bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design
Authors: Fazio Alessandro , Jewett Michael C , Daran-Lapujade Pascale , Mustacchi Roberta , Usaite Renata , Pronk Jack T , Workman Christopher T , Nielsen Jens 
Published: July 2008

AbstractBackgroundCharacterization of cellular growth is central to understanding living systems. Here, we applied a three-factor design to study the relationship between specific growth rate and genome-wide gene expression in 36 steady-state chemostat cultures ofSaccharomyces cerevisiae. The three factors we considered were specific growth rate, nutrient limitation, and oxygen availability.ResultsWe identified 268 growth rate dependent genes, independent of nutrient limitation and oxygen availability. The transcriptional response was used to identify key areas in metabolism around which mRNA expression changes are significantly associated. Among key metabolic pathways, this analysis revealedde novosynthesis of pyrimidine ribonucleotides and ATP producing and consuming reactions at fast cellular growth. By scoring the significance of overlap between growth rate dependent genes and known transcription factor target sets, transcription factors that coordinate balanced growth were also identified. Our analysis shows that Fhl1, Rap1, and Sfp1, regulating protein biosynthesis, have significantly enriched target sets for genes up-regulated with increasing growth rate. Cell cycle regulators, such as Ace2 and Swi6, and stress response regulators, such as Yap1, were also shown to have significantly enriched target sets.ConclusionOur work, which is the first genome-wide gene expression study to investigate specific growth rate and consider the impact of oxygen availability, provides a more conservative estimate of growth rate dependent genes than previously reported. We also provide a global view of how a small set of transcription factors, 13 in total, contribute to control of cellular growth rate. We anticipate that multi-factorial designs will play an increasing role in elucidating cellular regulation.
Composition and structure of the parasite faunas of cod, Gadus morhua L. (Teleostei: Gadidae), in the North East Atlantic
Authors: Perdiguero-Alonso Diana , Montero Francisco E , Raga Juan Antonio , Kostadinova Aneta 
Published: July 2008

AbstractBackgroundAlthough numerous studies on parasites of the Atlantic cod,Gadus morhuaL. have been conducted in the North Atlantic, comparative analyses on local cod parasite faunas are virtually lacking. The present study is based on examination of large samples of cod from six geographical areas of the North East Atlantic which yielded abundant baseline data on parasite distribution and abundance.Materials and MethodsA total of 826 fish was sampled in the Baltic, Celtic, Irish and North seas, Icelandic waters and Trondheimsfjord (Norway) in 2002 (spring and autumn) and 2003 (spring). The gills and internal organs (oesophagus, stomach, intestine, pyloric caeca, liver, heart, spleen, gall bladder and gonads) were examined for macroparasites following a standardised protocol. The taxonomic consistency of the identification was ensured thorough the entire study.ResultsWe discuss some problems in parasite identification, outline the composition of the parasite faunas in cod in the six North East Atlantic regions, provide novel data on parasite prevalence and abundance and a comparative assessment of the structure of the regional parasite faunas with respect to the higher-level taxonomic groupings, host specificity and zoogeographical distribution of the parasites. Altogether 57 different parasite forms were found including seven new host records (Diclidophora merlangi,Rhipidocotylesp.,Fellodistomumsp.,Steringotremasp.,Cucullanussp.,Spinitectussp., andChondracanthus ornatus). The predominant groups of cod parasites were trematodes (19 species) and nematodes (13 species) including larval anisakids which comprised 58.2% of the total number of individuals.ConclusionOur study reveals relatively rich regional parasite faunas in cod from the North East Atlantic which are dominated by generalist parasites with Arcto-Boreal distribution. Further, it provides more detailed data on the distribution in the North East Atlantic of the majority of cod parasites which may serve as baselines for future studies on the effect of climate change. Based on the faunal comparisons, predictions can be made in relation to the structure and diversity of the parasite communities in the North East Atlantic regions studied.
Chromosomal Rearrangements and Novel Genes in Disorders of Eye Development, Cataract and Glaucoma
Authors: Mihelec Marija , St Heaps Luke , Flaherty Maree , Billson Frank , Rudduck Christina , Tam Patrick P. L. , Grigg John R. , Peters Greg B. , Jamieson Robyn V. 
Published: July 2008

