bluuebunny/crossref_metadata_2025_split huggingface dataset:
Production of Retrovirus and Adenovirus Vectors for Gene Therapy: A Comparative Study Using Microcarrier and Stationary Cell Culture
Authors: Wu Suh‐Chin , Huang Gloria Yia‐Ling , Liu Jin‐Hwang 
Published: July 2002

AbstractIn gene therapy, retrovirus and adenovirus vectors are extensively used as gene‐delivery vehicles and further large‐scale processing of these viral vectors will be increasingly important. This study examined stationary and microcarrier cell culture systems with respect to the production of a retrovirus vector (encoding a monounit hammerhead ribozyme gene with an intron) and an adenovirus vector (encoding a reporter lacZ gene). Cytodex 1 and Cytodex 3 solid microcarriers were found to be able to provide good cell growth and high‐titer vector production in suspension cultures. Porous microcarriers such as Cytopore 2 gave slightly lower but still efficient growth but produced significantly lower titers of retrovirus and adenovirus vector from the producer cells. The specific retrovirus production was not proportionally related to the specific growth rate of the producer cells. High MOI infection was essential for high‐titer production of adenovirus vector in 293 cells. Hydrodynamic shear forces on microcarrier‐grown cells increased the production yield for retrovirus vector but decreased for adenovirus vector. The cellular productivity was much more efficient for adenovirus vector produced in 293 cells as compared to the retrovirus vector produced in PA317‐RCM1 cells. These findings can provide further insight into the feasibility of applying microcarrier cell culture technology to produce gene‐therapy virus vectors.
Effect of starvation time on the prey capture behaviour, functional response and population growth of Asplanchna sieboldi (Rotifera)
Authors: Nandini S. , Sarma S. S. S. 
Published: July 2002

1. We examined the effect of different periods of prior starvation(from 30 min to 16 h) on the prey capture behaviour, and functional and numerical responses of the predatory rotifer Asplanchna sieboldi using the rotifer Brachionus calyciflorus as prey.2. Feeding activity (i.e. encounter, attack, capture and ingestion) by Asplanchna increased significantly with increasing prey densities from 2 to 16 mL−−1 and with increasing prior starvation periods from 0.5 to 8 h.3. Asplanchna sieboldi showed a type II functional response at all the prior starvation periods tested. The asymptotic prey density was highest after 8 h of starvation.4. The instantaneous population growth rate of A. sieboldi ranged from 0.089 ± 0.044 (when starved for 8 h in every 24 h and at a prey density of 2 individuals mL−−1 for the other 16 h) to 1.015 ± 0.142 in the control (no starvation and at a prey density of 16 individuals mL−−1). The effect of starvation time on the numerical response was evident only at the higher prey density.
Characterization of ‘safe sites’ for pioneers in primary succession on recently deglaciated terrain
Authors: Jumpponen Ari , Väre Henry , Mattson Kim G. , Ohtonen Rauni , Trappe James M. 
Published: July 2002

1 We characterized safe sites for individuals of five early colonizers (Abies lasiocarpa, Juncus drummondii, J. mertensianus, Saxifraga ferruginea, S. tolmiei) that had survived at least one growing season on the recently deglaciated forefront of the Lyman Glacier in the North Cascade Mountains, Washington, USA. 2 Sites with concave surfaces, coarse surface substrate and in the vicinity of large rocks were more likely to be colonized by pioneering plant species. 3 We speculate that the distribution of plants is determined by the presence of sites that facilitate seed trapping and protect seeds and seedlings from desiccation. 4 The data identify the abiotic factors that determine initial recruitment and spatial distribution of plants. Such controls precede biotic interactions in this primary successional sere.
How does syringe distribution in prison affect consumption of illegal drugs by prisoners?
Authors: NELLES JOACHIM , FUHRER ANDREAS , HIRSBRUNNER HANS PETER 
Published: July 2002

