bluuebunny/crossref_metadata_2025 huggingface dataset:
Different experimental multiple trauma models induce comparable inflammation and organ injury
Authors: Relja Borna , Yang Bing , Bundkirchen Katrin , Xu Baolin , Köhler Kernt , Neunaber Claudia
Published: November 2020

Multiple injuries appear to be a decisive factor for experimental polytrauma. Therefore, our aim was to compare the inflammatory response and organ damage of five different monotrauma with three multiple trauma models. For this, mice were randomly assigned to 10 groups: Healthy control (Ctrl), Sham, hemorrhagic shock (HS), thoracic trauma (TxT), osteotomy with external fixation (Fx), bilateral soft tissue trauma (bsTT) or laparotomy (Lap); polytrauma I (PT I, TxT + HS + Fx), PT II (TxT + HS + Fx + Lap) and one multi-trauma group (MT, TxT + HS + bsTT + Lap). The inflammatory response and organ damage were quantified at 6 h by analyses of IL-6, IL-1β, IL-10, CXCL1, SAA1, HMGB1 and organ injury. Systemic IL-6 increased in all mono and multiple trauma groups, while CXCL1 increased only in HS, PT I, PT II and MT vs. control. Local inflammatory response was most prominent in HS, PT I, PT II and MT in the liver. Infiltration of inflammatory cells into lung and liver was significant in all multiple trauma groups vs. controls. Hepatic and pulmonary injury was prominent in HS, PT I, PT II and MT groups. These experimental multiple trauma models closely mimic the early post-traumatic inflammatory response in human. Though, the choice of read-out parameters is very important for therapeutic immune modulatory approaches.
Urolithin A augments angiogenic pathways in skeletal muscle by bolstering NAD+ and SIRT1
Authors: Ghosh Nandini , Das Amitava , Biswas Nirupam , Gnyawali Surya , Singh Kanhaiya , Gorain Mahadeo , Polcyn Carly , Khanna Savita , Roy Sashwati , Sen Chandan K.
Published: November 2020

Urolithin A (UA) is a natural compound that is known to improve muscle function. In this work we sought to evaluate the effect of UA on muscle angiogenesis and identify the underlying molecular mechanisms. C57BL/6 mice were administered with UA (10 mg/body weight) for 12–16 weeks. ATP levels and NAD+ levels were measured using in vivo 31P NMR and HPLC, respectively. UA significantly increased ATP and NAD+ levels in mice skeletal muscle. Unbiased transcriptomics analysis followed by Ingenuity Pathway Analysis (IPA) revealed upregulation of angiogenic pathways upon UA supplementation in murine muscle. The expression of the differentially regulated genes were validated using quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC). Angiogenic markers such as VEGFA and CDH5 which were blunted in skeletal muscles of 28 week old mice were found to be upregulated upon UA supplementation. Such augmentation of skeletal muscle vascularization was found to be bolstered via Silent information regulator 1 (SIRT1) and peroxisome proliferator-activated receptor-gamma coactivator-1-alpha (PGC-1α) pathway. Inhibition of SIRT1 by selisistat EX527 blunted UA-induced angiogenic markers in C2C12 cells. Thus this work provides maiden evidence demonstrating that UA supplementation bolsters skeletal muscle ATP and NAD+ levels causing upregulated angiogenic pathways via a SIRT1-PGC-1α pathway.
Spatially resolved fibre cavity ring down spectroscopy
Authors: Chen Rongzhang , Peng Zhaoqiang , Wang Mohan , Yan Aidong , Li Shuo , Huang Sheng , Li Ming-Jun , Chen Kevin P.
Published: November 2020

This paper presents a fibre cavity ring down spectroscopy probed by Rayleigh scattering optical frequency domain reflectometry (OFDR), which provides spatial location of stimuli and improved signal to noise ratio for distributed sensing measurements. A section of optical fibre was integrated into an active fibre ring cavity with optical gain and interrogated by the OFDR system for 11 cycles with a single laser scan. Through the cavity ring down configuration, root-mean-squared (RMS) noise of distributed temperature and strain measurements was reduced to 6.9 mK and less than 0.1 με, respectively for 1-cm spatially resolved measurements. Our work shows that the active fibre cavity configuration can be combined with distributed fibre sensing schemes to achieve both high spatial resolution and high sensitivity measurements.
Integrative quantitative-phase and airy light-sheet imaging
Authors: Subedi N. R. , Jung P. S. , Bredeweg E. L. , Nemati S. , Baker S. E. , Christodoulides D. N. , Vasdekis A. E.
Published: November 2020

Light-sheet microscopy enables considerable speed and phototoxicity gains, while quantitative-phase imaging confers label-free recognition of cells and organelles, and quantifies their number-density that, thermodynamically, is more representative of metabolism than size. Here, we report the fusion of these two imaging modalities onto a standard inverted microscope that retains compatibility with microfluidics and open-source software for image acquisition and processing. An accelerating Airy-beam light-sheet critically enabled imaging areas that were greater by more than one order of magnitude than a Gaussian beam illumination and matched exactly those of quantitative-phase imaging. Using this integrative imaging system, we performed a demonstrative multivariate investigation of live-cells in microfluidics that unmasked that cellular noise can affect the compartmental localization of metabolic reactions. We detail the design, assembly, and performance of the integrative imaging system, and discuss potential applications in biotechnology and evolutionary biology.
X-ray micro-computed tomography reveals a unique morphology in a new click-beetle (Coleoptera, Elateridae) from the Eocene Baltic amber
Authors: Kundrata Robin , Bukejs Andris , Prosvirov Alexander S. , Hoffmannova Johana
Published: November 2020

