bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frequency of nocturnal hypoxia in clinically stable patients during stroke rehabilitation
Authors: Roffe Christine , Frohnhofen Helmut , Sills Sheila , Hodsoll John , Allen Martin B , Jones Peter W 
Published: February 2010

Objective: Sleep disordered breathing is common in patients with cerebrovascular disease. Nocturnal hypoxia may lead to daytime tiredness and cognitive impairment, thus affecting progress. This study assessed the prevalence of nocturnal hypoxia during rehabilitation from stroke. Design: Prospective observational trial. Setting: The stroke rehabilitation wards of the North Staffordshire Hospital, UK and of Kreiskrankenhaus Grevenbroich, Germany. Subjects: Adult patients on a stroke rehabilitation ward, 10 days to 3 months (mean 32 days, SD18) after stroke onset (n = 160). Age and local environment-matched controls (n = 156) without a history of stroke were recruited from the community at both centres. Main measures: Pulse oximetry was performed overnight on the day of enrolment from 21:00 to 09:00. The baseline awake oxygen saturation, the mean nocturnal oxygen saturation, the lowest nocturnal oxygen saturation and the 4% Oxygen Desaturation Index were calculated for each participant. Results: The mean baseline awake oxygen saturation of stroke patients was at 95.3% (SD 1.7), 0.5% lower than that of controls (P = 0.005, independent t-test). The group means of the mean nocturnal oxygen saturation for stroke patients were 0.5% lower (at 93.8% SD 2.2) than controls (P = 0.03, independent t-test). The mean lowest nocturnal oxygen saturation was at 79.4% (SD 9.9), 5.9% lower than that of the controls (P<0.001, independent t-test). Considerably more stroke patients (n = 67, 42%) than controls (n = 24, 15%) had ≥10 desaturations below the baseline per hour (P<0.001 chi-square test). Conclusion: Clinically stable stroke patients enrolled in rehabilitation programmes have lower oxygen saturation and more nocturnal desaturations than non-stroke controls.
Errorless learning is superior to trial and error when learning a practical skill in rehabilitation: a randomized controlled trial
Authors: Donaghey CL , McMillan TM , O'Neill B. 
Published: February 2010

Objective: Errorless learning is an effective strategy for the cognitive rehabilitation of memory impairment, but there is little evidence to support its use for skill learning. This preliminary study investigates whether errorless learning is superior to treatment as usual (trial and error), when teaching people with amputations and comorbid risk of vascular cognitive impairment to fit a prosthetic limb. Design: A randomized control design. Setting: A regional limb-fitting clinic at the West of Scotland Mobility and Rehabilitation Centre in Glasgow. Participants: Thirty adults with transtibial amputations, recruited from a regional limb-fitting clinic. Of these 42% were cognitively impaired. Intervention: Random assignment to an errorless learning intervention (n = 15) or a treatment as usual control (n = 15). There were five training trials within a single session. Participants were then asked to fit their limb without assistance. Main measures: Performance was scored from videotape recording of the first occasion when the participant attempted to fit their limb without assistance. Addenbrookes Cognitive Examination — Revised (ACE-R) was used to assess general cognitive functioning. Results: The errorless learning group remembered more correct steps (mean 90.9, SD 12.1) than the control group (77.9; 8.4; P<0.001) and made fewer errors (mean 0.93, SD 1.3) than controls (2.1; 0.95); P =0.002). Conclusions: Errorless learning can benefit people with amputations in learning the practical skill of fitting a prosthetic limb. Further study that includes follow-up is warranted.
Respiratory muscle training improves cardiopulmonary function and exercise tolerance in subjects with subacute stroke: a randomized controlled trial
Authors: Sutbeyaz Serap Tomruk , Koseoglu Fusun , Inan Levent , Coskun Ozlem 
Published: February 2010

