bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recent advances of application of porous molecular cages for enantioselective recognition and separation
Authors: Zhang Jun‐Hui , Xie Sheng‐Ming , Zi Min , Yuan Li‐Ming 
Published: October 2019

AbstractPorous materials with well‐defined pore structures have received considerable attention in the past decades due to their unique structures and wide applications. Most porous materials such as zeolites, metal‐organic frameworks, covalent organic frameworks, and porous organic polymers are extended to infinite frameworks or networks by robust covalent or coordination bonds. Porous molecular cages composed of discrete molecules with permanent cavities are an emerging class of porous material and the discrete molecules assemble into solids by weak intermolecular interaction. In comparison to porous extended solids such as metal‐organic frameworks and covalent organic frameworks, porous molecular cage solids are generally soluble in organic solvents thus allowing solution processing, making them more convenient to apply in many fields. This review mainly focuses on the recent advances of application of porous molecular cages (porous organic cages and metal‐organic cages) for enantioselective recognition and separation from 2010 to present, including gas chromatography, capillary electrochromatography, chiral fluorescent recognition, chiral potentiometric sensing, and enantioselective adsorption. Furthermore, the two important family members of porous molecular cages, porous organic cages and metal‐organic cages, are also discussed.
Recent advances in sample preparation techniques in China
Authors: Xia Ling , Li Yanxia , Liu Yulan , Li Gongke , Xiao Xiaohua 
Published: October 2019

AbstractSample preparation is the procedure before instrumental analysis and significant to its effectiveness and efficiency. However, this procedure is usually time‐consuming, labor intensive, and prone to error. In the last decade, the development of sample preparation techniques has received increasing attention, especially in complex sample application. To pretreat samples faster and more effectively, advanced materials, instrumentation, and methods have been combined with typical techniques, including extraction, membrane separation, and chemical conversion techniques. Researchers in China focused on the development of simple, efficient sample preparation methods with selective enrichment and rapid separation capabilities for target analysis in complicated sample matrix and contribute almost a half of the publications in this specific field. In this review, a panorama of sample preparation techniques in China has been composed from more than 140 references, and we highlight some promising methods developed during recent years and introduce different separation materials with respect to these methods.
Extending the power transform approach for recovering areas of overlapping peaks
Authors: Wahab M. Farooq , Berthod Alain , Armstrong Daniel W. 
Published: October 2019

AbstractPower functions, , are embedded in some modern chromatography detectors and software which not only alter the linear dynamic range of such detectors but also improve the cosmetic aspects of the chromatograms. These aspects include a reduction in baseline noise, improved peak symmetry, and better resolution. However, after raising the electronic output of a detector to a selected power (n > 1), the original peak area information is lost as are very small peaks. Recent advances in the peak processing protocol allow us to recover peak areas from overlapping peak areas, even in noisy environments using power functions. One of the primary protocol requirements of this approach was to have resolution factors ≥0.9. An increasing positive bias in the recovered area was observed as the resolution factors decreased below 0.9. In this work, we extend the capabilities of power function to lower resolution values. This bias is addressed by considering the increasing contributions in peak height coming from adjacent peaks. It is shown that the power function can now be used as long as the peak maxima are visible, making = 0.5, the lower treatable resolution factor for two peaks of similar areas.
Alternative splicing of VEGFA is regulated by RBM10 in endometrial cancer
Authors: Dou Xiao‐Qing , Chen Xiu‐Juan , Wen Ming‐Xiao , Zhang Shu‐Zhen , Zhou Qun , Zhang Shi‐Qian 
Published: October 2019

