bluuebunny/crossref_metadata_2025_split huggingface dataset:
Initial results of an optimized perfusion system
Authors: Starck CT , Bettex D , Felix C , Reser D , Dreizler T , Hasenclever P , Falk V 
Published: February 2013

Background: In order to reduce the negative effects of extracorporeal circulation (ECC), the perfusion system and management were optimized at our institution. The goals of optimization were a reduction in the priming volume, in the foreign surface area and in microbubble activity, as well as optimization of suction blood management. Methods: Sixty patients were included in this retrospective study. Patients were assigned to two groups, with regard to the use of an optimized perfusion system (OPS-group, n=30) and a standard perfusion system (SPS-group, n=30). All patients underwent elective procedures. Results: There were no significant differences with respect to patient demographics and operation time. ECC time and cross-clamp time were significantly longer in the OPS group. Statistically significant differences in outcome between the two groups were seen with regard to the following variables: effective priming volume (OPS: 775±447ml; SPS: 1610±0ml; p<0.0001), hemoglobin drop after the start of ECC (OPS: 2.7±1.2g/dl; SPS: 4.2±0.8g/dl; p<0.0001), c-reactive protein on postoperative day 2 (OPS: 121.0±59.4 U/l; SPS: 164.0±50.2 U/l; p=0.003). With regard to the use of blood transfusions, a 33% reduction in the overall amount of transfused units was seen. The rate of patients without transfusions during the entire hospital stay increased from 37% (SPS) to 53% (OPS). The mean transfused red blood cell units per patient was lower in the OPS-group (1.6±2.4 units) than in the SPS-group (2.3±3.5 units). Conclusion: With the described optimized perfusion system, a significantly lower priming volume, leading to less hemodilution after the onset of CPB, was achieved. The amount of blood transfusions and the inflammatory response were reduced.
Pulmonary function and physical performance outcomes with preoperative physical therapy in upper abdominal surgery: a randomized controlled trial
Authors: Soares Silvia Maria de Toledo Piza , Nucci Luciana Bertoldi , da Silva Marcela Maria de Carvalho , Campacci Thaís Colombini 
Published: February 2013

Objective: Investigation of the effects of preoperative physical therapy on pulmonary function and physical performance before and after upper abdominal surgery. Design: Non-blind randomized controlled trial. Setting: Tertiary public hospital and private university, São Paulo state, Brazil. Subjects: Thirty-two patients undergoing abdominal surgery. Interventions: Patients were randomly assigned to receive physical therapy, with respiratory and global exercises, 2–3 weeks before surgery (treatment group; n = 16) or await operation without engaging in practicing (control group; n = 16). After surgery, a physical therapy protocol was administered to all subjects until the seventh postoperative day. Main measures: Pulmonary function outcome variables were inspiratory and expiratory strength, respiratory muscle endurance and spirometry, and physical performance outcome variables were the functional independence measure and 6-minute walk test distance. Any postoperative pulmonary complications were recorded. Results: There were no between-group differences at randomization. In the preoperative period, patients in the intervention group had higher inspiratory strength and respiratory muscle endurance than controls (88 cmH2O versus 64 cmH2O and 28 cmH2O versus 23 cmH2O, respectively; P <0 0.05). On the seventh postoperative day, in addition to inspiratory force and respiratory muscle endurance, the intervention group showed better results than controls in the functional independence measure score (118 versus 95) and 6-minute walk test distance (368.5 m versus 223 m), all P <0 0.05. Postoperative pulmonary complications occurred in 11 patients in the control group and five in the intervention group ( P = 0.03). Conclusion: Preoperative physical therapy improved pulmonary function and physical performance in the pre- and postoperative periods among patients undergoing upper abdominal surgery.
Subject-chosen activities in occupational therapy for the improvement of psychiatric symptoms of inpatients with chronic schizophrenia: a controlled trial
Authors: Hoshii Junko , Yotsumoto Kayano , Tatsumi Eri , Tanaka Chito , Mori Takashi , Hashimoto Takeshi 
Published: February 2013

