bluuebunny/crossref_metadata_2025 huggingface dataset:
Evidence supporting functional rhinoplasty or nasal valve repair: A 25‐year systematic review
Authors: Rhee John S. , Arganbright Jill M. , McMullin Brian T. , Hannley Maureen
Published: June 2008

Objective

To systematically review the existing literature supporting the efficacy of modern‐day rhinoplasty techniques for treatment of nasal obstruction due to nasal valve compromise.

Data Sources

PubMed search of the English‐language literature from January 1982 to August 2007 combined with manual review of citations within article bibliographies.

Review Methods

A systematic review of the literature for the targeted objective was conducted. Citations acquired from the targeted search were filtered and primary articles were reviewed to abstract information including interventions and outcome measures. Articles were then assigned level‐of‐evidence grades as defined by the Oxford Centre for Evidence‐Based Medicine.

Results

A total of 861 citations were generated and 291 abstracts were identified as potentially relevant articles. Of these abstracts, 82 articles merited full‐text review. A total of 44 articles met inclusion criteria. The majority of the studies were classified as level 4 evidence, and only two studies met level 2b criteria. There was considerable variation in the quality of the studies within the level 4 category. All articles generally supported the effectiveness of functional rhinoplasty techniques for treatment of nasal obstruction.

Conclusions

There is substantial level 4 evidence to support the efficacy of modern‐day rhinoplasty techniques for treatment of nasal obstruction due to nasal valve collapse. More recent studies have incorporated validated patient‐reported outcome measures, with more rigorous statistical analysis. Future study design improvements include the use of comparison cohorts and incorporating standardized objective outcome measures.
The preventive effect of halofuginone on posterior glottic stenosis in a rabbit model
Authors: Yoon Yeo‐Hoon , Rha Ki‐Sang , Koo Bon Seok , Park Jae Yong , Kim Yong Min , Park Yong Ho
Published: June 2008

Objective

The aim of this study was to investigate the preventive effect of halofuginone on posterior glottic stenosis (PGS) in an animal model.

Study Design

A randomized, controlled animal study.

Subjects and Methods

Sixteen male New Zealand White rabbits were used for this study. After the mucosa of posterior glottis was removed for producing PGS, the study group (eight rabbits) was given intraperitoneal halofuginone at 0.1 mg/kg/day for 4 weeks and saline was injected into peritoneum in the control group. At 4 weeks after injury, postsurgical changes of posterior glottis were evaluated by gross and histologic examination.

Results

PGS was induced by the mucosal stripping of the posterior glottis. The halofuginone‐treated group showed less scarring and granulation tissue formation. Also, the degree of synechia was significantly less than that of control group. Histologic analysis showed the decreased fibrosis in the halofuginone‐treated group.

Conclusion

This study suggests that halofuginone can be helpful in preventing PGS after laryngeal injury.
Topical budesonide via mucosal atomization device in refractory postoperative chronic rhinosinusitis
Authors: Kanowitz Seth J. , Batra Pete S. , Citardi Martin J.
Published: June 2008

Background

Nebulized budesonide (Pulmicort Respules, AstraZeneca, Wilmington, DE) provides control of respiratory tract inflammation in asthmatic patients. The Mucosal Atomization Device (MAD; Wolfe‐Tory Medical, Salt Lake City, UT) is a novel sinonasal atomization device.

Methods

Uncontrolled case series of postoperative patients with chronic rhinosinusitis (CRS) who received budesonide via MAD was performed.

Results

A total of 44 patients with a mean age of 53.5 years met inclusion criteria. The average follow‐up was 31.5 weeks (SD 17.55; range, 8 to 80 weeks). Overall, patient and physician global assessments demonstrated moderate to significant improvement. Average daily oral prednisone usage among patients who took systemic steroids (n = 27) was reduced from 7.96 to 1.94 mg/day without relapse of polyps, mucosal edema, and nasal discharge. Prednisone use was reduced to zero in 16 patients and reduced or stabilized in 10 other patients.

Conclusion

Topical budesonide via MAD may reduce the need for systemic prednisone and improve both physician and patient global assessment scores in postoperative CRS patients. Additional investigation is warranted to exclude placebo effect, spontaneous resolution, and regression to the mean as responsible factors for the reported findings.
Economic, family, and length‐of‐training issues that influence the selection of a clinician‐scientist career path in otolaryngology
Authors: Harris Jeffrey P. , Ariessohn Melanie L.
Published: June 2008

Objective

To understand the reasons for the decrease in clinician‐scientists in otolaryngology.

Study Design

An anonymous survey was prepared that questioned career preparation and personal demographics as well as motive for having done research in medical school. K awardees were also asked for concerns in choosing the clinician‐scientist career path and the obstacles encountered.

Subjects and Methods

A survey was conducted of the 2005 National Institute of Deafness and Other Communication Disorders otolaryngologist K‐awardees and otolaryngology residents from three research‐oriented U.S. medical schools.

Results

Residents felt that family issues ranked as a primary concern, followed by the time factor necessary to devote to research that would detract from their family and personal life. The K‐awardees' concern also appeared to be family issues; the lack of departmental support ranked second. The K‐awardees expressed that protected research time, a mentor, and departmental support were important to success.

Conclusion

This survey found that although young otolaryngologists are interested in research, they are deterred by financial and family constraints and a perceived paucity of departmental support.
Tonsillectomy in Australia: An audit of surgical technique and postoperative care
Authors: MacFarlane Patricia L. , Nasser Simon , Coman William B. , Kiss Gregory , Harris Penelope K. , Carney A. Simon
Published: June 2008

Objective

To assess current tonsillectomy practice among Australian otolaryngologists.

