bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Whole Proteome Inventory of Background Photocrosslinker Binding
Authors: Kleiner Philipp , Heydenreuter Wolfgang , Stahl Matthias , Korotkov Vadim S. , Sieber Stephan A. 
Published: December 2016

AbstractAffinity‐based protein profiling (AfBPP) is a widely applied method for the target identification of bioactive molecules. Probes containing photocrosslinkers, such as benzophenones, diazirines, and aryl azides, irreversibly link the molecule of interest to its target protein upon irradiation with UV light. Despite their prevalent application, little is known about photocrosslinker‐specific off‐targets, affecting the reliability of results. Herein, we investigated background protein labeling by gel‐free quantitative proteomics. Characteristic off‐targets were identified for each photoreactive group and compiled in a comprehensive inventory. In a proof‐of‐principle study, H8, a protein kinase A inhibitor, was equipped with a diazirine moiety. Application of this photoprobe revealed, by alignment with the diazirine background, unprecedented insight into its in situ proteome targets. Taken together, our findings guide the identification of biologically relevant binders in photoprobe experiments.
A Stable Neutral Radical in the Coordination Sphere of Aluminum
Authors: Li Bin , Kundu Subrata , Stückl A. Claudia , Zhu Hongping , Keil Helena , Herbst‐Irmer Regine , Stalke Dietmar , Schwederski Brigitte , Kaim Wolfgang , Andrada Diego M. , Frenking Gernot , Roesky Herbert W. 
Published: December 2016

AbstractThe neutral radical (Me2‐cAAC)2AlCl2 (2) is stabilized by cyclic (alkyl)(amino)carbenes (cAACs). Complex 2 was synthesized by reduction of the Me2‐cAAC:→AlCl3 (1) adduct with KC8 in the presence of another equivalent of Me2‐cAAC. The crystal structure of 2 shows that the Al−C bond lengths of the two carbenes bound to the Al center are considerably different, which is likely the result of intermolecular interactions. Quantum‐chemical calculations from the gas phase give an equilibrium structure with identical Al−C bond lengths. Compound 2 exhibits monoradical character, which was confirmed by EPR measurements. A bonding analysis indicates that the unpaired electron resides mainly at the carbene carbon atoms. Compound 2 is an example for an unusual neutral Al radical.
Hybrid Palladium Nanoparticles for Direct Hydrogen Peroxide Synthesis: The Key Role of the Ligand
Authors: Lari Giacomo M. , Puértolas Begoña , Shahrokhi Masoud , López Núria , Pérez‐Ramírez Javier 
Published: December 2016

AbstractLigand‐modified palladium nanoparticles deposited on a carbon carrier efficiently catalyze the direct synthesis of H2O2 and the unique performance is due to their hybrid nanostructure. Catalytic testing demonstrated that the selectivity increases with the HHDMA ligand content from 10 % for naked nanoparticles up to 80 %, rivalling that obtained with state‐of‐the‐art bimetallic catalysts (HHDMA=C20H46NO5P). Furthermore, it remains stable over five consecutive reaction runs owing to the high resistance towards leaching of the organic moiety, arising from its bond with the metal surface. As rationalized by density functional theory, this behavior is attributed to the adsorption mode of the reaction intermediates on the metal surface. Whereas they lie flat in the absence of the organic shell, their electrostatic interaction with the ligand result in a unique vertical configuration which prevents further dissociation and over‐hydrogenation. These findings demonstrate the importance of understanding substrate–ligand interactions in capped nanoparticles to develop smart catalysts for the sustainable manufacture of hydrogen peroxide.
A Novel Method for Constructing Histological Section Datasets of the Basal Ganglia in Digitized Human Brain
Authors: Xie Luoyingzi , Rong Jingjing , Li Qiyu 
Published: December 2016

