bluuebunny/crossref_metadata_2025 huggingface dataset:
Infiltration of myeloid cells into decidua is a critical early event in the labour cascade and post‐partum uterine remodelling
Authors: Shynlova Oksana , Nedd‐Roderique Tamara , Li Yunqing , Dorogin Anna , Nguyen Tina , Lye Stephen J.
Published: February 2013

Leucocyte infiltration in the decidua (maternal–foetal interface) before, during and after term (TL) and preterm labour (PTL) was studied in mouse. We also investigated the mechanism of peripheral leucocyte recruitment into decidua by analysing the tissue cytokine profiles. Decidual tissues were collected during late gestation, TL and post‐partum (PP). PTL was initiated on gestational day 15 by intrauterine injection of Lipopolysaccharide (LPS, 125 μg) or progesterone signalling antagonism by RU486. Animals were killed during PTL or PP. Decidua basalis was analysed using FACS and immunohistochemistry. Markers of myeloid cell differentiation (Gr1, Ly6G, Neu7/4, F4/80) were assessed to define tissue monocytes (M), neutrophils (N) and macrophages (Macs). Flow cytometry revealed a significant (P < 0.05) increase in decidual Macs prior to TL; M and N numbers increased during TL and further increased during PP, which correlated with immunohistochemistry data. Massive influx of N, but not Macs and M, was detected by FACS during LPS‐PTL (P < 0.05) but not RU486‐PTL. Highest levels of N infiltration into the decidua occurred PP in both LPS and RU486 groups. Decidual infiltration during TL and RU486‐PTL was accompanied by an increase in pro‐inflammatory cytokines (IL1b and IL6) and CCL2 chemokine; LPS‐PTL showed increases in multiple cytokines. PP period following TL and PTL was associated with further up‐regulation of multiple cytokines/chemokines (P < 0.05). Our data suggest a programme of myeloid cells involvement in parturition with the pre‐partum influx of Macs into the decidua contributing to the progression of labour, whereas the later influx of M and N contribute to PP decidual involution.
Enhanced hippocampus‐dependent memory and reduced anxiety in mice over‐expressing human catalase in mitochondria
Authors: Olsen Reid H. J. , Johnson Lance A. , Zuloaga Damian G. , Limoli Charles L. , Raber Jacob
Published: February 2013

Oxidative stress (OS) and reactive oxygen species (ROS) play a modulatory role in synaptic plasticity and signaling pathways. Mitochondria (MT), a major source of ROS because of their involvement in energy metabolism, are important for brain function. MT‐generated ROS are proposed to be responsible for a significant proportion of OS and are associated with developmental abnormalities and aspects of cellular aging. The role of ROS and MT function in cognition of healthy individuals is relatively understudied. In this study, we characterized behavioral and cognitive performance of 5‐ to 6‐month‐old mice over‐expressing mitochondrial catalase (MCAT). MCAT mice showed enhancements in hippocampus‐dependent spatial learning and memory in the water maze and contextual fear conditioning, and reduced measures of anxiety in the elevated zero maze. Catalase activity was elevated in MCAT mice in all brain regions examined. Measures of oxidative stress (glutathione, protein carbonyl content, lipid peroxidation, and 8‐hydroxyguanine) did not significantly differ between the groups. The lack of differences in these markers of oxidative stress suggests that the differences observed in this study may be due to altered redox signaling. Catalase over‐expression might be sufficient to enhance cognition and reduce measures of anxiety even in the absence of alteration in levels of OS.
Ultrasound‐accelerated catheter‐directed thrombolysis for the management of postpartum deep venous thrombosis
Authors: Dumantepe Mert , Tarhan Ibrahım Arif , Yurdakul Ilhan , Ozler Azmi
Published: February 2013

Pregnancy and the postpartum period are associated with an increased risk of venous thromboembolism, which remains an important cause of maternal morbidity and mortality. Although oral or systemic anticoagulation therapy may minimize thrombus propagation, it remains ineffective in removing thrombus burden and consequently does not prevent post‐thrombotic syndrome. A novel technique, ultrasound accelerated catheter directed thrombolysis (UACDT), has been developed to rapidly and completely resolve thrombus. While pregnancy and the postpartum period are generally considered as contraindications for thrombolysis, we demonstrate in this case study the safety and effectiveness of using UACDT to treat symptomatic, postpartum, iliofemoral deep vein thrombosis after only an overnight infusion.
Agroinoculation of Beet necrotic yellow vein virus cDNA clones results in plant systemic infection and efficient Polymyxa betae transmission
Authors: Delbianco Alice , Lanzoni Chiara , Klein Elodie , Rubies Autonell Concepcion , Gilmer David , Ratti Claudio
Published: February 2013

Agroinoculation is a quick and easy method for the infection of plants with viruses. This method involves the infiltration of tissue with a suspension of Agrobacterium tumefaciens carrying binary plasmids harbouring full‐length cDNA copies of viral genome components. When transferred into host cells, transcription of the cDNA produces RNA copies of the viral genome that initiate infection. We produced full‐length cDNA corresponding to Beet necrotic yellow vein virus (BNYVV) RNAs and derived replicon vectors expressing viral and fluorescent proteins in pJL89 binary plasmid under the control of the Cauliflower mosaic virus 35S promoter. We infected Nicotiana benthamiana and Beta macrocarpa plants with BNYVV by leaf agroinfiltration of combinations of agrobacteria carrying full‐length cDNA clones of BNYVV RNAs. We validated the ability of agroclones to reproduce a complete viral cycle, from replication to cell‐to‐cell and systemic movement and, finally, plant‐to‐plant transmission by its plasmodiophorid vector. We also showed successful root agroinfection of B. vulgaris, a new tool for the assay of resistance to rhizomania, the sugar beet disease caused by BNYVV.
Spectroscopic sensitivity of real‐time, rapidly induced phytochemical change in response to damage
Authors: Couture John J. , Serbin Shawn P. , Townsend Philip A.
Published: February 2013

An ecological consequence of plant–herbivore interactions is the phytochemical induction of defenses in response to insect damage. Here, we used reflectance spectroscopy to characterize the foliar induction profile of cardenolides in Asclepias syriaca in response to damage, tracked in vivo changes and examined the influence of multiple plant traits on cardenolide concentrations.

