bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing global models of terrestrial net primary productivity (NPP): the importance of water availability
Authors: Churkina G. , Running S. W. , Schloss A. L. , Intercomparison ThE. Participants OF. ThE. Potsdam NpP. Model 
Published: July 2002

SummaryGiven that neither absolute measures nor direct model validations of global terrestrial net primary productivity (NPP) are feasible, intercomparison of global NPP models provides an effective tool to check model consistency. For this study, we tested the assumption that water availability is the primary limiting factor of NPP in global terrestrial biospheric models. We compared a water balance coefficient (WBC), calculated as the difference of mean annual precipitation and potential evapotranspiration to NPP for each grid cell (0.5° × 0.5° longitude/latitude) in each of 14 models. We also evaluated different approaches used for introducing water budget limitations on NPP: (1) direct physiological control on evapotranspiration through canopy conductance; (2) climatological computation of constraints from supply/demand for ecosystem productivity; and (3) water limitation inferred from satellite data alone. Plots of NPP vs. WBC showed comparable patterns for the models using the same method for water balance limitation on NPP. While correlation plots revealed similar patterns for most global models, other environmental controls on NPP introduced substantial variability.
K+ channels of Cf‐9 transgenic tobacco guard cells as targets for Cladosporium fulvum Avr9 elicitor‐dependent signal transduction
Authors: Blatt Michael R. , Grabov Alexander , Brearley Jane , Hammond‐Kosack Kim , Jones Jonathan D. G. 
Published: July 2002

SummaryThe Cf‐9 gene encodes an extracytosolic leucine‐rich repeat (LRR) protein that is membrane anchored near its C‐terminus. The protein confers resistance in tomato to races of the fungus Cladosporium fulvum expressing the corresponding avirulence gene Avr9. In Nicotiana tabacum the Cf‐9 transgene confers sensitivity to the Avr9 elicitor, and leads on elicitation to a subset of defence responses qualitatively similar to those normally seen in the tomato host. One of the earliest responses, both in the native and transgenic hosts, results in K+ salt loss from the infected tissues. However, the mechanism(s) underlying this solute flux and its control is poorly understood. We have explored the actions of Avr9 on Cf‐9 transgenic Nicotiana using guard cells as a model. Much detail of guard cell ion channels and their regulation is already known. Measurements were carried out on intact guard cells in epidermal peels, and the currents carried by inward‐ (IK,in) and outward‐rectifying (IK,out) K+ channels were characterized under voltage clamp. Exposures to Avr9‐containing extracts resulted in a 2.5‐ to 3‐fold stimulation of IK,out and almost complete suppression of IK,in within 3–5 min. The K+ channel responses were irreversible. They were specific for the Avr9 elicitor, were not observed in guard cells of Nicotiana lacking the Cf‐9 transgene and, from kinetic analyses, could be ascribed to changes in channel gating. Both K+ channel responses were found to be saturable functions of Avr9 concentration and were completely blocked in the presence of 0.5 μM staurosporine and 100 μM H7, both broad‐range protein kinase antagonists. These results demonstrate the ability of the Cf‐9 transgene to couple Avr9 elicitation specifically to a concerted action on two discrete K+ channels and they indicate a role for protein phosphorylation in Avr9/Cf‐9 signal transduction leading to transport control.
Non‐vascular intervention with real‐time CT fluoroscopy
Authors: Law Eu Meng , Little Andrew F , Salanitri John C 
Published: July 2002

SUMMARYThe emerging technology of CT fluoroscopy (CTF) represents the first opportunity for real‐time CT guidance in non‐vascular intervention. As with any new technology, its efficacy requires validation before widespread application can be advocated. A review of our initial experience is presented with particular attention to room, procedure and fluoroscopy time savings, complication rates and dosimetry. Computed tomography fluoroscopy is useful for pulmonary, pelvic, retroperitoneal and other deep organ lesions that are not easily accessible by other modalities. Computed tomography fluoroscopy decreases procedure time by at least a factor of 2 compared with conventional CT (C‐CT) guidance, resulting in improved throughput in a busy interventional CT department. Accurate targeting of small lesions, previously considered inaccessible, can also be achieved with CTF. Exposure to the physician’s hands can be reduced to a level that is acceptable to the International Commission on Radiological Protection guidelines.
Efficacy and safety of transurethral alprostadil therapy in men with erectile dysfunction
Authors: Williams  , Abbou  , Amar  , Desvaux  , Flam  , Lycklama à Nijeholt  , Lynch  , Morgan  , MÜller  , Porst  , Pryor  , Ryan  , Witzsch  , Hall  , Place  , Spivack  , Gesundheit on behalf of the Muse Study Group  
Published: July 2002