Objective: To determine whether two types of exercise — breathing retraining (BRT) and inspiratory muscle training (IMT) — improve on cardiopulmonary functions and exercise tolerance in patients with stroke. Design: A randomized controlled trial. Setting: Education and research hospital. Subjects: Forty-five inpatients with stroke (24 men, 21 women) were recruited for the study. The subjects were randomized into three groups: 15 assigned to receive inspiratory muscle training (IMT); 15 assigned to received breathing retraining, diaphragmatic breathing and pursed-lips breathing (BRT); 15 assigned to a control group. Interventions: All study groups participated in a conventional stroke rehabilitation programme. For the same period, the IMT and BRT groups trained daily, six times a week, with each session consisting of one half-hour of training for six weeks. Main measures: Each subject underwent pulmonary function and cardiopulmonary exercise tests. Subjects were also assessed for exertional dyspnoea, stages of motor recovery, ambulation status, activity of daily living and quality of life. Results: After the training programme, the IMT group had significantly improved forced expiratory volume at 1 second (FEV1), forced vital capacity (FVC), vital capacity (VC), forced expiratory flow rate 25—75% (FEF 25—75%) and maximum voluntary ventilation (MVV) values compared with the BRT and control groups, although there were no significant differences between the BRT and control groups (P<0.01). Peak expiratory flow rate (PEF) value was increased significantly in the BTR group compared with the IMT and control groups. The IMT group also had significantly higher peak oxygen consumption (Vo2peak) than the BRT and control groups, although there were no significant differences between the BRT and control groups (P<0.001). There was a statistically significant increase in maximum inspiratory pressure (PImax) and maximum inspiratory and expiratory pressure (PEmax) in the BRT group and, PImax in the IMT group compared with baseline and the control group. In the IMT group, this was associated with improvements in exercise capacity, sensation of dyspnoea and quality of life. Conclusions: Significant short-term effects of the respiratory muscle training programme on respiratory muscle function, exercise capacity and quality of life were recorded in this study.
Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of Hepatic Nuclear Factor 4 Alpha
Authors: Koh Winston , Sheng Chen Tian , Tan Betty , Lee Qian Yi , Kuznetsov Vladimir , Kiang Lim Sai , Tanavde Vivek 
Published: February 2010

Abstract

Background
Recent literature has revealed that genetic exchange of microRNA between cells can be essential for cell-cell communication, tissue-specificity and developmental processes. In stem cells, as in other cells, this can be accomplished through microvesicles or exosome mediated transfer. However, molecular profiles and functions of microRNAs within the cells and in their exosomes are poorly studied. Next generation sequencing technologies could provide a broad-spectrum of microRNAs and their expression and identify possible microRNA targets. In this work, we performed deep sequencing of microRNAs to understand the profile and expression of the microRNAs in microvesicles and intracellular environment of human embryonic stem cells derived mesenchymal stem cells (hES-MSC).
We outline a workflow pertaining to visualizing, statistical analysis and interpreting deep sequencing data of known intracellular and extracellular microRNAs from hES-MSC). We utilized these results of which directed our attention towards establishing hepatic nuclear factor 4 alpha (HNF4A) as a downstream target of let-7 family of microRNAs.

Results
In our study, significant differences in expression profile of microRNAs were found in the intracellular and extracellular environment of hES-MSC. However, a high level of let-7 family of microRNAs is predominant in both intra- and extra- cellular samples of hES-MSC. Further results derived from visualization of our alignment data and network analysis showed that let-7 family microRNAs could affect the downstream target HNF4A, which is a known endodermal differentiation marker. The elevated presence of let-7 microRNA in both intracellular and extra cellular environment further suggests a possible intercellular signalling mechanism through microvesicles transfer. We suggest that let-7 family microRNAs might play a signalling role via such a mechanism amongst populations of stem cells in maintaining self renewal property by suppressing HNF4A expression. This is in line with recent paradigm where microRNAs regulate self-renewal and differentiation pathways of embryonic stem cells by forming an integral biological network with transcription factors.