AbstractVascular endothelial growth factor A (VEGFA) gene has three alternative exons which results in multiple isoforms. VEGFA has been found overexpressed in patients with endometrial cancer, but the VEGFA expression pattern and how it is regulated are still unknown. The level of VEGFA transcripts and protein isoforms were detected by semi‐quantitative Polymerase chain reaction (PCR) and immunoblotting in 29 paired endometrial tumor and adjacent nontumor control tissues. The level of three alternative splicing related proteins: RBM5, RBM6, and RBM10 was determined by immunoblotting. The H3K27Ac level in RBM10 promoter region was detected by ChIP‐PCR. The RBM10 promoter region methylation level were quantified by methylation‐sensitive high resolution melting. VEGFA165a was overexpressed and VEGFA165b level was reduced in tumors. RBM10 level was reduced in tumors. RBM10 level was negatively correlated with VEGFA165a level and positively correlated with VEGFA165b level in tumors. Using HEC‐1‐A and RL95‐2 cells, we confirmed that VEGFA165a/b expressed pattern was controlled by RBM10. MALAT1 level was increased in tumors but not involved in VEGFA alternative splicing. Reduced H3K27Ac level and increased DNA methylation in the promoter region controlled RBM10 expression in tumors. VEGFA alternative splicing in endometrial cancer was regulated by RBM10, the expression of which was controlled by histone acetylation and DNA methylation.
Helium Plasma Skin Regeneration: Evaluation of Skin Tissue Effects in a Porcine Model and Comparison to Nitrogen Plasma Skin Regeneration
Authors: Holcomb J. David , Schucker Adrienne 
Published: October 2019

Background and ObjectivesHelium plasma skin regeneration (PSR) is a novel skin rejuvenation technology with significant differences compared with nitrogen PSR technology but that may exert similar skin tissue effects. Study objectives included a comparison of acute and chronic skin tissue changes among the two plasmas in a porcine animal model.Study Design/Materials and MethodsIn this study, both helium and nitrogen gas plasmas were used to treat the dorsal skin of Yorkshire cross mini pigs with 20% (8.6 J/cm2) and 40% (17.8 J/cm2) power helium plasma single pass treatment (4 liter gas flow, continuous energy delivery, and linear non‐overlapping passes) compared with high energy nitrogen plasma double pass treatment (PSR3 @ 14.1 J/cm2: 4.0 J, 2.5 Hz pulse rate, overlapping horizontal, and vertical passes). Acute and chronic skin contraction, maximum acute depth of injury and chronic reparative healing depth were assessed along with representative histopathology in each treatment paradigm.ResultsHigh‐energy nitrogen plasma treatment exhibited greatest mean depth of acute tissue injury 4 hours post‐treatment whereas helium plasma treatment exhibited greater acute skin tissue contraction. Then, 20% and 40% power helium plasma treatment results were each very similar among animals as a percentage of nitrogen plasma treatment results for both depths of acute tissue injury and acute skin tissue contraction. Mean depths of reparative tissue healing were similar among treatment paradigms 30 days after treatment with significant intra‐ and inter‐animal variability observed within each treatment paradigm. Thirty‐day mean skin tissue contraction was greater for helium plasma treatment; however, the data varied significantly between animals in all paradigms. Histopathologic tissue evaluation after 30 days showed similar findings among the treatment paradigms with epidermal hyperplasia, flattening of rete ridges and with regenerative granulation tissue expanding the superficial and papillary dermis.ConclusionsThis study demonstrates modestly reduced depth of the thermal effect, greater skin tissue contraction and similarity of acute and chronic histopathological findings for helium plasma when compared with nitrogen plasma in a porcine animal model. © 2019 The Authors. Lasers in Surgery and Medicine published by Wiley Periodicals, Inc.
An Optical Surface Applicator for Intraoperative Photodynamic Therapy
Authors: Chamberlain Sarah , Bellnier David , Yendamuri Sai , Lindenmann Joerg , Demmy Todd , Nwogu Chukwumere , Ramer Max , Tworek Larry , Oakley Emily , Mallory Matthew , Carlsen Lindsey , Sexton Sandra , Curtin Leslie , Shafirstein Gal 
Published: October 2019