ABSTRACTTo investigate the construction of the histological section datasets in the basal ganglia of digitized human brain to provide a reference for the meso‐level histological data acquisition. A fresh adult brain from a cadaver with no neurological disease was selected, and tissue blocks of the basal ganglia in the right hemisphere was extracted using the visualization method, followed by pretreatments including gradient dehydrating, gelatin‐embedding and setting of calibration points. And then the tissue blocks was cryosectioned into 60‐μm‐thick coronal sections and the sectional images were captured simultaneously by a digital camera at a fixed position. Two series of sections (one section out of ten) were Nissl‐stained with Toluidine blue and immunostained with the calbindin D‐28K, respectively. Stained sections were digitized by a high resolution scanner. After alignment and registration, contours of nuclei and different nucleic function divisions in the digital images of stained sections were identified, and then were segmented and labeled using software exploited by ourselves. Datasets of one set of registrated serial sectional images and two sets of registrated histochemically stained images in basal ganglia area were obtained, which provide a histological reference for the neurosurgery and diagnostic imaging. a systematic method of cutting, slicing, staining, data acquisition and image registration of large tissue blocks was established, providing a reference for histological data acquisition on the digital human. Anat Rec, 300:1011–1021, 2017. © 2016 Wiley Periodicals, Inc.
Thalamic dopaminergic neurons projects to the paraventricular nucleus‐rostral ventrolateral medulla/C1 neural circuit
Authors: Ogundele Olalekan M. , Lee Charles C. , Francis Joseph 
Published: December 2016

ABSTRACTParaventricular nuclei (PVN) projections to the rostral ventrolateral medulla (RVLM)/C1 catecholaminergic neuron group constitute the pre‐autonomic sympathetic center involved in the neural control of systemic cardiovascular function. However, the role of extra‐hypothalamic and thalamic dopaminergic (DA) inputs in this circuit remains underexplored. Using retrograde neuroanatomical tracing and high contrast confocal imaging methods, we investigated the projections and morphology of the discrete thalamic DA neuron groups in the dorsal hypothalamic area and their contribution to the PVN‐RVLM neural circuit. We found that DA neuron subgroups in the Zona Incerta (Zi; 60%) and Reuniens thalamic nuclei (Re; 40%) were labeled comparably to the PVN (85%) after a retrograde tracer was injected into the RVLM/C1 (P < 0.01 mean ± SEM). The Re/Zi DA neuron subgroups were characterized by angulated cell bodies, superiomedial and inferiomedial projections reaching the contralateral Re/Zi and ipsilateral PVN DA neurons respectively. Ultimately, we deduced that the DA projections of the Re/Zi to the PVN contribute to the PVN‐RVLM/C1 neural circuit. As a result of these connections, the Re/Zi DA neuron groups may regulate preautonomic sympathetic events associated with the PVN‐RVLM pathway. Anat Rec, 300:1307–1314, 2017. © 2016 Wiley Periodicals, Inc.
Morphological Study: Ultrastructural Aspects of Articular Cartilage and Subchondral Bone in Patients Affected by Post‐Traumatic Shoulder Instability
Authors: Baudi Paolo , Catani Fabio , Rebuzzi Manuela , Ferretti Marzia , Smargiassi Alberto , Campochiaro Gabriele , Serafini Fabio , Palumbo Carla 
Published: December 2016

ABSTRACTPost‐traumatic shoulder instability is a frequent condition in active population, representing one of most disabling pathologies, due to altered balance involving joints. No data are so far available on early ultrastructural osteo‐chondral damages, associated with the onset of invalidating pathologies, like osteoarthritis‐OA. Biopsies of glenoid articular cartilage and sub‐chondral bone were taken from 10 adult patients underwent arthroscopic stabilization. Observations were performed under Transmission Electron Microscopy‐TEM in tangential, arcuate and radial layers of the articular cartilage and in the sub‐chondral bone. In tangential and arcuate layers chondrocytes display normal and very well preserved ultrastructure, probably due to the synovial liquid supply; otherwise, throughout the radial layer (un‐calcified and calcified) chondrocytes show various degrees of degeneration; occasionally, in the radial layer evidences of apoptosis/autophagy were also observed. Concerning sub‐chondral bone, osteocytes next to the calcified cartilage also show signs of degeneration, while osteocytes farther from the osteo‐chondral border display normal ultrastructure, probably due to the bone vascular supply. The ultrastructural features of the osteo‐chondral complex are not age‐dependent. This study represents the first complete ultrastructural investigation of the articular osteo‐chondral complex in shoulder instability, evaluating the state of preservation/viability of both chondrocytes and osteocytes throughout the successive layers of articular cartilage and sub‐chondral bone. Preliminary observations here collected represent the morphological basis for further deepening of pathogenesis related to shoulder instability, enhancing the relationship between cell shape and microenvironment; in particular, they could be useful in understanding if the early surgical treatment in shoulder instability could avoid the onset of OA. Anat Rec, 300:1208–1218, 2017. © 2016 Wiley Periodicals, Inc.
Reproductive Tract Histology in South American Fur Seal Pups (Arctophoca australis)
Authors: Katz Helena , Johansson Olle 
Published: December 2016

