bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digital Halftones
Authors: Vanderhaeghe David , Ostromoukhov Victor 
Published: March 2015

AbstractThis chapter presents in detail how halftoning algorithms are designed and can be implemented, from the simplest and widely used to the latest improvements.There are two main types of digital halftoning approaches. Three algorithmic classes exist to perform digital halftoning : point algorithms, neighborhood algorithms, and iterative algorithms. Point algorithms are local, parallelizable, processes that use a single original image pixel to decide whether a microdot should receive ink or not. Majority of algorithms in this class use a matrix‐based approach.The second class of digital halftoning approaches uses local neighborhood knowledge to compute the output image. A typical example is error diffusion. Error diffusion is a sequential process: it processes one microdot after the other, propagating an error value to unprocessed pixels. We present both the original error diffusion methods and the improvements, with a comparative study of their pros and cons.The last class is iterative algorithms which consider original and output images globally during the computation. The distribution of microdots becomes a global iterative process. Iterative algorithms are generally costly; but the resulting halftones show very good distribution and can take into account complex model of printers and the human visual system.
Digital Microscopy
Authors: Stuurman Nico , Thorn Kurt 
Published: March 2015

AbstractLight microscopes can visualize structures down to 200 nm (or sometimes less) and are therefore the tool of choice to visualize cells, the basic unit of life. No longer do researchers peer through the microscope's eyepieces and document their findings through drawings or on film, rather, digital image acquisition and motorized control of the microscope play a key role. Modern light microscopes capture data on digital detectors and are often fully automated, providing computer control of fluorescence excitation and detection and sample positioning. This makes it possible to automatically acquire multicolor three‐dimensional time‐lapse movies. Moreover, accurate, sensitive detectors enable quantification of microscope images and are a key component of various strategies to improve the spatial and temporal resolution of the microscope. Here, we review modern biological light microscopes, discuss their components, and describe how these tools are utilized experimentally.
Phosphates: Solid‐State Chemistry
Authors: Attfield J. Paul 
Published: February 2015

AbstractPhosphates contain oxyanions of phosphorus(V). The most common anion is the orthophosphate groupPO43−, which is found in many solid phosphates, including hydrated and acid phosphate salts. Oligomeric polyphosphate chains PnO3n+1(n+2)−up ton= 6 and cyclophosphate rings PnO3nn−up ton= 12 are also observed, and a unique cage ultraphosphate anion P8O236−is found in the Na3FeP8O23structure. Polymeric phosphate anions include the infinite chain catenaphosphate anion (PO3−)∞and the ultraphosphate networks found in CaP4O11and the lanthanide MP5O14structures. Many compound anions and neutral frameworks such as silicophosphates, aluminophosphates, and molybdenum phosphates also exist. Phosphate species are characterized through P–O stretching and bending vibrations in infrared and Raman spectroscopies, and by31P NMR. Phosphate structures are generally rigid, resistant to chemical attack, and (when anhydrous) insoluble and thermally stable. Some phosphate crystals have important physical properties such as ferroelectricity in KH2PO4(potassium dihydrogenphosphate,KDP). Diffusion of extra‐framework ions leads to potential uses of solid phosphates as ion exchangers and conductors, for example, NASICON based on NaZr2(PO4)3, and LiFePO4as a cathode material for lithium‐ion batteries. Vanadium phosphates are important selective oxidation catalysts. Large pore phosphates in which molecules can be adsorbed and undergo acid‐catalyzed reactions have been intensively studied. These materials are crystalline microporous solids such as aluminophosphates, or lamellar structures, typically based on α‐Zr(HPO4)2·H2O that can be pillared. This area of interest has led to the synthesis of many new organically templated metal phosphates, usually through hydrothermal reactions. Hydrated and acid orthophosphates can also be prepared in solution, and anhydrous phosphates are synthesized by direct high‐temperature reactions and from phosphate‐rich melts or fluxes. Slow cooling of melts is used to grow crystals, and quenching can result in many stable phosphate glasses. Phosphate anions do not absorb significantly in the UV–visible region and so solid phosphates also find use as optical materials such as phosphors, nonlinear crystals (e.g., KTiOPO4), and lasers. Solid phosphates constitute many minerals, notably apatites, which are also found in living organisms as rigid components such as bones and teeth. Synthetic calcium phosphate biomaterials are used for bone implants.
Sol–Gel Synthesis of Solids
Authors: Coradin Thibaud 
Published: February 2015

