bluuebunny/crossref_metadata_2025_split huggingface dataset:
COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations
Authors: Jothi Raja , Zotenko Elena , Tasneem Asba , Przytycka Teresa M. 
Published: January 2006

Abstract
Motivation: Determining orthology relations among genes across multiple genomes is an important problem in the post-genomic era. Identifying orthologous genes can not only help predict functional annotations for newly sequenced or poorly characterized genomes, but can also help predict new protein–protein interactions. Unfortunately, determining orthology relation through computational methods is not straightforward due to the presence of paralogs. Traditional approaches have relied on pairwise sequence comparisons to construct graphs, which were then partitioned into putative clusters of orthologous groups. These methods do not attempt to preserve the non-transitivity and hierarchic nature of the orthology relation.
Results: We propose a new method, COCO-CL, for hierarchical clustering of homology relations and identification of orthologous groups of genes. Unlike previous approaches, which are based on pairwise sequence comparisons, our method explores the correlation of evolutionary histories of individual genes in a more global context. COCO-CL can be used as a semi-independent method to delineate the orthology/paralogy relation for a refined set of homologous proteins obtained using a less-conservative clustering approach, or as a refiner that removes putative out-paralogs from clusters computed using a more inclusive approach. We analyze our clustering results manually, with support from literature and functional annotations. Since our orthology determination procedure does not employ a species tree to infer duplication events, it can be used in situations when the species tree is unknown or uncertain.
Contact: jothi@mail.nih.gov, przytyck@mail.nih.gov
Supplementary information: Supplementary materials are available at Bioinformatics online.
Disabling conditions and registration for child abuse and neglect: a population‐based study
Authors: Reading Richard 
Published: January 2006

.

Spencer N.,
Devereux E.,
Wallace A.,
Sundrum R.,
Shenoy M.,
Bacchus C. &
Logan S.
(
2005
)

,
116
,
609
–
613
.
Objective  To study the relationship between disabling conditions and registration for child abuse and neglect in a 19‐year whole‐population birth cohort.Setting  West Sussex area of the United Kingdom.Study design  Retrospective whole‐population cohort.Main outcomes  Child‐protection registration, physical abuse, sexual abuse, emotional abuse and neglect.Population and participants  Infants born in West Sussex (119 729) between January 1983 and December 2001 with complete data including birthweight, gestational age, maternal age and postal code.Results  Cerebral palsy, speech and language disorder, learning difficulties, conduct disorders and non‐conduct psychological disorders were all significantly associated with child‐protection registration before adjustment, and all but cerebral palsy retained significance after adjustment for birthweight, gestational age and socioeconomic status. Autism and sensory disabilities (vision and hearing) were not associated with an increased risk of child‐protection registration. Conduct disorders and moderate/severe learning difficulty were associated with registration in each of the four categories after adjustment for socioeconomic status, birthweight and gestational age. Children with speech and language disorders and mild learning difficulties were at increased risk of physical abuse, emotional abuse and neglect. Non‐conduct psychological disorders were associated with all categories except neglect, and cerebral palsy was associated with all categories except physical abuse and neglect.Conclusions  Children with disabling conditions seem to be at increased risk of registration for child abuse and neglect, although the pattern of registration varies with the specific disabling condition. The strong association with registration noted for conditions such as conduct disorder and learning difficulties is likely to arise, in part, because these conditions share a common aetiological pathway with child abuse and neglect.
Surveying biotransformations with à la carte genetic traps: translating dehydrochlorination of lindane (gamma‐hexachlorocyclohexane) into lacZ‐based phenotypes
Authors: Mohn William W. , Garmendia Junkal , Galvao Teca C. , De Lorenzo Víctor 
Published: January 2006

