bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tudor Nuclease Genes and Programmed DNA Rearrangements in
Tetrahymena thermophila
Authors: Howard-Till Rachel A. , Yao Meng-Chao 
Published: August 2007

ABSTRACT

Proteins containing a Tudor domain and domains homologous to staphylococcal nucleases are found in a number of eukaryotes. These “Tudor nucleases” have been found to be associated with the RNA-induced silencing complex (A. A. Caudy, R. F. Ketting, S. M. Hammond, A. M. Denli, A. M. Bathoorn, B. B. Tops, J. M. Silva, M. M. Myers, G. J. Hannon, and R. H. Plasterk, Nature
425
:411-414, 2003). We have identified two Tudor nuclease gene homologs,
TTN1
and
TTN2
, in the ciliate
Tetrahymena thermophila
, which has two distinct small-RNA pathways. Characterization of single and double KOs of
TTN1
and
TTN2
shows that neither of these genes is essential for growth or sexual reproduction. Progeny of
TTN2
KOs and double knockouts occasionally show minor defects in the small-RNA-guided process of DNA deletion but appear to be normal in hairpin RNA-induced gene silencing, suggesting that Tudor nucleases play only a minor role in RNA interference in
Tetrahymena
. Previous studies of
Tetrahymena
have shown that inserted copies of the
neo
gene from
Escherichia coli
are often deleted from the developing macronucleus during sexual reproduction (Y. Liu, X. Song, M. A. Gorovsky, and K. M. Karrer, Eukaryot. Cell
4:
421-431, 2005; M. C. Yao, P. Fuller, and X. Xi, Science
300:
1581-1584, 2003). This transgene deletion phenomenon is hypothesized to be a form of genome defense. Analysis of the Tudor nuclease mutants revealed exceptionally high rates of deletion of the
neo
transgene at the
TTN2
locus but no deletion at the
TTN1
locus. When present in the same genome, however, the
neo
gene is deleted at high rates even at the
TTN1
locus, further supporting a role for
trans
-acting RNA in this process. This deletion is not affected by the presence of the same sequence in the macronucleus, thus providing a counterargument for the role of the macronuclear genome in specifying all sequences for deletion.
Human Immunodeficiency Virus Type 1 (HIV-1) Plasma Load Discrepancies between the Roche COBAS AMPLICOR HIV-1 MONITOR Version 1.5 and the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 Assays
Authors: Damond F. , Roquebert B. , Bénard A. , Collin G. , Miceli M. , Yéni P. , Brun-Vezinet F. , Descamps D. 
Published: August 2007

ABSTRACT

We compared plasma viral load values obtained with COBAS AMPLICOR human immunodeficiency virus type 1 (HIV-1) MONITOR version 1.5 and with COBAS TaqMan HIV-1 assays. Mean values were 4.2 and 2.9 log
10
copies/ml, respectively, showing the lack of agreement between the two assays.
Functional Genomic and Serological Analysis of the Protective Immune Response Resulting from Vaccination of Macaques with an NS1-Truncated Influenza Virus
Authors: Baskin C. R. , Bielefeldt-Ohmann H. , García-Sastre A. , Tumpey T. M. , Van Hoeven N. , Carter V. S. , Thomas M. J. , Proll S. , Solórzano A. , Billharz R. , Fornek J. L. , Thomas S. , Chen C.-H. , Clark E. A. , Murali-Krishna Kaja , Katze M. G. 
Published: August 2007