Abstract
The synthesis of glasses and ceramics via the sol–gel route is based on the inorganic polymerization of molecular precursors such as metal alkoxides. Precursor structure and reactivity can be chemically controlled via complexation or acid–base catalysis. Sol–gel chemistry allows the powderless processing of glasses and ceramics, at much lower temperatures than that at usual solid‐state reactions. It provides a convenient and flexible access to nanoparticles, films, and fibers. Moreover, precursors are mixed at the molecular level and multicomponent materials can be formed. Thus, hybrid organic–inorganic materials have been made via the sol–gel route. The organic component can be used as a network modifier during the sol–gel synthesis and then withdrawn, allowing the formation of structured porous materials. It can also remain entrapped in the mineral matrix via weak interactions. Alternatively, organoalkoxysilanes allow covalent binding of organic moieties to silica networks. Such composites fill the gap between polymers and glasses, opening new possibilities for the design of functional materials in the fast developing areas of energy, biotechnology, and medicine.
Hydrogenase Maturation Protein HypF
Authors: Cygler Miroslaw , Petkun Svetlana 
Published: February 2015

Abstract

HypF
is an accessory protein for assembling the
NiFe
(
CN
)
2
CO
active center of [
NiFe
]‐hydrogenases.
HypF
together with
HypE
catalyzes the synthesis of the
CN
‐ ligands using carbamoylphosphate as the initial substrate.
HypF
comprises four domains: the acylphosphatase domain, the Zn finger domain, the
YrdC
‐like domain with a nucleotide‐binding site and the Kae1‐like “universal domain” with a second nucleotide‐binding site coordinated by a metal. The
YrdC
‐ and Kae1‐like domains are juxtaposed with their nucleotide‐binding sites facing each other and sequestered in an internal cavity. The distance between the two sites is approximately 14 Å. The carbamoylphosphate is hydrolyzed to carbamate within the acylphosphatase domain, which then likely migrates through a tunnel in the
YrdC
‐like domain toward the
ATP
molecule bound within this domain's nucleotide‐binding site. The end of the tunnel is near the α‐phosphate of
ATP
where the carbamate is converted to carbamoyl adenylate intermediate. This intermediate presumably diffuses across the cavity to the nucleotide‐binding site in Kae1‐like domain where the transfer of
CN
moiety to the C‐terminal cysteine of
HypE
finally occurs. While the structure discloses the architecture of the various active sites, the details of each catalytic step require further investigations.
Traumatic brain injury in later life increases risk for Parkinson disease
Authors: Gardner Raquel C. , Burke James F. , Nettiksimmons Jasmine , Goldman Sam , Tanner Caroline M. , Yaffe Kristine 
Published: February 2015

ObjectiveTraumatic brain injury (TBI) is thought to be a risk factor for Parkinson disease (PD), but results are conflicting. Many studies do not account for confounding or reverse causation. We sought to address these concerns by quantifying risk of PD after TBI compared to non‐TBI trauma (NTT; defined as fractures).MethodsUsing inpatient/emergency department (ED) International Classification of Disease, Ninth Revision code data for California hospitals from 2005–2006, we identified patients aged ≥55 years with TBI (n = 52,393) or NTT (n = 113,406) and without baseline PD or dementia who survived hospitalization. Using Kaplan–Meier estimates and Cox proportional hazards models (adjusted for age, sex, race/ethnicity, income, comorbidities, health care use, and trauma severity), we estimated risk of PD after TBI during follow‐up ending in 2011. We also assessed interaction with mechanism of injury (fall vs nonfall) and effect of TBI severity (mild vs moderate/severe) and TBI frequency (1 TBI vs >1 TBI).ResultsTBI patients were significantly more likely to be diagnosed with PD compared to NTT patients (1.7% vs 1.1%, p < 0.001, adjusted hazard ratio [HR] = 1.44, 95% confidence interval [CI] = 1.31–1.58). Risk of PD was similar for TBI sustained via falls versus nonfalls (interaction p = 0.6). Assessment by TBI severity (mild TBI: HR = 1.24, 95% CI = 1.04–1.48; moderate/severe TBI: HR = 1.50, 95% CI = 1.35–1.66) and TBI frequency (1 TBI: HR = 1.45, 95% CI = 1.30–1.60; >1 TBI: HR = 1.87, 95% CI = 1.58–2.21) revealed a dose response.InterpretationAmong patients aged ≥55 years presenting to inpatient/ED settings with trauma, TBI is associated with a 44% increased risk of developing PD over 5 to 7 years that is unlikely to be due to confounding or reverse causation. Ann Neurol 2015;77:987–995
Electrical stimulation enhances sensory recovery: A randomized controlled trial
Authors: Wong Joshua N. , Olson Jaret L. , Morhart Michael J. , Chan K. Ming 
Published: February 2015