Objective To examine the safety and efficacy of transurethral pharmacotherapy for erectile dysfunction, involving the use of a novel therapeutic system to administer alprostadil (prostaglandin E1) to the urethral mucosa in a double‐blind, randomized, parallel, placebo‐controlled study conducted in five countries in Europe.Patients and methods In an outpatient setting, patients with primarily organic erectile dysfunction of at least 3 months’ duration were treated with transurethral alprostadil, in an open‐label, dose‐escalating study. Testing stopped when the dose provided an erection sufficient for intercourse, as assessed by the patient and the investigator. Patients who achieved a sufficient response were then randomized to either active medication at the selected dose or to placebo for use at home for 3 months. After each home administration, patients recorded in diaries whether or not sexual intercourse occurred and any adverse reactions to the drug.Results A total of 249 patients were treated in an outpatient setting; of these patients, 159 (64%) achieved an erection sufficient for intercourse and were randomized (1:1) to either active medication or placebo for home treatment. Of the patients randomized to alprostadil for home treatment, 69% reported intercourse at least once, compared with 11% of patients randomized to placebo (P<0.001). The most common adverse reaction, urethral pain/burning, was reported by 7% of patients in the clinic. Most patients (83%) graded transurethral alprostadil as causing minimal or no discomfort in the clinic. No patient reported priapism or developed penile fibrosis.Conclusion Alprostadil delivered transurethrally by this system was well tolerated and effective in treating erectile dysfunction.
Concordance between fasting and 2‐h post‐glucose challenge criteria for the diagnosis of diabetes mellitus and glucose intolerance in high risk individuals
Authors: Drzewoski J. , Czupryniak L. 
Published: July 2002

SUMMARY Aims  To compare the new fasting with the 2‐h post glucose challenge diagnostic criteria for diabetes mellitus in a high‐risk Central European population.Methods  The results of the 75‐g oral glucose tolerance tests (OGTT) performed between 1st January 1990 and 31st December 1998 in patients at high risk of glucose metabolism disturbance were analysed.Results  From 1554 patients with OGTT results available for the study, 1360 (759 women and 601 men, aged 65.5 ± 6.9 years, body mass index 28.2 ± 4.5 kg/m2) were included into the study. With the use of the post‐challenge criteria, 41.3% of the analysed population had diabetes or impaired diabetes tolerance (IGT), whereas with the new fasting system only 16.6% would have been be diagnosed with any type of glucose intolerance. Diabetes was significantly more often diagnosed with the post‐challenge criteria than with the fasting ones: 16.2 vs. 5.3% (P < 0.0001). The subjects with diabetes diagnosed upon fasting glucose value were significantly younger than the subjects with diabetes diagnosed according to the 2‐h glucose challenge: 65.7 ± 6.2 vs. 68.8 ± 7.0 years, respectively (P < 0.01). The sensitivity of the new criteria for the diagnosis of diabetes was 18.2%, and specificity 97.2%. A total of 77.8% of IGT cases would have been diagnosed as having normal glucose metabolism according to the fasting glucose. The sensitivity of the new criteria for the diagnosis of impaired glucose tolerance (IGT or impaired fasting glucose) was 14.6%, and specificity 89.8%. The overall kappa statistic (κ) was low: 0.211 (95% confidence interval 0.149–0.27).Conclusions  The new lower fasting criteria might be too insensitive to identify a large proportion of individuals with diabetes or impaired glucose intolerance, particularly in a high‐risk population.
CAUSE AND CLINICAL–NEUROPHYSIOLOGICAL PICTURE OF PERONEAL NEUROPATHY
Authors: Aprile I. , Padua L. , Meloni A. , D'amico P. , Tonali P. 
Published: July 2002