AbstractDrug injection and syringe sharing is common among IDUs in prison. As a consequence, the prevalence of blood‐borne viral infections is several‐fold higher in prison than in the corresponding communities. Prisoners have been denied access to syringe exchange programmes, even though they have been proven to be highly effective in community settings. A 12‐month harm reduction programme which included syringe exchange was introduced into the only female prison (Hindelbank) in Switzerland. The programme was studied for 12 months (pilot phase). After the programme was completed, there was follow‐up 12 months later (follow‐up phase). Baseline data were collected on 137 of 161 prisoners. Follow up‐data were collected on 57 of 64 prisoners. Participants were interviewed several times about their use and injection of drugs and their shared use of syringes. Additional data on the number of syringes exchanged were also collected. Reports of drug use and injection in prison did not increase. The exchange of syringes was related to drug availability. Frequency of drug use increased in relation to duration of incarceration. Frequency of drug use decreased the longer the project had been implemented. None of the main arguments raised against the introduction of syringe distribution into prison, such as assault or an increase in drug injecting, was evident in this study. The results, although limited by the nature and the size of the prison, suggest that syringe exchange has a role in the prison setting.
Involvement of CNS cholinergic systems in alcohol drinking of P rats
Authors: KATNER S. N. , McBRIDE W. J. , LUMENG L. , LI T.‐K. , MURPHY J. M. 
Published: July 2002

AbstractAbstract Experiments were undertaken to determine if CNS muscarinic‐ and nicotinic‐cholinergic receptors are involved in regulating alcohol drinking of rats from the selectively‐bred alcohol‐preferring P line. Intracerebroventricular (i.c.v.) drug infusions were administered into the lateral ventricle of female P rats 15 minutes before ethanol access. The muscarinic antagonists pirenzepine and scopolamine were tested on limited access (4 hours/day) to a 10% (v/v) ethanol solution. Food and water were available ad libitum. Nicotine and the nicotinic antagonist mecamylamine were tested on limited access (4 hours/day) to 10% (v/v) ethanol and 0.0125% saccharin solutions. Food was available ad libitum and water was available during the remaining 20 hours. The baseline ethanol intakes ranged between an average of 3.0 ± 0.3 g/kg/4 hours and 3.4 ± 0.3 g/kg/4 hours. Administration of 40‐100 m g pirenzepine (M1‐selective antagonist) had no effect on ethanol, food or water consumption. However, 20‐80 m g scopolamine, a non‐selective muscarinic antagonist, dosedependently decreased ethanol intake as much as 60% (p < 0.05) without altering food or water consumption. The nicotinic antagonist mecamylamine (20‐120 m g) did not alter ethanol intake, but nicotine (40‐80 m g) dose‐dependently decreased ethanol drinking as much as 60% within the first 30 minutes (p < 0.05) without an effect on saccharin intake. The results suggest that: (a), muscarinic receptors, with the possible exception of the M1 subtype, are involved in regulating alcohol drinking and (b), activation of nicotinic receptors can reduce alcohol drinking of the P line of rats.
Mutations in the Essential Spindle Checkpoint Gene bub1 Cause Chromosome Missegregation and Fail to Block Apoptosis in Drosophila
Authors: Basu Joydeep , Bousbaa Hassan , Logarinho Elsa , Li ZeXiao , Williams Byron C. , Lopes Carla , Sunkel Claudio E. , Goldberg Michael L. 
Published: July 2002

We have characterized the Drosophila mitotic checkpoint control protein Bub1 and obtained mutations in the bub1 gene. Drosophila Bub1 localizes strongly to the centromere/kinetochore of mitotic and meiotic chromosomes that have not yet reached the metaphase plate. Animals homozygous for P-element–induced, near-null mutations of bub1 die during late larval/pupal stages due to severe mitotic abnormalities indicative of a bypass of checkpoint function. These abnormalities include accelerated exit from metaphase and chromosome missegregation and fragmentation. Chromosome fragmentation possibly leads to the significantly elevated levels of apoptosis seen in mutants.
We have also investigated the relationship between Bub1 and other kinetochore components. We show that Bub1 kinase activity is not required for phosphorylation of 3F3/2 epitopes at prophase/prometaphase, but is needed for 3F3/2 dephosphorylation at metaphase. Neither 3F3/2 dephosphorylation nor loss of Bub1 from the kinetochore is a prerequisite for anaphase entry. Bub1's localization to the kinetochore does not depend on the products of the genes zw10, rod, polo, or fizzy, indicating that the kinetochore is constructed from several independent subassemblies.
Just one more 'zine? Maintaining and improving the scholarly journal in the electronic present: a view from the humanities
Authors: Tomlins Christopher L. 
Published: July 2002

