Advances in high-throughput molecular biology, genomics and epigenetics, coupled with exponential increases in computing power and data storage, have led to a new era in biological research and information. Bioinformatics, the discipline devoted to storing, analysing and interpreting large volumes of biological data, has become a crucial component of modern biomedical research. Research in otolaryngology has evolved along with these advances.

This review highlights several modern high-throughput research methods, and focuses on the bioinformatics principles necessary to carry out such studies. Several examples from recent literature pertinent to otolaryngology are provided. The review is divided into two parts; this first part discusses the bioinformatics approaches applied in nucleotide sequencing and gene expression analysis.

This paper demonstrates how high-throughput nucleotide sequencing and transcriptomics are changing biology and medicine, and describes how these changes are affecting otorhinolaryngology. Sound bioinformatics approaches are required to obtain useful information from the vast new sources of data.

To determine whether the distribution of membrane lesions associated with Ménière's disease is random, as might be expected from a pervasive process such as hydrops, or orderly, as might be expected if membrane resistance is graded.

A meta-analysis of temporal bone reports on 184 specimens demonstrating endolymphatic hydrops was undertaken to determine membrane lesion evolution and distribution.

Lesion distribution was found to be orderly and cochleocentric. No random scattershot lesions were reported in any study. Disease always started in the cochlear apex, even in non-symptomatic cases, and then involved the saccule, utricle, ampullae and canal system in that precise sequence as the disease progressed.

The orderly lesion progression in the otopathology associated with Ménière's disease suggests that the hydropic process has a graded non-random effect on the labyrinth. These findings suggest a pathological staging system that may be useful in temporal bone evaluation.

To observe the long-term outcome of ossiculoplasty using autogenous mastoid cortical bone in chronic otitis media in-patients.

Sixty-one ears of 57 in-patients with chronic otitis media, with or without cholesteatoma, underwent type III tympanoplasty using autogenous mastoid cortical bone as the prosthetic material. Twenty-one ears were treated by canal wall down mastoidectomy and 40 ears by canal wall up mastoidectomy. The follow-up period was 3 to 6 years (average 4.2 years). Pure tone averages for thresholds at 0.5, 1, 2 and 3 kHz were calculated using standard conventional audiometry.

The pre-operative mean air–bone gap of 31.6 dB, for all ears, was reduced to 20.3 dB post-operatively. For the 40 canal wall up ears, this value decreased from 30.8 dB to 19.9 dB, and for the 21 canal wall down ears it decreased from 33.0 dB to 21.0 dB. The differences between the pre- and post-operative mean air–bone gap values were significant.

No cases of extrusion, necrosis or resorption were exhibited for the autogenous mastoid cortical bone prosthesis. A significant hearing improvement was obtained in the majority of cases and this remained stable over time.

There has been no previous research to demonstrate the risk of noise-induced hearing loss in industry in Nepal. Limited research on occupational noise-induced hearing loss has been conducted within small-scale industry worldwide, despite it being a substantial and growing cause of deafness in the developing world.

The study involved a cross-sectional audiometric assessment, with questionnaire-based examinations of noise and occupational history, and workplace noise level assessment.

A total of 115 metal workers and 123 hotel workers (control subjects) were recruited. Noise-induced hearing loss prevalence was 30.4 per cent in metal workers and 4.1 per cent in hotel workers, with a significant odds ratio of 10.3. Except for age and time in occupation, none of the demographic factors were significant in predicting outcomes in regression analyses. When adjusted for this finding, and previous noise-exposed occupations, the odds ratio was 13.8. Workplace noise was significantly different between the groups, ranging from 65.3 to 84.7 dBA in metal worker sites, and from 51.4 to 68.6 dBA in the control sites.

Metal workers appear to have a greater risk of noise-induced hearing loss than controls. Additional research on occupational noise-induced hearing loss in Nepal and small-scale industry globally is needed.

Established middle-ear cleft cholesteatoma is associated with keratinous debris, which is likely to be an ideal medium for saprophytic fungal colonisation. This prospective case study aimed to explore the incidence and nature of fungal elements in cholesteatoma keratin samples obtained during primary mastoid surgery.

All cases of middle-ear cleft cholesteatoma treated with primary mastoid surgery at the El-Sahel Teaching Hospital over a seven-month period were included. Keratinous debris obtained from the mastoid antrum was subjected to mycological analysis at the Department of Medical Microbiology and Immunology, Faculty of Medicine, Cairo University. A literature search was performed to determine the clinical and pathological relevance of fungal colonisation in cholesteatoma.

Eighteen patients underwent primary mastoid surgery for cholesteatoma (nineteen ears in total) in a seven-month period starting 30 March 2013. Patients included 13 males and 5 females, with an age range of 9 to 45 years (mean 23 years). Fungal cultures were obtained from 17 keratin samples (89 per cent). Of these, five fungal isolates belonged to the dermatophyte group (21 per cent).