We retrospectively analysed 40 patients with peroneal neuropathy (PN) referred to our EMG laboratory during the last 4 years. Aim of the study was to evaluate the incidence and causes of PN. Moreover, the relationship between causes and clinical‐neurophysiological picture was assessed and a follow‐up was performed.Preliminary results showed that, in most cases, association between PN and surgical event was present (27,5%): unexpectedly, the higher occurrence of PN was observed in patients who underwent operation in the hip region (prosthesis). In 20% of cases, a damaging event was not identified. Erroneous postures (kneeling and crossing leg) caused PN in 12% of cases. Prolonged allurement was related in 10% of PN (50% of these in intensive care unit admission ).PN was not significantly related to gender. The age range of the patients was extremely wide: from 7 to 80 years (mean 50 years). In more than 50% of cases, neuroapraxic block was demonstrated to neurophysiological evaluation.
Identification of Grb2 As a Novel Binding Partner of  Tumor Necrosis Factor (TNF) Receptor I
Authors: Hildt Eberhard , Oess Stefanie 
Published: July 2002

Tumor necrosis factor α (TNF-α) is a proinflammatory cytokine. Its pleiotropic biological properties are signaled through two distinct cell surface receptors: the TNF receptor type I (TNFR-I) and the TNF receptor type II. Neither of the two receptors possesses tyrosine kinase activity. A large majority of TNF-α–dependent activities can be mediated by TNFR-I. Recently, c-Raf-1 kinase was identified as an intracellular target of a signal transduction cascade initiated by binding of TNF-α to TNFR-I. However, the mechanism engaged in TNF-α–dependent activation of c-Raf-1 kinase is still enigmatic.
Here we report that the cytosolic adapter protein Grb2 is a novel binding partner of TNFR-I. Grb2 binds with its COOH-terminal SH3 domain to a PLAP motif within TNFR-I and with its NH2-terminal SH3 domain to SOS (son of sevenless). A PLAP deletion mutant of TNFR-I fails to bind Grb2. The TNFR-I/Grb2 interaction is essential for the TNF-α–dependent activation of c-Raf-1 kinase; activation of c-Raf-1 kinase by TNF-α can be blocked by coexpression of Grb2 mutants harboring inactivating point mutations in the NH2- or COOH-terminal SH3 domain, cell-permeable peptides that disrupt the Grb2/TNFR-I interaction or transdominant negative Ras. Functionality of the TNFR-I/Grb2/SOS/Ras interaction is a prerequisite but not sufficient for TNF-α–dependent activation of c-Raf-1 kinase. Inhibition of the TNFR-I/FAN (factor associated with neutral sphingomyelinase) interaction, which is essential for TNF-α–dependent activation of the neutral sphingomyelinase, either by cell-permeable peptides or by deletion of the FAN binding domain, prevents activation of c-Raf-1 kinase. In conclusion, binding of the Grb2 adapter protein via its COOH-terminal SH3 domain to the nontyrosine kinase receptor TNFR-I results in activation of a signaling cascade known so far to be initiated, in the case of the tyrosine kinase receptors, by binding of the SH2 domain of Grb2 to phosphotyrosine.
Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.
Authors: Eisenhaber F , Bork P 
Published: July 2002

