bluuebunny/crossref_metadata_2025 huggingface dataset:
Rationalising the use of cardiac catheterisation before Glenn completion
Authors: James Lorraine , Tandon Animesh , Nugent Alan , Malik Sadia , Ramaciotti Claudio , Greil Gerald , Zabala Luis , Forbess Joseph , Hussain Tarique
Published: March 2018

Previous studies have shown that cardiac MRI can be used to evaluate the suitability for infants to undergo the Glenn operation after having undergone the Norwood procedure. We sought to analyse our institutional data retrospectively to identify whether such a policy would be advisable in the current era. We reviewed patients who underwent the Norwood procedure between 1 January, 2006 and 1 January, 2016. All patients undergoing evaluation for the Glenn procedure received clinical evaluation, echocardiography, and cardiac catheterisation. A total of 179 patients were identified; 154 patients (86%) survived to undergo cardiac catheterisation as part of evaluation for the Glenn, and all who were evaluated did not eventually receive the Glenn. Using said algorithm, if cardiac MRI or CT were to be used to rationalise the use of catheterisation, 26 of 154 patients would have required catheterisation after cross-sectional imaging identified vascular obstruction; 83 of 154 patients would have received cross-sectional imaging only; and 45 of 154 would have had catheterisation only. All cases that required intervention, excluding aortopulmonary collaterals, and all cases that were not suitable to progress would have been correctly identified using clinical and echocardiographic criteria in addition to cardiac cross-sectional imaging to rationalise the use of catheterisation. Thus, in cases with acceptable clinical, echocardiographic, and angiographic findings, the additional haemodynamic information from catheterisation is rarely of use for decision-making, and interventions can largely be predicted by angiographic imaging modalities.
Persistent social inequality in low intake of vegetables among adolescents, 2002–2014
Authors: Rasmussen Mette , Pedersen Trine Pagh , Johnsen Nina Føns , Krølner Rikke Fredenslund , Holstein Bjørn E
Published: March 2018

Objective

To examine the trend in social inequality in low intake of vegetables among adolescents in Denmark from 2002 to 2014 using occupational social class (OSC) as socio-economic indicator.

Design

Repeated cross-sectional school surveys including four waves of data collection in 2002–2014. The analyses focused on absolute social inequality (difference between high and low OSC in low vegetable intake) as well as relative social inequality (OR for low vegetable intake by OSC).

Setting

The nationally representative Health Behaviour in School-aged Children (HBSC) study in Denmark.

Subjects

The study population was 11–15-year olds (n 17 243).

Results

Low intake of vegetables was defined as less than weekly intake measured by food frequency items. OSC was measured by student reports of parents’ occupation. The proportion of participants who reported eating vegetables less than once weekly was 8·9 %, with a notable decrease from 11·9 % in 2002 to 5·9 % in 2014. The OR (95 % CI) for less than weekly vegetable intake was 2·28 (1·98, 2·63) in the middle compared with high OSC and 3·12 (2·67, 3·66) in the low compared with high OSC. The absolute social inequality in low vegetable intake decreased from 2002 to 2014 but the relative social inequality remained unchanged.

Conclusions

The study underscores that it is important to address socio-economic factors in future efforts to promote vegetable intake among adolescents. The statistical analyses of social inequality in vegetable intake demonstrate that it is important to address both absolute and relative social inequality as these two phenomena may develop differently.
Synaptic loss in schizophrenia: a meta-analysis and systematic review of synaptic protein and mRNA measures
Authors: Osimo Emanuele Felice , Beck Katherine , Reis Marques Tiago , Howes Oliver D
Published: March 2018

Although synaptic loss is thought to be core to the pathophysiology of schizophrenia, the nature, consistency and magnitude of synaptic protein and mRNA changes has not been systematically appraised. Our objective was thus to systematically review and meta-analyse findings. The entire PubMed database was searched for studies from inception date to the 1st of July 2017. We selected case-control postmortem studies in schizophrenia quantifying synaptic protein or mRNA levels in brain tissue. The difference in protein and mRNA levels between cases and controls was extracted and meta-analysis conducted. Among the results, we found a significant reduction in synaptophysin in schizophrenia in the hippocampus (effect size: −0.65, p < 0.01), frontal (effect size: −0.36, p = 0.04), and cingulate cortices (effect size: −0.54, p = 0.02), but no significant changes for synaptophysin in occipital and temporal cortices, and no changes for SNAP-25, PSD-95, VAMP, and syntaxin in frontal cortex. There were insufficient studies for meta-analysis of complexins, synapsins, rab3A and synaptotagmin and mRNA measures. Findings are summarised for these, which generally show reductions in SNAP-25, PSD-95, synapsin and rab3A protein levels in the hippocampus but inconsistency in other regions. Our findings of moderate–large reductions in synaptophysin in hippocampus and frontal cortical regions, and a tendency for reductions in other pre- and postsynaptic proteins in the hippocampus are consistent with models that implicate synaptic loss in schizophrenia. However, they also identify potential differences between regions and proteins, suggesting synaptic loss is not uniform in nature or extent.
MiR-16-5p targets SESN1 to regulate the p53 signaling pathway, affecting myoblast proliferation and apoptosis, and is involved in myoblast differentiation
Authors: Cai Bolin , Ma Manting , Chen Biao , Li Zhenhui , Abdalla Bahareldin Ali , Nie Qinghua , Zhang Xiquan
Published: March 2018

