bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic error threshold; additivity and epistasis in RNA evolution
Authors: Takeuchi Nobuto , Poorthuis Petrus H , Hogeweg Paulien 
Published: February 2005

Abstract
Background
The error threshold puts a limit on the amount of information maintainable in Darwinian evolution. The error threshold was first formulated in terms of genotypes. However, if a genotype-phenotype map involves redundancy ("mutational neutrality"), the error threshold should be formulated in terms of phenotypes since there is no unique fittest genotype. A previous study formulated the error threshold in terms of phenotypes, and their results showed that a rather low degree of mutational neutrality can increase the error threshold unlimitedly.

Results
We obtain an analytical formulation of the phenotypic error threshold by considering the "additive assumption", in which base substitutions do not influence each other (no epistasis). Our formulation shows that an increase of the error threshold due to mutational neutrality is limited. Computer simulations of RNA evolution are conducted to verify our formulation, and the results show a good agreement between the analytical prediction and the simulations. The comparison with the previous formulation illustrates that it is important for the prediction of the error threshold to consider that the number of base substitutions per replication is rather large near the error threshold. To examine the additive assumption, a detailed analysis of additivity and epistasis in RNA folding of a particular sequence is performed. The results show a high degree of epistasis in RNA folding; furthermore, the analysis also elucidates the reason of the success of the additive assumption.

Conclusions
We conclude that an increase of the error threshold by mutational neutrality is limited, and that the additive assumption achieves a good prediction of the error threshold in spite of a high degree of epistasis in RNA folding because the average number of base substitutions of sequences retaining the phenotype per replication is sufficiently small to avoid of the effect of epistasis.
Herpesvirus pan encodes a functional homologue of BHRF1, the Epstein-Barr virus v-Bcl-2
Authors: Howell Melanie , Williams Tracey , Hazlewood Sheila A 
Published: February 2005

Abstract
Background
Epstein-Barr virus (EBV) latently infects about 90% of the human population and is associated with benign and malignant diseases of lymphoid and epithelial origin. BHRF1, an early lytic cycle antigen, is an apoptosis suppressing member of the Bcl-2 family. In vitro studies imply that BHRF1 is dispensable for both virus replication and transformation. However, the fact that BHRF1 is highly conserved not only in all EBV isolates studied to date but also in the analogous viruses Herpesvirus papio and Herpesvirus pan that infect baboons and chimpanzees respectively, suggests BHRF1 may play an important role in vivo.

Results
Herpesvirus papio BHRF1 has been shown to function in an analogous manner to EBV BHRF1 in response to DNA damaging agents in human keratinocytes. In this study we show that the heterologous expression of the previously uncharacterised Herpesvirus pan BHRF1 in the human Burkitt's lymphoma cell line Ramos-BL provides similar anti-apoptotic functions to that of EBV BHRF1 in response to apoptosis triggered by serum withdrawal, etoposide treatment and ultraviolet (UV) radiation. We also map the amino acid changes onto the recently solved structure of the EBV BHRF1 and reveal that these changes are unlikely to alter the 3D structure of the protein.

Conclusions
These findings show that the functional conservation of BHRF1 extends to a lymphoid background, suggesting that the primate virus proteins interact with cellular proteins that are themselves highly conserved across the higher primates. Further weight is added to this suggestion when we show that the difference in amino acid sequences map to regions on the 3D structure of EBV BHRF1 that are unlikely to change the conformation of the protein.
Proteolytic cleavage of pertussis toxin S1 subunit is not essential for its activity in mammalian cells
Authors: Carbonetti Nicholas H , Mays R Michael , Artamonova Galina V , Plaut Roger D , Worthington Zoë EV 
Published: February 2005

Abstract
Background
Pertussis toxin (PT) is an exotoxin virulence factor produced by Bordetella pertussis, the causative agent of whooping cough. PT consists of an active subunit (S1) that ADP-ribosylates the alpha subunit of several mammalian G proteins, and a B oligomer (S2–S5) that binds glycoconjugate receptors on cells. PT appears to enter cells by endocytosis, and retrograde transport through the Golgi apparatus may be important for its cytotoxicity. A previous study demonstrated that proteolytic processing of S1 occurs after PT enters mammalian cells. We sought to determine whether this proteolytic processing of S1 is necessary for PT cytotoxicity.