AbstractDisorders of eye development such as microphthalmia and anophthalmia (small and absent eyes respectively), anterior segment dysgenesis where there may be pupillary and iris anomalies, and associated cataract and glaucoma, often lead to visual impairment or blindness. Currently treatment options are limited, as much is unknown about the molecular pathways that control normal eye development and induce the aberrant processes that lead to ocular defects. Mutation detection rates in most of the known genes are generally low, emphasizing the genetic heterogeneity of developmental ocular defects. Identification of the disease genes in these conditions improves the clinical information available for affected individuals and families, and provides new insights into the underlying biological processes for facilitation of better treatment options. Investigation of chromosomal rearrangements associated with an ocular phenotype has been especially powerful for disease gene identification. Molecular characterization of such rearrangements, which pinpoints the region by physically disrupting the causative gene or its regulatory sequences, allows for rapid elucidation of underlying genetic factors that contribute to the phenotype. Genes includingPAX6, PITX2, FOXC1, MAF, TMEM114, SOX2, OTX2andBMP4have been identified in this way to be associated with developmental eye disorders. More recently, new methods in chromosomal analysis such as comparative genomic hybridization (CGH) microarray, have also enhanced our ability in disease gene identification.
Complications in a contemporary series of patients who underwent transsphenoidal surgery for Cushing's disease
Authors: Semple Patrick L. , Laws Edward R. 
Published: July 2008

Object
Transsphenoidal surgery is the usual treatment of choice for adrenocorticotropic hormone-secreting pituitary adenomas associated with Cushing's disease. In this paper the authors investigate the complications of transsphenoidal surgery in the treatment of a contemporary series of patients with Cushing's disease.

Methods
Between January 1992 and December 1997, 105 patients with Cushing's disease underwent transsphenoidal surgery at the University of Virginia Health Sciences Center. A retrospective analysis of the complications was conducted, and the mortality rate was found to be 0.9% and permanent morbidity was 1.8%. The overall number of complications was 14 (13.3%), which included seven complications directly related to surgery; one instance of permanent diabetes insipidus; one syndrome of inappropriate secretion of antidiuretic hormone; and five medical complications (four patients developed deep vein thrombosis and one developed pneumonia).

Conclusions
Transsphenoidal surgery for Cushing's disease has a higher complication rate than that for pituitary adenomas in general. This is primarily related to a greater number of medical complications, most notably deep vein thrombosis, resulting from the generally debilitated state of most patients with Cushing's disease. In view of the high incidence of deep vein thrombosis in these patients, prophylaxis for thromboembolism during the perioperative period is recommended.
The dysmorphic cervical spine in Klippel-Feil syndrome: interpretations from developmental biology
Authors: David Karoly M. , Thorogood Peter V. , Stevens John M. , Crockard H. Alan 
Published: July 2008

The authors conducted a study to identify radiological patterns of Klippel-Feil syndrome (KFS), and they present a new interpretation of the origin of these patterns based on recent advances in understanding of embryonic development of the spine and its molecular genetic control.
The authors studied radiographs and computerized tomography (CT) scans as well as magnetic resonance images or CT myelograms obtained in 30 patients with KFS who were referred for treatment between 1982 and 1996; the patients had complained of various neuroorthopedic complications. Homeotic transformation due to mutations or disturbed expression of Hox genes is a possible mechanism responsible for C-1 assimilation, which was found to have occurred in 19 cases (63%). Notochordal defects and/or signaling problems, which result in reduced or impaired Pax-1 gene expression, may underlie vertebral fusions. This, together with asymmetrical distribution of paraxial mesoderm cells and a possible lack of communication across the embryonic midline, could cause asymmetrical fusion patterns, which were present in 17 cases (57%). The wide and flattened shape of the fused vertebral bodies and their resemblance to the embryonic cartilaginous vertebrae as well as the process of progressive bone fusion with age suggest that the fusions occur before or, at the latest, during chondrification of vertebrae.
The authors suggest that the aforementioned mechanisms are likely to be, at least in part, responsible for the observed patterns in KFS that affect the craniovertebral junction and the cervical spine.
Pathogenesis, dynamics, and management of os odontoideum
Authors: Menezes Arnold H. 
Published: July 2008

