bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge
Authors: Krallinger Martin , Morgan Alexander , Smith Larry , Leitner Florian , Tanabe Lorraine , Wilbur John , Hirschman Lynette , Valencia Alfonso 
Published: September 2008

Abstract
Background:
Genome sciences have experienced an increasing demand for efficient text-processing tools that can extract biologically relevant information from the growing amount of published literature. In response, a range of text-mining and information-extraction tools have recently been developed specifically for the biological domain. Such tools are only useful if they are designed to meet real-life tasks and if their performance can be estimated and compared. The BioCreative challenge (Critical Assessment of Information Extraction in Biology) consists of a collaborative initiative to provide a common evaluation framework for monitoring and assessing the state-of-the-art of text-mining systems applied to biologically relevant problems.

Results:
The Second BioCreative assessment (2006 to 2007) attracted 44 teams from 13 countries worldwide, with the aim of evaluating current information-extraction/text-mining technologies developed for one or more of the three tasks defined for this challenge evaluation. These tasks included the recognition of gene mentions in abstracts (gene mention task); the extraction of a list of unique identifiers for human genes mentioned in abstracts (gene normalization task); and finally the extraction of physical protein-protein interaction annotation-relevant information (protein-protein interaction task). The 'gold standard' data used for evaluating submissions for the third task was provided by the interaction databases MINT (Molecular Interaction Database) and IntAct.

Conclusion:
The Second BioCreative assessment almost doubled the number of participants for each individual task when compared with the first BioCreative assessment. An overall improvement in terms of balanced precision and recall was observed for the best submissions for the gene mention (F score 0.87); for the gene normalization task, the best results were comparable (F score 0.81) compared with results obtained for similar tasks posed at the first BioCreative challenge. In case of the protein-protein interaction task, the importance and difficulties of experimentally confirmed annotation extraction from full-text articles were explored, yielding different results depending on the step of the annotation extraction workflow. A common characteristic observed in all three tasks was that the combination of system outputs could yield better results than any single system. Finally, the development of the first text-mining meta-server was promoted within the context of this community challenge.
Leydig Cells Express Follicle-Stimulating Hormone Receptors in African Catfish
Authors: García-López Ángel , Bogerd Jan , Granneman Joke C. M. , van Dijk Wytske , Trant John M. , Taranger Geir Lasse , Schulz Rüdiger W. 
Published: August 2008

This report aimed to establish, using African catfish, Clarias gariepinus, as model species, a basis for understanding a well-known, although not yet clarified, feature of male fish reproductive physiology: the strong steroidogenic activity of FSHs. Assays with gonadotropin receptor-expressing cell lines showed that FSH activated its cognate receptor (FSHR) with an at least 1000-fold lower EC50 than when challenging the LH receptor (LHR), whereas LH stimulated both receptors with similar EC50s. In androgen release bioassays, FSH elicited a significant response at lower concentrations than those required to cross-activate of the LHR, indicating that FSH stimulated steroid release via FSHR-dependent mechanisms. LHR/FSHR-mediated stimulation of androgen release was completely abolished by H-89, a specific protein kinase A inhibitor, pointing to the cAMP/protein kinase A pathway as the main route for both LH- and FSH-stimulated steroid release. Localization studies showed that intratubular Sertoli cells express FSHR mRNA, whereas, as reported for the first time in a vertebrate, catfish Leydig cells express both LHR and FSHR mRNA. Testicular FSHR and LHR mRNA expression increased gradually during pubertal development. FSHR, but not LHR, transcript levels continued to rise between completion of the first wave of spermatogenesis at about 7 months and full maturity at about 12 months of age, which was associated with a previously recorded approximately 3-fold increase in the steroid production capacity per unit testis weight. Taken together, our data strongly suggest that the steroidogenic potency of FSH can be explained by its direct trophic action on FSHR-expressing Leydig cells.
In search of a mechanistic basis for the strong steroidogenic activity of fish FSH, we demonstrate FSH receptor expression by Leydig cells in catfish.
Why Would You Do It? Age and Motivation to Become a Fire Service Volunteer
Authors: McLennan Jim , Birch Adrian 
Published: September 2008