Beetle fossils are a rich source of information about the palaeodiversity and evolutionary history of the order Coleoptera. Despite the increasing rate of fossil research on click-beetles (Coleoptera: Elateridae), the most diverse group in the superfamily Elateroidea, their fossil record has remained largely unstudied. This may be caused by the combination of their rather uniform external morphology and the suboptimal state of preservation and visibility in most fossil specimens. Here, we used X-ray micro-computed tomography to reconstruct the morphology of an interesting click-beetle from Eocene Baltic amber, which had some principal diagnostic characters obscured by opaque bubbles and body position. Our results suggest that the newly describedBaltelater bipectinatusgen. et sp. nov. belongs to tribe Protelaterini within subfamily Lissominae. Since Protelaterini have a predominantly Gondwanan distribution, our discovery is of a great importance for the historical biogeography of the group. Very distinctive are the bipectinate antennae with 11 antennomeres and with rami beginning on antennomere IV, which are not found in any recent Elateridae. The discovery of a new click-beetle lineage from European Eocene amber sheds further light on the palaeodiversity and historical diversification of the family as well as on the composition of the extinct amber forest ecosystem.
Ex vivo rectal explant model reveals potential opposing roles of Natural Killer cells and Marginal Zone-like B cells in HIV-1 infection
Authors: Smith S. Abigail , Murray Phillip M. , Amancha Praveen Kumar , Ackerley Cassie G. , Hu Yi-Juan , Amara Rama R. , Kelley Colleen F.
Published: November 2020

Our understanding of innate immune responses in human rectal mucosal tissues (RM) and their contributions to promoting or restricting HIV transmission is limited. We defined the RM composition of innate and innate-like cell subsets, including plasmacytoid dendritic cells; CD1c + myeloid DCs; neutrophils; macrophages; natural killer cells (NK); Marginal Zone-like B cells (MZB); γδ T cells; and mucosal-associated invariant T cells in RM from 69 HIV-negative men by flow cytometry. Associations between these cell subsets and HIV-1 replication in ex vivo RM explant challenge experiments revealed an inverse correlation between RM-NK and p24 production, in contrast to a positive association between RM-MZB and HIV replication. Comparison of RM and blood-derived MZB and NK illustrated qualitative and quantitative differences between tissue compartments. Additionally, 22 soluble molecules were measured in a subset of explant cultures (n = 26). Higher production of IL-17A, IFN-γ, IL-10, IP-10, GM-CSF, sFasL, Granzyme A, Granzyme B, Granulysin, and Perforin following infection positively correlated with HIV replication. These data show novel associations between MZB and NK cells and p24 production in RM and underscore the importance of inflammatory cytokines in mucosal HIV infection, demonstrating the likely critical role these innate immune responses play in early mucosal HIV replication in humans.
Genomic determinants for initiation and length of natural antisense transcripts in Entamoeba histolytica
Authors: Mornico Damien , Hon Chung-Chau , Koutero Mikael , Weber Christian , Coppee Jean-Yves , Dillies Marie-Agnes , Guillen Nancy
Published: November 2020

Natural antisense transcripts (NAT) have been reported in prokaryotes and eukaryotes. While the functions of most reported NATs remain unknown, their potentials in regulating the transcription of their counterparts have been speculated. Entamoeba histolytica, which is a unicellular eukaryotic parasite, has a compact protein-coding genome with very short intronic and intergenic regions. The regulatory mechanisms of gene expression in this compact genome are under-described. In this study, by genome-wide mapping of RNA-Seq data in the genome of E. histolytica, we show that a substantial fraction of its protein-coding genes (28%) has significant transcription on their opposite strand (i.e. NAT). Intriguingly, we found the location of transcription start sites or polyadenylation sites of NAT are determined by the specific motifs encoded on the opposite strand of the gene coding sequences, thereby providing a compact regulatory system for gene transcription. Moreover, we demonstrated that NATs are globally up-regulated under various environmental conditions including temperature stress and pathogenicity. While NATs do not appear to be consequences of spurious transcription, they may play a role in regulating gene expression in E. histolytica, a hypothesis which needs to be tested.
Moving targets in drug discovery
Authors: Zdrazil Barbara , Richter Lars , Brown Nathan , Guha Rajarshi
Published: November 2020

Drug Discovery is a lengthy and costly process and has faced a period of declining productivity within the last two decades resulting in increasing importance of integrative data-driven approaches. In this paper, data mining and integration is leveraged to inspect target innovation trends in drug discovery. The study highlights protein families and classes that have received more attention and those that have just emerged in the scientific literature, thus highlighting novel opportunities for drug intervention. In order to delineate the evolution of target-driven research interest from a biological perspective, trends in biological process annotations from Gene Ontology and disease annotations from DisGeNET are captured. The analysis reveals an increasing interest in targets related to immune system processes, and a recurrent trend for targets involved in circulatory system processes. At the level of diseases, targets associated with cancer-related pathologies, intellectual disability, and schizophrenia are increasingly investigated in recent years. The methodology enables researchers to capture trends in research attention in target space at an early stage during the drug discovery process. Workflows, scripts, and data used in this study are publicly available from https://github.com/BZdrazil/Moving_Targets. An interactive web application allows the customized exploration of target, biological process, and disease trends (available at https://rguha.shinyapps.io/MovingTargets/).
Factors affecting stability of plasma brain-derived neurotrophic factor
Authors: Wessels Jocelyn M. , Agarwal Ravi K. , Somani Aamer , Verschoor Chris P. , Agarwal Sanjay K. , Foster Warren G.
Published: November 2020