ABSTRACTHumanities journals have been laggards in exploration of opportunities that the online environment offers, and such attention as editors have given the matter has focused on distribution. This article describes how history journals in the USA are moving to establish a collective presence for scholarly history online. It suggests that editors should give equal attention to current opportunities to improve journals' operational efficiencies through full exploitation of desktop publishing in production and the reorganization of manuscript management (submissions, peer review, and author–editor interactions) as online processes. It concludes that cooperation in online distribution of journal scholarship could well lead on to cooperative use of online production and management tools.
The evaluation of peer‐review quality
Authors: van Rooyen Susan 
Published: July 2002

ABSTRACTThis paper discusses the role of peer review in the decision‐making processes of scientific journals. It outlines the objectives of peer review and some of the problems. It then goes on to describe research into the quality of peer review, in particular the BMJ's programme of research to date, the results obtained, and consequent changes in practice. It also looks briefly at future possibilities for research into the peer‐review process.
Never mind the textbook — here's the chapters
Authors: Taylor David 
Published: July 2002

ABSTRACTThis paper first looks at the current supply model for the paper textbook in the UK market and its peculiar vulnerability not only to the new internet‐based entrants, but also to the changing nature of the very product itself. It then looks at the emerging supply model for the electronic version of the textbook – the e‐book – and why that mode of delivery is especially appropriate to the UK student market. It concludes by describing what the future supply model might look like for this material: the delivery of the electronic chapter.
Virtual and non‐virtual realities: the changing roles of libraries and librarians
Authors: Klugkist Alex C. 
Published: July 2002

ABSTRACTWhat is the future for libraries and their librarians? In trying to give an answer to this pressing question we do not deal with utopian libraries of the next century, but with the library and the librarian of the next decade. The emphasis is on libraries within educational and research institutions, especially university libraries. We examine the changes confronting the library of the future and identify four key aspects of the library of the future. It will be (i) a gateway to information, whatever format this information comes in and wherever it is located; (ii) an expertise centre; (iii) a physical entity, not only in the sense of being a social meeting place and place of scholarly interaction, but also as a place where students and other users are provided with modern study facilities and adequate user support; and (iv) a collection centre of printed material. Such libraries can only take on an appropriate shape and will only survive if the institutions that librarians serve in meet the four criteria outlined above. We look at the demands that will be made on professional library knowledge and skills and the new job responsibilities and job attitudes required.
A year without print at Princeton, and what we plan next
Authors: Goodman David 
Published: July 2002

ABSTRACTPrinceton began to receive some major titles as electronic only, starting with the 2000 subscription year. We are expanding this in appropriate cases where we have confidence in the publisher, and the financial advantage is significant. There have been no complaints, and also almost no comments. Apparently users now look for current journal articles online, using the paper versions only if online is not available. We plan further developments to facilitate user convenience.
Fast solvers of integral and pseudodifferential equations on closed curves
Authors: Saranen J. , Vainikko G. 
Published: July 2002

On the basis of a fully discrete trigonometric Galerkin method and two grid iterations we propose solvers for integral and pseudodifferential equations on closed curves which solve the problem with an optimal convergence order

‖

u
N

−
u

‖
λ

≤

c

λ
,
μ

N

λ
−
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‖
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‖
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\|u_N-u\|_\lambda \leq c_{\lambda ,\mu }N^{\lambda -\mu }\|u\|_\mu

,

λ
≤
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\lambda \leq \mu

(Sobolev norms of periodic functions) in

O

(
N
log
⁡
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)

\mathrm {O}(N\log N)

arithmetical operations.
Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets.
Authors: Backofen R , Will S , Bornberg-Bauer E 
Published: July 2002