Conclusion
In summary, our study using a combination of alignment, statistical and network analysis tools to examine deep sequencing data of microRNAs in hES-MSC has led to a result that (i) identifies intracellular and exosome microRNA expression profiles of hES-MSCwith a possible mechanism of miRNA mediated intercellular regulation by these cells and (ii) placed HNF4A within the cross roads of regulation by the let-7 family of microRNAs.
In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection
Authors: Bolduc François , Hoareau Christopher , St-Pierre Patrick , Perreault Jean-Pierre 
Published: February 2010

Abstract

Background
It has been observed that following viroid infection, there is an accumulation of viroid-derived siRNAs in infected plants. Some experimental results suggest that these small RNAs may be produced by the plant defense system to protect it from infection, indicating that viroids can elicit the RNA-silencing pathways. The objective of this study is to identify in the peach latent mosaic viroid (PLMVd), a model RNA genome, the regions that are most susceptible to RNA interference machinery.

Results
The RNA isolated from an infected tree have been used to sequence in parallel viroid species and small non-coding RNA species. Specifically, PLMVd RNAs were amplified, cloned and sequenced according to a conventional approach, while small non-coding RNAs were determined by high-throughput sequencing. The first led to the typing of 18 novel PLMVd variants. The second provided a library of small RNAs including 880 000 sequences corresponding to PLMVd-derived siRNAs, which makes up 11.2% of the sequences of the infected library. These siRNAs contain mainly 21-22 nucleotide RNAs and are equivalently distributed between the plus and the minus polarities of the viroid. They cover the complete viroid genome, although the amount varies depending on the regions. These regions do not necessarily correlate with the double-stranded requirement to be a substrate for Dicer-like enzymes. We noted that some sequences encompass the hammerhead self-cleavage site, indicating that the circular conformers could be processed by the RNA-silencing machinery. Finally, a bias in the relative abundance of the nature of the 5' nucleotides was observed (A, U >> G, C).

Conclusions
The approach used provided us a quantitative representation of the PLMVd-derived siRNAs retrieved from infected peach trees. These siRNAs account for a relatively large proportion of the small non-coding RNAs. Surprisingly, the siRNAs from some regions of the PLMVd genome appear over-represented, although these regions are not necessarily forming sufficiently long double-stranded structures to satisfy Dicer-like criteria for substrate specificity. Importantly, this large library of siRNAs gave several hints as to the components of the involved silencing machinery.
Sleep triggered by an immune response in Drosophila is regulated by the circadian clock and requires the NFκB Relish
Authors: Kuo Tzu-Hsing , Pike Douglas H , Beizaeipour Zahra , Williams Julie A 
Published: February 2010

Abstract

Background
Immune challenge impacts behavior in many species. In mammals, this adaptive behavior is often manifested as an increase in sleep. Sleep has therefore been proposed to benefit the host by enhancing immune function and thereby overcome the challenge. To facilitate genetic studies on the relationship between sleep and immune function, we characterized the effect of the immune response on sleep in Drosophila melanogaster. Behavioral features of sleep as well as the innate immune response signaling pathways are well characterized in flies and are highly conserved in mammals.

Results
An immune response induced by infection with Gram-negative bacteria or by aseptic injury increased sleep in flies. The increase in sleep occurred during the morning hours after treatment and the magnitude of the effect was dependent on the time-of-day of inoculation or injury such that night-time treatment had a stronger effect than that during the daytime. This pattern persisted in constant darkness, indicating a role of the circadian clock. Mutants of the circadian clock gene, period, eliminated the increase in sleep observed in the morning, but instead showed enhanced sleep immediately after injury or infection.
Null mutants of the Nuclear Factor κB (NFκB) Relish, which is central to the innate immune response, do not increase sleep in response to injury or infection at any time of day. Instead, they maintain a normal sleep pattern until they die. Expression of a full-length Relish transgene in the fat bodies of Relish mutants restored the morning increase in sleep during an immune response. Fat bodies are a major site of immune signalling in flies and have a key role in host defense.

