bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of three mydriatic drug regimens on pupil size in rhesus (Macaca mulatta) and African green monkeys (Chlorocebus aethiops)
Authors: Merrill N.L. , Burge R. 
Published: July 2006

AbstractBackground  Human mydriatric drug use in non‐human primates (NHPs) has been documented but not quantified and compared for effectiveness. The objective of this study was to determine which drug regimen provided the most effective and consistent mydriatic effect for ophthalmologic examinations and other procedures. Secondary objectives were to determine average time to maximum dilation and whether species differences existed.Methods  Twelve rhesus and 12 African green monkeys were randomly assigned to one of six treatment combinations to test the mydriatic effects of three drug regimens: (1) tropicamide 1% (T); (2) tropicamide 1% and phenylephrine hydrochloride 2.5% (TP); and (3) tropicamide 1%, phenylephrine HCL 2.5% and cyclopentolate 1% (TPC). Left and right eyes of each monkey received a different drug regimen, depending on random assignment.Results  TPC showed a significantly larger mydriatic response in both species than T alone. Average time to maximum dilation with all three drug regimens was 50–60 minutes. Rhesus had a larger response to the mydriatic drug regimens than the African green monkeys.Conclusions  The TPC regimen had the largest and longest lasting mydriatic effect in both species.
Initiation of antiretroviral therapy during chronic SIV infection leads to rapid reduction in viral loads and the level of T‐cell immune response
Authors: Boyer Jean D. , Kumar Sanjeev , Robinson Tara , Parkinson Rose , Wu Ling , Lewis Mark , Watkins David I. , Weiner David B. 
Published: July 2006

AbstractIn the present era of increasing resistance of human immunodeficiency virus (HIV) to antiviral drugs, exploration of adjunct therapies directed at immune responses in combination with antiretroviral drugs may be of value for the treatment of acquired immunodeficiency syndrome. In this study, we designed a model for immune therapy using SIVmac251 infection in rhesus macaques. We explored the outcomes of primary infection on viral loads and the resulting T‐cell immune responses in primates. The SIV‐infected rhesus macaque model exhibited features similar to those observed in HIV‐1 infection of humans. Major histocompatibility complex (MHC) segregation with viral loads were found to associate with viral containment and hence the duration of the disease‐free latency period. Thus a better understanding of the relative roles of MHC class I allele in control of viral replication may provide important information for prophylactic or therapeutic vaccine designs. Mamu‐A01 is significantly associated with higher immune response and control of viral replication. This allele is frequent in rhesus macaques of Indian origin (22%). Interestingly, Mamu‐B01 (26% animals) was associated with lower immune responses and higher viral loads. Another allele, A08 was also predominantly present in 37% of the animals in this study. We observed higher viral replication in individual SIV‐infected rhesus monkeys that did not demonstrate strong cellular immune responses. The results are important for understanding SIV disease progression in different MHC Mamu alleles and also for improving the interpretation and quality of pre‐clinical studies in rhesus monkeys.
Gene expression profiling of gut mucosa and mesenteric lymph nodes in simian immunodeficiency virus‐infected macaques with divergent disease course
Authors: George M.D. , Verhoeven D. , McBride Z. , Dandekar S. 
Published: July 2006

AbstractBackground  Although the majority of drug‐naïve HIV‐infected patients develop acquired immunodeficiency syndrome (AIDS), a small percentage remains asymptomatic without therapeutic intervention.Methods  We have utilized the simian immunodeficiency virus (SIV)‐infected rhesus macaque model to gain insights into the molecular mechanisms of long‐term protection against simian AIDS.Results  Chronically SIV‐infected macaques with disease progression had high viral loads and CD4+ T‐cell depletion in mucosal tissue and peripheral blood. These animals displayed pathologic changes in gut‐associated lymphoid tissue (GALT) and mesenteric lymph node that coincided with increased expression of genes associated with interferon induction, inflammation and immune activation. In contrast, the animal with long‐term asymptomatic infection suppressed viral replication and maintained CD4+ T cells in both GALT and peripheral blood while decreasing expression of genes involved in inflammation and immune activation.Conclusions  Our findings suggest that reduced immune activation and effective repair and regeneration of mucosal tissues correlate with long‐term survival in SIV‐infected macaques.
A COMBINATION OF GLUTAMINASE AND pH CONTROL PREVENTS THE NONENZYMATIC CONVERSION OF l‐GLUTAMINE INTO l‐2‐PYRROLIDINE‐5‐CARBOXYLIC ACID IN FOOD PROCESSING
Authors: YOSHIMUNE KAZUAKI , ABE TAKURO , MORIGUCHI MITSUAKI 
Published: July 2006