Foliar cardenolide concentrations were measured at specific time points following damage to capture their induction profile. Partial least‐squares regression (PLSR) modeling was employed to calibrate cardenolide concentrations to reflectance spectroscopy. In addition, subsets of plants were either repeatedly sampled to track in vivo changes or modified to reduce latex flow to damaged areas.

Cardenolide concentrations and the induction profile of A. syriaca were well predicted using models derived from reflectance spectroscopy, and this held true for repeatedly sampled plants. Correlations between cardenolides and other foliar‐related variables were weak or not significant. Plant modification for latex reduction inhibited an induced cardenolide response.

Our findings show that reflectance spectroscopy can characterize rapid phytochemical changes in vivo. We used reflectance spectroscopy to identify the mechanisms behind the production of plant secondary metabolites, simultaneously characterizing multiple foliar constituents. In this case, cardenolide induction appears to be largely driven by enhanced latex delivery to leaves following damage.
Clinical relevance of antibody development in renal transplantation
Authors: Mehra Narinder K. , Siddiqui Jamshaid , Baranwal Ajay , Goswami Sanjeev , Kaur Gurvinder
Published: February 2013

The detection and characterization of anti‐HLA antibodies and the clinical impact of their appearance following renal transplantation are areas of immense interest. In particular, de novo development of donor‐specific antibodies (DSA) has been associated with acute and chronic antibody‐mediated graft rejection (AMR). Recently, methods for antibody detection have evolved remarkably from conventional cell‐based assays to advanced solid phase systems. These systems have revolutionized the art of defining clinically relevant antibodies that are directed toward a renal graft. While anti‐HLA DSAs have been widely associated with poor graft survival, the role of non‐HLA antibodies, particularly those directed against endothelial cells, is beginning to be realized. Appreciation of the mechanisms underlying T cell recognition of alloantigens has generated great interest in the use of synthetic peptides to prevent graft rejection. Hopefully, continued progress in unraveling the molecular mechanisms of graft rejection and posttransplant monitoring of antibodies using highly sensitive testing systems will prove beneficial to immunological risk assessment and early prediction of renal allograft failure.
The health care professionals' perspectives of collaboration in rehabilitation – an interview study
Authors: Kraft Mia , Blomberg Karin , Hedman Ann‐Marie Rydholm
Published: February 2013

Background

In previous literature, it has been recognised that the extent to which different healthcare professionals collaborate may affect both the quality and safety of care, and patient outcomes. Collaboration appears to be an essential part of professional practice, yet there is a lack of knowledge and understanding of collaboration in the context of short‐term care units. Therefore, this study was undertaken to better understand how professionals in this context view collaboration.

Aim

To describe collaboration in rehabilitation from the perspective of healthcare professionals.

Methods

Qualitative interviews were conducted with ten healthcare professionals, including: occupational therapists, physiotherapists and nurses, who worked in three different short‐term care settings. The interviews were transcribed, and qualitative content analysis was used.

Findings

Four categories, all of which included both positive and negative descriptions of collaboration, were identified: (i) Crossing professional and organisational boundaries (ii) Awareness of own professional identity (iii) Information and knowledge transfer and (iv) Balancing between patient, system and process.

Conclusions

The findings indicate the importance of leadership and organisational structures for stimulating communication, and promoting collaboration between team members. In addition, working as a professional in short‐term care requires individual skills in collaboration efforts, including awareness of one's own professional identity.

Relevance to clinical practice

Opportunities for supervision could be one way to increase individuals' awareness of their own role in the team.
Susceptibility evaluation of Picea abies and Cupressus lusitanica to the pine wood nematode (Bursaphelenchus xylophilus)
Authors: Nunes da Silva M. , Lima M. R. M. , Vasconcelos M. W.
Published: February 2013

Pine wilt disease (PWD), recently introduced into Europe, is caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus and is a devastating illness that affects mainly pine trees. It is known that the PWN is capable of infecting other conifers; however, there is currently no information on which other plant species may be susceptible to PWD. In this study, the potential susceptibility of two common species of European forests, Picea abies and Cupressus lusitanica, to PWN was assessed through the monitoring of visual external symptoms, dimension and localization of the nematode population in stems, quantification of total chlorophyll, total soluble phenolics and lignin, at 7, 14, 21 and 28 days after inoculation. The degree of susceptibility was established through the comparison of symptoms with Pinus pinaster, a well‐known PWN host. Furthermore, the stem ultrastructure of P. abies, C. lusitanica and Pn. pinaster was analysed by scanning electron microscopy. The results suggest that P. abies and C. lusitanica are resistant to PWN, and that lignin biosynthesis in these species is affected at an early stage of the infestation. Nevertheless, P. abies seems to be a compatible host that could act as a repository for PWN.
Subclavian Vein Thrombosis following Acute Internal Fixation of a Clavicular Fracture
Authors: Rahman Jeeshan R. , Magan Ahmad , Tytherleigh-Strong Graham M.
Published: February 2013

