bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Hepatitis C Virus (HCV) infection on biomolecular markers influencing the pathogenesis of bladder cancer
Authors: Hemmaid Kamel Z , Awadalla Amira , Elsawy Essam , Hussein Abdel-aziz M , Abdel-aziz Azza , Shokeir Ahmed A , El-Hefnawy Ahmed S , Abol-enein Hassan 
Published: June 2013

Abstract

Objective
The present study was designed to determine the possible impact of hepatitis C virus (HCV) infection on the expression of telomerase (TERT), retinoblastoma (RB1), E2F3, TP53, CDKN1A (p21) and fibroblast growth factor receptor- 3 (FGFR3) genes in patients with bladder cancer (BC).

Materials and methods
100 patients with bladder cancer (15 female and 85 male) were divided into 2 groups; Group I: 50 HCV negative subjects (age range 36–79), and Group II: 50 HCV positive subjects (age range 42–80). Expressions of the telomerase, retinoblastoma (Rb), E2F3, TP53 and FGFR3 genes were tested by immunohistochemistry and real time PCR in tumour tissues and healthy bladder tissues. Also, telomerase activity was assessed by telomeric repeats amplification protocol (TRAP).

Results
Bladder tumors associated with HCV infection were of high grade and invasive squamous cell carcinomas (SCCs). Expressions of hTERT, Rb, E2F3, TP53 and FGFR3 as well as telomerase activity were significantly higher in bladder tissues of HCV-infected patients compared with bladder tissues of non infected patients (p<0.05). On the contrary, CDKN1A (p21) expression was significantly lower in bladder tissues of HCV-infected patients compared to bladder tissues of non infected patients (p<0.05).

Conclusion
The expressions of hTERT, Rb, E2F3, TP53 and FGFR3 as well as the activity of telomerase were significantly high in malignant bladder tissues associated with HCV infection. On the other hand, CDKN1A (p21) expression was low in bladder tissues of HCV-infected subjects. Moreover, there was a positive correlation between HCV infection and expression of telomerase, E2F3, TP53 and FGFR3. There was a negative correlation between HCV infection and expression of Rb and p21.
Molecular analysis of appendiceal mucinous cystadenoma and rectal adenocarcinoma in a patient with urothelial carcinoma: a case report
Authors: Pulighe Fabio , Paliogiannis Panagiotis , Cossu Antonio , Palmieri Giuseppe , Colombino Maria , Scognamillo Fabrizio , Trignano Mario 
Published: June 2013

Abstract

Introduction
In this report, we present the case of a patient affected by appendiceal cystadenoma, a colorectal adenocarcinoma, and a concomitant bladder carcinoma, as well as the results of the molecular study of the most relevant mutational pathways involved in these tumors.

Case presentation
A 68-year-old Italian man was admitted to our unit complaining of macrohematuria, rectorrhagia, and rectal tenesmus for about 2 months. A colonoscopy showed the presence of a rectal lesion at 11cm from the anal margin; multiple biopsies were performed and a diagnosis of moderately differentiated adenocarcinoma was made. Abdominal ultrasonography and total body computed tomography performed subsequently to stage the rectal cancer showed the presence of two round nodules, interpreted as swollen lymph nodes of neoplastic origin, at the anterior aspect of the iliopsoas muscle and a budding lesion affecting the bladder. The patient underwent transurethral biopsy of the lesion in the right retrotrigonal region; the diagnosis was grade II urothelial carcinoma. The patient underwent an open anterior rectal resection with loco-regional lymphadenectomy. An enlarged appendix and a voluminous whitish soft-tissue lesion requiring an appendicectomy were detected perioperatively. Transurethral resection of the bladder lesion was also performed. The histological examination revealed that the nodular lesions in the appendix were due to a cystadenoma. For mutation analysis, genomic deoxyribonucleic acid was isolated from tumor tissue samples; for PIK3CA mutations, screening revealed that all three samples analyzed carried mutations in exon 9.

