Development and Optimization of a Subtraction-Normalized Immunocyte Profiling Signature for Prostate Cancer Active Surveillance Risk Stratification.

PURPOSE: Less invasive decision support tools are desperately needed to identify occult high-risk disease in men with prostate cancer (PCa) on active surveillance (AS). For a variety of reasons, many men on AS with low- or intermediate-risk disease forgo the necessary repeat surveillance biopsies needed to identify potentially higher-risk PCa. Here, we describe the development of a blood-based immunocyte transcriptomic signature to identify men harboring occult aggressive PCa. We then validate it on a biopsy-positive population with the goal of identifying men who should not be on AS and confirm those men with indolent disease who can safely remain on AS. This model uses subtraction-normalized immunocyte transcriptomic profiles to risk-stratify men with PCa who could be candidates for AS. MATERIALS AND METHODS: Men were eligible for enrollment in the study if they were determined by their physician to have a risk profile that warranted prostate biopsy. Both training (n = 1017) and validation cohort (n = 1198) populations had blood samples drawn coincident to their prostate biopsy. Purified CD2+ and CD14+ immune cells were obtained from peripheral blood mononuclear cells, and RNA was extracted and sequenced. To avoid overfitting and unnecessary complexity, a regularized regression model was built on the training cohort to predict PCa aggressiveness based on the National Comprehensive Cancer Network PCa guidelines. This model was then validated on an independent cohort of biopsy-positive men only, using National Comprehensive Cancer Network unfavorable intermediate risk and worse as an aggressiveness outcome, identifying patients who were not appropriate for AS. RESULTS: The best final model for the AS setting was obtained by combining an immunocyte transcriptomic profile based on 2 cell types with PSA density and age, reaching an AUC of 0.73 (95% CI: 0.69-0.77). The model significantly outperforms (P < .001) PSA density as a biomarker, which has an AUC of 0.69 (95% CI: 0.65-0.73). This model yields an individualized patient risk score with 90% negative predictive value and 50% positive predictive value. CONCLUSIONS: While further validation in an intended-use cohort is needed, the immunocyte transcriptomic model offers a promising tool for risk stratification of individual patients who are being considered for AS.

Adverse events following BNT162b2 mRNA COVID-19 vaccination among healthcare workers: A single-centre experience in Malaysia.

INTRODUCTION: The COVID-19 pandemic is a global health crisis that has resulted in a massive disease burden worldwide. Mass vaccination plays an important role in controlling the spread and severity of COVID-19 infections worldwide. MATERIALS AND METHODS: A cross-sectional study was conducted in Hospital Tuanku Ja'afar Seremban between 1 March 2021 and 4 May 2021 to describe the adverse events (AE) following BNT162b2 (Pfizer-BioNTech) vaccination. Healthcare personnel who received at least one dose of the vaccine were invited to complete an online questionnaire. RESULTS: Of 2282 analysed samples, AE were experienced in up to 64.5% (n=1472) of the study participants. Most AE were encountered after the second dose (56.5%, n=832). Pain at the injection site (41.5%, n=944), fever (35.1%, n=798) and lethargy (34.8%, n=792) were the most commonly reported AE. Severe AEFI were reported in a minority (2.9%, n=68). There were no documented anaphylaxis, vaccine-induced thrombosis, or myocarditis. The proportion of female recipients and recipients with a history of allergy were higher in the AE group compared to the non-AE group. CONCLUSION: Our study reinforces the safety of the BNT162b2 mRNA vaccine in the local population. The main adverse events were mild, although they occurred in most patients.

Potential Role of Serum Intestinal Fatty Acid-Binding Protein as a Marker for Early Prediction and Diagnosis of Necrotizing Enterocolitis in Preterm Neonates.