Abstract
MOTIVATION: Computer-based selection of entries from sequence databases with respect to a related functional description, e.g. with respect to a common cellular localization or contributing to the same phenotypic function, is a difficult task. Automatic semantic analysis of annotations is not only hampered by incomplete functional assignments. A major problem is that annotations are written in a rich, non-formalized language and are meant for reading by a human expert. This person can extract from the text considerably more information than is immediately apparent due to his extended biological background knowledge and logical reasoning. APPROACH: A technique of automated annotation evaluation based on a combination of lexical analysis and the usage of biological rule libraries has been developed. The proposed algorithm generates new functional descriptors from the annotation of a given entry using the semantic units of the annotation as prepositions for implications executed in accordance with the rule library. RESULTS: The prototype of a software system, the Meta_A(nnotator) program, is described and the results of its application to sequence attribute assignment and sequence selection problems, such as cellular localization and sequence domain annotation of SWISS-PROT entries, are presented. The current software version assigns useful subcellular localization qualifiers to approximately 88% of all SWISS-PROT entries. As shown by demonstrative examples, the combination of sequence and annotation analysis is a powerful approach for the detection of mutual annotation/sequence inconsistencies. AVAILABILITY: Results for the cellular localization assignment can be viewed at the URL http://www.bork. embl-heidelberg.de/CELL_LOC/CELL_LOC.html.
T-REX: reconstructing and visualizing phylogenetic trees and

reticulation networks
Authors: Makarenkov Vladimir 
Published: July 2002

Abstract
Summary: T-REX (tree and reticulogram reconstruction) is an application to reconstruct phylogenetic trees and reticulation networks from distance matrices. The application includes a number of tree fitting methods like NJ, UNJ or ADDTREE which have been very popular in phylogenetic analysis. At the same time, the software comprises several new methods of phylogenetic analysis such as: tree reconstruction using weights, tree inference from incomplete distance matrices or modeling a reticulation network for a collection of objects or species. T-REX also allows the user to visualize obtained tree or network structures using Hierarchical, Radial or Axial types of tree drawing and manipulate them interactively.
Availability: T-REX is a freeware package available online at: http://www.fas.umontreal.ca/biol/casgrain/en/labo/t-rex
Contact: makarenv@magellan.umontreal.ca or casgrain@magellan.umontreal.ca
The Binding Database: data management and interface design
Authors: Chen Xi , Lin Yuhmei , Liu Ming , Gilson Michael K. 
Published: July 2002

Abstract
Motivation: The large and growing body of experimental data on biomolecular binding is of enormous value in developing a deeper understanding of molecular biology, in developing new therapeutics, and in various molecular design applications. However, most of these data are found only in the published literature and are therefore difficult to access and use. No existing public database has focused on measured binding affinities and has provided query capabilities that include chemical structure and sequence homology searches.
Methods & results: We have created Binding DataBase (BindingDB), a public, web-accessible database of measured binding affinities. BindingDB is based upon a relational data specification for describing binding measurements via Isothermal Titration Calorimetry (ITC) and enzyme inhibition. A corresponding XML Document Type Definition (DTD) is used to create and parse intermediate files during the on-line deposition process and will also be used for data interchange, including collection of data from other sources. The on-line query interface, which is constructed with Java Servlet technology, supports standard SQL queries as well as searches for molecules by chemical structure and sequence homology. The on-line deposition interface uses Java Server Pages and JavaBean objects to generate dynamic HTML and to store intermediate results. The resulting data resource provides a range of functionality with brisk response-times, and lends itself well to continued development and enhancement.
Availability: The BindingDB is publicly available at http://www.bindingdb.org. The database schema and DTD file are available at http://www.bindingdb.org/bind/entity˙report.html, and http://www.bindingdb.org/bind/deposition/xml/BindingDB.xml, respectively.
Contact: gilson@umbi.umd.edu
* To whom correspondence should be addressed.
2 Present address: NovaScreen, 7170 Standard Drive, Hanover, MD 21076, USA.
A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups
Authors: Consortium The Y Chromosome 
Published: July 2002

The Y chromosome contains the largest nonrecombining block in the human genome. By virtue of its many polymorphisms, it is now the most informative haplotyping system, with applications in evolutionary studies, forensics, medical genetics, and genealogical reconstruction. However, the emergence of several unrelated and nonsystematic nomenclatures for Y-chromosomal binary haplogroups is an increasing source of confusion. To resolve this issue, 245 markers were genotyped in a globally representative set of samples, 74 of which were males from the Y Chromosome Consortium cell line repository. A single most parsimonious phylogeny was constructed for the 153 binary haplogroups observed. A simple set of rules was developed to unambiguously label the different clades nested within this tree. This hierarchical nomenclature system supersedes and unifies past nomenclatures and allows the inclusion of additional mutations and haplogroups yet to be discovered.[Supplementary Table 1, available as an online supplement at www.genome.org, lists all published markers included in this survey and primer information.]
Crystal structure of the collagen triple helix model [(Pro‐Pro‐Gly)10]3
Authors: Berisio Rita , Vitagliano Luigi , Mazzarella Lelio , Zagari Adriana 
Published: July 2002

