bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of pretreatment on morphology, chemical composition and enzymatic digestibility of eucalyptus bark: a potentially valuable source of fermentable sugars for biofuel production – part 1
Authors: Lima Marisa A , Lavorente Gabriela B , da Silva Hana KP , Bragatto Juliano , Rezende Camila A , Bernardinelli Oigres D , deAzevedo Eduardo R , Gomez Leonardo D , McQueen-Mason Simon J , Labate Carlos A , Polikarpov Igor
Published: May 2013

Background

In recent years, the growing demand for biofuels has encouraged the search for different sources of underutilized lignocellulosic feedstocks that are available in sufficient abundance to be used for sustainable biofuel production. Much attention has been focused on biomass from grass. However, large amounts of timber residues such as eucalyptus bark are available and represent a potential source for conversion to bioethanol. In the present paper, we investigate the effects of a delignification process with increasing sodium hydroxide concentrations, preceded or not by diluted acid, on the bark of two eucalyptus clones: Eucalyptus grandis (EG) and the hybrid, E. grandis x urophylla (HGU). The enzymatic digestibility and total cellulose conversion were measured, along with the effect on the composition of the solid and the liquor fractions. Barks were also assessed using Fourier-transform infrared spectroscopy (FTIR), solid-state nuclear magnetic resonance (NMR), X-Ray diffraction, and scanning electron microscopy (SEM).

Results

Compositional analysis revealed an increase in the cellulose content, reaching around 81% and 76% of glucose for HGU and EG, respectively, using a two-step treatment with HCl 1%, followed by 4% NaOH. Lignin removal was 84% (HGU) and 79% (EG), while the hemicellulose removal was 95% and 97% for HGU and EG, respectively. However, when we applied a one-step treatment, with 4% NaOH, higher hydrolysis efficiencies were found after 48 h for both clones, reaching almost 100% for HGU and 80% for EG, in spite of the lower lignin and hemicellulose removal. Total cellulose conversion increased from 5% and 7% to around 65% for HGU and 59% for EG. NMR and FTIR provided important insight into the lignin and hemicellulose removal and SEM studies shed light on the cell-wall unstructuring after pretreatment and lignin migration and precipitation on the fibers surface, which explain the different hydrolysis rates found for the clones.

Conclusion

Our results show that the single step alkaline pretreatment improves the enzymatic digestibility of Eucalyptus bark. Furthermore, the chemical and physical methods combined in this study provide a better comprehension of the pretreatment effects on cell-wall and the factors that influence enzymatic digestibility of this forest residue.
Direct detection of alpha synuclein oligomers in vivo
Authors: Dimant Hemi , Kalia Suneil K , Kalia Lorraine V , Zhu Liya N , Kibuuka Laura , Ebrahimi-Fakhari Darius , McFarland Nikolaus R , Fan Zhanyun , Hyman Bradley T , McLean Pamela J
Published: May 2013

Background

Rat models of Parkinson’s disease are widely used to elucidate the mechanisms underlying disease etiology or to investigate therapeutic approaches. Models were developed using toxins such as MPTP or 6-OHDA to specifically target dopaminergic neurons resulting in acute neuronal loss in the substantia nigra or by using viral vectors to induce the specific and gradual expression of alpha synuclein in the substantia nigra. The detection of alpha- synuclein oligomers, the presumed toxic species, in these models and others has been possible using only indirect biochemical approaches to date. Here we coinjected AAVs encoding alpha-synuclein fused to the N- or C-terminal half of VenusYFP in rat substantia nigra pars compacta and describe for the first time a novel viral vector rodent model with the unique ability to directly detect and track alpha synuclein oligomers ex vivo and in vivo.

Results

Viral coinjection resulted in widespread VenusYFP signal within the nigrostriatal pathway, including cell bodies in the substantia nigra and synaptic accumulation in striatal terminals, suggestive of in vivo alpha-synuclein oligomers formation. Transduced rats showed alpha-synuclein induced dopaminergic neuron loss in the substantia nigra, the appearance of dystrophic neurites, and gliosis in the striatum. Moreover, we have applied in vivo imaging techniques in the living mouse to directly image alpha-synuclein oligomers in the cortex.

Conclusion

We have developed a unique animal model that provides a tool for the Parkinson’s disease research community with which to directly detect alpha- synuclein oligomers in vivo and screen therapeutic approaches targeting alpha-synuclein oligomers.
NG2 cells, a new trail for Alzheimer’s disease mechanisms?
Authors: Nielsen Henrietta M , Ek Danyal , Avdic Una , Orbjörn Camilla , Hansson Oskar ,   The Netherlands Brain Bank, Veerhuis Robert , Rozemuller Annemieke JM , Brun Arne , Minthon Lennart , Wennström Malin
Published: May 2013

Background

Neuron Glial 2 (NG2) cells are glial cells known to serve as oligodendrocyte progenitors as well as modulators of the neuronal network. Altered NG2 cell morphology and up-regulation as well as increased shedding of the proteoglycan NG2 expressed on the cell surface have been described in rodent models of brain injury. Here we describe alterations in the human NG2 cell population in response to pathological changes characteristic of Alzheimer’s disease (AD).