Abstract
MOTIVATION: Predicting the ground state of biopolymers is a notoriously hard problem in biocomputing. Model systems, such as lattice proteins, are simple tools and valuable to test and improve new methods. Best known are models with sequences composed from a binary (hydrophobic and polar) alphabet. The major drawback is the degeneracy, i.e. the number of different ground state conformations. RESULTS: We show how recently developed constraint programming techniques can be used to solve the structure prediction problem efficiently for a higher order alphabet. To our knowledge it is the first report of an exact and computationally feasible solution to model proteins of length up to 36 and without resorting to maximally compact states. We further show that degeneracy is reduced by more than one order of magnitude and that ground state conformations are not necessarily compact. Therefore, more realistic protein simulations become feasible with our model.
Investigating extended regulatory regions of genomic DNA sequences.
Authors: Babenko V N , Kosarev P S , Vishnevsky O V , Levitsky V G , Basin V V , Frolov A S 
Published: July 2002

Abstract
MOTIVATION: Despite the growing volume of data on primary nucleotide sequences, the regulatory regions remain a major puzzle with regard to their function. Numerous recognising programs considering a diversity of properties of regulatory regions have been developed. The system proposed here allows the specific contextual, conformational and physico-chemical properties to be revealed based on analysis of extended DNA regions. RESULTS: The Internet-accessible computer system RegScan, designed to analyse the extended regulatory regions of eukaryotic genes, has been developed. The computer system comprises the following software: (i) programs for classification dividing a set of promoters into TATA-containing and TATA-less promoters and promoters with and without CpG islands; (ii) programs for constructing (a) nucleotide frequency profiles, (b) sequence complexity profiles and (c) profiles of conformational and physico-chemical properties; (iii) the program for constructing the sets of degenerate oligonucleotide motifs of a specified length; and (iv) the program searching for and visualising repeats in nucleotide sequences. The system has allowed us to demonstrate the following characteristic patterns of vertebrate promoter regions: the TATA box region is flanked by regions with an increased G+C content and increased bending stiffness, the TATA box content is asymmetric and promoter regions are saturated with both direct and inverted repeats. AVAILABILITY: The computer system RegScan is available via the Internet at http://www.mgs.bionet.nsc. ru/Systems/RegScan, http://www.cbil.upenn.edu/mgs/systems/r egscan/.
Functional and structural genomics using PEDANT
Authors: Frishman Dmitrij , Albermann Kaj , Hani Jean , Heumann Klaus , Metanomski Agnes , Zollner Alfred , Mewes Hans-Werner 
Published: July 2002

Abstract
Motivation: Enormous demand for fast and accurate analysis of biological sequences is fuelled by the pace of genome analysis efforts. There is also an acute need in reliable up-to-date genomic databases integrating both functional and structural information. Here we describe the current status of the PEDANT software system for high-throughput analysis of large biological sequence sets and the genome analysis server associated with it.
Results: The principal features of PEDANT are: (i) completely automatic processing of data using a wide range of bioinformatics methods, (ii) manual refinement of annotation, (iii) automatic and manual assignment of gene products to a number of functional and structural categories, (iv) extensive hyperlinked protein reports, and (v) advanced DNA and protein viewers. The system is easily extensible and allows to include custom methods, databases, and categories with minimal or no programming effort. PEDANT is actively used as a collaborative environment to support several on-going genome sequencing projects. The main purpose of the PEDANT genome database is to quickly disseminate well-organized information on completely sequenced and unfinished genomes. It currently includes 80 genomic sequences and in many cases serves as the only source of exhaustive information on a given genome. The database also acts as a vehicle for a number of research projects in bioinformatics. Using SQL queries, it is possible to correlate a large variety of pre-computed properties of gene products encoded in complete genomes with each other and compare them with data sets of special scientific interest. In particular, the availability of structural predictions for over 300 000 genomic proteins makes PEDANT the most extensive structural genomics resource available on the web.
Availability: The PEDANT genome analysis server is available at http://pedant.mips.biochem.mpg.de.
Contact: Genome sequencing centres interested in inclusion of their sequences in the PEDANT database should contact Dmitrij Frishman (frishman@mips.biochem.mpg.de).
* To whom correspondence should be addressed.
Experiences and viewpoints of PhD students completing their dissertations during crises
Authors: Znamenak Kyle , Lieberth Mitch , Murphy Jennifer L. , Sheaffer Auburn 
Published: June 2022