Background and ObjectivesIntraoperative photodynamic therapy (IO‐PDT) is typically administered by a handheld light source. This can result in uncontrolled distribution of light irradiance that impacts tissue and tumor response to photodynamic therapy. The objective of this work was to characterize a novel optical surface applicator (OSA) designed to administer controlled light irradiance in IO‐PDT.Study Design/Materials and MethodsAn OSA was constructed from a flexible silicone mesh applicator with multiple cylindrically diffusing optical fibers (CDF) placed into channels of the silicone. Light irradiance distribution, at 665 nm, was evaluated on the OSA surface and after passage through solid tissue‐mimicking optical phantoms by measurements from a multi‐channel dosimetry system. As a proof of concept, the light administration of the OSA was tested in a pilot study by conducting a feasibility and performance test with 665‐nm laser light to activate 2‐(1′‐hexyloxyethyl) pyropheophorbide‐a (HPPH) in the thoracic cavity of adult swine.ResultsAt the OSA surface, the irradiance distribution was non‐uniform, ranging from 128 to 346 mW/cm2. However, in the tissue‐mimicking phantoms, beam uniformity improved markedly, with irradiance ranges of 39–153, 33–87, and 12–28 mW/cm2 measured at phantom thicknesses of 3, 5, and 10 mm, respectively. The OSA safely delivered the prescribed light dose to the thoracic cavities of four swine.ConclusionsThe OSA can provide predictable light irradiances for administering a well‐defined and potentially effective therapeutic light in IO‐PDT. Lasers Surg. Med. © 2019 Wiley Periodicals, Inc.
Parameterizing the seasonal–diurnal wind climate of Rome: Fiumicino and Ciampino
Authors: Cook Nicholas J. 
Published: October 2019

AbstractThis study uses the Offset Elliptical Normal (OEN) mixture model to parameterize the seasonal–diurnal wind climate of Rome, Italy, for engineering design purposes, and also to reveal the physical meteorology of this “mixed” wind climate. The joint probability density function (PDF) of the wind vectors in the zonal–meridional plane are represented by a mixture of disjoint bivariate‐Normal ellipses. Each OEN ellipse is tentatively attributed to a physical wind mechanism: sea/land breezes; transient coastal jets; katabatic flows; the migrating atmospheric tide; and (non‐diurnal) geostrophic winds. The model enables a fuzzy probability of each wind mechanism to be assigned to each observation, allowing the progression of the various diurnal cycles to be tracked through time. This seasonal–diurnal parametric model is directly applicable to wind energy resource estimation, pollution studies, pedestrian comfort, and heating and ventilation design. The model is also an essential starting point in methods to simulate realistic time series of wind speed and direction.
A theoretical investigation of erbium‐doped fiber laser as a function of ion‐clustering, temperature, pumping wavelength, and configuration
Authors: Kabir Md. Aminul , Hossain Md. Mahbub , Amin Md. Ziaul , Ahsan Md. Shamim 
Published: October 2019

AbstractThe lasing performance of an erbium‐doped fiber laser (EDFL) is affected by several factors such as doping concentrations, erbium‐ion clustering, pumping wavelength, pumping configuration, and temperature. In this article, the performance of an EDFL has been investigated as a function of erbium‐ion clustering, pumping wavelength, pumping configuration, and temperature. In our investigation, we have found that power degradation, which happens due to ion‐clustering, at around 1530 nm is less affected for 980 nm pumping than for 1480 nm pumping. Moreover, a wider tuning range is achieved for 980 nm pumping than 1480 nm pumping. Our simulation results also show that the forward pumping configuration is suitable for a wider tuning range. To our best knowledge, pumping wavelength and configuration effects on an EDFL performance have not been investigated yet. We have also investigated the temperature effects on an EDFL performance and found little influence on lasing performance, at least within 30°C to 80°C.
CT and MRI compatibility of flexible 3D‐printed materials for soft actuators and robots used in image‐guided interventions
Authors: Neumann Wiebke , Pusch Tim P. , Siegfarth Marius , Schad Lothar R. , Stallkamp Jan L. 
Published: October 2019

