bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioengineering of Bacteria To Assemble Custom-Made Polyester Affinity Resins
Authors: Hay Iain D. , Du Jinping , Burr Natalie , Rehm Bernd H. A. 
Published: October 2014

ABSTRACT

Proof of concept for the
in vivo
bacterial production of a polyester resin displaying various customizable affinity protein binding domains is provided. This was achieved by engineering various protein binding domains into a bacterial polyester-synthesizing enzyme. Affinity binding domains based on various structural folds and derived from molecular libraries were used to demonstrate the potential of this technique. Designed ankyrin repeat proteins (DARPins), engineered OB-fold domains (OBodies), and V
HH
domains from camelid antibodies (nanobodies) were employed. The respective resins were produced in a single bacterial fermentation step, and a simple purification protocol was developed. Purified resins were suitable for most lab-scale affinity chromatography purposes. All of the affinity domains tested produced polyester beads with specific affinity for the target protein. The binding capacity of these affinity resins ranged from 90 to 600 nmol of protein per wet gram of polyester affinity resin, enabling purification of a recombinant protein target from a complex bacterial cell lysate up to a purity level of 96% in one step. The polyester resin was efficiently produced by conventional lab-scale shake flask fermentation, resulting in bacteria accumulating up to 55% of their cellular dry weight as polyester. A further proof of concept demonstrating the practicality of this technique was obtained through the intracellular coproduction of a specific affinity resin and its target. This enables
in vivo
binding and purification of the coproduced “target protein.” Overall, this study provides evidence for the use of molecular engineering of polyester synthases toward the microbial production of specific bioseparation resins implementing previously selected binding domains.
Selection for Growth on 3-Nitrotoluene by 2-Nitrotoluene-Utilizing Acidovorax sp. Strain JS42 Identifies Nitroarene Dioxygenases with Altered Specificities
Authors: Mahan Kristina M. , Penrod Joseph T. , Ju Kou-San , Al Kass Natascia , Tan Watumesa A. , Truong Richard , Parales Juanito V. , Parales Rebecca E. 
Published: October 2014

ABSTRACT

Acidovorax
sp. strain JS42 uses 2-nitrotoluene as a sole source of carbon and energy. The first enzyme of the degradation pathway, 2-nitrotoluene 2,3-dioxygenase, adds both atoms of molecular oxygen to 2-nitrotoluene, forming nitrite and 3-methylcatechol. All three mononitrotoluene isomers serve as substrates for 2-nitrotoluene dioxygenase, but strain JS42 is unable to grow on 3- or 4-nitrotoluene. Using both long- and short-term selections, we obtained spontaneous mutants of strain JS42 that grew on 3-nitrotoluene. All of the strains obtained by short-term selection had mutations in the gene encoding the α subunit of 2-nitrotoluene dioxygenase that changed isoleucine 204 at the active site to valine. Those strains obtained by long-term selections had mutations that changed the same residue to valine, alanine, or threonine or changed the alanine at position 405, which is just outside the active site, to glycine. All of these changes altered the regiospecificity of the enzymes with 3-nitrotoluene such that 4-methylcatechol was the primary product rather than 3-methylcatechol. Kinetic analyses indicated that the evolved enzymes had enhanced affinities for 3-nitrotoluene and were more catalytically efficient with 3-nitrotoluene than the wild-type enzyme. In contrast, the corresponding amino acid substitutions in the closely related enzyme nitrobenzene 1,2-dioxygenase were detrimental to enzyme activity. When cloned genes encoding the evolved dioxygenases were introduced into a JS42 mutant lacking a functional dioxygenase, the strains acquired the ability to grow on 3-nitrotoluene but with significantly longer doubling times than the evolved strains, suggesting that additional beneficial mutations occurred elsewhere in the genome.
Transfer RNA Modification: Presence, Synthesis, and Function
Authors: Björk Glenn R. , Hagervall Tord G. 
Published: October 2014

Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from
Escherichia coli
/
Salmonella enterica
serovar Typhimurium contains 33 different modified nucleosides, which are all, except one (Queuosine [Q]), synthesized on an oligonucleotide precursor, which by specific enzymes later matures into tRNA. The structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The synthesis of the tRNA-modifying enzymes is not regulated similarly, and it is not coordinated to that of their substrate, the tRNA. The synthesis of some of them (e.g., several methylated derivatives) is catalyzed by one enzyme, which is position and base specific, whereas synthesis of some has a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines,
N
6
-cyclicthreonyladenosine [ct
6
A], and Q). Several of the modified nucleosides are essential for viability (e.g., lysidin, ct
6
A, 1-methylguanosine), whereas the deficiency of others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those that are present in the body of the tRNA primarily have a stabilizing effect on the tRNA. Thus, the ubiquitous presence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
Association of fasting insulin and C peptide with diabetic retinopathy in Latinos with type 2 diabetes
Authors: Kuo Jane Z , Guo Xiuqing , Klein Ronald , Klein Barbara E , Weinreb Robert N , Genter Pauline , Hsiao Fone-Ching , Goodarzi Mark O , Rotter Jerome I , Chen Yii-Der Ida , Ipp Eli 
Published: October 2014

ObjectiveResidual insulin secretion provides important protection against the development of diabetic retinopathy in type 1 diabetes. The data to support this in type 2 diabetes are unclear. We therefore tested in type 2 diabetes whether markers of residual beta-cell function are associated with the development of diabetic retinopathy, an important microvascular complication of diabetes.DesignProspective, cross-sectional, family-based study.Participants585 Latino type 2 diabetic participants, ascertained in families via a proband either with known diabetes duration of greater than 10 years and/or with diabetic retinopathy.Outcome measuresCirculating levels of fasting insulin and C peptide measured and correlated to degree of diabetic retinopathy, assessed by digital fundus photography and graded using the Modified Airlie House Classification and the Early Treatment Diabetic Retinopathy Study scale (range: levels 10–85).ResultsFasting plasma insulin (β=−0.29; 95% CI −0.38 to −0.20; p<0.0001) and C peptide (β=−0.21; 95% CI −0.30 to −0.13; p<0.0001) concentrations in these diabetic participants were significantly correlated with retinopathy and its degree of severity. This relationship remained significant after adjusting for potential covariates including age, gender, glycosylated hemoglobin, duration of diabetes, blood pressure, and renal function.ConclusionsThese data suggest that residual endogenous insulin secretion is associated with the presence of diabetic retinopathy and its severity in Latinos with familial type 2 diabetes. It remains to be proven whether beta-cell targeted therapies, to maintain beta-cell mass and/or function in addition to glycemic control, will further the goal of preventing diabetic microvascular disease.
Treatment crossovers in time-to-event non-inferiority randomised trials of radiotherapy in patients with breast cancer
Authors: Parpia Sameer , Julian Jim A , Thabane Lehana , Gu Chushu , Whelan Timothy J , Levine Mark N 
Published: October 2014

BackgroundIn non-inferiority trials of radiotherapy in patients with early stage breast cancer, it is inevitable that some patients will cross over from the experimental arm to the standard arm prior to initiation of any treatment due to complexities in treatment planning or subject preference. Although the intention-to-treat (ITT) analysis is the preferred approach for superiority trials, its role in non-inferiority trials is still under debate. This has led to the use of alternative approaches such as the per-protocol (PP) analysis or the as-treated (AT) analysis, despite the inherent biases of such approaches.MethodsUsing simulations, we investigate the effect of 2%, 5% and 10% random and non-random crossovers prior to radiotherapy initiation on the ITT, PP, AT and the combination of ITT and PP analyses with respect to type I error in trials with time-to-event outcomes. We also evaluate bias and SE of the estimates from the ITT, PP and AT approaches.ResultsThe AT approach had the best performance in terms of type I error, but was anticonservative as non-random crossover increased. The ITT and PP approaches were anticonservative under all percentages of random and non-random crossover. Similarly, lowest bias was seen with the AT approach; however, bias increased as the percentage of non-random crossover increased. The ITT and PP had poor performance in terms of bias as crossovers increased.ConclusionsIf minimal crossovers were to occur, we have shown that the AT approach has the lowest type I error rates and smallest opportunity for bias. Results of trials with a high number of crossovers should be interpreted with caution, especially when crossover is non-random. Attempts to prevent crossovers should be maximised.
How to communicate with patients about future illness progression and end of life: a systematic review
Authors: Parry Ruth , Land Victoria , Seymour Jane 
Published: October 2014