SummaryThe ability of the product of a desired reaction to activate a bacterial transcriptional regulator was exploited to develop genetic traps that render the catalytic activity born by a DNA clone into a selectable/scorable phenotype. We established this strategy with a system to expose the activity of dehydrochlorinases acting upon gamma‐hexachlorocyclohexane (γ‐HCH or lindane). To this end, the effector‐binding protein, XylR, was evolved by gene shuffling plus mutagenic polymerase chain reaction to be optimally responsive to the major product of γ‐HCH dehydrochlorination, 1,2,4‐trichlorobenzene (TCB). We then derived Escherichia coli strains that constitutively expressed the modified XylR variant (named XylR5) and had lacZ under control of the Pu promoter, which is activated by XylR. A robotic β‐galactosidase assay indicated that when the resulting strain was transformed with a linA+ clone (expressing a γ‐HCH dehydrochlorinase from Sphingomonas paucimobilis UT26), it had levels of β‐galactosidase that were dependent on the γ‐HCH concentration. This à la carte host thus translated the conversion of γ‐HCH to TCB into upregulation of lacZ. An alternate host additionally expressing LacY grew efficiently on lactose only when LacZ was upregulated in a fashion dependent on TCB or other effectors of XylR5. These results demonstrated the power of deriving a host for the genetic scrutiny, rather than enzymatic screening, of clones expressing a given catabolic enzyme.
No evidence of population structure across three isolated subpopulations of Russula brevipes in an oak/pine woodland
Authors: Bergemann Sarah E. , Douhan Greg W. , Garbelotto Matteo , Miller Steven L. 
Published: January 2006

Summary

Russula brevipes is common ectomycorrhizal (EM) fungus that is associated with several hosts across temperate forest ecosystems. A previous study has demonstrated that substructuring across large geographic distances (1500 km) occurs in the western USA.
To examine genetic structure over a more localized scale, basidiocarps of Russula brevipes from three subpopulations, separated by distances of 230–1090 m, were collected over two consecutive years in an oak/pine woodland. Microsatellite loci were used to test for population differentiation both among subpopulations and by year.
No significant population differentiation was detected between subpopulations (θST = 0.01) or between years (θST = 0.01). Most loci were consistent with a Hardy–Weinburg equilibrium and 82% of the genets between seasons from similar sampling localities constituted new genotypes.
These results indicate that R. brevipes constitutes a randomly mating population with no genetic differentiation between locations or across successive fruiting seasons.
Access to Health Care Services for the Disabled Elderly
Authors: Taylor Donald H. , Hoenig Helen 
Published: January 2006

Objective. To determine whether difficulty walking and the strategies persons use to compensate for this deficit influenced downstream Medicare expenditures.Data Source. Secondary data analysis of Medicare claims data (1999–2000) for age‐eligible Medicare beneficiaries (N=4,997) responding to the community portion of the 1999 National Long Term Care Survey (NLTCS).Study Design. Longitudinal cohort study. Walking difficulty and compensatory strategy were measured at the 1999 NLTCS, and used to predict health care use as measured in Medicare claims data from the survey date through year‐end 2000.Data Extraction. Respondents to the 1999 community NLTCS with complete information on key explanatory variables (walking difficulty and compensatory strategy) were linked with Medicare claims to define outcome variables (health care use and cost).Principal Findings. Persons who reported it was very difficult to walk had more downstream home health visits (1.1/month, p<.001), but fewer outpatient physician visits (−0.16/month, p<.001) after controlling for overall disease burden. Those using a compensatory strategy for walking also had increased home health visits/month (0.55 for equipment, 1.0 for personal assistance, p<.001 for both) but did not have significantly reduced outpatient visits. Persons reporting difficulty walking had increased downstream Medicare costs ranging from $163 to $222/month (p<.001) depending upon how difficult walking was. Less than half of the persons who used equipment to adapt to walking difficulty had their difficulty fully compensated by the use of equipment. Persons using equipment that fully compensated their difficulty used around $300/month less in Medicare‐financed costs compared with those with residual difficulty.Conclusions. Difficulty walking and use of compensatory strategies are correlated with the use of Medicare‐financed services. The potential impact on the Medicare program is large, given how common such limitations are among the elderly.
Adverse outcome of pregnancy following air travel: A myth or a concern?
Authors: CHIBBER Rachana , AL‐SIBAI M. Hisham , QAHTANI Noura 
Published: January 2006