Circulating concentrations of brain-derived neurotrophic factor (BDNF) have been linked to cancer, neuropsychiatric, diabetes, and gynecological disorders. However, factors influencing plasma storage and subsequent BDNF quantification are incompletely understood. Therefore, the anticoagulant used in plasma separator tubes, storage-time, storage-temperature, and repeated freeze–thaw cycles on circulating BDNF concentrations was evaluated. Peripheral blood samples were collected from healthy women (n = 14) and men (n = 10) recruited prospectively from McMaster University (August 2014). Blood was collected from the cubital vein into plasma separator tubes containing five different anticoagulant systems [K2EDTA, Li-Hep, Li-Hep (gel), Na-Hep, Na-Hep (glass)], and placed on ice for transport to the lab for centrifugation. Plasma samples (n = 16) collected in K2EDTA tubes from women recruited to a previous study (April 2011 to December 2012) were used to determine the effect of multiple freeze–thaw cycles. Plasma BDNF was quantified using a commercially available ELISA kit. Plasma concentrations of BDNF were significantly affected by the type of plasma separator tube, storage-time, and number of freeze–thaw cycles. Storage temperature (− 20 vs. − 80 °C) did not significantly affect the quantity of BDNF measured as mean BDNF concentrations generally fell within our calculated acceptable change limit up to 6 months in the freezer. Our results suggest that for quantification of circulating BDNF blood collected in K2EDTA tubes and plasma stored up to 6 months at either − 20 or − 80 °C produces reproducible results that fall within an acceptable range. However, plasma samples stored beyond 6 months and repeated freeze–thaw cycles should be avoided.
Efficacy of P11-4 for the treatment of initial buccal caries: a randomized clinical trial
Authors: Sedlakova Kondelova Paulina , Mannaa Alaa , Bommer Claudine , Abdelaziz Marwa , Daeniker Laurent , di Bella Enrico , Krejci Ivo
Published: November 2020

To investigate the safety and efficacy of Self-Assembling Peptide P11-4 (SAP P11-4) compared to placebo or fluoride varnish (FV), a randomized, controlled, blinded, split-mouth study with sequential design was conducted. Subjects presenting two teeth with White-Spot-Lesions (WSLs) were included and teeth were randomly assigned to test or control. Control received placebo at baseline (D0) and test SAP P11-4, all received FV at Day 90 (D90). Standardized photographs were taken at each visit, and WSL size changes were morphometrically assessed. Hierarchical Linear Modelling, considering paired and sequential design, was used to test four hypotheses. SAP P11-4 lesions (test, D90–D0) showed significant WSL size reduction compared to placebo (control, D90–D0; p = 0.008) or FV (control, D180–D90; p = 0.001). Combination of SAP P11-4 and delayed FV after 90 days (test, D180–D0), showed a significant difference compared to FV alone (control D270–D90; p = 0.003). No significant difference on FV efficacy was found when SAP P11-4 was applied 3 months before FV (test D270–D90; control D270–D90, p = 0.70). SAP P11-4 treatment resulted in superior caries regression compared to either placebo or FV, and FV efficacy seems not to be affected by SAP P11-4. SAP P11-4 was found to be a safe and effective WSL treatment.
Culture systems influence the physiological performance of the soft coral Sarcophyton glaucum
Authors: Chang Tai-Chi , Mayfield Anderson B. , Fan Tung-Yung
Published: November 2020

There is an urgent need to develop means of ex situ biobanking and biopreserving corals and other marine organisms whose habitats have been compromised by climate change and other anthropogenic stressors. To optimize laboratory growth of soft corals in a way that could also benefit industry (e.g., aquarium trade), three culture systems were tested herein with Sarcophyton glaucum: (1) a recirculating aquaculture system (RAS) without exogenous biological input (RAS−B), (2) a RAS with “live” rocks and an exogenous food supply (RAS+B), and (3) a simple flow-through system (FTS) featuring partially filtered natural seawater. In each system, the effects of two levels of photosynthetically active radiation (100 or 200 μmol quanta m−2 s−1) and flow velocity (5 or 15 cm s−1) were assessed, and a number of soft coral response variables were measured. All cultured corals survived the multi-month incubation, yet those of the RAS−B grew slowly and even paled; however, once they were fed (RAS−B modified to RAS+B), their pigmentation increased, and their oral discs readily expanded. Light had a more pronounced effect in the RAS−B system, while flow affected certain coral response variables in the FTS tanks; there were few effects of light or flow in the RAS+B system, potentially highlighting the importance of heterotrophy. Unlike the ceramic pedestals of the FTS, those of the RAS+B did not regularly become biofouled by algae. In concert with the aforementioned physiological findings, we therefore recommend RAS+B systems as a superior means of biopreservating and biobanking soft corals.
Dopamine receptor D1- and D2-agonists do not spark brown adipose tissue thermogenesis in mice
Authors: Raffaelli Francesca-Maria , Resch Julia , Oelkrug Rebecca , Iwen K. Alexander , Mittag Jens
Published: November 2020

