging. To assess clinical efficacy, the numerical-analog-quality-of-life (QoL) score was routinely obtained from patients at our centre. MRI morphological data were analysed. Statistical analysis was conducted using Wilcoxon signed-rank test, uni- and multivariate regression models, Pearson product-moment correlation, and Kruskal-Wallis tests. RESULTS: From our database of 801 patients who underwent UAE between Jan 2008 to Dec 2021, preprocedural MR images were available in 577 cases and, 15 patients had pure adenomyosis (15/577, 2.6%). Uterine volume, JZmax, and JZdiff decreased significantly after UAE; QoL score increased significantly. A significant correlation was found between QoL change vs. JZmax and JZdiff change. Permanent amenorrhoea and elective hysterectomy 5 years after UAE were both 7.1%. CONCLUSION: Change of JZdiff after UAE in adenomyosis is a potential marker of clinical success. UAE is a clinically safe and effective treatment for adenomyosis.

Randomized clinical trial of fluid and salt restriction compared with a controlled liberal regimen in elective gastrointestinal surgery.

BACKGROUND: Excessive intravenous fluid prescription may play a causal role in postoperative complications following major gastrointestinal resectional surgery. The aim of this study was to investigate whether fluid and salt restriction would decrease postoperative complications compared with a more modern controlled liberal regimen. METHODS: In this observer-blinded single-site randomized clinical trial consecutive patients undergoing major gastrointestinal resectional surgery were randomized to receive either a liberal control fluid regimen or a restricted fluid and salt regimen. The primary outcome was postoperative complications of grade II and above (moderate to severe). RESULTS: Some 240 patients (194 colorectal resections and 46 oesophagogastric resections) were enrolled in the study; 121 patients were randomized to the restricted regimen and 119 to the control (liberal) regimen. During surgery the control group received a median (interquartile range) fluid volume of 2033 (1576-2500) ml and sodium input of 282 (213-339) mmol, compared with 1000 (690-1500) ml and 142 (93-218) mmol respectively in the restricted group. There was no significant difference in major complication rate between groups (38·0 and 39·0 per cent respectively). Median (range) hospital stay was 8 (3-101) days in the controls and 8 (range 3-76) days among those who received restricted fluids. There were four in-hospital deaths in the control group and two in the restricted group. Substantial differences in weight change, serum sodium, osmolality and urine : serum osmolality ratio were observed between the groups. CONCLUSION: There were no significant differences in major complication rates, length of stay and in-hospital deaths when fluid restriction was used compared with a more liberal regimen. REGISTRATION NUMBER: ISRCTN39295230 (http://www.controlled-trials.com).

Tissue attenuation imaging and tissue scatter imaging for quantitative ultrasound evaluation of hepatic steatosis.

We aimed to assess the feasibility of ultrasound-based tissue attenuation imaging (TAI) and tissue scatter distribution imaging (TSI) for quantification of liver steatosis in patients with nonalcoholic fatty liver disease (NAFLD). We prospectively enrolled 101 participants with suspected NAFLD. The TAI and TSI measurements of the liver were performed with a Samsung RS85 Prestige ultrasound system. Based on the magnetic resonance imaging proton density fat fraction (MRI-PDFF), patients were divided into ≤5%, 5-10%, and ≥10% of MRI-PDFF groups. We determined the correlation between TAI, TSI, and MRI-PDFF and used multiple linear regression analysis to identify any association with clinical variables. The diagnostic performance of TAI, TSI was determined based on the area under the receiver operating characteristic curve (AUC). The intraclass correlation coefficient (ICC) was calculated to assess interobserver reliability. Both TAI (rs = 0.78, P < .001) and TSI (rs = 0.68, P < .001) showed significant correlation with MRI-PDFF. TAI overperformed TSI in the detection of both ≥5% MRI-PDFF (AUC = 0.89 vs 0.87) and ≥10% (AUC = 0.93 vs 0.86). MRI-PDFF proved to be an independent predictor of TAI (ß = 1.03; P < .001), while both MRI-PDFF (ß = 50.9; P < .001) and liver stiffness (ß = -0.86; P < .001) were independent predictors of TSI. Interobserver analysis showed excellent reproducibility of TAI (ICC = 0.95) and moderate reproducibility of TSI (ICC = 0.73). TAI and TSI could be used successfully to diagnose and estimate the severity of hepatic steatosis in routine clinical practice.

