bluuebunny/crossref_metadata_2025 huggingface dataset:
Nosology and classification of genetic skeletal disorders: 2019 revision
Authors: Mortier Geert R. , Cohn Daniel H. , Cormier‐Daire Valerie , Hall Christine , Krakow Deborah , Mundlos Stefan , Nishimura Gen , Robertson Stephen , Sangiorgi Luca , Savarirayan Ravi , Sillence David , Superti‐Furga Andrea , Unger Sheila , Warman Matthew L.
Published: October 2019

The application of massively parallel sequencing technology to the field of skeletal disorders has boosted the discovery of the underlying genetic defect for many of these diseases. It has also resulted in the delineation of new clinical entities and the identification of genes and pathways that had not previously been associated with skeletal disorders. These rapid advances have prompted the Nosology Committee of the International Skeletal Dysplasia Society to revise and update the last (2015) version of the Nosology and Classification of Genetic Skeletal Disorders. This newest and tenth version of the Nosology comprises 461 different diseases that are classified into 42 groups based on their clinical, radiographic, and/or molecular phenotypes. Remarkably, pathogenic variants affecting 437 different genes have been found in 425/461 (92%) of these disorders. By providing a reference list of recognized entities and their causal genes, the Nosology should help clinicians achieve accurate diagnoses for their patients and help scientists advance research in skeletal biology.
Detecting riparian habitat preferences in “savanna” chimpanzees and associated Fauna with strontium isotope ratios: Implications for reconstructing habitat use by the chimpanzee‐human last common ancestor
Authors: Hamilton Marian , Nelson Sherry V. , Fernandez Diego P. , Hunt Kevin D.
Published: October 2019

Objectives

Riparian or gallery forests are critical habitats for numerous plants and animals today. Paleoanthropologically, reliance on such habitats informs behavioral and ecological reconstructions; for example, gallery forest habitats likely played a critical role in the transition from ape to hominin in the early Pliocene and may represent a preferred habitat for the last common ancestor of chimpanzees and humans. Direct indicators for gallery forest habitats preference are lacking. The objective of this article is to assess whether strontium isotope ratios are a reliable indicator of habitat preference for fauna living in and around gallery forests.

Materials and methods

We report bioavailable strontium isotope ratios from the Mugiri River, its tributaries, and its gallery forest (Toro‐Semliki Wildlife Reserve, southwestern Uganda), and compare them to surrounding savanna‐grassland values. We compare these environmental values to strontium isotopes ratios in faunal tooth enamel to determine if habitat preferences are accurately reflected.

Results

Gallery forest and savanna‐grassland vegetations have significantly different strontium isotope ratio profiles. We trace these isotopic differences to the influence of the Mugiri tributaries, which originate on Paleoproterozoic gneiss deposits on top of the surrounding escarpments. These isotopic differences in vegetation are mirrored in the tissues of fauna with habitat preferences for either the gallery forest or the surrounding grasslands.

Discussion

This research demonstrates the potential of strontium isotope ratios to identify habitat preferences in modern or fossil fauna under proper geologic variability. It provides a methodological model for future studies seeking to reconstruct habitat preferences in early hominins.
Population history of southern Italy during Greek colonization inferred from dental remains
Authors: Rathmann Hannes , Kyle Britney , Nikita Efthymia , Harvati Katerina , Saltini Semerari Giulia
Published: October 2019

Objectives

We are testing competing scenarios regarding the population history of the ancient Greek colonization of southern Italy using dental phenotypic evidence.

Materials and Methods

We collected dental metric and nonmetric trait data for 481 human skeletons from six archaeological sites along the Gulf of Taranto, dating to pre‐colonial (900–700 BC) and post‐colonial periods (700–200 BC). We are evaluating scenarios through an individual‐level biodistance analysis using a three‐pronged approach: (a) by analyzing levels of mobility in pre‐ and post‐colonial periods under a model of isolation‐by‐distance; (b) by quantifying differences in group means and variances in pre‐ and post‐colonial periods utilizing permutational multivariate analysis of variance and Betadisper analyses; and (c) by identifying ancestries of post‐colonial individuals using naïve Bayes classification.

Results

Southern Italy during pre‐colonial times was characterized by low levels of mobility and marked differences in group means and variances. During post‐colonial times, mobility increased and there were no differences in group means and variances. About 18% of the people in post‐colonial times were of Greek ancestry and lived equally distributed across Greek colonies and indigenous villages. Nevertheless, the overall biological composition and variability of southern Italy remained relatively unchanged across pre‐ and post‐colonial periods.

Discussion

Our results support a scenario in which only few Greek colonists migrated to southern Italy and lived in smaller numbers alongside indigenous people in Greek colonies as well as in indigenous villages. Our results contradict a scenario in which large numbers of Greek invaders founded biologically isolated and substantially homogeneous colonial enclaves within conquered territories.
Robotic surgery of the anterior skull base
Authors: Campbell Raewyn G.
Published: October 2019

Background

Significant advances have been made in transoral robotic surgery (TORS), yet its application in anterior skull‐base surgery has yet to be defined. This work explores the history of endoscopic sinus and anterior skull‐base surgery, and its advantages and disadvantages. The development of robotic surgery is then discussed as well as the advantages and disadvantages of TORS as it relates to the anterior skull base. The current applications for robotic surgery to the anterior skull base are presented with details of future applications.