Results

Immunohistological stainings of postmortem brain specimens from clinically diagnosed and postmortem verified AD patients and non-demented controls revealed reduced NG2 immunoreactivity as well as large numbers of NG2 positive astrocytes in individuals with high amyloid beta plaque load. Since fibrillar amyloid beta (Aβ)1-42 is the major component of AD-related senile plaques, we exposed human NG2 cells to oligomer- and fibril enriched preparations of Aβ1-42. We found that both oligomeric and fibrillar Aβ1-42 induced changes in NG2 cell morphology. Further, in vitro exposure to fibrillar Aβ1-42 decreased the NG2 concentrations in both cell lysates and supernatants. Interestingly, we also found significantly decreased levels of soluble NG2 in the cerebrospinal fluid (CSF) from clinically diagnosed AD patients compared to non-demented individuals. Additionally, the CSF NG2 levels were found to significantly correlate with the core AD biomarkers Aß1-42, T-tau and P-tau.

Conclusion

Our results demonstrate major alterations in the NG2 cell population in relation to AD pathology which highlights the NG2 cell population as a new attractive research target in the search for cellular mechanisms associated with AD pathogenesis.
Production of ethanol and arabitol by Debaryomyces nepalensis: influence of process parameters
Authors: Kumdam Himabindu , Narayana Murthy Shweta , Gummadi Sathyanarayana N
Published: May 2013

Debaryomyces nepalensis, osmotolerant yeast isolated from rotten apple, is known to utilize both hexoses and pentoses and produce industrially important metabolites like ethanol, xylitol and arabitol. In the present study, the effect of different growth substrates, trace elements, nitrogen concentration and initial pH on growth and formation of ethanol and arabitol were examined. Optimum conditions for maximizing the product yields were established: glucose as carbon source, an initial pH of 6.0, 6 g/L of ammonium sulphate and addition of micronutrients. Under these best suited conditions, a concentration of 11g/L of arabitol and 19 g/L of ethanol was obtained in shake flask fermentations. The fermentation was scaled up to 2.5 L bioreactor and the influence of aeration, agitation and initial substrate concentration was also determined. Under optimal conditions (150 g/L glucose, 400 rpm and 0.5 vvm) ethanol concentration reached 52 g/L, which corresponds to a yield of 0.34 g/g and volumetric productivity of 0.28 g/L/h, whereas arabitol production reached a maximum of 14 g/L with a yield and volumetric productivity of 0.1 g/g and 0.07 g/L/h respectively.
Adult attention-deficit hyperactivity disorder and obesity: epidemiological study
Authors: Cortese Samuele , Faraone Stephen V. , Bernardi Silvia , Wang Shuai , Blanco Carlos
Published: May 2013

Background

A significant association between attention-deficit hyperactivity disorder (ADHD) and obesity has been reported. This study addresses unexplored aspects of this relationship.

Aims

To evaluate the association between adult obesity and: (a) persistent, remitted or lifetime ADHD; (b) number of childhood ADHD symptoms, controlling for socioeconomic status and mood, anxiety and substance use disorders.

Method

Face-to-face psychiatric interviews in 34653 US adults from the National Epidemiologic Study on Alcohol and Related Conditions. Obesity was defined as a body mass index ⩾30.

Results

Persistent, lifetime or remitted ADHD were not associated with obesity after controlling for confounders. The number of childhood ADHD symptoms was significantly associated with adult obesity, even after adjustment, in women.

Conclusions

Childhood ADHD symptoms are associated with obesity in women even after comorbid psychiatric disorders are accounted for. This provides a rationale for longitudinal studies assessing the impact of the treatment of childhood ADHD symptoms on obesity in women.
Fertilisation is not a new beginning: sperm environment affects offspring developmental success
Authors: Ritchie Hannah , Marshall Dustin J.
Published: May 2013

For organisms with complex life histories, the direction and magnitude of phenotypic links among life-history stages can have important ecological and evolutionary effects. While the phenotypic links between mothers and offspring, as well as between larvae and adults, are well recognised, the links between sperm phenotype and offspring phenotype are less explored. Here we use a split-clutch/split-ejaculate design to examine whether the environment that sperm experience affects the subsequent performance of larvae in the broadcast spawning marine invertebrate Galeolaria geminoa. The environment that sperm experienced affected the developmental success of larvae sired by these sperm; larvae sired by sperm that experienced low salinities had poorer developmental success than larvae sired by sperm that experienced a normal salinity. When we explored the interactive effects of the sperm environment and the larval environment with an orthogonal design, we found an interaction; when sperm and larvae experienced the same environment, performance was generally higher than when the sperm and larval environments differed. These effects could be due to selection on specific sperm phenotypes, phenotypic modification of the sperm or both. Together, our results challenge the traditional notion that sperm are merely transporters of genetic material, instead, significant covariance between sperm and offspring phenotypes exists. Our study adds to a growing list that demonstrates that fertilisation does have a homogenising effect on the phenotype of the zygote, and that events before fertilisation during the gamete phase can carry through to affect performance in later life-history stages.
Affinity purification of T7 RNA transcripts with homogeneous ends using ARiBo and CRISPR tags
Authors: Salvail-Lacoste Alix , Di Tomasso Geneviève , Piette Benjamin L. , Legault Pascale
Published: May 2013