AbstractThe first report of the full‐length structure of the collagen‐like polypeptide [(Pro‐Pro‐Gly)10]3is given. This structure was obtained from crystals grown in a microgravity environment, which diffracted up to 1.3 Å, using synchrotron radiation. The final model, which was refined to an Rfactorof 0.18, is the highest‐resolution description of a collagen triple helix reported to date. This structure provides clues regarding a series of aspects related to collagen triple helix structure and assembly. The strict dependence of proline puckering on the position inside the Pro‐Pro‐Gly triplets and the correlation between backbone and side chain dihedral angles support the propensity‐based mechanism of triple helix stabilization/destabilization induced by hydroxyproline. Furthermore, the analysis of [(Pro‐Pro‐Gly)10]3packing, which is governed by electrostatic interactions, suggests that charges may act as locking features in the axial organization of triple helices in the collagen fibrils.
Single‐domain antibody fragments with high conformational stability
Authors: Dumoulin Mireille , Conrath Katja , Van Meirhaeghe Annemie , Meersman Filip , Heremans Karel , Frenken Leon G.J. , Muyldermans Serge , Wyns Lode , Matagne Andre 
Published: July 2002

AbstractA variety of techniques, including high‐pressure unfolding monitored by Fourier transform infrared spectroscopy, fluorescence, circular dichroism, and surface plasmon resonance spectroscopy, have been used to investigate the equilibrium folding properties of six single‐domain antigen binders derived from camelid heavy‐chain antibodies with specificities for lysozymes, β‐lactamases, and a dye (RR6). Various denaturing conditions (guanidinium chloride, urea, temperature, and pressure) provided complementary and independent methods for characterizing the stability and unfolding properties of the antibody fragments. With all binders, complete recovery of the biological activity after renaturation demonstrates that chemical‐induced unfolding is fully reversible. Furthermore, denaturation experiments followed by optical spectroscopic methods and affinity measurements indicate that the antibody fragments are unfolded cooperatively in a single transition. Thus, unfolding/refolding equilibrium proceeds via a simple two‐state mechanism (N⇋U), where only the native and the denatured states are significantly populated. Thermally‐induced denaturation, however, is not completely reversible, and the partial loss of binding capacity might be due, at least in part, to incorrect refolding of the long loops (CDRs), which are responsible for antigen recognition. Most interestingly, all the fragments are rather resistant to heat‐induced denaturation (apparent Tm = 60–80°C), and display high conformational stabilities (ΔG(H2O) = 30–60 kJ mole−1). Such high thermodynamic stability has never been reported for any functional conventional antibody fragment, even when engineered antigen binders are considered. Hence, the reduced size, improved solubility, and higher stability of the camelid heavy‐chain antibody fragments are of special interest for biotechnological and medical applications.
Involuntary autobiographical memories: The question of function
Authors: Mace John H. , Zhu Jian , Kruchten Emilee A. , McNally Kevin 
Published: April 2023

AbstractResearch on involuntary autobiographical memories has made significant progress over the past two decades. One question in this area concerns whether involuntary memories are functional, or merely cognitive failures. Survey methods have been used to assess the question of involuntary memory functionality, but with mixed results, with some suggesting that most involuntary memories are functional, and others suggesting the opposite. In this study, we argued that the variable findings were due to differences in survey design. In Study 1, we showed that closed‐ended questionnaires on function (where participants select from a number of function choices) produce significantly more positive function responses than open‐ended questionnaires (where participants freely articulate perceived functions). Study 2 showed that allowing participants to select more than one function greatly inflated positive function responses. We used these findings to outline a number of possible answers to the question of involuntary memory functions.