Methods

A structured search of the current literature using MEDLINE, PubMed, and EMBASE was performed from inception to May 2019. Search terms related to topics of robotic skull‐base surgery were identified and queried to identify relevant articles.

Results

Fifty‐four papers were identified from the literature search and a hand search of the references. Twenty‐one other references were discovered from personal communication, websites, and books relevant to the topic.

Conclusion

Anterior skull‐base surgery has the potential for significant morbidity compared to head and neck surgery, yet the application of the robot in sinus and anterior skull‐base surgery has yet to be formally defined. Currently, there are certain limitations that need to be overcome; however, research to address these barriers is currently underway and promises an exciting future for robotic sinus and anterior skull‐base surgery.
Thermally Driven Structure and Performance Evolution of Atomically Dispersed FeN4 Sites for Oxygen Reduction
Authors: Li Jiazhan , Zhang Hanguang , Samarakoon Widitha , Shan Weitao , Cullen David A. , Karakalos Stavros , Chen Mengjie , Gu Daming , More Karren L. , Wang Guofeng , Feng Zhenxing , Wang Zhenbo , Wu Gang
Published: October 2019

FeN4 moieties embedded in partially graphitized carbon are the most efficient platinum group metal free active sites for the oxygen reduction reaction in acidic proton‐exchange membrane fuel cells. However, their formation mechanisms have remained elusive for decades because the Fe−N bond formation process always convolutes with uncontrolled carbonization and nitrogen doping during high‐temperature treatment. Here, we elucidate the FeN4 site formation mechanisms through hosting Fe ions into a nitrogen‐doped carbon followed by a controlled thermal activation. Among the studied hosts, the ZIF‐8‐derived nitrogen‐doped carbon is an ideal model with well‐defined nitrogen doping and porosity. This approach is able to deconvolute Fe−N bond formation from complex carbonization and nitrogen doping, which correlates Fe−N bond properties with the activity and stability of FeN4 sites as a function of the thermal activation temperature.
A New Dimension for Coordination Polymers and Metal–Organic Frameworks: Towards Functional Glasses and Liquids
Authors: Horike Satoshi , Nagarkar Sanjog S. , Ogawa Tomohiro , Kitagawa Susumu
Published: October 2019

There are two categories of coordination polymers (CPs): inorganic CPs (i‐CPs) and organic ligand bridged CPs (o‐CPs). Based on the successful crystal engineering of CPs, we here propose noncrystalline states and functionalities as a new research direction for CPs. Control over the liquid or glassy states in materials is essential to obtain specific properties and functions. Several studies suggest the feasibility of obtaining liquid/glassy states in o‐CPs by design principles. The combination of metal ions and organic bridging ligands, together with the liquid/glass phase transformation, offer the possibility to transform o‐CPs into ionic liquids and other ionic soft materials. Synchrotron measurements and computational approaches contribute to elucidating the structures and dynamics of the liquid/glassy states of o‐CPs. This offers the opportunity to tune the porosity, conductivity, transparency, and other material properties. The unique energy landscape of liquid/glass o‐CPs offers opportunities for properties and functions that are complementary to those of the crystalline state.
A Simplified Method for Fractionation and Analysis of Waxes and Oils from Sorghum (Sorghum bicolor (L.) Moench) Bran
Authors: Hums Megan E. , Moreau Robert A.
Published: October 2019

In the United States, sorghum is primarily used for animal feed and ethanol production but has potential to provide value‐added coproducts including waxes and oil. The surface of sorghum contains 0.1–0.4% wax; however, wax extraction from whole kernels before fermentation may not be economical. An alternative method for this extraction could be facilitated through decortication, abrasion of the surface to remove bran. Decortication increases the starch content of decorticated sorghum, potentially improving ethanol yields, while concentrating wax and oil to the bran. Typically, oil (triacylglycerols) and waxes are extracted from bran in one extraction and waxes are precipitated from oil using cold temperatures then filtration. This research compared traditional fractionation (simulated with a two‐step, single‐temperature extraction) to a two‐step, dual‐temperature extraction, whereby oil is first extracted at room temperature and then waxes at elevated temperature. Extractions were performed using an accelerated solvent extractor with hexane or ethanol as solvents. Ethanol extraction showed greater yields (~15% w/w) compared to those of hexane (~11% w/w) because polar materials were extracted. Using hexane, the two‐step, dual‐temperature fractionation separated waxes from oils via the temperature of extraction solvent with similar purity to the traditional method that fractionated via cold precipitation and filtration. For ethanol, the traditional single‐step method fractionated with higher wax purity but lower oil purity compared to the two‐step, dual‐temperature fractionation.
Enhancing flame retardance of epoxy resin by incorporation into ammonium polyphosphate/boron nitride nanosheets/zinc ferrite three‐dimensional porous aerogel via vacuum‐assisted infiltration
Authors: Zhang Qiaoran , Zhang Mengmeng , Shi Huili , Li Zhiwei , Yu Laigui , Li Xiaohong , Zhang Zhijun , Wu Zhishen
Published: October 2019