Brown adipose tissue (BAT) thermogenesis is considered a potential target for treatment of obesity and diabetes. In vitro data suggest dopamine receptor signaling as a promising approach; however, the biological relevance of dopamine receptors in the direct activation of BAT thermogenesis in vivo remains unclear. We investigated BAT thermogenesis in vivo in mice using peripheral administration of D1-agonist SKF38393 or D2-agonist Sumanirole, infrared thermography, and in-depth molecular analyses of potential target tissues; and ex vivo in BAT explants to identify direct effects on key thermogenic markers. Acute in vivo treatment with the D1- or D2-agonist caused a short spike or brief decrease in BAT temperature, respectively. However, repeated daily administration did not induce lasting effects on BAT thermogenesis. Likewise, neither agonist directly affected Ucp1 or Dio2 mRNA expression in BAT explants. Taken together, the investigated agonists do not seem to exert lasting and physiologically relevant effects on BAT thermogenesis after peripheral administration, demonstrating that D1- and D2-receptors in iBAT are unlikely to constitute targets for obesity treatment via BAT activation.
Initial assessment of treatment of talar posterior process fractures with open reduction and percutaneous fixation
Authors: Mao Haijiao , Wang Haiqing , Zhao Jiyuan , Wang Linger , Yao Liwei , Wei Ke
Published: November 2020

The purpose of this study was to provide an initial assessment of treatment for talar posterior process fractures using open reduction and internal fixation (ORIF) through posteromedial approach and percutaneous screw fixation. From January 2014 to December 2018, 12 cases with displaced fracture of talar posterior process were treated in our department. The clinical and radiological results were assessed after 4 and 12 months of operation with Visual Analog Scale (VAS) pain and American Orthopedic Foot and Ankle Society (AOFAS) scores. ORIF was performed in four of the cases and percutaneous screw fixation was performed in eight of the cases. The average follow-up period was 13 months. Complications such as wound infection, nerve injury, screw loosening, malunion or nonunion of fracture were absent. For clinical assessment, considerable mprovements were observed for the AOFAS and VAS scores at 4 and 12 months postoperatively for both techniques. There was no significant difference for AOFAS scores and VAS scores between the two techniques (p > 0.05). Both techniques showed good functional outcome and were performed for posterior talar process fracture following the fracture displacement guidelines. Percutaneous screw fixation treatment with computer-assisted three-dimensional evaluation shortened the operation time and reduced incidences of surgical complications.
Novel nonlinear reconstruction method with grey-level quantisation units for electron tomography
Authors: Baba Norio , Kaneko Kenji , Baba Misuzu
Published: November 2020

We report a new computed tomography reconstruction method, named quantisation units reconstruction technique (QURT), applicable to electron and other fields of tomography. Conventional electron tomography methods such as filtered back projection, weighted back projection, simultaneous iterative reconstructed technique, etc. suffer from the ‘missing wedge’ problem due to the limited tilt-angle range. QURT demonstrates improvements to solve this problem by recovering a structural image blurred due to the missing wedge and substantially reconstructs the structure even if the number of projection images is small. QURT reconstructs a cross-section image by arranging grey-level quantisation units (QU pieces) in three-dimensional image space via unique discrete processing. Its viability is confirmed by model simulations and experimental results. An important difference from recently developed methods such as discrete algebraic reconstruction technique (DART), total variation regularisation—DART, and compressed sensing is that prior knowledge of the conditions regarding the specimen or the expected cross-section image is not necessary.
In vitro modeling of solid tumor interactions with perfused blood vessels
Authors: Kwak Tae Joon , Lee Esak
Published: November 2020

Molecular crosstalk between intra-tumor blood vessels and tumor cells plays many critical roles in tumorigenesis and cancer metastasis. However, it has been very difficult to investigate the biochemical mechanisms underlying the overlapping, multifactorial processes that occur at the tumor-vascular interface using conventional murine models alone. Moreover, traditional two-dimensional (2D) culture models used in cancer research do not recapitulate aspects of the 3D tumor microenvironment. In the present study, we introduce a microfluidic model of the solid tumor-vascular interface composed of a human umbilical vein endothelial cell (HUVEC)-lined, perfusable, bioengineered blood vessel and tumor spheroids embedded in an extracellular matrix (ECM). We sought to optimize our model by varying the composition of the tumor spheroids (MDA-MB-231 breast tumor cells + mesenchymal stem cells (MSCs)/human lung fibroblasts (HLFs)/HUVECs) and the extracellular matrix (ECM: collagen, Matrigel, and fibrin gels with or without free HLFs) that we used. Our results indicate that culturing tumor spheroids containing MDA-MB-231 cells + HUVECs in an HLF-laden, fibrin-based ECM within our microfluidic device optimally (1) enhances the sprouting and migration of tumor spheroids, (2) promotes angiogenesis, (3) facilitates vascular invasion, and (4) preserves the structural integrity and functionality of HUVEC-lined microfluidic channels. This model may provide a platform for drug screening and mechanism studies on solid tumor interactions with functional blood vessels.
Preemptive interferon-α treatment could protect against relapse and improve long-term survival of ALL patients after allo-HSCT
Authors: Liu Sining , Luo Xueyi , Zhang Xiaohui , Xu Lanping , Wang Yu , Yan Chenhua , Chen Huan , Chen Yuhong , Han Wei , Wang Fengrong , Wang Jingzhi , Liu Kaiyan , Huang Xiaojun , Mo Xiaodong
Published: November 2020

