bluuebunny/crossref_metadata_2025_split huggingface dataset:
An integrated approach for the systematic identification and characterization of heart-enriched genes with unknown functions
Authors: Uchida Shizuka , Schneider André , Wiesnet Marion , Jungblut Benno , Zarjitskaya Polina , Jenniches Katharina , Kreymborg Karsten grosse , Seeger Werner , Braun Thomas 
Published: March 2009

Abstract

Background
High throughput techniques have generated a huge set of biological data, which are deposited in various databases. Efficient exploitation of these databases is often hampered by a lack of appropriate tools, which allow easy and reliable identification of genes that miss functional characterization but are correlated with specific biological conditions (e.g. organotypic expression).

Results
We have developed a simple algorithm (DGSA = D atabase-dependent G ene S election and A nalysis) to identify genes with unknown functions involved in organ development concentrating on the heart. Using our approach, we identified a large number of yet uncharacterized genes, which are expressed during heart development. An initial functional characterization of genes by loss-of-function analysis employing morpholino injections into zebrafish embryos disclosed severe developmental defects indicating a decisive function of selected genes for developmental processes.

Conclusion
We conclude that DGSA is a versatile tool for database mining allowing efficient selection of uncharacterized genes for functional analysis.
The properties of bioengineered chondrocyte sheets for cartilage regeneration
Authors: Mitani Genya , Sato Masato , Lee Jeong IK , Kaneshiro Nagatoshi , Ishihara Miya , Ota Naoshi , Kokubo Mami , Sakai Hideaki , Kikuchi Tetsutaro , Mochida Joji 
Published: March 2009

Abstract

Background
Although the clinical results of autologous chondrocyte implantation for articular cartilage defects have recently improved as a result of advanced techniques based on tissue engineering procedures, problems with cell handling and scaffold imperfections remain to be solved. A new cell-sheet technique has been developed, and is potentially able to overcome these obstacles. Chondrocyte sheets applicable to cartilage regeneration can be prepared with this cell-sheet technique using temperature-responsive culture dishes. However, for clinical application, it is necessary to evaluate the characteristics of the cells in these sheets and to identify their similarities to naive cartilage.

Results
The expression of SOX 9, collagen type 2, 27, integrin α10, and fibronectin genes in triple-layered chondrocyte sheets was significantly increased in comparison to those in conventional monolayer culture and in a single chondrocyte sheet, implying a nature similar to ordinary cartilage. In addition, immunohistochemistry demonstrated that collagen type II, fibronectin, and integrin α10 were present in the triple-layered chondrocyte sheets.

Conclusion
The results of this study indicate that these chondrocyte sheets with a consistent cartilaginous phenotype and adhesive properties may lead to a new strategy for cartilage regeneration.
Improving consensus structure by eliminating averaging artifacts
Authors: KC Dukka B 
Published: March 2009

Abstract

Background
Common structural biology methods (i.e., NMR and molecular dynamics) often produce ensembles of molecular structures. Consequently, averaging of 3D coordinates of molecular structures (proteins and RNA) is a frequent approach to obtain a consensus structure that is representative of the ensemble. However, when the structures are averaged, artifacts can result in unrealistic local geometries, including unphysical bond lengths and angles.

Results
Herein, we describe a method to derive representative structures while limiting the number of artifacts. Our approach is based on a Monte Carlo simulation technique that drives a starting structure (an extended or a 'close-by' structure) towards the 'averaged structure' using a harmonic pseudo energy function. To assess the performance of the algorithm, we applied our approach to Cα models of 1364 proteins generated by the TASSER structure prediction algorithm. The average RMSD of the refined model from the native structure for the set becomes worse by a mere 0.08 Å compared to the average RMSD of the averaged structures from the native structure (3.28 Å for refined structures and 3.36 A for the averaged structures). However, the percentage of atoms involved in clashes is greatly reduced (from 63% to 1%); in fact, the majority of the refined proteins had zero clashes. Moreover, a small number (38) of refined structures resulted in lower RMSD to the native protein versus the averaged structure. Finally, compared to PULCHRA [1], our approach produces representative structure of similar RMSD quality, but with much fewer clashes.