ObjectiveBrief postsurgical electrical stimulation (ES) has been shown to enhance peripheral nerve regeneration in animal models following axotomy and crush injury. However, whether this treatment is beneficial in humans with sensory nerve injury has not been tested. The goal of this study was to test the hypothesis that ES would enhance sensory nerve regeneration following digital nerve transection compared to surgery alone.MethodsPatients with complete digital nerve transection underwent epineurial nerve repair. After coaptation of the severed nerve ends, fine wire electrodes were implanted before skin closure. Postoperatively, patients were randomized to receiving either 1 hour of 20Hz continuous ES or sham stimulation in a double‐blinded manner. Patients were followed monthly for 6 months by a blinded evaluator to monitor physiological recovery of spatial discrimination, pressure threshold, and quantitative small fiber sensory testing. Functional disability was measured using the Disability of Arm, Shoulder, and Hand questionnaire.ResultsA total of 36 patients were recruited, with 18 in each group. Those in the ES group showed consistently greater improvements in all sensory modalities by 5 to 6 months postoperatively compared to the controls. Although there was a trend of greater functional improvements in the ES group, it was not statistically significant (p > 0.01).InterpretationPostsurgical ES enhanced sensory reinnervation in patients who sustained complete digital nerve transection. The conferred benefits apply to a wide range of sensory functions. Ann Neurol 2015;77:996–1006
Complement C1q‐C3–associated synaptic changes in multiple sclerosis hippocampus
Authors: Michailidou Iliana , Willems Janske G. P. , Kooi Evert‐Jan , van Eden Corbert , Gold Stefan M. , Geurts Jeroen J. G. , Baas Frank , Huitinga Inge , Ramaglia Valeria 
Published: February 2015

ObjectiveMultiple sclerosis (MS) is a demyelinating disease of the central nervous system, leading to memory impairment in up to 65% of patients. Memory dysfunction in MS has been associated with loss of synapses in the hippocampus, but its molecular basis is unknown. Accumulating evidence suggests that components of the complement system, C1q and C3, can mediate elimination of synapses.MethodsTo investigate the involvement of complement in synaptic changes in MS, gene and protein expression and localization of C1q and C3 were analyzed in relation to neuropathological changes in myelinated and demyelinated hippocampi from postmortem MS brains. Findings were compared to hippocampi of Alzheimer disease (AD) and non‐neurological controls.ResultsC1q expression and C3 activation were increased in myelinated and demyelinated MS hippocampi, mainly in the CA3/2 and CA1 subfields, which also showed a marked decrease in synaptic density and increased neuronal staining for the mitochondrial heat shock protein 70 (mtHSP70) stress marker. Neurons were the major source of C1q mRNA. C1q protein and activated C3 localized at synapses within human leukocyte antigen–positive cell processes and lysosomes, suggesting engulfment of complement‐tagged synapses by microglia. A significant association (p < 0.0001) between the density of C1q and synaptophysin‐positive synapses or mtHSP70 was seen in myelinated MS hippocampi, further pointing toward a link between the complement pathway and synaptic changes. In contrast to AD, MS hippocampi were consistently negative for the terminal complement activation complex C5b9.InterpretationThese data support a role for the C1q‐C3 complement axis in synaptic alterations in the MS hippocampus. Ann Neurol 2015;77:1007–1026
Flurbiprofen axetil loaded coaxial electrospun poly(vinyl pyrrolidone)–nanopoly(lactic‐co‐glycolic acid) core–shell composite nanofibers: Preparation, characterization, and anti‐adhesion activity
Authors: Zhu Tonghe , Chen Sihao , Li Wenyao , Lou Jianzhong , Wang Jihu 
Published: February 2015