Study Design

An audit based on an anonymous 19‐item postal questionnaire on tonsillectomy technique and perioperative management sent to all Australian otolaryngology specialists.

Subjects and Methods

Two hundred eighty‐four otolaryngologists registered with the Australian Society of Otolaryngology‐Head and Neck Surgery database were sent the questionnaire.

Results

A 72.5 percent response rate was obtained. Monopolar diathermy was the most common technique for dissection (45%) and hemostasis (54%). Bipolar diathermy was used for hemostasis in 20 percent. Cold‐steel dissection was routinely used by 36 percent, ties were used for hemostasis only by 11 percent of surgeons. The use of local anesthetic, dexamethasone, and postoperative antibiotics was 45 percent, 40 percent, and 20 percent, respectively. Seventy‐six percent of surgeons always observed tonsil patients overnight.

Conclusion

Australian surgeons still use monopolar diathermy as their preferred technique for tonsillectomy. Local anesthetic, dexamethasone, and postoperative antibiotics are used infrequently, and fewer than 1:4 surgeons perform day‐case tonsillectomy.
Laser‐assisted stapedotomy with a Nitinol heat‐crimping prosthesis: Outcomes compared with a platinum fluoroplastic prosthesis
Authors: Pudel Eduard I. , Briggs Robert J.S.
Published: June 2008

Objective

To assess the hearing outcomes achieved with a Nitinol heat‐crimping prosthesis when used with a laser‐assisted stapedotomy for otosclerosis.

Study Design

Prospective assessment of 50 stapedotomies performed in 48 patients. Data collected included audiological results and duration of hospital admission. Outcomes were compared with a previously reported series of 66 stapedotomies performed in 59 patients.

Setting

Tertiary referral center and private practice.

Results

In the Nitinol group, hearing was improved in all cases (100%). The air‐bone gap (ABG) was closed to within 10 dB in 48 (96%). This group's results are significantly better (P ≥ 0.01) than those of the platinum fluoroplastic group, in whom ABG was within 10 dB in 74 percent.

Conclusion

Laser‐assisted stapedotomy, under local anesthesia with sedation, using a Nitinol heat‐crimping prosthesis is a safe, well‐tolerated technique with which excellent audiological results can be achieved.
Impact of shoulder complaints after neck dissection on shoulder disability and quality of life
Authors: Stuiver Martijn M. , van Wilgen Cornelis P. , de Boer Erlijn M. , de Goede Cees J. T. , Koolstra Muriel , van Opzeeland Anita , Venema Piet , Sterken Margriet W. , Vincent Andrew , Dijkstra Pieter U.
Published: June 2008

Objective

To explore relationships between shoulder complaints after neck dissection, shoulder disability, and quality of life. To find clinical predictors for mid‐ to long‐term shoulder disability.

Study Design

Prospective.

Patients and Methods

Shoulder pain, shoulder mobility, and shoulder droop, as well as scores on shoulder disability questionnaire and RAND‐36 (quality of life), were measured at baseline, discharge (T1), and 4 months postoperatively (T2) on 139 patients admitted for neck dissection to major head and neck centers in the Netherlands.

Results

Shoulder mobility was significantly decreased at T1 and did not improve. Significant relationships between shoulder function, shoulder disability score, and RAND‐36 domains were found. Two clusters of clinical symptoms could be identified as independent predictors for shoulder disability.

Conclusions

Objective deterioration in shoulder function after neck dissection is associated with perceived shoulder disability and related to physical functioning and bodily pain. Predictors for shoulder disability can be found.
The effects of Peroxisome Proliferator‐Activated Receptor‐γ agonist on a murine model of experimental allergic rhinitis
Authors: Jeon Eun‐Ju , Lee Seung Kyun , Park Yong‐Soo , Kim Dong‐Hyun , Yum Jin Ho , Park Chan‐Soon
Published: June 2008

Objectives

To investigate the effect of rosiglitazone, a synthetic selective peroxisome proliferator‐activated receptor (PPAR)‐γ agonist, for cytokine production and PPAR‐γ expression in nasal mucosa.

Methods

Mice in allergic rhinitis group received ovalbumin sensitization followed by ovalbumin intranasal challenge. Mice in the rosiglitazone group received rosiglitazone treatment additionally. Various allergic responses were then assessed.

Results

The frequency of nasal rubs and ovalbumin‐specific immunoglobulin E decreased significantly in the rosiglitazone group compared with the allergic rhinitis group. The rosiglitazone group also showed that inflammation was markedly reduced by rosiglitazone administration. Immunohistochemistry showed that PPAR‐γ protein expression in nasal mucosa was enhanced in the allergic rhinitis group and the rosiglitazone group compared with control mice.

Conclusion

PPAR‐γ activation with rosiglitazone effectively inhibited allergic symptom development, nasal mucosal inflammation, and production of ovoalbumin‐specific immunoglobulin E and Th2‐type cytokine. Our results provide evidence of the therapeutic potential of PPAR‐γ agonist for the treatment of allergic rhinitis.
Baseline laryngeal effects among individuals with dust mite allergy
Authors: Krouse John H. , Dworkin James P. , Carron Michael A. , Stachler Robert J.
Published: June 2008

Objective

To examine baseline effects of perennial allergy on laryngeal appearance, laryngeal function, and perceived vocal handicap among individuals without current allergy or voice symptoms.

Data Sources

This pilot study included 47 adults: 21 with positive and 26 with negative skin test responses for the dust mite, Dermatophagoides pteronyssinus.

