bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data
Authors: Grigoriadis Anita , Mackay Alan , Reis-Filho Jorge S , Steele Dawn , Iseli Christian , Stevenson Brian J , Jongeneel C Victor , Valgeirsson Haukur , Fenwick Kerry , Iravani Marjan , Leao Maria , Simpson Andrew JG , Strausberg Robert L , Jat Parmjit S , Ashworth Alan , Neville A Munro , O'Hare Michael J 
Published: October 2006

Abstract
Introduction
Diverse microarray and sequencing technologies have been widely used to characterise the molecular changes in malignant epithelial cells in breast cancers. Such gene expression studies to identify markers and targets in tumour cells are, however, compromised by the cellular heterogeneity of solid breast tumours and by the lack of appropriate counterparts representing normal breast epithelial cells.

Methods
Malignant neoplastic epithelial cells from primary breast cancers and luminal and myoepithelial cells isolated from normal human breast tissue were isolated by immunomagnetic separation methods. Pools of RNA from highly enriched preparations of these cell types were subjected to expression profiling using massively parallel signature sequencing (MPSS) and four different genome wide microarray platforms. Functional related transcripts of the differential tumour epithelial transcriptome were used for gene set enrichment analysis to identify enrichment of luminal and myoepithelial type genes. Clinical pathological validation of a small number of genes was performed on tissue microarrays.

Results
MPSS identified 6,553 differentially expressed genes between the pool of normal luminal cells and that of primary tumours substantially enriched for epithelial cells, of which 98% were represented and 60% were confirmed by microarray profiling. Significant expression level changes between these two samples detected only by microarray technology were shown by 4,149 transcripts, resulting in a combined differential tumour epithelial transcriptome of 8,051 genes. Microarray gene signatures identified a comprehensive list of 907 and 955 transcripts whose expression differed between luminal epithelial cells and myoepithelial cells, respectively. Functional annotation and gene set enrichment analysis highlighted a group of genes related to skeletal development that were associated with the myoepithelial/basal cells and upregulated in the tumour sample. One of the most highly overexpressed genes in this category, that encoding periostin, was analysed immunohistochemically on breast cancer tissue microarrays and its expression in neoplastic cells correlated with poor outcome in a cohort of poor prognosis estrogen receptor-positive tumours.

Conclusion
Using highly enriched cell populations in combination with multiplatform gene expression profiling studies, a comprehensive analysis of molecular changes between the normal and malignant breast tissue was established. This study provides a basis for the identification of novel and potentially important targets for diagnosis, prognosis and therapy in breast cancer.
Ancient genomic architecture for mammalian olfactory receptor clusters
Authors: Aloni Ronny , Olender Tsviya , Lancet Doron 
Published: October 2006

Abstract
Background
Mammalian olfactory receptor (OR) genes reside in numerous genomic clusters of up to several dozen genes. Whole-genome sequence alignment nets of five mammals allow their comprehensive comparison, aimed at reconstructing the ancestral olfactory subgenome.

Results
We developed a new and general tool for genome-wide definition of genomic gene clusters conserved in multiple species. Syntenic orthologs, defined as gene pairs showing conservation of both genomic location and coding sequence, were subjected to a graph theory algorithm for discovering CLICs (clusters in conservation). When applied to ORs in five mammals, including the marsupial opossum, more than 90% of the OR genes were found within a framework of 48 multi-species CLICs, invoking a general conservation of gene order and composition. A detailed analysis of individual CLICs revealed multiple differences among species, interpretable through species-specific genomic rearrangements and reflecting complex mammalian evolutionary dynamics. One significant instance involves CLIC #1, which lacks a human member, implying the human-specific deletion of an OR cluster, whose mouse counterpart has been tentatively associated with isovaleric acid odorant detection.

