bluuebunny/crossref_metadata_2025 huggingface dataset:
Two types of amyloidosis presenting in a single patient: a case series
Authors: Sidiqi M. Hasib , McPhail Ellen D. , Theis Jason D. , Dasari Surendra , Vrana Julie A. , Drosou Maria Eleni , Leung Nelson , Hayman Suzanne , Rajkumar S. Vincent , Warsame Rahma , Ansell Stephen M. , Gertz Morie A. , Grogan Martha , Dispenzieri Angela
Published: March 2019

The amyloidoses are a group of disorders with overlapping clinical presentations, characterized by aggregation and tissue deposition of misfolded proteins. The nature and source of the amyloidogenic protein determines therapy, therefore correct subtyping is critical to patient management. We report the clinicopathologic features of nine patients diagnosed with two amyloid types confirmed by liquid chromatography-coupled tandem mass spectrometry. The most common types were transthyrethin (n = 9) and immunoglobulin-derived (n = 7). Two patients did not have immunoglobulin-derived amyloidosis despite the presence of a monoclonal gammopathy. Eight patients were diagnosed with two types concurrently, and one patient had an 11-year interval between diagnoses. Histopathological distribution of amyloid was variable with vascular, interstitial, and periosteal deposits seen. Identification of a second type was incidental in seven patients, but led to genetic counselling in one patient and therapy directed at both amyloid subtypes in another. With longer survival of myeloma and AL amyloidosis patients and increasing prevalence of patients with wild-type transthyretin amyloidosis due to an aging population, the phenomenon of two amyloid types in a single patient will be encountered more frequently. In light of revolutionary new therapies for transthyretin amyloidosis (patisiran, tafamidis, and inotersen), recognition of dual amyloid types is highly clinically relevant.
Quantum electrodynamics at room temperature coupling a single vibrating molecule with a plasmonic nanocavity
Authors: Ojambati Oluwafemi S. , Chikkaraddy Rohit , Deacon William D. , Horton Matthew , Kos Dean , Turek Vladimir A. , Keyser Ulrich F. , Baumberg Jeremy J.
Published: March 2019

Interactions between a single emitter and cavity provide the archetypical system for fundamental quantum electrodynamics. Here we show that a single molecule of Atto647 aligned using DNA origami interacts coherently with a sub-wavelength plasmonic nanocavity, approaching the cooperative regime even at room temperature. Power-dependent pulsed excitation reveals Rabi oscillations, arising from the coupling of the oscillating electric field between the ground and excited states. The observed single-molecule fluorescent emission is split into two modes resulting from anti-crossing with the plasmonic mode, indicating the molecule is strongly coupled to the cavity. The second-order correlation function of the photon emission statistics is found to be pump wavelength dependent, varying from g(2)(0) = 0.4 to 1.45, highlighting the influence of vibrational relaxation on the Jaynes-Cummings ladder. Our results show that cavity quantum electrodynamic effects can be observed in molecular systems at ambient conditions, opening significant potential for device applications.
Urban pollution greatly enhances formation of natural aerosols over the Amazon rainforest
Authors: Shrivastava Manish , Andreae Meinrat O. , Artaxo Paulo , Barbosa Henrique M. J. , Berg Larry K. , Brito Joel , Ching Joseph , Easter Richard C. , Fan Jiwen , Fast Jerome D. , Feng Zhe , Fuentes Jose D. , Glasius Marianne , Goldstein Allen H. , Alves Eliane Gomes , Gomes Helber , Gu Dasa , Guenther Alex , Jathar Shantanu H. , Kim Saewung , Liu Ying , Lou Sijia , Martin Scot T. , McNeill V. Faye , Medeiros Adan , de Sá Suzane S. , Shilling John E. , Springston Stephen R. , Souza R. A. F. , Thornton Joel A. , Isaacman-VanWertz Gabriel , Yee Lindsay D. , Ynoue Rita , Zaveri Rahul A. , Zelenyuk Alla , Zhao Chun
Published: March 2019

One of the least understood aspects in atmospheric chemistry is how urban emissions influence the formation of natural organic aerosols, which affect Earth’s energy budget. The Amazon rainforest, during its wet season, is one of the few remaining places on Earth where atmospheric chemistry transitions between preindustrial and urban-influenced conditions. Here, we integrate insights from several laboratory measurements and simulate the formation of secondary organic aerosols (SOA) in the Amazon using a high-resolution chemical transport model. Simulations show that emissions of nitrogen-oxides from Manaus, a city of ~2 million people, greatly enhance production of biogenic SOA by 60–200% on average with peak enhancements of 400%, through the increased oxidation of gas-phase organic carbon emitted by the forests. Simulated enhancements agree with aircraft measurements, and are much larger than those reported over other locations. The implication is that increasing anthropogenic emissions in the future might substantially enhance biogenic SOA in pristine locations like the Amazon.
Shuttling a single charge across a one-dimensional array of silicon quantum dots
Authors: Mills A. R. , Zajac D. M. , Gullans M. J. , Schupp F. J. , Hazard T. M. , Petta J. R.
Published: March 2019