The proliferation, apoptosis, and differentiation of myoblasts are essential processes in skeletal muscle development. During this developmental process, microRNAs (miRNAs) play crucial roles. In our previous RNA-seq study (accession number GSE62971), we found that miR-16-5p was differentially expressed between fast and slow growth in chicken. In this study, we report that miR-16-5p could inhibit myoblast proliferation, promote myoblast apoptosis, and repress myoblast differentiation by directly binding to the 3′ UTR of SESN1, which is also differentially expressed. Overexpression of SESN1 significantly promoted the proliferation, inhibited apoptosis, and induced differentiation of myoblasts. Conversely, its loss of function hampered myoblast proliferation, facilitated myoblast apoptosis, and inhibited myoblast differentiation. Interestingly, we found SESN1 could regulate p53 by a feedback mechanism, thereby participating in the regulation of p53 signaling pathway, which suggests that this feedback is indispensable for myoblast proliferation and apoptosis. Altogether, these data demonstrated that miR-16-5p directly targets SESN1 to regulate the p53 signaling pathway, and therefore affecting myoblast proliferation and apoptosis. Additionally, SESN1 targets myogenic genes to control myoblast differentiation.
Cytochrome c speeds up caspase cascade activation by blocking 14-3-3ε-dependent Apaf-1 inhibition
Authors: Elena-Real Carlos A. , Díaz-Quintana Antonio , González-Arzola Katiuska , Velázquez-Campoy Adrián , Orzáez Mar , López-Rivas Abelardo , Gil-Caballero Sergio , De la Rosa Miguel Á. , Díaz-Moreno Irene
Published: March 2018

Apoptosis is a highly regulated form of programmed cell death, essential to the development and homeostasis of multicellular organisms. Cytochrome c is a central figure in the activation of the apoptotic intrinsic pathway, thereby activating the caspase cascade through its interaction with Apaf-1. Our recent studies have revealed 14-3-3ε (a direct inhibitor of Apaf-1) as a cytosolic cytochrome c target. Here we explore the cytochrome c / 14-3-3ε interaction and show the ability of cytochrome c to block 14-3-3ε-mediated Apaf-1 inhibition, thereby unveiling a novel function for cytochrome c as an indirect activator of caspase-9/3. We have used calorimetry, NMR spectroscopy, site mutagenesis and computational calculations to provide an insight into the structural features of the cytochrome c / 14-3-3ε complex. Overall, these findings suggest an additional cytochrome c-mediated mechanism to modulate apoptosome formation, shedding light onto the rigorous apoptotic regulation network.
Group 2 innate lymphoid cells protect lung endothelial cells from pyroptosis in sepsis
Authors: Lai Dengming , Tang Jing , Chen Linsong , Fan Erica K. , Scott Melanie J. , Li Yuehua , Billiar Timothy R. , Wilson Mark A. , Fang Xiangming , Shu Qiang , Fan Jie
Published: March 2018

Group 2 innate lymphoid cells (ILC2) are one of three subgroups of innate lymphoid cells (ILC1, ILC2, and ILC3), and the major ILC population detected in the lungs. The function of ILC2 in the regulation of lung inflammation remains unclear. In the current study, we explored an important role of ILC2 in protecting lung endothelial cell (EC) from pyroptosis in sepsis-induced acute lung inflammation and the underlying mechanism. Using a cecal ligation and puncture (CLP) mouse sepsis model, we demonstrated that IL-33, which is released in response to sepsis, acting through its receptor ST2 mediates ILC2 expansion in the lungs. We further showed that the increased ILC2 in the lungs secrete IL-9, which in turn prevents lung EC from undergoing pyroptosis, a pro-inflammatory cell death form, by attenuating caspase-1 activation. These findings suggest a previously unidentified innate pathway that negatively regulates lung inflammation following sepsis.
Author Correction: Cancer-associated fibroblasts induce metalloprotease-independent cancer cell invasion of the basement membrane
Authors: Glentis Alexandros , Oertle Philipp , Mariani Pascale , Chikina Aleksandra , El Marjou Fatima , Attieh Youmna , Zaccarini Francois , Lae Marick , Loew Damarys , Dingli Florent , Sirven Philemon , Schoumacher Marie , Gurchenkov Basile G. , Plodinec Marija , Vignjevic Danijela Matic
Published: March 2018

In the original version of this Article, financial support and contributions in manuscript preparation were not fully acknowledged. The PDF and HTML versions of the Article have now been corrected to include the following:

‘M.P. and P.O. would like to thank Prof. Roderick Y.H. Lim for advice during manuscript preparation and for providing the laboratory and microscopy infrastructure.… [We also thank] the NanoteraProject, awarded to the PATLiSciII Consortium (M.P and P.O)…’
Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont
Authors: Pluvinage Benjamin , Grondin Julie M. , Amundsen Carolyn , Klassen Leeann , Moote Paul E. , Xiao Yao , Thomas Dallas , Pudlo Nicholas A. , Anele Anuoluwapo , Martens Eric C. , Inglis G. Douglas , Uwiera Richard E. R. , Boraston Alisdair B. , Abbott D. Wade
Published: March 2018

In red algae, the most abundant principal cell wall polysaccharides are mixed galactan agars, of which agarose is a common component. While bioconversion of agarose is predominantly catalyzed by bacteria that live in the oceans, agarases have been discovered in microorganisms that inhabit diverse terrestrial ecosystems, including human intestines. Here we comprehensively define the structure–function relationship of the agarolytic pathway from the human intestinal bacterium Bacteroides uniformis (Bu) NP1. Using recombinant agarases from Bu NP1 to completely depolymerize agarose, we demonstrate that a non-agarolytic Bu strain can grow on GAL released from agarose. This relationship underscores that rare nutrient utilization by intestinal bacteria is facilitated by the acquisition of highly specific enzymes that unlock inaccessible carbohydrate resources contained within unusual polysaccharides. Intriguingly, the agarolytic pathway is differentially distributed throughout geographically distinct human microbiomes, reflecting a complex historical context for agarose consumption by human beings.
Disentangling the role of floral sensory stimuli in pollination networks
Authors: Kantsa Aphrodite , Raguso Robert A. , Dyer Adrian G. , Olesen Jens M. , Tscheulin Thomas , Petanidou Theodora
Published: March 2018