INTRODUCTION: Intestinal fatty acid-binding protein (I-FABP) is located in the apex of mature enterocytes and released into circulation; once the injury of enterocyte happens, its circulating levels are considered an early and sensitive marker of intestinal ischemia as in necrotizing enterocolitis (NEC); because of its small molecular weight, it can be detected in urine. AIMS: The aim was to study the usefulness of both serum and urine I-FABP in early diagnosis of NEC and to correlate the serum and urinary levels. SETTINGS AND DESIGN: This study was case-control design. METHODS: Simultaneous serum and urine samples obtained at the onset of symptoms, in 40 preterms with suspected NEC, with gestational age ± 27.70 weeks and birth weight ± 1.11 kg, i.e., 20 preterms diagnosed at Stage I, 12 preterms at Stage II, and 8 preterms at Stage III, were compared with age- and weight-matched preterms with no NEC. STATISTICAL ANALYSIS: The collected data were tabulated, coded, and then analyzed using the computer program Statistical Package for the Social Science (SPSS version 22). RESULTS: Serum levels of I-FABP in NEC cases were significantly higher than the control group, with a mean of 6005.77 ± 6384.77 and 1480.79 ± 1276.48 pg/ml, respectively (P < 0.001). Urine levels of I-FABP in NEC cases were significantly higher than the control group, with a mean of 5009.22 ± 3941.64 and 2677.62 ± 2257.29 pg/ml, respectively (P = 0.04). Both serum and urine I-FABP levels not only in Stage II are significantly higher than Stage I but also in Stage III are significantly higher than Stage I and II (P < 0.001, P = 0.03, respectively), which showed significant positive correlation with stages of NEC (r = 0.618; P < 0.001; r = 0.306; P = 0.049, respectively). Both serum and urine I-FABP levels had a highly significant positive correlation with each other (r = 0.406 P < 0.0001). Receiving operating characteristic curve showed an area under the curve of 0.92 and 0.81 for serum and urine I-FABP, respectively. CONCLUSIONS: Whether serum or urinary I-FABP is valuable in the diagnosis and prediction of NEC and strongly correlated with the disease severity and with each other.

Silencing cathepsin L expression reduces Myzus persicae protein content and the nutritional value as prey for Coccinella septempunctata.

Gut-expressed aphid genes, which may be more easily inhibited by RNA interference (RNAi) constructs, are attractive targets for pest control efforts involving transgenic plants. Here we show that expression of cathepsin L, which encodes a cysteine protease that functions in aphid guts, can be reduced by expression of an RNAi construct in transgenic tobacco. The effectiveness of this approach is demonstrated by up to 80% adult mortality, reduced fecundity, and delayed nymph production of Myzus persicae (green peach aphids) when cathepsin L expression was reduced by plant-mediated RNAi. Consistent with the function of cathepsin L as a gut protease, M. persicae fed on the RNAi plants had a lower protein content in their bodies and excreted more protein and/or free amino acids in their honeydew. Larvae of Coccinella septempunctata (seven-spotted ladybugs) grew more slowly on aphids having reduced cathepsin L expression, suggesting that prey insect nutritive value, and not just direct negative effects of the RNAi construct, needs to be considered when producing transgenic plants for RNAi-mediated pest control.

The antisense 5' end of the V2 gene confers enhanced resistance against the monopartite begomovirus cotton leaf curl Kokhran virus-Burewala strain.

Whitefly-transmitted viruses of the genus Begomovirus (the family Geminiviridae) have become a limiting factor for agricultural productivity in many warmer parts of the world. The economies of Pakistan and India have, since the early 1990s, suffered losses due to cotton leaf curl disease (CLCuD). The disease is caused by begomoviruses, the most important of which at this time is cotton leaf curl Kokhran virus strain Burewala (CLCuKoV-Bu), and a disease-specific betasatellite, cotton leaf curl Multan betasatellite (CLCuMuB). Efforts to minimize losses due to CLCuD rely mainly on the use of insecticides to kill the whitefly vector; no resistant cotton varieties are currently commercially available. The study described here has investigated RNA interference technology for its potential to yield resistance against CLCuKoV-Bu and three other begomoviruses; CLCuKoV, tomato leaf curl New Delhi virus (ToLCNDV) and Pedilanthus leaf curl virus (PeLCV). Three fragments of the virion-sense V2 gene of CLCuKoV-Bu were transformed into Nicotiana benthamiana in antisense orientation and transgenic lines expressing virus-specific short RNAs were assessed for their ability to yield resistance. Only CLCuKoV-Bu with the V2 sequence closest to the promoter was resistant. Inoculation of CLCuKoV-Bu with CLCuMuB into transgenic plants did not significantly affect the outcome, although viral DNA was detected in number of plants, suggesting that the betasatellite may impair RNAi resistance. Overall the results indicate that targeting the 5' end of V2 gene using antisense-RNA has the potential to deliver resistance against begomoviruses and that RNAi-based resistance imparts some degree of resistance to heterologous viruses. Keywords: geminivirus; begomovirus; RNAi; resistance; CLCuKoV-Burewala; CLCuMuB.