Diagnosis of focal liver lesions with deep learning-based multi-channel analysis of hepatocyte-specific contrast-enhanced magnetic resonance imaging.

BACKGROUND: The nature of input data is an essential factor when training neural networks. Research concerning magnetic resonance imaging (MRI)-based diagnosis of liver tumors using deep learning has been rapidly advancing. Still, evidence to support the utilization of multi-dimensional and multi-parametric image data is lacking. Due to higher information content, three-dimensional input should presumably result in higher classification precision. Also, the differentiation between focal liver lesions (FLLs) can only be plausible with simultaneous analysis of multi-sequence MRI images. AIM: To compare diagnostic efficiency of two-dimensional (2D) and three-dimensional (3D)-densely connected convolutional neural networks (DenseNet) for FLLs on multi-sequence MRI. METHODS: We retrospectively collected T2-weighted, gadoxetate disodium-enhanced arterial phase, portal venous phase, and hepatobiliary phase MRI scans from patients with focal nodular hyperplasia (FNH), hepatocellular carcinomas (HCC) or liver metastases (MET). Our search identified 71 FNH, 69 HCC and 76 MET. After volume registration, the same three most representative axial slices from all sequences were combined into four-channel images to train the 2D-DenseNet264 network. Identical bounding boxes were selected on all scans and stacked into 4D volumes to train the 3D-DenseNet264 model. The test set consisted of 10-10-10 tumors. The performance of the models was compared using area under the receiver operating characteristic curve (AUROC), specificity, sensitivity, positive predictive values (PPV), negative predictive values (NPV), and f1 scores. RESULTS: The average AUC value of the 2D model (0.98) was slightly higher than that of the 3D model (0.94). Mean PPV, sensitivity, NPV, specificity and f1 scores (0.94, 0.93, 0.97, 0.97, and 0.93) of the 2D model were also superior to metrics of the 3D model (0.84, 0.83, 0.92, 0.92, and 0.83). The classification metrics of FNH were 0.91, 1.00, 1.00, 0.95, and 0.95 using the 2D and 0.90, 0.90, 0.95, 0.95, and 0.90 using the 3D models. The 2D and 3D networks' performance in the diagnosis of HCC were 1.00, 0.80, 0.91, 1.00, and 0.89 and 0.88, 0.70, 0.86, 0.95, and 0.78, respectively; while the evaluation of MET lesions resulted in 0.91, 1.00, 1.00, 0.95, and 0.95 and 0.75, 0.90, 0.94, 0.85, and 0.82 using the 2D and 3D networks, respectively. CONCLUSION: Both 2D and 3D-DenseNets can differentiate FNH, HCC and MET with good accuracy when trained on hepatocyte-specific contrast-enhanced multi-sequence MRI volumes.

Rapid detection and differentiation of Erysipelothrix spp. by a novel multiplex real-time PCR assay.

AIM: The aim of this study was to develop a multiplex real-time PCR assay for the identification and discrimination of Erysipelothrix rhusiopathiae, tonsillarum and Erysipelothrix sp. strain 2 for direct detection of Erysipelothrix spp. from animal specimens. METHODS AND RESULTS: A primer set and three species-specific probes with different end labelling were designed from the noncoding region downstream of the 5S rRNA coding region. The sensitivity, specificity and repeatability of the assay were validated by analysing 27 Erysipelothrix spp. reference serotype strains and ten septicemia-associated non-Erysipelothrix spp. bacterial isolates. Cross-reactivity with Erysipelothrix sp. strain 1 was not observed with any of the primer probe combinations. The detection limit was determined to be <10 colony forming units and as low as one genome equivalent per PCR . Further evaluation of the Erysipelothrix spp. multiplex PCR was performed by comparing an enrichment isolation culture method and a conventional differential PCR on 15 samples from pigs experimentally inoculated with Erysipelothrix spp. and 22 samples from pigs with suspected natural infection. CONCLUSION: The multiplex real-time PCR assay was found to be simple, rapid, reliable, specific and highly sensitive. SIGNIFICANCE AND IMPACT OF THE STUDY: The developed real-time multiplex PCR assay does not require cumbersome and lengthy cultivation steps prior to DNA extraction, obtained comparable results to enrichment isolation, and will be useful in diagnostic laboratories for rapid detection of Erysipelothrix spp.