Boron nitride nanosheets (BNNSs) were combined with ammonium polyphosphate (APP) and zinc ferrite (ZF) nanoparticle to prepare APP/BNNS/ZF composite aerogels via a freeze‐drying method. Then, epoxy resin (EP) was incorporated into the pores of the as‐obtained aerogels via a vacuum‐assisted infiltration method to afford APP/BNNS/ZF‐EP composites with greatly improved fire resistance. The flame‐retardant performance of the as‐prepared composites was evaluated by cone calorimetry test; and the flame‐retardant mechanism of the aerogels was discussed in relation to thermogravimetric‐infrared analysis of the pyrolysis products. Findings demonstrate that the APP/BNNS/ZF‐EP composite containing 24.0 wt % of the APP/BNNS/ZF aerogel exhibits superior flame‐retardant performance; and its peak heat release rate and total heat release are reduced by 86.2 and 86.5% as compared with those of pristine EP. The reason lies in that APP can be decomposed in the early stage of burning to generate phosphoric acid, thereby promoting the formation of char layer; ZF can catalyze the charring process; and BNNS can act as the physical barrier to retard the burning of EP. In addition, the APP10/BNNS1/ZF0.1‐EP composite can be endowed with superhydrophobicity via the modification of polydimethylsiloxane and hydrophobic nanosilica, which could contribute to broadening its scope of application. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2020, 137, 48609.

Highlights

Flame‐retardant APP/BNNS/ZF aerogels were prepared by a freeze‐drying method.

APP/BNNS/ZF‐EP composites were obtained via a vacuum‐assisted infiltration method.

The pHRR of composites are reduced by 86.2% as compared with that of pristine EP.

The EP composites exhibit excellent flame retardancy and superhydrophobicity.
Low‐defect graphene–polyamide‐6 composites and modeling the filler–matrix interface
Authors: Lee Kok Peng Marcian , Czajka Michael , Shanks Robert , Daver Fugen
Published: October 2019

Low‐defect graphene (G) was prepared via the thermal reduction of expanded graphite in a carbon monoxide environment. G exfoliated and suspended in p‐xylene was compounded in polyamide‐6 (PA6) with filler content ranging from 0.1 to 6%·w/w. Interactions between G and PA6 were characterized via Fourier‐transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and scanning electron microscopy (SEM). Elastic modulus (E)had increased with increasing G content, and had exceeded idealized Halpin–Tsai predictions at 0.1–1.0%·w/w G content, indicating good dispersion and filler–matrix interactions. However, further analysis with a modified rule‐of‐mixtures (RoM) mathematical model indicate that the quality of filler–matrix interface had been suboptimal and had deteriorated drastically with increasing G content. The evaluation of interface quality is in agreement with observed changes in thermal behavior trends. The modified RoM can be applied as a useful tool toward interpreting the mechanical properties of graphene‐reinforced composites. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci.2020,137, 48630.
Arginolipid: A membrane‐active antifungal agent and its synergistic potential to combat drug resistance in clinical Candida isolates
Authors: Patil Mrunal , Wanjare Shashir , Borse Vivek , Srivastava Rohit , Mehta Preeti , Vavia Pradeep
Published: October 2019

Antifungal drug resistance exhibits a major clinical challenge for treating nosocomial fungal infections. To find a possible solution, we synthesized and studied the antifungal activities of three different arginolipids (Nα‐acyl‐arginine ethyl ester) against clinical drug‐resistant isolates of Candida. The most active arginolipid, oleoyl arginine ethyl ester (OAEE) consisting of a long unsaturated hydrophobic chain, was tested for its mode of action, which revealed that it altered ergosterol biosynthesis and compromised the fungal cell membrane. Also, OAEE was found to exhibit synergistic interactions with fluconazole (FLU) or amphotericin B (AmB) against planktonic Candida cells, wherein it reduced the inhibitory concentrations of these drugs to their in vitro susceptible range. Studies conducted against the C. tropicalis biofilm revealed that the OAEE+AmB combination synergistically reduced the metabolic activity and hyphal density in biofilms, whereas OAEE+FLU was found to be additive against most cases. Finally, the evaluated selective toxicity of OAEE toward fungal cells over mammalian cells could establish it as an alternative treatment for combating drug‐resistant Candida infections.
Understanding task preparation and resumption behaviors in cross‐device search
Authors: Wu Dan , Dong Jing , Tang Yuan , Capra Rob
Published: October 2019

It is now common for individuals to have multiple computing devices, such as laptops, smart phones, and tablets. This multidevice environment increases the popularity of cross‐device search activities. Cross‐device search can be seen as a special case of cross‐session search. Previous studies regarded re‐finding behaviors in cross‐session search as task resumption. Based on this, this article proposes considering 2 phases of cross‐device search: task preparation and task resumption and to explore their features by modeling. A within‐subject user experiment was designed to collect data. Four groups of features were captured from specific behaviors of querying, clicking, gazing, and cognition. This article tested 3 machine‐learning methods and found that the C5.0 decision tree performed best. Five features were included in the task preparation behavior model, and 3 in the task resumption behavior model. The difference and relationship between task preparation and task resumption were investigated by comparing their behavioral features. It is concluded that information need remains blurred in task preparation and becomes clear in task resumption. The changing states of information need suggest an exploratory process in cross‐device search. We also identify some implications for search engine designers.
Green synthesis and physiochemical characterization of nickel oxide nanoparticles: Interaction studies with Calf thymus DNA
Authors: Sarkar Niloy , Sharma Radhey Shyam , Kaushik Mahima
Published: October 2019