ABSTRACT

We are still inadequately prepared for an influenza pandemic due to the lack of a vaccine effective for subtypes to which the majority of the human population has no prior immunity and which could be produced rapidly in sufficient quantities. There is therefore an urgent need to investigate novel vaccination approaches. Using a combination of genomic and traditional tools, this study compares the protective efficacy in macaques of an intrarespiratory live influenza virus vaccine produced by truncating NS1 in the human influenza A/Texas/36/91 (H1N1) virus with that of a conventional vaccine based on formalin-killed whole virus. After homologous challenge, animals in the live-vaccine group had greatly reduced viral replication and pathology in lungs and reduced upper respiratory inflammation. They also had lesser induction of innate immune pathways in lungs and of interferon-sensitive genes in bronchial epithelium. This postchallenge response contrasted with that shortly after vaccination, when more expression of interferon-sensitive genes was observed in bronchial cells from the live-vaccine group. This suggested induction of a strong innate immune response shortly after vaccination with the NS1-truncated virus, followed by greater maturity of the postchallenge immune response, as demonstrated with robust influenza virus-specific CD4
+
T-cell proliferation, immunoglobulin G production, and transcriptional induction of T- and B-cell pathways in lung tissue. In conclusion, a single respiratory tract inoculation with an NS1-truncated influenza virus was effective in protecting nonhuman primates from homologous challenge. This protection was achieved in the absence of significant or long-lasting adverse effects and through induction of a robust adaptive immune response.
Immunization of Primates with a Newcastle Disease Virus-Vectored Vaccine via the Respiratory Tract Induces a High Titer of Serum Neutralizing Antibodies against Highly Pathogenic Avian Influenza Virus
Authors: DiNapoli Joshua M. , Yang Lijuan , Suguitan Amorsolo , Elankumaran Subbiah , Dorward David W. , Murphy Brian R. , Samal Siba K. , Collins Peter L. , Bukreyev Alexander 
Published: August 2007

ABSTRACT

The ongoing outbreak of highly pathogenic avian influenza virus (HPAIV) in birds, the incidence of transmission to humans with a resulting high mortality rate, and the possibility of a human pandemic warrant the development of effective human vaccines against HPAIV. We developed an experimental live-attenuated vaccine for direct inoculation of the respiratory tract based on recombinant avian Newcastle disease virus (NDV) expressing the hemagglutinin (HA) glycoprotein of H5N1 HPAIV (NDV-HA). Expression of the HPAIV HA gene slightly reduced NDV virulence, as evidenced by the increased mean embryo death time and reduced replication in chickens. NDV-HA was administered to African green monkeys in two doses of 2 × 10
7
infectious units each with a 28-day interval to evaluate the systemic and local antibody responses specific to H5N1 HPAIV. The virus was shed only at low titers from the monkeys, indicative of safety. Two doses of NDV-HA induced a high titer of H5N1 HPAIV-neutralizing serum antibodies in all of the immunized monkeys. Moreover, a substantial mucosal immunoglobulin A response was induced in the respiratory tract after one and two doses. The titers of neutralizing antibodies achieved in this study suggest that the vaccine would be likely to prevent mortality and reduce morbidity caused by the H5N1 HPAIV. In addition, induction of a local immune response in the respiratory tract is an important advantage that is likely to reduce or prevent transmission of the virus during an outbreak or a pandemic. This vaccine is a candidate for clinical evaluation in humans.
Protection of Rabbits against Challenge with Rabbit Papillomaviruses by Immunization with the N Terminus of Human Papillomavirus Type 16 Minor Capsid Antigen L2
Authors: Gambhira Ratish , Jagu Subhashini , Karanam Balasubramanyam , Gravitt Patti E. , Culp Timothy D. , Christensen Neil D. , Roden Richard B. S. 
Published: August 2007