AbstractAustralian communities are very dependent on volunteer-based fire services for protection against fires and other hazards. However, overall volunteer numbers have declined significantly over the past decade, due mostly to the impact of economic and demographic changes on Australian society. One effect of these is that volunteer fire service memberships are ageing. Little is known with certainty about what motivates individuals to become fire service volunteers. A survey of 455 CFA volunteers suggested that those who volunteer do so because of a mix of community-safety, community-contribution, and self-oriented motivations. It appears that younger volunteers are more likely to be motivated by self-oriented perceived benefits from volunteering compared with older volunteers. However, they are no less motivated, on average, by community-safety concerns and community contribution desires than are older volunteers.
Antitumoral Activity and Osteogenic Potential of Mesenchymal Stem Cells Expressing the Urokinase-Type Plasminogen Antagonist Amino-Terminal Fragment in a Murine Model of Osteolytic Tumor
Authors: Fritz Vanessa , Noël Danièle , Bouquet Céline , Opolon Paule , Voide Romain , Apparailly Florence , Louis-Plence Pascale , Bouffi Carine , Drissi Hicham , Xie Chao , Perricaudet Michel , Müller Ralph , Schwarz Edward , Jorgensen Christian 
Published: August 2008

Abstract
Prostate cancer metastasis to bone results in mixed osteolytic and osteoblastic lesions associated with high morbidity, and there is mounting evidence that the urokinase-type plasminogen system is causatively involved in the progression of prostate cancer. Adult mesenchymal stem cells (MSCs) are promising tools for cell-mediated gene therapy with the advantage of osteogenic potential, a critical issue in the case of osteolytic metastases. In this study, we evaluated the therapeutic use of engineered murine MSCs for in vivo delivery of the urokinase-type plasminogen antagonist amino-terminal fragment (hATF) to impair osteolytic prostate cancer cell progression in bone and to repair bone lesions. Bioluminescence imaging revealed that both primary MSCs and the MSC line C3H10T1/2 (C3) expressing hATF (MSC-hATF) significantly inhibited intratibial PC-3 Luciferase (Luc) growth following coinjection in SCID mice. Furthermore, microcomputed tomography imaging of vascular network clearly demonstrated a significant decrease in tumor-associated angiogenesis and a protection from tumor-induced osteolysis in MSC-hATF-treated mice. Importantly, the osteogenic potential of MSC-hATF cells was unaffected, and an area of new bone formation was evidenced in 60% of animals. Together, these data support the concept of MSC-based therapy of tumor osteolysis disease, indicating that MSCs may combine properties of vehicle for angiostatic agent with osteogenic potential.
Disclosure of potential conflicts of interest is found at the end of this article.
Spatiotemporal Recapitulation of Central Nervous System Development by Murine Embryonic Stem Cell-Derived Neural Stem/Progenitor Cells
Authors: Okada Yohei , Matsumoto Arifumi , Shimazaki Takuya , Enoki Ryosuke , Koizumi Amane , Ishii Seiji , Itoyama Yasuto , Sobue Gen , Okano Hideyuki 
Published: August 2008

Abstract
Neural stem/progenitor cells (NS/PCs) can generate a wide variety of neural cells. However, their fates are generally restricted, depending on the time and location of NS/PC origin. Here we demonstrate that we can recapitulate the spatiotemporal regulation of central nervous system (CNS) development in vitro by using a neurosphere-based culture system of embryonic stem (ES) cell-derived NS/PCs. This ES cell-derived neurosphere system enables the efficient derivation of highly neurogenic fibroblast growth factor-responsive NS/PCs with early temporal identities and high cell-fate plasticity. Over repeated passages, these NS/PCs exhibit temporal progression, becoming epidermal growth factor-responsive gliogenic NS/PCs with late temporal identities; this change is accompanied by an alteration in the epigenetic status of the glial fibrillary acidic protein promoter, similar to that observed in the developing brain. Moreover, the rostrocaudal and dorsoventral spatial identities of the NS/PCs can be successfully regulated by sequential administration of several morphogens. These NS/PCs can differentiate into early-born projection neurons, including cholinergic, catecholaminergic, serotonergic, and motor neurons, that exhibit action potentials in vitro. Finally, these NS/PCs differentiate into neurons that form synaptic contacts with host neurons after their transplantation into wild-type and disease model animals. Thus, this culture system can be used to obtain specific neurons from ES cells, is a simple and powerful tool for investigating the underlying mechanisms of CNS development, and is applicable to regenerative treatment for neurological disorders.
Disclosure of potential conflicts of interest is found at the end of this article.
Comparison of two-dimensional and three-dimensional systems for kinematic analysis of the sagittal motion of canine hind limbs during walking
Authors: Kim Jongmin , Rietdyk Shirley , Breur Gert J. 
Published: September 2008