One of the most promising applications of nanomaterials is that of nanobiosensors, using biomolecules such as nucleic acids as receptors. This study aimed to synthesize nickel oxide nanoparticles (NiO NPs) by an environmentally friendly green synthesis, using the extract of the herb Coriandrum sativum (coriander). The synthesized NPs were characterized using UV–Visible spectroscopy, Fourier transform infrared spectroscopy, X‐ray diffraction, X‐ray photon spectroscopy, field emission scanning electron microscopy coupled with energy dispersive spectroscopy, dynamic light scattering, zeta potential and transmission electron microscopy. All results confirmed the synthesis of pure, spherical, positively charged NiO NPs of around 95 nm in diameter with prominent hydroxyl groups attached to the surface. Furthermore, interaction studies of synthesized NiO NPs with calf thymus DNA (CT DNA) were performed using UV–Visible spectroscopy, UV–thermal melting, circular dichroism, and fluorescence spectroscopy. CT DNA served as a substitute for nucleic acid biosensors. All experimental studies indicated that the NiO NPs bound electrostatically with CT DNA. These studies may facilitate exploring the potential of NiO NP–nucleic acid conjugated materials to be used as nanobiosensors for various applications, especially in pharmacological, epidemiological, and environmental diagnostic applications, and in detection.
Unraveling what makes a monoclonal antibody difficult‐to‐express: From intracellular accumulation to incomplete folding and degradation via ERAD
Authors: Mathias Sven , Wippermann Anna , Raab Nadja , Zeh Nikolas , Handrick René , Gorr Ingo , Schulz Patrick , Fischer Simon , Gamer Martin , Otte Kerstin
Published: October 2019

Although most therapeutic monoclonal antibodies (mAbs) can routinely be produced in the multigram per litre range, some mAb candidates turn out to be difficult‐to‐express (DTE). In addition, the class of more complex biological formats is permanently increasing and mammalian expression systems like Chinese hamster ovary (CHO) cell lines can show low performance. Hence, there is an urgent need to identify any rate limiting processing step during cellular synthesis. Therefore, we assessed the intracellular location of the DTE antibody mAb2 by fluorescence and electron microscopy (EM) and revealed an accumulation of the antibody, which led to an aberrant morphology of the endoplasmic reticulum (ER). Analysis of underlying cellular mechanisms revealed that neither aggregation nor antibody assembly, but folding represented the reason for hampered secretion. We identified that the disulfide bridge formation within the antibody light chain (LC) was impaired due to less recognition by protein disulfide isomerase (PDI). As a consequence, the DTE molecule was degraded intracellularly by the ubiquitin proteasome system via ER‐associated degradation (ERAD). This study revealed that with the continuous emergence of DTE therapeutic protein candidates, special attention needs to be drawn to optimization processes to ensure manufacturability.
Raman spectroscopy as a method to replace off‐line pH during mammalian cell culture processes
Authors: Rafferty Carl , O'Mahony Jim , Burgoyne Barbara , Rea Rosemary , Balss Karin M. , Latshaw David C.
Published: October 2019

Raman spectroscopy is a robust, well‐established tool utilized for measuring important cell culture process variables for example, feed, metabolites, and biomass in real‐time. This study further expands the functionality of in‐line Raman spectroscopy coupled with partial least squares (PLS) regression modelling to develop a pH measurement tool. Cell line specific models were developed to enhance the robustness for processes with different pH setpoints, deadbands, and cellular metabolism. The modelling strategy further improved robustness by reducing the temporal complexity of pH shifts by splitting data sets into two time zones reflective of major changes in pH. In addition, models were developed to assess if lactate and partial pressure of carbon dioxide (pCO2) could be used in a PLS model for pH. Splitting the data sets into early and late for the process resulted in errors of 0.035 pH and 0.034 pH for the two respective Raman cell lines models which was within acceptance criteria. The lactate and pCO2 PLS model with values provided by Raman models had a further 0.001 pH error reduction. This study illustrates the potential to eliminate off‐line samples to correct for in‐line measurements of pH and further illustrates the capabilities of Raman to measure additional process variables.
Awakening dormant glycosyltransferases in CHO cells with CRISPRa
Authors: Karottki Karen Julie la Cour , Hefzi Hooman , Xiong Kai , Shamie Isaac , Hansen Anders Holmgaard , Li Songyuan , Pedersen Lasse Ebdrup , Li Shangzhong , Lee Jae Seong , Lee Gyun Min , Kildegaard Helene Faustrup , Lewis Nathan E.
Published: October 2019

Chinese hamster ovary (CHO) cells are the preferred workhorse for the biopharmaceutical industry, and CRISPR/Cas9 has proven powerful for generating targeted gene perturbations in CHO cells. Here, we expand the CRISPR engineering toolbox with CRISPR activation (CRISPRa) to increase transcription of endogenous genes. We successfully increased transcription of Mgat3 and St6gal1, and verified their activity on a functional level by subsequently detecting that the appropriate glycan structures were produced. This study demonstrates that CRISPRa can make targeted alterations of CHO cells for desired phenotypes.
Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release
Authors: Duroy Pierre‐Olivier , Bosshard Sandra , Schmid‐Siegert Emanuel , Neuenschwander Samuel , Arib Ghislaine , Lemercier Philippe , Masternak Jacqueline , Roesch Lucien , Buron Flavien , Girod Pierre‐Alain , Xenarios Ioannis , Mermod Nicolas
Published: October 2019