ABSTRACT A strategy using Alicyclobacillus F‐62 glutaminase was established to minimize the nonenzymatic production of l‐2‐pyrrolidine‐5‐carboxylic acid (l‐pyroglutamic acid, savorless amino acid) and maximize the enzymatic production of l‐glutamic acid (savorous [umami] amino acid) from l‐glutamine in food‐protein processing. The nonenzymatic production rate of l‐pyroglutamic acid was influenced by pH and temperature, and decreased over a pH range of 4–6 at 30C. Under optimum conditions (30C and pH 5.0), the l‐glutamic and l‐pyroglutamic acids obtained from 1 mM l‐glutamine in the presence of glutaminase from Alicyclobacillus F‐62 were 0.96 and 0.03 mM, respectively. This novel method is useful for the efficient production of l‐glutamic acid during food‐protein processing.
MODELING AND OPTIMIZATION OF OSMOTIC DEHYDRATION OF BANANA FOLLOWED BY AIR DRYING
Authors: OLIVEIRA ISADORA M. , FERNANDES FABIANO A.N. , RODRIGUES SUELI , SOUSA PAULO H.M. , MAIA GERALDO A. , FIGUEIREDO RAIMUNDO W. 
Published: July 2006

ABSTRACT The process of osmotic dehydration followed by air drying was studied, modeled and optimized for the dehydration of bananas, which are an extremely perishable fruit unable to withstand freezing and, as such, need to be dried in order to preserve the fruit for later use. The mathematical model was validated with experimental data and the simulations show how the operating conditions affect the process. Process optimization was performed to obtain the best operating conditions that would reduce the total processing time. The results show the advantage of using moderate to high sucrose concentrations (55–65°Brix) for the osmotic solution, reduced pressure and the use of the osmotic treatment to reduce the total processing time of fruit drying.
CONJUGATE HEAT TRANSFER ASSOCIATED WITH A TURBULENT HOT AIR JET IMPINGING ON A CYLINDRICAL OBJECT
Authors: NITIN N. , GADIRAJU R.P. , KARWE M.V. 
Published: July 2006

ABSTRACT Numerical simulation of flow field and thermal transport processes for a turbulent jet impinging on the surface of a cylindrical object, e.g., hot dog, were carried out at different jet velocities. Numerical predictions for average surface heat transfer coefficient were compared with the experimental results obtained using a lumped mass approach for model aluminum cylinders. Results indicated good agreement between the numerical and experimental results over the range of jet velocities, i.e., 10–40 m/s. Further experiments were carried out with real beef hotdogs to obtain center point temperature–time history during hot air impingement baking process. The experimental data agreed well with the numerical predictions when the impinging jet temperature was below 100C.
THE EFFECT OF FERMENTATION ON CASSAVA STARCH MICROSTRUCTURE
Authors: MARCON M.J.A. , VIEIRA M.A. , SANTOS K. , DE SIMAS K.N. , DIAS DE MELLO CASTANHO AMBONI R. , AMANTE E.R. 
Published: July 2006

ABSTRACT The effect of glucose syrup addition on sour cassava starch fermentation was studied on cassava starch from three locations in Santa Catarina State (Brazil), following four treatments: traditional, 0.10, 0.25 and 0.50% of glucose syrup added to total cassava suspension volume. A glucose syrup concentration of 0.50% contributed to doubling fermentation yield. The objective of this work was to observe the effect of the cassava starch fermentation process on starch granule microstructure, as compared with industrial processing. Micrography was performed using a scanning electron microscope, at 2000× magnification. Fermentations with 0.50% glucose syrup presented the greatest effects on starch granule microstructure.
The Vacuole System Is a Significant Intracellular Pathway for Longitudinal Solute Transport in Basidiomycete Fungi
Authors: Darrah P. R. , Tlalka M. , Ashford A. , Watkinson S. C. , Fricker M. D. 
Published: July 2006

ABSTRACT
Mycelial
fungi have a growth form which is unique among multicellular organisms.
The data presented here suggest that they have developed a unique
solution to internal solute translocation involving a complex, extended
vacuole. In all filamentous fungi examined, this extended vacuole forms
an interconnected network, dynamically linked by tubules, which has
been hypothesized to act as an internal distribution system. We have
tested this hypothesis directly by quantifying solute movement within
the organelle by photobleaching a fluorescent vacuolar marker.
Predictive simulation models were then used to determine the transport
characteristics over extended length scales. This modeling showed that
the vacuolar organelle forms a functionally important, bidirectional
diffusive transport pathway over distances of millimeters to
centimeters. Flux through the pathway is regulated by the dynamic
tubular connections involving homotypic fusion and fission. There is
also a strongly predicted interaction among vacuolar organization,
predicted diffusion transport distances, and the architecture of the
branching colony
margin.
Function of Ammonium Transporter A in the Initiation of Culmination of Development in
Dictyostelium discoideum
Authors: Singleton Charles K. , Kirsten Janet H. , Dinsmore Colin J. 
Published: July 2006