AbstractThis article narrates the experiences of four former PhD students who completed the transition from graduate student to graduates with PhDs during unprecedented external events: The COVID‐19 pandemic and a period of civil unrest in response to the 2020 police killings of George Floyd and Breonna Taylor. The authors reflect on some commonalities in how they were able to adjust and persevere to completion.
Conversations with leaders: Sharing perspectives on the impact of and response to COVID‐19 and other crises
Authors: Schmidt Steven W. , English Leona M. , Carr‐Chellman Ali 
Published: June 2022

AbstractLessons learned during the COVID‐19 pandemic, through trial and error and sharing stories of successes and failures, have resulted in progress in the quest to resume what we refer to as normal or regular college life for students, faculty, and staff. However, it is doubtful that we will ever get back to the exact same situation that we were in prior to March of 2020, and that may not even be an appropriate goal for which to strive. We can learn from this pandemic and continuously improve what we do based on lessons learned rather than simply focusing on getting back to some sort of prepandemic “normal” state. This article and this entire edition of New Directions for Adult and Continuing Education are part of those efforts to document our experiences so we all can learn from them and move forward with that knowledge in mind.
Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention
Authors: Orchanian Stephanie B. , Gauglitz Julia M. , Wandro Stephen , Weldon Kelly C. , Doty Megan , Stillwell Kristina , Hansen Shalisa , Jiang Lingjing , Vargas Fernando , Rhee Kyung E. , Lumeng Julie C. , Dorrestein Pieter C. , Knight Rob , Kim Jae H. , Song Se Jin , Swafford Austin D. 
Published: June 2022

AbstractThe first week after birth is a critical time for the establishment of microbial communities for infants. Preterm infants face unique environmental impacts on their newly acquired microbiomes, including increased incidence of cesarean section delivery and exposure to antibiotics as well as delayed enteral feeding and reduced human interaction during their intensive care unit stay. Using contextualized paired metabolomics and 16S sequencing data, the development of the gut, skin, and oral microbiomes of infants is profiled daily for the first week after birth, and it is found that the skin microbiome appears robust to early life perturbation, while direct exposure of infants to antibiotics, rather than presumed maternal transmission, delays microbiome development and prevents the early differentiation based on body site regardless of delivery mode. Metabolomic analyses identify the development of all gut metabolomes of preterm infants toward full‐term infant profiles, but a significant increase of primary bile acid metabolism only in the non‐antibiotic treated vaginally birthed late preterm infants. This study provides a framework for future multi‐omic, multibody site analyses on these high‐risk preterm infant populations and suggests opportunities for monitoring and intervention, with infant antibiotic exposure as the primary driver of delays in microbiome development.
Snake Venom Hydrogels as a Rapid Hemostatic Agent for Uncontrolled Bleeding
Authors: Yegappan Ramanathan , Lauko Jan , Wang Zhao , Lavin Martin F. , Kijas Amanda W. , Rowan Alan E. 
Published: June 2022

AbstractUncontrolled bleeding from traumatic injury remains the leading cause of preventable death with loss of balance between blood clotting (coagulation) and blood clot breakdown (fibrinolysis). A major limitation of existing hemostatic agents is that they require a functioning clotting system to control the bleeding and are largely based on gauze delivery scaffolds. Herein, a novel rapid wound sealant, composed of two recombinant snake venom proteins, the procoagulant ecarin, to rapidly initiate blood clotting and the antifibrinolytic textilinin, to prevent blood clot breakdown within a synthetic thermoresponsive hydrogel scaffold is developed. In vitro, it is demonstrated that clotting is rapidly initiated with only nanomolar concentrations of venom protein and clot breakdown is effectively inhibited by textilinin. A stable clot is formed within 60 s compared to normal clot formation in 8 min. In vivo studies reveal that the snake venom hydrogel rapidly controls warfarin‐induced bleeding, reducing the bleed volume from 48% to 12% and has demonstrated immune compatibility. A new class of hemostatic agents that achieve formation of rapid and stable blood clots even in the presence of blood thinners is demonstrated here.