Conclusions
These data demonstrate that an immune response increases sleep in flies in a manner that is gated by the circadian clock and that requires the NFκB Relish. These findings support a role of sleep in a recovery process and demonstrate a conserved feature of the Drosophila model of sleep.
A novel DSPPmutation causes dentinogenesis imperfecta type II in a large Mongolian family
Authors: Bai Haihua , Agula Hasi , Wu Qizhu , Zhou Wenyu , Sun Yujing , Qi Yue , Latu Suya , Chen Yujie , Mutu Jiri , Qiu Changchun 
Published: February 2010

Abstract

Background
Several studies have shown that the clinical phenotypes of dentinogenesis imperfecta type II (DGI-II) may be caused by mutations in dentin sialophosphoprotein (DSPP). However, no previous studies have documented the clinical phenotype and genetic basis of DGI-II in a Mongolian family from China.

Methods
We identified a large five-generation Mongolian family from China with DGI-II, comprising 64 living family members of whom 22 were affected. Linkage analysis of five polymorphic markers flanking DSPP gene was used to genotype the families and to construct the haplotypes of these families. All five DSPP exons including the intron-exon boundaries were PCR-amplified and sequenced in 48 members of this large family.

Results
All affected individuals showed discoloration and severe attrition of their teeth, with obliterated pulp chambers and without progressive high frequency hearing loss or skeletal abnormalities. No recombination was found at five polymorphic markers flanking DSPP in the family. Direct DNA sequencing identified a novel A→G transition mutation adjacent to the donor splicing site within intron 3 in all affected individuals but not in the unaffected family members and 50 unrelated Mongolian individuals.

Conclusion
This study identified a novel mutation (IVS3+3A→G) in DSPP, which caused DGI-II in a large Mongolian family. This expands the spectrum of mutations leading to DGI-II.
Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue
Authors: Antonov Janine , Popovici Vlad , Delorenzi Mauro , Wirapati Pratyaksha , Baltzer Anna , Oberli Andrea , Thürlimann Beat , Giobbie-Hurder Anita , Viale Giuseppe , Altermatt Hans Jörg , Aebi Stefan , Jaggi Rolf 
Published: February 2010

AbstractBackgroundThe purpose of the work reported here is to test reliable molecular profiles using routinely processed formalin-fixed paraffin-embedded (FFPE) tissues from participants of the clinical trial BIG 1-98 with a median follow-up of 60 months.MethodsRNA from fresh frozen (FF) and FFPE tumor samples of 82 patients were used for quality control, and independent FFPE tissues of 342 postmenopausal participants of BIG 1-98 with ER-positive cancer were analyzed by measuring prospectively selected genes and computing scores representing the functions of the estrogen receptor (eight genes, ER_8), the progesterone receptor (five genes, PGR_5), Her2 (two genes, HER2_2), and proliferation (ten genes, PRO_10) by quantitative reverse transcription PCR (qRT-PCR) on TaqMan Low Density Arrays. Molecular scores were computed for each category and ER_8, PGR_5, HER2_2, and PRO_10 scores were combined into a RISK_25 score.ResultsPearson correlation coefficients between FF- and FFPE-derived scores were at least 0.94 and high concordance was observed between molecular scores and immunohistochemical data. The HER2_2, PGR_5, PRO_10 and RISK_25 scores were significant predictors of disease free-survival (DFS) in univariate Cox proportional hazard regression. PRO_10 and RISK_25 scores predicted DFS in patients with histological grade II breast cancer and in lymph node positive disease. The PRO_10 and PGR_5 scores were independent predictors of DFS in multivariate Cox regression models incorporating clinical risk indicators; PRO_10 outperformed Ki-67 labeling index in multivariate Cox proportional hazard analyses.ConclusionsScores representing the endocrine responsiveness and proliferation status of breast cancers were developed from gene expression analyses based on RNA derived from FFPE tissues. The validation of the molecular scores with tumor samples of participants of the BIG 1-98 trial demonstrates that such scores can serve as independent prognostic factors to estimate disease free survival (DFS) in postmenopausal patients with estrogen receptor positive breast cancer.Trial RegistrationCurrent Controlled Trials: NCT00004205
Genetic analysis of patients with Fuchs endothelial corneal dystrophy in India
Authors: Hemadevi Boomiraj , Srinivasan Muthiah , Arunkumar Jambulingam , Prajna Namperumalsamy V , Sundaresan Periasamy 
Published: February 2010