With the recent increase in popularity of early operative fixation for certain clavicular fracture configurations, it is important for orthopaedic surgeons to be mindful of the possible additional risk of thromboembolic complications that may arise as a consequence of an acute injury. We describe the case of a 41-year-old man who presented to our department with a left-sided, middle-third, displaced clavicular fracture. He underwent an acute open reduction and internal fixation, which was complicated by a postoperative subclavian vein thrombosis. This was treated with oral anticoagulation. The thrombus had completely resorbed by 3 months. Five months after surgery, the patient had a full range of movement of the left arm, with no swelling, after having completed a 4000-mile cycle ride. A review of the available literature suggests that the commonest and safest treatment for a subclavian vein thrombosis is subcutaneous unfractionated heparin followed by oral warfarin therapy. The present case report highlights the potential risk of upper limb thrombosis after acute osteo-synthesis of the clavicle and discusses the current evidence with respect to the treatment of upper limb venous thrombosis.
A case of pili torti in a young adult domestic short‐haired cat
Authors: Maina Elisa , Colombo Silvia , Abramo Francesca , Pasquinelli Gianandrea
Published: February 2013

Background

Pili torti is a congenital or acquired human disease characterized by flattening and twisting of the hair shaft by 180 degrees. A similar condition has been previously reported in a litter of kittens with generalized hair loss, associated with systemic signs and followed by death at a young age.

Animal

A 1‐year‐old castrated male domestic short‐haired cat was presented for noninflammatory and nonpruritic symmetrical multifocal alopecia involving the head, pinnae, forelimbs, tail and chest. The cat was otherwise healthy.

Methods and results

Microscopic examination of hair shafts revealed pili torti and a typical combination of anagen and telogen roots, occasionally spiral in shape, without evidence of mites or dermatophytes. Histopathological examination showed the same hair shaft abnormality, with normal epidermis, dermis, hair follicles and other adnexa. Scanning electron microscopy confirmed a hair shaft dysplasia characterized by pili torti, similar to that described in humans.

Conclusions and clinical importance

To the best of the authors' knowledge, this is the first case report of pili torti in a healthy young adult cat.
Differential responses of fast‐ and slow‐conducting pyramidal tract neurons to changes in accuracy demands during locomotion
Authors: Stout Erik E. , Beloozerova Irina N.
Published: February 2013

Key points

The motor cortex is highly involved in performing complex movements including skilled locomotion.

Slow‐conducting pyramidal tract neurons (PTNs) in the motor cortex are much more numerous than fast‐conducting PTNs, but little is known about their function during movements.

We find here that slow‐conducting PTNs show vigorous and concerted changes to their activities during accurate targeted stepping versus simple locomotion over a flat surface, while changes to the activities of fast‐conducting PTNs vary.

This suggests that slow‐conducting PTNs are involved to a greater extent in control of accuracy during locomotion.

The results may be relevant to developing therapies for stroke and traumatic brain injury.

Abstract  Most movements need to be accurate. The neuronal mechanisms controlling accuracy during movements are poorly understood. In this study we compare the activity of fast‐ and slow‐conducting pyramidal tract neurons (PTNs) of the motor cortex in cats as they walk over both a flat surface, a task that does not require accurate stepping and can be accomplished without the motor cortex, as well as along a horizontal ladder, a task that requires accuracy and the activity of the motor cortex to be successful. Fast‐ and slow‐conducting PTNs are known to have distinct biophysical properties as well as different afferent and efferent connections. We found that while the activity of all PTNs changes substantially upon transition from simple locomotion to accurate stepping on the ladder, slow‐conducting PTNs respond in a much more concerted manner than fast‐conducting ones. As a group, slow‐conducting PTNs increase discharge rate, especially during the late stance and early swing phases, decrease discharge variability, have a tendency to shift their preferred phase of the discharge into the swing phase, and almost always produce a single peak of activity per stride during ladder locomotion. In contrast, the fast‐conducting PTNs do not display such concerted changes to their activity. In addition, upon transfer from simple locomotion to accurate stepping on the ladder slow‐conducting PTNs more profoundly increase the magnitude of their stride‐related frequency modulation compared with fast‐conducting PTNs. We suggest that slow‐conducting PTNs are involved in control of accuracy of locomotor movements to a greater degree than fast‐conducting PTNs.
Therapeutic Hints from Analyzing the Attractor Landscape of the p53 Regulatory Circuit
Authors: Wang Wei
Published: February 2013

Analysis of network dynamics holds promise for development of novel therapies.
Modifying Deubiquitinases
Authors: Ray L. Bryan
Published: February 2013

A technique for developing specific and potent enzyme inhibitors is validated on enzymes of the ubiquitin‑proteasome system.
Inhibitors of eIF2α Dephosphorylation Slow Replication and Stabilize Latency in Toxoplasma gondii
Authors: Konrad Christian , Queener Sherry F. , Wek Ronald C. , Sullivan William J.
Published: February 2013