Toll-like receptor (TLR)7 expression in mycosis fungoides and psoriasis: a case-control study.

BACKGROUND: Toll-like receptors (TLRs) have been implicated in various dermatological diseases. TLR agonists have the capacity to potently activate the innate immune cells of patients with advanced, refractory, cutaneous T-cell lymphoma (CTCL). AIM: To detect TLR7 gene expression in mycosis fungoides (MF) (a neoplastic skin condition) and to compare it with psoriasis (an inflammatory skin condition) in an attempt to clarify the pathogenic role played by TLR7 in both conditions. METHODS: This case-control study enrolled 28 patients with MF: 30 patients with psoriasis, and 30 age- and sex-matched healthy controls (HCs). A 4-mm punch skin biopsy was obtained from lesional skin of patients and from normal skin of HCs for detection of TLR7 gene expression using real-time PCR. RESULTS: Mean TLR7 level in patients with MF (0.4 ± 0.23) was significantly lower than in patients with psoriasis (1.49 ± 0.46) and in HCs (1.22 ± 0.44) (P < 0.001), and mean TLR7 level in patients with psoriasis was significantly higher than in HCs (P < 0.03). Based on MF staging, 21.4% of patients had stage Ia, 28.6% had stage Ib, 28.6% had stage IIa and 21.4% had stage IIb disease. Comparing the TLR7 levels in relation to MF staging revealed the lowest mean value was in stage IIb and highest mean value in stage Ia, and this was significant (P < 0.001). CONCLUSION: Disturbed innate immunity might play a role in the pathogenesis of neoplastic and inflammatory skin conditions. TLR7 could be useful as a prognostic factor in MF.

Management of Myositis Ossificans of the Hand: A Case Report and a Review of the Literature.

Myositis ossificans is a rare form of self-limiting heterotopic ossification of muscles. Most cases are seen in the thigh; the standard approach to these cases has been nonsurgical management awaiting spontaneous resolution. We report on a rare case of myositis ossificans of the hand with severe symptoms treated with early marginal excision without a trial of nonsurgical management.

First Report of Tomato leaf curl Albatinah virus (ToLCABV) and its Associated Betasatellite Infecting Papaya in Oman.