ABSTRACTCurrent L1 virus-like particle (VLP) vaccines provide type-restricted protection against a small subset of the human papillomavirus (HPV) genotypes associated with cervical cancer, necessitating continued cytologic screening of vaccinees. Cervical cancer is most problematic in countries that lack the resources for screening or highly multivalent HPV VLP vaccines, suggesting the need for a low-cost, broadly protective vaccinogen. Here, N-terminal L2 polypeptides comprising residues 1 to 88 or 11 to 200 derived from HPV16, bovine papillomavirus type 1 (BPV1), or cottontail rabbit papillomavirus (CRPV) were produced in bacteria. Rabbits were immunized with these N-terminal L2 polypeptides and concurrently challenged with CRPV and rabbit oral papillomavirus (ROPV). Vaccination with either N-terminal L2 polypeptides of CRPV effectively protected rabbits from CRPV challenge but not from papillomas induced by cutaneous challenge with CRPV genomic DNA. Furthermore, papillomas induced by CRPV genomic DNA deficient for L2 expression grew at the same rate as those induced by wild-type CRPV genomic DNA, further suggesting that the L2 polypeptide vaccines lack therapeutic activity. Neutralizing serum antibody titers of >15 correlated with protection (P< 0.001), a finding consistent with neutralizing antibody-mediated protection. Surprisingly, a remarkable degree of protection against heterologous papillomavirus types was observed after vaccination with N-terminal L2 polypeptides. Notably, vaccination with HPV16 L2 11-200 protected against cutaneous and mucosal challenge with CRPV and ROPV, respectively, papillomaviruses that are evolutionarily divergent from HPV16. Further, vaccination with HPV16 L2 11-200 generates broadly cross-neutralizing serum antibody, suggesting the potential of L2 as a second-generation preventive HPV vaccine antigen.
The Deaths of God in Hegel and Nietzsche and the Crisis of Values in Secular Modernity and Post-secular Postmodernity
Authors: Franke William 
Published: August 2007

AbstractAlthough declarations of the death of God seem to be provocations announcing the end of the era of theology, this announcement is actually central to the Christian revelation in its most classic forms, as well as to its reworkings in contemporary religious thought. Indeed provocative new possibilities for thinking theologically open up precisely in the wake of the death of God. Already Hegel envisaged a revolutionary new realization of divinity emerging in and with the secular world through its establishment of a total order of immanence. However, in postmodern times this comprehensive order aspired to by modern secularism implodes or cracks open towards the wholly Other. A hitherto repressed demand for the absolute diff erence of the religious, or for "transcendence," returns with a vengeance. is difference is what could not be stated in terms of the Hegelian System, for reasons that post-structuralist writers particularly have insisted on: all representations of God are indeed dead. Yet this does not mean that they cannot still be powerful, but only that they cannot assign God any stable identity. Nietzsche's sense of foreboding concerning the death of God is coupled with his intimations of the demise of representation and “grammar” as epistemologically bankrupt, but also with his vision of a positive potential for creating value in the wake of this collapse of all linguistically articulated culture. He points the way towards the emergence of a post-secular religious thinking of what exceeds thought and representation.
Prisoner Behavior and Social System in the Nazi Concentration Camps
Authors: Luchterhand Elmer 
Published: August 2007