BackgroundConversation and discourse analytic research has yielded important evidence about skills needed for effective, sensitive communication with patients about illness progression and end of life.ObjectivesTo: ▸ Locate and synthesise observational evidence about how people communicate about sensitive future matters;▸ Inform practice and policy on how to provide opportunities for talk about these matters;▸ Identify evidence gaps.DesignSystematic review of conversation/discourse analytic studies of recorded interactions in English, using a bespoke appraisal approach and aggregative synthesis.Results19 publications met the inclusion criteria. We summarised findings in terms of eight practices: ‘fishing questions’—open questions seeking patients’ perspectives (5/19); indirect references to difficult topics (6/19); linking to what a patient has already said—or noticeably not said (7/19); hypothetical questions (12/19); framing difficult matters as universal or general (4/19); conveying sensitivity via means other than words, for example, hesitancy, touch (4/19); encouraging further talk using means other than words, for example, long silences (2/19); and steering talk from difficult/negative to more optimistic aspects (3/19).ConclusionsPractices vary in how strongly they encourage patients to engage in talk about matters such as illness progression and dying. Fishing questions and indirect talk make it particularly easy to avoid engaging—this may be appropriate in some circumstances. Hypothetical questions are more effective in encouraging on-topic talk, as is linking questions to patients’ cues. Shifting towards more ‘optimistic’ aspects helps maintain hope but closes off further talk about difficulties: practitioners may want to delay doing so. There are substantial gaps in evidence.
Torsion constraints from cosmological magnetic field and QCD domain walls
Authors: Garcia de Andrade L. C. 
Published: October 2014

Earlier Kostelecky [Phys. Rev. D 69, 105009 (2004)] has investigated the role of gravitational sector in Riemann–Cartan (RC) spacetime with torsion, in Lorentz and CPT violating (LV) Standard Model extension (SME). In his paper use of quantum electrodynamic (QED) extension in RC spacetime is made. More recently L. C. Garcia de Andrade [Phys. Lett. B 468, 28 (2011)] obtained magnetic field galactic dynamo seeds in the bosonic sector with massless photons, which proved to decay faster than necessary [Phys. Lett. B 711, 143 (2012)] to be able to seed galactic dynamos. In this paper it is shown that by using the fermionic sector of Kostelecky–Lagrangian and torsion written as a chiral current, one obtains torsion and magnetic fields explicitly from a Heisenberg–Ivanenko form of Dirac equation whose solution allows us to express torsion in terms of LV coefficients and magnetic field in terms of fermionic matter fields. When minimal coupling between electromagnetic and torsion fields is used it is shown that the fermionic sector of QED with torsion leads to resonantly amplify magnetic fields which mimics an α2-dynamo mechanism. Fine-tuning of torsion is shown to result in the dynamo reversal, a phenomenon so important in solar physics and geophysics. Of course this is only an analogy since torsion is very weak in solar and geophysics contexts. An analogous expression for the α-effect of mean-field dynamos is also obtained where the α-effect is mimic by torsion. Similar resonant amplification mechanisms connected to early universe have been considered by Finelli and Gruppuso.
Building volumetric appearance models of fabric using micro CT imaging
Authors: Zhao Shuang , Jakob Wenzel , Marschner Steve , Bala Kavita 
Published: October 2014