Leaf curl disease with severe curling, vein darkening, and vein thickening was observed on papaya plants in a field in Qurayat district of Oman during December 2013. Disease incidence ranged from 50 to 70%, particularly in young papaya plants. The presence of a large population of whiteflies and symptoms observed on papaya plants suggested that the causal agent could be begomoviruses (family Geminiviridae) and associated satellites. Four leaf samples with mild and severe leaf curling were collected from the field. Total nucleic acid extracted from symptomatic and healthy plants using the CTAB method were used as a template to amplify circular DNAs using Φ29 DNA polymerase, and products were digested with restriction enzymes to identify fragments of 2.6 to 2.8 kb typical of geminiviruses. BamHI yielded fragments of ~2.8 and 1.4 kb when the digested products were resolved by electrophoresis on a 1% agarose gel. These fragments were cloned and sequenced using a primer walking strategy in both directions. Sequencing results confirmed the exact sizes of 1,303, 1,358, and 2,765 bp; the sequences were deposited in GenBank under the accession numbers HG969296, HG969297, and HG969260, respectively. BLAST results showed that the first two sequences are Tomato leaf curl betasatellite (ToLCB; isolates Pap-2 and Pap-3) showing 97% sequence identity with a previously reported ToLCB sequence (Accession No. KF229728). Both satellites encode a single gene in the complementary sense strand referred to as ßC1, which showed 97% sequence identity to ToLCB (HE800551). The viral sequence (isolate Pap-6) showed four genes in the complementary sense (the replication-associated protein [Rep] gene, the transcription-activator protein [TrAP] gene, the replication-enhancer protein [REn] gene, and the C4 gene) and two genes (pre-coat protein [V2] and coat protein [CP]) in virion-sense (2). BLAST analysis showed 95.2% sequence identity to Tomato leaf curl Albatinah virus (ToLCABV; FJ956700), reported earlier to infect tomato in Oman (3). Amino acid sequence comparison of the four predicted proteins (Rep, TrAP, Ren, and C4) encoded by Pap-6 shared 95, 96, 100, and 100% sequence identity, whereas virion-sense proteins (V1 and V2) shared 99% sequence identity with ToLCABV (FJ956700). According to the recommendations of the International Committee on Taxonomy of Viruses, these results indicate that the virus identified in association with papaya leaf curl disease in Oman is a variant of ToLCABV (1). All infected samples showed the presence of ToLCABV, while no hybridization was observed in healthy control DNA using ToLCABV probe. These findings are indicative of the rapid spread of diseases involving Begomovirus and betasatellites, which often result in increased host range, as is evident from this study. References: (1) C. M. Fauquet et al. Arch. Virol. 148:405, 2003. (2) L. Hanley-Bowdoin et al. Crit. Rev. Plant Sci. 18:71, 1999. (3) A. J. Khan et al. Arch. Virol. 159:445, 2013.

Extensive Phenotypic Variability in Syndrome Dysmorphic Facies, Renal Agenesis, Ambiguous Genitalia, Microcephaly, Polydactyly, and Lissencephaly (DREAM-PL): A Case Report Highlighting Diagnostic and Management Challenges.

The dysmorphic facies, renal agenesis, ambiguous genitalia, microcephaly, polydactyly, and lissencephaly (DREAM-PL) syndrome is a rare autosomal recessive disorder characterized by dysmorphic facies, renal agenesis, ambiguous genitalia in males, microcephaly, polydactyly, and lissencephaly. The CTU2 gene, which encodes a protein involved in the post-transcriptional modification of tRNAs is the source of the syndrome's mutation. Several developmental abnormalities can result from a disruption of this modification, which is necessary for the proper translation of genes. The severity of the symptoms of DREAM-PL syndrome can range from moderate to severe, and its clinical characteristics are quite diverse. Some patients might have some of the distinguishing characteristics, whereas others might have all of them. The most typical characteristics include ambiguous genitalia, dysmorphic facies, and microcephaly. DREAM-PL syndrome is diagnosed based on clinical signs and genetic testing which can show mutations in the CTU2 gene. Although there is no known cure for this syndrome, the treatment aims to manage the symptoms. Other lines of treatment like surgical correction of birth defects can sometimes be beneficial to these patients in addition to supportive care. This study is a report of a 37-week-old male neonate, delivered by lower segment cesarean section. The baby's birth weight is 2.760 kg with a heterozygous confirmed pathogenic mutation of the CTU2 gene confirmed by whole-exome sequencing.

Management of the open abdomen: a national study of clinical outcome and safety of negative pressure wound therapy.