Methods

Subjects were tested for sensitivity to dust mite antigen by prick testing. Laryngeal appearance and function were studied with laryngovideostroboscopy, acoustic and speech aerodynamic analysis, and voice sampling. These parameters were blindly analyzed by three trained examiners. Subjects also completed the Voice Handicap Index (VHI) as a measure of vocal handicap.

Results

Subjects allergic to dust mites perceived significantly greater vocal handicap on the VHI than did nonallergic subjects. No significant differences were noted between groups in laryngeal appearance or function.

Conclusion

These pilot data suggest that, at baseline, allergic individuals perceive greater vocal handicap than their nonallergic counterparts (P = 0.04), even in the absence of current allergy symptoms or observable physical or functional abnormalities. These preliminary observations can serve as an impetus for further research into this important area, including the potential interrelationship between acid reflux disease and allergic laryngeal inflammation.
Adequacy of surgeon‐performed ultrasound‐guided thyroid fine‐needle aspiration biopsy
Authors: Bhatki Amol M. , Brewer Brad , Robinson‐Smith Toni , Nikiforov Yuri , Steward David L.
Published: June 2008

Objective

To determine the diagnostic accuracy of specimens obtained by a surgeon performing office‐based ultrasound (US)‐guided fine‐needle aspiration biopsy (FNAB) of thyroid nodules.

Subjects and Methods

From 2003 to 2006, a single surgeon performed 447 consecutive office‐based US‐guided FNABs without on‐site cytological specimen evaluation. Adequate specimens had at least six clusters of follicular cells from at least two separate needle passes.

Results

Non‐diagnostic specimens occurred in 16 of 447 (3.6%) nodules, whereas suboptimal specimens occurred in 17 of 447 (3.8%). Adequate samples were obtained in 413 of 447 (92.6%) of specimens. Malignancy was present in 20 of 447 (4.5%) and atypical features were present in 37 of 447 (8.3%). Benign diagnoses were rendered in 357 of 447 (79.9%) of specimens, of which four of 357 (1.1%) represented false‐negative results.

Conclusion

Prior publications recommend that obtaining adequate thyroid cytology specimens requires use of US‐guided FNAB and on‐site evaluation of cytology adequacy. This study demonstrates that a combination of experienced US guidance, both capillary and aspiration sampling, and three to four needle passes produce comparable results while conserving costs and resources.
Digital images for postsurgical follow‐up of tympanostomy tubes in remote Alaska
Authors: Kokesh John , Ferguson A. Stewart , Patricoski Chris , Koller Kathryn , Zwack Greg , Provost Ellen , Holck Peter
Published: June 2008

Objective

To determine if video otoscope still images of the tympanic membrane taken in remote clinics are comparable to an in‐person microscopic examination for follow‐up care.

Design

Comparative concordance, diagnostic reliability.

Methods

Community health aide/practitioners in remote Alaska imaged 70 ears following tympanostomy tube placement. The patients were then examined in person by two otolaryngologists. Images were later reviewed at 8 and 14 weeks.

Results

Intraprovider concordance for physical examination findings was: “Tube in,” 94 percent‐97 percent (κ = 0.89‐0.94); “Tube patent,” 94 percent −97 percent (κ = 0.89‐0.94); “Drainage,” 90 percent‐96 percent (κ = –0.04‐0.38); “Perforation,” 90 percent −96 percent (κ = 0.61‐0.82); “Granulation,” 97 percent −100 percent (κ = 0.49‐1.0); “Middle ear fluid,” 88 percent −96 percent (κ = 0.28‐0.71); “Retracted,” 83 percent‐91 percent (κ = 0.26‐0.58). These agreement rates are similar to interprovider concordance when two otolaryngologists examine the same patient in person. Intraprovider concordance for diagnoses was 76 percent −80 percent (κ = 0.64‐0.71) and 77 percent −88 percent (κ = 0.66‐0.81) when poor images were excluded. Interprovider diagnostic concordance for the in‐person exam was 89 percent (κ = 0.83).

Conclusion

Video‐otoscopy images of the tympanic membrane are comparable to an in‐person examination for assessment and treatment of patients following tympanostomy tubes. Store‐and‐forward telemedicine is an acceptable method of following patients post tympanostomy tube placement.
A brief history of medicine's Hippocratic Oath, or how times have changed
Authors: Smith Larry
Published: June 2008

Medicine has experienced many changes over the last three thousand years and surprisingly, the good and the bad of these changes can be found in the evolution of the wording of the Hippocratic Oath. This commentary reveals why the original Oath became a part of modern medicine's rite of passage and how society is now changing the very reason that the Hippocratic Oath was brought into the world of medical ethics. By examining the modern language of the Oath, it is possible to understand how these words have diluted its meaning and intent. The long‐term consequences of these changes cannot be foreseen, but history has shown what can happen without a strong oath to guide the practitioner.
Impact of newly revised sterile medication compounding guidelines USP (797) on allergy vial preparation
Authors: Lin Sandra Y. , Houser Steven M. , Gross Gary , Aaronson Donald
Published: June 2008

Objectives

To highlight newly revised guidelines on sterile medication compounding released by the United States Pharmacopeia (USP (797)) in December 2007, and the implications on immunotherapy vial preparation.

Study Design and Methods

A policy review.

Results

The newly revised USP chapter on sterile medication guidelines was released December 2007 and becomes effective June 2008. The revised USP (797) now has specific guidelines addressing immunotherapy vial preparation that are a significant change from the previous version. The revised guidelines should be a useful tool for clinicians who are developing and setting office mixing standards.