Despite progress in understanding pollination network structure, the functional roles of floral sensory stimuli (visual, olfactory) have never been addressed comprehensively in a community context, even though such traits are known to mediate plant–pollinator interactions. Here, we use a comprehensive dataset of floral traits and a novel dynamic data-pooling methodology to explore the impacts of floral sensory diversity on the structure of a pollination network in a Mediterranean scrubland. Our approach tracks transitions in the network behaviour of each plant species throughout its flowering period and, despite dynamism in visitor composition, reveals significant links to floral scent, and/or colour as perceived by pollinators. Having accounted for floral phenology, abundance and phylogeny, the persistent association between floral sensory traits and visitor guilds supports a deeper role for sensory bias and diffuse coevolution in structuring plant–pollinator networks. This knowledge of floral sensory diversity, by identifying the most influential phenotypes, could help prioritize efforts for plant–pollinator community restoration.
Efficient molecular evolution to generate enantioselective enzymes using a dual-channel microfluidic droplet screening platform
Authors: Ma Fuqiang , Chung Meng Ting , Yao Yuan , Nidetz Robert , Lee Lap Man , Liu Allen P. , Feng Yan , Kurabayashi Katsuo , Yang Guang-Yu
Published: March 2018

Directed evolution has long been a key strategy to generate enzymes with desired properties like high selectivity, but experimental barriers and analytical costs of screening enormous mutant libraries have limited such efforts. Here, we describe an ultrahigh-throughput dual-channel microfluidic droplet screening system that can be used to screen up to ~107 enzyme variants per day. As an example case, we use the system to engineer the enantioselectivity of an esterase to preferentially produce desired enantiomers of profens, an important class of anti-inflammatory drugs. Using two types of screening working modes over the course of five rounds of directed evolution, we identify (from among 5 million mutants) a variant with 700-fold improved enantioselectivity for the desired (S)-profens. We thus demonstrate that this screening platform can be used to rapidly generate enzymes with desired enzymatic properties like enantiospecificity, chemospecificity, and regiospecificity.
An assessment of neuronal calcium sensor-1 and response to neoadjuvant chemotherapy in breast cancer patients
Authors: Moore Lauren M. , Wilkinson Rachel , Altan Mehmet , Toki Maria , Carvajal-Hausdorf Daniel E. , McGuire John , Ehrlich Barbara E. , Rimm David L.
Published: March 2018

Neuronal calcium sensor-1 (NCS-1) has been identified as a binding partner of the taxane, paclitaxel. Our previous study showed that overexpression of NCS-1 increased the efficacy of paclitaxel in vitro, but was associated with poor clinical outcome. Here, we determine if NCS-1 expression is associated with pathological complete response (pCR) to taxane-based neoadjuvant chemotherapy in 105 pre-treatment breast cancer biopsies. Elevated expression of NCS-1 was found to be positively associated with pCR. These results suggest that NCS-1 may be a predictive biomarker for response to taxane-based neoadjuvant chemotherapy in breast cancer.
Structural model of human dUTPase in complex with a novel proteinaceous inhibitor
Authors: Nyíri Kinga , Mertens Haydyn D. T. , Tihanyi Borbála , Nagy Gergely N. , Kőhegyi Bianka , Matejka Judit , Harris Matthew J. , Szabó Judit E. , Papp-Kádár Veronika , Németh-Pongrácz Veronika , Ozohanics Olivér , Vékey Károly , Svergun Dmitri I. , Borysik Antoni J. , Vértessy Beáta G.
Published: March 2018

Human deoxyuridine 5′-triphosphate nucleotidohydrolase (dUTPase), essential for DNA integrity, acts as a survival factor for tumor cells and is a target for cancer chemotherapy. Here we report that the Staphylococcal repressor protein StlSaPIBov1 (Stl) forms strong complex with human dUTPase. Functional analysis reveals that this interaction results in significant reduction of both dUTPase enzymatic activity and DNA binding capability of Stl. We conducted structural studies to understand the mechanism of this mutual inhibition. Small-angle X-ray scattering (SAXS) complemented with hydrogen-deuterium exchange mass spectrometry (HDX-MS) data allowed us to obtain 3D structural models comprising a trimeric dUTPase complexed with separate Stl monomers. These models thus reveal that upon dUTPase-Stl complex formation the functional homodimer of Stl repressor dissociates, which abolishes the DNA binding ability of the protein. Active site forming dUTPase segments were directly identified to be involved in the dUTPase-Stl interaction by HDX-MS, explaining the loss of dUTPase activity upon complexation. Our results provide key novel structural insights that pave the way for further applications of the first potent proteinaceous inhibitor of human dUTPase.
A Highly Potent and Broadly Neutralizing H1 Influenza-Specific Human Monoclonal Antibody
Authors: Nogales Aitor , Piepenbrink Michael S. , Wang Jiong , Ortega Sandra , Basu Madhubanti , Fucile Christopher F. , Treanor John J. , Rosenberg Alexander F. , Zand Martin S. , Keefer Michael C. , Martinez-Sobrido Luis , Kobie James J.
Published: March 2018