Cloth is essential to our everyday lives; consequently, visualizing and rendering cloth has been an important area of research in graphics for decades. One important aspect contributing to the rich appearance of cloth is its complex 3D structure. Volumetric algorithms that model this 3D structure can correctly simulate the interaction of light with cloth to produce highly realistic images of cloth. But creating volumetric models of cloth is difficult: writing specialized procedures for each type of material is onerous, and requires significant programmer effort and intuition. Further, the resulting models look unrealistically "perfect" because they lack visually important features like naturally occurring irregularities.
This paper proposes a new approach to acquiring volume models, based on density data from X-ray computed tomography (CT) scans and appearance data from photographs under uncontrolled illumination. To model a material, a CT scan is made, yielding a scalar density volume. This 3D data has micron resolution details about the structure of cloth but lacks all optical information. So we combine this density data with a reference photograph of the cloth sample to infer its optical properties. We show that this approach can easily produce volume appearance models with extreme detail, and at larger scales the distinctive textures and highlights of a range of very different fabrics such as satin and velvet emerge automatically---all based simply on having accurate mesoscale geometry.<!-- END_PAGE_1 -->
ISA 2013 workshop report: a report on the Fifth International Workshop on Indoor Spatial Awareness
Authors: Tomko Martin , Bell Scott , Li Ki-Joune 
Published: October 2014

In our increasingly urbanized world, the World's population spends more and more time indoors. Indoor environments become our new natural habitat, and we conduct more and more activities enclosed by walls, moving vertically rather then horizontally, and without direct access to sunlight. Our daily activities are assisted by a range of sensors and human-machine interfaces that assist our senses and facilitate the transition between indoor and outdoor environments.
The combination of the unnatural indoor environments, novel technologies augmenting our interaction, and the ubiquitous connection to the Internet results in an entirely new ecosystem with particular challenges to our spatial abilities, spatial interactions (between humans, machines and the built environment) and spatial needs.
The series of ACM Workshops on Indoor Spatial Awareness addresses these challenges and explores the cognitive and semantic challenges, positioning and data processing requirements and technological innovations needed to facilitate the smooth transition to this ecosystem.
Mechanisms of Hypoxia-Mediated Immune Escape in Cancer
Authors: Barsoum Ivraym B. , Koti Madhuri , Siemens D. Robert , Graham Charles H. 
Published: October 2014

Abstract
An important aspect of malignant progression is the acquired ability of tumor cells to avoid recognition and destruction by the immune system (immune escape). Clinical cancer progression is also associated with the development of tumor hypoxia, which is mechanistically linked to the acquisition of malignant phenotypes in cancer cells. Despite the well-established role of hypoxia in tumor cell invasion and metastasis, and resistance to therapy, relatively few studies have examined the contribution of hypoxia to cancer immune escape. Accumulating evidence reveals that hypoxia can impair anticancer immunity by altering the function of innate and adaptive immune cells and/or by increasing the intrinsic resistance of tumor cells to the cytolytic activity of immune effectors. Here, we discuss certain aspects of the contribution of hypoxia to tumor immune escape and provide evidence for a novel role of cyclic guanosine monophosphate (cGMP) signaling in the regulation of hypoxia-induced immune escape. Thus, we propose that activation of cGMP signaling in cancer cells may have important immunotherapeutic applications. Cancer Res; 74(24); 7185–90. ©2014 AACR.
Elevated LIM Kinase 1 in Nonmetastatic Prostate Cancer Reflects Its Role in Facilitating Androgen Receptor Nuclear Translocation
Authors: Mardilovich Katerina , Gabrielsen Mads , McGarry Lynn , Orange Clare , Patel Rachana , Shanks Emma , Edwards Joanne , Olson Michael F. 
Published: October 2014

Abstract
Prostate cancer affects a large proportion of the male population, and is primarily driven by androgen receptor (AR) activity. First-line treatment typically consists of reducing AR signaling by hormone depletion, but resistance inevitably develops over time. One way to overcome this issue is to block AR function via alternative means, preferably by inhibiting protein targets that are more active in tumors than in normal tissue. By staining prostate cancer tumor sections, elevated LIM kinase 1 (LIMK1) expression and increased phosphorylation of its substrate Cofilin were found to be associated with poor outcome and reduced survival in patients with nonmetastatic prostate cancer. A LIMK-selective small molecule inhibitor (LIMKi) was used to determine whether targeted LIMK inhibition was a potential prostate cancer therapy. LIMKi reduced prostate cancer cell motility, as well as inhibiting proliferation and increasing apoptosis in androgen-dependent prostate cancer cells more effectively than in androgen-independent prostate cancer cells. LIMK inhibition blocked ligand-induced AR nuclear translocation, reduced AR protein stability and transcriptional activity, consistent with its effects on proliferation and survival acting via inhibition of AR activity. Furthermore, inhibition of LIMK activity increased αTubulin acetylation and decreased AR interactions with αTubulin, indicating that the role of LIMK in regulating microtubule dynamics contributes to AR function. These results indicate that LIMK inhibitors could be beneficial for the treatment of prostate cancer both by reducing nuclear AR translocation, leading to reduced proliferation and survival, and by inhibiting prostate cancer cell dissemination. Mol Cancer Ther; 14(1); 246–58. ©2014 AACR.
Surgical Fires in Laser Laryngeal Surgery: Are We Safe Enough?
Authors: Roy Soham , Smith Lee P. 
Published: October 2014