Conclusions
Appendiceal mucoceles are rare but require adequate surgical treatment, given their malignant potential and the possibility of causing peritoneal pseudomyxoma. It is essential to make a correct preoperative evaluation based on a colonoscopy rather than ultrasound and computed tomography to exclude synchronous neoplasias often associated with mucoceles and to plan the optimum surgical strategy. The association between appendiceal mucoceles and other neoplasias is relatively frequent, especially with colorectal cancer. Oncogenic activation in the PIK3CA-depending pathway may contribute substantially to the pathogenesis of the different solid tumors in the same patient.
Alteration of human blood cell transcriptome in uremia
Authors: Scherer Andreas , Günther Oliver P , Balshaw Robert F , Hollander Zsuzsanna , Wilson-McManus Janet , Ng Raymond , McMaster W Robert , McManus Bruce M , Keown Paul A 
Published: June 2013

Abstract

Background
End-stage renal failure is associated with profound changes in physiology and health, but the molecular causation of these pleomorphic effects termed “uremia” is poorly understood. The genomic changes of uremia were explored in a whole genome microarray case-control comparison of 95 subjects with end-stage renal failure (n = 75) or healthy controls (n = 20).

Methods
RNA was separated from blood drawn in PAXgene tubes and gene expression analyzed using Affymetrix Human Genome U133 Plus 2.0 arrays. Quality control and normalization was performed, and statistical significance determined with multiple test corrections (qFDR). Biological interpretation was aided by knowledge mining using NIH DAVID, MetaCore and PubGene

Results
Over 9,000 genes were differentially expressed in uremic subjects compared to normal controls (fold change: -5.3 to +6.8), and more than 65% were lower in uremia. Changes appeared to be regulated through key gene networks involving cMYC, SP1, P53, AP1, NFkB, HNF4 alpha, HIF1A, c-Jun, STAT1, STAT3 and CREB1. Gene set enrichment analysis showed that mRNA processing and transport, protein transport, chaperone functions, the unfolded protein response and genes involved in tumor genesis were prominently lower in uremia, while insulin-like growth factor activity, neuroactive receptor interaction, the complement system, lipoprotein metabolism and lipid transport were higher in uremia. Pathways involving cytoskeletal remodeling, the clathrin-coated endosomal pathway, T-cell receptor signaling and CD28 pathways, and many immune and biological mechanisms were significantly down-regulated, while the ubiquitin pathway and certain others were up-regulated.

Conclusions
End-stage renal failure is associated with profound changes in human gene expression which appears to be mediated through key transcription factors. Dialysis and primary kidney disease had minor effects on gene regulation, but uremia was the dominant influence in the changes observed. This data provides important insight into the changes in cellular biology and function, opportunities for biomarkers of disease progression and therapy, and potential targets for intervention in uremia.
Treatment reality in elderly patients with advanced ovarian cancer: a prospective analysis of the OVCAD consortium
Authors: Trillsch Fabian , Woelber Linn , Eulenburg Christine , Braicu Ioana , Lambrechts Sandrina , Chekerov Radoslav , van Nieuwenhuysen Els , Speiser Paul , Zeimet Alain , Castillo-Tong Dan Cacsire , Concin Nicole , Zeillinger Robert , Vergote Ignace , Mahner Sven , Sehouli Jalid 
Published: June 2013

Abstract

Background
Approximately one third of women diagnosed with ovarian cancer is 70 years or older. Information on the treatment reality of these elderly patients is limited.

Methods
275 patients with primary epithelial ovarian cancer FIGO stage II-IV undergoing cytoreductive surgery and platinum-based chemotherapy were prospectively included in this European multicenter study. Patients <70 and ≥70 years were compared regarding clinicopathological variables and prognosis.

Results
Median age was 58 years (18–85); 47 patients (17.1%) were 70 years or older. The postoperative 60-day-mortality rate was 2.1% for elderly and 0.4% for younger patients (p < 0.001). Elderly patients were less likely to receive optimal therapy (no residual disease after surgery and platinum combination chemotherapy) compared to patients <70 years (40.4% vs. 70.1%, p < 0.001) and their outcome was less favorable regarding median PFS (12 vs. 20 months, p = 0.022) and OS (30 vs. 64 months, p < 0.001). However, in multivariate analysis age itself was not a prognostic factor for PFS while the ECOG performance status had prognostic significance in elderly patients.

Conclusions
Elderly patients with ovarian cancer are often treated less radically. Their outcome is impaired despite no consistent prognostic effect of age itself. Biological age and functional status should be considered before individualized treatment plans are defined.
Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection
Authors: Vincent Caroline , Stephens David A , Loo Vivian G , Edens Thaddeus J , Behr Marcel A , Dewar Ken , Manges Amee R 
Published: June 2013