Fungal colonisation in middle-ear cleft cholesteatoma probably plays a significant role in disease progression. Moreover, saprophytic fungal colonisation in cholesteatoma keratin may be responsible for the fetor commonly associated with the ear discharge.

Adhesion formation is a frequent and serious post-operative problem in ENT surgery. This study assessed the effect of two anti-adhesive haemostatic agents on an experimental guinea pig model.

The middle-ear mucosa of 14 guinea pigs was exposed to surgical trauma. After surgery, Arista™ AH was injected into the right middle ear of seven animals, while Ankaferd Blood Stopper was injected into the right middle ear of the other seven animals. The left ears were left untreated and regarded as the control group. The three groups were compared by histological examination at post-operative week 4.

In each of the three groups, consolidation of the lamina propria and epithelium mucosae, increments in the number of active fibroblasts, collagen fibrils and inflammatory cells, and increased vascular dilation were observed on haematoxylin and eosin-stained sections, and were more prominent in the control and Ankaferd Blood Stopper groups. Epithelial thickness and capillary vasodilation were significantly lower in the Arista™ AH group compared with the control and Ankaferd Blood Stopper groups (p < 0.008).

Arista™ AH may prevent the formation of adhesions in middle-ear surgery. Further experimental studies are required to determine its ototoxic potential.

Allergic rhinitis is the most common form of non-infectious rhinitis, affecting 500 million people worldwide, with one-fifth of those affected living in the Indian subcontinent. The skin prick test is the most valuable test for detecting offending allergens, and can be helpful for patient education, allergen avoidance and immunotherapy planning.

The skin prick test was performed with 49 allergens in 486 patients who presented with symptoms of allergic rhinitis, and the allergen profile was studied.

Of the 486 allergic rhinitis patients, 335 (68.93 per cent) showed allergen positivity to the skin prick test. Dust mite was the most common allergen, with positive results in 44.65 per cent of cases.

The most common offending allergen in our study was the dust mite. Identification of specific allergens for a particular geographical area aids patient education and enables allergen-specific immunotherapy.

Sialendoscopy can be followed by swelling and infection of the salivary gland. A possible pathomechanism is damage of the deeper salivary duct system by intraductal pressure generated by the irrigation fluid.

After measuring the physiological intraductal pressures which arise during sialendoscopy, these pressures were simulated in freshly excised salivary glands and the tissue was analysed histologically.

Normal intraductal filling pressure during sialendoscopy is 100–250 daPa, and pressure peaks can be up to 2000 daPa during flushing. A filling pressure of more than 400 daPa results in dilatation of the salivary ducts and acinar area. No direct damage to any duct structures could be observed histologically.

Irrigation fluid should be administered intermittently rather than continuously during sialendoscopy. The intraductal filling pressure should not exceed 400 daPa to minimise the trauma to the salivary duct system and reduce the risk of developing oedema and inflammation.

Epidermal growth factor receptor (EGFR) overexpression and prognostic value in head and neck squamous cell cancer is the basis for targeting by anti-EGFR antibodies, which increase the efficacy of radiotherapy. In order to evaluate the best therapeutic schedule, the effects of cetuximab (C225) on Hep-2 cell proliferation, alone and in combination with cisplatin, were studied.

Hep-2 cells were treated with cetuximab alone or in combination with cisplatin. After determining cell viability with trypan blue, morphological features of apoptotic degeneration were analysed by fluorescence microscopy with Hoechst 33258 stain.

Cetuximab alone mildly inhibited Hep-2 proliferation and showed no pro-apoptotic effects. When administered concomitantly with cisplatin, cetuximab synergistically increased inhibition of proliferation and apoptosis.

The antiproliferative activity of cetuximab is consistent with its hypothesised role in inhibiting repopulation. However, the increase in the effects of pro-apoptotic agents induced by cetuximab may be even more relevant to its clinical effectiveness than the inhibition of repopulation.

To discover the anatomist who first identified the upper oesophageal sphincter.

The authors searched dozens of antique anatomy textbooks kept in the old section of the ‘Vincenzo Pinali’ Medical Library of Padua University, looking for descriptions of the upper oesophageal sphincter.

The oesophageal sphincter was drawn correctly only in 1601, by Julius Casserius, in the book De vocis auditusque organis historia anatomica… (which translates as ‘An Anatomical History on the Organs of Voice and Hearing …’), and was properly described by Antonio Maria Valsalva in 1704 in the book De aure humana tractatus… (‘Treatise on the Human Ear …’).

Anatomists Casserius and Valsalva can be considered the discoverers of the ‘oesophageal sphincter’.

