bluuebunny/crossref_metadata_2025_split huggingface dataset:
BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events
Authors: Gerner Martin , Sarafraz Farzaneh , Bergman Casey M. , Nenadic Goran 
Published: June 2012

Abstract
Motivation: Although the amount of data in biology is rapidly increasing, critical information for understanding biological events like phosphorylation or gene expression remains locked in the biomedical literature. Most current text mining (TM) approaches to extract information about biological events are focused on either limited-scale studies and/or abstracts, with data extracted lacking context and rarely available to support further research.
Results: Here we present BioContext, an integrated TM system which extracts, extends and integrates results from a number of tools performing entity recognition, biomolecular event extraction and contextualization. Application of our system to 10.9 million MEDLINE abstracts and 234 000 open-access full-text articles from PubMed Central yielded over 36 million mentions representing 11.4 million distinct events. Event participants included over 290 000 distinct genes/proteins that are mentioned more than 80 million times and linked where possible to Entrez Gene identifiers. Over a third of events contain contextual information such as the anatomical location of the event occurrence or whether the event is reported as negated or speculative.
Availability: The BioContext pipeline is available for download (under the BSD license) at http://www.biocontext.org, along with the extracted data which is also available for online browsing.
Contact: martin.gerner@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Will disruptive mood dysregulation disorder reduce false diagnosis of bipolar disorder in children?
Authors: Margulies David M , Weintraub Sheldon , Basile Joann , Grover Paul J , Carlson Gabrielle A 
Published: June 2012

Margulies DM, Weintraub S, Basile J, Grover PJ, Carlson GA. Will disruptive mood dysregulation disorder reduce false diagnosis of bipolar disorder in children? Bipolar Disord 2012: 14: 488–496. © 2012 The Authors Journal compilation © 2012 John Wiley & Sons A/S.Objectives:  The frequency of diagnosis of bipolar disorder has risen dramatically in children and adolescents. The DSM‐V Work Group has suggested a new diagnosis termed disruptive mood dysregulation disorder (DMDD) (formerly temper dysregulation disorder with dysphoria) to reduce the rate of false diagnosis of bipolar disorder in young people. We sought to determine if the application of the proposed diagnostic criteria for DMDD would reduce the rate of diagnosis of bipolar disorder in children.Patients and methods:  Eighty‐two consecutively hospitalized children, ages 5 to 12 years, on a children’s inpatient unit were rigorously diagnosed using admission interviews of the parents and the child, rating scales, and observation over the course of hospitalization.Results:  Overall, 30.5% of inpatient children met criteria for DMDD by parent report, and 15.9% by inpatient unit observation. Fifty‐six percent of inpatient children had parent‐reported manic symptoms. Of those, 45.7% met criteria for DMDD by parent‐report, though only 17.4% did when observed on the inpatient unit.Conclusion:  Although DMDD does decrease the rate of diagnosis of bipolar disorder in children, how much depends on whether history or observation is used.
COMT polymorphisms as predictors of cognitive dysfunction during manic and mixed episodes in bipolar I disorder
Authors: Soeiro‐de‐Souza Márcio Gerhardt , Machado‐Vieira Rodrigo , Soares Bio Danielle , Do Prado Carolina Martins , Moreno Ricardo Alberto 
Published: June 2012

Soeiro‐de‐Souza MG, Machado‐Vieira R, Soares Bio D, Do Prado CM, Moreno RA. COMT polymorphisms as predictors of cognitive dysfunction during manic and mixed episodes in bipolar I disorder. Bipolar Disord 2012: 14: 554–564. © 2012 The Authors.  Journal compilation © 2012 John Wiley & Sons A/S.Objective:  The dopaminergic system plays an important role in the prefrontal cortex (PFC) and is believed to mediate cognitive dysfunction (CD) in bipolar disorder (BD). The enzyme catechol‐O‐methyltransferase (COMT) is involved in the catabolism of dopamine in the PFC, and an association between COMT single nucleotide polymorphisms (SNPs) and BD has been reported. COMT SNPs have also been associated with executive and working memory performance in healthy subjects, patients with schizophrenia, and euthymic BD patients. The objective of this study was to investigate the association between COMT SNPs and acute CD during BD mood episodes.Methods:  Seventy‐two symptomatic, medication‐free subjects with bipolar I disorder (BD‐I) and 76 healthy controls were evaluated using neuropsychological tests, and genotyped for COMT SNPs rs4680 and rs165599.Results:  Patients undergoing mania and mixed episodes carrying the COMT allele G had better performance on executive function, memory, verbal fluency, and intelligence tests. Moreover, an interaction was detected between the COMT allele G and the Young Mania Rating Scale in BD CD.Conclusions:  Allele G from COMT SNPs rs4680 and rs165599 may represent reliable state‐dependent predictors of global CD during manic and mixed episodes in BD. Further studies in larger samples are necessary to confirm these findings.
Latitude and Date of Sowing Influences Phenology of Photoperiod‐Sensitive Sorghums
Authors: Abdulai A. L. , Kouressy M. , Vaksmann M. , Asch F. , Giese M. , Holger B. 
Published: June 2012