Objective: To compare the therapeutic effects of subject-chosen and therapist-chosen activities in occupational therapy for inpatients with chronic schizophrenia. Design: Prospective comparative study. Setting: A psychiatric hospital in Japan. Subjects: Fifty-nine patients with chronic schizophrenia who had been hospitalized for many years. Interventions: The subjects received six-months occupational therapy, participating in either activities of their choice (subject-chosen activity group, n = 30) or activities chosen by occupational therapists based on treatment recommendations and patient consent (therapist-chosen activity group, n = 29). Main measures: The Positive and Negative Syndrome Scale and the Global Assessment of Functioning (GAF) Scale were used to evaluate psychiatric symptoms and psychosocial function, respectively. Results: After six-months occupational therapy, suspiciousness and hostility scores of the positive scale and preoccupation scores of the general psychopathology scale significantly improved in the subject-chosen activity group compared with the therapist-chosen activity group, with 2(2) (median (interquartile range)) and 3(1.25), 2(1) and 2.5(1), and 2(1) and 3(1), respectively. There were no significant differences in psychosocial functions between the two groups. In within-group comparisons before and after occupational therapy, suspiciousness scores of the positive scale, preoccupation scores of the general psychopathology scale, and psychosocial function significantly improved only in the subject-chosen activity group, with 3(1) to 2(2), 3(1) to 2(1), and 40(9) to 40(16) respectively, but not in the therapist-chosen activity group. Conclusions: The results suggested that the subject-chosen activities in occupational therapy could improve the psychiatric symptoms, suspiciousness, and preoccupation of the inpatients with chronic schizophrenia.
Early Events of Overused Supraspinatus Tendons Involve Matrix Metalloproteinases and EMMPRIN/CD147 in the Absence of Inflammation
Authors: Attia Mohamed , Huet Eric , Gossard Camille , Menashi Suzanne , Tassoni Marie-Claude , Martelly Isabelle 
Published: February 2013

Background: The principal feature of tendon degeneration is structural change of the extracellular matrix (ECM) including collagens. In painful tendons, alterations of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) have been described; however, the initial molecular mechanism at the origin of these alterations is still poorly understood. A rat model of supraspinatus tendon overuse has been developed, which may be predictive of pathological tendon alterations. Purpose: To determine which MMPs are involved in early ECM remodeling during overuse and their relationship with the inflammatory context. Study Design: Controlled laboratory study. Methods: Analyses were performed on rat supraspinatus tendons at 2 and 4 weeks of overuse on a downhill treadmill. Transcript levels of MMPs and TIMPs were assessed by semiquantitative reverse transcription polymerase chain reaction. Western blotting and/or immunolabeling were used for MMP-2, MMP-3, MMP-13, and extracellular MMP inducer (EMMPRIN, also called cluster of differentiation [CD] 147) detection. In situ and/or sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) gelatin zymography was performed for MMP-2 and MMP-9. TIMP activity was revealed by reverse zymography. Inflammation was assessed by cytokine antibody array and/or immunolabeling. Results: Compared with a control, overused supraspinatus tendons showed a significantly higher gelatinolytic activity at 2 weeks, which slightly decreased at 4 weeks. MMP-9 and MMP-13 were undetectable; MMP-3 was downregulated in overused tendons. Only MMP-2, particularly its active form, and the MMP-2 activator MMP-14 were upregulated at 2 weeks of overuse when an increase in TIMP-2 transcripts was observed. MMP-2 upregulation occurred in the absence of inflammation but was associated with an increase of EMMPRIN/CD147. Conclusion: EMMPRIN/CD147-regulated MMP-2 and MMP-14, associated with low MMP-3, appear as the main characteristics of ECM remodeling in early overused tendons. Whether alterations in the pattern of these MMPs are an adaptive response or a repair response that may degenerate into tendinosis, is still uncertain. Moreover, there seems to be no indication for an inflammatory response to overuse, suggesting that the increased metalloproteinase activity is rather a response to a mechanical stress than an inflammatory one. Clinical Relevance: Any strategy aimed at preventing full-thickness tears resulting from initial tendon matrix alterations should consider these changes in MMP-3, MMP-2, and MMP-14, or further upstream, EMMPRIN.
Patient Origin Is Associated With Duration of Endotracheal Intubation and PICU Length of Stay for Children With Status Asthmaticus
Authors: Shibata Shinpei , Khemani Robinder G. , Markovitz Barry 
Published: February 2013

