bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical significance of ESR1 gene copy number changes in breast cancer as measured by fluorescence in situ hybridisation
Authors: Lin Ching-Hung , Liu Jacqueline M , Lu Yen-Shen , Lan Chieh , Lee Wei-Chung , Kuo Kuan-Ting , Wang Chung-Chieh , Chang Dwan-Ying , Huang Chiun-Sheng , Cheng Ann-Lii 
Published: December 2012

AimsTheESR1gene encodes for oestrogen receptor (ER) α, which plays a crucial role in mammary carcinogenesis and clinical outcome in patients with breast cancer. However, the clinical significance of theESR1gene copy number change for breast cancer has not been clarified.MethodsESR1gene copy number was determined by fluorescence in situ hybridisation (FISH) on tissue sections. A minimum of 20 tumour cells were counted per section, and a FISH ratio ofESR1gene to CEP6 ≥2.0 was consideredESR1amplification. A ratio >1.2 but <2.0 was consideredESR1gain. TheESR1copy number was further measured by quantitative real-time PCR (Q-PCR) with ASXL2 as a reference.ResultsFISH revealedESR1amplification in six cases (4.0%) andESR1gain in 13 cases (8.7%) from a total of 150 cases.ESR1gain and amplification were more common in older patients (p<0.001), and correlated well with ER protein expression (p=0.03) measured by immunohistochemistry, andESR1copy number (p<0.001) measured by Q-PCR. Furthermore, the multivariate analysis revealed thatESR1amplification was associated with a shorter disease-free survival (HR=5.56, p=0.03) and a shorter overall survival (HR=5.11, p=0.04).ConclusionsIn general, the frequency ofESR1amplification in breast cancer is low when measured by FISH in large sections.ESR1gain and amplification in breast cancer may be associated with older age and poorer outcomes.
Correlation between placental bacterial culture results and histological chorioamnionitis: a prospective study on 376 placentas
Authors: Queiros da Mota Vanessa , Prodhom Guy , Yan Pu , Hohlfheld Patrick , Greub Gilbert , Rouleau Caroline 
Published: December 2012

ObjectiveTo study the correlation between the bacteriological and histopathological findings in placentas from women with suspected or proven chorioamnionitis (CA).MethodsOver a 1-year period, 376 placentas were prospectively collected and processed for bacteriological and pathological studies in cases of confirmed or suspected maternal or neonatal infection.ResultsHistological CA was diagnosed in 26.9% of placentas (101/376), and 27.7% (28/101) of these placentas had positive bacteriological cultures. A monomicrobial culture, mainly represented by Gram-positive cocci and Gram-negative bacilli, was identified in 27% of the positive bacterial cultures. The proportion of positive cultures was higher (p=0.03) when CA was associated with funisitis, as compared with placental samples with early CA. In placentas without histological CA, bacteriological cultures were mostly negative (230/275), although pathogenic bacteria were identified in 16.3% of them (45/275).ConclusionsThe histological and bacteriological results were concordant in about 70% of the examined placentas, with 61.1% negative cases (CA absent and negative bacterial cultures), and only 7.4% placentas with positive histological and bacteriological results. Discordant results (positive histology with negative bacteriology) were obtained in placentas with early CA documented by histology although possibly in relation with antibiotic prophylaxis and the presence of fastidious bacteria. Conversely, negative histology with positive bacteriology could be explained by the presence of an early-stage bacterial infection that has not yet led to detectable microscopic lesions.
Adenocarcinoma of gallbladder: an immunohistochemical profile and comparison with cholangiocarcinoma
Authors: Hughes Norman Richard , Bhathal Prithi S 
Published: December 2012