Relapse was the major cause of treatment failure in patients with acute lymphoblastic leukemia (ALL) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). We aimed to identify the efficacy and safety of preemptive interferon-α (IFN-α) treatment in ALL patients who had minimal residual disease (MRD) after allo-HSCT. Multiparameter flow cytometry and polymerase chain reaction assays were applied for MRD monitoring. Recombinant human IFN-α-2b injections were administered subcutaneously twice weekly in every 4 weeks cycle. Twenty-four (35.3%), 5 (7.4%), 6 (8.8%), and 13 (19.1%) patients achieved MRD negativity at 1, 2, 3, and > 3 months, respectively, after treatment. Seven patients showed grade ≥ 3 toxicities after IFN-α treatment. The 4-year cumulative incidence of total acute graft-versus-host disease (aGVHD), severe aGVHD, total chronic GVHD (cGVHD), and severe cGVHD after treatment was 14.7%, 2.9%, 40.0%, and 7.5%, respectively. The 4-year cumulative incidences of relapse and non-relapse mortality after treatment was 31.9% and 6.0%, respectively. The 4-year probabilities of disease-free survival and overall survival after IFN-α treatment were 62.1% and 71.1%, respectively. Thus, preemptive IFN-α treatment could protect against relapse and improve long-term survival for ALL patients who had MRD after allo-HSCT. The study was registered athttps://clinicaltrials.govas #NCT02185261 (09/07/2014).
Ocular surface manifestation of COVID-19 and tear film analysis
Authors: Meduri Alessandro , Oliverio Giovanni William , Mancuso Giuseppe , Giuffrida Angela , Guarneri Claudio , Venanzi Rullo Emmanuele , Nunnari Giuseppe , Aragona Pasquale
Published: November 2020

To evaluate the ocular manifestation in patients hospitalized with coronavirus disease 2019 (COVID-19) and to search for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in tears. This study was conducted in 29 hospitalized patients who were admitted to the COVID center at the Policlinic Hospital of the University of Messina, Italy. All patients underwent an ophthalmologic assessment comprising a Standardized Patient Evaluation of Eye Dryness (SPEED) questionnaire, anterior segment, and the ocular surface examination of both eyes using a portable slit lamp. The Schirmer I test was performed, and the filter paper strip was used to search for the presence of SARS-CoV-2 on the ocular surface by real-time quantitative polymerase chain reaction (RT-qPCR). A total of 10 patients reported ocular symptoms; in particular, four reported eye burning, three reported foreign body sensation, and three reported tearing. Moreover, seven patients presented conjunctival hyperemia and/or chemosis, eleven patients presented blepharitis signs such as lid margin hyperemia and/or telangiectasia, crusted eyelashes, and meibomian orifices alterations. Tear analysis did not reveal the presence of SARS-CoV-2. Ocular symptoms are common in patients with COVID-19; although, tear analysis did not reveal the presence of SARS-CoV-2.
In situ casting of rice husk ash in metal organic frameworks induces enhanced CO2 capture performance
Authors: Panda Debashis , Saini Chanchal , Kumar E. Anil , Singh Sanjay Kumar
Published: November 2020

Incorporation of rice-husk-ash (RHA), an agricultural waste, in situ during the synthesis of MIL-101(Cr) resulted in a significant improvement in the CO2 adsorption properties over the synthesized RHA-MIL-101(Cr). The newly synthesized RHA-MIL-101(Cr) composite exhibited an enhancement of 14–27% in CO2 adsorption capacity as compared to MIL-101(Cr) at 25 °C and 1 bar. The content of RHA incorporated in RHA-MIL-101(Cr) fine tuned the CO2 capture performance to achieve high working capacity (0.54 mmol g−1), high purity (78%), superior CO2/N2 selectivity (18) and low isosteric heat of adsorption (20–30 kJ mol−1). The observed superior CO2 adsorption performance of RHA-MIL-101(Cr) is attributed to the fine tuning of textural characteristics—enhancement of 12–27% in BET surface area, 12–33% in total pore volume and 18–30% in micropore volume—upon incorporation of RHA in MIL-101(Cr).
Brassica oleracea var. acephala (kale) improvement by biological activity of root endophytic fungi
Authors: Poveda Jorge , Zabalgogeazcoa Iñigo , Soengas Pilar , Rodríguez Victor M. , Cartea M. Elena , Abilleira Rosaura , Velasco Pablo
Published: November 2020

