tbuckley/cabot-search huggingface dataset:
Preoperative Prediction of Surgical Margin Status in Patients With Prostate Cancer Treated by Radical Prostatectomy
Authors: Liang Cheng, Jeff Slezak, Erik J. Bergstralh, Robert P. Myers, Horst Zincke, David G. Bostwick
Journal: Journal of Clinical Oncology (2000)

We sought to determine the preoperative factors associated with surgical margin status in patients who underwent radical prostatectomy for prostate cancer.The study group consisted of 339 patients who were treated by radical retropubic prostatectomy and bilateral pelvic lymphadenectomy at the Mayo Clinic. None received preoperative adjuvant therapy. The mean age at the time of surgery was 66 years (range, 45 to 79 years). All specimens were totally embedded and whole-mounted. Positive surgical margin was defined as the presence of cancer cells at the inked margins. Numerous pathologic characteristics in needle biopsies and preoperative clinical findings were analyzed.The overall margin positivity rate was 24%. In univariate analysis, preoperative serum prostate-specific antigen (PSA) level, Gleason score, perineural invasion, percentage of cancer in the biopsy specimens, and number and percentage of biopsy cores involved by cancer were all associated with positive surgical margins. In multivariate analysis, preoperative serum PSA level (odds ratio for a doubling of PSA levels, 1.9; 95% confidence interval, 1.5 to 2.4; P <.001) and percentage of cancer in the biopsy specimens (odds ratio for a 10% increase, 1.3; 95% confidence interval, 1.2 to 1.4; P <.001) were predictive of margin status in radical prostatectomy. With use of preoperative serum PSA level and percentage of cancer in the biopsy as predictors of surgical margins, the overall accuracy as measured by the area under the receiver operating characteristic curve was 0.74.Preoperative serum PSA level and percentage of cancer in the biopsy specimens were independently associated with surgical margin status in patients who underwent radical prostatectomy for prostate cancer. The combination of these two factors provides a high level of predictive accuracy for margin status.
Nodule Bioassay of the Mouse Mammary Tumor Virus: Modifications and Quantitative Considerations&lt;xref ref-type="fn" rid="FN2"&gt;2&lt;/xref&gt;
Authors: S. Nandi, Sandra Haslam, Cheryl Helmich, Ross I. Ritter
Journal: JNCI Journal of the National Cancer Institute (1971)

The standard nodule assay of mammary tumor virus (MTV), and various modifications of it, were used in the assay of viral activity in mammary tissues (M-MTV) and blood (R-MTV). Incidence of nodules was not consistently correlated with the dose of M-MTV in test mice implanted with estradiol plus deoxycorticosterone pellets. Nodule assays with pituitary isografts under the kidney capsule of test mice reduced the mortality rate and the time necessary for the qualitative assay of MTV in naturally or artificially infected mice. The pituitary isograft procedure can also be used in the quantitative determination of R-MTV within a period of 12 weeks.
Ultramicroscopic Changes in the Endometrial Cells of Spontaneous Adenocarcinoma of Rabbits&lt;xref ref-type="fn" rid="FN2"&gt;2&lt;/xref&gt;&lt;xref ref-type="fn" rid="FN3"&gt;3&lt;/xref&gt;
Authors: Nobuhisa Baba, Emmerich von Haam
Journal: JNCI Journal of the National Cancer Institute (1967)

Journal Article Ultramicroscopic Changes in the Endometrial Cells of Spontaneous Adenocarcinoma of Rabbits Get access Nobuhisa Baba, M.D., Ph.D., Nobuhisa Baba, M.D., Ph.D. Department of Pathology, College of Medicine, The Ohio State University, Columbus, Ohio 43210 Search for other works by this author on: Oxford Academic PubMed Google Scholar Emmerich von Haam, M.D. Emmerich von Haam, M.D. Department of Pathology, College of Medicine, The Ohio State University, Columbus, Ohio 43210 Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 38, Issue 5, May 1967, Pages 657–672, https://doi.org/10.1093/jnci/38.5.657 Published: 01 May 1967 Article history Received: 25 May 1966 Revision received: 05 January 1967 Published: 01 May 1967
Phenotypically aberrant and clonal T cell in the lung of patients with refractory coeliac disease
Authors: Jean Pastre, Karine Juvin, Georgia Malamut, Amandine Vial-Dupuy, Benoit Douvry, Christophe Cellier, Dominique Israel-Biet
Journal: European Respiratory Journal (2013)