Os odontoideum is an uncommon craniovertebral junction (CVJ) abnormality that exists as a separate ossicle apart from a hypoplastic dens. It usually moves with the clivus or the anterior arch of C-1 (dystopic) or rarely with the dens (orthotopic). Its genesis and natural history have been debated, and its proper treatment remains uncertain.
Two hundred and sixty patients, with symptomatic os odontoideum, were evaluated by the author over a 20-year period; the author performed surgery in 134 of these patients. In a prospective study the author evaluated the early childhood history of trauma, the dynamic studies of motion, and the effects of traction by using pleuridirectional tomography, computerized tomography (CT), CT myelography and magnetic resonance (MR) imaging. Operative findings were documented.
Early childhood trauma to the CVJ was recorded in 74 patients, in 30 of whom normal odontoid processes were documented at initial examination prior to the patient reaching age 4 years.
Acute neurological deterioration following trauma occurred in 63 of 134 patients. Symptoms were insidious in 71 of 134 patients. In six patients, who presented with acute neurological deterioration after trauma and in whom an abnormal spinal cord signal in the cervicomedullary junction was demonstrated on MR imaging, normal CVJ motion dynamics were shown. Motion dynamics varied and were unique to each patient. Irreducible ventral CVJ disease causing cervicomedullary compromise occurred in 28 patients in whom a transpharyngeal ventral decompressive procedure was necessitated. During the transoral operation, the transverse portion of the cruciate ligament was found to be located anterior to the axis body. All patients required dorsal CVJ arthrodesis, which, in 46, was limited to the C1-2 segment. Instability at the C1-2 joints was always multidirectional, as demonstrated on preoperative neuroimaging studies as well as at operation.
Sixteen patients presented after completed primary C1-2 dorsal fusion and with worsening deficits. They improved when the range of the fusion was extended to the occiput or if the ventrally located lesion was excised.
Os odontoideum is associated with early childhood trauma and is an acquired phenomenon. The presence of abnormal motion dynamics necessitates surgical intervention as do associated neurological deficits. Asymptomatic patients in whom os odontoideum is incidentally discovered and in whom no abnormal motion dynamics are demonstrated should be followed closely.
Comprehensive approach to Chiari malformation in pediatric patients
Authors: Greenlee Jeremy , Garell P. Charles , Stence Nicholas , Menezes Arnold H. 
Published: July 2008

Chiari malformation is a developmental disorder that is often associated with other abnormalities of the cerebrospinal axis. Despite widespread recognition of this association, there is relatively little information on the treatment of these coexisting disorders in the setting of cerebellar tonsillar ectopia. In an effort to improve the care provided to pediatric patients with Chiari malformations the authors reviewed their management practices over the last 20 years. Specifically, they recorded presenting symptoms, radiological studies, comorbidities, and management (surgical and nonsurgical) of 112 patients (all < 20 years of age) with Chiari malformation without myelodysplasia.
They found an associated syrinx in 29% of patients, basilar invagination in 17%, and scoliosis in 14%. The basal angle varied from 120 to 190° and Boogard's angle varied from 120 to 220°; both angles were larger than those measured in normal controls. The vertical height of the posterior fossa was shortened and the volume decreased as compared with normal controls.
The surgical management of this group of patients included posterior decompressive (44%), combined transoral and posterior decompressive (31%), combined posterior decompressive and posterior fusion (8%), and multiple posterior decompressive procedures in the same patient (5%).
The authors conclude that pediatric patients with a Chiari malformation should be specifically examined for evidence of additional craniovertebral malformations so that procedures are directed at correcting both the comorbidities and the herniation of the cerebellar tonsils through the foramen magnum.
The anatomical suitability of C1-2 transarticular screw placement in pediatric patients
Authors: Brockmeyer Douglas L. , York Julie E. , Apfelbaum Ronald I. 
Published: July 2008