Until recently, American theory and discussion on prisoner behavior in the Nazi concentration camps differed in important ways from most European work. The American peculiarities stem from two main sources. First, there were gross reporting errors which added to the common difficulties in making sense of the camp system and genocide. Second, before the end of World War II and after, there was quick publication of poorly-grounded theories, reflecting concern with narrowly psychodynamic processes, rather than social processes. The present paper reviews study findings on the importance of human groups in the struggle for survival. Particular attention is given to the emergence of a prisoner social system and to the normative aspects of such a system. Along with references to the relevant work of others, the author deals at some length with his own early research, involving intensive interviews with fifty-two camp sur vivors who emigrated to the United States. In that study, data were gathered on changes with time in the camps in (1) patterns of interpersonal relations, (2) sharing with other prisoners and assisting them, and (3) thefts from other prisoners. The paper considers several propositions on human behavior in extreme situations. These include the proposition by Bruno Bettelheim that the longer prisoners were confined, the more they identified with the SS; that a prisoner had reached the final stage of adjustment to the camp situation when he had changed his personality so as to accept as his own the values11 of his captors. The paper summarizes the author's findings on prisoner behavior in especially extreme situations such as prolonged punishment assemblies and winter- time transports of Auschwitz evacuees; on the attitudes of respondents toward "old" prisoners and toward members of prisoner underground organizations; and on the length of imprisonment of members of various national and inter national camp committees. Evidence is offered which suggests that stable pairing was the most common type of interpersonal relationship pattern and that most survivors had a sharing relationship of mutuality with one or more persons; that the pair was the basic unit of survival. Respondents showing decline in sharing behavior were in the camps sub stantially less time than those showing no change. Those respondents who showed greater and more stable general social participation were in the camps con siderably longer than those whose participation declined. Respondents showing decline in thefts (taking from other prisoners only) or consideration of theft, were in the camps longer than those showing increasing theft behavior. The study findings offered conflict at many points with narrowly psycho dynamic interpretations of prisoner behavior. It is concluded that in the camps the human group and social change system emerge as the most fruitful foci for scientific analysis.
Degree of Pathology as Related To Readiness To Accept Labels in Process and Reactive Schizophrenics
Authors: Johnson James E. , Petzel Thomas P. , Becker Paul A. , Rudinsky Mark F. 
Published: August 2007

TWO experiments were performed in order to determine whether readiness to accept deviant labels, as measured by acquiescence set, interacts with type of schizophrenia (process vs. reactive) to influence level of pathology. It was found on both a behavioral measure and a psychometric measure of psychopathology that high acquiescent process schizophrenics manifested more pathology than did either low acquiescent process or reactive schizophrenics, both of whom showed more pathology than high acquiescent reactive schizophrenics. The results suggest that one's ac ceptance of deviant labels as well as one's past history of being assigned social and evaluative labels may influence the patient's level of pathology. Scheff (1966), in viewing the mental patient from a sociological perspective, suggests that an important determinant of mental disorder is the acceptance by the deviant individual of the various labels which stigmatize him as mentally ill. If this is the case, then individual differences in readiness to accept or agree with labels about oneself may be related to the degree of pathology manifested in a psychiatric population. The present authors sought to determine if acquiescence set, as measured by the Agreement Response Scale (Couch & Keniston, 1960), is related to degree of pathology in schizophrenic patients. The Agreement Response Scale was used as a measure of the general tendency to acquiesce to or agree with personality statements or labels. The investigators performed two experiments, in Experiment 1 a behavioral measure of pathology was used and in Experiment 2 a psychometric measure of pathology was used. In addition, the schizophrenic Ss were grouped according to the process-reactive distinction as the reactive schizophrenic may be expected to have a more favorable history of labeling than would the process schizophrenic.
Sex Roles At the Indian-Majority Interface in Minnesota
Authors: Westermeyer Joseph 
Published: August 2007

Recently Indian men have played a major role in the new activist—sometimes militant—organisations acting on behalf of Indian people. However, this major role contrasts markedly with the situation usually encountered in most social institutions. There one finds more Indian women in influential positions, with more Indian men relegated to custodial positions. This paper addresses the patterns and distribution of this bias against Indian men. It contrasts this bias in the general society with the major social role played by men within Indian social forms. Hypotheses are included that may aid our under standing of both the psychological and social dimensions of this phenomenon. Remedial measures are suggested.
Epidemiological Aspects of the Repatriate Syndrome
Authors: Burke A.W. 
Published: August 2007