AimCholangiocarcinomas display intestinal and pyloric gland metaplasia-cell phenotypes. Those that arise in chronically inflamed (fluke infested) bile ducts more frequently express the intestinal metaplasia-cell phenotype and p53 than sporadic cholangiocarcinomas. We wished to determine if adenocarcinomas of the gallbladder display a similar profile.MethodsAdenocarcinoma, adenoma, and dysplastic and metaplastic epithelia were studied in 55 gallbladders. Serial paraffin sections were stained for five foregut antigens characteristically present in pyloric gland metaplasia, three intestinal-specific antigens and p53. Antigen expression was compared with that shown by 65 fluke-associated and 47 sporadic cholangiocarcinomas.ResultsPyloric gland metaplasia in gallbladders with chronic cholecystitis invariably displayed the five foregut antigens. The frequency of expression of these five antigens by the gallbladder cancers and cholangiocarcinomas did not differ significantly. An intestinal goblet-cell marker and p53 were more frequently expressed by gallbladder carcinoma (59% and 45%, respectively) and fluke-associated cholangiocarcinoma (45% and 46%) than by sporadic cholangiocarcinoma (17% and 23%). K20 was more frequently expressed by gallbladder carcinoma (52%) than either fluke-associated (21%) or sporadic (17%) cholangiocarcinoma. Dysplastic epithelium and adenomas also displayed the pyloric gland and intestinal metaplasia-cell phenotypes. Cells staining for pyloric gland metaplasia-cell phenotypes were distinct from the intestinal metaplasia-cell phenotypes when present together in a gallbladder carcinoma, cholangiocarcinoma, dysplastic epithelium or adenoma.ConclusionsAdenocarcinomas of gallbladder generally arise from a foregut cell lineage via a metaplasia-dysplasia-carcinoma sequence. A background of chronic inflammation increases the frequency of expression of an intestinal goblet-cell phenotype and p53 in the cancers.
Helicobacter pylori-associated hypochlorhydria in children, and development of iron deficiency
Authors: Harris Paul R , Serrano Carolina A , Villagrán Andrea , Walker Marjorie M , Thomson Melanie , Duarte Ignacio , Windle Henry J , Crabtree Jean E 
Published: December 2012

AimsAcuteHelicobacter pyloriinfection is associated with transient hypochlorhydria. InH pylori-associated atrophy, hypochlorhydria has a role in iron deficiency (ID) through changes in the physiology of iron-complex absorption. The aims were to evaluate the association betweenH pylori-associated hypochlorhydria and ID in children.MethodsSymptomatic children (n=123) were prospectively enrolled. Blood, gastric juice and gastric biopsies were taken, respectively, for haematological analyses, pH assessment andH pyloridetermination, and duodenal biopsies for exclusion of coeliac disease. Stool samples were collected for parasitology/microbiology. Thirteen children were excluded following parasitology and duodenal histopathology, and five due to impaired blood analysis.ResultsTen children were hypochlorhydric (pH>4) and 33 wereH pyloripositive. InH pylori-positive children with pH>4 (n=6) serum iron and transferrin saturation levels % were significantly lower (p<0.01) thanH pylori-positive children with pH≤4. No differences in ferritin, or total iron binding capacity, were observed. InH pylori-negative children with pH>4, iron and transferrin saturation were not significantly different from children with pH≤4.ConclusionsLow serum iron and transferrin in childhoodH pyloriinfection is associated with hypochlorhydria. In uninfected children, hypochlorhydria was not associated with altered serum iron parameters, indicating a combination ofH pyloriinfection and/or inflammation, and hypochlorhydria has a role in the aetiology of ID. AlthoughH pylori-associated hypochlorhydria is transient during acute gastritis, this alters iron homeostasis with clinical impact in developing countries with a highH pyloriprevalence.
Host gene expression profiling of cervical smear is eligible for cancer risk evaluation
Authors: Bourmenskaya Olga , Shubina Ekaterina , Trofimov Dmitry , Rebrikov Denis , Sabdulaeva Elina , Nepsha Oksana , Bozhenko Vladimir , Rogovskaya Svetlana , Sukhikh Gennady 
Published: December 2012

AimsUterine cervical carcinoma (CC) is known to be a delayed consequence of human papillomavirus (HPV) infection. Considering the reported influence of HPV on host genome activity, we conceived an approach to capture human gene expression profiles corresponding to increased risks of carcinogenesis.MethodsA sample set of 143 female participants included a ‘control’ group of 23, a ‘pathology’ group of 83 (cervical abnormalities of varied grade including 10 cases of CC), and a ‘HPV carrier’ group of 37 (infected but manifesting normal cytology). HPV detection, viral load measurements and gene expression profiling were performed by real-time PCR assays.ResultsGradual increase in expression of proliferation markers and a decrease in expression of proapoptotic genes, some receptors,PTENandPTGS2were demonstrated for progressive grades of cervical intraepithelial neoplasia leading to cancer. All reported trends were statistically significant, for instance, correlation of gene expression values forMKI67,CCNB1andBIRC5.A model was proposed that employed mRNA concentrations for genesMKI67,CDKN2A,PGRandBAX. Prompt distinction between the norm and the cancer, provided by initial calculation, suggested that positive values of the function could indicate the higher individual risks. Indeed, all patients assigned to high risk by calculation were HPV infected and showed elevated viral E6, E7 mRNA concentration known to be associated with CC onset.ConclusionsThe research was concentrated on dynamical gene expression profiling upon pathological changes ultimately leading to CC. Differences of normalised mRNA concentrations were used for quantitative model design and its primary approbation.
Preoperative Onyx embolization of hypervascular head, neck, and spinal tumors. Experience with 100 consecutive cases from a single tertiary center
Authors: Rangel-Castilla Leonardo , Shah Ankit H , Klucznik Richard Paul , Diaz Orlando M 
Published: December 2012