AbstractBackgroundAntimicrobial use is thought to suppress the intestinal microbiota, thereby impairing colonization resistance and allowingClostridium difficileto infect the gut. Additional risk factors such as proton-pump inhibitors may also alter the intestinal microbiota and predispose patients toClostridium difficileinfection (CDI). This comparative metagenomic study investigates the relationship between epidemiologic exposures, intestinal bacterial populations and subsequent development of CDI in hospitalized patients. We performed a nested case–control study including 25 CDI cases and 25 matched controls. Fecal specimens collected prior to disease onset were evaluated by 16S rRNA gene amplification and pyrosequencing to determine the composition of the intestinal microbiota during the at-risk period.ResultsThe diversity of the intestinal microbiota was significantly reduced prior to an episode of CDI. Sequences corresponding to the phylum Bacteroidetes and to the families Bacteroidaceae and Clostridiales Incertae Sedis XI were depleted in CDI patients compared to controls, whereas sequences corresponding to the family Enterococcaceae were enriched. In multivariable analyses, cephalosporin and fluoroquinolone use, as well as a decrease in the abundance of Clostridiales Incertae Sedis XI were significantly and independently associated with CDI development.ConclusionsThis study shows that a reduction in the abundance of a specific bacterial family - Clostridiales Incertae Sedis XI - is associated with risk of nosocomial CDI and may represent a target for novel strategies to prevent this life-threatening infection.
Evaluation of Fenton oxidation process coupled with biological treatment for the removal of reactive black 5 from aqueous solution
Authors: Bahmani Pegah , Rezaei Kalantary Roshanak , Esrafili Ali , Gholami Mitra , Jonidi Jafari Ahmad 
Published: June 2013

Abstract
Biodegradation of azo dyes is difficult due to their complex structures and low BOD to COD ratios. In the present study, the efficiency of using Fenton’s reagent (H2O2 + Fe2+) as a pretreatment process to enhance microbial transformation of reactive black 5 (RB5) in an aqueous system was evaluated. The RB5 with an initial concentration of 250 mg/L was decolorized up to 90% in 60 h by using a bacterial consortium. Fenton’s reagent at a Fe2+ concentration of 0.5 mM and H2O2 concentration of 2.9 mM (molar ratio, 1:5.8) was most effective for decolorization at pH = 3.0. The extent of RB5 removal by the combined Fenton–biotreatment was about 2 times higher than that of biotreatment alone. The production of some aromatic amines intermediates implied partial mineralization of the RB5 in Fenton treatment alone; in addition, decreasing of GC-MS peaks suggested that dearomatization occurred in Fenton-biological process. Fenton pretreatment seems to be a cost–effective option for the biotreatment of azo dyes, due mainly to the lower doses of chemicals, lower sludge generation, and saving of time. Our results demonstrated positive effects of inoculating bacterial consortium which was capable of dye biodegradation with a Fenton’s pretreatment step as well as the benefits of low time required for the biological process. In addition, the potential of field performance of Fenton-biological process because of using bacterial consortium is an other positive effect of it.
Peripheral blood derived gene panels predict response to infliximab in rheumatoid arthritis and Crohn's disease
Authors: Mesko Bertalan , Poliska Szilard , Váncsa Andrea , Szekanecz Zoltan , Palatka Karoly , Hollo Zsolt , Horvath Attila , Steiner Laszlo , Zahuczky Gabor , Podani Janos , Nagy and Laszlo 
Published: June 2013

Abstract
Background
Biological therapies have been introduced for the treatment of chronic inflammatory diseases including rheumatoid arthritis (RA) and Crohn's disease (CD). The efficacy of biologics differs from patient to patient. Moreover these therapies are rather expensive, therefore treatment of primary non-responders should be avoided.

Method
We addressed this issue by combining gene expression profiling and biostatistical approaches. We performed peripheral blood global gene expression profiling in order to filter the genome for target genes in cohorts of 20 CD and 19 RA patients. Then RT-quantitative PCR validation was performed, followed by multivariate analyses of genes in independent cohorts of 20 CD and 15 RA patients, in order to identify sets ofinterrelated genes that can separate responders from non-responders to the humanized chimeric anti-TNFalpha antibody infliximab at baseline.

Results
Gene panels separating responders from non-responders were identified using leave-one-out cross-validation test, and a pool of genes that should be tested on larger cohorts was created in both conditions.