Conclusions/Significance

Offices preparing immunotherapy vials should consider formalizing and implementing vial preparation guidelines. These guidelines should be based on expert opinion, experience, and scientific literature.
Induction of chondrogenic differentiation in cultured fibroblasts isolated from the inferior turbinate
Authors: Kim Sung Won , Cho Jin Hee , Hong Myung Wha , Rhie Jong‐Won , Yoon He Ro
Published: June 2008

Objectives:

To explore options of cell sources for regeneration of cartilage, turbinate fibroblasts were tested for their differentiation potential when cultured in three‐dimensional scaffolds with growth factors and co‐cultured with septal chondrocytes.

Methods

Fibroblasts and chondrocytes were seeded on to an alginate sponge in different proportions and were stimulated with TGF‐β1 and IGF‐I. Chondrogenic differentiation of fibroblasts was assessed by histology including immunohistochemical staining, which was examined by reverse transcriptase polymerase chain reaction (RT‐PCR).

Results

Chondroid cells with extracellular matrices occupied the porous structures of alginate sponge and immunolocalizations for type II collagen became prominent at four weeks in culture. Expression of type II collagen and aggrecan mRNA were detected by RT‐PCR. Co‐culture of fibroblasts and chondrocytes showed comparable expansion of cells and extracellular matrix to culture of chondrocytes only.

Conclusion

These findings suggest that human turbinate fibroblasts are apparently redirected toward chondrogenic phenotype by in vitro culture system under specific conditions. Co‐culture of turbinate fibroblasts with septal chondrocytes would be an effective method to expand cartilage specific extracellular matrix.
Nasopharyngectomy: Does the approach to the nasopharynx influence survival?
Authors: Vlantis Alexander C , Yu Brian KH , Kam Michael KM , Hung Terry , Lo Phoebe SY , King Ann D , Tong Michael CF , van Hasselt C Andrew
Published: June 2008

Objective

To investigate whether the approach used to the nasopharynx to perform a salvage nasopharyngectomy for recurrent or residual nasopharyngeal carcinoma influences survival.

Study Design

A retrospective case series.

Subjects and Methods

Eighty patients underwent a nasopharyngectomy via a transpalatal, maxillary swing, or midfacial degloving approach. Local progression‐free, locoregional progression‐free, and overall survival rates were calculated for each approach.

Results

For the whole group (N = 80), there were no significant differences in the survival rates between the three approaches. For the subgroup of patients with recurrent T1 and T2 tumors (n = 68), the local progression‐free and locoregional progression‐free survival rates were significantly better when a maxillary swing approach was used than when a midfacial degloving approach was used.

Conclusion

The maxillary swing approach is associated with significantly better survival rates than the midfacial degloving approach when used to perform a salvage nasopharyngectomy for residual or recurrent T1 and T2 nasopharyngeal carcinoma.
Effects of endoscopic sinus surgery and delivery device on cadaver sinus irrigation
Authors: Harvey Richard J. , Goddard John C. , Wise Sarah K. , Schlosser Rodney J.
Published: June 2008

Objective

Assess paranasal sinus distribution of topical solutions following endoscopic sinus surgery (ESS) using various delivery devices.

Study Design

Experimental prospective study.

Subjects and Methods

Ten cadaver sinus systems were irrigated with Gastroview before surgery, after ESS, and after medial maxillectomy. Delivery was via pressurized spray (NasaMist), neti pot (NasaFlo), and squeeze bottle (Sinus Rinse). Scans were performed before and after each delivery with a portable CT machine (Xoran xCAT), and blinded assessments were made for distribution to individual sinuses.

Results

Total sinus distribution was greater post‐ESS (P < 0.001). Additional distribution was gained with medial maxillectomy (P = 0.02). Influence of delivery device on distribution was significantly higher with neti pot > squeeze bottle > pressurized spray (P < 0.001). Frontal sinus penetration was greatest after surgery (P = 0.001).

Conclusion

ESS greatly enhances the delivery of nasal solutions, regardless of delivery device. Pressurized spray solutions in un‐operated sinuses provide little more than nasal cavity distribution. Use of squeeze bottle/neti pot post‐ESS offers a greatly enhanced ability to deliver solutions to the paranasal sinuses.
Evaluation of acoustic rhinometry in a nasal provocation test with allergic rhinitis
Authors: Kim Young Hyo , Yang Tae Yong , Lee Dong Youl , Ko Kook Jin , Shin Seung Ho , Jang Tae Young
Published: June 2008

Objective

The nasal provocation test is not widely available due to lack of standardized methods and related research. We evaluated the clinical utility of the nasal provocation test using acoustic rhinometry.

Study Design

All patients underwent skin tests and were graded according to severity of reaction.

Methods

We performed nasal provocation tests using acoustic rhinometry in patients with allergic rhinitis from January 2003 to December 2006. A total of 836 patients participated in our study. The mean age was 36 years and the male:female ratio was 5:4.

Results

The mean nasal volume was 10.86 cm3 and the mean minimal cross‐sectional area (MCA) was 0.66 cm3 before the study. Relationship between the severity of the reaction and change in mean nasal volume and MCA was statistically significant. The relationship between the severity of the reaction against the antigen and the severity of clinical symptoms was also statistically significant.

Conclusion

The nasal provocation test can be helpful in evaluating the severity of allergic rhinitis. However, we must be careful in interpreting the results alone.
Electrical stimulation facilitates rat facial nerve recovery from a crush injury
Authors: Lal Devyani , Hetzler Laura T. , Sharma Nijee , Wurster Robert D. , Marzo Sam J. , Jones Kathryn J. , Foecking Eileen M.
Published: June 2008

Objective

To study the effect of electrical stimulation on accelerating facial nerve functional recovery from a crush injury in the rat model.