Background/purposePreoperative embolization of head, neck, and spinal tumors is frequently used to control tumor bleeding, reduce operative time, and achieve better resection. Numerous embolic materials have been used. The use of the liquid embolic agent Onyx is rapidly increasing but current experience is limited to small case series. Our purpose was to evaluate the indications, techniques, angiographic devascularization, blood loss, outcome, and general efficacy of preoperative tumor embolization with Onyx in a large series.MethodsRetrospective analysis of 100 consecutive cases of head, neck, and spinal tumors embolized with Onyx and prospective follow-up.Results100 patients (63 women, 37 men) were included. Tumors included 39 meningiomas, 23 metastases, 16 parangliomas, five juvenile nasal angiofibromas, five giant cell bone tumors, three Ewing's sarcomas, three hemangiomas, three hemangioblastomas, two multiple myelomas, and one osteoblastoma. In all patients, angiographic analysis of the feeding arteries and branches was performed and all embolizations were completed in a single session. Additional materials were used in 28 patients. No mortality or major complications were observed. Minor complications were seen in 11 patients. 85 patients underwent surgery; 79 within the next 48 h and six of them 4–188 days after embolization.ConclusionsEmbolization of intracranial, head, neck, and spinal tumors with Onyx is effective and safe by a transarterial route or by direct puncture. Onyx penetrates well into the tumor capillary with less arterial catheterization. Studies are necessary to establish long term utility in adjunct or palliative tumor embolization.
Clinical, microbiological and histological findings in lambs affected by ‘salivary abomasum disease’
Authors: Christodoulopoulos G. , Scott P. R. , Jehl N. , Filioussis G. , Smith S. H. 
Published: December 2012

‘Salivary abomasum disease’ is a common syndrome in Greece affecting lambs and kids from three to 17 days of age. In this case series, we present clinical and laboratory findings from 37 affected lambs presented alive and subsequently euthanased for welfare reasons and necropsied, and also from 24 other lambs submitted dead that were also necropsied. The clinical signs in the 37 lambs presented alive included lethargy (100 per cent), absence of sucking (83.8 per cent), weakness (37.8 per cent), abdominal distension (40.5 per cent) and increased frequency of urination (24.3 per cent). Diarrhoea was not observed in any affected lambs. At necropsy of these 37 lambs, the abomasum was distended with gas (70.3 per cent), saliva (43.2 per cent) along with mixed milk clots and gastric secretions; while multiple small mucosal and serosal haemorrhages with blood clots (‘coffee grains’) were recorded (91.9 per cent). Eight of 37 lambs that were examined alive, had elevated blood urea nitrogen concentrations (21.6 per cent). The pH of the abomasal contents ranged from 1.0 to 2.8;Escherichia coliwas cultured from six of 37 (16.2 per cent) abomasal fluid samples. A mild to moderate inflammatory cell infiltrate was present in the mucosal lamina propria of 13 of 15 abomasal samples (86.6 per cent). Kidneys were paler than normal in 13 of the total 61 lambs necropsied (21.3 per cent); while acute tubular necrosis was evident on histopathological examination of 11 of 12 examined pale kidneys (91.6 per cent). The low abomasal pH and reported successful treatment with oral sodium bicarbonate suggest that metabolic acidosis may develop during the disease; however, further studies, including blood gas analysis, and determination of D‐ and L‐lactic acid concentrations, are necessary to confirm this hypothesis.
In ovo serial skeletal muscle diffusion tractography of the developing chick embryo using DTI: feasibility and correlation with histology
Authors: Zhou Zien , DelProposto Zachary , Wu Lianming , Xu Jianrong , Hua Jia , Zhou Yan , Ye Yongquan , Zhang Zishu , Hu Jiani , Haacke E Mark 
Published: December 2012

Abstract

Background
Magnetic resonance imaging is a noninvasive method of evaluating embryonic development. Diffusion tensor imaging (DTI), based on the directional diffusivity of water molecules, is an established method of evaluating tissue structure. Yet embryonic motion degrades the in vivo acquisition of long-duration DTI. We used a dual-cooling technique to avoid motion artifact and aimed to investigate whether DTI can be used to monitor chick embryonic skeletal muscle development in ovo, and to investigate the correlation between quantitative DTI parameters fractional anisotropy (FA) and fiber length and quantitative histologic parameters fiber area percentage (FiberArea%) and limb length.