Results
Protease inhibitor studies suggested that S1 processing may involve a metalloprotease, and processing does not involve furin, a mammalian cell protease that cleaves several other bacterial toxins. However, inhibitor studies showed a general lack of correlation of S1 processing with PT cellular activity. A combination of replacement, insertion and deletion mutations in the C-terminal region of S1, as well as mass spectrometry data, suggested that the cleavage site is located around residue 203–204, but that cleavage is not strongly sequence-dependent. Processing of S1 was abolished by each of 3 overlapping 8 residue deletions just downstream of the putative cleavage site, but not by smaller deletions in the same region. Processing of the various mutant forms of PT did not correlate with cellular activity of the toxin, nor with the ability of the bacteria producing them to infect the mouse respiratory tract. In addition, S1 processing was not detected in transfected cells expressing S1, even though S1 was fully active in these cells.

Conclusions
S1 processing is not essential for the cellular activity of PT. This distinguishes it from the processing of various other bacterial toxins, which has been shown to be important for their cytotoxicity. S1 processing may be mediated primarily by a metalloprotease, but the cleavage site on S1 is not sequence-dependent and processing appears to depend on the general topology of the protein in that region, indicating that multiple proteases may contribute to this cleavage.
Role of Leishmania (Leishmania) chagasi amastigote cysteine protease in intracellular parasite survival: studies by gene disruption and antisense mRNA inhibition
Authors: Mundodi Vasanthakrishna , Kucknoor Ashwini S , Gedamu Lashitew 
Published: February 2005

Abstract
Background
The parasitic protozoa belonging to Leishmania (L.) donovani complex possess abundant, developmentally regulated cathepsin L-like cysteine proteases. Previously, we have reported the isolation of cysteine protease gene, Ldccys2 from Leishmania (L.) chagasi. Here, we have further characterized this cysteine protease gene and demonstrated its role during infection and survival of Leishmania (L.) chagasi within the U937 macrophage cells.

Results
The amastigote specific Ldccys2 genes of L. (L.) chagasi and L. (L.) donovani have identical gene organization, as determined by southern blots. In vivo expression analyses by Northern blots showed that Ldccys2 is amastigote specific. Western blot using anti-Ldccys2 antibody confirmed the amastigote specific protein expression. Recombinant expression of Ldccys2, a 30 kDA protein, was functionally active in a gelatin assay. Results from Ldccys2 heterozygous knockout mutants showed its role during macrophage infection and in intra-macrophage survival of the parasites. Since attempts to generate null mutants failed, we used antisense RNA inhibition to regulate Ldcccys2 gene expression. Not surprisingly, the results from antisense studies further confirmed the results from heterozygous knockout mutants, reiterating the importance of amastigote specific cysteine proteases in Leishmania infection and pathogenesis.

Conclusions
The study shows that Ldccys2 is a developmentally regulated gene and that Ldccys2 is expressed only in infectious amastigote stages of the parasite. The collective results from both the heterozygous knockout mutants and antisense mRNA inhibition studies shows that Ldccys2 helps in infection and survival of L. (L.) chagasi amastigotes within the macrophage cells. Finally, antisense RNA technique can be used as an alternate approach to gene knockout, for silencing gene expression in L. (L.) chagasi, especially in cases such as this, where a null mutant cannot be achieved by homologous recombination.
Nucleus accumbens core lesions retard instrumental learning and performance with delayed reinforcement in the rat
Authors: Cardinal Rudolf N , Cheung Timothy HC 
Published: February 2005

Abstract
Background
Delays between actions and their outcomes severely hinder reinforcement learning systems, but little is known of the neural mechanism by which animals overcome this problem and bridge such delays. The nucleus accumbens core (AcbC), part of the ventral striatum, is required for normal preference for a large, delayed reward over a small, immediate reward (self-controlled choice) in rats, but the reason for this is unclear. We investigated the role of the AcbC in learning a free-operant instrumental response using delayed reinforcement, performance of a previously-learned response for delayed reinforcement, and assessment of the relative magnitudes of two different rewards.