Conclusion
The identified multi-species CLICs demonstrate that most of the mammalian OR clusters have a common ancestry, preceding the split between marsupials and placental mammals. However, only two of these CLICs were capable of incorporating chicken OR genes, parsimoniously implying that all other CLICs emerged subsequent to the avian-mammalian divergence.
Developing Models for Patient Flow and Daily Surge Capacity Research
Authors: Asplin Brent R. , Flottemesch Thomas J. , Gordon Bradley D. 
Published: October 2006

Between 1993 and 2003, visits to U.S. emergency departments (EDs) increased by 26%, to a total of 114 million visits annually. At the same time, the number of U.S. EDs decreased by more than 400, and almost 200,000 inpatient hospital beds were taken out of service. In this context, the adequacy of daily surge capacity within the system is clearly an important issue. However, the research agenda on surge capacity thus far has focused primarily on large‐scale disasters, such as pandemic influenza or a serious bioterrorism event. The concept of daily surge capacity and its relationship to the broader research agenda on patient flow is a relatively new area of investigation. In this article, the authors begin by describing the overlap between the research agendas on daily surge capacity and patient flow. Next, they propose two models that have potential applications for both daily surge capacity and hospitalwide patient‐flow research. Finally, they identify potential research questions that are based on applications of the proposed research models.
Impact on Survival of Time From Definitive Surgery to Initiation of Adjuvant Chemotherapy for Early-Stage Breast Cancer
Authors: Lohrisch Caroline , Paltiel Charles , Gelmon Karen , Speers Caroline , Taylor Suzanne , Barnett Jeff , Olivotto Ivo A. 
Published: October 2006

Purpose To determine if time to start of adjuvant chemotherapy after curative surgery influences survival in early-stage breast cancer. Patients and Methods A retrospective review was conducted of 2,594 patients receiving adjuvant chemotherapy for stage I and II breast cancer between 1989 and 1998 at the British Columbia Cancer Agency. Relapse-free survival (RFS) and overall survival (OS) were compared among patients grouped by time from definitive curative surgery to start of adjuvant chemotherapy (≤ 4 weeks, > 4 to 8 weeks, > 8 to 12 weeks, and >12 to 24 weeks). Results RFS and OS were similar for women starting chemotherapy up to 12 weeks after surgery. OS hazard ratio (univariate) for initiation of chemotherapy more than 12 weeks compared with 12 weeks or less after surgery was 1.5 (95% CI, 1.07 to 2.10; P = .017). Five-year OS rates were 84%, 85%, 89%, and 78%, (log-rank P = .013); RFS rates were 74%, 79%, 82%, and 69% (log-rank P = .004) for patients starting chemotherapy 4 weeks or fewer, more than 4 to 8 weeks, more than 8 to 12 weeks, and more than 12 to 24 weeks after surgery, respectively. In multivariate analysis, independent prognostic factors were grade, size, nodal status, estrogen receptor, age, and lymphatic and/or vascular invasion. Initiation of adjuvant chemotherapy more than 12 weeks from surgery remained significantly associated with inferior survival, with a hazard ratio of 1.6 (95% CI, 1.2 to 2.3; P = .005). Conclusion This retrospective analysis suggests that adjuvant chemotherapy is equally effective up to 12 weeks after definitive surgery but that RFS and OS appear to be compromised by delays of more than 12 weeks after definitive surgery.
Rhinoscleroma of the lower respiratory tract
Authors: Holinger Paul H. , Gelman Howard K. , Wolfe Charles K. 
Published: October 2006

AbstractRhinoscleroma is a chronic granulomatous disease of the respiratory tract endemic to Eastern Europe and Central America which is being recognized with increasing frequency in other countries, including the United States. It was initially described as a lesion of the nose and upper respiratory tract, but is now known to involve the larynx, trachea and bronchi as well to cause slowly progressive asphyxia.Eleven cases of rhinoscleroma with varying degrees of involvement of the lower respiratory tract (larynx, trachea and bronchi) are presented. Present day treatment is both medical, consisting primarily of streptomycin and tetracycline, and endoscopic dilatation.Prolonged medication with careful dose control is necessary. Lower respiratory tract involvement should be considered in patients with chronic destructive granulomatous nasal pathology. This should be especially emphasized if they have an Eastern European or Central American background, or have travelled in these areas in which rhinoscleroma is endemic.
Inverting papilloma of the nose and paranasal sinuses
Authors: Suh Ku W. , Facer George W. , Devine Kenneth D. , Weiland Louis H. , Zujko Richard D. 
Published: October 2006