Brassica oleracea var. acephala (kale) is a cruciferous vegetable widely cultivated for its leaves and flower buds in Atlantic Europe and the Mediterranean area, being a food of great interest as a "superfood" today. Little has been studied about the diversity of endophytic fungi in the Brassica genus, and there are no studies regarding kale. In this study, we made a survey of the diversity of endophytic fungi present in the roots of six different Galician kale local populations. In addition, we investigated whether the presence of endophytes in the roots was beneficial to the plants in terms of growth, cold tolerance, or resistance to bacteria and insects. The fungal isolates obtained belonged to 33 different taxa. Among those, a Fusarium sp. and Pleosporales sp. A between Setophoma and Edenia (called as Setophoma/Edenia) were present in many plants of all five local populations, being possible components of a core kale microbiome. For the first time, several interactions between endophytic fungus and Brassica plants are described and is proved how different interactions are beneficial for the plant. Fusarium sp. and Pleosporales sp. B close to Pyrenophora (called as Pyrenophora) promoted plant growth and increased cold tolerance. On the other hand, isolates of Trichoderma sp., Pleosporales sp. C close to Phialocephala (called as Phialocephala), Fusarium sp., Curvularia sp., Setophoma/Edenia and Acrocalymma sp. were able to activate plant systemic resistance against the bacterial pathogen Xanthomonas campestris. We also observed that Fusarium sp., Curvularia sp. and Setophoma/Edenia confered resistance against Mamestra brassicae larvae.
Accuracy and efficiency of germline variant calling pipelines for human genome data
Authors: Zhao Sen , Agafonov Oleg , Azab Abdulrahman , Stokowy Tomasz , Hovig Eivind
Published: November 2020

Advances in next-generation sequencing technology have enabled whole genome sequencing (WGS) to be widely used for identification of causal variants in a spectrum of genetic-related disorders, and provided new insight into how genetic polymorphisms affect disease phenotypes. The development of different bioinformatics pipelines has continuously improved the variant analysis of WGS data. However, there is a necessity for a systematic performance comparison of these pipelines to provide guidance on the application of WGS-based scientific and clinical genomics. In this study, we evaluated the performance of three variant calling pipelines (GATK, DRAGEN and DeepVariant) using the Genome in a Bottle Consortium, “synthetic-diploid” and simulated WGS datasets. DRAGEN and DeepVariant show better accuracy in SNP and indel calling, with no significant differences in their F1-score. DRAGEN platform offers accuracy, flexibility and a highly-efficient execution speed, and therefore superior performance in the analysis of WGS data on a large scale. The combination of DRAGEN and DeepVariant also suggests a good balance of accuracy and efficiency as an alternative solution for germline variant detection in further applications. Our results facilitate the standardization of benchmarking analysis of bioinformatics pipelines for reliable variant detection, which is critical in genetics-based medical research and clinical applications.
Maternal plasma folate concentration is positively associated with serum total cholesterol and low-density lipoprotein across the three trimesters of pregnancy
Authors: da Silva Manoela T. , Mujica-Coopman Maria F. , Figueiredo Amanda C. C. , Hampel Daniela , Vieira Luna S. , Farias Dayana R. , Shahab-Ferdows Setareh , Allen Lindsay H. , Brito Alex , Lamers Yvonne , Kac Gilberto , S. Vaz Juliana
Published: November 2020

Increased first-trimester low-density lipoprotein (LDL-C) concentration has been associated with adverse pregnancy outcomes, such as gestational diabetes. The B vitamins folate, B-6, and total B-12 are key for the methyl group-dependent endogenous synthesis of phosphatidylcholine, which is needed for lipoprotein synthesis, e.g., very low-density lipoprotein (VLDL), the precursor of circulating LDL-C. Maternal B-vitamin concentration usually declines across trimesters. Whether changes in maternal B-vitamin concentrations are associated with total cholesterol (TC), triglycerides (TG), and lipoprotein concentrations is unknown. Therefore, we explored the association between plasma folate, vitamin B-6 in the form of pyridoxal 5′-phosphate (PLP), and total B-12 with serum TC, LDL-C, HDL-C, and TG concentrations across trimesters. This secondary analysis used data of a prospective pregnancy cohort study included apparently healthy adult women (n = 179) from Rio de Janeiro, Brazil. The biomarkers were measured in fasting blood samples collected at 5–13, 20–26, and 30–36 weeks of gestation. The associations between B vitamins and lipid concentrations across trimesters were explored using linear mixed-effect models. Among B vitamins, only plasma folate was positively associated with TC (β = 0.244, 95% CI 0.034–0.454) and LDL-C (β = 0.193, 95% CI 0.028–0.357) concentrations. The positive relationship of maternal folate and TC and LDL-C concentrations may indicate the importance of folate as a methyl donor for lipoprotein synthesis during pregnancy.
In vivo oscillations of the soleus muscle can be quantified using b-mode ultrasound imaging during walking and running in humans
Authors: Lai A. K. M. , Hodson-Tole E. F.
Published: November 2020

Impact forces, due to the foot contacting the ground during locomotion, can be considered input signals to the body that must be dissipated to prevent impact-related injuries. One proposed mechanism employed by the body to damp the impact is through vibrations of the skeletal muscles. However, there is yet to be direct in vivo measures of muscle oscillations during locomotion. This study investigated the use of 2D ultrasound imaging to quantify transverse muscle oscillations (deep-superficial displacement of the muscle boundary relative to the skin) in response to impact forces elicited by walking and running at a range of speeds. Increases in vertical impact forces with faster walking and running was consistent with changes in both magnitude and frequency in the measured oscillations of the soleus muscle; one of the main human ankle plantar flexors. Muscle oscillations contained more higher frequency components at fast running (50% signal power in frequencies below ~ 14 Hz) compared with slow walking (50% signal power contained in frequencies below ~ 5 Hz). This study provides a platform for ultrasound imaging to examine muscle oscillation responses to impact forces induced by changes in external interfaces such as shoe material, locomotion type and ground surface properties.
Formation of the hollow nanopillar arrays through the laser-induced transformation of TiO2 nanotubes
Authors: Wawrzyniak Jakub , Karczewski Jakub , Kupracz Piotr , Grochowska Katarzyna , Coy Emerson , Mazikowski Adam , Ryl Jacek , Siuzdak Katarzyna
Published: November 2020