AbstractMatching phenology with prevalent abiotic and biotic conditions is a prerequisite for varietal adaptation to the environment. That is particularly important in the context of climate change because an increase in temperature is most likely to modify the precocity of the varieties. The forecast of flowering time in photoperiod‐sensitive sorghum is complex as flowering depends on temperature, day length and soil fertility. The objectives of this work were to quantify effects of latitude on the development of selected sorghum varieties and to verify the precision of our models to predict sorghum maturity. A field experiment at three locations along the latitudinal gradient in Mali with staggered sowing dates (SDs) was conducted. Seven sorghum cultivars covering a wide range of the diversity of cultivated sorghums in Mali were sown on the 10 of June, July and August in 2009 and 2010. Duration of the vegetative phase strongly decreased with latitude. Although the maximum day length difference between locations was < 8 min, for some varieties, we observed a reduction in crop duration of up to 3 weeks. Some varieties were photoperiod insensitive at one location but became photoperiod sensitive at another. The effect of latitude on the phenology is underestimated by the existing models. To determine the optimal areas for the varieties in West Africa and to forecast the effects of climate change, a correction of the simulation coefficients taking account of latitude is proposed. But, in the end, it will be necessary to develop a new model that will be able to predict the effects of both SD and latitude. More research is needed to understand physiological response mechanisms of the pronounced latitude effects on sorghum phenology.
Downregulation of TWIK‐related arachidonic acid‐activated K+ channel in the spinal cord of rats after complete bladder outlet obstruction
Authors: Wu Xilian , Liang Yueyou , Zhang Zhongyun , Cao Mingxin , Liang Weijie 
Published: June 2012

Objectives:  To study the altered expression of TWIK‐related arachidonic acid‐activated K+ channel in the L6–S1 spinal cord of rats after complete bladder outlet obstruction, and to investigate the role of TWIK‐related arachidonic acid‐activated K+ channel in the neurogenic mechanism of bladder dysfunction.Methods:  Female Sprague–Dawley rats were randomly divided into a complete bladder outlet obstruction group and a sham‐operated control group. Cystometry was carried out and tissues of L6–S1 spinal cord were obtained for detection of TWIK‐related arachidonic acid‐activated K+ channel mRNA and protein by real‐time polymerase chain reaction, western blot and immunohistochemistry.Results:  The bladder outlet obstruction rat model was established. Real‐time polymerase chain reaction, western blot and immunohistochemistry showed that the expression of TWIK‐related arachidonic acid‐activated K+ channel was lower in the L6–S1 spinal cord of the bladder outlet obstruction rats, compared with the control rats.Conclusions:  Downregulation of TWIK‐related arachidonic acid‐activated K+ channel might enhance the excitability of the neurons and increase the sensitivity of the bladder, probably providing a new study model of overactive bladder secondary to bladder outlet obstruction.
Diffusion tensor magnetic resonance imaging reveals visual pathway damage that correlates with clinical severity in glaucoma
Authors: Chen Zhiqi , Lin Fuchun , Wang Junming , Li Zheng , Dai Hui , Mu Ketao , Ge Jian , Zhang Hong 
Published: June 2012