Toxoplasma gondii
is an obligate intracellular parasite that permanently infects warm-blooded vertebrates through its ability to convert into a latent tissue cyst form. The latent form (bradyzoite) can reinitiate a life-threatening acute infection if host immunity wanes, most commonly in AIDS or organ transplant patients. We have previously shown that bradyzoite development is accompanied by phosphorylation of the parasite eukaryotic initiation factor 2 alpha subunit (eIF2α), which dampens global protein synthesis and reprograms gene expression. In this study, we analyzed the activities of two specific inhibitors of eIF2α dephosphorylation, salubrinal (SAL) and guanabenz (GA). We establish that these drugs are able to inhibit the dephosphorylation of
Toxoplasma
eIF2α. Our results show that SAL and GA reduce tachyzoite replication
in vitro
and
in vivo
. Furthermore, both drugs induce bradyzoite formation and inhibit the reactivation of latent bradyzoites
in vitro
. To address whether the antiparasitic activities of SAL and GA involve host eIF2α phosphorylation, we infected mutant mouse embryonic fibroblast (MEF) cells incapable of phosphorylating eIF2α, which had no impact on the efficacies of SAL and GA against
Toxoplasma
infection. Our findings suggest that SAL and GA may serve as potential new drugs for the treatment of acute and chronic toxoplasmosis.
Effects of Biofilm Growth on Plasmid Copy Number and Expression of Antibiotic Resistance Genes in Enterococcus faecalis
Authors: Cook L. C. , Dunny G. M.
Published: February 2013

Biofilm growth causes increased average plasmid copy number as well as increased copy number heterogeneity in
Enterococcus faecalis
cells carrying plasmid pCF10. In this study, we examined whether biofilm growth affected the copy number and expression of antibiotic resistance determinants for several plasmids with diverse replication systems. Four different
E. faecalis
plasmids, unrelated to pCF10, demonstrated increased copy number in biofilm cells. In biofilm cells, we also observed increased transcription of antibiotic resistance genes present on these plasmids. The increase in plasmid copy number correlated with increased plating efficiency on high concentrations of antibiotics. Single-cell analysis of strains carrying two different plasmids suggested that the increase in plasmid copy number associated with biofilm growth was restricted to a subpopulation of biofilm cells. Regrowth of harvested biofilm cells in liquid culture resulted in a rapid reduction of plasmid copy number to that observed in the planktonic state. These results suggest a possible mechanism by which biofilm growth could reduce susceptibility to antibiotics in clinical settings.
Time Series Analysis as a Tool To Predict the Impact of Antimicrobial Restriction in Antibiotic Stewardship Programs Using the Example of Multidrug-Resistant Pseudomonas aeruginosa
Authors: Willmann Matthias , Marschal Matthias , Hölzl Florian , Schröppel Klaus , Autenrieth Ingo B. , Peter Silke
Published: February 2013

The association between antimicrobial consumption and resistance in nonfermentative Gram-negative bacteria is well-known. Antimicrobial restriction, implemented in clinical routines by antibiotic stewardship programs (ASPs), is considered a means to reduce resistance rates. Whether and how antimicrobial restriction can accomplish this goal is still unknown though. This leads to an element of uncertainty when designing strategies for ASPs. From January 2002 until December 2011, an observational study was performed at the University Hospital Tübingen, Tübingen, Germany, to investigate the association between antimicrobial use and resistance rates in
Pseudomonas aeruginosa
. Transfer function models were used to determine such associations and to simulate antimicrobial restriction strategies. Various positive associations between antimicrobial consumption and resistance were observed in our setting. Surprisingly, impact estimations of different antimicrobial restriction strategies revealed relatively low intervention expenses to effectively attenuate the observed increase in resistance. For example, a simulated intervention of an annual 4% reduction in the use of meropenem over 3 years from 2009 until 2011 yielded a 62.5% attenuation (95% confidence interval, 15% to 110%) in the rising trend of multidrug-resistant
Pseudomonas aeruginosa
(three- and four-class-resistant
P. aeruginosa
[34MRGN-PA]). Time series analysis models derived from past data may be a tool to predict the outcome of antimicrobial restriction strategies, and could be used to design ASPs.
Efficacy of Tenofovir in Patients with Lamivudine Failure Is Not Different from That in Nucleoside/Nucleotide Analogue-Naïve Patients with Chronic Hepatitis B
Authors: Baran Bulent , Soyer Ozlem Mutluay , Ormeci Asli Cifcibasi , Gokturk Suut , Evirgen Sami , Bozbey Hamza Ugur , Akyuz Filiz , Karaca Cetin , Demir Kadir , Besisik Fatih , Onel Derya , Gulluoglu Mine , Badur Selim , Kaymakoglu Sabahattin
Published: February 2013