Detection of inducible clindamycin resistance among Staphylococcal isolates from different clinical specimens in western India.

BACKGROUND: Macrolide (MLS B ) resistance is the most widespread and clinically important mechanism of resistance encountered with Gram-positive organisms. Resistance may be constitutive (cMLS B phenotype) or inducible (iMLS B phenotype). The iMLS B phenotypes are not differentiated by using standard susceptibility test methods, but can be distinguished by erythromycin-clindamycin disk approximation test (D-test) and demonstration of resistance genes by molecular methods. AIMS: To demonstrate in vitro inducible clindamycin resistance (iMLS B ) in erythromycin-resistant (ER) and clindamycin-susceptible (CLI-S) clinical isolates of Staphylococci spp., and interpretation of susceptibility tests to guide therapy. MATERIALS AND METHODS: Eight hundred and fifty-one isolates of Staphylococci spp. were recovered from various clinical specimens. All the Staphylococcal spp. were identified by conventional microbiological methods including colony morphology, Gram stain, catalase, slide coagulase and tube coagulase. Antibiotic susceptibility testing was performed by Kirby Bauer disc diffusion method. Erythromycin-resistant isolates were examined for inducible clindamycin resistance (iMLS B ) by using double disk approximation test (D-test) at 15 mm disk separation. RESULTS: The Staphylococci spp. isolated were 379 S. aureus [31.60% methicillin-resistant S. aureus (MRSA), 12.92% methicillin-sensitive S. aureus (MSSA)] and 472 coagulase-negative Staphylococci (CNS) [37.60% methicillin-resistant coagulase-negative Staphylococci (MRCNS), 17.86% methicillin-sensitive coagulase-negative Staphylococci (MSCNS)]. Four hundred and thirty (50.52%) Staphylococcal spp. isolates showed erythromycin resistance. Constitutive resistance was demonstrated in 202 (46.97%), inducible clindamycin resistance (iMLS B ) in 101 (23.48%), and non-inducible (MS) in 127 (29.53%). Two distinct induction phenotypes, D (18.13%) and D + (5.34%) were observed. All iMLS B isolates were susceptible to linezolid and vancomycin while 78.78% to ciprofloxacin. CONCLUSIONS: Fifty percent of Staphylococcal spp. were ER among which 23.48% were iMLS B phenotypes. Eighty-seven per cent of iMLS B phenotypes were observed to be methicillin-resistant. The high frequency of methicillin resistance isolates (87.12%) with in vitro inducible clindamycin resistance at our institute raises concern of clindamycin treatment failures with methicillin-resistant infections. So we recommend that microbiology laboratories should include the D-test for inducible resistance to clindamycin in the routine antibiotic susceptibility testing.

Alcohol dependence produced in mice by inhalation of ethanol: grading the withdrawal reaction.

Intoxicating blood levels of ethanol are maintained for several days in mice housed in an atmosphere of ethanol vapor. On removal from the alcohol, all the mice develop withdrawal signs. The signs can be graded to indicate the time course and intensity of the withdrawal reaction.

Tobacco seedlings: damage by excessive nitrogen lessened by added phosphorus.

Concentrations of nitrogen (as ammonium nitrate) of 50 kilo-grams per hectare and greater are toxic to tobacco seedlings; symptoms are poor growth and white leaves. The leaves have markedly less chlorophylls (especially chlorophyll a) and more carotene and xanthophyll than seedlings grown in media low in nitrogen. These ill eflects are aggravated by short supply of phosphorus; they can be counteracted by more liberal supply of phosphorus.