Affinity purification of RNA using the ARiBo tag technology currently provides an ideal approach to quickly prepare RNA with 3′ homogeneity. Here, we explored strategies to also ensure 5′ homogeneity of affinity-purified RNAs. First, we systematically investigated the effect of starting nucleotides on the 5′ heterogeneity of a small SLI RNA substrate from the Neurospora VS ribozyme purified from an SLI-ARiBo precursor. A series of 32 SLI RNA sequences with variations in the +1 to +3 region was produced from two T7 promoters (class III consensus and class II ϕ2.5) using either the wild-type T7 RNA polymerase or the P266L mutant. Although the P266L mutant helps decrease the levels of 5′-sequence heterogeneity in several cases, significant levels of 5′ heterogeneity (≥1.5%) remain for transcripts starting with GGG, GAG, GCG, GGC, AGG, AGA, AAA, ACA, AUA, AAC, ACC, AUC, and AAU. To provide a more general approach to purifying RNA with 5′ homogeneity, we tested the suitability of using a small CRISPR RNA stem–loop at the 5′ end of the SLI-ARiBo RNA. Interestingly, we found that complete cleavage of the 5′-CRISPR tag with the Cse3 endoribonuclease can be achieved quickly from CRISPR–SLI-ARiBo transcripts. With this procedure, it is possible to generate SLI-ARiBo RNAs starting with any of the four standard nucleotides (G, C, A, or U) involved in either a single- or a double-stranded structure. Moreover, the 5′-CRISPR-based strategy can be combined with affinity purification using the 3′-ARiBo tag for quick purification of RNA with both 5′ and 3′ homogeneity.
Improving educational environment in medical colleges through transactional analysis practice of teachers
Authors: Rajan Marina , Chacko Thomas
Published: May 2013

Context: A FAIMER (Foundation for Advancement in International Medical Education and Research) fellow organized a comprehensive faculty development program to improve faculty awareness resulting in changed teaching practices and better teacher student relationships using Transactional Analysis (TA). Practicing TA tools help development of ‘awareness’ about intrapersonal and interpersonal processes.

Objectives:

To improve self-awareness among medical educators.

To bring about self-directed change in practices among medical educators.

To assess usefulness of TA tools for the same.

Methods: An experienced trainer conducted a basic course (12 hours) in TA for faculty members. The PAC model of personality structure, functional fluency model of personal functioning, stroke theory on motivation, passivity and script theories of adult functional styles were taught experientially with examples from the Medical Education Scenario. Self-reported improvement in awareness and changes in practices were assessed immediately after, at three months, and one year after training.

Findings: The mean improvement in self-'awareness' is 13.3% (95% C.I 9.3-17.2) among nineteen participants. This persists one year after training. Changes in practices within a year include, collecting feedback, new teaching styles and better relationship with students.

Discussion and Conclusions: These findings demonstrate sustainable and measurable improvement in self-awareness by practice of TA tools. Improvement in self-'awareness' of faculty resulted in self-directed changes in teaching practices. Medical faculty has judged the TA tools effective for improving self-awareness leading to self-directed changes.
Expression of erythropoietin in Indian tetraploid potato variety
Authors: Desai Priti N , Padh Harish
Published: May 2013

With the advent of protein-based biotech drugs in the market, the quest for the “perfect” protein expression system, which is both economical and effective, has come into focus. Currently bacteria, yeast, insect cells, mammalian cells, transgenic animal and transgenic plants are widely used for the expression of therapeutic proteins. Among these, transgenic plants provide advantages in terms of low production cost, lower capital investment in infrastructure, and suitable post-translational modifications. The major limitation of plants as an expression host is the low level of transgene expression. To increase the expression of heterologous proteins in plants, a number of approaches have been used. One of the approaches is to increase the transgene expression by using tissue-specific promoter(s) which can concentrate the protein of interest in targeted tissues and, thus, prove advantageous in downstream purification. In the present report, a protocol for expression of heterologous protein erythropoietin in potato tuber using patatin, the tuber-tissue-specific promoter, was standardized. Expression vectors for production of the erythropoietin gene under tissue-specific promoter were successfully constructed. For production of a transgenic plant, tissue culture techniques for regeneration of the whole plant from single explants were standardized. Polymerase chain reaction (PCR) analysis was performed to confirm the stable integration of the erythropoietin gene in the potato plant by using sequence-specific primers.
Evolution of alarm cues: a role for kin selection?
Authors: Meuthen Denis , Baldauf Sebastian A , Thünken Timo
Published: May 2013