Objective: To describe intubation practices and duration of mechanical ventilation in children with status asthmaticus admitted from emergency departments (ERs) to pediatric intensive care units (PICUs). Design: Retrospective cohort study using the Virtual PICU Performance System database (VPS, LLC) of children with status asthmaticus admitted to a participating PICU between December 2003 and September 2006. The primary outcome measure was intubation prior to intensive care unit (ICU) admission. Secondary outcomes included length of intubation and medical length of stay. Setting: Thirty-five PICUs in the United States. Patients: Children who were intubated and mechanically ventilated during their ICU stay for asthma and were admitted from an ER. Results: A total of 4051 patients with status asthmaticus were identified. Intubation data were available from 35 of the 53 centers. Of all, 187 children were intubated for asthma, of which 157 were admitted from an ER and had complete data. Of all, 85 patients were from community hospital ERs and 72 were from the institution’s own ER. In all, 115 (73%) patients were intubated prior to ICU admission and 42 (27%) patients were intubated after PICU admission. Of patients who received mechanical ventilation for status asthmaticus and were intubated prior to PICU admission, a greater proportion were intubated at community hospital ERs than in the institutions’ own ERs. Eighty-five percent of the patients from community hospital ERs were intubated prior to PICU admission as opposed to 60% from institution’s own ERs ( P = .0004). However, median duration of intubation and PICU stay from community hospital ERs was significantly shorter than from the hospitals’ own ERs (25 vs 42 hours P = .011; 57 vs 98 hours P = .0013, respectively). Logistic regression analysis revealed that after controlling for the effects of age, race, gender, and a revised version of the Paediatric Index of Mortality score of patients who were admitted for status asthmaticus and required mechanical ventilations, patients treated in community hospital ERs represented a greater proportion of preadmission intubation. The odds ratio for preadmission intubation was 5.1 if the patients arrived from community hospital ERs (95% confidence interval 1.91-13.6). Conclusion: Patients with status asthmaticus are more likely to be intubated when they are admitted from community hospital emergency rooms, although the duration of intubation and PICU stay is shorter.
Syndesmosis Fixation Using Dual 3.5 mm and 4.5 mm Screws With Tricortical and Quadricortical Purchase
Authors: Markolf Keith L. , Jackson Steven R. , McAllister David R. 
Published: February 2013

Background: Grade 3 syndesmosis (high ankle) sprains of the ankle are frequently treated using screws that fix the distal fibula to the tibia. We hypothesized that forces acting on the distal fibula and displacements of the distal fibula relative to the tibia recorded during simulated ankle loading tests would be significantly affected by syndesmosis screw size and the number of engaged tibial cortices. Methods: Distal fibular forces and displacements were measured after cutting the distal inferior tibiofibular ligaments and fixing the distal fibula to the distal fibula with 2 syndesmosis screws. Screws of 3.5 mm and 4.5 mm were applied with tricortical and quadricortical purchase. Results: There were no significant differences in distal fibular forces or displacements between any combination of screw size and cortical purchase tested. The highest mean fibular force recorded in the study (110.2 N) occurred when 10 N-m of external foot torque was applied to a dorsiflexed ankle loaded with 1000 N axial weight-bearing force. For ankle dorsiflexion and external foot torque tests, the distal fibula always displaced posteriorly with respect to the tibia. Mean displacements of the fibula from 1000 N applied axial weight-bearing force (maximum 0.15 mm) and from 10 N-m of forced foot dorsiflexion (maximum 0.43 mm) were considerably less than those from 10 N-m external foot torque (1.7 mm to 2.7 mm). Conclusions: Screw size and the number of engaged tibial cortices had no significant effect on mechanical stability of the distal fibula during these tests. Application of external foot torque (internal tibial torque) to a weight-bearing ankle produced the greatest bending displacements of the screws, and should be avoided during rehabilitation to reduce the possibility of screw breakage. Clinical Relevance: In terms of mechanical stability, surgeons may have considerable flexibility with regard to screw fixation of high ankle sprains.
Combined inhibition of PI3K-related DNA damage response kinases and mTORC1 induces apoptosis in MYC-driven B-cell lymphomas
Authors: Shortt Jake , Martin Benjamin P. , Newbold Andrea , Hannan Katherine M. , Devlin Jennifer R. , Baker Adele J. , Ralli Rachael , Cullinane Carleen , Schmitt Clemens A. , Reimann Maurice , Hall Michael N. , Wall Meaghan , Hannan Ross D. , Pearson Richard B. , McArthur Grant A. , Johnstone Ricky W. 
Published: February 2013