ObjectiveLaser surgery of the larynx and airway remains high risk for the formation of operating room fire. Traditional methods of fire prevention have included use of “laser safe” tubes, inflation of a protective cuff with saline, and wet pledgets to protect the endotracheal tube from laser strikes. We tested a mechanical model of laser laryngeal surgery to evaluate the fire risk.Study DesignMechanical model.SettingLaboratory.Subjects and MethodsAn intubation mannequin was positioned for suspension microlaryngoscopy. A Laser‐Shield II cuffed endotracheal tube was placed through the larynx and the cuff inflated using saline. Wet pledgets covered the inflated cuff. A CO2 laser created an inadvertent cuff strike at varying oxygen concentrations. Risk reduction measures were implemented to discern any notable change in the outcome after fire.ResultsAt 100% FiO2 an immediate fire with sustained flame was created and at 40% FiO2 a near immediate sustained flame was created. At 29% FiO2, a small nonsustained flame was noted. At room air, no fire was created. There was no discernible difference in the severity of laryngeal damage after the fire occurred whether the tube was immediately pulled from the mannequin or if saline was poured down the airway as a first response.ConclusionsWhile “laser safe” tubes provide a layer of protection against fires, they are not fire proof. Inadvertent cuff perforation may result in fire formation in low‐level oxygen enriched environments. Placement of wet pledgets do not provide absolute protection. Endotracheal tube (ETT) cuffs should be placed distally well away from an inadvertent laser strike while maintaining the minimum supplemental oxygen necessary.
Ten-year follow-up of the ‘minimal MRI lesion’ subgroup from the original CHAMPS Multiple Sclerosis Prevention Trial
Authors: Simon JH , Kinkel RP , Kollman C , O’Connor P , Fisher E , You X , Hyde R ,   for the CHAMPIONS Investigators Group
Published: October 2014

Background: Patients with clinically isolated syndrome (CIS) and characteristic magnetic resonance imaging (MRI) lesions are at high risk for multiple sclerosis (MS). However, patients with a minimal MRI lesion burden (a low T2-hyperintense [low T2] lesion count) may have borderline formal diagnostic criteria, presenting a clinical management challenge. Objective: Compare the 10-year disease progression of patients with low and higher T2 lesion counts treated over most intervals. Methods: CIS patients from the original CHAMPS MS trial were retrospectively assigned to low-T2 (first quartile; 2–8 lesions) or higher-T2 (second through fourth quartiles; ≥ 9 lesions) groups using baseline T2 lesion counts. The 5- and 10-year open-label extension of CHAMPS (CHAMPIONS) evaluated conversion to clinically definite MS (CDMS), MRI activity, relapses, and disability. Results: The vast majority of patients showed new disease activity by MRI and/or clinical criteria at 10 years (low-T2 86%; higher-T2 98%). Fewer low-T2 than higher-T2 patients developed CDMS (40% vs. 63%; p = 0.013); low-T2 patients also had fewer new brain lesions, less brain volume loss, and less disability progression. Conclusion: CIS patients with low T2 lesion counts show continued disease activity. However, all assessments of disease progression over 10 years indicated a significantly less severe disease course for low-T2 patients.
Thrombospondin 1 requires von Willebrand factor to modulate arterial thrombosis in mice
Authors: Prakash Prem , Kulkarni Paresh P. , Chauhan Anil K. 
Published: October 2014

Key PointsThrombospondin 1 requires the presence of VWF to modulate arterial thrombosis. Platelet thrombospondin 1 contributes to arterial thrombosis.