Conclusions
Our data show that peripheral blood gene expression profiles are suitable for determining gene panels with high discriminatory power to differentiate responders from non-responders in infliximab therapy at baseline in CD and RA, which could be cross-validated successfully. Biostatistical analysis of peripheral blood gene expression data leads to the identification of gene panels that can help predict responsiveness of therapy and support the clinical decision-making process.
Cobalt-catalyzed Branched-selective Addition of Aromatic Ketimines to Styrenes under Room-temperature Conditions
Authors: Dong Jinghua , Lee Pin-Sheng , Yoshikai Naohiko 
Published: June 2013

Abstract
An improved cobalt-based catalytic system has been developed for the branched-selective addition of aromatic ketimines to styrenes. With an appropriate combination of triarylphosphine and the Grignard reagent, the reaction takes place smoothly at room temperature to afford 1,1-diarylethane derivatives with high regioselectivity.
Facile Preparation of Poly(3-substituted thiophene) Block Copolymers by Nickel-catalyzed Deprotonative Polycondensation without External Generation of Thiophene Organometallic Species
Authors: Nakamura Karin , Tamba Shunsuke , Sugie Atsushi , Mori Atsunori 
Published: June 2013

Abstract
Thiophene-based block copolymers are synthesized by addition of bromothiophene and the Knochel–Hauser base (TMPMgCl·LiCl). Nickel-catalyzed deprotonative C–H coupling polycondensation of 3-substituted-thiophenes proceeds to give head-to-tail-type poly(3-substituted thiophen-2,5-diyl) bearing nickel at the polymer end. Block copolymers of thiophene derivatives are obtained by successive addition of 2-bromo-3-alkylthiophene and magnesium amide to a living polythiophene end. The use of nickel catalyst bearing an o-tolyl group gives the tolyl-group-terminated thiophene diblock copolymers in high efficiency. Triblock copolymer is also synthesized by the iterative addition of bromothiophene and TMPMgCl·LiCl.
Prediction of Acidity in Streams Affected by Mine Drainage
Authors: Park Daeryong , Park Byungtae , Mendinsky Justin J , Paksuchon Benjaphon , Suhataikul Ratda , Dempsey Brian A 
Published: June 2013

Abstract
Prediction of total acidity can be used in lieu of measured acidity and for quality assurance purposes. In order to test the accuracy of the prediction methods, we compared the measured hot peroxide acidity values (E1) by three methods (E2, E3, and E4) of predicting total acidity. This study showed that improved prediction of total acidity can be achieved by considering the effects of pH on aluminum hydrolysis and sulfate speciation with respect to water quality.
Does fusion improve the outcome after decompressive surgery for lumbar spinal stenosis?
Authors: Försth P. , Michaëlsson K. , Sandén B. 
Published: June 2013

Whether to combine spinal decompression with fusion in patients with symptomatic lumbar spinal stenosis remains controversial. We performed a cohort study to determine the effect of the addition of fusion in terms of patient satisfaction after decompressive spinal surgery in patients with and without a degenerative spondylolisthesis. The National Swedish Register for Spine Surgery (Swespine) was used for the study. Data were obtained for all patients in the register who underwent surgery for stenosis on one or two adjacent lumbar levels. A total of 5390 patients fulfilled the inclusion criteria and completed a two-year follow-up. Using multivariable models the results of 4259 patients who underwent decompression alone were compared with those of 1131 who underwent decompression and fusion. The consequence of having an associated spondylolisthesis in the operated segments pre-operatively was also considered. At two years there was no significant difference in patient satisfaction between the two treatment groups for any of the outcome measures, regardless of the presence of a pre-operative spondylolisthesis. Moreover, the proportion of patients who required subsequent further lumbar surgery was also similar in the two groups. In this large cohort the addition of fusion to decompression was not associated with an improved outcome. Cite this article: Bone Joint J 2013;95-B:960–5.
Is there an association between the individual anatomy of the scapula and the development of rotator cuff tears or osteoarthritis of the glenohumeral joint?
Authors: Moor B. K. , Bouaicha S. , Rothenfluh D. A. , Sukthankar A. , Gerber C. 
Published: June 2013

We hypothesised that a large acromial cover with an upwardly tilted glenoid fossa would be associated with degenerative rotator cuff tears (RCTs), and conversely, that a short acromion with an inferiorly inclined glenoid would be associated with glenohumeral osteoarthritis (OA). This hypothesis was tested using a new radiological parameter, the critical shoulder angle (CSA), which combines the measurements of inclination of the glenoid and the lateral extension of the acromion (the acromion index).The CSA was measured on standardised radiographs of three groups: 1) a control group of 94 asymptomatic shoulders with normal rotator cuffs and no OA; 2) a group of 102 shoulders with MRI-documented full-thickness RCTs without OA; and 3) a group of 102 shoulders with primary OA and no RCTs noted during total shoulder replacement. The mean CSA was 33.1° (26.8° to 38.6°) in the control group, 38.0° (29.5° to 43.5°) in the RCT group and 28.1° (18.6° to 35.8°) in the OA group. Of patients with a CSA > 35°, 84% were in the RCT group and of those with a CSA < 30°, 93% were in the OA group.We therefore concluded that primary glenohumeral OA is associated with significantly smaller degenerative RCTs with significantly larger CSAs than asymptomatic shoulders without these pathologies. These findings suggest that individual quantitative anatomy may imply biomechanics that are likely to induce specific types of degenerative joint disorders.Cite this article: Bone Joint J 2013;95-B:935–41.
Lower bounds on Ricci flow invariant curvatures and geometric applications
Authors: Richard Thomas 
Published: June 2013