Conclusion
The benchmarking results demonstrate that our approach for removing averaging artifacts can be very beneficial for the structural biology community. Furthermore, the same approach can be applied to almost any problem where averaging of 3D coordinates is performed. Namely, structure averaging is also commonly performed in RNA secondary prediction [2], which could also benefit from our approach.
Molecular assays for the detection of microRNAs in prostate cancer
Authors: Siva Amara C , Nelson Luke J , Fleischer Chad L , Majlessi Mehrdad , Becker Michael M , Vessella Robert L , Reynolds Mark A 
Published: March 2009

Abstract

Background
MicroRNAs (miRNAs) are small non-coding RNAs (about 21 to 24 nucleotides in length) that effectively reduce the translation of their target mRNAs. Several studies have shown miRNAs to be differentially expressed in prostate cancer, many of which are found in fragile regions of chromosomes. Expression profiles of miRNAs can provide information to separate malignancies based upon stage, progression and prognosis. Here we describe research prototype assays that detect a number of miRNA sequences with high analytical sensitivity and specificity, including miR-21, miR-182, miR-221 and miR-222, which were identified through expression profiling experiments with prostate cancer specimens. The miRNAs were isolated, amplified and quantified using magnetic bead-based target capture and a modified form of Transcription-Mediated Amplification (TMA).

Results
Analytical sensitivity and specificity were demonstrated in model system experiments using synthetic mature microRNAs or in vitro miRNA hairpin precursor transcripts. Research prototype assays for miR-21, miR-182, miR-221 and miR-222 provided analytical sensitivities ranging from 50 to 500 copies of target per reaction in sample transport medium. Specific capture and detection of mature miR-221 from complex samples was demonstrated in total RNA isolated from human prostate cancer cell lines and xenografts.

Conclusion
Research prototype real-time TMA assays for microRNAs provide accurate and reproducible quantitation using 10 nanograms of input total RNA. These assays can also be used directly with tissue specimens, without the need for a preanalytic RNA isolation step, and thus provide a high-throughput method of microRNA profiling in clinical specimens.
Predicting clinically unrecognized coronary artery disease: use of two- dimensional echocardiography
Authors: Chang Su Min , Hakeem Abdul , Nagueh Sherif F 
Published: March 2009

Abstract

Background
2-D Echo is often performed in patients without history of coronary artery disease (CAD). We sought to determine echo features predictive of CAD.

Methods
2-D Echo of 328 patients without known CAD performed within one year prior to stress myocardial SPECT and angiography were reviewed. Echo features examined were left ventricular and atrial enlargement, LV hypertrophy, wall motion abnormality (WMA), LV ejection fraction (EF) < 50%, mitral annular calcification (MAC) and aortic sclerosis/stenosis (AS). High risk myocardial perfusion abnormality (MPA) was defined as >15% LV perfusion defect or multivessel distribution. Severe coronary artery stenosis (CAS) was defined as left main, 3 VD or 2VD involving proximal LAD.

Results
The mean age was 62 ± 13 years, 59% men, 29% diabetic (DM) and 148 (45%) had > 2 risk factors. Pharmacologic stress was performed in 109 patients (33%). MPA was present in 200 pts (60%) of which, 137 were high risk. CAS was present in 166 pts (51%), 75 were severe. Of 87 patients with WMA, 83% had MPA and 78% had CAS. Multivariate analysis identified age >65, male, inability to exercise, DM, WMA, MAC and AS as independent predictors of MPA and CAS. Independent predictors of high risk MPA and severe CAS were age, DM, inability to exercise and WMA.
2-D echo findings offered incremental value over clinical information in predicting CAD by angiography. (Chi square: 360 vs. 320 p = 0.02).