AbstractBackground:  To investigate nerve fibre damage of the visual pathway in patients with primary open‐angle glaucoma using tract‐based spatial statistical analysis of diffusion tensor imaging and correlate these measures with the clinical severity of glaucoma.Design:  Cross‐sectional study.Participants:  Twenty‐five individuals with primary open‐angle glaucoma and 24 healthy controls were recruited.Methods:  All subjects underwent detailed ophthalmological examinations, including the cup‐to‐disc ratio, retinal nerve fibre layer thickness and visual fields test. Diffusion tensor imaging of the visual pathway was performed using a 3.0‐T magnetic resonance scanner.Main Outcome Measures:  Diffusivity changes of the nerve fibres in the visual pathway were calculated through tract‐based spatial statistical analysis. The mean diffusivity and fractional anisotropy were assessed and compared with ophthalmological measurements.Results:  Compared with controls, bilateral optic tracts and optic radiations in primary open‐angle glaucoma patients showed significantly decreased fractional anisotropy and increased mean diffusivity (P < 0.05). In the glaucoma group, the fractional anisotropy of the optic tracts and optic radiations varied consistently with the cup‐to‐disc ratio, retinal nerve fibre layer thickness and visual function analysis, respectively (P < 0.05). The mean diffusivity of the optic tracts correlated with these ophthalmological measurements (P < 0.05). However, no significant correlation was observed between the mean diffusivity of the optic radiations and the ophthalmological measurements (P > 0.05).Conclusions:  The optic tracts and optic radiations of primary open‐angle glaucoma patients demonstrated radiological evidence of neurodegeneration. This varied with damage to the optic disc and with the loss of visual function. Tract‐based spatial statistical analysis of diffusion tensor imaging is an objective and effective tool for detecting the loss of cortical nerve fibres in primary open‐angle glaucoma.
Cortical interneurons, immune factors and oxidative stress as early targets for schizophrenia
Authors: O’Donnell Patricio 
Published: June 2012

AbstractSchizophrenia is a common disorder in which strong genetic predisposition is combined with environmental factors. Despite the widely recognized developmental nature of the disease, symptoms do not emerge until late adolescence. Current therapeutic approaches are therefore employed too late, as brain alterations may have been present earlier than symptom onset. Here I review the developmental trajectory of the cortical circuits responsible for excitation–inhibition balance, which are at the center of current pathophysiological views, and propose that oxidative stress in cortical interneurons may be a final common pathway by which several different etiological factors can yield the cortical dysfunction characteristic of schizophrenia. If this scenario is correct, redox modulators may be beneficial for the disease. It is critical that the developmental trajectories of the factors yielding oxidative stress are taken into account for those approaches to succeed.
Mitochondrial sirtuins – a new therapeutic target for repair and protection in multiple sclerosis
Authors: Rice C. M. , Sun M. , Kemp K. , Gray E. , Wilkins A. , Scolding N. J. 
Published: June 2012

AbstractGiven the significant socioeconomic impact of progressive multiple sclerosis (MS) and the paucity of treatment options, there is an urgent need to develop new and effective therapies for this disabling condition. The relatively recent appreciation that progressive disability is largely driven by neuronal loss has focused considerable research attention on neuroprotective strategies. This has coincided with the emergence of oxidative damage as a prominent effector mechanism of axonal damage in studies of MS pathogenesis, which has opened up a new range of putative targets for neuroprotective therapy in MS. Mitochondrial sirtuins are NAD+‐dependent protein deacetylases associated with the control of metabolism, aging, and stem cell proliferation and differentiation. Their role in inflammatory demyelinating disease has not been fully characterized, and is the subject of ongoing research. Here, we expound the rationale behind selecting mitochondrial sirtuins as a therapeutic target in demyelinating disease, and report preliminary data that warrant further investigation.
Different effects of spinalization and locomotor training of spinal animals on cholinergic innervation of the soleus and tibialis anterior motoneurons
Authors: Skup Malgorzata , Gajewska‐Wozniak Olga , Grygielewicz Paulina , Mankovskaya Tatsyana , Czarkowska‐Bauch Julita 
Published: June 2012