Abstract
Objective—To test the hypotheses that kinematic data of the sagittal motion of canine hind limbs during walking obtained with a 2-dimensional (2-D) system correlate well with those obtained with a 3-dimensional (3-D) system and that the data obtained with the 2-D system are repeatable.
Animals—6 adult dogs with no evidence of lameness.
Procedures—Hind limb motions of 6 walking dogs were recorded via 2-D video and 3-D optoelectric systems simultaneously. Five valid trials were digitized, and 5 data sets (2-D 60 Hz, 3-D 180 Hz, 3-D sagittal 180 Hz, 3-D 60 Hz, and 3-D sagittal 60 Hz) of a complete gait cycle were created for each dog. In sagittal data sets, 3-D data were reduced to exclude coordinates for mediolateral orientation. Temporospatial parameters; angles of hip, stifle, and tarsal joints; and coefficients of variation of angular measurements of each dog were calculated for each data set. Accuracy of the 2-D analysis was determined by calculating mean absolute differences and estimating agreement between the 2-D and 3-D 180-Hz data sets.
Results—Values of joint angles and angular excursions measured with the 2-D system were repeatable and agreed with respective values obtained with the 3-D system. Reduction of the sampling rate had a greater impact on values of kinematic variables obtained with the 3-D system than did elimination of data on mediolateral orientation.
Conclusions and Clinical Relevance—Kinematic analysis using a 2-D video system provided accurate and repeatable data of the sagittal angular motion of canine hind limbs during walking.
Use of high-frequency ultrasonography for evaluation of skin thickness in relation to hydration status and fluid distribution at various cutaneous sites in dogs
Authors: Diana Alessia , Guglielmini Carlo , Fracassi Federico , Pietra Marco , Balletti Erika , Cipone Mario 
Published: September 2008

Abstract
Objective—To assess the usefulness of high-frequency diagnostic ultrasonography for evaluation of changes of skin thickness in relation to hydration status and fluid distribution at various cutaneous sites in dogs.
Animals—10 clinically normal adult dogs (6 males and 4 females) of various breeds.
Procedures—Ultrasonographic examination of the skin was performed before and after hydration via IV administration of an isotonic crystalloid solution (30 mL/kg/h for 30 minutes). A 13-MHz linear-array transducer was used to obtain series of ultrasonographic images at 4 different cutaneous sites (the frontal, sacral, flank, and metatarsal regions). Weight and various clinicopathologic variables (PCV; serum osmolality; and serum total protein, albumin, and sodium concentrations) were determined before and after the infusion. These variables and ultrasonographic measurements of skin thickness before and after hydration were compared.
Results—Among the 10 dogs, mean preinfusion skin thickness ranged from 2,211 μm (metatarsal region) to 3,249 μm (sacral region). Compared with preinfusion values, weight was significantly increased, whereas PCV; serum osmolality; and serum total protein, albumin, and sodium concentrations were significantly decreased after infusion. After infusion, dermal echogenicity decreased and skin thickness increased significantly by 21%, 14%, 15%, and 13% in the frontal, sacral, flank, and metatarsal regions, respectively.
Conclusions and Clinical Relevance—Cutaneous site and hydration were correlated with cutaneous characteristics and skin thickness determined by use of high-frequency ultrasonography in dogs. Thus, diagnostic ultrasonography may be a useful tool for the noninvasive evaluation of skin hydration in healthy dogs and in dogs with skin edema.
Evaluation of the effect of ranitidine on gastroduodenal contractile activity and gastric emptying in horses
Authors: Maher Omar , Nieto Jorge E. , Stanley Scott D. , Dore Elizabeth , Snyder Jack R. 
Published: September 2008