Conclusion
2-D Echo was valuable in predicting presence of physiological and anatomical CAD in addition to clinical information.
Molecular diagnosis of Toxoplasma gondii infection in cerebrospinal fluid from AIDS patients
Authors: Alfonso Yenisey , Fraga Jorge , Fonseca Carlos , Jiménez Narciso , Pinillos Taimy , Dorta-Contreras Alberto J , Cox Raymundo , Capó Virginia , Pomier Olga , Bandera Francisco , Ginorio Dora 
Published: March 2009

Abstract

Background
Toxoplasmic encephalitis (TE) is one of the most common opportunistic infections in immunocompromised patients. In Cuba, despite the highly active antiretroviral therapy, TE is still the most important cause of cerebral mass lesions in patients infected with the human immunodeficiency virus (HIV). The detection of Toxoplasma gondii by PCR may facilitate the diagnosis and follow-up of TE in acquired immunodeficiency syndrome (AIDS) patients by direct identification of parasite DNA in clinical samples. The aim of the present study was to evaluate a rapid PCR method using the B1 gene to detect T. gondii in cerebrospinal fluid (CSF) samples from patients with suspected TE.

Methods
CSF samples from AIDS and HIV-negative patients were analyzed. Patients were divided into two groups according to the Centre for Disease Control and Prevention (CDC) criteria for AIDS-related TE: AIDS patients with suspected neurotoxoplasmosis and AIDS and HIV-negative patients with other confirmed neurological diseases but no suspicions of TE. Predictive values, diagnostic accuracy, sensitivity and specificity of the PCR B1 method were calculated.

Results
The results obtained from 190 patients showed that this assay has a good sensitivity and specificity (83.3% and 95.7%, respectively) for the diagnosis of TE in AIDS patients.

Conclusion
PCR using the B1 gene and B22/B23 set of primers is a single, rapid and reliable method that may be valuable for discrimination between toxoplasmosis and other central nervous system (CNS) diseases.
Treatment of focal degenerative cartilage defects with polymer-based autologous chondrocyte grafts: four-year clinical results
Authors: Kreuz Peter C , Müller Sebastian , Ossendorf Christian , Kaps Christian , Erggelet Christoph 
Published: March 2009

Abstract
Introduction
Second-generation autologous chondrocyte implantation with scaffolds stabilizing the grafts is a clinically effective procedure for cartilage repair. In this ongoing prospective observational case report study, we evaluated the effectiveness of BioSeed®-C, a cell-based cartilage graft based on autologous chondrocytes embedded in fibrin and a stable resorbable polymer scaffold, for the treatment of clinical symptomatic focal degenerative defects of the knee.

Methods
Clinical outcome after 4-year clinical follow-up was assessed in 19 patients with preoperatively radiologically confirmed osteoarthritis and a Kellgren-Lawrence score of 2 or more. Clinical scoring was performed before implantation of the graft and 6, 12, and 48 months after implantation using the Lysholm score, the Knee injury and Osteoarthritis Outcome Score (KOOS), the International Knee Documentation Committee (IKDC) score, and the International Cartilage Repair Society (ICRS) score. Cartilage regeneration and articular resurfacing were assessed by magnetic resonance imaging (MRI) 4 years after implantation of the autologous cartilage graft.

Results
Significant improvement (P < 0.05) of the Lysholm and ICRS scores was observed as early as 6 months after implantation of BioSeed®-C and remained stable during follow-up. The IKDC score showed significant improvement compared with the preoperative situation at 12 and 48 months (P < 0.05). The KOOS showed significant improvement in the subclasses pain, activities of daily living, and knee-related quality of life 6 months as well as 1 and 4 years after implantation of BioSeed®-C in osteoarthritic defects (P < 0.05). MRI analysis showed moderate to complete defect filling with a normal to incidentally hyperintense signal in 16 out of 19 patients treated with BioSeed®-C. Two patients without improvement in the clinical and MRI scores received a total knee endoprosthesis after 4 years.

Conclusions
The results show that the good clinical outcome achieved 1 year after implantation of BioSeed®-C remains stable over the course of a period of 4 years and suggest that implanting BioSeed®-C is a promising treatment option for the repair of focal degenerative defects of the knee.
Prosodic discrimination in patients with
schizophrenia
Authors: Matsumoto K. , Samson G. T. , O'Daly O. D. , Tracy D. K. , Patel A. D. , Shergill S. S. 
Published: March 2009