In the following article, we present a simple, two-step method of creating spaced, hollow nanopillars, from the titania nanotube arrays via pulsed laser-treatment. Due to the high ordering of the structure, the prepared material exhibits photonic properties, which has been shown to increase the overall photoefficiency. The optical and morphological changes in the titania nanotubes after pulsed laser-treatment with 532, 355, and 266 nm wavelengths in the 10–50 mJ/cm2 fluence range are studied. The investigation reveals, that by using appropriate wavelength and energy, the number of surface defects, geometrical features, or both can be tailored.
In vitro dexamethasone treatment does not induce alternative ATM transcripts in cells from Ataxia–Telangiectasia patients
Authors: Pozzi Elisa , Giorgio Elisa , Mancini Cecilia , Lo Buono Nicola , Augeri Stefania , Ferrero Marta , Di Gregorio Eleonora , Riberi Evelise , Vinciguerra Maria , Nanetti Lorenzo , Bianchi Federico Tommaso , Sassi Maria Paola , Costanzo Vincenzo , Mariotti Caterina , Funaro Ada , Cavalieri Simona , Brusco Alfredo
Published: November 2020

Short term treatment with low doses of glucocorticoid analogues has been shown to ameliorate neurological symptoms in Ataxia–Telangiectasia (A–T), a rare autosomal recessive multisystem disease that mainly affects the cerebellum, immune system, and lungs. Molecular mechanisms underlying this clinical observation are unclear. We aimed at evaluating the effect of dexamethasone on the induction of alternative ATM transcripts (ATMdexa1). We showed that dexamethasone cannot induce an alternative ATM transcript in control and A–T lymphoblasts and primary fibroblasts, or in an ATM-knockout HeLa cell line. We also demonstrated that some of the reported readouts associated with ATMdexa1 are due to cellular artifacts and the direct induction of γH2AX by dexamethasone via DNA-PK. Finally, we suggest caution in interpreting dexamethasone effects in vitro for the results to be translated into a rational use of the drug in A–T patients.
Introduction to Challenges for Health and Safety in Research
Authors: Kuzmina O. , Hoyle S.
Published: November 2020

Results from the University and Research Institutions survey are presented in this chapter revealing what are the most common challenges faced by health and safety professionals, managers and researchers in these organisations. Barriers discovered are collated in five categories: physical, economical, organisational, behavioural and industry specific. Where appropriate this chapter directs the reader to a relevant chapter for further in-depth analysis. The appendix at the end of the chapter is a collection of feedback from survey responders on how workplace health and safety, in their view, could be improved.
Managing Legal Risks in an Uncertain Environment
Authors: Crosbie Philip
Published: November 2020

In this chapter, we consider how organisations and individuals are able to manage the legal duties upon them in an environment that was not necessarily their intended target. The requirement within health and safety legislation to do what is ‘reasonably practicable’ should provide some comfort to organisations; they are not expected to create a risk-free environment, and it is accepted that individuals may be exposed to suitably controlled risk without fear of criminal sanction. However, the risk profile and audience of those working in academia and research environments presents unique challenges. Throughout this chapter, we have considered the ways in which an organisation dealing with the uncertain can be certain about one thing; that the right decision will be taken when the time comes. We suggest that there are some fundamental aspects of good health and safety management that, if properly understood and exercised by organisations, will produce a regime that can progress academic interests in a safe setting. In essence, organisations should seek to develop an environment and culture that inspires and rewards the right behaviours so that its individuals can ‘break the mould’ and not the law.
Stress and Workplace Wellbeing in a Higher Education and Research Organisation
Authors: Kanwar Monica
Published: November 2020

This chapter will look at stress and workplace wellbeing in Higher Education (HE) and research establishments, which tend to have more complex management structures than traditional commercial companies. The information presented is aimed to help progress safety culture in the organisation including consideration of how safety culture, management of stress and wellbeing are all connected. This chapter looks at possible influences of culture in an HE environment and how the culture of an organisation influences the stress and wellbeing of individuals. It looks at practical resources that could assist locally to enable steps to be taken to support the HE environment. A case study demonstrates an example of an institution's wellbeing approach which has evolved over a ten-year period.
Educate Don't Indoctrinate: Planning and Delivering Training and Support for Workplaces with High Staff Turnover
Authors: Healy D. M. , O'Leary P.
Published: November 2020

This chapter discusses the challenges associated with the design and implementation of safety training programmes within large complex organisations with a high rate of staff turnover on a research university example. The authors guide you through a simplified process of planning and delivery of safety training, highlighting some of the challenges and innovative solutions they have seen along the way. Using the information provided throughout the chapter you will be able to develop and deliver your own unique strategy, combining the different elements discussed to suit your organisation.
Safety Outside of the Classroom
Authors: Coulahan P.
Published: November 2020