A careful analysis of the mental hospital case notes of 55 Jamaicans who had become ill in Britain and were successfully traced in Jamaica show that most had suffered from recurrent episodes of schizophrenia but that few were predisposed develop this illness. After an average period of 42 months follow-up it was found that there had been an excessive mortality and that others were living in the Bush. The most important finding of the study is that the chronic symptoms of illness which have been previously described as characteristic of the repatriate syndrome, had taken place in a half of the sample. Nevertheless there was evidence of a good outcome in a third of those who were living and interviewed during the field survey. These findings have been discussed. It has been concluded that repatriation may be of therapeutic benefit but only following more careful selection of cases.
MLN3897, a novel CCR1 inhibitor, impairs osteoclastogenesis and inhibits the interaction of multiple myeloma cells and osteoclasts
Authors: Vallet Sonia , Raje Noopur , Ishitsuka Kenji , Hideshima Teru , Podar Klaus , Chhetri Shweta , Pozzi Samantha , Breitkreutz Iris , Kiziltepe Tanyel , Yasui Hiroshi , Ocio Enrique M. , Shiraishi Norihiko , Jin Janice , Okawa Yutaka , Ikeda Hiroshi , Mukherjee Siddhartha , Vaghela Nileshwari , Cirstea Diana , Ladetto Marco , Boccadoro Mario , Anderson Kenneth C. 
Published: August 2007

Abstract
The interaction between osteoclasts (OCs) and multiple myeloma (MM) cells plays a key role in the pathogenesis of MM-related osteolytic bone disease (OBD). MM cells promote OC formation and, in turn, OCs enhance MM cell proliferation. Chemokines are mediators of MM effects on bone and vice versa; in particular, CCL3 enhances OC formation and promotes MM cell migration and survival. Here, we characterize the effects of MLN3897, a novel specific antagonist of the chemokine receptor CCR1, on both OC formation and OC-MM cell interactions. MLN3897 demonstrates significant impairment of OC formation (by 40%) and function (by 70%), associated with decreased precursor cell multinucleation and down-regulation of c-fos signaling. OCs secrete high levels of CCL3, which triggers MM cell migration; conversely, MLN3897 abrogates its effects by inhibiting Akt signaling. Moreover, MM cell-to-OC adhesion was abrogated by MLN3897, thereby inhibiting MM cell survival and proliferation. Our results therefore show novel biologic sequelae of CCL3 and its inhibition in both osteoclastogenesis and MM cell growth, providing the preclinical rationale for clinical trials of MLN3897 to treat OBD in MM.
Clinical determinants of exacerbations in severe, early-onset COPD
Authors: Foreman M. G. , DeMeo D. L. , Hersh C. P. , Reilly J. J. , Silverman E. K. 
Published: August 2007

Chronic obstructive pulmonary disease (COPD) exacerbations impair health. The present authors analysed participants in the Boston Early-Onset COPD Study for familial aggregation and propensity for COPD exacerbations.In the present study, two exacerbation outcomes, episodes of cough and phlegm, and frequent exacerbations were analysed with multivariable modelling and generalised estimating equations.In early-onset COPD probands, passive tobacco smoke exposure within the home was strongly associated with episodes of cough and phlegm. Chronic phlegm production was associated with both exacerbation phenotypes in probands. In first-degree relatives of early-onset COPD probands, chronic bronchitis, episodic wheezing, pneumonia and active smoking were associated with the episodes of cough and phlegm phenotype. In relatives, identical characteristics plus exertional dyspnoea were associated with frequent exacerbations. Exacerbation risk increased with declining lung function. Familial aggregation for episodes of cough and phlegm was observed in relatives with severe obstruction.In conclusion, passive smoke exposure increases morbidity in severe early-onset chronic obstructive pulmonary disease probands, and chronic obstructive pulmonary disease exacerbations correlate with chronic sputum production in probands and relatives. The familial aggregation of exacerbations suggests a genetic basis for susceptibility to chronic obstructive pulmonary disease exacerbations.
Protein structural similarity search by Ramachandran codes
Authors: Lo Wei-Cheng , Huang Po-Jung , Chang Chih-Hung , Lyu Ping-Chiang 
Published: August 2007

AbstractBackgroundProtein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases.ResultsWe propose a new linear encoding method, SARST (Structural similarity searchAided byRamachandranSequentialTransformation). SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE) and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms.ConclusionAs a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.