Reproductive failure experimentally induced in sows via artificial insemination with semen spiked with porcine circovirus type 2.

Porcine circovirus type 2 (PCV2) is associated with reproductive failure in female pigs. However, the association of PCV2-positive semen in the pathogenesis has not been elucidated. The objectives of this study were to determine whether semen spiked with PCV2 causes infection in PCV2-naïve, mature female pigs and whether delivery of PCV2 via artificial insemination causes reproductive failure or fetal infection. Nine sows were randomly allocated into 3 groups of 3 sows each and artificially inseminated with PCV2 DNA-negative semen (group 1), PCV2 DNA-negative semen spiked with PCV2a (group 2), or PCV2b (group 3). All sows in groups 2 and 3 developed PCV2 viremia 7 to 14 days after insemination. None of the group 2 sows became pregnant, whereas all group 3 sows (3/3) farrowed at the expected date. At parturition, presuckle serum samples were collected, and live-born piglets, stillborn fetuses, and mummified fetuses were necropsied. All live-born piglets (n = 8) in group 3 were PCV2 viremic at birth. Stillborn fetuses (n = 2) had gross lesions of congestive heart failure. Mummified fetuses (n = 25) varied in crown-rump length from 7 to 27 cm, indicating fetal death between 42 and 105 days of gestation. PCV2 antigen was detected in the myocardium by immunohistochemistry of 7/8 (88%) live-born piglets, 2/2 (100%) of the stillborn fetuses, and 25/25 (100%) of the mummified fetuses. In addition, 4/25 mummified fetuses had PCV2 antigen associated with smooth muscle cells and fibroblasts. The results of this study indicate that intrauterine administration of PCV2 causes reproductive failure in naïve sows.

In vitro activity of gentamicin and amikacin against Salmonella enterica serovar Typhi: a search for a treatment regimen for typhoid fever.

The emergence of Salmonella enterica serovar Typhi isolates resistant to ciprofloxacin and 3rd-generation cephalosporins is a concern for physicians in developing countries. This study assessed the in vitro activity of gentamicin and amikacin against 464 S. entenca serovar Typhi isolates obtained from blood of patients clinically suspected of enteric fever who attended the Calcutta School of Tropical Medicine from 1991 to 2003. The isolates were sensitive to gentamicin and amikacin, showing minimum inhibitory concentrations 0.01-4 microg/mL and 0.005-3.5 microg/mL respectively. Both agents showed bactericidal activity at concentrations of 2 microg/mL after incubation for 6 hours. Aminoglycoside antibiotics such as gentamicin and amikacin may thus be introduced as a treatment regimen for typhoid fever.

Regional variation in gene expression in the healthy colon is dysregulated in ulcerative colitis.

OBJECTIVE: To investigate differential intestinal gene expression in patients with ulcerative colitis and in controls. DESIGN: Genome-wide expression study (41,058 expression sequence tags, 215 biopsies). SETTING: Western General Hospital, Edinburgh, UK, and Genentech, San Francisco, USA. PATIENTS: 67 patients with ulcerative colitis and 31 control subjects (23 normal subjects and 8 patients with inflamed non-inflammatory bowel disease biopsies). INTERVENTIONS: Paired endoscopic biopsies were taken from 5 specific anatomical locations for RNA extraction and histology. The Agilent microarray platform was used and confirmation of results was undertaken by real time polymerase chain reaction and immunohistochemistry. RESULTS: In healthy control biopsies, cluster analysis showed differences in gene expression between the right and left colon. (chi(2) = 25.1, p<0.0001). Developmental genes, homeobox protein A13 (HOXA13), (p = 2.3x10(-16)), HOXB13 (p<1x10(-45)), glioma-associated oncogene 1 (GLI1) (p = 4.0x10(-24)), and GLI3 (p = 2.1x10(-28)) primarily drove this separation. When all ulcerative colitis biopsies and control biopsies were compared, 143 sequences had a fold change of >1.5 in the ulcerative colitis biopsies (0.01>p>10(-45)) and 54 sequences had a fold change of <-1.5 (0.01>p>10(-20)). Differentially upregulated genes in ulcerative colitis included serum amyloid A1 (SAA1) (p<10(-45)) the alpha defensins 5 and 6 (DEFA5 and 6) (p = 0.00003 and p = 6.95x10(-7), respectively), matrix metalloproteinase 3 (MMP3) (p = 5.6x10(-10)) and MMP7 (p = 2.3x10(-7)). Increased DEFA5 and 6 expression was further characterised to Paneth cell metaplasia by immunohistochemistry and in situ hybridisation. Sub-analysis of the inflammatory bowel disease 2 (IBD2) and IBD5 loci, and the ATP-binding cassette (ABC) transporter genes revealed a number of differentially regulated genes in the ulcerative colitis biopsies. CONCLUSIONS: Key findings are the expression gradient in the healthy adult colon and the involvement of novel gene families, as well as established candidate genes in the pathogenesis of ulcerative colitis.