AbstractObjective:  To assess whether air travel elevates the risk of adverse pregnancy outcomes in essentially healthy women with single non‐anomalous fetuses at a gestational age greater than 20 weeks.Methods:  A retrospective analysis of air travel during the current pregnancy and pregnancy outcome was undertaken in 992 women admitted for delivery over a 12‐month period. The study group of 546 (55%) women, of whom 57% were primigravidae, travelled at least once during pregnancy, and were compared with a control group of 447 women (45%), of whom 54% were primigravidae, who did not travel by air.Results:  The primigravidae in the study group showed an increased risk of preterm birth, and this risk was statistically significant between the gestations of 34 and 37 weeks (adjusted odds ratio 1.5, 95% confidence intervals 1.2, 1.8); this risk remained elevated after adjustment for covariates. These women's pregnancies were appreciably shorter than those of primigravidae who did not fly (36.1 ± 0.8 vs. 39.2 ± 2.1 weeks) and their babies had lower birthweights (2684 ± 481 vs. 3481 ± 703 g). and were more likely to be admitted to the neonatal intensive care unit. This group of air travellers is unusual for the uncommonly long and frequent duration of air travel, which is not routinely undertaken in most parts of the world. There were no thromboembolic events complicating any pregnancies.Conclusions:  Primigravid women who travel by air appear to be at higher risk for preterm birth. Multicentre large studies are required to confirm or repute these findings.
Biocompatible properties of surgical mesh using an animal model
Authors: KRAUSE Hannah G. , GALLOWAY Stuart J. , KHOO Soo K. , LOURIE Richard , GOH Judith T. W. 
Published: January 2006

AbstractAim:  To study the biocompatibility of surgical meshes for use in pelvic reconstructive surgery using an animal model.Methods:  Eight different types of mesh: Atrium, Dexon, Gynemesh, IVS tape, Prolene, SPARC tape, TVT tape and Vypro II, were implanted into the abdominal walls of rats for 3 months’ duration. Explanted meshes were assessed, using light microscopy, for parameters of rejection and incorporation.Results:  Type 1 (Atrium, Gynemesh, Prolene, SPARC and TVT) and type 3 (Vypro II, Dexon and IVS) meshes demonstrated different biocompatible properties. Inflammatory cellular response and fibrosis at the interface of mesh and host tissue was most marked with Vypro II and IVS. All type 1 meshes displayed similar cellular responses despite markedly different mesh architecture.Conclusions:  The inflammatory response and fibrous reaction in the non‐absorbable type 3 meshes tested (IVS and Vypro II) was more marked than the type 1 meshes. The increased inflammatory and fibrotic response may be because of the multifilamentous polypropylene components of these meshes. Material and filament composition of mesh is the main factor in determining cellular response.
Challenges and future of renal replacement therapy
Authors: DE FRANCISCO Angel L. M. , PIÑERA Celestino 
Published: January 2006

AbstractRenal community increasingly recognizes the challenges of very high mortality, morbidity and low quality of life among dialysis patients. Current hemodialysis (HD) schedule provides less than 10% of the clearance power of the natural kidneys and therefore current standard HD treatment is still a long way from providing adequate renal replacement. In the future it would be expected to improve dialysis control with the development of new technology: membranes, dialysate buffer, electrolyte concentration, system interface, arteriovenous access monitoring. Online technology must be adapted to routine HD for new prescription monitoring such as creatinine online sensing technology, sodium‐specific electrode or hydrogen ion concentration. Online convective therapies offer the opportunity for a more biological renal replacement therapy increasing convective transport in order to “reproduce” glomerular function and improving small and middle molecular clearance in an economically feasible and safe way. The paradigm of thrice‐weekly dialysis is faced with diminishing returns, with the possible exception of long dialysis sessions. More frequent (daily) dialysis represents a very promising tool for improving dialysis outcomes and quality of life. Future technologies for renal replacement include bioartificial kidneys based in continuous hemofiltration and bioartificial tubules. Although Phase I/II clinical trial on 10 patients with acute renal failure has been reported the procedure requires further evaluation. Organogenesis, therapeutic cloning, or cloning and organogenesis combined might in the future produce a functional and histocompatible kidney. The continuous increase in incidence and prevalence of renal‐replacement therapy is a world‐wide phenomenon, although the rates in Europe are still much lower than in the U.S. The increase in rates applies especially to older patients, patients with diabetes mellitus and renal vascular disease and the consequences of this important comorbidity are very important in terms of mortality.
Online hemodiafiltration: 4 years of clinical experience
Authors: MUÑOZ Rosa , GALLARDO Isabel , VALLADARES Evandro , SARACHO Ramón , MARTÍNEZ Isabel , OCHARAN Julen , MONTENEGRO Jesús 
Published: January 2006