Results
Groups of rats with excitotoxic or sham lesions of the AcbC acquired an instrumental response with different delays (0, 10, or 20 s) between the lever-press response and reinforcer delivery. A second (inactive) lever was also present, but responding on it was never reinforced. As expected, the delays retarded learning in normal rats. AcbC lesions did not hinder learning in the absence of delays, but AcbC-lesioned rats were impaired in learning when there was a delay, relative to sham-operated controls. All groups eventually acquired the response and discriminated the active lever from the inactive lever to some degree. Rats were subsequently trained to discriminate reinforcers of different magnitudes. AcbC-lesioned rats were more sensitive to differences in reinforcer magnitude than sham-operated controls, suggesting that the deficit in self-controlled choice previously observed in such rats was a consequence of reduced preference for delayed rewards relative to immediate rewards, not of reduced preference for large rewards relative to small rewards. AcbC lesions also impaired the performance of a previously-learned instrumental response in a delay-dependent fashion.

Conclusions
These results demonstrate that the AcbC contributes to instrumental learning and performance by bridging delays between subjects' actions and the ensuing outcomes that reinforce behaviour.
Differences in need for antihypertensive drugs among those aware and unaware of their hypertensive status: a cross sectional survey
Authors: Khan Nadia A , Wardman Dennis , Campbell Norman RC 
Published: February 2005

Abstract
Background
Lack of antihypertensive use among hypertensive individuals is a major public health problem. It remains unclear as to how much of this lack of treatment is because of failure to diagnose hypertension or failure to initiate drug treatment for those with a diagnosis of hypertension. The primary aim of this study was to determine the proportion of those untreated individuals who would be recommended to start drug therapy for control of blood pressure among those aware or unaware of their diagnosis of hypertension.

Methods
The Canadian Heart Health Surveys (1986 – 1992), a national, cross-sectional descriptive survey (n = 23 129), was used to determine the proportion of individuals who were untreated, yet satisfied the 2004 Canadian hypertension guidelines for initiating drug therapy. Patients were divided into subgroups of those aware and unaware of having a diagnosis of hypertension according to self reported awareness from the survey.

Results
Of those with untreated hypertension (= 140/90 mmHg), only 37% were aware of their diagnosis. 74% of untreated individuals aware of their diagnosis of hypertension would require drug therapy, compared to 57% of those who were unaware. Of those >65 years of age, 52% of aware individuals needed drug therapy whereas only 34% of unaware elderly would need drug treatment.

Conclusion
In both unaware and aware subgroups, the majority of patients with untreated hypertension would benefit from antihypertensive drug therapy according to the 2004 Canadian Hypertension recommendations. The proportion of untreated patients that still need drug therapy was higher among those who were aware compared to those who were unaware. This finding suggests that the major gap in hypertension control may be in initiating drug therapy rather than in diagnosing hypertension. Further studies are needed to confirm these results to ultimately help strategize public health efforts in controlling hypertension.
International outbreak of SalmonellaOranienburg due to German chocolate
Authors: Werber Dirk , Dreesman Johannes , Feil Fabian , van Treeck Ulrich , Fell Gerhard , Ethelberg Steen , Hauri Anja M , Roggentin Peter , Prager Rita , Fisher Ian ST , Behnke Susanne C , Bartelt Edda , Weise Ekkehard , Ellis Andrea , Siitonen Anja , Andersson Yvonne , Tschäpe Helmut , Kramer Michael H , Ammon Andrea 
Published: February 2005

Abstract
Background
This report describes a large international chocolate-associated Salmonella outbreak originating from Germany.

Methods
We conducted epidemiologic investigations including a case-control study, and food safety investigations. Salmonella (S.) Oranienburg isolates were subtyped by the use of pulsed-field gel electrophoresis (PFGE).