The evolution of alarm signals has puzzled evolutionary ecologists for decades. This is particularly true for alarm cues (‘Schreckstoff’) which are present in many fishes. They are passively released through injuries and signal the presence of a predator. Although the benefits for conspecific receivers are obvious (they can adjust their behavior to avoid predation), those for the senders are not which is, however, a necessary requirement for the evolution of alarm signals. Several hypotheses relying on potential direct benefits for the senders have been suggested. Alarm cues might attract secondary predators which in turn might increase the escape probability of the sender. A primary immune enhancing role was suggested as well. An alternative explanation is based on Hamilton’s inclusive fitness theory stating that individuals can indirectly increase their fitness by increasing the survival of genetically related individuals (‘kin selection theory’). If related individuals preferentially benefit from alarm signals, for instance by being more receptive to kin-alarm cues, senders could increase their inclusive fitness. Here, we investigate whether individuals of the cichlid fishPelvicachromis taeniatus respond differentially to alarm cues derived from kin and non-kin. P. taeniatuspossesses alarm cues and is known to adjust its behavior when exposed to alarm cues. We measured the change in activity after the addition of alarm cues (derived from kin- and non-kin) relative to a control treatment. Reduced activity is a widespread behavioral adaptation to reduce predation risk in prey organisms. Fish of the alarm cue treatments significantly reduced their activity relative to control fish. However, fish did not respond differentially to alarm cues derived from kin and non-kin suggesting that potential inclusive fitness benefits are not mediated by responses specific to individual alarm cues. We discuss alternative mechanisms such as kin-related grouping and mating preferences potentially leading to kin-biased alarm cue perception.
Common ground for biodiversity and ecosystem services: the “partial protection” challenge
Authors: Faith Daniel P
Published: May 2013

New global initiatives require clarity about similarities and differences between biodiversity and ecosystem services. One argument is that ecosystem services capture utilitarian values, while biodiversity captures intrinsic values. However, the concept of biodiversity equally emerges from anthropogenic use values. Measures of biodiversity indicate broad option values, and so provide different information about future uses and benefits. Such differences nevertheless can be the basis for “common ground” for biodiversity and ecosystem services. Systematic conservation planning and related frameworks acknowledge such differences through effective trade-offs and synergies among different values of society. The early work on regional biodiversity trade-offs includes a little-explored aspect that could enhance this common ground. Regional planning here takes into account the “partial protection” of biodiversity provided by some land uses. Common-ground will be promoted by better integrating the ecosystem services and biodiversity conservation offered by ecosystems at the “natural end of the spectrum” with the partial protection and other benefits/services provided by more intensively-transformed places.
Rapamycin-insensitive mTORC1 activity controls eIF4E:4E-BP1 binding
Authors: Livingstone Mark , Bidinosti Michael
Published: May 2013

The recent development of mammalian target of rapamycin (mTOR) kinase domain inhibitors and genetic dissection of rapamycin-sensitive and -insensitive mTOR protein complexes (mTORC1 and mTORC2) have revealed that phosphorylation of the mTOR substrate 4E-BP1 on amino acids Thr37 and/or Thr46 represents a rapamycin-insensitive activity of mTORC1. Despite numerous previous reports utilizing serine (Ser)-to-alanine (Ala) and threonine (Thr)-to-Ala phosphorylation site mutants of 4E-BP1 to assess which post-translational modification(s) directly regulate binding to eIF4E, an ambiguous understanding persists. This manuscript demonstrates that the initial, rapamycin-insensitive phosphorylation event at Thr46 is sufficient to prevent eIF4E:4E-BP1 binding. This finding is relevant, particularly as mTOR kinase domain inhibitors continue to be assessed for clinical efficacy, since it clarifies a difference between the action of these second-generation mTOR inhibitors and those of rapamycin analogues.
NIH Portfolio Allocation, Lemmings, and the Silent Spring: A Time-Capsule Commentary & Its Update
Authors: Boothby Mark
Published: May 2013

With the release of the US President’s proposed budget for the Federal Fiscal year (FY) 2013, to start October 1, 2012, we’ve spun yet again into the mad vortex of an appropriation season. Fundamental re-thinks of how biological and medical research are prioritized and funded are urgently needed, but sadly appear to be unlikely unless the research and advocacy communities push harder and in a more unified manner. Early in the Obama presidency and the NIH Directorship of Dr Francis Collins, the FASEB Office of Public Affairs performed an analysis of trends in funding of R01 and other Research Project Grants and shared that with the Director and his office. Using the FASEB analysis, whose numbers drew on NIH data, an independent commentary (below) was submitted to (but not published in) Science. With the analysis a few years old, this older viewpoint is followed by updates that touch on how the trends have fared since early 2010 and comment on other aspects of the ongoing cull in biomedical research. In particular, data on some of the growth areas that continue to prosper at the expense of the ever-declining direct support for R01 science are discussed.
Does vitamin D deficiency contribute to post-burn bone loss?
Authors: Klein Gordon L
Published: May 2013