We evaluated the efficacy of tenofovir disoproxil fumarate (TDF) in patients with lamivudine failure (LAM-F) in comparison with that in nucleoside/nucleotide analogue (NA)-naïve patients with chronic hepatitis B (CHB). The criteria for inclusion were being NA naïve or having previous LAM-F and receiving TDF therapy for at least 6 months. Biochemical and virological tests were performed at the baseline, at 3-month intervals in the first year, and every 6 months thereafter. The primary outcome measure for efficacy was a complete virological response (CVR), defined as an HBV DNA level of <20 IU/ml. CVR rates were calculated by Kaplan-Meier analysis, and a multivariate Cox proportional-hazard model was generated in order to find predictive factors independently associated with the time to a CVR. We included 197 patients in the study (136 males; mean age, 43 ± 12 years; 105 patients were NA naïve). Sixty-five patients had hepatitis B e antigen (HBeAg)-positive CHB. The median duration of TDF treatment was 29 (range, 6 to 52) months. Seventy-one patients (77%) in the LAM-F group were treated with TDF add-on therapy. The CVR rates of the NA-naïve and LAM-F groups were comparable in HBeAg-negative (94% versus 96% at month 36,P= 0.10) and HBeAg-positive patients (67% versus 83% at month 36,P= 0.48). According to the multivariate Cox regression model, only HBeAg positivity (hazard ratio [HR], 0.39; 95% confidence interval [CI], 0.26 to 0.59;P< 0.001) and a high baseline HBV DNA level (HR, 0.44; 95% CI, 0.29 to 0.67;P< 0.001) had a significant influence on the time to a CVR. The similar cumulative CVR rates during the follow-up show that TDF has comparable efficacy in lamivudine-experienced and NA-naïve patients, and the presence of resistance mutations did not alter the response rates.
SR-Like RNA-Binding Protein Slr1 Affects Candida albicans Filamentation and Virulence
Authors: Ariyachet Chaiyaboot , Solis Norma V. , Liu Yaoping , Prasadarao Nemani V. , Filler Scott G. , McBride Anne E.
Published: February 2013

Candida albicans
causes both mucosal and disseminated infections, and its capacity to grow as both yeast and hyphae is a key virulence factor. Hyphal formation is a type of polarized growth, and members of the SR (serine-arginine) family of RNA-binding proteins influence polarized growth of both
Saccharomyces cerevisiae
and
Aspergillus nidulans
. Therefore, we investigated whether SR-like proteins affect filamentous growth and virulence of
C. albicans
. BLAST searches with
S. cerevisiae
SR-like protein Npl3 (ScNpl3) identified two
C. albicans
proteins: CaNpl3, an apparent ScNpl3 ortholog, and Slr1, another
S
R-
l
ike
R
NA-binding protein with no close
S. cerevisiae
ortholog. Whereas ScNpl3 was critical for growth, deletion of
NPL3
in
C. albicans
resulted in few phenotypic changes. In contrast, the
slr1
Δ/Δ mutant had a reduced growth rate
in vitro
, decreased filamentation, and impaired capacity to damage epithelial and endothelial cells
in vitro
. Mice infected intravenously with the
slr1
Δ/Δ mutant strain had significantly prolonged survival compared to that of mice infected with the wild-type or
slr1
Δ/Δ mutant complemented with
SLR1
(
slr1
Δ/Δ+
SLR1
) strain, without a concomitant decrease in kidney fungal burden. Histopathology, however, revealed differential localization of
slr1
Δ/Δ hyphal and yeast morphologies within the kidney. Mice infected with
slr1
Δ/Δ cells also had an increased brain fungal burden, which correlated with increased invasion of brain, but not umbilical vein, endothelial cells
in vitro
. The enhanced brain endothelial cell invasion was likely due to the increased surface exposure of the Als3 adhesin on
slr1
Δ/Δ cells. Our results indicate that Slr1 is an SR-like protein that influences
C. albicans
growth, filamentation, host cell interactions, and virulence.
Staphylococcus aureus Nuclease Is an SaeRS-Dependent Virulence Factor
Authors: Olson Michael E. , Nygaard Tyler K. , Ackermann Laynez , Watkins Robert L. , Zurek Oliwia W. , Pallister Kyler B. , Griffith Shannon , Kiedrowski Megan R. , Flack Caralyn E. , Kavanaugh Jeffrey S. , Kreiswirth Barry N. , Horswill Alexander R. , Voyich Jovanka M.
Published: February 2013

Several prominent bacterial pathogens secrete nuclease (Nuc) enzymes that have an important role in combating the host immune response. Early studies of
Staphylococcus aureus
Nuc attributed its regulation to the
agr
quorum-sensing system. However, recent microarray data have indicated that
nuc
is under the control of the SaeRS two-component system, which is a major regulator of
S. aureus
virulence determinants. Here we report that the
nuc
gene is directly controlled by the SaeRS two-component system through reporter fusion, immunoblotting, Nuc activity measurements, promoter mapping, and binding studies, and additionally, we were unable identify a notable regulatory link to the
agr
system. The observed SaeRS-dependent regulation was conserved across a wide spectrum of representative
S. aureus
isolates. Moreover, with community-associated methicillin-resistant
S. aureus
(CA MRSA) in a mouse model of peritonitis, we observed
in vivo
expression of Nuc activity in an SaeRS-dependent manner and determined that Nuc is a virulence factor that is important for
in vivo
survival, confirming the enzyme's role as a contributor to invasive disease. Finally, natural polymorphisms were identified in the SaeRS proteins, one of which was linked to Nuc regulation in a CA MRSA USA300 endocarditis isolate. Altogether, our findings demonstrate that Nuc is an important
S. aureus
virulence factor and part of the SaeRS regulon.
An inflammatory myofibroblastic tumour of the breast with ALK overexpression
Authors: Zhou Yan , Zhu Jiang , Zhang Yi , Jiang Jun , Jia Ming
Published: February 2013

Inflammatory myofibroblastic tumours (IMTs), also known as inflammatory pseudotumours, include a diverse group of lesions characterised by inflammatory cell infiltration and variable fibrotic responses. Their occurrence in the breast is unusual. We present a case of an IMT of the breast in a 46-year-old woman who complained of a breast mass with palpable axillary lymph node. The initial clinical diagnosis was breast cancer, and the patient underwent a conservative excision with apparently negative margins and an axillary lymph node excisional biopsy. A histopathological examination showed the presence of myofibroblastic spindle cells with mixed inflammatory infiltrates, and the pathological diagnosis was IMT. Significantly, the case we present here is unique in showing anaplastic lymphoma kinase 1 (ALK1) overexpression and ALK1 gene amplification in IMT of the breast. Therefore, our case suggests that ALK1 gene amplification in IMT of the breast has important diagnostic and therapeutic implications.
Modified technique of soft liner application
Authors: Gupta Narendra , Misra Neeta , Kumar Sulabh , Uppal Saurabh
Published: February 2013