AbstractOnline hemodiafiltration (online HDF) is a new hemodialysis technique combining convection and diffusion and thus also enabling the purification of large molecules. As yet, only a small number of clinical experiences have been published about the effectiveness and safety of online HDF. We present a prospective and observational study conducted on 31 patients treated with online HDF in our center in the last 4 years. The purpose of the study is to compare the evolution of the following aspects before and after starting online HDF: dose of dialysis, purification of medium‐sized/large molecules, inflammation, nutrition, Ca‐P metabolism, anemia, and intradialytic complications. Online HDF increased Kt/V to 31.0% (p>0.001) and reduced postdialysis β2‐M to 66.4% (p>0.001). The rest of the parameters analyzed did not vary significantly. During online HDF, episodes of symptomatic hypotension fell by 45% in relation to conventional hemodialysis, and no relevant complication occurred. Online HDF is very useful in patients in whom we need to increase replacement therapy, such as patients with a large body surface, those in whom we suspect a residual syndrome or those who have been receiving dialysis for a long time and for whom we wish to prevent amyloidosis. Online HDF is safe and better tolerated than conventional hemodialysis.
Low Levels of Pyrazinamide and Ethambutol in Children with Tuberculosis and Impact of Age, Nutritional Status, and Human Immunodeficiency Virus Infection
Authors: Graham S. M. , Bell D. J. , Nyirongo S. , Hartkoorn R. , Ward S. A. , Molyneux E. M. 
Published: January 2006

ABSTRACT

Recent pharmacokinetic studies that included children found that serum drug levels were low compared to those of adults for whom the same dosages were used. This study aimed to characterize the pharmacokinetics of pyrazinamide and ethambutol in Malawian children and to examine the impact of age, nutritional status, and human immunodeficiency virus (HIV) infection. We conducted a pharmacokinetic study of children treated for tuberculosis with thrice-weekly pyrazinamide (
n
= 27; mean age, 5.7 years) and of a separate group of children treated with thrice-weekly ethambutol (
n
= 18; mean age, 5.5 years) as portions of tablets according to national guidelines. Malnutrition and HIV infection were common in both groups. Blood samples were taken just prior to oral administration of the first dose, and subsequent samples were taken at intervals of 2, 3, 4, 7, 24, and 48 h after drug administration. Serum drug levels were low in all children for both drugs; in almost all cases, the maximum concentration of the drug in serum (
C
max
) failed to reach the MIC for
Mycobacterium tuberculosis
. The
C
max
of pyrazinamide was significantly lower in younger children (<5 years) than in older children. The
C
max
of pyrazinamide was also lower for HIV-infected children and children with severe malnutrition, but these differences did not reach statistical significance. No differences were found for ethambutol in relation to age, HIV infection, or malnutrition, but the
C
max
was <2 mg/liter in all cases. Studies of pharmacokinetic parameters and clinical outcomes obtained by using higher dosages of drugs for treatment of childhood tuberculosis are needed, and recommended dosages may need to be increased.
Novel Yeast Cell-Based Assay To Screen for Inhibitors of Human Cytomegalovirus Protease in a High-Throughput Format
Authors: Cottier Valérie , Barberis Alcide , Lüthi Urs 
Published: January 2006