Burn injury results in the acute loss of bone as well as the development of progressive vitamin D deficiency. Bone loss occurs acutely due to resorption, which is then followed by apoptosis of osteoblasts preventing repair of the bone loss. The acute resorption is due to a combination of the inflammatory response and the stress response to the burn injury. The resultant production of inflammatory cytokines and endogenous glucocorticoids initially stimulate the osteoblasts to produce RANK ligand, which stimulates marrow stem cell differentiation into osteoclasts. As the stress response persists for approximately one year post-burn the glucocorticoids produced by the body will cause osteoblast apoptosis and adynamic bone, impairing the ability of bone to recover its resorptive losses. The vitamin D deficiency is due to the failure to supplement the diet of burn patients with vitamin D on discharge from hospital and to failure of the skin to make normal quantities of vitamin D on sunlight exposure. Because the bone resorption can be prevented by the acute administration of bisphosphonates it is unlikely that vitamin D deficiency is responsible for the early-onset bone loss following burns. However, because a deficit in trabecular bone remains for at least two years post-burn, it is possible that vitamin D deficiency prevents the recovery of trabecular bone density over the long term.
Identification of two telomere-proximal fission yeast DNA replication origins constrained by nearby cis-acting sequences to replicate in late S phase
Authors: Chaudari Amna , Huberman Joel A
Published: May 2013

Telomeres of the fission yeast, Schizosaccharomyces pombe, are known to replicate in late S phase, but the reasons for this late replication are not fully understood. We have identified two closely-spaced DNA replication origins, 5.5 to 8 kb upstream from the telomere itself. These are the most telomere-proximal of all the replication origins in the fission yeast genome. When located by themselves in circular plasmids, these origins fired in early S phase, but if flanking sequences closer to the telomere were included in the circular plasmid, then replication was restrained to late S phase – except in cells lacking the replication-checkpoint kinase, Cds1. We conclude that checkpoint-dependent late replication of telomere-associated sequences is dependent on nearby cis-acting sequences, not on proximity to the physical end of a linear chromosome.
Misunderstanding publication bias: editors are not blameless after all
Authors: Senn Stephen
Published: May 2013

In analysing whether there is an editorial bias in favour of positive studies, researchers have made implicit assumptions that are implausible. In particular, to justify the conclusion that there is no bias because observed editorial acceptance rates do not favour positive studies, the assumption that the decision to submit an article is based solely on quality would be required. If, on the other hand, submission were based on perceived probability of acceptance, negative and positive studies would not differ in terms of acceptance rates, but in terms of quality.

It is shown, using a simple graphical model, how similar underlying situations as regards the relationship between quality and probability of acceptance on the one hand and study outcome (positive or negative) and probability of acceptance on the other could produce dramatically different results depending on the behaviour of authors.

Furthermore, there is, in fact, some evidence that submitted negative studies are, on average, of higher quality than positive ones. This calls into question the standard interpretation of the studies examining editorial bias. It would appear that despite similar probabilities of acceptance for negative and positive studies, editors could be discriminating against negative studies.
Capecitabine-induced radiation recall phenomenon: a case report
Authors: Aguilar José , García Elena , García-Garre Elisa
Published: May 2013

Radiation recall dermatitis is defined as an inflammatory reaction of the skin at the site of previous irradiation. Different drugs have been associated with triggering this phenomenon, and it can also affect other areas and organs where previous radiotherapy has been administered. The time gap between the inflammatory reaction and previous radiation can range from days to several years.

We report what we believe to be the first case of Capecitabine-induced Radiation Therapy Oncology Group (RTOG) Grade 4 recall skin toxicity (ulcerating dermatitis), which occurred three years after skin irradiation. Clinicians should be aware of this phenomenon, even when considering patients for whom it has been a long time since previous radiation therapy. This unusual and late drug side effect should be borne in mind in the differential diagnosis and management of advanced-disease patients as it may be confused with local relapse or infectious complication of previously operated areas.
Respiratory functions of conservancy workers working in solid waste management sector of Chennai, India
Authors: Roopa Srinivasan , Padmavathi Ramaswamy , Akolkar Avinash , Sankar Sambandam , Ravishankar Pitani , Vijayalakshmi Thanasekharaan , Subhashini AS , Kalpana Balakrishnan
Published: May 2013

Chennai is the fourth largest metropolitan city in India. Around 10,000 conservancy workers of the Chennai Corporation handle about 4500 to 5200 tons of solid wastes per day. These workers are exposed to a lot of environmental and occupational hazards affecting the respiratory system. This paper presents the results of pulmonary function assessment in 178 conservancy workers (100 sweepers & 78 loaders) of the Chennai Corporation. Detailed medical and occupational history was obtained and clinical examination was performed after obtaining informed consent. Pulmonary functions (forced vital capacity [FVC], forced expiratory volume in 1 second [FEV1] and peak expiratory flow rate [PEFR]) were measured using a portable spirometer. Since normal pulmonary function values for healthy non-smoking South Indian adults are available through previously published studies, the pulmonary function test (PFT) values from the study group were compared with the predicted values after corrections for age and anthropometry. The pulmonary functions of the conservancy workers were significantly lower than their predicted values. Moreover, the pulmonary functions declined with increasing years of working. Among both the groups of conservancy workers, the pulmonary functions were significantly lower in sweepers than loaders (P<0.01). This study has generated lung function data of the Chennai Corporation conservancy workers that can aid the concerned authorities to implement specific interventions to reduce the exposure and improve the health status of the workers.
Glenoid Labral Tear: follow up case series on ultrasound guided autologous platelet rich plasma in conjunction with a progressive rehabilitation program
Authors: Vander Kraats Robert , Doss Arockia
Published: May 2013

Background: Labral tears commonly occur in both the general and sporting population, often leading to significant pain and dysfunction. Patients often engage in progressive rehabilitative programs, and surgical intervention may be required in severe cases. Autologous platelet rich plasma (PRP) injections have been growing in popularity in musculoskeletal medicine as an alternative to corticosteroid injections. This paper looks at the effectiveness of PRP injections in glenoid labral lesions.