Craniovertebral instability is a challenging problem in pediatric spinal surgery. Recently, C1-2 transarticular screw fixation in pediatric patients has been used to assist in the stabilization of the craniovertebral joint. Currently there are no data that define the anatomical suitability of this technique in the pediatric population. The authors report their experience in 32 pediatric patients in whom craniovertebral instability was treated by placement of C1-2 transarticular screws.
From March 1991 to October 1998, 32 patients 16 years of age or younger with atlantooccipital, or atlantoaxial instability, or both were evaluated at our institution. There were 22 boys and 10 girls. Their ages ranged from 4 to 16 years (mean age 10.2 years). The most common causes of instability were os odontoideum (12 patients) and ligamentous laxity (nine patients). Six patients had undergone a total of nine previous attempts at posterior fusion at outside institutions.
All patients underwent extensive preoperative radiological evaluation including thin cut (1-mm) computerized tomography scanning with multiplanar reconstruction to evaluate the C1-2 joint space anatomy. Of the 64 possible C1-2 joint spaces in 32 patients, 55 sides (86%) were considered suitable for transarticular screw placement preoperatively. In three patients the C1-2 joint space anatomy was considered unsuitable for screw placement bilaterally. In three patients the anatomy was considered inadequate on one side. Fifty-five C1-2 transarticular screws were subsequently placed, with no resulting neurological or vascular complications. We conclude that C1-2 transarticular screw fixation is technically possible in a large proportion of pediatric patients with craniovertebral instability.
Cranial cruciate ligament repair in dogs with and without meniscal lesions treated by different minimally invasive methods
Authors: Fehr M. , Ertelt J. 
Published: July 2008

SummaryThe goal of this study was to evaluate different minimally invasive surgical options as therapy for cranial cruciate ligament rupture and resulting meniscal injuries. In this study, 81 stifle joints of dogs with complete or partial rupture of the cranial cruciate ligament were treated with minimally invasive surgery at the Small Animal Clinic of the University of Veterinary Medicine in Hannover. The patients were divided into three groups depending on intraoperative diagnosis and the surgical technique applied. The dogs in group I (n = 26) had an isolated rupture of the cranial cruciate ligament (CCLR), while those in groups II (n = 26) and III (n = 29) also had an injury of the medial meniscus. Re-section of the damaged meniscal part was performed by arthroscopically guided partial meniscectomy (AGPM) on the dogs in group II, while minimally invasive medial arthrotomy (MIMA) was used on the dogs of group III. All of the stifles were stabilized with a modified lateral imbrication technique using a braided, synthetic, absorbable suture material (Panacryl®). Six months after surgery 76.5% of all patients were examined clinically and 74.1% radiographically for evaluation of the success of the different treatment techniques. At this examination, there were no signs of lameness in 42.1% of group I (CCLR), 65.0% of group II (AGPM) and 87.0% of group III (MIMA). Upon palpation, 75.8% of these stifle joints were found to be stable. Radiographic evaluations did not show any indication of progression of gonarthrosis in 73.3% of all stifle joints examined here.
A Sequential Assignment Procedure for Proteins that have Intermediate Line Widths in MAS NMR Spectra: Amyloid Fibrils of Human CA150.WW2
Authors: Becker Johanna , Ferguson Neil , Flinders Jeremy , van Rossum Barth‐Jan , Fersht Alan R. , Oschkinat Hartmut 
Published: July 2008