ABSTRACT

The histidine kinase DhkC controls a phosphorelay involved in regulating the slug versus culmination choice during the multicellular developmental program of
Dictyostelium discoideum
. When the relay is active, slug migration is favored due to the activation of a cyclic AMP (cAMP) phosphodiesterase and the resultant lowering of the intracellular and extracellular levels of cAMP. Ammonia signaling represents one input into the DhkC phosphorelay, and previous studies indicated that the ammonium transporter C inhibits the relay in response to low ammonia levels. Evidence is presented that another member of the family of ammonium transporters, AmtA, also regulates the slug/culmination choice. Under standard conditions of development, the wild-type strain requires a transitional period of 2 to 3 h to go from fingers to culminants, with some slugs forming and migrating briefly prior to culmination. In contrast,
amtA
null cells, like cells that lack DhkC, possessed a transitional period of only 1 to 2 h and rarely formed slugs. Disruption of
amtA
in an
amtC
null strain overcame the slugger phenotype of that strain and restored its ability to culminate. Strains lacking AmtA were insensitive to the ability of ammonia to promote and prolong slug migration. These findings lead to the proposal that AmtA functions in ammonia sensing as an activator of the DhkC phosphorelay in response to perceived high ammonia levels.
TFIIA Plays a Role in the Response to Oxidative Stress
Authors: Kraemer Susan M. , Goldstrohm David A. , Berger Ann , Hankey Susan , Rovinsky Sherry A. , Scott Moye-Rowley W. , Stargell Laurie A. 
Published: July 2006

ABSTRACT

To characterize the role of the general transcription factor TFIIA in the regulation of gene expression by RNA polymerase II, we examined the transcriptional profiles of TFIIA mutants of
Saccharomyces cerevisiae
using DNA microarrays. Whole-genome expression profiles were determined for three different mutants with mutations in the gene coding for the small subunit of TFIIA,
TOA2
. Depending on the particular mutant strain, approximately 11 to 27% of the expressed genes exhibit altered message levels. A search for common motifs in the upstream regions of the pool of genes decreased in all three mutants yielded the binding site for Yap1, the transcription factor that regulates the response to oxidative stress. Consistent with a TFIIA-Yap1 connection, the TFIIA mutants are unable to grow under conditions that require the oxidative stress response. Underexpression of Yap1-regulated genes in the TFIIA mutant strains is not the result of decreased expression of Yap1 protein, since immunoblot analysis indicates similar amounts of Yap1 in the wild-type and mutant strains. In addition, intracellular localization studies indicate that both the wild-type and mutant strains localize Yap1 indistinguishably in response to oxidative stress. As such, the decrease in transcription of Yap1-dependent genes in the TFIIA mutant strains appears to reflect a compromised interaction between Yap1 and TFIIA. This hypothesis is supported by the observations that Yap1 and TFIIA interact both in vivo and in vitro. Taken together, these studies demonstrate a dependence of Yap1 on TFIIA function and highlight a new role for TFIIA in the cellular mechanism of defense against reactive oxygen species.
Sequential Processing of a Mitochondrial Tandem Protein: Insights into Protein Import in
Schizosaccharomyces pombe
Authors: Khalimonchuk Oleh , Ott Martin , Funes Soledad , Ostermann Kai , Rödel Gerhard , Herrmann Johannes M. 
Published: July 2006

ABSTRACT

The sequencing of the genome of
Schizosaccharomyces pombe
revealed
the presence of a number of genes encoding tandem proteins, some of
which are mitochondrial components. One of these proteins
(pre-Rsm22-Cox11) consists of a fusion of Rsm22, a component of the
mitochondrial ribosome, and Cox11, a factor required for copper
insertion into cytochrome oxidase. Since in
Saccharomyces
cerevisiae
, Cox11 is physically attached to the mitochondrial
ribosome, it was suggested that the tandem organization of Rsm22-Cox11
is used to covalently tie the mitochondrial ribosome to Cox11 in
S.
pombe
. We report here that pre-Rsm22-Cox11 is matured in two
subsequent processing events. First, the mitochondrial presequence is
removed. At a later stage of the import process, the Rsm22 and Cox11
domains are separated by cleavage of the mitochondrial processing
peptidase at an internal processing site. In vivo data obtained using a
tagged version of pre-Rsm22-Cox11 confirmed the proteolytic separation
of Cox11 from the Rsm22 domain. Hence, the tandem organization of
pre-Rsm22-Cox11 does not give rise to a persistent fusion protein but
rather might be used to increase the import efficiency of Cox11 and/or
to coordinate expression levels of Rsm22 and Cox11 in
S.
pombe
.
A HYBRID GENE TEAM MODEL AND ITS APPLICATION TO GENOME ANALYSIS
Authors: KIM SUN , CHOI JEONG-HYEON , SAPLE AMIT , YANG JIONG 
Published: July 2006