Results
From 1 October 2001 through 24 March 2002, an estimated excess of 439 S. Oranienburg notifications was registered in Germany. Simultaneously, an increase in S. Oranienburg infections was noted in other European countries in the Enter-net surveillance network. In a multistate matched case-control study in Germany, daily consumption of chocolate (matched odds ratio [MOR]: 4.8; 95% confidence interval [CI]: 1.3–26.5), having shopped at a large chain of discount grocery stores (MOR: 4.2; CI: 1.2–23.0), and consumption of chocolate purchased there (MOR: 5.0; CI: 1.1–47.0) were associated with illness. Subsequently, two brands from the same company, one exclusively produced for that chain, tested positive for S. Oranienburg. In two other European countries and in Canada chocolate from company A was ascertained that also contained S. Oranienburg. Isolates from humans and from chocolates had indistinguishable PFGE profiles. No source or point of contamination was identified. Epidemiological identification of chocolate as a vehicle of infections required two months, and was facilitated by proxy measures.

Conclusions
Despite the use of improved production technologies, the chocolate industry continues to carry a small risk of manufacturing Salmonella-containing products. Particularly in diffuse outbreak-settings, clear associations with surrogates of exposure should suffice to trigger public health action. Networks such as Enter-net have become invaluable for facilitating rapid and appropriate management of international outbreaks.
Association between fetal growth restriction and polymorphisms at sites -1 and +3 of pituitary growth hormone: a case-control study
Authors: Adkins Ronald M , Campese Caroline , Vaidya Rehana , Boyd Theonia K 
Published: February 2005

Abstract
Background
Fetal growth restriction is associated with significantly increased risks of neonatal death and morbidity and with susceptibility to hypertension, cardiovascular disease and NIDDM later in life. Human birth weight has a substantial genetic component, with at least a quarter of the variation attributable to additive genetic effects.

Methods
One hundred twenty-five subjects (83 control and 42 case) were selected using stringent inclusion/exclusion criteria. DNA sequencing was used to identify 26 single nucleotide polymorphisms in the pituitary growth hormone gene (GH1) at which all subjects were genotyped. Association with fetal growth restriction was tested by logistic regression for all sites with minor allele frequencies greater than 5%.

Results
Logistic regression identified significant association with fetal growth restriction of C alleles at sites -1 and +3 (relative to the start of transcription) that are in complete linkage disequilibrium. These alleles are present at higher frequency (6% vs. 0.4%) in fetal growth restricted subjects and are associated with an average reduction in birth weight of 152 g in normal birth weight and 97 g in low birth weight subjects.

Conclusions
There is suggestive association between fetal growth restriction and the presence of C alleles at sites -1 and +3 of the pituitary growth hormone gene.
Psychometric properties and clinical utility of the Scale for Suicidal Ideation (SSI) in adolescents
Authors: Holi Matti M , Pelkonen Mirjami , Karlsson Linnea , Kiviruusu Olli , Ruuttu Titta , Heilä Hannele , Tuisku Virpi , Marttunen Mauri 
Published: February 2005

Abstract
Background
Accurate assessment of suicidality is of major importance in both clinical and research settings. The Scale for Suicidal Ideation (SSI) is a well-established clinician-rating scale but its suitability to adolescents has not been studied. The aim of this study was to evaluate the reliability and validity, and to test an appropriate cutoff threshold for the SSI in a depressed adolescent outpatient population and controls.

Methods
218 adolescent psychiatric outpatient clinic patients suffering from depressive disorders and 200 age- and sex-matched school-attending controls were evaluated by the SSI for presence and severity of suicidal ideation. Internal consistency, discriminative-, concurrent-, and construct validity as well as the screening properties of the SSI were evaluated.