Soft liners are materials that can be advocated successfully to manage clinical situations like atrophic edentulous ridges with flabby displaceable tissues and in cases of severely resorbed ridges which adversely affect the retention and stability of complete dentures and further enhance bone loss. Soft liner provides a cushioning effect and distributes uniform occlusal forces to compromised residual ridges. In this paper a modified technique of soft liner application in mandibular denture has been discussed.
A ray of hope for a woman with Sheehan's syndrome
Authors: Jain Deepti
Published: February 2013

A 25-year-old woman presented with a history of secondary amenorrhoea for the last 3 years, coinciding with her delivery. She delivered at home and had massive postpartum haemorrhage. She was brought in a state of circulatory collapse to the nearest teaching hospital, where she was resuscitated. She developed anaemia, septicaemia and extradural empyema. The complications were managed and the woman improved. Presently, she approached us for infertility. She was investigated and diagnosed with postpartum hypopituitarism, that is, Sheehan's syndrome. Her gonadotrophin levels, luteinising hormone/follicle-stimulating hormone, were normal, serum oestradiol was low and serum prolactin was also on the lower side. She had started with genital atrophy and was given three cycles of cyclic oestrogen +progesterone combination. Ovulation was induced. She conceived and her antenatal period was uneventful. She delivered a full-term baby vaginally. However, she had inadequate lactation after delivery and lost the baby at one-and-a-half months’ age due to gastroenteritis.
MODELING BY FITTING A UNION OF POLYNOMIAL FUNCTIONS TO DATA IN AN ERRORS-IN-VARIABLES CONTEXT
Authors: HUNYADI LEVENTE , VAJK ISTVÁN
Published: February 2013

We present a model construction method based on a local fitting of polynomial functions to noisy data and building the entire model as a union of regions explained by such polynomial functions. Local fitting is shown to reduce to solving a polynomial eigenvalue problem where the matrix coefficients are data covariance and approximated noise covariance matrices that capture distortion effects by noise. By defining the asymmetric distance between two points as the projection of one onto the function fitted to the neighborhood of the other, we use a best weighted cut method to find a proper partitioning of the entire set of data into feasible regions. Finally, the partitions are refined using a modified version of a k-planes algorithm.
INTERVENTION IN BIOLOGICAL PHENOMENA REPRESENTED BY GENETIC REGULATORY NETWORKS: A VARIABLE STRUCTURE APPROACH
Authors: FNAIECH MOHAMED AMINE , NOUNOU HAZEM N. , NOUNOU MOHAMED N. , DATTA ANIRUDDHA
Published: February 2013

The utilization of mathematical tools in the analysis and synthesis of models representing biological phenomena is rapidly growing. Adding to these efforts, in this paper, a mathematical method based on the sliding mode control approach will be used for the purpose of developing a therapeutic intervention strategy for a class of biological phenomena. Such an intervention scheme aims at moving an undesirable state of a diseased network towards a more desirable state using drugs to act on some genes/metabolites that characterize the undesirable behavior. S-systems, which offer a good compromise between accuracy and mathematical flexibility, are a promising framework for modeling the dynamical behavior of biological phenomena as well as genetic regulatory networks. Since biological phenomena modeled by S-systems are complex nonlinear processes, the need for robust nonlinear intervention strategies that are capable of guiding the target variables to their desired values often arises. The main objective of this paper is to develop an intervention scheme based on sliding mode control theory, sometimes referred to as variable structure control theory, and evaluate the robustness of the sliding mode intervention scheme in the presence of model parameter uncertainties. The proposed intervention strategy is applied to a glycolytic-glycogenolytic pathway model and the simulation results demonstrate the effectiveness of the proposed scheme.
GENE EXPRESSION DATA CLASSIFICATION COMBINING HIERARCHICAL REPRESENTATION AND EFFICIENT FEATURE SELECTION
Authors: BOSIO MATTIA , BELLOT PAU , SALEMBIER PHILIPPE , OLIVERAS-VERGÉS ALBERT
Published: February 2013

A general framework for microarray data classification is proposed in this paper. It produces precise and reliable classifiers through a two-step approach. At first, the original feature set is enhanced by a new set of features called metagenes. These new features are obtained through a hierarchical clustering process on the original data. Two different metagene generation rules have been analyzed, called Treelets clustering and Euclidean clustering. Metagenes creation is attractive for several reasons: first, they can improve the classification since they broaden the available feature space and capture the common behavior of similar genes reducing the residual measurement noise. Furthermore, by analyzing some of the chosen metagenes for classification with gene set enrichment analysis algorithms, it is shown how metagenes can summarize the behavior of functionally related probe sets. Additionally, metagenes can point out, still undocumented, highly discriminant probe sets numerically related to other probes endowed with prior biological information in order to contribute to the knowledge discovery process.