Background and objectives : coeliac disease (CD) is sometimes associated with extra-intestinal manifestations including cough, airway obstruction, pulmonary hemosiderosis and/or infiltrates. Tissue extra-intestinal aberrant lymphocytes have also been reported in skin lesions of type II refractory coeliac disease (RCD). We report here the first cases of RCD characteristic T cells and clones in the lung of patients with RCD.   Methods : 5 patients (aged 51 ± 6 years) with confirmed RCD were referred to us for pulmonary symptoms (cough, dyspnea on exertion) and/or scanographic signs (mild infiltrates, micronodules). Mean time elapsed since RCD diagnosis was 22 months. Fiberoptic bronchoscopy was performed with bronchial biopsies (BB) and bronchoalveolar lavage (BAL) being analyzed for cytologic or histopathology, immunophenotyping and molecular status.   Results : BAL exhibited a lymphocytic alveolitis in 3 cases (210±74.10 3  cells/mL, 27±4% lymphocytes, CD4/CD8 ratio: 3.5±1, mean±SEM). Aberrant CD3-/CD4-/CD8- alveolar T lymphocytes were found in all cases. Three of them exhibited clonal TCRγ rearrangements. BB showed no inflammatory infiltrates but T cell clones identical to those present in the intestinal epithelium in 3/5 cases. Two of 5 patients died of intestinal or skin lymphoma, none of pulmonary complication so far (mean follow up: 3.4 years).   Conclusion : These data highlight the importance of a systematic pulmonary work-up in patients with RCD, at high risk of developing aggressive lymphomas. Ongoing studies are assessing the prevalence of such pulmonary abnormalities in RCD subjects and will tell us about their specific impact on the disease outcome.
Single-lung retransplantation for late graft failure
Authors: M Fournier, C Sleiman, H Mal, O Groussard, J L Mollo, J P Duchatelle, B Andreassian, R Pariente
Journal: European Respiratory Journal (1993)

In lung or heart-lung recipients, an irreversible graft-failure may develop in connection with chronic rejection, infection or bronchial complications. A limited number of transplant-recipients have undergone a retransplantation procedure in several centres. First results are discouraging, especially in the case of early retransplantation. We decided, 3 yrs ago, to evaluate the feasibility and benefits of single-lung retransplantation in lung-transplant recipients with late graft-failure. Eight consecutive single-lung retransplantations were performed in patients with previous single-lung (n = 7), or double-lung (n = 1) transplant. Primary graft and native lung were removed in 5 and 3 patients, respectively. The delay between the two surgical procedures was 16 +/- 10 months (range 6-37 months). Three patients died within 3 months. Long-term survivors experienced stable and satisfactory functional results (forced expiratory volume in one second (FEV1 63 +/- 21% predicted; range 40-103% predicted), with survival values ranging 8-20 months. One patient died of septic shock 16.5 months after retransplantation. The remaining four patients are alive. These data suggest that the retransplantation option could be considered in selected patients with late graft-failure. The final decision for retransplantation, however, is largely influenced by the current shortage of donor lungs.
Assessment of the COPD patients' care: An audit of clinical practice
Authors: Abdellatif Med Bennani, Fatima Zohra Drissi, Souad Kebbati, Malika Guermaz
Journal: European Respiratory Journal (2013)

Introduction:  The care of COPD remains serious and insufficient despite the guidelines dissemination. Its morbidity is ever-increasing.   Aims : To evaluate the COPD patients’ care in clinical practice.   Methods:  An audit achieved through a questionnaire sent to all physicians’ pulmonologists (PP) and general practitioners (GPs) in the North West Algerian taking care of the COPD patients.   Results:  Two hundred and sixty eight practitioners participated in this study, 194 GPs and 74 pulmonologists with a respective response rate of 46 and 74%. Smoking status systematically searched for each examination by 70% of GPs and 95% of PP. 25% of GPs and 13% of PP track down the COPD from the age of 50. Cough and expectoration among smokers are searched systematically by 69% of GPs and 74% of PP. Dyspnea is searched systematically by 57% of GPs and 78% of PP. Only 20% of GPs and 51% of PP use dyspnea’s rating scales.The access to spirometry is easy for 20% of GPs and 85% of PP. 40% of GPs and 80% of PP regularly ask for a spirometric test patients’ observation. In practice, the diagnosis of COPD is based on symptoms alone in over 1/3 of MG. Only 38% of GPs and 68% of PP use guides for the care of COPD. Comorbidities linked to COPD are routinely sought by 44% MG and 69% PP. All practitioners declared that they never assess the impact of COPD on patients9 sexuality. Anxiety is sought by 76% of GPs and 73% of PP. Depression is sought by 56% of GPs and 55.4% of PP. Physical activity is routinely recommended by 36% of GPs and 42% of PP. Flu vaccine is routinely recommended by 57% of GPs and 65% of PP. 22% GPS and 8% of PP prescribe long-term oral corticosteroids in combination with LABA for patients with frequent exacerbations.
CD38 in Hairy Cell Leukemia Is a Marker of Poor Prognosis and a New Target for Therapy
Authors: Nicolas Poret, Qiangwei Fu, Soizic Guihard, Meyling Cheok, Katie Miller, Gordon Zeng, Bruno Quesnel, Xavier Troussard, Sylvie Galiègue-Zouitina, Carl Simon Shelley
Journal: Cancer Research (2015)