ABSTRACTIn the present study, a detailed histological description of the female reproductive tract of South American fur seal (Arctophoca australis) pups has been conducted. The uterine tube was covered by cuboidal to columnar epithelium; nerve fibers were present in the mesosalpinx and beneath the muscular layer. The uterus was bipartitus; the endometrial surface of the horns was lined by a simple cuboidal or columnar epithelium with deep tubular glands; caudally (“the transition area”), the epithelium changed to pseudostratified columnar, few tubular glands were present and the myometrium increased in width. A bistratified epithelium internally coated the uterine body, whereas it changed to cylindrical stratified epithelium with a highly vascularized lamina propria and a strong muscular layer in the cervix; no endometrial glands were observed in this region. From the transition area of the uterus to the vagina there were several nerve fibers and ganglia belonging to the uterovaginalis plexus. In the vestibule, hymenal folds were poorly developed; adnexa structures included the major vestibular glands and a neurovascular structure similar to the vestibular bulb. Minor vestibular glands were associated with the clitoris. The skin of the perineum was lined by a keratinized stratified epithelium, pigmented, with sebaceous glands, sweat glands and hair follicles. This is the first detailed histological description of the reproductive tract of South American fur seal pups, including the glandular adnexa and nerve structures. These results contribute to the reproductive biology in Pinniped species, and give a better understanding of the utero‐placental perfusion mechanism during diving. Anat Rec, 2017. © 2017 Wiley Periodicals, Inc. Anat Rec, 300:600–613, 2017. © 2016 Wiley Periodicals, Inc.
Efficient Hydrogenation of Biomass Oxoacids to Lactones by Using NHC–Iridium Coordination Polymers as Solid Molecular Catalysts
Authors: Liu Yaoqi , Sun Zheming , Huang Changyu , Tu Tao 
Published: December 2016

AbstractA series of NHC–iridium coordination polymers have proven to be robust, efficient and recyclable solid molecular catalysts toward the hydrogenation of biomass levulinic acid (LA) to γ‐valerolactone. Along with quantitative yields attained at 0.01 mol % catalyst loading under 50 atm of H2, the solid molecular catalyst was readily recovered and reused for 12 runs without obvious loss of the selectivity and activity. Remarkably, up to 1.2×105 TON, an unprecedented value could be achieved in this important transformation. In addition, a number of LA homologues, analogues and derivatives were well tolerated to deliver various intriguing and functional lactones in good to excellent yields, which further confirmed the feasibility of the solid molecular catalysts.
Design of an Optimal Fuzzy Sliding Mode Control using Scalar Sign Function
Authors: Chaouech Lotfi , Soltani Moez , Dhahri Slim , Chaari Abdelkader 
Published: December 2016

AbstractThe purpose of this paper is to present a new design for an optimal fuzzy sliding mode control based on a modified parallel distributed compensator and using a scalarsignfunction method. The proposed fuzzy sliding mode control uses a modified parallel distributed compensator scheme to find the optimal gains. To do this, the control gains are not considered constant through the linearized subsystem. Among these, we find state feedback gains, which are determined in offline mode using some prescribed performance criteria. Moreover, the fuzzy sliding surface of the system is designed using a stable eigenvector and the scalarsignfunction. The advantages of the proposed design are minimum energy control effort, faster response, and zero steady‐state error. We analyze and test the performance and stability of the new optimal fuzzy sliding mode control using simulation results that show that the proposed approach is very effective.
Optical detection of different phenolic compounds by means of a novel biosensor based on sol–gel immobilized laccase
Authors: Lepore Maria , Portaccio Marianna 
Published: December 2016