ABSTRACTFlurbiprofen axetil (FA)‐loaded coaxial electrospun poly(vinyl pyrrolidone) (PVP)–nanopoly(lactic‐co‐glycolic acid) core–shell composite nanofibers were successfully fabricated by a facile coaxial electrospinning, and an electrospun drug‐loaded system was formed for anti‐adhesion applications. The FA, which is a kind of lipid microsphere nonsteroidal anti‐inflammatory drug, was shown to be successfully adsorbed in the PVP, and the formed poly(lactic‐co‐glycolic acid) (PLGA)/PVP/FA composite nanofibers exhibited a uniform and smooth morphology. The cell viability assay and cell morphology observation revealed that the formed PLGA/PVP/FA composite nanofibers were cytocompatible. Importantly, the loaded FA within the PLGA/PVP coaxial nanofibers showed a sustained‐release profile and anti‐adhesion activity to inhibit the growth of the IEC‐6 and NIH3T3 model cells. With the significantly reduced burst‐release profile, good cytocompatibility, and anti‐adhesion activity, the developed PLGA/PVP/FA composite nanofibers were proposed to be a promising material in the fields of tissue engineering and pharmaceutical science. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci.2015,132, 41982.
Selective retinol production by modulating the composition of retinoids from metabolically engineered E. coli
Authors: Jang Hui‐Jeong , Ha Bo‐Kyung , Zhou Jia , Ahn Jiyoon , Yoon Sang‐Hwal , Kim Seon‐Won 
Published: February 2015

ABSTRACTRetinoids can be produced from E. coli when introduced with the β‐carotene biosynthesis pathway and the BCMO gene. E. coli has no inherent metabolic pathways related to retinoids, therefore only retinal should be produced from the cleavage of β‐carotene by BCMO. However, retinol and retinyl acetate were also produced in significant amounts, by the non‐specific activity of inherent promiscuous enzymes or the antibiotic resistance marker of the retinal‐producing plasmids. Retinol was produced by the ybbO gene of E. coli which encodes oxidoreductase and retinyl acetate was produced by the chloramphenicol resistance gene, called cat gene which encodes chloramphenicol acetyltransferase, present within the pS‐NA plasmid that also contains the mevalonate pathway. The composition of retinoids could be modulated by manipulating the relevant genes. The composition of retinol, a commercially important retinoid, was significantly increased by the overexpression of ybbO gene and the removal of cat gene in the recombinant E. coli, which suggests the possibility of selective retinoid production in the future. Biotechnol. Bioeng. 2015;112: 1604–1612. © 2015 Wiley Periodicals, Inc.
Robust kinetics of an RNA virus: Transcription rates are set by genome levels
Authors: Timm Collin , Gupta Ankur , Yin John 
Published: February 2015

ABSTRACTIn order to persist in nature, RNA viruses have evolved strategies to grow in diverse host environments. To better understand how such strategies might work, we used qRT‐PCR to measure viral RNA species during cellular infections by a model RNA virus, vesicular stomatitis virus (VSV). Absolute levels of the VSV major transcript and genome were measured for infections in BHK and PC3 cells, across different multiplicities of infection (MOI 1, 10, 100), in the absence or presence of protein synthesis, as well as in cells in an interferon‐activated anti‐viral state. While viral genome replication was delayed in more resistant host cells, kinetic modeling of these data revealed a simple linear relationship between the mRNA production rate and genome levels under all tested conditions. These results indicate that while viral transcription and genome replication both depend on the availability of the viral RNA‐dependent RNA polymerase and host cellular resources, transcription proceeds without apparent limits on these resources. Biotechnol. Bioeng. 2015;112: 1655–1662. © 2015 Wiley Periodicals, Inc.
Fluid and cell behaviors along a 3D printed alginate/gelatin/fibrin channel
Authors: Xu Yufan , Wang Xiaohong 
Published: February 2015