Influenza’s propensity for antigenic drift and shift, and to elicit predominantly strain specific antibodies (Abs) leaves humanity susceptible to waves of new strains with pandemic potential for which limited or no immunity may exist. Subsequently new clinical interventions are needed. To identify hemagglutinin (HA) epitopes that if targeted may confer universally protective humoral immunity, we examined plasmablasts from a subject that was immunized with the seasonal influenza inactivated vaccine, and isolated a human monoclonal Ab (mAb), KPF1. KPF1 has broad and potent neutralizing activity against H1 influenza viruses, and recognized 83% of all H1 isolates tested, including the pandemic 1918 H1. Prophylactically, KPF1 treatment resulted in 100% survival of mice from lethal challenge with multiple H1 influenza strains and when given as late as 72 h after challenge with A/California/04/2009 H1N1, resulted in 80% survival. KPF1 recognizes a novel epitope in the HA globular head, which includes a highly conserved amino acid, between the Ca and Cb antigenic sites. Although recent HA stalk-specific mAbs have broader reactivity, their potency is substantially limited, suggesting that cocktails of broadly reactive and highly potent HA globular head-specific mAbs, like KPF1, may have greater clinical feasibility for the treatment of influenza infections.
A smartphone app to reduce excessive alcohol consumption: Identifying the effectiveness of intervention components in a factorial randomised control trial
Authors: Crane David , Garnett Claire , Michie Susan , West Robert , Brown Jamie
Published: March 2018

Our aim was to evaluate intervention components of an alcohol reduction app: Drink Less. Excessive drinkers (AUDIT> =8) were recruited to test enhanced versus minimal (reduced functionality) versions of five app modules in a 25 factorial trial. Modules were: Self-monitoring and Feedback, Action Planning, Identity Change, Normative Feedback, and Cognitive Bias Re-training. Outcome measures were: change in weekly alcohol consumption (primary); full AUDIT score, app usage, app usability (secondary). Main effects and two-way interactions were assessed by ANOVA using intention-to-treat. A total of 672 study participants were included. There were no significant main effects of the intervention modules on change in weekly alcohol consumption or AUDIT score. There were two-way interactions between enhanced Normative Feedback and Cognitive Bias Re-training on weekly alcohol consumption (F = 4.68, p = 0.03) and between enhanced Self-monitoring and Feedback and Action Planning on AUDIT score (F = 5.82, p = 0.02). Enhanced Self-monitoring and Feedback was used significantly more often and rated significantly more positively for helpfulness, satisfaction and recommendation to others than the minimal version. To conclude, in an evaluation of the Drink Less smartphone application, the combination of enhanced Normative Feedback and Cognitive Bias Re-training and enhanced Self-monitoring and Feedback and Action Planning yielded improvements in alcohol-related outcomes after 4-weeks.
A Prognostic Nomogram for Postoperative Bone Remodeling in Patients with ADDWoR
Authors: Liu Xiaohan , Shen Pei , Wang Xiangyu , Zhang Shanyong , Zheng Jiawei , Yang Chi
Published: March 2018

This study aimed to establish an effective prognostic nomogram for predicting the probability of postoperative bone remodeling of patients with anterior disc displacement without reduction (ADDWoR). The nomogram was based on a retrospective study on patients underwent surgical approaches for ADDWoR at Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University from January, 2007 to January, 2017. A multivariate logistic regression analysis was used to develop variables suitable for probability estimation model. The predictive accuracy and discriminative ability were determined by ROC (AUC-index) and calibration curve. Results were validated using bootstrap resampling with all statistical tests two-sided. 1110 patients were included in the analysis. The probability of postoperative bone remodeling in ADDWoR was 0.51. Six independent prognostic factors including age of onset, nocturnal bruxism, disc morphology, BMD, Wilkes’ classification, and postoperative splint therapy were integrated to construct the nomogram. The probability estimation model showed good discrimination in both internal and external validation with AUC-index of 0.84. The calibration curves for probability of postoperative bone remodeling showed optimal agreement with actual observation. In conclusion, a nomogram was established to provide individual prediction of postoperative bone remodeling for patients with ADDWoR treated by arthroscopy surgery.
Combined effects of elevated temperature and CO2 enhance threat from low temperature hazard to winter wheat growth in North China
Authors: Tan Kaiyan , Zhou Guangsheng , Lv Xiaomin , Guo Jianping , Ren Sanxue
Published: March 2018

We examined the growth and yield of winter wheat (Triticum aestivum) in response to the predicted elevated CO2 concentration and temperature to determine the mechanism of the combined impacts in North China Plain. An elevated treatment (CO2: 600 μmol mol−1, temperature: +2.5~3.0 °C, ECTI) and a control treatment (ambient CO2 and temperature, CK) were conducted in open-top chambers from October 2013 to June 2016. Post-winter growth stages of winter wheat largely advanced and shifted to a cooler period of nature season under combined impact of elevated CO2 and temperature during the entire growing season. The mean temperature and accumulated photosynthetic active radiations (PAR) over the post-winter growing period in ECTI decreased by 0.8–1.5 °C and 10–13%, respectively compared with that in CK, negatively impacted winter wheat growth. As a result, winter wheat in ECTI suffered from low temperature hazards during critical period of floret development and anthesis and grain number per ear was reduced by 10–31% in the three years. Although 1000-kernel weight in ECTI increased by 8–9% mainly due to elevated CO2, increasing CO2 concentration from 400 to 600 μmol mol−1 throughout the growth stage was not able to offset the adverse effect of warming on winter wheat growth and yield.
Spatially explicit poisoning risk affects survival rates of an obligate scavenger
Authors: Monadjem A. , Kane A. , Botha A. , Kelly C. , Murn C.
Published: March 2018