AbstractInverting papilloma of the nose and paranasal sinuses has been classified as a true neoplasm by most authors. It is distinct from the ordinary nasal polyps in that it has a different cause, different histologic features, a higher recurrence rate, and is occasionally associated with carcinoma.This study includes 57 patients seen over a 30‐year period who had inverting papilloma and for whom the history, clinical and radiologic findings, treatment methods, pathologic sections, and recurrences were analyzed. Features associated with higher recurrence rate were epithelial atypia and extent of lesions. Females showed higher recurrence rates than males. External approaches (lateral rhinotomy) reduced recurrence remarkably compared with transnasal removal (13 percent versus 45 percent).Four patients had associated carcinoma with inverting papilloma, and more extensive operations were performed in these cases; one patient died of the tumor. Radical aggressive treatment and careful follow‐up are advocated because of the higher recurrence rate after inadequate removal and because of possible malignant transformation.
The jugular bulb: Its anatomic and clinical considerations in contemporary otology
Authors: Graham Malcolm D. 
Published: October 2006

AbstractAdvances in neurotologic diagnosis and surgery has pointed to the need for a complete reassessment of the relationship and significance of the jugular bulb and sigmoid sinus in the temporal bone.The purpose of this paper is to bring together in a comprehensive, up‐to‐date, and relevant manner knowledge of the jugular bulb and sigmoid sinus.The anatomy of the bulb and sinus is discussed and selected temporal bone sections presented to illustrate the varying locations of the jugular bulb. Considerations in differential diagnosis are presented and examples of surgical procedures are discussed wherein the jugular bulb was encountered and the methods of management are detailed in these instances.
A study of nasal airway function in the postoperative period of nasal surgery
Authors: Sherman Allen H. 
Published: October 2006

AbstractOne hundred fifty‐seven consecutive nasal surgery cases were followed for a minimum of one year or more. Ten cases were considered to have unsatisfactory mechanical airways, caused either by return of the original pathology (alar collapse or atrophic rhinitis) or by inadequate mechanical results.Nineteen cases in which the mechanical airways were satisfactory had soft tissue obstruction secondary to chronic inferior turbinate congestion.The effects of nasal allergy and the trauma of postnasal packing on chronic congestion of the turbinates are tabulated according to the type of surgery performed and results discussed.
Glottic and subglottic stenosis from endotracheal intubation
Authors: Hawkins Donald B. 
Published: October 2006

AbstractAs a result of increased use of prolonged endotracheal intubation, complications of intubation are now being seen more often. Stenosis of the airway may develop at the level of the glottic or subglottic larynx, or in the trachea. Discussions of management do not always distinguish clearly between laryngeal stenosis and tracheal stenosis. Yet, these are two separate entities. Discussions of laryngeal stenosis usually deal with subglottic stenosis, with less emphasis on obstruction at the glottic level.Of 20 patients, 14 adults and six children, with stenosis of the larynx secondary to intubation, we were successful in establishing adequate airways in 16. An analysis of these 20 patients leads to the following conclusions:

Scarring in the glottic posterior commissure between the arytenoid cartilages is a frequent cause of laryngeal stenosis after intubation.
Endoscopic management can be successful in many cases if it is started early enough, and repeated as often as is necessary. The earlier it is begun, the better the results will be.
Indwelling stents which are extremely valuable in laryngeal stenosis from external trauma, may not be as useful in stenosis from endotracheal tube trauma.
Mucormycosis
Authors: Eisenberg Lee , Wood Terry , Boles Roger 
Published: October 2006

AbstractThree cases of mucormycosis are presented; two with unusual aspects: One with previously unreported involvement of the mandible, and one presenting as a cavernous sinus thrombosis.Review of the literature reveals a limited number of survivors. Survival in two of the cases presented here suggests that early diagnosis, aggressive therapy with surgery, and amphotericin B should improve the prognosis.
Spontaneous and traumatic perilymph fistulas
Authors: Althaus Sean R. 
Published: October 2006