ABSTRACTThree‐dimensional (3D) cell manipulation is available with the integration of microfluidic technology and rapid prototyping techniques. High‐Fidelity (Hi‐Fi) constructs hold enormous therapeutic potential for organ manufacturing and regenerative medicine. In the present paper we introduced a quasi‐three‐dimensional (Q3D) model with parallel biocompatible alginate/gelatin/fibrin hurdles. The behaviors of fluids and cells along the microfluidic channels with various widths were studied. Cells inside the newly designed microfluidic channels attached and grew well. Morphological changes of adipose‐derived stem cells (ADSCs) in both two‐dimensional (2D) and 3D milieu were found on the printed constructs. Endothelialization occurred with the co‐cultures of ADSCs and hepatocytes. This study provides insights into the interactions among fluids, cells and biomaterials, the behaviors of fluids and cells along the microfluidic channels, and the applications of Q3D techniques. Biotechnol. Bioeng. 2015;112: 1683–1695. © 2015 Wiley Periodicals, Inc.
High throughput screening of particle conditioning operations: II. Evaluation of scale‐up heuristics with prokaryotically expressed polysaccharide vaccines
Authors: Noyes Aaron , Huffman Ben , Berrill Alex , Merchant Nick , Godavarti Ranga , Titchener‐Hooker Nigel , Coffman Jonathan , Sunasara Khurram , Mukhopadhyay Tarit 
Published: February 2015

ABSTRACTMultivalent polysaccharide conjugate vaccines are typically comprised of several different polysaccharides produced with distinct and complex production processes. Particle conditioning steps, such as precipitation and flocculation, may be used to aid the recovery and purification of such microbial vaccine products. An ultra scale‐down approach to purify vaccine polysaccharides at the micro‐scale would greatly enhance productivity, robustness, and speed the development of novel conjugate vaccines. In part one of this series, we described a modular and high throughput approach to develop particle conditioning processes (HTPC) for biologicals that combines flocculation, solids removal, and streamlined analytics. In this second part of the series, we applied HTPC to industrially relevant feedstreams comprised of capsular polysaccharides (CPS) from several bacterial species. The scalability of HTPC was evaluated between 0.8 mL and 13 L scales, with several different scaling methodologies examined. Clarification, polysaccharide yield, impurity clearance, and product quality achieved with HTPC were reproducible and comparable with larger scales. Particle sizing was the response with greatest sensitivity to differences in processing scale and enabled the identification of useful scaling rules. Scaling with constant impeller tip speed or power per volume in the impeller swept zone offered the most accurate scale up, with evidence that time integration of these values provided the optimal basis for scaling. The capability to develop a process at the micro‐scale combined with evidence‐based scaling metrics provide a significant advance for purification process development of vaccine processes. The USD system offers similar opportunities for HTPC of proteins and other complex biological molecules. Biotechnol. Bioeng. 2015;112: 1568–1582. © 2015 Wiley Periodicals, Inc.
Expansion, harvest and cryopreservation of human mesenchymal stem cells in a serum‐free microcarrier process
Authors: Heathman Thomas R. J. , Glyn Veronica A. M. , Picken Andrew , Rafiq Qasim A. , Coopman Karen , Nienow Alvin W. , Kara Bo , Hewitt Christopher J. 
Published: February 2015

ABSTRACTHuman mesenchymal stem cell (hMSC) therapies are currently progressing through clinical development, driving the need for consistent, and cost effective manufacturing processes to meet the lot‐sizes required for commercial production. The use of animal‐derived serum is common in hMSC culture but has many drawbacks such as limited supply, lot‐to‐lot variability, increased regulatory burden, possibility of pathogen transmission, and reduced scope for process optimization. These constraints may impact the development of a consistent large‐scale process and therefore must be addressed. The aim of this work was therefore to run a pilot study in the systematic development of serum‐free hMSC manufacturing process. Human bone‐marrow derived hMSCs were expanded on fibronectin‐coated, non‐porous plastic microcarriers in 100 mL stirred spinner flasks at a density of 3 × 105 cells.mL−1 in serum‐free medium. The hMSCs were successfully harvested by our recently‐developed technique using animal‐free enzymatic cell detachment accompanied by agitation followed by filtration to separate the hMSCs from microcarriers, with a post‐harvest viability of 99.63 ± 0.03%. The hMSCs were found to be in accordance with the ISCT characterization criteria and maintained hMSC outgrowth and colony‐forming potential. The hMSCs were held in suspension post‐harvest to simulate a typical pooling time for a scaled expansion process and cryopreserved in a serum‐free vehicle solution using a controlled‐rate freezing process. Post‐thaw viability was 75.8 ± 1.4% with a similar 3 h attachment efficiency also observed, indicating successful hMSC recovery, and attachment. This approach therefore demonstrates that once an hMSC line and appropriate medium have been selected for production, multiple unit operations can be integrated to generate an animal component‐free hMSC production process from expansion through to cryopreservation. Biotechnol. Bioeng. 2015;112: 1696–1707. © 2015 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.