AbstractCholinergic input modulates excitability of motoneurons and plays an important role in the control of locomotion in both intact and spinalized animals. However, spinal cord transection in adult rats affects cholinergic innervation of only some hindlimb motoneurons, suggesting that specificity of this response is related to functional differences between motoneurons. Our aim was therefore to compare cholinergic input to motoneurons innervating the soleus (Sol) and tibialis anterior (TA) motoneurons following spinal cord transection at a low‐thoracic level. The second aim was to investigate whether deficits in cholinergic input to these motoneurons could be modified by locomotor training. The Sol and TA motoneurons were identified by retrograde labelling with fluorescent dyes injected intramuscularly. Cholinergic terminals were detected using anti‐vesicular acetylcholine transporter (VAChT) antibody. Overall innervation of motoneurons was evaluated with anti‐synaptophysin antibody. After spinalization we found a decrease in the number of VAChT‐positive boutons apposing perikarya of the Sol (to 49%) but not TA motoneurons. Locomotor training, resulting in moderate functional improvement, partly reduced the deficit in cholinergic innervation of Sol motoneurons by increasing the number of VAChT‐positive boutons. However, the optical density of VAChT‐positive boutons terminating on various motoneurons, which decreased after spinalization, continued to decrease despite the training, suggesting an impairment of acetylcholine availability in the terminals. Different effects of spinal cord transection on cholinergic innervation of motoneurons controlling the ankle extensor and flexor muscles point to different functional states of these muscles in paraplegia as a possible source of activity‐dependent signaling regulating cholinergic input to the motoneurons.
Exploration of data partitioning in an eight‐gene data set: phylogeny of metalmark moths (Lepidoptera, Choreutidae)
Authors: Rota Jadranka , Wahlberg Niklas 
Published: June 2012

Rota, J. & Wahlberg, N. (2012). Exploration of data partitioning in an eight‐gene data set: phylogeny of metalmark moths (Lepidoptera, Choreutidae). —Zoologica Scripta, 41, 536–546.Molecular data sets for phylogenetic inference continue to increase in size, especially with respect to the number of genes sampled. As more and more genes are included in analyses, the importance of partitioning the data to avoid problems that can arise from underparameterization becomes more apparent. With an eight‐gene data set from 38 metalmark moth species (12 genera represented) and three outgroups, we explored different data partitioning strategies and their influence on convergence and mixing of Markov Chains Monte Carlo in a Bayesian setting. We found that in larger data sets, with an increase in the number of partitions that are made a priori (e.g. by gene and codon position), convergence and mixing become poor. This problem can be overcome by using a recently published algorithm in which homologous sites are grouped into blocks with similar evolutionary rates that can then be modelled as separate data subsets. Using this novel approach to data partitioning, our analyses resolve with strong support relationships among the genera of metalmark moths. Support for the monophyly of the family, the two subfamilies and all genera except Hemerophila is strong. Hemerophila is broken into two separate clades, Hemerophila sensu stricto and another well‐supported clade. To render Hemerophila monophyletic, we describe a new genus, Ornarantia Rota, gen. nov., and transfer 18 species from Hemerophila to it. The type species of Ornarantia is Hemerophila laciniosella Busck, 1914.
Greening the Counterinsurgency: The Deceptive Effects of Guatemala's Rural Development Plan of 1970
Authors: Copeland Nicholas 
Published: June 2012

ABSTRACTThis article examines the role of USAID's 1970 Rural Development Plan (RDP) for Guatemala in normalizing US military support for the Guatemalan government despite concerns about excessive state violence in the late 1960s. I argue that the RDP presented a depoliticized vision of Guatemala's agrarian problem and generated optimism that this problem could be resolved through market mechanisms and within the existing social order. Rather than promoting prosperity and stability, the RDP framed state terror as a temporary exception, and helped set the stage for genocide in the 1980s. This highlights complicities between discourses of development and political violence.
Heightened attention to supplementation is needed to improve the vitamin D status of breastfeeding mothers and infants when sunshine exposure is restricted
Authors: Dawodu Adekunle , Zalla Lauren , Woo Jessica G. , Herbers Patricia M. , Davidson Barbara S. , Heubi James E. , Morrow Ardythe L. 
Published: June 2012