‘R staging’ is a new ultrasonographic scoring system developed and used by our specialist head and neck radiologist for reporting sonographic risk of malignancy to those at our thyroid multidisciplinary team meeting. This study aimed to: classify the R staging system, examine its relationship with the eventual histopathological diagnosis and define its clinical utility.

The pre-operative ultrasound scans of 78 patients were assigned an R status by our specialist head and neck radiologist. The final histopathology report for each thyroid nodule was used as the ‘gold standard’ for analysis.

When thyroid nodules were classified as low risk (R stages 1–3) or high risk (R stages 4–5) for malignancy, the sensitivity of R staging was 74.2 per cent and specificity was 80.9 per cent. An R5 status was 100 per cent predictive of malignancy.

Our results compare favourably with other suggested ultrasonographic staging systems for thyroid nodules.

Papillary microcarcinoma of the thyroid has been described as either a normal variant or a serious malignancy. We describe our experience with papillary microcarcinoma and lymph node metastases.

A total of 685 consecutive total thyroidectomies with central compartment neck dissection were reviewed for papillary microcarcinoma. Association of central compartment lymph node metastases with age, gender, tumour multifocality, bilaterality and extrathyroidal extension was analysed.

Out of 170 papillary microcarcinoma cases, multifocality was found in 72 (42.4 per cent), bilaterality in 49 (28.8 per cent) and extrathyroidal extension in 16 (9.4 per cent). In all, 23 patients (13.5 per cent) had lymph node metastases. There was a significant association (p < 0.05) between extrathyroidal extension (but no other tumour characteristics) and lymph node metastases.

In all, 13.5 per cent of papillary microcarcinomas in our series showed lymph node metastases. Lymph node metastases were associated with extrathyroidal invasion of the papillary microcarcinoma.

This study examined whether the occurrence of late neck metastasis in early tongue squamous cell carcinoma can be predicted by evaluating HMGB1 (high mobility group box 1) expression in the primary lesion.

A case–control study was conducted. The cases comprised 10 patients with late neck metastasis. The controls consisted of 16 patients without recurrence. All were examined immunohistochemically for HMGB1 protein expression. The odds ratio for late neck metastasis in relation to HMGB1 was estimated.

Results for HMGB1 were dichotomised into positive staining scores (score, 5–7) and negative scores (0–4). Six cases (60 per cent) and four controls (25 per cent) were HMGB1-positive. Although no significant result was seen, compared with HMGB1-negative patients the odds ratio for late neck metastasis in HMGB1-positive patients was 3.8 (95 per cent confidence interval, 0.6–26.5) after adjusting for other factors.

In the present study, immunohistochemical study of HMGB1 in early tongue squamous cell carcinoma did not appear to be very useful for predicting occult neck metastasis. Further study is necessary to clarify the relationship between HMGB1 expression and late neck metastasis in early tongue squamous cell carcinoma.

Having observed variation in the breadth of surgeons' fingers whilst they are placing the incision for submandibular gland surgery, we aimed to examine this technique of incision siting, quantify the differences in fingerbreadths and consider any consequences of variability.

Surgeons trained in salivary gland surgery were questioned on their method of incision placement for submandibular gland surgery. The breadth of index and middle fingers were subsequently measured using Vernier calipers.

The majority of surgeons use a measure of two fingerbreadths below the mandible in planning their approach to the submandibular gland. There is a significant difference in the size of surgeons' fingers, particularly between men and women (mean, 4.2 cm vs 3.6 cm).

Fingerbreadth measurements are somewhat arbitrary, with significant inter-surgeon variability. However, based on the results of cadaveric studies, the findings indicate that the technique is safe for marking the incision in submandibular surgery.

Revision laryngeal framework surgery is usually performed for medialisation laryngoplasty failure, rather than for failure after arytenoid adduction. We describe a new method for revision arytenoid adduction surgery, performed by directly pulling the lateral cricoarytenoid muscle (‘lateral cricoarytenoid muscle pull surgery’).

We describe a case of revision laryngeal framework surgery, present a literature review and describe the advantages of lateral cricoarytenoid muscle pull surgery over the original method of arytenoid adduction using a posterior approach.

Medialisation laryngoplasty combined with arytenoid adduction was performed following unilateral vocal fold paralysis from mediastinal surgery, resulting in severe glottic insufficiency. The patient's voice improved after the initial surgery, but had deteriorated 18 months later. Revision surgery was performed using lateral cricoarytenoid muscle pull surgery, and her voice recovered normally in terms of perceptual impression. The post-operative course was uneventful for 10 months following revision surgery.

To our knowledge, this is the first case of revision arytenoid adduction performed using a lateral cricoarytenoid muscle pull approach. Lateral cricoarytenoid muscle pull surgery should therefore be considered as a new fenestration approach for arytenoid adduction.