Study Design

Experimental.

Method

The main trunk of the right facial nerve was crushed just distal to the stylomastoid foramen, causing right‐sided facial paralysis in 17 Sprague‐Dawley rats. An electrode apparatus was implanted in all rats. Nine rats underwent electrical stimulation and eight were sham stimulated until complete facial nerve recovery. Facial nerve function was assessed daily by grading eyeblink reflex, vibrissae orientation, and vibrissae movement.

Results

An electrical stimulation model of the rat facial nerve following axotomy was established. The semi‐eyeblink returned significantly earlier (3.71 + 0.97 vs 9.57 + 1.86 days post axotomy) in stimulated rats (P= 0.008). Stimulated rats also recovered all functions earlier, and showed less variability in recovery time.

Conclusion

Electrical stimulation initiates and accelerates facial nerve recovery in the rat model as it significantly reduces recovery time for the semi‐eyeblink reflex, a marker of early recovery. It also hastens recovery of other functions.
Extracts from The Cochrane Library: Antibiotics to reduce post‐tonsillectomy morbidity
Authors: Burton Martin J. , Archer Sanford M. , Rosenfeld Richard M.
Published: June 2008

The “Cochrane Corner” is a quarterly section in the journal that highlights systematic reviews relevant to otolaryngology‐head and neck surgery, with invited commentary to highlight implications for clinical decision making. This installment features a Cochrane Review entitled “Antibiotics to reduce post‐tonsillectomy morbidity,” which concludes there is little or no evidence that antibiotics reduce pain or hemorrhage after tonsillectomy.
Passage of Tropical Storm Allison (2001) over southeast Texas recorded in δ18O values of Ostracoda
Authors: Lawrence James R. , Hyeong Kiseong , Maddocks Rosalie F. , Lee Kwang-Sik
Published: June 2008

Freshwater Ostracoda collected in ephemeral pond-waters derived from Tropical Storm Allison (2001, Texas) recorded the unusually low oxygen-isotope values of that storm. Therefore, the potential clearly exists, in locations where tropical cyclones make landfall, to obtain a long-term record of tropical cyclone activity from fossil ostracode calcite.
Guardians at the gate: quarantine and racialism in two Pacific Rim port cities, 1870–1914
Authors: MAYNE ALAN
Published: June 2008

This article examines the ambivalent relationship that San Francisco and Darwin developed with Asia during the late nineteenth and early twentieth centuries. On the one hand they presented themselves as gateways that facilitated trade with Asia. On the other hand they acted as sentinels that protected Europeans from Asian immigration. This quirky behaviour is encapsulated in the quarantine regulations that were applied in both ports to Asian commodities and people. The two case studies suggest a broader paradox in the history of port cities. Their prosperity and vitality rested upon the free flow of goods and people, but those flows generated enormous frictions.
Mapping, tissue distribution and polymorphism of porcine genes encoding retinol binding proteins (RBP1 and RBP4)
Authors: Wei-Hua Gong , Zhong-Lin Tang , Wen-Tao Cui , Shu-Lin Yang , Kui Li
Published: June 2008

Using the INRA – University of Minnesota porcine 7000 Rad Radiation Hybrid panel (IMpRH) containing 118 clones, porcine cellular retinol binding protein gene 1 (RBP1) and plasma retinol binding protein gene 4 (RBP4) were assigned to porcine chromosomes 13 and 14, respectively. The mRNA distributions of the two genes in adult Wuzhishan pig tissues (lung, skeletal muscle, spleen, heart, stomach, large intestine, lymph node, small intestine, liver, brain, kidney and fat) were examined. One single nucleotide polymorphism (SNP) was identified in Laiwu, Wuzhishan, Guizhou, Bama pig breeds and a Tongcheng experimental population and analysed using a polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) method. Significant associations were found between different genotypes of A/G156 and maximum carcass length (LM), minimum carcass length (LN), haemoglobin (HGB), mean corpuscular volume haemoglobin (MCH), and day to slaughter weight (age) traits in the Tongcheng experimental population. This SNP locus might be used as a genetic marker in pig breeding and production.
A near uniform basin‐wide sea level fluctuation over the Japan/East Sea: A semienclosed sea with multiple straits
Authors: Kim Seung‐Bum , Fukumori Ichiro
Published: June 2008

Sea level of the Japan/East Sea observed by the TOPEX/Poseidon (T/P) satellite altimeter is analyzed using a 1/4°‐resolution ocean general circulation model. A significant fraction of the Japan/East Sea sea level variability is found to be spatially uniform with periods ranging from 20 d to a year. The model simulation is consistent with T/P records in terms of the basin‐wide sea level fluctuation's spectral energy and coherence. The simulation indicates that the changes are barotropic in nature and controlled, notably at high frequencies, by the net mass transport through the straits of the Japan/East Sea driven by winds in the vicinity of the Korea/Tsushima and Soya Straits. A series of barotropic simulations suggest that the sea level fluctuations are the result of a dynamic balance at the straits among near‐strait winds, friction, and geostrophic control. The basin‐wide sea level response is a linear superposition of changes due to winds near the individual straits. In particular, a basin‐wide sea level response can be established by winds near either one of the straits alone. For the specific geometry and winds, winds near the Soya Strait have a larger impact on the Japan/East Sea mean sea level than those near the Korea/Tsushima Strait.
High-resolution mass spectrometry of viral assemblies: Molecular composition and stability of dimorphic hepatitis B virus capsids
Authors: Uetrecht Charlotte , Versluis Cees , Watts Norman R. , Roos Wouter H. , Wuite Gijs J. L. , Wingfield Paul T. , Steven Alasdair C. , Heck Albert J. R.
Published: June 2008