The Chinese hamster ovary (CHO) cells used to produce biopharmaceutical proteins are known to contain type‐C endogenous retrovirus (ERV) sequences in their genome and to release retroviral‐like particles. Although evidence for their infectivity is missing, this has raised safety concerns. As the genomic origin of these particles remained unclear, we characterized type‐C ERV elements at the genome, transcriptome, and viral particle RNA levels. We identified 173 type‐C ERV sequences clustering into three functionally conserved groups. Transcripts from one type‐C ERV group were full‐length, with intact open reading frames, and cognate viral genome RNA was loaded into retroviral‐like particles, suggesting that this ERV group may produce functional viruses. CRISPR‐Cas9 genome editing was used to disrupt the gag gene of the expressed type‐C ERV group. Comparison of CRISPR‐derived mutations at the DNA and RNA level led to the identification of a single ERV as the main source of the release of RNA‐loaded viral particles. Clones bearing a Gag loss‐of‐function mutation in this ERV showed a reduction of RNA‐containing viral particle release down to detection limits, without compromising cell growth or therapeutic protein production. Overall, our study provides a strategy to mitigate potential viral particle contaminations resulting from ERVs during biopharmaceutical manufacturing.
Xylose assimilation enhances the production of isobutanol in engineered Saccharomyces cerevisiae
Authors: Lane Stephan , Zhang Yanfei , Yun Eun Ju , Ziolkowski Leah , Zhang Guochang , Jin Yong‐Su , Avalos José L.
Published: October 2019

Bioconversion of xylose—the second most abundant sugar in nature—into high‐value fuels and chemicals by engineered Saccharomyces cerevisiae has been a long‐term goal of the metabolic engineering community. Although most efforts have heavily focused on the production of ethanol by engineered S. cerevisiae, yields and productivities of ethanol produced from xylose have remained inferior as compared with ethanol produced from glucose. However, this entrenched focus on ethanol has concealed the fact that many aspects of xylose metabolism favor the production of nonethanol products. Through reduced overall metabolic flux, a more respiratory nature of consumption, and evading glucose signaling pathways, the bioconversion of xylose can be more amenable to redirecting flux away from ethanol towards the desired target product. In this report, we show that coupling xylose consumption via the oxidoreductive pathway with a mitochondrially‐targeted isobutanol biosynthesis pathway leads to enhanced product yields and titers as compared to cultures utilizing glucose or galactose as a carbon source. Through the optimization of culture conditions, we achieve 2.6 g/L of isobutanol in the fed‐batch flask and bioreactor fermentations. These results suggest that there may be synergistic benefits of coupling xylose assimilation with the production of nonethanol value‐added products.
Development of a robust nitrilase by fragment swapping and semi‐rational design for efficient biosynthesis of pregabalin precursor
Authors: Zhang Qin , Lu Xia‐Feng , Zhang Yan , Tang Xiao‐Ling , Zheng Ren‐Chao , Zheng Yu‐Guo
Published: October 2019

Protein engineering is a powerful tool for improving the properties of enzymes. However, large changes in enzyme properties are still challenging for traditional evolution strategies because they usually require multiple amino acid substitutions. In this study, a feasible evolution approach by a combination of fragment swapping and semi‐rational design was developed for the engineering of nitrilase. A chimera BaNIT harboring 12 amino acid substitutions was obtained using nitrilase from Arabis alpine (AaNIT) and Brassica rapa (BrNIT) as parent enzymes, which exhibited higher enantioselectivity and activity toward isobutylsuccinonitrile for the biosynthesis of pregabalin precursor. The semi‐rational design was executed on BaNIT to further generate variant BaNIT/L223Q/H263D/Q279E with the concurrent improvement of activity, enantioselectivity, and solubility. The robust nitrilase displayed a 5.4‐fold increase in whole‐cell activity and the enantiomeric ratio (E) increased from 180 to higher than 300. Molecular dynamics simulation and molecular docking demonstrated that the substitution of residues on the A and C surface contributed to the conformation alteration of nitrilase, leading to the simultaneous enhancement of enzyme properties. The results obtained not only successfully engineered the nitrilase with great industrial potential for the production of pregabalin precursor, but also provided a new perspective for the development of novel industrially important enzymes.
Engineered Fn3 protein has targeted therapeutic effect on mesothelin‐expressing cancer cells and increases tumor cell sensitivity to chemotherapy
Authors: Sirois Allison R. , Deny Daniela A. , Li Yanxuan , Fall Yacine D. , Moore Sarah J.
Published: October 2019

Mesothelin is a protein expressed at high levels on the cell surface in a variety of cancers, with limited expression in healthy tissues. The presence of mesothelin on tumor tissue correlates with increased invasion and metastasis, and resistance to traditional chemotherapies, through mechanisms that remain poorly understood. Molecules that specifically recognize mesothelin and interrupt its contribution to tumor progression have significant potential for targeted therapy and targeted drug delivery applications. A number of mesothelin‐targeting therapies are in preclinical and clinical development, although none are currently approved for routine clinical use. In this work, we report the development of a mesothelin‐targeting protein based on the fibronectin type‐III non‐antibody protein scaffold, which offers opportunities for applications where antibodies have limitations. We engineered protein variants that bind mesothelin with high affinity and selectively initiate apoptosis in tumor cells expressing mesothelin. Interestingly, apoptosis does not occur through a caspase‐mediated pathway and does not require downregulation of cell‐surface mesothelin, suggesting a currently unknown pathway through which mesothelin contributes to cancer progression. Importantly, simultaneous treatment with mesothelin‐binding protein and chemotherapeutic mitomycin C had a greater cytotoxic effect on mesothelin‐positive cells compared to either molecule alone, underscoring the potential for combination therapy including biologics targeting mesothelin.
Automatic real‐time calibration, assessment, and maintenance of generic Raman models for online monitoring of cell culture processes
Authors: Tulsyan Aditya , Wang Tony , Schorner Gregg , Khodabandehlou Hamid , Coufal Myra , Undey Cenk
Published: October 2019