AbstractAlthough exclusively breastfed infants are at increased risk of vitamin D (vit D) deficiency if vit D supplementation is lacking and sun exposure is limited, assessment of both risk factors in the first year of life is lacking. We evaluated the contribution of vit D intake and sunlight exposure to vit D status in 120 healthy, breastfeeding mother–infant dyads, who were followed up for 1 year. Vitamin D intake and skin sunlight exposure were evaluated using questionnaires. Serum 25‐hydroxyvitamin D, parathyroid hormone (PTH) and alkaline phosphatase levels were determined post‐natally in mothers at 4 weeks and in infants at 4, 26 and 52 weeks. Vitamin D supplementation was low (<20%) and sunlight exposure was common (93%) in study infants. At 4 weeks, 17% of mothers were vit D deficient (<50 nmol L−1) and 49% were insufficient (50–<75 nmol L−1), while 18% of infants were severely vit D deficient (<25 nmol L−1) and 77% were deficient (<50 nmol L−1). At 26 weeks, winter/spring birth season and shorter duration of months of exclusive breastfeeding were protective of vit D deficiency in infants. Vitamin D deficiency in infants decreased to 12% at 52 weeks with sunlight exposure. Serum PTH levels were significantly higher in severely vit D deficient than sufficient infants. Vitamin D deficiency was widespread in early post‐partum breastfeeding mothers and infants, and declined to one in eight infants at 52 weeks due mostly to sunshine exposure. When sunlight exposure is limited or restricted, intensified vit D supplementation of breastfeeding mothers and infants is needed to improve vit D status.
‘Lessons learned’: A comparative case study analysis of an emergency department response to two burns disasters
Authors: Little Mark , Cooper Jim , Gope Monica , Hahn Kelly A , Kibar Cem , McCoubrie David , Ng Conrad , Robinson Annie , Soderstrom Jessamine , Leclercq Muriel 
Published: June 2012

AbstractObjectiveThe Royal Perth Hospital (RPH; Perth, Australia) has been the receiving facility for burns patients in two separate disasters. In 2002, RPH received 28 severely injured burns patients after the Bali bombing, and in 2009 RPH received 23 significantly burnt patients as a result of an explosion on board a foreign vessel in the remote Ashmore Reef Islands (840 km west of Darwin). The aim of this paper is to identify the interventions developed following the Bali bombing in 2002 and review their effectiveness of their implementation in the subsequent burns disaster.MethodsA comparative case study analysis using a standardised approach was used to describe context with debrief reports and ED photographs from both disasters used for evaluation.ResultsThe implementation of regular ED disaster response planning and training, early Code Brown notification of the entire hospital with regular updates, early clearing of inpatient beds, use of Short Message Service to communicate regularly with ED staff, control of the public and media access to the ED, visual identification of staff within the ED, early panendoscopy to ascertain intubation needs, and senior clinical decision makers in all areas of the ED were all acknowledged as effective based on the debrief reports. There was a reduction in ED length of stay (150 to 55 min) and no deaths occurred; however, quantitative analysis can only be suggestive rather than a direct measure of improvement given the likelihood of other system changes.ConclusionThere were a number of lessons observed from the Bali experience in 2002 that have led to improvements in practice and lessons learned.
Forage nutritive value of Texas bluegrass harvested in the morning and afternoon in northwest Oklahoma
Authors: Goldman Jason J. , Gunter Stacey A. 
Published: June 2012

Abstract
Texas bluegrass (
Poa arachnifera
Torr.) is a highly rhizomatous, dioecious, sexual, perennial, cool‐season grass native to southern Kansas, Oklahoma, western Arkansas and most of Texas. This native species is of particular interest for development into an improved cool‐season forage plant because of its heat tolerance and persistence under the extreme environmental conditions of the southern Great Plains. The objectives of this experiment were to determine water‐soluble, non‐structural carbohydrate and crude protein concentrations, forage dry matter yield, and in situ organic matter and crude protein disappearance from Texas bluegrass as affected by germplasm, maturity and time of harvest (morning and afternoon) at Woodward, Oklahoma. Crude protein concentrations ranged from 9 to 12% across seasons and did not differ between a morning and afternoon harvest. Dry matter yield ranged from 2130 to 5580 kg ha−1 over all harvest dates. Water‐soluble, non‐structural carbohydrate concentration was greater in the afternoon compared to morning harvests and ranged from 11 to 26%. Based on estimates from in situ digestion, the ratio of ruminally degradable crude protein to ruminally degraded organic matter in Texas bluegrass, it may compensate for the ruminally degraded nitrogen deficiency associated with dormant warm‐season grasses during the winter. The forage nutritive value parameters estimated in this study indicate that Texas bluegrass has potential as an improved cool‐season pasture grass.