Hepatitis B virus (HBV) is a major human pathogen. In addition to its importance in human health, there is growing interest in adapting HBV and other viruses for drug delivery and other nanotechnological applications. In both contexts, precise biophysical characterization of these large macromolecular particles is fundamental. HBV capsids are unusual in that they exhibit two distinct icosahedral geometries, nominally composed of 90 and 120 dimers with masses of ≈3 and ≈4 MDa, respectively. Here, a mass spectrometric approach was used to determine the masses of both capsids to within 0.1%. It follows that both lattices are complete, consisting of exactly 180 and 240 subunits. Nanoindentation experiments by atomic-force microscopy indicate that both capsids have similar stabilities. The data yielded a Young's modulus of ≈0.4 GPa. This experimental approach, anchored on very precise and accurate mass measurements, appears to hold considerable potential for elucidating the assembly of viruses and other macromolecular particles.
Disruption of Tsc2 in pancreatic β cells induces β cell mass expansion and improved glucose tolerance in a TORC1-dependent manner
Authors: Rachdi Latif , Balcazar Norman , Osorio-Duque Fernando , Elghazi Lynda , Weiss Aaron , Gould Aaron , Chang-Chen Karen J. , Gambello Michael J. , Bernal-Mizrachi Ernesto
Published: June 2008

Regulation of pancreatic β cell mass and function is a major determinant for the development of diabetes. Growth factors and nutrients are important regulators of β cell mass and function. The signaling pathways by which these growth signals modulate these processes have not been completely elucidated. Tsc2 is an attractive candidate to modulate these processes, because it is a converging point for growth factor and nutrient signals. In these experiments, we generated mice with conditional deletion ofTsc2in β cells (βTsc2−/−). These mice exhibited decreased glucose levels and hyperinsulinemia in the fasting and fed state. Improved glucose tolerance in these mice was observed as early as 4 weeks of age and was still present in 52-week-old mice. Deletion ofTsc2in β cells induced expansion of β cell mass by increased proliferation and cell size. Rapamycin treatment reversed the metabolic changes in βTsc2−/−mice by induction of insulin resistance and reduction of β cell mass. The reduction of β cell mass in βTsc2−/−mice by inhibition of the mTOR/Raptor (TORC1) complex with rapamycin treatment suggests that TORC1 mediates proliferative and growth signals induced by deletion ofTsc2in β cells. These studies uncover a critical role for the Tsc2/mTOR pathway in regulation of β cell mass and carbohydrate metabolismin vivo.
Integrins α1β1 and α2β1 are receptors for the rotavirus enterotoxin
Authors: Seo Neung-Seon , Zeng Carl Q.-Y. , Hyser Joseph M. , Utama Budi , Crawford Sue E. , Kim Kate J. , Höök Magnus , Estes Mary K.
Published: June 2008

Rotavirus NSP4 is a viral enterotoxin capable of causing diarrhea in neonatal mice. This process is initiated by the binding of extracellular NSP4 to target molecule(s) on the cell surface that triggers a signaling cascade leading to diarrhea. We now report that the integrins α1β1 and α2β1 are receptors for NSP4. NSP4 specifically binds to the α1 and α2 I domains with apparent
K
d
= 1–2.7 μM. Binding is mediated by the I domain metal ion-dependent adhesion site motif, requires Mg
2+
or Mn
2+
, is abolished with EDTA, and an NSP4 point mutant, E
120
A, fails to bind α2 integrin I domain. NSP4 has two distinct integrin interaction domains. NSP4 amino acids 114–130 are essential for binding to the I domain, and NSP4 peptide 114–135 blocks binding of the natural ligand, collagen I, to integrin α2. NSP4 amino acids 131–140 are not associated with the initial binding to the I domain, but elicit signaling that leads to the spreading of attached C2C12-α2 cells, mouse myoblast cells stably expressing the human α2 integrin. NSP4 colocalizes with integrin α2 on the basolateral surface of rotavirus-infected polarized intestinal epithelial (Caco-2) cells as well as surrounding noninfected cells. NSP4 mutants that fail to bind or signal through integrin α2 were attenuated in diarrhea induction in neonatal mice. These results indicate that NSP4 interaction with integrin α1 and α2 is an important component of enterotoxin function and rotavirus pathogenesis, further distinguishing this viral virulence factor from other microbial enterotoxins.
Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import
Authors: Rubio Mary Anne T. , Rinehart Jesse J. , Krett Bethany , Duvezin-Caubet Stéphane , Reichert Andreas S. , Söll Dieter , Alfonzo Juan D.
Published: June 2008