It is well-known that functionally related genes occur in a physically clustered form, especially operons in bacteria. By leveraging on this fact, there has recently been an interesting problem formulation known as gene team model, which searches for a set of genes that co-occur in a pair of closely related genomes. However, many gene teams, even experimentally verified operons, frequently scatter within other genomes. Thus, the gene team model should be refined to reflect this observation.In this paper, we generalized the gene team model, that looks for gene clusters in a physically clustered form, to multiple genome cases with relaxed constraints. We propose a novel hybrid pattern model that combines the set and the sequential pattern models. Our model searches for gene clusters with and/or without physical proximity constraint. This model is implemented and tested with 97 genomes (120 replicons). The result was analyzed to show the usefulness of our model. We also compared the result from our hybrid model to those from the traditional gene team model. We also show that predicted gene teams can be used for various genome analysis: operon prediction, phylogenetic analysis of organisms, contextual sequence analysis and genome annotation. Our program is fast enough to provide a service on the web at . Users can select any combination of 97 genomes to predict gene teams.
SELECTIVE TARGETING OF INDEL-INFERRED DIFFERENCES IN SPATIAL STRUCTURES OF HOMOLOGOUS PROTEINS
Authors: LI YVONNE Y. , JONES STEVEN J. M. , CHERKASOV ARTEM 
Published: July 2006

The eukaryotic pathogen Leishmania donovani possesses a housekeeping protein Elongation-Factor-1α (EF-1α) which has been found to be unexpectedly involved in the pathogen's virulence. Because it is associated with virulence and essential for cell survival, this protein is an attractive choice for drug targeting; however, its sequence is highly similar (> 80% sequence identity) to that of its human homolog, rendering it a risky choice for a drug target.The chief difference between these two proteins has been found to be a 12 amino acid sequence present in human EF-1α but absent from leishmania EF-1α. Furthermore, it has been shown that this 12 amino acid insert in the human sequence corresponds to a hairpin loop on the surface of the protein. In this study, we searched for those spatial features in leishmania EF-1α that are impacted or obscured by the extra hairpin loop in the human counterpart.We have also conducted a large-scale in silico screening for small molecules that could plausibly bind to these protein features. While experimental evidence is required to verify our results, our findings thus far appear to support this approach as a new strategy for the development of antagonists against pathogenic targets having close human homologs.
A Multiplex Tissue Immunoblotting Assay for Proteomic Profiling: A Pilot Study of the Normal to Tumor Transition of Esophageal Squamous Cell Carcinoma
Authors: Chung Joon-Yong , Braunschweig Till , Hu Nan , Roth Mark , Traicoff June L. , Wang Quan-Hong , Knezevic Vladimir , Taylor Philip R. , Hewitt Stephen M. 
Published: July 2006

Abstract
Esophageal cancer remains a highly lethal malignancy for which the genetic and proteomic events are poorly understood. Studies have reported dysregulated proteins in esophageal carcinoma; however, the magnitude of these changes remains largely uncharacterized. Little is known about alterations early in the neoplastic pathway. Using multiplex tissue immunoblotting, we quantified the expression of seven proteins in esophageal carcinogenesis. Regions of normal, dysplasia, and invasive carcinoma of the squamous esophagus in six patients were characterized. Pan-cytokeratin (CK) was essentially unchanged across the transition (0.96 in dysplasia and 0.69 in tumor). Expression levels of annexin 1, CK-4, and CK-14 were all decreased in dysplasia and tumor compared with normal (reference, 1.00): annexin 1, 0.30 in dysplasia and 0.15 in tumor; CK-4, 0.20 in dysplasia and 0.16 in tumor; and CK-14, 0.54 in dysplasia and 0.40 in tumor. Expression of two proteins was increased in dysplasia and tumor versus normal: cyclooxygenase-2, 1.35 in dysplasia and 2.32 in tumor and p53, 1.29 in dysplasia and 2.37 in tumor. Secreted protein, acidic and rich in cysteine, which is expressed in the adjacent stroma, was 1.56-fold higher in stroma underlying dysplasia and 6.20-fold increased in dysplastic stroma surrounding invasive tumor. These findings suggest that changes in protein expression can be detected during the transition to dysplasia and may be useful biomarkers. (Cancer Epidemiol Biomarkers Prev 2006;15(7):1403–8)
Human Papillomavirus Type–Specific 18-Month Risk of High-Grade Cervical Intraepithelial Neoplasia in Women with a Normal or Borderline/Mildly Dyskaryotic Smear
Authors: Berkhof Johannes , Bulkmans Nicole W.J. , Bleeker Maaike C.G. , Bulk Saskia , Snijders Peter J.F. , Voorhorst Feja J. , Meijer Chris J.L.M. 
Published: July 2006