OBJECTIVE: To determine clinical outcome of open abdomen therapy and assess the influence of negative pressure wound therapy on outcome. BACKGROUND: Leaving the abdomen open (laparostomy) is an option following laparotomy for severe abdominal sepsis or trauma. Negative pressure wound therapy (NPWT) has become a popular means of managing laparostomy wounds. It may facilitate nursing care and delayed primary wound closure but the evidence to support its use is poor and concern has arisen about the risk of intestinal fistulation from exposed bowel, leading to an increased risk of death. METHODS: Prospective observational study of 578 patients treated with an open abdomen in 105 hospitals in the United Kingdom between January 1, 2010, and June 30, 2011. Propensity analysis was used to compare adverse outcomes (fistulation, death, intestinal failure, bleeding requiring intervention) and delayed primary closure rates in patients who did and did not receive NPWT. FINDINGS: The most common indication for an open abdomen (n = 398, 68.9%) was abdominal sepsis. Overall hospital mortality was 28.2%. The majority of patients (n = 355, 61.4%) were treated with NPWT. Intestinal fistulation [relative risk (RR) = 0.83, 95% confidence interval (CI): 0.44-1.58], death (RR = 0.87, 95% CI: 0.64-1.20), bleeding (RR = 0.74, 95% CI: 0.45-1.23), and intestinal failure (RR = 1.00, 95% CI: 0.64-1.57) were no more common in patients receiving NPWT, but the rate of delayed primary closure was significantly lower (RR = 0.74, 95% CI: 0.60-0.90, P = 0.002) when NPWT was used. CONCLUSIONS: The indications for an open abdomen in the United Kingdom appear to be significantly different to those described in N. America, where its use in the management of trauma predominates. NPWT in patients with an open abdomen is not associated with an increase in mortality or intestinal fistulation. It is, however, associated with a reduced rate of delayed primary closure. Although this may be related to patient selection, NPWT may leave patients with abdominal wall defects that require further treatment.

In vitro radiosensitization by gold nanoparticles during continuous low-dose-rate gamma irradiation with I-125 brachytherapy seeds.

This communication reports the first experimental evidence of gold nanoparticle (AuNP) radiosensitization during continuous low-dose-rate (LDR) gamma irradiation with low-energy brachytherapy sources. HeLa cell cultures incubated with and without AuNP were irradiated with an I-125 seed plaque designed to produce a relatively homogeneous dose distribution in the plane of the cell culture slide. Four sets of irradiation experiments were conducted at low-dose rates ranging from 2.1 to 4.5cGy/h. Residual γH2AX was measured 24h after irradiation and used to compare radiation damage to the cells with and without AuNP. The data demonstrate that the biological effect when irradiating in the presence of 0.2mg/ml concentration of AuNP is about 70%-130% greater than without AuNP. Meanwhile, without radiation, the AuNP showed minimal effect on the cancer cells. These findings provide in vitro evidence that AuNP may be employed as radiosensitizers during continuous LDR brachytherapy. FROM THE CLINICAL EDITOR: In this basic science paper, the application of gold nanoparticles as radiosensitizing agents for low dose rate gamma radiation therapy is discussed, demonstrating efficacy in cell culture models.

Significantly higher expression of high-mobility group AT hook protein 2 (HMGA2) in the border zone of glioblastoma.

BACKGROUND: High-mobility group AT-hook protein 2 (HMGA2) is a gene regulatory protein that is correlated with metastatic potential and poor prognosis. It has been shown that HMGA2 is overexpressed in various tumors such as lung cancer or pancreatic cancer. The invasive character and highly aggressive structure of glioblastoma let us to investigate HMGA2 expression in the border zone of the tumor more closely. We compared HMGA2 expression between glioblastoma and normal brain tissue. In addition, we analyzed and compared HMGA2 expression in the border and center zones of tumors. Correlation tests between HMGA expression and clinical parameters such as MGMT-status and survival were performed. METHODS: Samples from 23 patients with WHO grade 4 glioblastomas were analyzed for HMGA2 expression using quantitative real-time polymerase chain reaction (qPCR) and immunohistochemistry (IHC) and correlated with clinical parameters. The areas from the tumor center and border were analyzed separately. Two normal brain tissue specimens were used as the controls. RESULTS: Our results confirm that HMGA2 is higher expressed in glioblastoma compared to healthy brain tissue (qPCR, P=0.013; IHC, P=0.04). Moreover, immunohistochemistry revealed significantly higher HMGA2 expression in the border zone of the tumor than in the tumor center zone (P=0.012). Survival analysis revealed a tendency for shorter survival when HMGA2 was highly expressed in the border zone. CONCLUSIONS: The results reveal an overexpression of HMGA2 in the border zone of glioblastomas; thus, the expression cluster of HMGA2 seems to be heterogenous and thorough borough surgical resection of the vital and aggressive border cells might be important to inhibit the invasive character of the tumor.