Mitochondrial genomes generally encode a minimal set of tRNAs necessary for protein synthesis. However, a number of eukaryotes import tRNAs from the cytoplasm into their mitochondria. For instance,
Saccharomyces cerevisiae
imports cytoplasmic tRNA
Gln
into the mitochondrion without any added protein factors. Here, we examine the existence of a similar active tRNA import system in mammalian mitochondria. We have used subcellular RNA fractions from rat liver and human cells to perform RT-PCR with oligonucleotide primers specific for nucleus-encoded tRNA
CUG
Gln
and tRNA
UUG
Gln
species, and we show that these tRNAs are present in rat and human mitochondria
in vivo
. Import of
in vitro
transcribed tRNAs, but not of heterologous RNAs, into isolated mitochondria also demonstrates that this process is tRNA-specific and does not require the addition of cytosolic factors. Although this
in vitro
system requires ATP, it is resistant to inhibitors of the mitochondrial electrochemical gradient, a key component of protein import. tRNA
Gln
import into mammalian mitochondria proceeds by a mechanism distinct from protein import. We also show that both tRNA
Gln
species and a bacterial pre-tRNA
Asp
can be imported
in vitro
into mitochondria isolated from myoclonic epilepsy with ragged-red fiber cells if provided with sufficient ATP (2 mM). This work suggests that tRNA import is more widespread than previously thought and may be a universal trait of mitochondria. Mutations in mitochondrial tRNA genes have been associated with human disease; the tRNA import system described here could possibly be exploited for the manipulation of defective mitochondria.
Sexual assault centers: Attendance rates, and differences between early and late presenting cases
Authors: NESVOLD HELLE , FRIIS SVEIN , ORMSTAD KARI
Published: June 2008

Objective. Sexual assault centers (SACs) aim at assisting victims and to provide forensic medical examination (FME). This study explores the gap between assaults actually occurring and those seen at SAC; and the characteristics of cases presented in time/too late for FME (early and late cohorts). Design. Retrograde descriptive study. Setting and sample. A two‐year series from a self‐referral SAC; characteristics of victims, assaults, use of services. Methods. Chi‐quadrate, uni‐ and multivariate logistic regression analyses. Main outcome measures. Number of female victims seen/female at‐risk population (attendance rates). Case and service profiles in the two cohorts. Adjusted odds for late presentation. Results. Attendance rates for females were 0.12% (14–55 years); an estimated 4–7% of sexually assaulted females in the catchment area. Two hundred and seventy eight victims arrived in time for FME, 76 later; 6% males. Assaults in the early cohort were more often performed by strangers. Two hundred and thirty‐eight victims underwent FME, 55% complied with follow‐up, 55% reported to the police. The late cohort contained more adolescent victims, more acquainted/partner perpetrators, more verbal coercion; 45% medically examined, 80% follow‐up compliance; 34% reported to police. Further referrals occurred equally often in both cohorts; 12% to somatic and 39% to psychiatric services. Among victims seen, 5% died within 7 years of consultation. Conclusion. Cases seen at SAC are strongly selected. The late cohort seems more representative of the commonly occurring assaults; young victims, known assailants. Even late presenters are in need of a multidisciplinary approach.
FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space
Authors: Chen Xiang , He Si-Min , Bu Dongbo , Zhang Fa , Wang Zhiyong , Chen Runsheng , Gao Wen
Published: June 2008

Motivation: RNA secondary structures with pseudoknots are often predicted by minimizing free energy, which is proved to be NP-hard. Due to kinetic reasons the real RNA secondary structure often has local instead of global minimum free energy. This implies that we may improve the performance of RNA secondary structure prediction by taking kinetics into account and minimize free energy in a local area.

Result: we propose a novel algorithm named FlexStem to predict RNA secondary structures with pseudoknots. Still based on MFE criterion, FlexStem adopts comprehensive energy models that allow complex pseudoknots. Unlike classical thermodynamic methods, our approach aims to simulate the RNA folding process by successive addition of maximal stems, reducing the search space while maintaining or even improving the prediction accuracy. This reduced space is constructed by our maximal stem strategy and stem-adding rule induced from elaborate statistical experiments on real RNA secondary structures. The strategy and the rule also reflect the folding characteristic of RNA from a new angle and help compensate for the deficiency of merely relying on MFE in RNA structure prediction. We validate FlexStem by applying it to tRNAs, 5SrRNAs and a large number of pseudoknotted structures and compare it with the well-known algorithms such as RNAfold, PKNOTS, PknotsRG, HotKnots and ILM according to their overall sensitivities and specificities, as well as positive and negative controls on pseudoknots. The results show that FlexStem significantly increases the prediction accuracy through its local search strategy.

Availability: Software is available at http://pfind.ict.ac.cn/FlexStem/

Contact:  xchen@jdl.ac.cn; wgao@pku.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors
Authors: Liu Jiajian , Stormo Gary D.
Published: June 2008

Motivation: Modeling and identifying the DNA-protein recognition code is one of the most challenging problems in computational biology. Several quantitative methods have been developed to model DNA-protein interactions with specific focus on the C2H2 zinc-finger proteins, the largest transcription factor family in eukaryotic genomes. In many cases, they performed well. But the overall the predictive accuracy of these methods is still limited. One of the major reasons is all these methods used weight matrix models to represent DNA-protein interactions, assuming all base-amino acid contacts contribute independently to the total free energy of binding.

Results: We present a context-dependent model for DNA–zinc-finger protein interactions that allows us to identify inter-positional dependencies in the DNA recognition code for C2H2 zinc-finger proteins. The degree of non-independence was detected by comparing the linear perceptron model with the non-linear neural net (NN) model for their predictions of DNA–zinc-finger protein interactions. This dependency is supported by the complex base-amino acid contacts observed in DNA–zinc-finger interactions from structural analyses. Using extensive published qualitative and quantitative experimental data, we demonstrated that the context-dependent model developed in this study can significantly improves predictions of DNA binding profiles and free energies of binding for both individual zinc fingers and proteins with multiple zinc fingers when comparing to previous positional-independent models. This approach can be extended to other protein families with complex base-amino acid residue interactions that would help to further understand the transcriptional regulation in eukaryotic genomes.