Raman spectroscopy is a multipurpose analytical technology that has found great utility in real‐time monitoring and control of critical performance parameters of cell culture processes. As a process analytical technology (PAT) tool, the performance of Raman spectroscopy relies on chemometric models that correlate Raman signals to the parameters of interest. The current calibration techniques yield highly specific models that are reliable only on the operating conditions they are calibrated in. Furthermore, once models are calibrated, it is typical for the model performance to degrade over time due to various recipe changes, raw material variability, and process drifts. Maintaining the performance of industrial Raman models is further complicated due to the lack of a systematic approach to assessing the performance of Raman models. In this article, we propose a real‐time just‐in‐time learning (RT‐JITL) framework for automatic calibration, assessment, and maintenance of industrial Raman models. Unlike traditional models, RT‐JITL calibrates generic models that can be reliably deployed in cell culture experiments involving different modalities, cell lines, media compositions, and operating conditions. RT‐JITL is a first fully integrated and fully autonomous platform offering a self‐learning approach for calibrating and maintaining industrial Raman models. The efficacy of RT‐JITL is demonstrated on experimental studies involving real‐time predictions of various cell culture performance parameters, such as metabolite concentrations, viability, and viable cell density. RT‐JITL framework introduces a paradigm shift in the way industrial Raman models are calibrated, assessed, and maintained, which to the best of authors' knowledge, have not been done before.
Massive computational identification of somatic variants in exonic splicing enhancers using The Cancer Genome Atlas
Authors: Tanimoto Kousuke , Muramatsu Tomoki , Inazawa Johji
Published: October 2019

Owing to the development of next‐generation sequencing (NGS) technologies, a large number of somatic variants have been identified in various types of cancer. However, the functional significance of most somatic variants remains unknown. Somatic variants that occur in exonic splicing enhancer (ESE) regions are thought to prevent serine and arginine‐rich (SR) proteins from binding to ESE sequence motifs, which leads to exon skipping. We computationally identified somatic variants in ESEs by compiling numerous open‐access datasets from The Cancer Genome Atlas (TCGA). Using somatic variants and RNA‐seq data from 9635 patients across 32 TCGA projects, we identified 646 ESE‐disrupting variants. The false positive rate of our method, estimated using a permutation test, was approximately 1%. Of these ESE‐disrupting variants, approximately 71% were located in the binding motifs of four classical SR proteins. ESE‐disrupting variants occurred in proportion to the number of somatic variants, but not necessarily in the specific genes associated with the biological processes of cancer. Existing bioinformatics tools could not predict the pathogenicity of ESE‐disrupting variants identified in this study, although these variants could cause exon skipping. We demonstrated that ESE‐disrupting nonsense variants tended to escape nonsense‐mediated decay surveillance. Using integrated analyses of open access data, we could specifically identify ESE‐disrupting variants. We have generated a powerful tool, which can handle datasets without normal samples or raw data, and thus contribute to reducing variants of uncertain significance because our statistical approach only uses the exon‐junction read counts from the tumor samples.
Strategies for the Development of Metallic‐Nanoparticle‐Based Label‐Free Biosensors and Their Biomedical Applications
Authors: Kaushal Sandeep , Nanda Sitansu Sekhar , Samal Shashadhar , Yi Dong Kee
Published: October 2019

Label‐free biosensors offer accurate sensing capabilities due to the reliable quantification of biological and biochemical processes. These devices function by establishing a dynamic interaction of analyte and receptor molecules and convert this interaction into a measurable signal through a transducer. In recent decades, label‐free biosensors have attracted attention in biomedical applications due to the ease of linking nanomaterials with bioreceptor molecules. In this review, recent advances in sensitivity, specificity, and sensing mechanism related to label‐free biosensors of metallic nanoparticles of gold, silver, aluminium, copper, and zinc oxide are presented. Selected sensing methods based on fluorescence, surface plasmon resonance, surface‐enhanced Raman scattering, metal‐enhanced fluorescence, and electrochemical sensors are discussed. New measurement techniques and rapid progress of label‐free biosensors are going to play a vital role in the real‐time detection of biomarkers in clinical samples, such as blood plasma, serum, and urine, as well as in targeted drug delivery. Future trends of these label‐free biosensing mechanisms and their development are also discussed.
Cellular senescence and EMT crosstalk in bleomycin‐induced pathogenesis of pulmonary fibrosis—an in vitro analysis
Authors: Muthuramalingam Karthika , Cho Moonjae , Kim Youngmee
Published: October 2019