Xanthium strumarium: a weed host of components of begomovirus-betasatellite complexes affecting crops.

Xanthium strumarium is a common weed that often shows symptoms typical of begomovirus infection, such as leaf curling and vein thickening. The virus complex isolated from the weed consisted of two begomoviruses along with a betasatellite and an alphasatellite. The first begomovirus was shown to be an isolate of Cotton leaf curl Burewala virus, a new recombinant begomovirus species that is associated with resistance breaking in previously resistant cotton varieties in Pakistan, whereas the second was shown to be an isolate of Tomato leaf curl Gujarat virus (ToLCGV), a begomovirus previously reported to be bipartite. However, there was no evidence for the presence of the second genomic component, DNA B, of ToLCGV in X. strumarium. The betasatellite was shown to be an isolate of Tomato yellow leaf curl Thailand betasatellite, the first time this satellite has been identified in Pakistan. The alphasatellite associated with infection of X. strumarium was shown to be a species recently identified in potato and various weeds; Potato leaf curl alphasatellite. Although each component has been identified previously, this is the first time they have been identified in a single host. These findings reinforce the hypothesis that weeds are reservoirs of crop-infecting begomoviruses that may contribute to virus diversity by virtue of harboring multiple viruses and virus associated components, which may lead to interspecific recombination and component exchange.

Does the outcome of colonic flexure cancers differ from the other colonic sites?

BACKGROUND: Anecdotally, colonic flexure cancers (FC) appear to have a poorer prognosis compared to other colonic cancers (OCC). The aim of this study was to determine the outcome of colonic flexure cancers compared to the cancers of the rest of the colon. METHODS: Patients with a diagnosis of colonic cancer over a 5-year period (2002-2006) were retrieved from a prospective database. Analysis was performed on flexure (hepatic/splenic) cancers versus remaining colon cancers. Overall, 1-, 3- and 5-year survival rates were calculated. All patients were followed up until death or end of study period (December 2008), with median follow-up of 32 months. Statistical analysis was performed using Kaplan-Meier with log rank statistic and Pearson chi-square test. RESULTS: Of 613 patients (54% males) with colonic cancers with median age 71 years, range (30-100), 67 (10.9%) were FC (35 hepatic/32 splenic) and 546 (89.1%) were arising from OCC. The curative resection rates were FC 73.2% (41 of 56) and OCC 83.4% (359 of 435) (p = 0.05). Post-operative mortality for FC and OCC was 10.7% (6 of 56) and 4.2% (18 of 434), respectively (p = 0.04). FC presented at a more advanced Dukes stage (p = 0.003). Recurrence rates were 9.8% (4 of 41) for FC and 20.9% (75 of 359) for OCC sites (p = 0.088). The overall mean survival was 48.8 and 58.2 m for FC and OCC, respectively (p = 0.158). Of 1-, 3- and 5-year survival, only 1-year survival was significantly different between the two groups (OCC (85%) vs FC (75%), p = 0.018). CONCLUSIONS: Nearly one in ten colonic cancers is located at a flexure. Despite FC presenting at an advanced stage, leading to a lower curative resection rate, no significant survival difference was noted compared to other colonic sites, beyond the first year.

Intracerebral mucormycosis after COVID-19: illustrative cases.