Abstract Hairy cell leukemia (HCL) is characterized by underexpression of the intracellular signaling molecule RhoH. Reconstitution of RhoH expression limits HCL pathogenesis in a mouse model, indicating this could represent a new therapeutic strategy. However, while RhoH reconstitution is theoretically possible as a therapy, it is technically immensely challenging as an appropriately functional RhoH protein needs to be specifically targeted. Because of this problem, we sought to identify druggable proteins on the HCL surface that were dependent upon RhoH underexpression. One such protein was identified as CD38. Analysis of 51 HCL patients demonstrated that 18 were CD38-positive. Interrogation of the clinical record of 23 relapsed HCL patients demonstrated those that were CD38-positive had a mean time to salvage therapy 71 months shorter than patients who were CD38-negative. Knockout of the CD38 gene in HCL cells increased apoptosis, inhibited adherence to endothelial monolayers, and compromised ability to produce tumors in vivo. Furthermore, an anti-CD38 antibody proved effective against pre-existing HCL tumors. Taken together, our data indicate that CD38 expression in HCL drives poor prognosis by promoting survival and heterotypic adhesion. Our data also indicate that CD38-positive HCL patients might benefit from treatments based on CD38 targeting. Cancer Res; 75(18); 3902–11. ©2015 AACR.
Incidence of Kaposi's Sarcoma and Mycosis Fungoides in the United States Including Puerto Rico, 1973–81
Authors: Robert J. Biggar, John Horm, Joseph F. Fraumeni, Mark H. Greene, James J. Goedert
Journal: JNCI Journal of the National Cancer Institute (1984)

The incidence of Kaposi's sarcoma (KS) was examined with the use of data from the Surveillance, Epidemiology, and End Results (SEER) Program of the National Cancer Institute. KS is a manifestation of the recent epidemic of acquired immunodeficiency syndrome (AIDS) that has occurred particularly among homosexual men. The incidence of KS in 1973-79 was found to be higher (0.29 male and 0.07 female cases/100,000/yr) than is usually cited for the pre-AIDS KS incidence rates. Collectively, the 9 SEER registries in the United States showed only a slight increase in the incidence of KS between 1973-79 and 1980-81. However, the SEER registry covering San Francisco, which is a high-risk area for AIDS, showed a marked excess of KS in 1981. The KS case rate among never-married men younger than 50 years old, a surrogate index of homosexuality, was found to be markedly elevated in the post-AIDS period, compared with the case rate of a reference disease, mycosis fungoides. Never-married men younger than 50 years old, therefore, constitute a SEER-identifiable population who can be monitored for risk of KS and other neoplasms that might be related to AIDS. In addition, the incidence rate of KS in the SEER registry of Puerto Rico was generally higher than that in the U.S. SEER registries, despite data that suggested that KS may be underreported. The demographic characteristics of patients diagnosed as having KS in Puerto Rico suggested the classical rather than the AIDS-related form of KS.
Who is That? Brain Networks and Mechanisms for Identifying Individuals
Authors: Catherine Perrodin, Christoph Kayser, Taylor J. Abel, Nikos K. Logothetis, Christopher I. Petkov
Journal: Trends in Cognitive Sciences (2015)