AbstractA novel sol–gel‐based biosensor exploiting the optical absorption properties of sol–gel immobilized laccase has been constructed to increase enzyme specificity toward different phenolic substrates. Laccase from Trametes versicolor has been immobilized in optically transparent sol–gel matrices. Using Fourier transform infrared spectroscopy and data analysis based on a wavelet algorithm, a successful enzyme immobilization has been determined. The changes in the optical absorption spectra of laccase reaction products at 425, 375, and 400 nm have been used to determine hydroquinone, resorcinol, and catechol concentrations, respectively. Owing to the slow response time of the hydroquinone–laccase reaction, our optical biosensor has been tested with resorcinol and catechol. Linear ranges up to 1.4 and 0.2 mM, limit‐of‐detection (LOD) of 4.5 and 0.6 μΜ, have been evidenced for resorcinol and catechol, respectively. Data for determining the resorcinol concentration have been particularly interesting since no other biosensor device has been reported in the literature. In comparison with other biosensors using laccase from the same native source, our biosensor has been characterized by larger linear ranges, significant sensitivities, and good LODs. To challenge our biosensor with real samples, tap water samples spiked with known amount of catechol and resorcinol have been employed.
Unequivocal evidence supporting the segregated flow intestinal model that discriminates intestine versus liver first‐pass removal with PBPK modeling
Authors: Pang K. Sandy , Yang Qi Joy , Noh Keumhan 
Published: December 2016

AbstractMerits of the segregated flow model (SFM), highlighting the intestine as inert serosa and active enterocyte regions, with a smaller fractional (fQ < 0.3) intestinal flow (QI) perfusing the enterocyte region, are described. Less drug in the circulation reaches the enterocytes due to the lower flow (fQQI) in comparison with drug administered into the gut lumen, fostering the idea of route‐dependent intestinal removal. The SFM has been found superior to the traditional model (TM), which views the serosa and enterocytes totally as a well‐mixed tissue perfused by 100% of the intestinal flow, QI. The SFM model is able to explain the lower extents of intestinal metabolism of enalapril, morphine and midazolam with i.v. vs. p.o. dosing. For morphine, the urine/bile ratio of the metabolite, morphine glucuronide
for p.o. was 2.6× that of i.v. This was due to the higher proportion of intestinally formed morphine glucuronide, appearing more in urine than in bile due to its low permeability and greater extent of intestinal formation with p.o. administration. By contrast, the TM predicted the same
for p.o. vs. i.v. The TM predicted that the contributions of the intestine:liver to first‐pass removal were 46%:54% for both p.o. and i.v. The SFM predicted same 46%:54% (intestine:liver) for p.o., but 9%:91% for i.v. By contrast, the kinetics of codeine, the precursor of morphine, was described equally well by the SFM‐ and TM‐PBPK models, a trend suggesting that intestinal metabolism of codeine is negligible. Fits to these PBPK models further provide insightful information towards metabolite formation: available fractions and the fractions of hepatic and total clearances that form the metabolite in question. The SFM‐PBPK model is useful to identify not only the presence of intestinal metabolism but the contributions of the intestine and liver for metabolite formation. Copyright © 2016 John Wiley & Sons, Ltd.
Modeling of complex antibody elution behavior under high protein load densities in ion exchange chromatography using an asymmetric activity coefficient
Authors: Huuk Thiemo C. , Hahn Tobias , Doninger Katharina , Griesbach Jan , Hepbildikler Stefan , Hubbuch Jürgen 
Published: December 2016

AbstractA main requirement for the implementation of model‐based process development in industry is the capability of the model to predict high protein load densities. The frequently used steric mass action isotherm assumes a thermodynamically ideal system and, hence constant activity coefficients. In this manuscript, an industrial antibody purification problem under high load conditions is considered where this assumption does not hold. The high protein load densities, as commonly applied in industrial downstream processing, may lead to complex elution peak shapes. Using Mollerup's generalized ion‐exchange isotherm (GIEX), the observed elution peak shapes could be modeled. To this end, the GIEX isotherm introduced two additional parameters to approximate the asymmetric activity coefficient. The effects of these two parameters on the curvature of the adsorption isotherm and the resulting chromatogram are investigated. It could be shown that they can be determined by inverse peak fitting and conform with the mechanistic demands of model‐based process development.
Microbiome precision editing: Using PEG as a selective fermentation initiator against methicillin‐resistant Staphylococcus aureus
Authors: Kao Ming‐Shan , Huang Stephen , Chang Wei‐Lin , Hsieh Ming‐Fa , Huang Chun‐Jen , Gallo Richard L. , Huang Chun‐Ming 
Published: December 2016