Methods: The clinical and radiological findings are presented for two patients who have been treated with autologous PRP into the glenohumeral joint adjacent to the labral tear, in conjunction with a progressive rehabilitative program. Follow up occurred at 18 months and 13 months, respectively.

Results: Both subjects tolerated the PRP injection well with no adverse effects, and were compliant with their rehabilitative programs. On initial presentation, pain on the visual analogue scale (VAS) was 7/10 and 6/10 and at follow up it was reported as 0/10. Both subjects have now returned to normal sporting and work activities.

Conclusions: The findings from this case series suggest that PRP in conjunction with appropriate rehabilitation can assist in the clinical recovery of glenoid labral tears. Further research is required with greater sample numbers and improved methodological parameters.
Exploring the membrane topology of prohormone convertase 1 in AtT20 Cells: in situ analysis by immunofluorescence microscopy
Authors: Cawley Niamh X , Sridhar Meera , Hong Hong , Loh Peng
Published: May 2013

Prohormone convertase 1 (PC1) was previously characterized as a partially transmembrane protein in purified chromaffin granules of bovine adrenal medulla1. This was challenged with experiments on transfected PC1 in COS1 cells, a non-endocrine cell line2. To address this issue, we undertook to analyze its extraction properties in vitro and its immunocytochemical localization in situ in AtT20 cells, an endocrine cell line that expresses PC1. Most of the 87 kDa form of PC1 was resistant to carbonate extraction suggesting that it had properties of a transmembrane protein. Under semi-permeabilized conditions whereby only the plasma membrane was permeabilized, the carboxy-terminus of PC1 was specifically immunostained whereas the amino-terminus was not. These results indicate that the amino-terminus of PC1 was within the lumen of the Golgi and granules, and some of the C-terminus was exposed to the cytosol. Thus, endogenous PC1 can assume a transmembrane orientation in situ in AtT20 cells.
Biased under-reporting of research reflects biased under-submission more than biased editorial rejection
Authors: Chalmers Iain , Dickersin Kay
Published: May 2013

Stephen Senn challenges Ben Goldacre’s assertion in ‘Bad Pharma’ that biased editorial acceptance of reports with ‘positive’ findings is not a cause of biased under-reporting of research. We agree with Senn that biased editorial decisions may contribute to reporting bias, but Senn ignores the evidence that biased decisions by researchers to submit reports for possible publication are the main causes of the problem.
Rhinoscleroma presenting as a nasal-palatal mass with airway obstruction
Authors: Domanski Mark C , Rivero Alexander , Kardon David E
Published: May 2013

We report a case of a 45-year-old male with severe rhinoscleroma. The patient presented to the emergency room with dyspnea from a long-standing nasal-palatal mass. A tracheostomy was required for airway control. While dyspnea in the presence of an upper airway mass is typical of malignancy, consideration of non-oncological etiologies is important. We review the epidemiology, pathology, diagnosis, and treatment of rhinoscleroma.
Authors are also reviewers: problems in assigning cause for missing negative studies
Authors: Senn Stephen
Published: May 2013

I compare two possible extreme hypotheses regarding submission of papers to journals: the Q hypothesis, whereby the decision to submit is based on quality of research; and the P hypothesis, whereby it is based on probability of acceptance. I give five reasons as to why the P hypothesis is more plausible and suggest that problems of missing data may previously have caused researchers to misinterpret the evidence on editorial bias.
Human iPSC-derived mesoangioblasts, like their tissue-derived counterparts, suppress T cell proliferation through IDO- and PGE-2-dependent pathways
Authors: Li Ou , English Karen , Tonlorenzi Rossana , Cossu Giulio , Saverio Tedesco Francesco , Wood Kathryn J
Published: May 2013

Human mesoangioblasts are currently in a phase I/II clinical trial for the treatment of patients with Duchenne muscular dystrophy. However, limitations associated with the finite life span of these cells combined with the significant numbers of mesoangioblasts required to treat all of the skeletal muscles in these patients restricts their therapeutic potential. Induced pluripotent stem cell (iPSC)-derived mesoangioblasts may provide the solution to this problem. Although, the idea of using iPSC-derived cell therapies has been proposed for quite some time, our understanding of how the immune system interacts with these cells is inadequate. Herein, we show that iPSC-derived mesoangioblasts (HIDEMs) from healthy donors and, importantly, limb-girdle muscular dystrophy 2D patients exert immunosuppressive effects on T cell proliferation.  Interferon gamma (IFN-γ) and tumour necrosis factor alpha (TNF-α) play crucial roles in the initial activation of HIDEMs and importantly indoleamine 2,3 dioxygenase (IDO) and prostaglandin E2 (PGE-2) were identified as key mechanisms involved in HIDEM suppression of T cell proliferation. Together with recent studies confirming the myogenic function and regenerative potential of these cells, we suggest that HIDEMs could provide an unlimited alternative source for mesoangioblast-based therapies.
Proteins and lipids of glycosomal membranes from Leishmania tarentolae and Trypanosoma brucei
Authors: Colasante Claudia , Voncken Frank , Manful Theresa , Ruppert Thomas , Tielens Aloysius G M , van Hellemond Jaap J , Clayton Christine
Published: May 2013