Obligate scavengers such as vultures provide critical ecosystem services and their populations have undergone severe declines in Asia and Africa. Intentional poisoning is a major threat to vultures in Africa, yet the impact on vulture populations of where poisoned carcasses are positioned is not known. We used re-sightings of 183 African white-backed vultures captured and tagged in two regions of South Africa, some 200 km apart, to estimate spatial differences in relative survival rates across life stages. Juvenile survival rates were similar in the two regions, whilst subadult and adult survival rates differed significantly. Using agent-based modelling, we show that this pattern of relative survival rates is consistent between regions that differ in intensity of poisoning, despite the proximity of the two regions. This may have important consequences for vulture conservation and the targeting of conservation efforts, particularly with regard to the efficacy of “vulture safe zones” around vulture breeding populations.
A Multi-modality Approach Towards Elucidation of the Mechanism for Human Achilles Tendon Bending During Passive Ankle Rotation
Authors: Kinugasa Ryuta , Taniguchi Keigo , Yamamura Naoto , Fujimiya Mineko , Katayose Masaki , Takagi Shu , Edgerton V. Reggie , Sinha Shantanu
Published: March 2018

The in vitro unconstrained Achilles tendon is nearly straight, while in vivo experiments reveal that the proximal region of the Achilles tendon, adjacent to Kager’s fat pad, bends ventrally during plantarflexion but remains nearly straight during dorsiflexion. Tendon bending is an important factor in determining the displacement of the foot compared to the shortening of the muscle fibers. The objective of this study was to elucidate the various mechanisms that could cause tendon bending, which currently remain unknown. Examination of Thiel-embalmed cadavers, with preservation of native articular joint mobility, revealed that the Achilles tendon still bent ventrally even when its surrounding tissues, including the skin surface, Kager’s fat pad, and distal portions of the soleus muscle were removed. Shear modulus and collagen fiber orientation were distributed homogeneously with respect to the longitudinal line of the tendon, minimizing their causative contributions to the bending. Given that tendon bending is not caused by either the nature of the deformations of the tissues surrounding the Achilles tendon or its physical properties, we conclude that it results from the geometric architecture of the Achilles tendon and its configuration with respect to the surrounding tissues.
Nutritionally recommended food for semi- to strict vegetarian diets based on large-scale nutrient composition data
Authors: Kim Seunghyeon , Fenech Michael F. , Kim Pan-Jun
Published: March 2018

Diet design for vegetarian health is challenging due to the limited food repertoire of vegetarians. This challenge can be partially overcome by quantitative, data-driven approaches that utilise massive nutritional information collected for many different foods. Based on large-scale data of foods’ nutrient compositions, the recent concept of nutritional fitness helps quantify a nutrient balance within each food with regard to satisfying daily nutritional requirements. Nutritional fitness offers prioritisation of recommended foods using the foods’ occurrence in nutritionally adequate food combinations. Here, we systematically identify nutritionally recommendable foods for semi- to strict vegetarian diets through the computation of nutritional fitness. Along with commonly recommendable foods across different diets, our analysis reveals favourable foods specific to each diet, such as immature lima beans for a vegan diet as an amino acid and choline source, and mushrooms for ovo-lacto vegetarian and vegan diets as a vitamin D source. Furthermore, we find that selenium and other essential micronutrients can be subject to deficiency in plant-based diets, and suggest nutritionally-desirable dietary patterns. We extend our analysis to two hypothetical scenarios of highly personalised, plant-based methionine-restricted diets. Our nutrient-profiling approach may provide a useful guide for designing different types of personalised vegetarian diets.
Retinal S-opsin dominance in Ansell’s mole-rats (Fukomys anselli) is a consequence of naturally low serum thyroxine
Authors: Henning Yoshiyuki , Mladěnková Nella , Burda Hynek , Szafranski Karol , Begall Sabine
Published: March 2018

Mammals usually possess a majority of medium-wavelength sensitive (M-) and a minority of short-wavelength sensitive (S-) opsins in the retina, enabling dichromatic vision. Unexpectedly, subterranean rodents from the genusFukomysexhibit an S-opsin majority, which is exceptional among mammals, albeit with no apparent adaptive value. Because thyroid hormones (THs) are pivotal forM-opsinexpression and metabolic rate regulation, we have, for the first time, manipulated TH levels in the Ansell’s mole-rat (Fukomys anselli) using osmotic pumps. In Ansell’s mole-rats, the TH thyroxine (T4) is naturally low, likely as an adaptation to the harsh subterranean ecological conditions by keeping resting metabolic rate (RMR) low. We measured gene expression levels in the eye, RMR, and body mass (BM) in TH-treated animals. T4 treatment increased both,S-andM-opsinexpression, albeitM-opsinexpression at a higher degree. However, this plasticity was only given in animals up to approximately 2.5 years. Mass-specific RMR was not affected following T4 treatment, although BM decreased. Furthermore, the T4 inactivation rate is naturally higher inF.ansellicompared to laboratory rodents. This is the first experimental evidence that the S-opsin majority in Ansell’s mole-rats is a side effect of low T4, which is downregulated to keep RMR low.
Transcriptional landscape of human endogenous retroviruses (HERVs) and other repetitive elements in psoriatic skin
Authors: Lättekivi Freddy , Kõks Sulev , Keermann Maris , Reimann Ene , Prans Ele , Abram Kristi , Silm Helgi , Kõks Gea , Kingo Külli
Published: March 2018