Abstract
Objective—To determine the effect of ranitidine on gastric emptying in horses.
Animals—11 adult horses.
Procedures—In vitro, isolated muscle strips from the pyloric antrum and duodenum of 5 horses were suspended in baths and attached to isometric force transducers. Once stable spontaneous contractions were observed, ranitidine or diluent was added at cumulative increasing concentrations. Isometric stress responses were compared. In vivo, 6 horses were assigned to a group in a prospective randomized crossover study design with a wash-out period of 2 weeks between trials. Ranitidine (2.2 mg/kg) or saline (0.9% NaCl) solution was administered IV, and 15 minutes later, acetaminophen (20 mg/kg), diluted in 400 mL of water, was administered via nasogastric tube to evaluate the liquid phase of gastric emptying. Serum acetaminophen concentration was measured at several time points for 3 hours by use of liquid chromatography tandem mass spectrometry. Frequency of defecation was recorded during the 3 hours of the study.
Results—Ranitidine increased the contractile activity of the pyloric antrum smooth muscle at a concentration of 10−4 M. No significant effect of ranitidine on plasma kinetics of acetaminophen was identified. Frequency of defecation did not differ between groups.
Conclusions and Clinical Relevance—Ranitidine did increase gastric motility in vitro, but no effect on liquid phase gastric emptying was identified in healthy horses by use of the acetaminophen absorption model. Results do not support the use of ranitidine to promote gastric emptying.
Effects of topical application of taurolidine on second intention healing of experimentally induced wounds in rats
Authors: Simpson Jennifer M. , Séguin Bernard , Gitelman Alix I. 
Published: September 2008

Abstract
Objective—To determine the macroscopic effects of topical application of taurolidine on second intention healing of experimentally induced wounds in rats.
Animals—32 adult Sprague-Dawley female rats.
Procedures—In each rat, 2 skin wounds were created in the lumbar area. Groups of 7 rats were assigned to have 1 wound treated topically with hydroxycellulose gel (HDCG), 2% taurolidine in HDCG (T-HDCG), 2% taurolidine–sodium citrate solution, or bacitracin-neomycin-polymyxin B ointment; the other wound was not treated. Four control rats (8 untreated wounds) were used. Wounds were monitored for contraction, epithelialization, and complete healing at 4, 8, and 14 days after wound creation. The number of days to complete healing was also recorded for each wound.
Results—Compared with other treatments or untreated wounds, wounds treated with T-HDCG had decreased total healing at day 8 and decreased epithelialization and decreased total healing at day 14. Wounds treated with T-HDCG required approximately 3 days longer to completely heal than all other treated and untreated wounds. Application of bacitracinneomycin-polymyxin B ointment did not enhance wound healing. Mean time to complete healing of untreated wounds in all treatment and control groups was 10.00 to 10.14 days.
Conclusions and Clinical Relevance—In rats, topical application of T-HDCG to wounds had a negative effect on second intention healing by delaying the epithelialization process. In mammals, generally, wounds treated topically with taurolidine may need to be treated and monitored for a longer period than other wounds treated with other common woundhealing compounds or untreated wounds.
Diagnosis and treatment of dynamic closed-mouth jaw locking in a dog
Authors: Frazho Jean K. , Tano Cheryl A. , Ferrell Eric A. 
Published: September 2008