Abstract
Introduction: High-risk human papillomavirus (hrHPV) DNA testing is an increasingly used instrument in cervical cancer prevention along cervical cytology. The inclusion of hrHPV testing in cervical screening requires efficient management as many hrHPV infections are transient. We investigated the potential value of hrHPV genotyping in normal and borderline/mildly dyskaryotic (BMD) smears.
Materials and Methods: From a screening population of 44,102 women in the Netherlands, we included hrHPV-positive women with a normal or BMD smear. We assessed the type-specific 18-month risk of high-grade cervical intraepithelial neoplasia (CIN).
Results: In hrHPV-positive women, 18-month risk of CIN grade 3 or invasive cancer (≥CIN3) was 6% [95% confidence interval (95% CI), 4-9] after normal cytology and 20% (95% CI, 16-25) after BMD. If positive for HPV16, ≥CIN3 risks were 14% (95% CI, 9-21) and 37% (95% CI, 28-48), respectively. In the subset of hrHPV-positive women without HPV16, HPV18 was associated with an increased risk of high-grade CIN after normal cytology and HPV31 and HPV33 were associated with an increased risk, particularly after BMD. HPV16 and HPV18 were also associated with an increased risk of high-grade CIN in women with an hrHPV-positive normal baseline smear and a repeat normal smear at 6 months.
Discussion: HrHPV-positive women without type 16, 18, 31, or 33 had a relatively low risk of high-grade CIN. Among women with baseline normal cytology and among women with a baseline and repeat normal smear, HPV16/18–positive women showed an increased risk of high-grade CIN. This warrants more aggressive management of HPV16/18–positive women compared with other hrHPV-positive women. (Cancer Epidemiol Biomarkers Prev 2006;15(7):1268–73)
Factors Associated with Enrollment in Cancer Genetics Research
Authors: Ford Beth M. , Evans James S. , Stoffel Elena M. , Balmaña Judith , Regan Meredith M. , Syngal Sapna 
Published: July 2006

Abstract
Previous studies have identified low patient accrual in large-scale cancer clinical trials, particularly for underrepresented groups, such as ethnic minorities, females, and patients &gt;65 years. As there have been few studies examining participation in cancer genetics epidemiologic research, our objective was to identify clinical and demographic factors predicting enrollment in these studies. A total of 1,111 patients diagnosed with colorectal cancer presenting to a gastrointestinal oncology clinic were approached to enroll in a study investigating the role of the MSH6 gene in familial colorectal cancer. Patient consent was sought for providing a blood specimen for DNA analysis and review of medical records/tumor specimens and contacting family members to confirm the family history of cancer. Seven predictor variables for enrollment (age, sex, ethnicity, family history of colorectal cancer in a first-degree relative, presence of children, insurance type, and type of visit) were analyzed using logistic regression analysis to determine the effect on decision to enroll. Of 1,111 patients approached, 696 (62.6%) enrolled in the study. Of these approached individuals, 4.2% were of nonwhite ethnicity and 33.5% were age ≥65 years. Patients of white ethnicity [odds ratio (OR), 2.10; P = 0.018], males (OR, 1.47; P = 0.002), those ages ≤65 years (OR, 1.42; P = 0.009), and those with a first-degree relative with colorectal cancer (OR, 1.57; P = 0.005) were significantly more likely to enroll. Fewer than 4% of all participants denied permission for the study researchers to access information from medical records or to be recontacted by researchers to discuss the enrollment of additional family members. Our data suggest that, once subjects decided to enroll, the majority (88%) was comfortable with consenting to all study components, including the creation of cell lines and future recontact. Low participation rates for ethnic minorities, females, and elderly patients are similar for both cancer genetics and clinical trial studies. (Cancer Epidemiol Biomarkers Prev 2006;15(7):1355–9)