Human endogenous retrovirus (HERV) sequences make up at least 8% of the human genome. Transcripts originating from these loci as well as proteins encoded by them have been detected in various tissues. HERVs are believed to be implicated in autoimmune diseases, however the extent to which, has remained unclear. Differential expression studies have so far been limited to certain HERV subfamilies with conserved sequences. No studies have been published describing the genome-wide expression pattern of HERVs and repetitive elements in the context of psoriasis. In the present study, we analysed total RNA sequencing data from skin samples of 12 psoriasis patients and 12 healthy controls, which enabled us to describe the entire transcriptional landscape of repetitive elements. We report high levels of repetitive element expression in the skin of psoriasis patients as well as healthy controls. The majority of differentially expressed elements were downregulated in lesional and non-lesional skin, suggesting active HERV suppression in the pro-inflammatory environment of psoriatic skin. However, we also report upregulation of a small subset of HERVs previously described in the context of autoimmune diseases, such as members of the HERV-K and W families, with the potential to affect the immunopathogenesis of psoriasis.
Intravenous administration of anti-inflammatory mesenchymal stem cell spheroids reduces chronic alcohol intake and abolishes binge-drinking
Authors: Ezquer Fernando , Morales Paola , Quintanilla María Elena , Santapau Daniela , Lespay-Rebolledo Carolyne , Ezquer Marcelo , Herrera-Marschitz Mario , Israel Yedy
Published: March 2018

Chronic alcohol intake leads to neuroinflammation and astrocyte dysfunction, proposed to perpetuate alcohol consumption and to promote conditioned relapse-like binge drinking. In the present study, human mesenchymal stem cells (MSCs) were cultured in 3D-conditions to generate MSC-spheroids, which greatly increased MSCs anti-inflammatory ability and reduced cell volume by 90% versus conventionally 2D-cultured MSCs, enabling their intravenous administration and access to the brain. It is shown, in an animal model of chronic ethanol intake and relapse-drinking, that both the intravenous and intra-cerebroventricular administration of a single dose of MSC-spheroids inhibited chronic ethanol intake and relapse-like drinking by 80–90%, displaying significant effects over 3–5 weeks. The MSC-spheroid administration fully normalized alcohol-induced neuroinflammation, as shown by a reduced astrocyte activation, and markedly increased the levels of the astrocyte Na-glutamate (GLT-1) transporter. This research suggests that the intravenous administration of MSC-spheroids may constitute an effective new approach for the treatment of alcohol-use disorders.
ChIP-seq and ChIP-exo profiling of Pol II, H2A.Z, and H3K4me3 in human K562 cells
Authors: Mchaourab Zenab F. , Perreault Andrea A. , Venters Bryan J.
Published: March 2018

The human K562 chronic myeloid leukemia cell line has long served as an experimental paradigm for functional genomic studies. To systematically and functionally annotate the human genome, the ENCODE consortium generated hundreds of functional genomic data sets, such as chromatin immunoprecipitation coupled to sequencing (ChIP-seq). While ChIP-seq analyses have provided tremendous insights into gene regulation, spatiotemporal insights were limited by a resolution of several hundred base pairs. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq that overcomes this limitation by providing higher precision mapping of protein-DNA interactions. To study the interplay of transcription initiation and chromatin, we profiled the genome-wide locations for RNA polymerase II (Pol II), the histone variant H2A.Z, and the histone modification H3K4me3 using ChIP-seq and ChIP-exo. In this Data Descriptor, we present detailed information on parallel experimental design, data generation, quality control analysis, and data validation. We discuss how these data lay the foundation for future analysis to understand the relationship between the occupancy of Pol II and nucleosome positions at near base pair resolution.
Molecular interaction-dependent surface potentials of sequentially polymerized alucone films
Authors: Choi Ui-Jin , Kim Hyein , Park Yi-Seul , Lee Hyemi , Lee Jin Seok
Published: March 2018

Here, we investigated the relationship between the surface potentials and molecular interactions in the alucone films grown by molecular layer deposition.
Evaluating excited state atomic polarizabilities of chromophores
Authors: Heid Esther , Hunt Patricia A. , Schröder Christian
Published: March 2018

Ground and excited state atomic polarizabilities of the chromophoresN-methyl-6-oxyquinolinium betaine and coumarin 153 have been evaluatedviaquantum mechanics.
Insights into exfoliation possibility of MAX phases to MXenes
Authors: Khazaei Mohammad , Ranjbar Ahmad , Esfarjani Keivan , Bogdanovski Dimitri , Dronskowski Richard , Yunoki Seiji
Published: March 2018

Chemical exfoliation of MAX phases into two-dimensional (2D) MXenes can be considered as a major breakthrough in the synthesis of novel 2D systems.
Life cycle assessment of the production of surface-active alkyl polyglycosides from acid-assisted ball-milled wheat straw compared to the conventional production based on corn-starch
Authors: Brière Raphaël , Loubet Philippe , Glogic Edis , Estrine Boris , Marinkovic Sinisa , Jérôme François , Sonnemann Guido
Published: March 2018

The environmental impacts of alkyl polyglycosides production from wheat straw are assessed and compared to the conventional process based on corn starch.
Development of a peptide-based bifunctional chelator conjugated to a cytotoxic drug for the treatment of melanotic melanoma
Authors: Gaonkar Raghuvir H. , Baishya Rinku , Paul Brahamacharry , Dewanjee Saikat , Ganguly Shantanu , Debnath Mita C. , Ganguly Soumya
Published: March 2018