Abstract
Case Description—A 5-year-old neutered male English Bulldog was evaluated for intermittent closed-mouth jaw locking of approximately 1 week's duration.
Clinical Findings—Initial physical examination revealed a nonpainful inability to open the jaw with and without manual assistance; however, manipulation of the jaw after the dog was sedated for diagnostic imaging restored jaw function. Anesthesia was subsequently induced, and computed tomography was performed with the jaw open and closed; contrast agent–enhanced images of the closed jaw were also obtained. No abnormalities of the temporomandibular joints or retrobulbar space were detected. Fluoroscopic examination of movement of the temporomandibular joints revealed a dynamic interference of the rostrodorsal aspect of the coronoid process of the left mandibular ramus with the medial surface of the frontal process of the left zygomatic bone or the left orbital ligament.
Treatment and Outcome—Partial excision of the coronoid process of the left mandibular ramus was performed. The dog recovered without complication and was able to open and close its jaw and eat within 6 hours after surgery. No additional episodes of jaw locking were detected during the 6 months after surgery.
Clinical Relevance—To the authors' knowledge, closed-mouth jaw locking in animals attributable to dynamic interference of the rostrodorsal aspect of the coronoid process of a mandibular ramus with the medial surface of the frontal process of a zygomatic bone or an orbital ligament has not been described. Surgical excision of the coronoid process of the mandibular ramus appeared to provide a successful outcome in the dog of this report.
Thrombi in the trachea of a dog secondary to placement of a tracheotomy tube
Authors: Fitzwater Kathryn L. , Marks Steven L. , Hanel Rita M. 
Published: September 2008

Abstract
Case Description—A 7-year-old Spaniel-crossbreed dog was evaluated for stertorous breathing and inspiratory stridor.
Clinical Findings—A temporary tracheotomy tube was placed prior to referral. Results of physical examination at our facility, including thoracic auscultation, were unremarkable. Examination of the larynx revealed a 2 × 2-cm nodular mass on the lateral aspect of the epiglottis and left arytenoid cartilage. Cytologic examination of the mass indicated septic suppurative inflammation and intracellular rod-shaped bacteria. During the procedures, decreased air movement through the temporary tracheotomy tube was detected, and the tube was replaced. A thrombus was found on the distal end of the temporary tracheotomy tube; the thrombus obstructed 90% of the tube lumen. Approximately 12 hours later, auscultation revealed decreased sounds in all lung fields. Cervical and thoracic radiography revealed an intraluminal soft tissue opacity distal to the tracheotomy tube. A thrombus that contained hair and plant material was removed from the trachea by use of an embolectomy catheter and videogastroscope. Approximately 30 hours after removal of the initial thrombus, the dog had an episode of respiratory distress. Cervical radiography revealed another intraluminal opacity. It was another thrombus, which also was removed by use of the videogastroscope.
Treatment and Outcome—Tracheoscopy was performed with a videogastroscope in an attempt to remove the thrombi. A Fogarty catheter was used to remove the initial intraluminal thrombus from the trachea.
Clinical Relevance—Airway obstruction resulting from an intraluminal thrombus in the trachea should be considered as a secondary complication after tracheotomy tube placement.
Comparison of four methods to assess colostral IgG concentration in dairy cows
Authors: Chigerwe Munashe , Tyler Jeff W. , Middleton John R. , Spain James N. , Dill Jeffrey S. , Steevens Barry J. 
Published: September 2008

Abstract
Objective—To determine sensitivity and specificity of 4 methods to assess colostral IgG concentration in dairy cows and determine the optimal cutpoint for each method.
Design—Cross-sectional study.
Animals—160 Holstein dairy cows.
Procedures—171 composite colostrum samples collected within 2 hours after parturition were used in the study. Test methods used to estimate colostral IgG concentration consisted of weight of the first milking, 2 hydrometers, and an electronic refractometer. Results of the test methods were compared with colostral IgG concentration determined by means of radial immunodiffusion. For each method, sensitivity and specificity for detecting colostral IgG concentration < 50 g/L were calculated across a range of potential cutpoints, and the optimal cutpoint for each test was selected to maximize sensitivity and specificity.
Results—At the optimal cutpoint for each method, sensitivity for weight of the first milking (0.42) was significantly lower than sensitivity for each of the other 3 methods (hydrometer 1, 0.75; hydrometer 2, 0.76; refractometer, 0.75), but no significant differences were identified among the other 3 methods with regard to sensitivity. Specificities at the optimal cutpoint were similar for all 4 methods.
Conclusions and Clinical Relevance—Results suggested that use of either hydrometer or the electronic refractometer was an acceptable method of screening colostrum for low IgG concentration; however, the manufacturer-defined scale for both hydrometers overestimated colostral IgG concentration. Use of weight of the first milking as a screening test to identify bovine colostrum with inadequate IgG concentration could not be justified because of the low sensitivity.