With poor prognosis and aberrant lung remodeling, pulmonary fibrosis exhibits worldwide prevalence accompanied by an increase in burden in terms of hospitalization and death. Apart from genetic and non‐genetic factors, fibrosis occurs as a side effect of bleomycin antineoplastic activity. Elucidating the cellular and molecular mechanism could help in the development of effective anti‐fibrotic treatment strategies. In the present study, we investigated the underlying mechanism behind bleomycin‐induced fibrosis using human alveolar epithelial cells (A549 cells). On the basis of the experimental observation, it was demonstrated that with transforming growth factor‐β (TGF‐β) as a central mediator of fibrosis progression, a cross‐talk between epithelial–mesenchymal transition (EMT) and senescence upon bleomycin treatment occurs. This results in the advancement of this serious fibrotic condition. Fibrosis was initiated through integrin activation and imbalance in the redox state (NOX expression) of the cell. It progressed along the TGF‐β‐mediated non‐canonical pathway (via ERK phosphorylation) followed by the upregulation of α‐smooth muscle actin and collagen synthesis. Additionally, in this process, the loss of the epithelial marker E‐cadherin was observed. Furthermore, the expressions of senescence markers, such as p21 and p53, were upregulated upon bleomycin treatment, thereby intensifying the fibrotic condition. Accordingly, the molecular pathway mediating the bleomycin‐induced fibrosis was explored in the current study.
Sex‐related difference in the use of percutaneous left ventricular assist device in patients undergoing complex high‐risk percutaneous coronary intervention: Insight from the cVAD registry
Authors: Alraies M Chadi , Kaki Amir , Kajy Marvin , Blank Nimrod , Hasan Reema , Htun Wah Wah , Glazier James J. , Elder Mahir , O'Neill William W. , Grines Cindy L. , Schreiber Theodore
Published: October 2019

Objective

To assess the in‐hospital and short‐term outcome differences between males and females who underwent high‐risk PCI with mechanical circulatory support (MCS).

Background

Sex differences have been noted in several percutaneous coronary intervention (PCI) series with females less likely to be referred for PCI due increased risk of adverse events. However, data on sex differences in utilization and outcomes of high‐risk PCI with MCS is scarce.

Methods

Using the cVAD Registry, we identified 1,053 high‐risk patients who underwent PCI with MCS using Impella 2.5 or Impella CP. Patients with cardiogenic shock were excluded. A total of 792 (75.21%) males and 261 (24.79%) females were included in the analysis with median follow‐up of 81.5 days.

Results

Females were more likely to be African American, older (72.05 ± 11.66 vs. 68.87 ± 11.17, p < .001), have a higher prevalence of diabetes (59.30 vs. 49.04%, p = .005), renal insufficiency (35.41 vs. 27.39%, p = .018), and peripheral vascular disease (31.89 vs. 25.39%, p of .05). Women had a higher mean STS score (8.21 ± 8.21 vs. 5.04 ± 5.97, p < .001) and lower cardiac output on presentation (3.64 ± 1.30 vs. 4.63 ± 1.49, p < .001). Although women had more comorbidities, there was no difference in in‐hospital mortality, stroke, MI or need for recurrent revascularization compared to males. Females were more likely to have multivessel revascularization than males. Ejection fraction improved in both males and females at the time of discharge (26.59 to 31.40% and 30.75 to 36.05%, respectively, p < .0001). However, females had higher rate of bleeding requiring transfusion compared with males (9.58 vs. 5.30%, p = .019).

Conclusion

Female patients undergoing high PCI were older and had more comorbidities but had similar outcomes compared to males.
Enhanced High‐Temperature Electrochemical Performance of Layered Nickel‐Rich Cathodes for Lithium‐Ion Batteries after LiF Surface Modification
Authors: Huang Jinlong , Du Ke , Peng Zhongdong , Cao Yanbing , Xue Zhichen , Duan Jianguo , Wang Fei , Liu Yong , Hu Guorong
Published: October 2019

Layered nickel (Ni)‐rich materials have been widely studied as attractive cathode materials for lithium‐ion batteries, owing to their high theoretical specific capacity and low cost; however, most Ni‐rich materials have poor cycle performance, especially at high temperatures. This study reports a simple sol‐gel method for developing lithium fluoride (LiF)‐coated LiNi0.90Co0.08Al0.02O2 (NCA@LiF) by immersing NCA powder in a 1‐butyl‐2,3‐dimethylimidazolium tetrafluoroborate (BdmimBF4) solution. The residual Li compound on the surface of NCA can be converted into a uniform LiF coating layer through the in situ hydrolysis of BdmimBF4. The Li‐conducting LiF coating layer inhibits side reactions (LiPF6→PF5+LiF, PF5+H2O→POF3+HF, POF3+Li2O→LixPOFy+LiF, Li2O/LiOH+HF→H2O+2LiF) with the electrolyte and protects the electrode from HF corrosion. The NCA@LiF sample shows a high capacity retention rate of 79.9 % after 200 cycles at 1 C and an excellent capacity of 155.7 mAh g−1 at 10 C at room temperature. Additionally, the capacity retention rate of the NCA@LiF sample at high temperatures exhibited a significant improvement in comparison with the NCA sample, reaching 75.7 % after 100 cycles at 60 °C at 1 C. This simple and effective method can be used for improving the electrochemistry stability and high‐temperature performance of other Ni‐based cathode materials.
A Hydroperoxide‐Mediated Decarboxylation of α‐Ketoacids Enables the Chemoselective Acylation of Amines
Authors: Nanjo Takeshi , Kato Natsuki , Zhang Xuan , Takemoto Yoshiji
Published: October 2019