Peptide-conjugated cytotoxic gemcitabine for the treatment of melanotic melanoma.
Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease
Authors: Ackerman Cheri M. , Weber Peter K. , Xiao Tong , Thai Bao , Kuo Tiffani J. , Zhang Emily , Pett-Ridge Jennifer , Chang Christopher J.
Published: March 2018

Coregistering quantitative high-resolution metal imaging with fluorescence imaging identifies copper accumulation in megamitochondria within intact neuroretinal slices.
Nanocellulose templated growth of ultra-small bismuth nanoparticles for enhanced radiation therapy
Authors: Jiao Li , Li Qingxuan , Deng Junjie , Okosi Nsikak , Xia Junfei , Su Ming
Published: March 2018

An unmet need in nanomedicine is to prepare biocompatible and renal clearable nanoparticles by controlling the diameter, composition and surface properties of the nanoparticles.
Seawater splitting for hydrogen evolution by robust electrocatalysts from secondary M (M = Cr, Fe, Co, Ni, Mo) incorporated Pt
Authors: Zheng Jingjing , Zhao Yuanyuan , Xi He , Li Changhai
Published: March 2018

Water splitting is a promising technique for clean hydrogen energy harvesting.
A water-based room temperature synthesis of ZIF-93 for CO2 adsorption
Authors: Ramos-Fernandez E. V. , Grau-Atienza A. , Farrusseng D. , Aguado S.
Published: March 2018

ZIF-93 synthesized in water medium at room temperature with high yield for CO2/N2 separation.
“Ethanol–water exchange” nanobubbles templated hierarchical hollow β-Mo2C/N-doped carbon composite nanospheres as an efficient hydrogen evolution electrocatalyst
Authors: Diao Lechen , Qin Jian , Zhao Naiqin , Shi Chunsheng , Liu Enzuo , He Fang , Ma Liying , Li Jiajun , He Chunnian
Published: March 2018

“Ethanol–water exchange” nanobubbles were utilized to produce hollow β-Mo2C/N-doped carbon nanospheres for use as an efficient hydrogen evolution electrocatalyst.
A single-phase all-solid-state lithium battery based on Li1.5Cr0.5Ti1.5(PO4)3 for high rate capability and low temperature operation
Authors: Inoishi Atsushi , Nishio Akira , Yoshioka Yuto , Kitajou Ayuko , Okada Shigeto
Published: March 2018

We report a battery made from a single material using Li1.5Cr0.5Ti1.5(PO4)3 as the anode, cathode and electrolyte.
Characterization of the structural ensembles of p53 TAD2 by molecular dynamics simulations with different force fields
Authors: Ouyang Yanhua , Zhao Likun , Zhang Zhuqing
Published: March 2018

The conformations of p53 TAD2 in complexes and sampled in simulations with five force fields.
Long-range corrected density functional through the density matrix expansion based semilocal exchange hole
Authors: Patra Bikash , Jana Subrata , Samal Prasanjit
Published: March 2018

The exchange hole, which is one of the principal constituents of the density functional formalism, can be used to design accurate range-separated hybrid functionals in association with appropriate correlation.
The effect of dopant chirality on the properties of self-assembling materials with a ferroelectric order
Authors: Węgłowska Dorota , Perkowski Paweł , Chrunik Maciej , Czerwiński Michał
Published: March 2018

The first example of hockey-stick compounds exhibiting a smectic I phase with a direct transition to the isotropic phase.
Two-dimensional transition metal dichalcogenides: interface and defect engineering
Authors: Hu Zehua , Wu Zhangting , Han Cheng , He Jun , Ni Zhenhua , Chen Wei
Published: March 2018

This review summarizes the recent advances in understanding the effects of interface and defect engineering on the electronic and optical properties of TMDCs, as well as their applications in advanced (opto)electronic devices.
Hypotoxic copper complexes with potent anti-metastatic and anti-angiogenic activities against cancer cells
Authors: Shi Xiangchao , Chen Zhongyan , Wang Yanjun , Guo Zijian , Wang Xiaoyong
Published: March 2018

Phenanthroline Cu(ii) complexes with cationic substituents exhibit great potential to suppress metastasis, angiogenesis and proliferation of tumor cells through multiple pathways.
Catalytic cascade conversion of furfural to 1,4-pentanediol in a single reactor
Authors: Liu Fei , Liu Qiaoyun , Xu Jinming , Li Lei , Cui Yi-Tao , Lang Rui , Li Lin , Su Yang , Miao Shu , Sun Hui , Qiao Botao , Wang Aiqin , Jérôme Francois , Zhang Tao
Published: March 2018

The selective transformation of furfural to 1,4-pentanediol has been achieved with up to 90% yield in a CO2/H2/H2O system over Ru catalytic species supported on a mesoporous carbon.
FRET-based metal ion sensing by a crown-containing bisstyryl dye
Authors: Ustimova M. A. , Lebedeva A. Yu. , Fedorov Yu. V. , Berdnikova D. V. , Fedorova O. A.
Published: March 2018

A ratiometric cation FRET system containing two binding centers demonstrates distinct fluorescence changes upon interaction with alkaline, alkaline earth and heavy metal cations.
Sn-Doped defect pyrochlore oxide KNbWO6·H2O microcrystals and their photocatalytic reduction of CO2
Authors: Zeng Xu , Chen Yan , Jiao Shihui , Fang Zhenxing , Wang Boran , Pang Guangsheng , Feng Shouhua
Published: March 2018