AbstractClinicians have been aware of the problem of post‐stapedectomy peri‐lymph fistulas for some time. The existence of non‐surgical oval and round window fistulas has been known and was first described in detail by Fee in 1968. This paper concerns a small series of patients with spontaneous and traumatic perilymph fistulas. Five oval window fistulas and one round window fistula are reported. Clinical features, audiometric, radiographic and vestibular findings are discussed.The etiology of traumatic and spontaneous fistulas is not well understood, but seems to bear a relationship to sudden increases in intracran‐ial pressure transmitted to the inner ear through the cochlear aqueduct. Middle ear pressure changes, as seen in acoustic or barotrauma, may also cause these leaks.Indications for surgery and techniques of perilymph fistula identification and repair are discussed in the paper. Surgical correction led to relief of vertigo in 80 percent of patients in this series, and significant hearing improvements were seen in 50 percent of the patients.In evaluating patients with sudden sensori‐neural hearing loss, or persistent vestibular symptoms following head or ear trauma, the otologist should keep in mind the possibility of a perilymph fistula and actively investigate these patients. Evidence presented in this paper and in the literature suggests that identification and correction of spontaneous and traumatic perilymph fistulas can lead to resolution of vestibular symptoms and improved hearing in a significant number of patients with these lesions.
Auditory symptoms associated with herpes zoster or idiopathic facial paralysis
Authors: Byl Frederick M. , Adour Kedar K. 
Published: October 2006

AbstractAuditory symptoms (hyperacusis, tinnitus, decreased hearing) have long been recognized to accompany herpetic or idiopathic facial paralysis. Twenty‐nine percent of 1,080 patients with idiopathic facial paralysis and 37 percent of 172 with herpes zoster oticus facial paralysis had auditory symptoms. Abnormal related sensori‐neural hearing loss was documented in only 11 of these 377 patients with auditory complaints. All of the 11 had a diagnosis of herpes zoster oticus.Sensori‐neural hearing loss occurs in only about 6.5 percent of patients with herpes zoster facial paralysis, and no confirmed case of such loss in idiopathic facial paralysis has been reported. In patients presenting with sensori‐neural hearing loss accompanying facial paralysis believed to be idiopathic, herpes zoster should be suspected even in the absence of vesicles. Factors favorable for recovery of auditory function include age 64 years or younger, mild initial hearing loss, a cochlear pattern of hearing loss, and absence of vertigo. Recovery of auditory function does take place; however, a high‐tone sensori‐neural loss may persist except in younger patients.
Ossicular transplants: Histologic findings in Animals and Man
Authors: Linthicum Fred H. 
Published: October 2006

AbstractNumerous papers have been published in the past 15 years in which the authors attempted to predict the results of surgical procedures on humans by analyzing the findings in animals undergoing similar procedures. Our experience in analyzing animal and human temporal bones indicates that conclusions drawn on this basis are frequently invalid.We reviewed temporal bones of monkeys and cats that had had a variety of surgical procedures. There is much more middle ear fibrosis, particularly in the epitympanum, in these animals than one finds in human temporal bones. In a number of animals in which middle ear procedures were performed, hydrops of the inner ear or labyrinthitis occurred. This has not been the experience in human middle ear surgical procedures.An extensive review of the literature indicates that most investigators are of the same opinion. However, there are still those who are performing experiments using ossicular transplants, stapedectomy techniques, etc., who attempt to correlate the findings in animals in anticipation of what the same procedures might do to the human middle and inner ear.It appears from our experience, and that of many other investigators, that the ultimate fate of ossicular repositioning and transplantation in various animals cannot be used to predict what might happen in human beings.
Frontal sinus trauma: Experimental reconstruction with proplast
Authors: Schenck Nicholas L. , Tomlinson Michael J. 
Published: October 2006