Key PointsMYC-driven lymphomas demonstrate activation of mTORC1 and an endogenous DNA damage response. BEZ235 inhibits PI3K-related DNA damage response kinases and mTORC1, inducing p53-independent upregulation of proapoptotic BMF.
The risk of hemophagocytic lymphohistiocytosis in Hermansky-Pudlak syndrome type 2
Authors: Jessen Birthe , Bode Sebastian F. N. , Ammann Sandra , Chakravorty Subarna , Davies Graham , Diestelhorst Jana , Frei-Jones Melissa , Gahl William A. , Gochuico Bernadette R. , Griese Matthias , Griffiths Gillian , Janka Gritta , Klein Christoph , Kögl Tamara , Kurnik Karin , Lehmberg Kai , Maul-Pavicic Andrea , Mumford Andrew D. , Pace David , Parvaneh Nima , Rezaei Nima , de Saint Basile Geneviève , Schmitt-Graeff Annette , Schwarz Klaus , Karasu Gulsun T. , Zieger Barbara , zur Stadt Udo , Aichele Peter , Ehl Stephan 
Published: February 2013

Key Points
Hermansky-Pudlak syndrome type 2 confers a moderate risk for hemophagocytic lymphohistiocytosis.
Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus(Stramenopiles, Xanthophyceae)
Authors: Rybalka Nataliya , Wolf Matthias , Andersen Robert A , Friedl Thomas 
Published: February 2013

Abstract

Background

Heterococcus is a microalgal genus of Xanthophyceae (Stramenopiles) that is common and widespread in soils, especially from cold regions. Species are characterized by extensively branched filaments produced when grown on agarized culture medium. Despite the large number of species described exclusively using light microscopic morphology, the assessment of species diversity is hampered by extensive morphological plasticity.

Results
Two independent types of molecular data, the chloroplast-encoded psbA/rbcL spacer complemented by rbcL gene and the internal transcribed spacer 2 of the nuclear rDNA cistron (ITS2), congruently recovered a robust phylogenetic structure. With ITS2 considerable sequence and secondary structure divergence existed among the eight species, but a combined sequence and secondary structure phylogenetic analysis confined to helix II of ITS2 corroborated relationships as inferred from the rbcL gene phylogeny. Intra-genomic divergence of ITS2 sequences was revealed in many strains. The ‘monophyletic species concept’, appropriate for microalgae without known sexual reproduction, revealed eight different species. Species boundaries established using the molecular-based monophyletic species concept were more conservative than the traditional morphological species concept. Within a species, almost identical chloroplast marker sequences (genotypes) were repeatedly recovered from strains of different origins. At least two species had widespread geographical distributions; however, within a given species, genotypes recovered from Antarctic strains were distinct from those in temperate habitats. Furthermore, the sequence diversity may correspond to adaptation to different types of habitats or climates.

Conclusions
We established a method and a reference data base for the unambiguous identification of species of the common soil microalgal genus Heterococcus which uses DNA sequence variation in markers from plastid and nuclear genomes. The molecular data were more reliable and more conservative than morphological data.
A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover
Authors: Nagy Istvan , Barth Susanne , Mehenni-Ciz Jeanne , Abberton Michael T , Milbourne Dan 
Published: February 2013