In kinetoplastid protists, several metabolic pathways, including glycolysis and purine salvage, are located in glycosomes, which are microbodies that are evolutionarily related to peroxisomes. With the exception of some potential transporters for fatty acids, and one member of the mitochondrial carrier protein family, proteins that transport metabolites across the glycosomal membrane have yet to be identified. We show here that the phosphatidylcholine species composition ofTrypanosoma bruceiglycosomal membranes resembles that of other cellular membranes, which means that glycosomal membranes are expected to be impermeable to small hydrophilic molecules unless transport is facilitated by specialized membrane proteins. Further, we identified 464 proteins in a glycosomal membrane preparation fromLeishmania tarentolae. The proteins included approximately 40 glycosomal matrix proteins, and homologues of peroxisomal membrane proteins - PEX11, GIM5A and GIM5B; PXMP4, PEX2 and PEX16 - as well as the transporters GAT1 and GAT3. There were 27 other proteins that could not be unambiguously assigned to other compartments, and that had predicted trans-membrane domains. However, no clear candidates for transport of the major substrates and intermediates of energy metabolism were found. We suggest that, instead, these metabolites are transported via pores formed by the known glycosomal membrane proteins.
Presentation of an umbilical cord cyst with a surprising jet: a case report of a patent urachus
Authors: Svigos John , Khurana Sanjeev , Munt Christopher , Sinhal Sanjay , Bernardo Julie
Published: May 2013

We report a baby with an unusual true umbilical cord cyst detected at 12 weeks gestation which as the pregnancy progressed became increasingly difficult to distinguish from a pseudocyst of the umbilical cord. Concern of the possibility of cord compression/cord accident led to an elective caesarean section being performed at 35+ week’s gestation with delivery of a healthy female infant weighing 2170g. At birth the cyst ruptured and the resultant thickened elongated cord was clamped accordingly. After the cord clamp fell off at 5 days post delivery an elongated umbilical stump was left behind from which a stream of urine surprisingly jetted out from the umbilicus each time the baby cried. A patent urachus was confirmed on ultrasound and the umbilical jet of urine resolved at 4 weeks post delivery after treatment of an Escherichia coli urinary tract infection. At 11 weeks post delivery a laparoscopic excision of the urachus was successfully performed. The baby, now 18 months of age, continues to thrive without incident.
The prion dilemma confounding science educators
Authors: Zaitsev Igor V , Chen Ling , Boydston-White Susie , Pavel Manita , Shugaeva Svetlana N , Petrova Alla G , Williams Oksana V
Published: May 2013

In this paper, the issue of the prion hypothesis, a simmering controversy within the scientific community, is addressed. We inquire into the appropriateness of the use of certain augmentations and rhetoric approaches used during scientific debates, as well as the aptness of unequivocal statements in textbooks that indicate “abnormal prions” as a primary cause of Transmissible Spongiform Encephalopathies.
Rack ‘em, pack 'em and stack ‘em: challenges and opportunities in teaching large classes in higher education
Authors: Kumar Saravana
Published: May 2013

The higher education sector is undergoing tremendous change, driven by complex driving forces including financial, administrative, and organisational and stakeholder expectations. It is in this challenging environment, educators are required to maintain and improve the quality of teaching and learning outcomes while contending with increasing class sizes. Despite mixed evidence on the effectiveness of large classes on student outcomes, large classes continue to play an important part in higher education. While large classes pose numerous challenges, they also provide opportunities for innovative solutions. This paper provides an overview of these challenges and highlights opportunities for innovative solutions.
Critical care management of patients following transcatheter aortic valve replacement
Authors: Raiten Jesse M , Gutsche Jacob T , Horak Jiri , Augoustides John GT
Published: May 2013

Transcatheter aortic valve replacement (TAVR) is rapidly gaining popularity as a technique to surgically manage aortic stenosis (AS) in high risk patients. TAVR is significantly less invasive than the traditional approach to aortic valve replacement via median sternotomy. Patients undergoing TAVR often suffer from multiple comorbidities, and their postoperative course may be complicated by a unique set of complications that may become evident in the intensive care unit (ICU). In this article, we review the common complications of TAVR that may be observed in the ICU, and different strategies for their management.
Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes
Authors: Marin Michel A , Vicente Ana Carolina P
Published: May 2013

Background: Vibrio cholerae, the etiologic agent of cholera, is indigenous to aquatic environments. The V. cholerae genome consists of two chromosomes; the smallest of these harbors a large gene capture and excision system called the superintegron (SI), of ~120 kbp. The flexible nature of the SI that results from gene cassette capture, deletion and rearrangement is thought to make it a hotspot of V. cholerae diversity, but beyond the basic structure it is not clear if there is a core genome in the SI and if so how it is structured. The aim of this study was to explore the core genome structure and the differences in gene content among strains of V. cholerae.