Strategies for the formation of amide bonds, that is, one of the most basic and important transformations in organic synthesis, have so far focused predominantly on dehydration reactions. Herein, we report and demonstrate the practical utility of a novel decarboxylative amidation of α‐ketoacids by using inexpensive tert‐butyl hydroperoxide (TBHP), which is characterized by high yields, a broad substrate scope, mild reaction conditions, and a unique chemoselectivity. These features enable the synthesis of peptides from amino acid derived α‐ketoacids under preservation of the stereochemical information.
Tomographische Untersuchung der Fluiddynamik viskoser Systeme in Packungskolonnen
Authors: Bolenz Lukas , Fischer Florian , Toye Dominique , Kenig Eugeny Y.
Published: October 2019

Die Fluiddynamik in strukturierten Packungen wird anhand von Röntgentomographie untersucht. Dabei liegt der Fokus auf dem Einfluss der Viskosität der flüssigen Phase, die zwischen 5 und 50 mPa s variiert wird. Filmströmung ist die dominierende Strömungsform, aber es treten auch Flüssigkeitszwickel an den Kontaktstellen benachbarter Packungsbleche auf. Die Anteile der beiden Strömungsformen am Holdup werden quantifiziert und das mittlere Oberfläche‐zu‐Volumen‐Verhältnis wird bestimmt. Außerdem erfolgt eine Untersuchung des Benetzungsgrads der Packung bei verschiedenen Viskositäten und Flüssigkeitsbelastungen.
Chronic administration of Cl‐amidine, a pan‐peptidylarginine deiminase inhibitor, does not reverse bone loss in two different murine models of osteoporosis
Authors: Vargas‐Muñoz Virginia M. , Martínez‐Martínez Arisai , Muñoz‐Islas Enriqueta , Ramírez‐Rosas Martha B. , Acosta‐González Rosa I. , Jiménez‐Andrade Juan M.
Published: October 2019

Recent in vitro studies have shown a role for the peptidyl‐arginine deiminases (PADs) in bone resorption. However, it is unknown whether these enzymes are involved in bone loss in vivo. Thus, we evaluated the antiresorptive effect of a pan‐PAD inhibitor in two murine models of osteoporosis: (a) primary osteoporosis induced by ovariectomy (OVX); and (b) secondary osteoporosis associated to Type‐1 diabetes induced by streptozotocin (STZ, 50 mg/kg, i.p., five daily administrations). Five weeks after OVX and 15 weeks after injections of STZ, mice received daily administrations of Cl‐amidine (3 or 10 mg/kg, i.p.) or vehicle for 30 consecutive days. At the end of the treatment, femur and vertebra were harvested for microCT analysis. Blood samples were collected for determination of antibodies against cyclic citrullinated peptides (anti‐CCP) by enzyme‐linked immunosorbent assay. Serum levels of anti‐CCP antibodies from diabetic mice were not significantly different compared to control mice. However, a significant loss of both trabecular bone at the femoral neck and cortical bone at the femoral diaphysis was found in diabetic mice, and Cl‐amidine did not reverse the diabetes‐induced bone loss. Mice with OVX had significantly lower serum levels of anti‐CCP compared to mice with sham surgery. OVX resulted in significant loss of both trabecular bone at the L5 vertebra and distal femoral metaphysis. Cl‐amidine did not block the OVX‐induced bone loss. Our results suggest that chronic treatment with Cl‐amidine at the doses and period of time administered is not long enough to inhibit bone loss in two different murine models of osteoporosis.
Evaluating intraspecific genetic diversity using environmental DNA and denoising approach: A case study using tank water
Authors: Tsuji Satsuki , Miya Masaki , Ushio Masayuki , Sato Hirotoshi , Minamoto Toshifumi , Yamanaka Hiroki
Published: October 2019

Recent advances in environmental DNA (eDNA) analysis using high‐throughput sequencing (HTS) provide a noninvasive way to evaluate the intraspecific genetic diversity of aquatic macroorganisms. However, erroneous sequences present in HTS data can result in false positive haplotypes; therefore, reliable strategies are necessary to eliminate such erroneous sequences when evaluating intraspecific genetic diversity using eDNA metabarcoding. In this study, we propose an approach combining denoising using amplicon sequence variant (ASV) method and the removal of haplotypes with low detection rates. A mixture of rearing water of Ayu (Plecoglossus altivelis altivelis) was used as an eDNA sample. In total, nine haplotypes of Ayu mitochondrial D‐loop region were contained in the sample and amplified by two‐step tailed PCR. The 15 PCR replicates indexed with different tags were prepared from the eDNA sample to compare the detection rates between true haplotypes and false positive haplotypes. All PCR replications were sequenced by HTS, and the total number of detected true haplotypes and false positive haplotypes was compared with and without denoising using the two types of ASV methods, Divisive Amplicon Denoising Algorithm 2 (DADA2) and UNOISE3. The use of both ASV methods considerably reduced the number of false positive haplotypes. Moreover, all true haplotypes were detected in all 15 PCR replicates, whereas false positive haplotypes had detection rates varying from 1/15 to 15/15. Thus, by removing haplotypes with lower detection rates than 15/15, the number of false positive haplotypes was further reduced. The approach proposed in this study successfully eliminated most of the false positive haplotypes in the HTS data obtained from eDNA samples, which allowed us to improve the detection accuracy for evaluating intraspecific genetic diversity using eDNA analysis.