AbstractThe second WW domain (WW2) of CA150, a human transcriptional activator, forms amyloid fibrils in vitro under physiological conditions. Based on experimental constraints from MAS NMR spectroscopy experiments, alanine scanning and electron microscopy, a structural model of CA150.WW2 amyloid fibrils was calculated earlier. Here, the assignment strategy is presented and suggested as a general approach for proteins that show intermediate line width. The 13C,13C correlation experiments were recorded on fully or partially 13C‐labelled fibrils. The earlier 13C assignment (26 residues) was extended to 34 of the 40 residues by direct 13C‐excitation experiments by using a deuterated sample that showed strongly improved line width. A 3D HNC‐TEDOR (transferred‐echo double‐resonance) experiment with deuterated CA150.WW2 fibrils yielded 14 amide nitrogen and proton resonance assignments. The obtained chemical shifts were compared with the chemical shifts determined with the natively folded WW domain. TALOS (Torsion angle likelihood obtained from shift and sequence similarity) predictions confirmed that, under physiological conditions, the fibrillar form of CA150.WW2 adopts a significantly different β structure than the native WW‐domain fold.
A New Catalytic Route to Boryl‐ and Borylsilyl‐Substituted Buta‐1,3‐dienes
Authors: Walkowiak Jȩdrzej , Jankowska‐Wajda Magdalena , Marciniec Bogdan 
Published: July 2008

AbstractVinyl‐substituted boronates in the presence of complexes containing RuH bonds (preferably [Ru(CO)ClH(PCy3)2], Cy: cyclohexyl) react regioselectively with terminal ethynes (involving silylethynes), albeit with the exception of phenylacetylene, to produce boryl‐ and borylsilyl‐substituted buta‐1,3‐dienes with a preference for E,E‐diene. The reaction opens a new catalytic route for the preparation of dienylboronates, and particularly dienylsilylboronates, that are functionalised building blocks in the synthesis of organic and natural products. The mechanism of this new reaction was proved to involve an insertion of alkyne into RuH bonds followed by an insertion of coordinated vinyl boronate into the RuC bond and β‐hydrogen transfer to the metal to eliminate boryldiene or borylsilyldiene.
Aptamers and molecularly imprinted polymers as artificial biomimetic receptors in affinity capillary electrophoresis and electrochromatography
Authors: Giovannoli Cristina , Baggiani Claudio , Anfossi Laura , Giraudi Gianfranco 
Published: July 2008

AbstractArtificial biomimetic receptors, such as aptamers and molecular‐imprinted polymers, show antibody‐like properties which are due to molecular recognition phenomena characterized by high affinity and selectivity. These binding features have made them suitable in all those application fields in which selective recognition is required. Thus, it is not surprising that they are finding applications in affinity CE as well. Recently, a variety of ACE methods have shown themselves to be suitable tools to provide a detailed quantitative characterization of the thermodynamic and kinetic aspects of binding. At the same time, affinity CE can exploit the peculiarities of these binding interactions to set up CE‐based analytical tools for the separation and the determination of specific target molecules in microscale formats. This review will provide a detailed description of affinity CE methods recently reported in the literature and related to these topics.
Clinical evaluation of a membrane‐based voice‐producing element for laryngectomized women
Authors: Tack Johannes W. , Qiu Qingjun , Schutte Harm K. , Kooijman Piet G. C. , Meeuwis Cees A. , van der Houwen Eduard B. , Mahieu Hans F. , Verkerke Gijsbertus J. 
Published: July 2008

AbstractBackground.A newly developed artificial voice source was clinically evaluated in laryngectomized women for voice quality improvements. The prosthesis was placed in a commercially available, tracheoesophageal shunt valve.Methods.In 17 subjects, voice‐producing element (VPE) prototypes were compared with the subject's regular tracheo‐esophageal shunt voice in a randomized cross‐over trial. The evaluation was based on aeroacoustic measurements and perceptual analysis.Results.Considerably higher fundamental frequencies were attained with the use of the VPE. The sound pressure level also increased for most subjects. The required driving pressures of the lung and air flow rates were altered, allowing significantly longer phonation times in 1 breath. Accumulation of mucus did not interfere with the proper functioning of the device during these tests.Conclusion.A VPE with sound‐generating membranes is suitable for providing a substitute voice source for laryngectomized patients, especially patients suggestive of a severely hypotonic or atonic pharyngoesophageal segment who can benefit from a more melodious and louder voice. © 2008 Wiley Periodicals, Inc. Head Neck 2008