AbstractTrauma has become the most common pathologic entity requiring operative intervention in the frontal sinus. Treatment has evolved from simple open drainage to ablation with reconstruction at a later date. Methyl‐methacrylate, currently the most widely used alloplastic material, has inherent disadvantages such as two‐stage reconstruction, difficulty in handling and molding, and susceptibility to trauma.The present investigation evaluates Proplast(r), a biocompatible Teflon fluorocarbon polymer implant, in one and two‐stage frontal reconstruction following traumatic defects to the canine frontal sinus. Following the loss of anterior or posterior frontal bone, Proplast(r) provided excellent cosmetic reconstruction over a period of one year. Resistance to infection was good, reaction with dura and brain was absent, and cerebrospinal fluid leaks sealed rapidly. In contrast to other alloplastic materials, rapid vasculariza‐tion and collagen ingrowth lead to stabilization rather than sequestration.Several advantages over alloplastic and metallic implants may give Proplast(r) a unique potential in operative cranioplasty.
Contribution to therapy of dysphonia plica ventricularis
Authors: Kosokovic Franjo , Vecerina Santa , Cepelja Ivanka , Konic Vera 
Published: October 2006

AbstractExcision of the hypertrophic ventricular folds was performed in 35 patients by means of laryngomicroscopy. In most of our patients this therapy promptly resulted in a clear voice. Correlating the laryngomicroscopic finding and the histological picture we were able to classify hypertrophy of the ventricular folds into three stages, each of which presents with a characteristical clinical and histological picture and thus requires appropriate therapy. In Stage I the histological changes are reversible and conservative phoniatric therapy leads to success relatively quickly. In the second stage histological changes may also be reversible, and the prolonged and persistent phoniatric therapy leads to success but we prefer micro‐surgical excision because of the direct effect. In Stage III, however, we found irreversible histological changes in the sense of connective hyper‐plasia which prompted us to conclude that microsurgical excision alone may lead to regression of the hoarseness.
Effect of radiation therapy on facial nerve cable autografts
Authors: Mcguirt W. F. , Mccabe B. F. 
Published: October 2006

AbstractFacial nerve cable autografts were performed on 20 cats with 10 animals receiving 6,000 Rads of postoperative irradiation over six weeks. Testing by clinical appearance, pontograms, and axon counts showed no statistical difference in the operated only and the operated plus irradiated groups. Pontograms illustrated the clinical observance of spasticity, delay and weakness often seen after grafting. This animal work tends to verify the clinical impression that in patients requiring postoperative irradiation for a malignancy necessitating excision and grafting of the facial nerve, anticipated results should be equivalent to the facial nerve cable autografts without postoperative irradiation.
Laryngeal involvement in von recklinghausen's disease: A case report and review of the literature
Authors: Chang‐Lo Mary 
Published: October 2006

AbstractA case of neurofibromatosis involving the larynx is added to the 19 previously reported cases; furthermore, it represents the only reported case of plexiform ganglioneurofibroma of the larynx in Von Recklinghau‐sen's disease. The reported cases of neurofibromatosis with laryngeal involvement in the world literature are discussed and summarized. The main clinical symptoms are dyspnea, dysphonia and dysphagia which occasionally require tracheotomy when the condition is recognized. Elective surgical excision is the treatment of choice.
Management of malignancy of the temporal bone
Authors: Gacbk Richard R. , Goodman Max 
Published: October 2006

AbstractAn analysis was made of 31 patients with malignancy of the temporal bone treated at Massachusetts Eye and Ear Infirmary between 1959 and 1975. Treatment modalities included: partial temporal bone resection, subtotal temporal bone resection, total temporal bone resection, radical mas‐toidectomy followed by radiation therapy, radiation therapy alone, and chemotherapy. When tumor was limited to the external ear canal, partial temporal bone resection was effective in 10 out of 11 patients. When tumor involved the middle ear, subtotal temporal bone resection cured 3 out of 5 patients, and radical mastoidectomy followed by radiation therapy cured 5 out of 12 patients. Total temporal bone resection and chemotherapy failed to cure a patient each, but radiation therapy alone was successful in controlling tumor in one patient.
Problems of diagnosis in the evaluation of mediastinal sarcoidosis
Authors: Welsh Louis W. , Welsh John J. 
Published: October 2006

AbstractThe diagnosis of sarcoidosis can be established when the case meets the criteria of clinical course, radiologie findings, and supportive histology.When there is variation from the established criteria and the clinical course of age, systemic evidence of disease or the radiologie findings of unilateral or solitary adenopathy are encountered, then ongoing evaluation is necessary to identify a possible second disease existence.Cases have been presented which indicate some problem requiring further investigative studies before acceptance of the diagnosis of sarcoidosis.