ABSTRACT

The protease encoded by the human cytomegalovirus (HCMV) is an attractive target for antiviral drug development because of its essential function in viral replication. We describe here a cellular assay in the yeast
Saccharomyces cerevisiae
for the identification of small molecule inhibitors of HCMV protease by conditional growth in selective medium. In this system, the protease cleavage sequence is inserted into the
N
-(5′-phosphoribosyl)anthranilate isomerase (Trp1p), a yeast protein essential for cell proliferation in the absence of tryptophan. Coexpression of HCMV protease with the engineered Trp1p substrate in yeast cells results in site-specific cleavage and functional inactivation of the Trp1p enzyme, thereby leading to an arrest of cell proliferation. This growth arrest can be suppressed by the addition of validated HCMV protease inhibitors. The growth selection system presented here provides the basis for a high-throughput screen to identify HCMV protease inhibitors that are active in eukaryotic cells.
Discordances between Interpretation Algorithms for Genotypic Resistance to Protease and Reverse Transcriptase Inhibitors of Human Immunodeficiency Virus Are Subtype Dependent
Authors: Snoeck Joke , Kantor Rami , Shafer Robert W. , Van Laethem Kristel , Deforche Koen , Carvalho Ana Patricia , Wynhoven Brian , Soares Marcelo A. , Cane Patricia , Clarke John , Pillay Candice , Sirivichayakul Sunee , Ariyoshi Koya , Holguin Africa , Rudich Hagit , Rodrigues Rosangela , Bouzas Maria Belen , Brun-Vézinet Françoise , Reid Caroline , Cahn Pedro , Brigido Luis Fernando , Grossman Zehava , Soriano Vincent , Sugiura Wataru , Phanuphak Praphan , Morris Lynn , Weber Jonathan , Pillay Deenan , Tanuri Amilcar , Harrigan Richard P. , Camacho Ricardo , Schapiro Jonathan M. , Katzenstein David , Vandamme Anne-Mieke 
Published: January 2006

ABSTRACTThe major limitation of drug resistance genotyping for human immunodeficiency virus remains the interpretation of the results. We evaluated the concordance in predicting therapy response between four different interpretation algorithms (Rega 6.3, HIVDB-08/04, ANRS [07/04], and VGI 8.0). Sequences were gathered through a worldwide effort to establish a database of non-B subtype sequences, and demographic and clinical information about the patients was gathered. The most concordant results were found for nonnucleoside reverse transcriptase (RT) inhibitors (93%), followed by protease inhibitors (84%) and nucleoside RT inhibitor (NRTIs) (76%). For therapy-naive patients, for nelfinavir, especially for subtypes C and G, the discordances were driven mainly by the protease (PRO) mutational pattern 82I/V + 63P + 36I/V for subtype C and 82I + 63P + 36I + 20I for subtype G. Subtype F displayed more discordances for ritonavir in untreated patients due to the combined presence of PRO 20R and 10I/V. In therapy-experienced patients, subtype G displayed a lot of discordances for saquinavir and indinavir due to mutational patterns involving PRO 90 M and 82I. Subtype F had more discordance for nelfinavir attributable to the presence of PRO 88S and 82A + 54V. For the NRTIs lamivudine and emtricitabine, CRF01_AE had more discordances than subtype B due to the presence of RT mutational patterns 65R + 115 M and 118I + 215Y, respectively. Overall, the different algorithms agreed well on the level of resistance scored, but some of the discordances could be attributed to specific (subtype-dependent) combinations of mutations. It is not yet known whether therapy response is subtype dependent, but the advice given to clinicians based on a genotypic interpretation algorithm differs according to the subtype.
New TEM-Derived Extended-Spectrum β-Lactamase and Its Genomic Context in Plasmids from
Salmonella enterica
Serovar Derby Isolates from Uruguay
Authors: Vignoli Rafael , Cordeiro Nicolas F. , García Virginia , Mota María Inés , Betancor Laura , Power Pablo , Chabalgoity José A. , Schelotto Felipe , Gutkind Gabriel , Ayala Juan A. 
Published: January 2006

ABSTRACT

A small (8.2-kb) ColE1 plasmid encoding TEM-144 (a new β-lactamase with a ceftazidimase profile) was sequenced by a gene-walking strategy. The
bla
TEM
allele was carried on a Tn
2
element, disrupting a Rom protein gene. TEM-144 differs from TEM-1 by two mutations (R164C and E240K) and from the ceftazidime-hydrolyzing TEM-91 by one mutation (T182M).
In Vitro Activity of DX-619, a Novel Des-Fluoro(6) Quinolone, against a Panel of
Streptococcus pneumoniae
Mutants with Characterized Resistance Mechanisms
Authors: Wickman Paul A. , Moland Ellen Smith , Black Jennifer A. , Thomson Kenneth S. 
Published: January 2006

ABSTRACT

The in vitro activities of DX-619 and four other quinolones were compared against
Streptococcus pneumoniae
mutants that contained a variety of alterations within the quinolone resistance-determining regions. DX-619 was the most potent quinolone and was least affected by the mutations.