Results
From 84 normally developing chick embryos, 5 were randomly chosen each day from incubation days 5 to 18 and scanned using 3.0 Tesla magnetic resonance imaging. A dual-cooling technique is used before and during imaging. Eggs were cracked for making histological specimen after imaging. 3 eggs were serially imaged from days 5 to 18. We show that skeletal muscle fibers can be tracked in hind limb in DTI beginning with incubation day 8. Our data shows a good positive correlation between quantitative DTI and histologic parameters (FA vs FiberArea%: r= 0.943, p<0.0001; Fiber_length vs Limb_length: r=0.974, p<0.0001). The result of tracked fibers in DTI during incubation corresponds to the development of chick embryonic skeletal muscle as reported in the literature.

Conclusion
Diffusion tensor imaging can provide a noninvasive means of evaluating skeletal muscle development in ovo.
Evolution of cichlid vision via trans-regulatory divergence
Authors: O’Quin Kelly E , Schulte Jane E , Patel Zil , Kahn Nadia , Naseer Zan , Wang Helena , Conte Matthew A , Carleton Karen L 
Published: December 2012

Abstract

Background
Phenotypic evolution may occur through mutations that affect either the structure or expression of protein-coding genes. Although the evolution of color vision has historically been attributed to structural mutations within the opsin genes, recent research has shown that opsin regulatory mutations can also tune photoreceptor sensitivity and color vision. Visual sensitivity in African cichlid fishes varies as a result of the differential expression of seven opsin genes. We crossed cichlid species that express different opsin gene sets and scanned their genome for expression Quantitative Trait Loci (eQTL) responsible for these differences. Our results shed light on the role that different structural, cis-, and trans-regulatory mutations play in the evolution of color vision.

Results
We identified 11 eQTL that contribute to the divergent expression of five opsin genes. On three linkage groups, several eQTL formed regulatory “hotspots” associated with the expression of multiple opsins. Importantly, however, the majority of the eQTL we identified (8/11 or 73%) occur on linkage groups located trans to the opsin genes, suggesting that cichlid color vision has evolved primarily via trans-regulatory divergence. By modeling the impact of just two of these trans-regulatory eQTL, we show that opsin regulatory mutations can alter cichlid photoreceptor sensitivity and color vision at least as much as opsin structural mutations can.

Conclusions
Combined with previous work, we demonstrate that the evolution of cichlid color vision results from the interplay of structural, cis-, and especially trans-regulatory loci. Although there are numerous examples of structural and cis-regulatory mutations that contribute to phenotypic evolution, our results suggest that trans-regulatory mutations could contribute to phenotypic divergence more commonly than previously expected, especially in systems like color vision, where compensatory changes in the expression of multiple genes are required in order to produce functional phenotypes.
Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression
Authors: Luo Guan-Zheng , Hafner Markus , Shi Zhimin , Brown Miguel , Feng Gui-Hai , Tuschl Thomas , Wang Xiu-Jie , Li XiaoChing 
Published: December 2012

AbstractBackgroundMicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally in a wide range of biological processes. The zebra finch (Taeniopygia guttata), an oscine songbird with characteristic learned vocal behavior, provides biologists a unique model system for studying vocal behavior, sexually dimorphic brain development and functions, and comparative genomics.ResultsWe deep sequenced small RNA libraries made from the brain, heart, liver, and muscle tissues of adult male and female zebra finches. By mapping the sequence reads to the zebra finch genome and to known miRNAs in miRBase, we annotated a total of 193 miRNAs. Among them, 29 (15%) are avian specific, including three novel zebra finch specific miRNAs. Many of the miRNAs exhibit sequence heterogeneity including length variations, untemplated terminal nucleotide additions, and internal substitution events occurring at the uridine nucleotide within a GGU motif. We also identified seven Z chromosome-encoded miRNAs. Among them, miR-2954, an avian specific miRNA, is expressed at significantly higher levels in males than in females in all tissues examined. Target prediction analysis reveals that miR-2954, but not other Z-linked miRNAs, preferentially targets Z chromosome-encoded genes, including several genes known to be expressed in a sexually dimorphic manner in the zebra finch brain.ConclusionsOur genome-wide systematic analysis of mature sequences, genomic locations, evolutionary sequence conservation, and tissue expression profiles of the zebra finch miRNA repertoire provides a valuable resource to the research community. Our analysis also reveals a miRNA-mediated mechanism that potentially regulates sex-biased gene expression in avian species.
Human CD72 splicing isoform responsible for resistance to systemic lupus erythematosus regulates serum immunoglobulin level and is localized in endoplasmic reticulum
Authors: Hitomi Yuki , Adachi Takahiro , Tsuchiya Naoyuki , Honda Zen-Ichiro , Tokunaga Katsushi , Tsubata Takeshi 
Published: December 2012

AbstractBackgroundCD72 is an inhibitory co-receptor expressed on B cells. We previously demonstrated significant association of the polymorphism of theCD72gene with susceptibility to human systemic lupus erythematosus (SLE) in individuals carrying a SLE-susceptibleFCGR2Bgenotype (FCGR2B-232Thr/Thr). The humanCD72locus generates a splicing isoform that lacks exon 8 (CD72Δex8) as well as full-length CD72 (CD72fl), and theCD72polymorphism regulates exon 8 skipping.ResultsHere we demonstrated that individuals carrying the disease-protectiveCD72genotype exhibit significantly lower serum immunoglobulin levels than do individuals carrying otherCD72genotypes (P< 0.05). Although expression level of CD72fl in the peripheral blood B cells was similar regardless ofCD72genotype, the protein level of CD72Δex8 was increased in individuals carrying the disease-protectiveCD72genotype, suggesting a crucial role of CD72Δex8 in regulation of antibody production. By expressing these human CD72 isoforms in mouse cell lines, we further demonstrated that CD72Δex8 is accumulated in endoplasmic reticulum (ER) and fails to regulate BCR signaling whereas human CD72fl is efficiently transported to the cell surface and inhibits signaling through the B cell antigen receptor (BCR), as is the case for mouse CD72.ConclusionHumanCD72polymorphism appears to regulate antibody production as well as susceptibility to SLE by regulating expression of ER-localizing CD72Δex8.
Some ethylene biosynthesis and AP2/ERF genes reveal a specific pattern of expression during somatic embryogenesis in Hevea brasiliensis
Authors: Piyatrakul Piyanuch , Putranto Riza-Arief , Martin Florence , Rio Maryannick , Dessailly Florence , Leclercq Julie , Dufayard Jean-François , Lardet Ludovic , Montoro Pascal 
Published: December 2012

Abstract

Background
Ethylene production and signalling play an important role in somatic embryogenesis, especially for species that are recalcitrant in in vitro culture. The AP2/ERF superfamily has been identified and classified in Hevea brasiliensis. This superfamily includes the ERFs involved in response to ethylene. The relative transcript abundance of ethylene biosynthesis genes and of AP2/ERF genes was analysed during somatic embryogenesis for callus lines with different regeneration potential, in order to identify genes regulated during that process.

Results
The analysis of relative transcript abundance was carried out by real-time RT-PCR for 142 genes. The transcripts of ERFs from group I, VII and VIII were abundant at all stages of the somatic embryogenesis process. Forty genetic expression markers for callus regeneration capacity were identified. Fourteen markers were found for proliferating calli and 35 markers for calli at the end of the embryogenesis induction phase. Sixteen markers discriminated between normal and abnormal embryos and, lastly, there were 36 markers of conversion into plantlets. A phylogenetic analysis comparing the sequences of the AP2 domains of Hevea and Arabidopsis genes enabled us to predict the function of 13 expression marker genes.

Conclusions
This first characterization of the AP2/ERF superfamily in Hevea revealed dramatic regulation of the expression of AP2/ERF genes during the somatic embryogenesis process. The gene expression markers of proliferating callus capacity to regenerate plants by somatic embryogenesis should make it possible to predict callus lines suitable to be used for multiplication. Further functional characterization of these markers opens up prospects for discovering specific AP2/ERF functions in the Hevea species for which somatic embryogenesis is difficult.