SummaryFifteen patients with prominent positive symptoms of schizophrenia and 15
normal controls performed verbal prosodic and pure musical discrimination
tasks, with changes in pitch and timing parameters. The patients'
performance was comparable to that of controls on the discrimination of
terminal pitch changes, but significantly poorer on the more difficult
internal pitch discrimination. The latter deficit was positively correlated
with the severity of their positive symptoms. The results suggest that
patients have a deficit in processing fundamental aspects of prosody, which
is associated with the presence of positive symptoms.
Psychiatric presentation of voltage-gated potassium channel antibody-associated encephalopathy
Authors: Parthasarathi U. D. , Harrower T. , Tempest M. , Hodges J. R. , Walsh C. , McKenna P. J. , Fletcher P. C. 
Published: March 2009

SummaryVoltage-gated potassium channel antibody encephalopathy, a rare cause of limbic encephalopathy, typically presents with memory impairment and seizures. Psychiatric symptoms have not been emphasised in the literature. Here we describe a 58-year-old man who presented with panic attacks and psychogenic non-epileptic seizures and, later on, developed delusions and hallucinations and then confusion. He was found to have antibodies to voltage-gated potassium channels. Treatment with immuno-modulatory therapy resulted in almost complete recovery.
Mood switch in bipolar depression: comparison of adjunctive
venlafaxine, bupropion and sertraline
Authors: Post R. M. , Altshuler L. L. , Leverich G. S. , Frye M. A. , Nolen W A. , Kupka R. W. , Suppes T. , McElroy S. , Keck P. E. , Denicoff K. D. , Grunze H. , Walden J. , Kitchen C. M. R. , Mintz J. 
Published: March 2009

BackgroundFew studies have examined the relative risks of switching into hypomania
or mania associated with second-generation antidepressant drugs in
bipolar depression.AimsTo examine the relative acute effects of bupropion, sertraline and
venlafaxine as adjuncts to mood stabilisers.MethodIn a 10-week trial, participants receiving out-patient treatment for
bipolar disorder (stratified for rapid cycling) were randomly treated
with a flexible dose of one of the antidepressants, or their respective
matching placebos, as adjuncts to mood stabilisers.ResultsA total of 174 adults with bipolar disorder I, II or not otherwise
specified, currently in the depressed phase, were included. All three
antidepressants were associated with a similar range of acute response
(49–53%) and remission (34–41%). There was a significantly increased risk
of switches into hypomania or mania in participants treated with
venlafaxine compared with bupropion or sertraline.ConclusionsMore caution appears indicated in the use of venlafaxine rather than
bupropion or sertraline in the adjunctive treatment of bipolar
depression, especially if there is a prior history of rapid cycling.
Measuring memory impairment in community-based patients with schizophrenia
Authors: Al-Uzri M. M. , Reveley M. A. , Owen L. , Bruce J. , Frost S. , Mackintosh D. , Moran P. M. 
Published: March 2009

BackgroundThe majority of memory impairment studies in schizophrenia are cohort studies using laboratory-based tests, which make it difficult to estimate the true extent and relevance of memory impairment in patients with schizophrenia in the community.AimsTo examine the extent of memory impairment in community-based patients with schizophrenia using a clinically relevant test.MethodAll patients with schizophrenia (n= 190) in one catchment area were identified, of whom 133 were potentially eligible for the study; 73 patients volunteered to take part. They were assessed using the Rivermead Behavioural Memory Test (RBMT), the National Adult Reading Test, the Positive and Negative Syndrome Scale, the Health of the Nation Outcome Scales and the Office for National Statistics Classification of Occupation. Their performance on the memory test was compared with that of matched controls (n=71).ResultsPatients as a group performed significantly worse (P< 0.001) than controls on the RBMT. Using the RBMT normative scores, 81% of patients were found to have impaired memory compared with 28% of controls.ConclusionsUsing a clinically relevant test, the majority of community-based patients with schizophrenia may have memory impairment.
Socio-economic position and common mental disorders
Authors: Skapinakis Petros , Weich Scott , Lewis Glyn , Singleton Nicola , Araya Ricardo 
Published: March 2009