Availability:The software implemented as c programs and are available by request. http://ural.wustl.edu/softwares.html

Contact:  stormo@ural.wustl.edu
Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data
Authors: Li Huai , Zhan Ming
Published: June 2008

Motivation: Unraveling the transcriptional regulatory program mediated by transcription factors (TFs) is a fundamental objective of computational biology, yet still remains a challenge.

Method: Here, we present a new methodology that integrates microarray and TF binding data for unraveling transcriptional regulatory networks. The algorithm is based on a two-stage constrained matrix decomposition model. The model takes into account the non-linear structure in gene expression data, particularly in the TF-target gene interactions and the combinatorial nature of gene regulation by TFs. The gene expression profile is modeled as a linear weighted combination of the activity profiles of a set of TFs. The TF activity profiles are deduced from the expression levels of TF target genes, instead directly from TFs themselves. The TF-target gene relationships are derived from ChIP-chip and other TF binding data. The proposed algorithm can not only identify transcriptional modules, but also reveal regulatory programs of which TFs control which target genes in which specific ways (either activating or inhibiting).

Results: In comparison with other methods, our algorithm identifies biologically more meaningful transcriptional modules relating to specific TFs. We applied the new algorithm on yeast cell cycle and stress response data. While known transcriptional regulations were confirmed, novel TF-gene interactions were predicted and provide new insights into the regulatory mechanisms of the cell.

Contact:  zhanmi@mail.nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
Antidiabetic Indian Plants: A Good Source of Potent Amylase Inhibitors
Authors: Bhat Menakshi , Zinjarde Smita S. , Bhargava Shobha Y. , Kumar Ameeta Ravi , Joshi Bimba N.
Published: June 2008

Diabetes is known as a multifactorial disease. The treatment of diabetes (Type II) is complicated due to the inherent patho‐physiological factors related to this disease. One of the complications of diabetes is post‐prandial hyperglycemia (PPHG). Glucosidase inhibitors, particularly α‐amylase inhibitors are a class of compounds that helps in managing PPHG. Six ethno‐botanically known plants having antidiabetic property namely, Azadirachta indica Adr. Juss.; Murraya koenigii (L.) Sprengel; Ocimum tenuflorum (L.) (syn: Sanctum); Syzygium cumini (L.) Skeels (syn: Eugenia jambolana); Linum usitatissimum (L.) and Bougainvillea spectabilis were tested for their ability to inhibit glucosidase activity. The chloroform, methanol and aqueous extracts were prepared sequentially from either leaves or seeds of these plants. It was observed that the chloroform extract of O. tenuflorum; B. spectabilis; M. koenigii and S. cumini have significant α‐amylase inhibitory property. Plants extracts were further tested against murine pancreatic, liver and small intestinal crude enzyme preparations for glucosidase inhibitory activity. The three extracts of O. tenuflorum and chloroform extract of M. koenigi showed good inhibition of murine pancreatic and intestinal glucosidases as compared with acarbose, a known glucosidase inhibitor.
The distribution of chondrichthyans along the northern coast of Norway
Authors: Williams Tom , Helle Kristin , Aschan Michaela
Published: June 2008

Williams, T., Helle, K., and Aschan, M. 2008. The distribution of chondrichthyans along the northern coast of Norway. – ICES Journal of Marine Science, 65: 1161–1174. The relationship between temperature, latitude, and depth and the distribution and relative abundance of chondrichthyans along the northern coast of Norway was examined based on catches made in scientific trawls north of 62°N from 1992 to 2005. It appears that Chimaera monstrosa, Etmopterus spinax, Squalus acanthias, and Galeus melastomus were more abundant in the south, and Amblyraja radiata more common in the north. Between 1992 and 2005, the distribution and relative abundance did not appear to change significantly, although average water temperatures rose during the period. Current fishing levels do not appear to be impacting the populations of the more common species, but the status of species rarely found in the survey catches is unclear.
Antagonistic Interaction between Systemic Acquired Resistance and the Abscisic Acid–Mediated Abiotic Stress Response in Arabidopsis
Authors: Yasuda Michiko , Ishikawa Atsushi , Jikumaru Yusuke , Seki Motoaki , Umezawa Taishi , Asami Tadao , Maruyama-Nakashita Akiko , Kudo Toshiaki , Shinozaki Kazuo , Yoshida Shigeo , Nakashita Hideo
Published: June 2008

Systemic acquired resistance (SAR) is a potent innate immunity system in plants that is effective against a broad range of pathogens. SAR development in dicotyledonous plants, such as tobacco (Nicotiana tabacum) and Arabidopsis thaliana, is mediated by salicylic acid (SA). Here, using two types of SAR-inducing chemicals, 1,2-benzisothiazol-3(2H)-one1,1-dioxide and benzo(1,2,3)thiadiazole-7-carbothioic acid S-methyl ester, which act upstream and downstream of SA in the SAR signaling pathway, respectively, we show that treatment with abscisic acid (ABA) suppresses the induction of SAR in Arabidopsis. In an analysis using several mutants in combination with these chemicals, treatment with ABA suppressed SAR induction by inhibiting the pathway both upstream and downstream of SA, independently of the jasmonic acid/ethylene-mediated signaling pathway. Suppression of SAR induction by the NaCl-activated environmental stress response proved to be ABA dependent. Conversely, the activation of SAR suppressed the expression of ABA biosynthesis–related and ABA-responsive genes, in which the NPR1 protein or signaling downstream of NPR1 appears to contribute. Therefore, our data have revealed that antagonistic crosstalk occurs at multiple steps between the SA-mediated signaling of SAR induction and the ABA-mediated signaling of environmental stress responses.