Managing the safety of students and researchers in a Higher Education Institute (HEI) or Research Institute (RI) can be challenging. Those challenges can be exacerbated when researchers, and students in particular, leave the formal learning environment and are exposed to dynamic hazards outside of the classroom over which they or the HEI/RI have little or no control. This chapter examines how an organisation can manage the safety of students and researchers in three key areas outside of the classroom – (i) When engaged in approved sporting activities; (ii) When on professional work placements/internships; and (iii) When undertaking fieldwork. I chose sporting activity because in the almost twenty years I have been involved in managing and advising on safety in a university it is the only activity that I have first-hand experience of that has led directly to the death of a student; I chose work placements/internships as a subject because when students and researchers are engaged in such activities the HEI/RI loses control to a significant degree over their working environment and activities and consequently, their safety; and finally I chose fieldwork because I consider it to be one of the most dangerous activities that any academic, student or researcher can engage in. The guidance contained within this chapter is designed to help guide and assist safety practitioners and other stakeholders who are tasked with ensuring student and researcher safety outside of the classroom.
Liaising with the Emergency Services
Authors: Blunt J.
Published: November 2020

This chapter highlights some of the issues that arise when emergency services are needed to assist with incidents in scientific institutions. Incidents are often a result of the identified control measures failing. While the emergency services will take control in a situation to which they have been called, they will be very keen to liaise with those who have specialist knowledge in order to safeguard their personnel. Some risks are not obvious. This chapter explores some of the key hazards and risks that are often present in scientific institutions and proposes ways to minimise the risks to emergency personnel. If the department has suitable information and assistance available to the emergency services, most situations can be dealt with in an efficient and safe manner. The experience that has shaped this chapter is drawn from the author's experience, and experience shared with colleagues, in several institutions.
When the Walls Come Down: Secrets of Open Space Safety
Authors: Aspinall T. V. , Derbyshire R.
Published: November 2020

How do you ensure the health and safety (H&S) of workers in shared, open-plan workplaces? While the principles of safety management remain the same for all workplaces, additional challenges are present when developing H&S management plans in open-plan, shared discipline workspaces. Chapter 12 highlights the H&S management systems developed and implemented within the Manchester Institute of Biotechnology at the University of Manchester, the first purpose-built university multidisciplinary research Institute in the UK, with the potential to facilitate up to 600 research staff. It focuses on the challenges which were identified, and how the development and introduction of effective control systems, coupled with the development of competency, co-operation in using shared spaces and equipment, and the development of effective routes of communication, has resulted in tangible improvements to processes, procedures and behaviours within the Institute.
Health and Safety Considerations in the Design of Teaching and Research Laboratories
Authors: DiBerardinis Louis
Published: November 2020

The proper design of new or renovated laboratories is critical to the success of the research or teaching to be conducted in the laboratory as well as the safety and health of the occupants. The factors that can lead to the successful design, construction and operation of a laboratory are having the relevant disciplines represented and engaged from the beginning and following a defined process to assure that all potential issues are addressed. From a health and safety perspective the key design issues are the layout of the space, adequate contaminant control ventilation as well as ventilation for comfort control and the proper safety features such as emergency eye washes and showers, fire detection, alarm and suppression systems, and electrical and mechanical safety systems. Applicable regulatory requirements as well as building codes and best practices must also be considered. This chapter describes the process to follow as well as key issues that should be addressed depending on the type of laboratory and the materials, equipment, and procedures to be employed in the space. It also provides additional resources that can be consulted for guidance.
Translation of Safety from University Research to Spin-out
Authors: Johal Surrinder , Pedrero-Llamas Ana
Published: November 2020

Launching a spin-out is becoming increasingly attractive for students, academics and researchers worldwide. Once established as a company, the directors are automatically accountable and responsible for complying with local health and safety regulations. Currently, the advice available to them appears highly variable and the advantages of having a well-defined health and safety management system from the onset are not always obvious. This chapter explores potential pitfalls and provides guidance on the basic steps a new spin-out needs to take to establish a safe foundation for future growth. In the chapter we have provided a checklist aimed to help you to develop and implement a safety management system.
Green and Sustainable Whilst Avoiding Risks
Authors: Sheeley H. J.
Published: November 2020

There has been an increasing interest in and effort to ensure laboratory and research work practices are in line with ethical and social responsibility conduct including “green” objectives such as the elimination of waste, energy conservation and protection of the environment. Research and teaching laboratories are often at the cutting edge and exploratory, leading to potentially higher risk work and environments. Increasing health and safety legislation, product controls and other pressures have significantly reduced risk to workers but could be reversed by other conflicting priorities such as “green” replacements and the drive for sustainable goals. Successful opportunities and risks suggest it is possible but requires careful consideration and associated management.
Based on the synergistic effect of Mg2+ and antibacterial peptides to improve the corrosion resistance, antibacterial ability and osteogenic activity of magnesium-based degradable metals
Authors: Zhou Wenhao , Yan Jianglong , Li Yangyang , Wang Lan , Jing Lei , Li Ming , Yu Sen , Cheng Yan , Zheng Yufeng
Published: November 2020

Magnesium (Mg) and its alloys have been widely investigated as the most promising biodegradable metals for orthopedic device applications, but its surface properties should be further improved to overcome the restricted osteogenesis and fast degradation problems.
Boron: the first p-block element to fix inert N2 all the way to NH3
Authors: Walawalkar Mrinalini G.
Published: November 2020

Borylene is able to activate inert dinitrogen to the ammonium ion. The entire conversion was established through a successive reduction-cum protonation sequence, through the isolation of all intermediate species.