BackgroundIndividuals in lower socio-economic groups have an increased prevalence of common mental disorders.AimsTo investigate the longitudinal association between socio-economic position and common mental disorders in a general population sample in the UK.MethodParticipants (n=2406) were assessed at two time points 18 months apart with the Revised Clinical Interview Schedule. The sample was stratified into two cohorts according to mental health status at baseline.ResultsNone of the socio-economic indicators studied was significantly associated with an episode of common mental disorder at follow-up after adjusting for baseline psychiatric morbidity. The analysis of separate diagnostic categories showed that subjective financial difficulties at baseline were independently associated with depression at follow-up in both cohorts.ConclusionsThese findings support the view that apart from objective measures of socio-economic position, more subjective measures might be equally important from an aetiological or clinical perspective.
Gender differences in reoffending after discharge from
medium-secure units
Authors: Maden Anthony , Skapinakis Petros , Lewis Glyn , Scott Fiona , Burnett Rachel , Jamieson Elizabeth 
Published: March 2009

BackgroundPrevious research has shown that there are gender differences in
reoffending after discharge from medium-secure units, but these have not
been adequately explained.AimsTo investigate gender differences in reoffending after discharge from
medium-secure psychiatric units.MethodAll people discharged from medium-secure units in England and Wales
between April 1997 and March 1998 were followed up for 1 year
(n=959; 12% women). Reoffending was estimated by
collecting reconviction data from the Home Office's Offenders' Index or
from files at the mental health unit up to 2 years after discharge.ResultsWomen were less likely than men to be reconvicted within 2 years of
discharge (9% v. 16%, OR=0.49, 95% CI 0.25 – 0.98).
Adjustments for history of self-harm, drug or alcohol problems and
previous offending substantially reduced the gender difference. In the
full model the OR was 0.97 (95% CI 0.45–2.12).ConclusionsSome or all of the gender differences in reoffending between men and
women are explained by self-harm, alcohol and drug problems and previous
criminal history.
Psychological effects of ketamine in healthy
volunteers
Authors: Pomarol-Clotet E. , Honey G. D. , Murray G. K. , Corlett P. R. , Absalom A. R. , Lee M. , McKenna P. J. , Bullmore E. T. , Fletcher P. C. 
Published: March 2009

BackgroundThe psychosis-inducing effect of ketamine is important evidence
supporting the glutamate hypothesis of schizophrenia. However, the
symptoms the drug produces have not been described systematically.AimTo examine the effects of ketamine in healthy people using a structured
psychiatric interview.MethodKetamine (200 ng/ml) or placebo was administered by continuous infusion
to 15 healthy volunteers. Symptoms were rated using the Present State
Examination, the Thought, Language and Communication Scale and the Scale
for Assessment of Negative Symptoms.ResultsKetamine induced a range of perceptual distortions, but not
hallucinations. Referential ideas were seen in nearly half the sample.
There were only mild and infrequent ratings on the thought disorder
scale. Affective flattening and alogia were seen in some volunteers.ConclusionsKetamine does not reproduce the full picture of schizophrenia. The main
point of similarity concerns referential thinking. Phenomena resembling
negative symptoms are also seen, but the distinction of these from the
drug's sedative effects requires further elucidation.
Three decades of antidepressant, anxiolytic and hypnotic use in a national population birth cohort
Authors: Colman Ian , Wadsworth Michael E. J. , Croudace Tim J. , Jones Peter B. 
Published: March 2009

BackgroundPsychotropic medication use is common and increasing. Use of such drugs at the individual level over long periods has not been reported.AimsTo describe antidepressant, anxiolytic and hypnotic drug use, and associations between such medication use and common mental disorder, over a 22-year period.MethodQuestions about psychotropic medication use and symptoms of common mental disorder were asked of more than 3000 members of the 1946 British birth cohort at multiple time points between ages 31 and 53 years.ResultsPrevalence of any antidepressant, anxiolytic or hypnotic use increased significantly from 1977 (30.6 per 1000) to 1999 (59.1 per 1000) as the cohort aged. Less than 30% with mental disorder used antidepressants, anxiolytics or hypnotics. Previous use of antidepressant, anxiolytic or hypnotic was a strong predictor of future use during an episode of mental disorder (odds ratios 3.0–8.4); this association became weaker over time.ConclusionsPharmacotherapy is infrequently used by individuals with common mental disorder in Britain; this has not changed in the past three decades.