PurposeThree‐dimensional (3D) printing allows for the fabrication of medical devices with complex geometries, such as soft actuators and robots that can be used in image‐guided interventions. This study investigates flexible and rigid 3D‐printing materials in terms of their impact on multimodal medical imaging.MethodsThe generation of artifacts in clinical computer tomography (CT) and magnetic resonance (MR) imaging was evaluated for six flexible and three rigid materials, each with a cubical and a cylindrical geometry, and for one exemplary flexible fluidic actuator. Additionally, CT Hounsfield units (HU) were quantified for various parameter sets iterating peak voltage, x‐ray tube current, slice thickness, and convolution kernel.ResultsWe found the image artifacts caused by the materials to be negligible in both CT and MR images. The HU values mainly depended on the elemental composition of the materials and applied peak voltage was ranging between 80 and 140 kVp. Flexible, nonsilicone‐based materials were ranged between 51 and 114 HU. The voltage dependency was less than 29 HU. Flexible, silicone‐based materials were ranged between 60 and 365 HU. The voltage‐dependent influence was as large as 172 HU. Rigid materials ranged between −69 and 132 HU. The voltage‐dependent influence was <33 HU.ConclusionsAll tested materials may be employed for devices placed in the field of view during CT and MR imaging as no significant artifacts were measured. Moreover, the material selection in CT could be based on the desired visibility of the material depending on the application. Given the wide availability of the tested materials, we expect our results to have a positive impact on the development of devices and robots for image‐guided interventions.
Nonconforming quadrilateral finite element method for Ginzburg–Landau equation
Authors: Shi Dongyang , Liu Qian 
Published: October 2019

AbstractNonconforming finite element method is studied for a linearized backward fully‐discrete scheme of the Ginzburg–Landau equation with the quadrilateral element. The unconditional convergent result of order O(h + τ) in the broken H1‐norm is deduced rigorously based on a splitting technique, by which the ratio between the subdivision parameter h and the time step τ is removed. Furthermore, numerical results are provided to confirm the theoretical analysis. The analysis developed herein can be regarded as a framework to deal with the unconditional convergent analysis of the Ginzburg–Landau equation for other known low order nonconforming elements.
Impact of early caffeine therapy in preterm newborns on infant lung function
Authors: Sanchez‐Solis Manuel , Garcia‐Marcos Patricia W. , Agüera‐Arenas Juan , Mondejar‐Lopez Pedro , Garcia‐Marcos Luis 
Published: October 2019

AbstractObjectiveTo know the effect of caffeine therapy on infant lung function in preterm infants with a gestational age less than 31 weeks.Material and MethodsForced vital capacity (FVC), forced expiratory volume at 0.5 seconds (FEV0.5), and forced expiratory flows were measured by raised volume rapid thoracoabdominal compression technique; functional residual capacity was measured by plethysmography (FRCpleth). Compliance of the respiratory system was measured by a single interruption technique (Crs). The Student t test was used to compare lung function measurements between the two groups: treated versus nontreated with caffeine. A multivariate analysis was carried out considering each and every lung function parameter (z‐score) as the dependent variable; and gender, gestational age, birth weight (z‐score), corrected age, invasive mechanical ventilation (yes/no), and bronchopulmonary dysplasia (BPD) diagnosis (yes/no) as independent ones. Additionally, stratified analyses by BPD diagnosis were performed.ResultsThe multivariate analysis showed significant higher z‐scores of FVC and FEV0.5 in preterm infants treated with caffeine (P = .004 and P = .024, respectively). This result only being significant in the group of non‐BPD infants (P = .021 and P = .042), after stratifying by BPD diagnosis. Differences were not found in z‐scores of FEV0.5/FVC, FEF75, FEF25‐75, FRCpleth, nor Crs.ConclusionLung function (FVC and FEV0.5) is improved in infants born under 31 weeks of gestation when treated with caffeine. This improvement is driven by the group of infants who did not suffer from BPD. Overall, our results show that there is an early beneficial effect of caffeine treatment in infant lung function
In silico design and molecular basis for the selectivity of Olinone toward the first over the second bromodomain of BRD4
Authors: Rodríguez Yoel , Gerona‐Navarro Guillermo , Osman Roman , Zhou Ming‐Ming 
Published: October 2019