Abstract

Background
Mutations in COL8A2 gene which encodes the collagen alpha-2 (VIII) chain have been identified in both familial and sporadic cases of Fuchs endothelial corneal dystrophy (FECD). Heterozygous mutations in the SLC4A11 gene are also known to cause late-onset FECD. Therefore we screened for COL8A2, SLC4A11 gene variants in Indian FECD patients.

Methods
Eighty patients with clinically diagnosed FECD and 100 age matched normal individuals were recruited. Genomic DNA was isolated from peripheral blood leukocytes. Mutations in COL8A2, SLC4A11 coding regions were screened using bi-directional sequencing. Fischer's exact test or Pearson's chi squared test were used to predict the statistical association of genotypes with the phenotype.

Results
Screening of COL8A2 gene revealed 2 novel c.1610G>A, c.1643A>G and 3 reported variations c.112G>A, c.464G>A and c.1485G>A. In SLC4A11 gene, novel c.1659C>T, c.1974C>T and reported c.405G>A, c.481A>C and c.639G>A variants were identified. However all the variations in both the genes were also present in unaffected controls.

Conclusions
This is the first study analysing COL8A2 gene in Indian patients with FECD. No pathogenic mutations were identified in COL8A2. Merely silent changes, which showed statistically insignificant association with FECD, were identified in the screening of SLC4A11 gene. These results suggest that COL8A2, SLC4A11 genes may not be responsible for FECD in patients examined in this study.
Documentation of best interest by intensivists: a retrospective study in an Ontario critical care unit
Authors: Ratnapalan Mohana , Cooper Andrew B , Scales Damon C , Pinto Ruxandra 
Published: February 2010

Abstract

Background
Intensive care physicians often must rely on substitute decision makers to address all dimensions of the construct of "best interest" for incapable, critically ill patients. This task involves identifying prior wishes and to facilitate the substitute decision maker's understanding of the incapable patient's condition and their likely response to treatment. We sought to determine how well such discussions are documented in a typical intensive care unit.

Methods
Using a quality of communication instrument developed from a literature search and expert opinion, 2 investigators transcribed and analyzed 260 handwritten communications for 105 critically ill patients who died in the intensive care unit between January and June 2006. Cohen's kappa was calculated before analysis and then disagreements were resolved by consensus. We report results on a per-patient basis to represent documented communication as a process leading up to the time of death in the ICU. We report frequencies and percentages for discrete data, median (m) and interquartile range (IQR) for continuous data.

Results
Our cohort was elderly (m 72, IQR 58-81 years) and had high APACHE II scores predictive of a high probability of death (m 28, IQR 23-36). Length of stay in the intensive care unit prior to death was short (m 2, IQR 1-5 days), and withdrawal of life support preceded death for more than half (n 57, 54%). Brain death criteria were present for 18 patients (17%). Although intensivists' communications were timely (median 17 h from admission to critical care), the person consenting on behalf of the incapable patient was explicitly documented for only 10% of patients. Life support strategies at the time of communication were noted in 45% of charts, and options for their future use were presented in 88%. Considerations relevant to determining the patient's best interest in relation to the treatment plan were not well documented. While explicit survival estimates were noted in 50% of charts, physicians infrequently documented their own predictions of the patient's functional status (20%), anticipated need for chronic care (0%), or post ICU quality of life (3%). Similarly, documentation of the patient's own perspectives on these ranged from 2-18%.

Conclusions
Intensivists' documentation of their communication with substitute decision makers frequently outlined the proposed plan of treatment, but often lacked evidence of discussion relevant to whether the treatment plan was expected to improve the patient's condition. Legislative standards for determination of best interest, such as the Health Care Consent Act in Ontario, Canada, may provide guidance for intensivists to optimally document the rationales for proposed treatment plans.