Methods: From the complete genomes of seven V. cholerae and one Vibrio mimicus representative strains, we recovered the SI sequences based on the locations of the structural gene IntI4 and the V. cholerae repeats. Analysis of the pangenome, including cluster analysis of functional genes, pangenome profile analysis, genetic variation analysis of functional genes, strain evolution analysis and function enrichment analysis of gene clusters, was performed using a pangenome analysis pipeline in addition to the R scripts, splitsTree4 and genoPlotR.

Results and conclusions: Here, we reveal the genetic architecture of the V. cholerae SI. It contains eight core genes when V. mimicus is included and 21 core genes when only V. cholerae strains are considered; many of them are present in several copies. The V. cholerae SI has an open pangenome, which means that V. cholerae may be able to import new gene cassettes to SI. The set of dispensable SI genes is influenced by the niche and type species. The core genes are distributed along the SI, apparently without a position effect.
Reactive microglia after taste nerve injury: comparison to nerve injury models of chronic pain
Authors: Bartel Dianna L , Finger Thomas E
Published: May 2013

The chorda tympani (CT), which innervates taste buds on the anterior portion of the tongue, is susceptible to damage during inner ear surgeries. Injury to the CT causes a disappearance of taste buds, which is concurrent with significant microglial responses at central nerve terminals in the nucleus of the solitary tract (nTS). The resulting taste disturbances that can occur may persist for months or years, long after the nerve and taste buds have regenerated. These persistent changes in taste sensation suggest alterations in central functioning and may be related to the microglial responses. This is reminiscent of nerve injuries that result in chronic pain, where microglial reactivity is essential in maintaining the altered sensation (i.e., pain). In these models, methods that diminish microglial responses also diminish the corresponding pain behavior. Although the CT nerve does not contain nociceptive pain fibers, the microglial reactivity after CT damage is similar to that described in pain models. Therefore, methods that decrease microglial responses in pain models were used here to test if they could also affect microglial reactivity after CT injury. Treatment with minocycline, an antibiotic that dampens pain responsive microglia, was largely ineffective in diminishing microglial responses after CT injury. In addition, signaling through the toll-like 4 receptor (TLR4) does not seem to be required after CT injury as blocking or deleting TLR4 had no effect on microglial reactivity. These results suggest that microglial responses following CT injury rely on different signaling mechanisms than those described in nerve injuries resulting in chronic pain.
Streptococcal taxonomy based on genome sequence analyses
Authors: Thompson Cristiane C , Emmel Vanessa E , Fonseca Erica L , Marin Michel A , Vicente Ana Carolina P
Published: May 2013

The identification of the clinically relevant viridans streptococci group, at species level, is still problematic. The aim of this study was to extract taxonomic information from the complete genome sequences of 67 streptococci, comprising 19 species, by means of genomic analyses, multilocus sequence analysis (MLSA), average amino acid identity (AAI), genomic signatures, genome-to-genome distances (GGD) and codon usage bias. We then attempted to determine the usefulness of these genomic tools for species identification in streptococci. Our results showed that MLSA, AAI and GGD analyses are robust markers to identify streptococci at the species level, for instance,S. pneumoniae,S. mitis, andS. oralis. AStreptococcusspecies can be defined as a group of strains that share ≥ 95% DNA similarity in MLSA and AAI, and > 70% DNA identity in GGD. This approach allows an advanced understanding of bacterial diversity.
A p53-like transcription factor similar to Ndt80 controls the response to nutrient stress in the filamentous fungus, Aspergillus nidulans
Authors: Katz Margaret E , Braunberger Kathryn , Yi Gauncai , Cooper Sarah , Nonhebel Heather M , Gondro Cedric
Published: May 2013

TheAspergillus nidulans xprGgene encodes a putative transcriptional activator that is a member of the Ndt80 family in the p53-like superfamily of proteins. Previous studies have shown that XprG controls the production of extracellular proteases in response to starvation. We undertook transcriptional profiling to investigate whether XprG has a wider role as a global regulator of the carbon nutrient stress response. Our microarray data showed that the expression of a large number of genes, including genes involved in secondary metabolism, development, high-affinity glucose uptake and autolysis, were altered in anxprGΔnull mutant. Many of these genes are known to be regulated in response to carbon starvation. We confirmed that sterigmatocystin and penicillin production is reduced inxprG-mutants. The loss of fungal mass and secretion of pigments that accompanies fungal autolysis in response to nutrient depletion was accelerated in anxprG1gain-of-function mutant and decreased or absent in anxprG-mutant. The results support the hypothesis that XprG plays a major role in the response to carbon limitation and that nutrient sensing may represent one of the ancestral roles for the p53-like superfamily. Disruption of the AN6015 gene, which encodes a second Ndt80-like protein, showed that it is required for sexual reproduction inA. nidulans.