Social animals can identify conspecifics by many forms of sensory input. However, whether the neuronal computations that support this ability to identify individuals rely on modality-independent convergence or involve ongoing synergistic interactions along the multiple sensory streams remains controversial. Direct neuronal measurements at relevant brain sites could address such questions, but this requires better bridging the work in humans and animal models. Here, we overview recent studies in nonhuman primates on voice and face identity-sensitive pathways and evaluate the correspondences to relevant findings in humans. This synthesis provides insights into converging sensory streams in the primate anterior temporal lobe (ATL) for identity processing. Furthermore, we advance a model and suggest how alternative neuronal mechanisms could be tested.
Clinical and Pathologic Characteristics of Graft-Versus-Host Disease Produced in Cyclophosphamide-Treated Adult Mice<xref ref-type="fn" rid="FN2">2</xref>
Authors: J S Sandberg, A H Owens, G W Santos
Journal: JNCI Journal of the National Cancer Institute (1971)

This report describes the clinical and pathologic characteristics of the acute graft-versus-host disease produced in adult mice by cyclophosphamide and allogeneic immunologically competent cells. Lethargy, hunched posture, ruffled coat, facial edema, and severe wasting were noted within 5–6 days. Most mice died within 7–15 days. Histologic studies revealed a mixed mononuclear cell infiltration of various tissues associated with varying degrees of cellular degeneration. Changes were most marked in the lymphoid organs. These findings are analogous to the acute graft-versus-host disease described in other settings. Similar abnormalities were not seen in mice given cyclophosphamide or allogeneic cells alone or in mice treated with cyclophosphamide and heat-killed foreign cells. Neither did they occur in parent strain mice given cyclophosphamide and F1 hybrid spleen cells.
Evaluation of gene expression during in vitro ciliogenesis to search for novel candidate genes in primary ciliary dyskinesia
Authors: Tamara Paff, Eric Haarman, Hans Daniels, Youssef Moutaouakil, Dimitra Micha, Maarten Massink, Piet Postmus, Gerard Pals
Journal: European Respiratory Journal (2013)

Introduction

Mutations in genes that are important in ciliary motility often cause primary ciliary dyskinesia (PCD). In half of the patients, causal mutations in any of the eighteen known PCD genes cannot be identified.

Aim

The aim of this pilot study is to investigate gene expression in respiratory epithelial cells during ciliogenesis. We hypothesized that a) all known PCD genes show similar expression profiles and that b) clustering genes with similar expression may provide novel PCD candidate genes.

Methods

We collected nasal epithelial curette biopsies from 2 healthy controls. Cells were cultured using a monolayer-suspension cell culture (Willems,T et al. J Cyst Fibros 2004). RNA was isolated at three time points: at the end of the monolayer culture (no cilia), after three days in suspension culture (growing cilia) and at the end of the suspension culture (full grown cilia). Whole genome expression arrays were performed and differential gene expression was analyzed by ANOVA.

Results

Except for TXNDC3, we observed a time dependent increase in expression levels in all known PCD genes. However, for HEATR2 and CCDC40 this difference did not reach statistical significance. A total of 1511 genes were significantly up-regulated during ciliogenesis. This cluster was highly enriched for genes related to cilia.

Conclusion

We identified a cluster of 1511 genes that showed an increase in expression levels during in vitro ciliogenesis, including 15 of the 18 known PCD genes. Using this novel application on a larger sample size may provide a more accurate cluster of possible PCD candidate genes.
Prospective evaluation of endoscopic ultrasonography-guided double-balloon-occluded gastrojejunostomy bypass (EPASS) for malignant gastric outlet obstruction
Authors: Takao Itoi, Kentaro Ishii, Nobuhito Ikeuchi, Atsushi Sofuni, Takuji Gotoda, Fuminori Moriyasu, Vinay Dhir, Anthony Yuen Bin Teoh, Kenneth F Binmoeller
Journal: Gut (2015)

Surgical gastrojejunostomy (GJ), which has been the standard palliative treatment for malignant gastric outlet obstruction (MGOO), is associated with good functional outcome and the long-term relief of symptoms. Endoscopic placement of a metal stent for MGOO treatment has been gaining popularity as an alternative to surgical GJ because of its high technical success rates and less invasiveness. Interestingly, several investigators have attempted endoscopic GJ as ‘endoscopic bypass’ for longer efficacy while maintaining a less invasive procedure.1 We previously reported on the feasibility and safety of EUS-guided GJ (EUS-GJ) using a lumen-apposing metal stent (LAMS)2 ,3 and a special double-balloon enteric tube in an animal model and a pilot clinical study.3 Herein, we describe the first prospective clinical study of EUS-guided double-balloon-occluded gastrojejunostomy bypass (EPASS) using a LAMS (figure 1). We performed EPASS in 20 patients with MGOO. The double-balloon tube (figure 2) was correctly inserted into the jejunum across from the stomach in all cases. The technical success rate of stent placement was 90%.