AbstractBromodomains (BrDs), a conserved structural module in chromatin‐associated proteins, are well known for recognizing ε‐N‐acetyl lysine residues on histones. One of the most relevant BrDs is BRD4, a tandem BrD containing protein (BrD1 and BrD2) that plays a critical role in numerous diseases including cancer. Growing evidence shows that the two BrDs of BRD4 have different biological functions; hence selective ligands that can be used to study their functions are of great interest. Here, as a follow‐up of our previous work, we first provide a detailed characterization study of the in silico rational design of Olinone as part of a series of five tetrahydropyrido indole‐based compounds as BRD4 BrD1 inhibitors. Additionally, we investigated the molecular basis for Olinone's selective recognition by BrD1 over BrD2. Molecular dynamics simulations, free energy calculations, and conformational analyses of the apo‐BRD4‐BrD1|2 and BRD4‐BrD1|2/Olinone complexes showed that Olinone's selectivity is facilitated by five key residues: Leu92 in BrD1|385 in BrD2 of ZA loop, Asn140|433, Asp144|His437 and Asp145|Glu438 of BC loop, and Ile146|Val49 of helix C. Furthermore, the difference in hydrogen bonds number and in mobility of the ZA and BC loops of the acetyl‐lysine binding site between BRD4 BrD1/Olinone and BrD2/Olinone complexes also contribute to the difference in Olinone's binding affinity and selectivity toward BrD1 over BrD2. Altogether, our computer‐aided molecular design techniques can effectively guide the development of small‐molecule BRD4 BrD1 inhibitors, explain their selectivity origin, and further open doors to the design of new therapeutically improved derivatives.
Assessing the accuracy of contact predictions in CASP13
Authors: Shrestha Rojan , Fajardo Eduardo , Gil Nelson , Fidelis Krzysztof , Kryshtafovych Andriy , Monastyrskyy Bohdan , Fiser Andras 
Published: October 2019

AbstractThe accuracy of sequence‐based tertiary contact predictions was assessed in a blind prediction experiment at the CASP13 meeting. After 4 years of significant improvements in prediction accuracy, another dramatic advance has taken place since CASP12 was held 2 years ago. The precision of predicting the top L/5 contacts in the free modeling category, where L is the corresponding length of the protein in residues, has exceeded 70%. As a comparison, the best‐performing group at CASP12 with a 47% precision would have finished below the top 1/3 of the CASP13 groups. Extensively trained deep neural network approaches dominate the top performing algorithms, which appear to efficiently integrate information on coevolving residues and interacting fragments or possibly utilize memories of sequence similarities and sometimes can deliver accurate results even in the absence of virtually any target specific evolutionary information. If the current performance is evaluated by F‐score on L contacts, it stands around 24% right now, which, despite the tremendous impact and advance in improving its utility for structure modeling, also suggests that there is much room left for further improvement.
Delineation of a new structural motif involving NHN γ‐turn
Authors: Dhar Jesmita , Kishore Raghuvansh , Chakrabarti Pinak 
Published: October 2019

AbstractMacromolecules are characterized by distinctive arrangement of hydrogen bonds. Different patterns of hydrogen bonds give rise to distinct and stable structural motifs. An analysis of 4114 non‐redundant protein chains reveals the existence of a three‐residue, (i − 1) to (i + 1), structural motif, having two hydrogen‐bonded five‐membered pseudo rings (the first, an NH···OC involving the first residue, and the second being NH∙∙∙N involving the last two residues), separated by a peptide bond. There could be an additional hydrogen bond between the side‐chain at (i‐1) and the main‐chain NH of (i + 1). The average backbone torsion angles of −76(±21)° and – 12(±17)° at i creates a tight turn in the polypeptide chain, akin to a γ‐turn. Indeed, a search of three‐residue fragments with restriction on the terminal Cα···Cα distance and the existence of the two pseudo rings on either side revealed the presence 14 846 cases of a variant, termed NHN γ‐turn, distinct from the NHO γ‐turn (2032 cases) that has traditionally been characterized by the presence of NHO hydrogen bond linking the terminal main‐chain atoms. As in the latter, the newly identified γ‐turns are also of two types—classical and inverse, occurring in the ratio of 1:6. The propensities of residues to occur in these turns and their secondary structural features have been enumerated. An understanding of these turns would be useful for structure prediction and loop modeling, and may serve as models to represent some of the unfolded state or disordered region in proteins.