BACKGROUND: In this case report the authors present two female patients with intracranial mucormycosis after coronavirus disease 2019 (COVID-19). OBSERVATIONS: The first patient was a 30-year-old woman with no past medical history or allergies who presented with headaches and vomiting. Magnetic resonance imaging (MRI) and computed tomography of the skull showed an endonasal infection, which had already destroyed the frontal skull base and caused a large frontal intracranial abscess. The second patient was a 29-year-old woman with multiple pre-existing conditions, who was initially admitted to the hospital due to a COVID-19 infection and later developed a hemiparesis of the right side. Here, the MRI scan showed an abscess configuration in the left motor cortex. In both cases, rapid therapy was performed by surgical clearance and abscess evacuation followed by antifungal, antidiabetic, and further supportive treatment for several weeks. LESSONS: Both cases are indicative of a possible correlation of mucormycosis in the setting of severe immunosuppression involved with COVID-19, both iatrogenic with the use of steroids and previous medical history. Furthermore, young and supposedly healthy patients can also be affected by this rare disease.

General approach to identifying potential targets for cancer imaging by integrated bioinformatics analysis of publicly available genomic profiles.

Molecular imaging has moved to the forefront of drug development and biomedical research. The identification of appropriate imaging targets has become the touchstone for the accurate diagnosis and prognosis of human cancer. Particularly, cell surface- or membrane-bound proteins are attractive imaging targets for their aberrant expression, easily accessible location, and unique biochemical functions in tumor cells. Previously, we published a literature mining of potential targets for our in-house enzyme-mediated cancer imaging and therapy technology. Here we present a simple and integrated bioinformatics analysis approach that assembles a public cancer microarray database with a pathway knowledge base for ascertaining and prioritizing upregulated genes encoding cell surface- or membrane-bound proteins, which could serve imaging targets. As examples, we obtained lists of potential hits for six common and lethal human tumors in the prostate, breast, lung, colon, ovary, and pancreas. As control tests, a number of well-known cancer imaging targets were detected and confirmed by our study. Further, by consulting gene-disease and protein-disease databases, we suggest a number of significantly upregulated genes as promising imaging targets, including cell surface-associated mucin-1, prostate-specific membrane antigen, hepsin, urokinase plasminogen activator receptor, and folate receptors. By integrating pathway analysis, we are able to organize and map "focused" interaction networks derived from significantly dysregulated entity pairs to reflect important cellular functions in disease processes. We provide herein an example of identifying a tumor cell growth and proliferation subnetwork for prostate cancer. This systematic mining approach can be broadly applied to identify imaging or therapeutic targets for other human diseases.

Novel method for quantifying radiation-induced single-strand-break yields in plasmid DNA highlights 10-fold discrepancy.

The widely used agarose gel electrophoresis method for assessing radiation-induced single-strand-break (SSB) yield in plasmid DNA involves measurement of the fraction of relaxed-circular (C) form that migrates independently from the intact supercoiled (SC) form. We rationalized that this method may underestimate the SSB yield since the position of the relaxed-circular form is not altered when the number of SSB per DNA molecule is >1. To overcome this limitation, we have developed a novel method that directly probes and quantifies SSBs. Supercoiled (3)H-pUC19 plasmid samples were irradiated with γ-rays, alkali-denatured, dephosphorylated, and kinated with γ-[(32)P]ATP, and the DNA-incorporated (32)P activities were used to quantify the SSB yields per DNA molecule, employing a standard curve generated using DNA molecules containing a known number of SSBs. The same irradiated samples were analyzed by agarose gel and SSB yields were determined by conventional methods. Comparison of the data demonstrated that the mean SSB yield per plasmid DNA molecule of [21.2±0.59]×10(-2)Gy(-1) as measured by direct probing is ~10-fold higher than that obtained from conventional gel-based methods. These findings imply that the SSB yields inferred from agarose gels need reevaluation, especially when they were utilized in the determination of radiation risk.

Change in hepatitis C virus clades: a cross-sectional study of chronic HCV patients in Pakistan from 2000-2010.