Figure 1 
Schema of EUS-guided double-balloon-occluded gastrojejunostomy bypass (EPASS) using a lumen-apposing metal stent.





Figure 2 
Double-balloon enteric tube allows the filling-water between two balloons.



EPASS was performed in 20 patients with MGOO between March 2014 and March 2015 (10 male) (supplementary tables 1 and 2). The median intubation time of the double-balloon tube insertion was 10.5 min (range 6–28 min). The technical success rate of stent placement was 90% (18/20) (figure 3 and supplementary table 3). The median intubation time from the double-balloon tube intubation to stent placement was 25.5 min (range 10–39 min). In the two failed cases, we recognised the maldeployment of the distal flange immediately after deployment of the proximal flange by the presence of pneumoperitonium on fluoroscopy and endoscopic visualisation of the abdominal cavity through the LAMS. Post-treatment gastric outlet obstruction …
Next-generation sequencing for inherited cancer risk assessment: Under the hood at Counsyl.
Authors: Jared Robert Maguire
Journal: Journal of Clinical Oncology (2014)

22 Background: Next-generation DNA sequencing (NGS) is the universal nucleic acid assay technology, with the capability to replace nearly all existing DNA assay technologies. In most cases it is more affordable, more accurate, more flexible, and less subject to human error than prior assay technologies such as capillary electrophoresis or genotyping arrays. In the last year especially, NGS utilization in the clinic has increased. The use of NGS to detect single nucleotide polymorphisms (SNPs) and short insertions/deletions (indels) is well established. However, primarily due to novelty, NGS for has not yet often been used in the clinic for the detection of larger copy number variants (CNVs). Instead, supplementary technologies such as multiplex ligation-probe amplification (MLPA) and quantitative PCR (qPCR) have been used to probe large CNVs. Methods: Counsyl’s Family Prep and Inherited Cancer Screens use NGS for detecting SNPs and indels, and also CNV analysis in the genes of interest. Here we present the technical details of the platform and our validation results showing that CNV analysis by NGS meets or exceeds the performance of such analysis by MLPA or endpoint TaqMan. Only two discordant CNV genotypes were found out of 20,086 calls; both discordances are errors in the control assay, and are attributable to technical limitations. Results: See Table. Conclusions: CNVs account for a significant proportion of BRCA1 and BRCA2 associated cancer risk. Our NGS methodology achieves analytical performance previously obtained only by multiple assays, decreasing testing costs and thereby potentially widening access. [Table: see text]
Familial pulmonary fibrosis: Clinical-functional and radiological features
Authors: David Bennett, Maria Antonietta Mazzei, Fabrizio Mezzasalma, Rosa Metella Refini, Elena Bargagli, Luca Volterrani, Paola Rottoli
Journal: European Respiratory Journal (2013)

Familial pulmonary fibrosis (FPF) is defined as an idiopathic interstitial pneumonia in two or more consanguineous. Starting from our database, we performed a retrospective analysis of clinical, functional and HRCT features of 35 patients (15 males, age at the diagnosis 58.9±9.2 years), belonging to 23 different families with FPF. Prevalent symptoms at onset were dry cough and dyspnoea, but 10% of the patients were asymptomatic and referred to us for ILD assessment because of their familiar history of pulmonary fibrosis. Two main HRCT patterns have been documented: possible UIP (20/35 patients; 57%) and fibrotic-NSIP (14/35 patients; 40%), only one patient showed a typical UIP pattern. In CT analysis hiatal hernia and mediastinal lipomatosis were statistically more frequent in patients with possible UIP pattern than in fibrotic NSIP (p 0.05) between probable UIP and fibrotic NSIP. Following the patients routinely with PFTs every 3 months we observed that no significant worsening in FVC%, FEV1% and DLCO% was evident after 1-year follow-up. Our study shows that functional deterioration is less evident in FPF than expected for sporadic IPF, suggesting that the disease progression is slower. FPF does not present with a single HRCT pattern, being possible UIP and fibrotic NSIP the prevalent ones. Interestingly, hiatal hernia and mediastinal lipomatosis were more frequently observed in the possible UIP group.