AbstractRecent creation of a Unified Microbiome Initiative (UMI) has the aim of understanding how microbes interact with each other and with us. When pathogenic Staphylococcus aureus infects the skin, the interplay between S. aureus and skin commensal bacteria occurs. Our previous data revealed that skin commensal bacteria can mediate fermentation against the growth of USA300, a community‐acquired methicillin‐resistant S. aureus MRSA. By using a fermentation process with solid media on a small scale, we define poly(ethylene glycol) dimethacrylate (PEG‐DMA) as a selective fermentation initiator which can specifically intensify the probiotic ability of skin commensal Staphylococcus epidermidis bacteria. At least five short‐chain fatty acids including acetic, butyric and propionic acids with anti‐USA300 activities are produced by PEG‐DMA fermentation of S. epidermidis. Furthermore, the S. epidermidis‐laden PEG‐DMA hydrogels effectively decolonized USA300 in skin wounds in mice. The PEG‐DMA and its derivatives may become novel biomaterials to specifically tailor the human skin microbiome against invading pathogens.
Translation system engineering in Escherichia coli enhances non‐canonical amino acid incorporation into proteins
Authors: Gan Rui , Perez Jessica G. , Carlson Erik D. , Ntai Ioanna , Isaacs Farren J. , Kelleher Neil L. , Jewett Michael C. 
Published: December 2016

ABSTRACTThe ability to site‐specifically incorporate non‐canonical amino acids (ncAAs) into proteins has made possible the study of protein structure and function in fundamentally new ways, as well as the bio synthesis of unnatural polymers. However, the task of site‐specifically incorporating multiple ncAAs into proteins with high purity and yield continues to present a challenge. At the heart of this challenge lies the lower efficiency of engineered orthogonal translation system components compared to their natural counterparts (e.g., translation elements that specifically use a ncAA and do not interact with the cell's natural translation apparatus). Here, we show that evolving and tuning expression levels of multiple components of an engineered translation system together as a whole enhances ncAA incorporation efficiency. Specifically, we increase protein yield when incorporating multiple p‐azido‐phenylalanine(pAzF) residues into proteins by (i) evolving the Methanocaldococcus jannaschii p‐azido‐phenylalanyl‐tRNA synthetase anti‐codon binding domain, (ii) evolving the elongation factor Tu amino acid‐binding pocket, and (iii) tuning the expression of evolved translation machinery components in a single vector. Use of the evolved translation machinery in a genomically recoded organism lacking release factor one enabled enhanced multi‐site ncAA incorporation into proteins. We anticipate that our approach to orthogonal translation system development will accelerate and expand our ability to site‐specifically incorporate multiple ncAAs into proteins and biopolymers, advancing new horizons for synthetic and chemical biotechnology. Biotechnol. Bioeng. 2017;114: 1074–1086. © 2016 Wiley Periodicals, Inc.
Responses to romidepsin by line of therapy in patients with relapsed or refractory peripheral T‐cell lymphoma
Authors: Foss Francine , Pro Barbara , Miles Prince H. , Sokol Lubomir , Caballero Dolores , Horwitz Steven , Coiffier Bertrand 
Published: December 2016

AbstractPeripheral T‐cell lymphoma (PTCL) is a heterogeneous group of aggressive non‐Hodgkin lymphomas typically associated with poor prognosis. Most patients with PTCL receive chemotherapy as first‐line treatment, but many experience rapid relapse. For patients with relapsed/refractory PTCL, responses to treatment and long‐term outcomes tend to worsen with increasing lines of therapy. Romidepsin is a potent class I histone deacetylase inhibitor approved by the US Food and Drug Administration for the treatment of PTCL in patients who have received ≥1 prior therapy. A pivotal phase 2 trial of romidepsin in patients with relapsed/refractory PTCL demonstrated an objective response rate of 25% (33/130), including 15% with confirmed/unconfirmed complete response, and a median duration of response of 28 months. In the analysis presented herein, romidepsin was shown to have similar responses and long‐term outcomes in patients with 1, 2, and ≥3 prior lines of treatment, including in patients with disease refractory to the last prior therapy. Although adverse events increased with increasing lines of treatment, the rate of dose modifications and discontinuations due to adverse events was not significantly different. These data support the use of romidepsin as salvage treatment for PTCL irrespective of the number of prior therapies.