The second step of the framework is the feature selection which applies the Improved Sequential Floating Forward Selection algorithm (IFFS) to properly choose a subset from the available feature set for classification composed of genes and metagenes. Considering the microarray sample scarcity problem, besides the classical error rate, a reliability measure is introduced to improve the feature selection process. Different scoring schemes are studied to choose the best one using both error rate and reliability. The Linear Discriminant Analysis classifier (LDA) has been used throughout this work, due to its good characteristics, but the proposed framework can be used with almost any classifier. The potential of the proposed framework has been evaluated analyzing all the publicly available datasets offered by the Micro Array Quality Control Study, phase II (MAQC). The comparative results showed that the proposed framework can compete with a wide variety of state of the art alternatives and it can obtain the best mean performance if a particular setup is chosen. A Monte Carlo simulation confirmed that the proposed framework obtains stable and repeatable results.
UNCOVER CONTEXT-SPECIFIC GENE REGULATION BY TRANSCRIPTION FACTORS AND microRNAs USING BAYESIAN SPARSE NONNEGATIVE FACTOR REGRESSION
Authors: MENG JIA , CHEN YIDONG , HUANG YUFEI
Published: February 2013

In multicellular organisms, transcription factors (TFs) and microRNAs (miRNA) embody two largest families of molecules that modulate messenger RNA (mRNA) expressions through transcriptional and post-transcriptional regulations. While mRNA and microRNA expressions can be measured by microarray technique, the activities of transcription factors manifested by their protein expression are still difficult to observe, making it usually a complex problem to reconstruct a collaborative gene regulatory network (GRN) by TFs and miRNAs from expression data.

In this paper, a novel Bayesian sparse non-negative factor regression (BSNFR) model is proposed for modeling the joint regulations of mRNAs by TFs and miRNAs and integration of multiple data types including gene expressions, microRNA expressions, TF targeted genes, and microRNA targets. Powered by a Gibbs sampling solution, BSNFR can infer both the TF/microRNA-mediated mRNA regulations and the unknown TF activities. Additionally, since BSNFR directly models the non-negative activities of TFs, it avoids the common problem of sign ambiguity with factor models and is capable of accurate prediction of the types (up or down) of regulations as well. BSNFR also includes a nonparametric Bayesian model for the latent factor activities, which enables the discovery of the clustering effects among samples due to (disease) subtypes.

The proposed BSNFR model and the developed Gibbs sampling solution were validated on simulated systems and applied to real data of glioblastoma multiforme (GBM) patients from The Cancer Genome Atlas (TCGA). A GBM specific gene regulatory network by TFs and miRNAs was reconstructed. This GBM network includes 107 regulations recorded in the existing databases and 16 new regulations. Functional analysis suggests that the regulated genes are enriched in cell cycle and P53 pathways. In addition, BSNFR also identified 3 clusters among GBM patient samples, two of which demonstrates significant survival differences (p=0.004). Finally, the estimated TF activities imply that EGR-1 is significantly correlated with patient survivals (p=0.004) and may be used as a prognostic biomarker.

The data and matlab code are available at: http://compgenomics.cbi.utsa.edu/BSNFR .
NOT THAT RIGID MIDGETS AND NOT SO FLEXIBLE GIANTS: ON THE ABUNDANCE AND ROLES OF INTRINSIC DISORDER IN SHORT AND LONG PROTEINS
Authors: HOWELL MARK , GREEN RYAN , KILLEEN ALEXIS , WEDDERBURN LAMAR , PICASCIO VINCENT , RABIONET ALEJANDRO , PENG ZHENLING , LARINA MAYA , XUE BIN , KURGAN LUKASZ , UVERSKY VLADIMIR N.
Published: February 2013

Intrinsically disordered proteins or proteins with disordered regions are very common in nature. These proteins have numerous biological functions which are complementary to the biological activities of traditional ordered proteins. A noticeable difference in the amino acid sequences encoding long and short disordered regions was found and this difference was used in the development of length-dependent predictors of intrinsic disorder. In this study, we analyze the scaling of intrinsic disorder in eukaryotic proteins and investigate the presence of length-dependent functions attributed to proteins containing long disordered regions.
QUANTUM TYPE COHOMOLOGIES ON CONTACT MANIFOLDS
Authors: CHO YONG SEUNG
Published: February 2013

We extend the notion of a pseudoholomorphic map in a symplectic manifold to the one of an almost coholomorphic map on a contact manifold M of an odd dimension. We study the moduli space of stable almost coholomorphic maps that represent a two-dimensional integral homology class of M, Gromov–Witten type invariants, quantum type products and quantum type cohomologies.
VALIDITY OF THE GELL-MANN FORMULA FOR sl(n, ℝ) AND su(n) ALGEBRAS
Authors: SALOM IGOR , ŠIJAČKI DJORDJE
Published: February 2013

The so-called Gell-Mann formula, a prescription designed to provide an inverse to the Inönü–Wigner Lie algebra contraction, has a great versatility and potential value. This formula has no general validity as an operator expression. The question of applicability of Gell-Mann's formula to various algebras and their representations was only partially treated. The validity constraints of the Gell-Mann formula for the case of sl(n, ℝ) and su(n) algebras are clarified, and the complete list of representations spaces for which this formula applies is given. Explicit expressions of the sl(n, ℝ) generators matrix elements are obtained for all these cases in a closed form by making use of the Gell-Mann formula.
DEFECT FORMATION AND MAGNETIC PROPERTIES OF Co-DOPED ZnO NANOWIRES
Authors: SHI LI BIN , QI GUO QUAN , FEI YING
Published: February 2013