Profiling CpG island field methylation in both morphologically normal and neoplastic human colonic mucosa.

Aberrant CpG island (CGI) methylation occurs early in colorectal neoplasia. Quantitative methylation-specific PCR profiling applied to biopsies was used to quantify low levels of CGI methylation of 18 genes in the morphologically normal colonic mucosa of neoplasia-free subjects, adenomatous polyp patients, cancer patients and their tumours. Multivariate statistical analyses distinguished tumour from mucosa with a sensitivity of 78.9% and a specificity of 100% (P=3 x 10(-7)). In morphologically normal mucosa, age-dependent CGI methylation was observed for APC, AXIN2, DKK1, HPP1, N33, p16, SFRP1, SFRP2 and SFRP4 genes, and significant differences in CGI methylation levels were detected between groups. Multinomial logistic regression models based on the CGI methylation profiles from normal mucosa correctly identified 78.9% of cancer patients and 87.9% of non-cancer (neoplasia-free+polyp) patients (P=4.93 x 10(-7)) using APC, HPP1, p16, SFRP4, WIF1 and ESR1 methylation as the most informative variables. Similarly, CGI methylation of SFRP4, SFRP5 and WIF1 correctly identified 61.5% of polyp patients and 78.9% of neoplasia-free subjects (P=0.0167). The apparently normal mucosal field of patients presenting with neoplasia has evidently undergone significant epigenetic modification. Methylation of the genes selected by the models may play a role in the earliest stages of the development of colorectal neoplasia.

Restoration of impaired free radical generation and proinflammatory cytokines by MCP-1 in mycobacterial pathogenesis.

Mycobacterium tuberculosis exerts its pathogenic effects mainly via its cell wall glycolipid called Mannosylated Lipoarabinomannan (Man-LAM), which subverts the cellular inflammatory responses by the suppression of superoxide anion generation in earlier hours, and nitric oxide (NO) generation at later hours of pathogenic invasion. In this paper, we have shown the prophylactic effect of C-C chemokines, both in vitro and in vivo. Exogenous administration of C-C chemokines, particularly monocyte chemoattractant protein (MCP)-1, led to the induction of superoxide anion generation via the restoration of impaired protein kinase C (PKC) signalling in Man-LAM-treated macrophages. Monocyte chemoattractant protein-1 could also potently induce NO generation by upregulation of the proinflammatory cytokines tumour necrosis factor-alpha and interleukin-12 from Man-LAM-treated macrophages accompanied by inhibition of anti-inflammatory responses. Our in vivo observations clearly exhibited effective restoration of impaired PKC signalling as well as proinflammatory cytokine expression by MCP-1 in Man-LAM treated as well as M. tuberculosis H37Rv-infected C57BL/6 mice. We also observed, as direct evidence, that MCP-1 induced a significant reduction of the number of viable tubercle bacilli in the lungs and spleen of infected mice. Collectively, our findings strongly suggest the effectiveness of MCP-1 as a potent immunoprophylactic tool for controlling the mycobacterial establishment within the host.