The changing pattern in hepatitis C virus (HCV) clades overtime is not well known in Pakistan. To find out the changing pattern of different HCV clades over time in this country 22,125 patients were genotyped and tracked for a period of 11 years (2000-2010). A changing pattern in HCV clades was seen in this region during the study period. Sub-clade 3a remained the dominant sub-clade circulating in different areas of the country in the study era. HCV sub-clade 3a demonstrated significantly high correlation with time (p < 0.05) whereas undetermined clades were seen with statistically non-significant correlation with time (years). All the other clades showed negative correlation with time. In general a significant decline was observed in the percentages of HCV clades 2, 4, 5 and 6 (p < 0.001). Among sub-clades, HCV 1a, 2c, 2b and 3b significantly decreased overtime (p < 0.05), while an increase has been observed for HCV 3a sub-clade and mixed clades (p <0.001). The ratio of undetermined clades remained constant over the study period. In conclusion, a changing pattern of HCV clades was observed over the 11-year study period, and this changed pattern might have direct impact on HCV disease outcome.

Insulin-like growth factor-1 in psoriatic plaques treated with PUVA and methotrexate.

BACKGROUND: The pathogenesis of psoriasis is thought to depend on the activation of immune cells and their secreted cytokines, chemokines and growth factors like IGF-1 which may contribute to the epidermal hyperplasia of psoriasis. Treatment of psoriasis with PUVA and methotrexate are associated with clinical improvement and decrease in epidermal hyperplasia. OBJECTIVE: To examine the effects of PUVA and methotrexate therapy on IGF-1 expression in psoriatic plaques and whether this change correlates with clinical response. METHODS: For 24 psoriatic patients, the PASI score and levels of lesional IGF-1 and its mRNA were determined by RT-PCR before and after treatment with either methotrexate or PUVA. Skin biopsies from 12 healthy volunteers served as control for IGF-1 levels in normal skin. RESULTS: Lesional skin of psoriatic patients showed a statistically significant elevation in IGF-1 and its mRNA levels in comparison to control (P = 0.0001). Both methotrexate and PUVA treatment were associated with a significant decrease in both PASI scores and lesional IGF-1 after 10 month treatment. CONCLUSION: Both methotrexate and PUVA therapy for psoriasis are associated with a decrease in PASI score and IGF-1. The IGF-1 down-regulation may possibly be a consequence of the decrease in cytokines and inflammatory cellular infiltrate that occur following treatment with either modalities or due to their effect on local fibroblast activity and proliferation.

Natural occurrence of mesta yellow vein mosaic virus and DNA-satellites in ornamental sunflower (Helianthus spp.) in Pakistan.

Weeds and ornamental plants serve as a reservoir for geminiviruses and contribute to their dissemination, genome recombination and/or satellite capture. Ornamental sunflower (Helianthus spp.) plants exhibiting mild leaf curl symptoms were subjected to begomovirus and DNA-satellites isolation. The full-length genome of the isolated begomovirus clone (Od1-A) showed 96.8% nucleotide (nt) sequence identity with mesta yellow vein mosaic virus (MeYVMV; accession no. FR772081) whereas, alphasatellite (Od1-a) and betasatellite (Od1-b) clones showed their highest nt sequence identities at 97.4% and 98.2% with ageratum enation alphasatellite (AEA; accession no. FR772085) and papaya leaf curl betasatellite (PaLCuB; accession. no. LN878112), respectively. The evolutionary relationships, average evolutionary divergence and the recombination events were also inferred. The MeYVMV exhibited 9.5% average evolutionary divergence and its CP and Rep had 9.3% and 12.2%, concomitantly; the alphasatellite and the betasatellite had 8.3% and 5.2%, respectively. The nt substitution rates (site-1 year-1) were found to be 6.983 × 10-04 and 5.702 × 10-05 in the CP and Rep of MeYVMV, respectively. The dN/dS ratio and the Tajima D value of MeYVMV CP demonstrated its possible role in host switching. The absolute quantification of the begomovirus demonstrated that mild symptoms might have a correlation with low virus titer. This is the first identification of MeYVMV and associated DNA-satellites from ornamental sunflower in Pakistan. The role of sequence divergence, recombination and importance of MeYVMV along with DNA-satellites in extending its host range is discussed.