The defect formation energies and magnetic properties in Co -doped ZnO nanowires (NWs) are studied using the first-principle density functional method within the generalized gradient approximation (GGA) and GGA + U schemes. It is found that Co impurity has lower formation energies in the surface sites, indicating that Co impurity occupies preferably surface sites of NWs. Ferromagnetic (FM) and antiferromagnetic (AFM) coupling are investigated by GGA and GGA + U methods. The results show that the AFM coupling in energy is lower than the FM coupling, which indicates that AFM coupling is more stable. The magnetic properties can be mediated by the vacancies [ VO(B) and VZn(B) ] and interstitials [ IZn(oct) ]. The stability of the FM and AFM can be explained by the Co 3d energy level coupling.
PREPARATION AND ELECTROMAGNETIC PROPERTIES OF BaFe12O19–Ni0.8Zn0.2Fe2O4/POLYPYRROLE COMPOSITE FILM
Authors: WANG YAN , HUANG YING , WANG QIUFEN , HE QIAN
Published: February 2013

BaFe12O19 – Ni0.8Zn0.2Fe2O4 /Polypyrrole composite film [including three doping acids, dodecyl benzene sulfonic acid (DBSA), camphor sulfonic acid (CSA) and p-toluenesulfonic acid (TSA)] was prepared by sol–gel method and in situ chemical oxidative polymerization. The structure, morphologies, conductivities, magnetic properties and microwave absorption properties of the composite film were characterized by using XRD, FESEM, FTIR, Four-probe tester, VSM and Vector network analyzer. The results show that the conductivity of acid-doped Polypyrrole composite film is higher than that of pure Polypyrrole composite film. The saturation magnetization (Ms) and remanent magnetization (Mr) of the composite film are lower than those of BaFe12O19 – Ni0.8Zn0.2Fe2O4 film. However, the electromagnetic properties are in the contrary. The microwave absorption properties of the composite film are much better than those of BaFe12O19 – Ni0.8Zn0.2Fe2O4 , which mainly depends on the increasing of the dielectric loss. A minimum reflection loss of the DBSA-doped composite film is −17.6 dB at 9.3 GHz with the thickness at 3.0 mm.
An approach to social recommendation for context-aware mobile services
Authors: Biancalana Claudio , Gasparetti Fabio , Micarelli Alessandro , Sansonetti Giuseppe
Published: February 2013

Nowadays, several location-based services (LBSs) allow their users to take advantage of information from the Web about points of interest (POIs) such as cultural events or restaurants. To the best of our knowledge, however, none of these provides information taking into account user preferences, or other elements, in addition to location, that contribute to define the context of use. The provided suggestions do not consider, for example, time, day of week, weather, user activity or means of transport. This article describes a social recommender system able to identify user preferences and information needs, thus suggesting personalized recommendations related to POIs in the surroundings of the user's current location. The proposed approach achieves the following goals: (i) to supply, unlike the current LBSs, a methodology for identifying user preferences and needs to be used in the information filtering process; (ii) to exploit the ever-growing amount of information from social networking, user reviews, and local search Web sites; (iii) to establish procedures for defining the context of use to be employed in the recommendation of POIs with low effort. The flexibility of the architecture is such that our approach can be easily extended to any category of POI. Experimental tests carried out on real users enabled us to quantify the benefits of the proposed approach in terms of performance improvement.
Introduction to special section on CAMRa2010
Authors: Said Alan , Berkovsky Shlomo , De Luca Ernesto W.
Published: February 2013

The challenge and workshop on Context-Aware Movie Recommendation (CAMRa2010) were conducted jointly in 2010 with the Recommender Systems conference. The challenge focused on three context-aware recommendation scenarios: time-based, mood-based, and social recommendation. The participants were provided with anonymized datasets from two real-world online movie recommendation communities and competed against each other for obtaining the highest accuracy of recommendations. The datasets contained contextual features, such as tags, annotation, social relationsips, and comments, normally not available in public recommendation datasets. More than 40 teams from 21 countries participated in the challenge. Their participation was summarized by 10 papers published by the workshop, which have been extended and revised for this special section. In this preface we overview the challenge datasets, tasks, evaluation metrics, and the obtained outcomes.
An empirical comparison of social, collaborative filtering, and hybrid recommenders
Authors: Bellogín Alejandro , Cantador Iván , Díez Fernando , Castells Pablo , Chavarriaga Enrique
Published: February 2013

In the Social Web, a number of diverse recommendation approaches have been proposed to exploit the user generated contents available in the Web, such as rating, tagging, and social networking information. In general, these approaches naturally require the availability of a wide amount of these user preferences. This may represent an important limitation for real applications, and may be somewhat unnoticed in studies focusing on overall precision, in which a failure to produce recommendations gets blurred when averaging the obtained results or, even worse, is just not accounted for, as users with no recommendations are typically excluded from the performance calculations. In this article, we propose a coverage metric that uncovers and compensates for the incompleteness of performance evaluations based only on precision. We use this metric together with precision metrics in an empirical comparison of several social, collaborative filtering, and hybrid recommenders. The obtained results show that a better balance between precision and coverage can be achieved by combining social-based filtering (high accuracy, low coverage) and collaborative filtering (low accuracy, high coverage) recommendation techniques. We thus explore several hybrid recommendation approaches to balance this trade-off. In particular, we compare, on the one hand, techniques integrating collaborative and social information into a single model, and on the other, linear combinations of recommenders. For the last approach, we also propose a novel strategy to dynamically adjust the weight of each recommender on a user-basis, utilizing graph measures as indicators of the target user's connectedness and relevance in a social network.