Results
Cronbach's α for the whole SSI was 0.95. The SSI total score differentiated patients and controls, and increased statistically significantly in classes with increasing severity of suicidality derived from the suicidality items of the K-SADS-PL diagnostic interview. Varimax-rotated principal component analysis of the SSI items yielded three theoretically coherent factors suggesting construct validity. Area under the receiver operating characteristic (ROC) curve was 0.84 for the whole sample and 0.80 for the patient sample. The optimal cutoff threshold for the SSI total score was 3/4 yielding sensitivity of 75% and specificity of 88.9% in this population.

Conclusions
SSI appears to be a reliable and a valid measure of suicidal ideation for depressed adolescents.
Patient characteristics and clinical management of patients with shoulder pain in U.S. primary care settings: Secondary data analysis of the National Ambulatory Medical Care Survey
Authors: Wofford James L , Mansfield Richard J , Watkins Raquel S 
Published: February 2005

Abstract
Background
Although shoulder pain is a commonly encountered problem in primary care, there are few studies examining its presenting characteristics and clinical management in this setting.

Methods
We performed secondary data analysis of 692 office visits for shoulder pain collected through the National Ambulatory Medical Care Survey (Survey years 1993–2000). Information on demographic characteristics, history and place of injury, and clinical management (physician order of imaging, physiotherapy, and steroid intraarticular injection) were examined.

Results
Shoulder pain was associated with an injury in one third (33.2% (230/692)) of office visits in this population of US primary care physicians. Males, and younger adults (age ≤ 52) more often associated their shoulder pain with previous injury, but there were no racial differences in injury status. Injury-related shoulder pain was related to work in over one-fifth (21.3% (43/202)) of visits.
An x-ray was performed in 29.0% (164/566) of office visits, a finding that did not differ by gender, race, or by age status. Other imaging (CT scan, MRI, or ultrasound) was infrequently performed (6.5%, 37/566).
Physiotherapy was ordered in 23.9% (135/566) of visits for shoulder pain. Younger adults and patients with a history of injury more often had physiotherapy ordered, but there was no significant difference in the ordering of physiotherapy by gender or race. Examination of the use of intraarticular injection was not possible with this data set.

Conclusion
These data from the largest sample of patients with shoulder pain presenting to primary care settings offer insights into the presenting characteristics and clinical management of shoulder pain at the primary care level. The National Ambulatory Medical Care Survey is a useful resource for examining the clinical management of specific symptoms in U.S. primary care offices.
A novel surgical procedure for bridging of massive bone defects
Authors: Knothe Ulf R , Springfield Dempsey S 
Published: February 2005

Abstract
Background
Bony defects arising from tumor resection or debridement after infection, non-union or trauma present a challenging problem to orthopedic surgeons, as well as patients due to compliance issues. Current treatment options are time intensive, require more than one operation and are associated with high rate of complications. For this reason, we developed a new surgical procedure to bridge a massive long bone defect.

Methods
To bridge the gap, an in situ periosteal sleeve is elevated circumferentially off of healthy diaphyseal bone adjacent to the bone defect. Then, the adjacent bone is osteotomized and the transport segment is moved along an intramedullary nail, out of the periosteal sleeve and into the original diaphyseal defect, where it is docked. Vascularity is maintained through retention of the soft tissue attachments to the in situ periosteal sleeve. In addition, periosteal osteogenesis can be augmented through utilization of cancellous bone graft or in situ cortical bone adherent to the periosteal sleeve.

Results
The proposed procedure is novel in that it exploits the osteogenic potential of the periosteum by replacing the defect arising from resection of tissue out of a pathological area with a defect in a healthy area of tissue, through transport of the adjacent bone segment. Furthermore, the proposed procedure has several advantages over the current standard of care including ease of implementation, rapid patient mobilization, and no need for specialized implants (intramedullary nails are standard inventory for surgical oncology and trauma departments) or costly orthobiologics.

Conclusions
The proposed procedure offers a viable and potentially preferable alternative to the current standard treatment modalities, particularly in areas of the world where few surgeons are trained for procedures such as distraction osteogenesis (e.g. the Ilizarov procedure) as well as areas of the world where surgeons have little access to expensive, complex devices and orthobiologics.