Abstract

We
consider Ricci flow invariant cones 𝒞 in the space of curvature
operators lying between the cones “nonnegative Ricci curvature” and
“nonnegative curvature operator”. Assuming some mild control on the scalar curvature
of the Ricci flow, we show that if a solution to the Ricci flow has its
curvature operator which satisfies

R
+
ε
I
∈
𝒞

$\textup {R}+\varepsilon \textup {I}\in \mathcal {C}$

at the
initial time,
then it satisfies

R
+
K
ε
I
∈
𝒞

$\textup {R}+K\varepsilon \textup {I}\in \mathcal {C}$

on some time interval
depending only on
the scalar curvature control.
This allows us to link Gromov–Hausdorff
convergence and Ricci flow convergence when the limit is smooth and

R
+
I
∈
𝒞

$\textup {R}+\textup {I}\in \mathcal {C}$

along the sequence of initial
conditions. Another application is a stability result for
manifolds whose curvature operator is almost in 𝒞.
Finally, we study the case where 𝒞 is contained in the
cone of operators whose sectional curvature is nonnegative. This allows
us to weaken the assumptions of the previously mentioned
applications. In particular, we construct a Ricci flow for a class of
(not too) singular Alexandrov spaces.
Acute neonatal appendicitis: the potential value of laparoscopy as a diagnostic and therapeutic tool
Authors: Dias Joana , Cerqueira Arnaldo , Pinheiro Liliana , Rezende Daria , Sá Carla , Abreu Eduarda , Silva Albina , Marques Matos , Pereira Almerinda , Manuel José , Pinto Jorge Correia 
Published: June 2013

Abstract
Appendicitis is the most common cause of acute abdominal pain requiring surgical intervention in children, but it is very rare in infants and neonates. Nonspecific clinical features and low index of suspicion make its diagnosis and management particularly challenging, which may result in high chances of complications such as perforation and peritonitis, thus increasing morbidity and mortality. We present the case of a female late preterm newborn with bloody stools and bilious gastric aspirates on the second day of life. After 24 h of clinical, laboratory and radiological surveillance, which evidenced deterioration in the newborn’s condition, an exploratory laparoscopy was performed, showing generalized peritonitis and perforated inflammatory appendix. A laparoscopic appendicectomy was performed. Histology confirmed the appendicitis diagnosis. The authors enhance the value of diagnostic laparoscopy and its potential as a therapeutic tool in neonates.
Trisomy 13 with anorectal malformation: an association or an incidental finding?
Authors: Arora Puneet Kumar , Mohandas Sindhu , Aladangady Narendra 
Published: June 2013

Abstract
This report describes a baby with trisomy 13 (Patau syndrome) with imperforate anus. It is very unusual for Patau syndrome to be associated with anorectal malformation. In the English medical literature, there are only four reported cases of trisomy13 being associated with imperforate anus: a partial trisomy of chromosome 13q and 20p [Nagai et al. Currarino triad (anorectal malformation, sacral bony abnormality and presacral mass) with partial trisomy of chromosomes 13q and 20p. Clin Genet. 1994;45:272–3.], a mosaic form [46,XX,t(13q13q)/46,XX,–13,+r(13)] (Jalal et al. Unusual mosaic trisomy 13 through 13/13 translocation and monosomy 13 with a small ring. Ann Genet. 1990;33:173–5.) of trisomy 13, a third case in which the form of trisomy 13 was not described (Cho et al. One hundred three consecutive patients with anorectal malformations and their associated anomalies. Arch Pediatr Adolesc Med. 2001;155:587–91.) and a fourth case of trisomy 13 with a Robertsonian translocation of the extra chromosome 13 to chromosome 14 (Lewis and Lander. Trisomy 13 is associated with anorectal malformations. Arch Dis Child. 2007;92:185.).