AbstractBackgroundWhite clover (Trifolium repensL.) is an allotetraploid species possessing two highly collinear ancestral sub-genomes. The apparent existence of highly similar homeolog copies for the majority of genes in white clover is problematic for the development of genome-based resources in the species. This is especially true for the development of genetic markers based on single nucleotide polymorphisms (SNPs), since it is difficult to distinguish between homeolog-specific and allelic variants. Robust methods for categorising single nucleotide variants as allelic or homeolog-specific in large transcript datasets are required. We illustrate one potential approach in this study.ResultsWe used 454-pyrosequencing sequencing to generate ~760,000 transcript sequences from an 8th generation white clover inbred line. These were assembled and partially annotated to yield a reference transcript set comprising 71,545 sequences. We subsequently performed Illumina sequencing on three further white clover samples, generating 14 million transcript reads from a mixed sample comprising 24 divergent white clover genotypes, and 50 million reads on two further eighth generation white clover inbred lines. Mapping these reads to the reference transcript set allowed us to develop a significant SNP resource for white clover, and to partition the SNPs from the inbred lines into categories reflecting allelic or homeolog-specific variation. The potential for using haplotype reconstruction and progenitor genome comparison to assign haplotypes to specific ancestral sub-genomes of white clover is demonstrated for sequences corresponding to genes encoding dehydration responsive element binding protein and acyl-coA oxidase.ConclusionsIn total, 208,854 independent SNPs in 31,715 reference sequences were discovered, approximately three quarters of which were categorised as representing allelic or homeolog-specific variation using two inbred lines. This represents a significant resource for white clover genomics and genetics studies. We discuss the potential to extend the analysis to identify a “core set” of ancestrally derived homeolog specific variants in white clover.
AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications
Authors: Van Geystelen Anneleen , Decorte Ronny , Larmuseau Maarten HD 
Published: February 2013

Abstract

Background
Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase the resolution of the phylogenetic Y chromosomal tree. Moreover, the exponential growth of known Y chromosomal lineages will require an automatic determination of the phylogenetic position of an individual based on whole genome SNP calling data and an up to date Y chromosomal tree.

Results
We present an automated approach, ‘AMY-tree’, which is able to determine the phylogenetic position of a Y chromosome using a whole genome SNP profile, independently from the NGS platform and SNP calling program, whereby mistakes in the SNP calling or phylogenetic Y chromosomal tree are taken into account. Moreover, AMY-tree indicates ambiguities within the present phylogenetic tree and points out new Y-SNPs which may be phylogenetically relevant. The AMY-tree software package was validated successfully on 118 whole genome SNP profiles of 109 males with different origins. Moreover, support was found for an unknown recurrent mutation, wrong reported mutation conversions and a large amount of new interesting Y-SNPs.

Conclusions
Therefore, AMY-tree is a useful tool to determine the Y lineage of a sample based on SNP calling, to identify Y-SNPs with yet unknown phylogenetic position and to optimize the Y chromosomal phylogenetic tree in the future. AMY-tree will not add lineages to the existing phylogenetic tree of the Y-chromosome but it is the first step to analyse whole genome SNP profiles in a phylogenetic framework.
S-Adenosyl-L-Methionine protects the probiotic yeast, Saccharomyces boulardii,from acid-induced cell death
Authors: Cascio Vincent , Gittings Daniel , Merloni Kristen , Hurton Matthew , Laprade David , Austriaco Nicanor 
Published: February 2013

Abstract

Background

Saccharomyces boulardii is a probiotic yeast routinely used to prevent and to treat gastrointestinal disorders, including the antibiotic-associated diarrhea caused by Clostridium difficile infections. However, only 1-3% of the yeast administered orally is recovered alive in the feces suggesting that this yeast is unable to survive the acidic environment of the gastrointestinal tract.

Results
We provide evidence that suggests that S. boulardii undergoes programmed cell death (PCD) in acidic environments, which is accompanied by the generation of reactive oxygen species and the appearance of caspase-like activity. To better understand the mechanism of cell death at the molecular level, we generated microarray gene expression profiles of S. boulardii cells cultured in an acidic environment. Significantly, functional annotation revealed that the up-regulated genes were significantly over-represented in cell death pathways Finally, we show that S-adenosyl-L-methionine (AdoMet), a commercially available, FDA-approved dietary supplement, enhances the viability of S. boulardii in acidic environments, most likely by preventing programmed cell death.

Conclusions

In toto, given the observation that many of the proven health benefits of S. boulardii are dependent on cell viability, our data suggests that taking S. boulardii and AdoMet together may be a more effective treatment for gastrointestinal disorders than taking the probiotic yeast alone.