KNbWO6·H2O:0.208Sn2+ has been used as a photocatalyst for the conversion of CO2, utilizing abundant solar light to cope with energy and environmental issues.
Synthesis of plasmodione metabolites and13C-enriched plasmodione as chemical tools for drug metabolism investigation
Authors: Feng Liwen , Lanfranchi Don Antoine , Cotos Leandro , Cesar-Rodo Elena , Ehrhardt Katharina , Goetz Alice-Anne , Zimmermann Herbert , Fenaille François , Blandin Stephanie A. , Davioud-Charvet Elisabeth
Published: March 2018

A 10-step synthesis of the antimalarial lead,13C18-enriched plasmodione, and of seven putative metabolites is described.
Tri- and di-fluoroethylation of alkenes by visible light photoredox catalysis
Authors: Pan Xiao-Yang , Zhao Yue , Qu Hong-An , Lin Jin-Hong , Hang Xiao-Chun , Xiao Ji-Chang
Published: March 2018

The photoredox-catalyzed solvent-dependent tri-/di-fluoroethylation of alkenes with sulfonium salts (Ph2S+CH2RF TfO−) (RF = CF3 or HCF2) is described.
Silver-catalyzed ring-opening difluoromethylthiolation/trifluoromethylthiolation of cycloalkanols with PhSO2SCF2H or PhSO2SCF3
Authors: Xu Bin , Wang Decai , Hu Yonghong , Shen Qilong
Published: March 2018

A silver-catalyzed ring-opening difluoromethylthiolation/trifluoromethylthiolation of cycloalkanols including cyclopropanols, cyclobutanols, cyclopentanols, cyclohexanols and cycloheptanols was described.
Tailoring of pore structure in mesoporous carbon for favourable flavin mediated interfacial electron transfer in microbial fuel cells
Authors: Tang Wei , Wu Xiao-Shuai , Qiao Yan , Wang Rui-Jie , Luo Xian
Published: March 2018

Spherical mesopores with large pore width are more favorable to flavin mediated interfacial electron transfer in microbial fuel cells.
Discovery and preliminary SAR of 14-aryloxy-andrographolide derivatives as antibacterial agents with immunosuppressant activity
Authors: Li Feng , Li Xiao-Min , Sheng Dekuan , Chen Shao-Ru , Nie Xin , Liu Zhuyun , Wang Decai , Zhao Qi , Wang Yitao , Wang Ying , Zhou Guo-Chun
Published: March 2018

6b17 and 9b are active against 3 tested bacteria while they block IL-6/STAT3, TLR4/NF-κB and TNF-α/NF-κB pathways. 7b1 and 8b1 are selectively active against E. faecalis but 7b1 selectively blocks TNF-α/NF-κB pathway and 8b1 selectively blocks TLR4/NF-κB pathway.
Formation of complexes in aqueous solutions of amphiphilic triblock polyelectrolytes of different topologies and an oppositely charged protein
Authors: Papagiannopoulos Aristeidis , Karayianni Maria , Pispas Stergios , Radulescu Aurel
Published: March 2018

The complexation of lysozyme with aggregates of two triblock amphiphilic polyelectrolytes of different molecular topologies is investigated by scattering techniques.
Graphitic carbon nitride quantum dot decorated three-dimensional graphene as an efficient metal-free electrocatalyst for triiodide reduction
Authors: Yuan Hong , Liu Jia , Li Hansheng , Li Yongjian , Liu Xiufeng , Shi Daxin , Wu Qin , Jiao Qingze
Published: March 2018

Graphitic carbon nitride quantum dot decorated three-dimensional graphene as an efficient electrocatalyst exhibited synergistically enhanced electrochemical performance for triiodide reduction.
Unravelling the reaction chemistry and degradation mechanism in aqueous Zn/MnO2 rechargeable batteries
Authors: Zhao Shuai , Han Bo , Zhang Datong , Huang Qun , Xiao Lei , Chen Libao , Ivey Douglas G. , Deng Yida , Wei Weifeng
Published: March 2018

Two-step redox reactions (Mn(ii) ions ⇌ ZnMn2O4 spinel ⇌ layered Zn-birnessite) during the charge–discharge process.
Thermokinetic profile of NDM-1 and its inhibition by small carboxylic acids
Authors: Wang Qian , He Yuan , Lu Rui , Wang Wen-Ming , Yang Ke-Wu , Fan Hai Ming , Jin Yi , Blackburn G. Michael
Published: March 2018

The New Delhi metallo-β-lactamase (NDM-1) is an important clinical target for antimicrobial research, but there are insufficient clinically useful inhibitors and the details of NDM-1 enzyme catalysis remain unclear. The aim of this work is to provide a thermodynamic profile of NDM-1 catalysed hydrolysis of β-lactams using an isothermal titration calorimetry (ITC) approach and to apply this new method to the identification of new low-molecular-weight dicarboxylic acid inhibitors. The results reveal that hydrolysis of penicillin G and imipenem by NDM-1 share the same thermodynamic features with a significant intrinsic enthalpy change and the release of one proton into solution, while NDM-1 hydrolysis of cefazolin exhibits a different mechanism with a smaller enthalpy change and the release of two protons. The inhibitory constants of four carboxylic acids are found to be in the micromolar range. The compounds pyridine-2,6-dicarboxylic acid and thiazolidine-2,4-dicarboxylic acid show the best inhibitory potency and are confirmed to inhibit NDM-1 using a clinical strain of Escherichia coli. The pyridine compound is further shown to restore the susceptibility of this E. coli strain to imipenem, at an inhibitor concentration of 400 μM, while the thiazoline compound also shows a synergistic effect with imipenem. These results provide valuable information to enrich current understanding on the catalytic mechanism of NDM-1 and to aid the future optimisation of β-lactamase inhibitors based on these scaffolds to tackle the problem of antibiotic resistance.