Significant advances have been made towards fault-tolerant operation of silicon spin qubits, with single qubit fidelities exceeding 99.9%, several demonstrations of two-qubit gates based on exchange coupling, and the achievement of coherent single spin-photon coupling. Coupling arbitrary pairs of spatially separated qubits in a quantum register poses a significant challenge as most qubit systems are constrained to two dimensions with nearest neighbor connectivity. For spins in silicon, new methods for quantum state transfer should be developed to achieve connectivity beyond nearest-neighbor exchange. Here we demonstrate shuttling of a single electron across a linear array of nine series-coupled silicon quantum dots in ~50 ns via a series of pairwise interdot charge transfers. By constructing more complex pulse sequences we perform parallel shuttling of two and three electrons at a time through the array. These experiments demonstrate a scalable approach to physically transporting single electrons across large silicon quantum dot arrays.
Loss of a proteostatic checkpoint in intestinal stem cells contributes to age-related epithelial dysfunction
Authors: Rodriguez-Fernandez Imilce A. , Qi Yanyan , Jasper Heinrich
Published: March 2019

A decline in protein homeostasis (proteostasis) has been proposed as a hallmark of aging. Somatic stem cells (SCs) uniquely maintain their proteostatic capacity through mechanisms that remain incompletely understood. Here, we describe and characterize a ‘proteostatic checkpoint’ in Drosophila intestinal SCs (ISCs). Following a breakdown of proteostasis, ISCs coordinate cell cycle arrest with protein aggregate clearance by Atg8-mediated activation of the Nrf2-like transcription factor cap-n-collar C (CncC). CncC induces the cell cycle inhibitor Dacapo and proteolytic genes. The capacity to engage this checkpoint is lost in ISCs from aging flies, and we show that it can be restored by treating flies with an Nrf2 activator, or by over-expression of CncC or Atg8a. This limits age-related intestinal barrier dysfunction and can result in lifespan extension. Our findings identify a new mechanism by which somatic SCs preserve proteostasis, and highlight potential intervention strategies to maintain regenerative homeostasis.
Topological transitions among skyrmion- and hedgehog-lattice states in cubic chiral magnets
Authors: Fujishiro Y. , Kanazawa N. , Nakajima T. , Yu X. Z. , Ohishi K. , Kawamura Y. , Kakurai K. , Arima T. , Mitamura H. , Miyake A. , Akiba K. , Tokunaga M. , Matsuo A. , Kindo K. , Koretsune T. , Arita R. , Tokura Y.
Published: March 2019

Manipulating topological spin textures is a key for exploring unprecedented emergent electromagnetic phenomena. Whereas switching control of magnetic skyrmions, e.g., the transitions between a skyrmion-lattice phase and conventional magnetic orders, is intensively studied towards development of future memory device concepts, transitions among spin textures with different topological orders remain largely unexplored. Here we develop a series of chiral magnets MnSi1−xGex, serving as a platform for transitions among skyrmion- and hedgehog-lattice states. By neutron scattering, Lorentz transmission electron microscopy and high-field transport measurements, we observe three different topological spin textures with variation of the lattice constant controlled by Si/Ge substitution: two-dimensional skyrmion lattice in x = 0–0.25 and two distinct three-dimensional hedgehog lattices in x = 0.3–0.6 and x = 0.7–1. The emergence of various topological spin states in the chemical-pressure-controlled materials suggests a new route for direct manipulation of the spin-texture topology by facile mechanical methods.
Metastable brain waves
Authors: Roberts James A. , Gollo Leonardo L. , Abeysuriya Romesh G. , Roberts Gloria , Mitchell Philip B. , Woolrich Mark W. , Breakspear Michael
Published: March 2019

Traveling patterns of neuronal activity—brain waves—have been observed across a breadth of neuronal recordings, states of awareness, and species, but their emergence in the human brain lacks a firm understanding. Here we analyze the complex nonlinear dynamics that emerge from modeling large-scale spontaneous neural activity on a whole-brain network derived from human tractography. We find a rich array of three-dimensional wave patterns, including traveling waves, spiral waves, sources, and sinks. These patterns are metastable, such that multiple spatiotemporal wave patterns are visited in sequence. Transitions between states correspond to reconfigurations of underlying phase flows, characterized by nonlinear instabilities. These metastable dynamics accord with empirical data from multiple imaging modalities, including electrical waves in cortical tissue, sequential spatiotemporal patterns in resting-state MEG data, and large-scale waves in human electrocorticography. By moving the study of functional networks from a spatially static to an inherently dynamic (wave-like) frame, our work unifies apparently diverse phenomena across functional neuroimaging modalities and makes specific predictions for further experimentation.
Tensor network simulation of multi-environmental open quantum dynamics via machine learning and entanglement renormalisation
Authors: Schröder Florian A. Y. N. , Turban David H. P. , Musser Andrew J. , Hine Nicholas D. M. , Chin Alex W.
Published: March 2019

The simulation of open quantum dynamics is a critical tool for understanding how the non-classical properties of matter might be functionalised in future devices. However, unlocking the enormous potential of molecular quantum processes is highly challenging due to the very strong and non-Markovian coupling of ‘environmental’ molecular vibrations to the electronic ‘system’ degrees of freedom. Here, we present an advanced but general computational strategy that allows tensor network methods to effectively compute the non-perturbative, real-time dynamics of exponentially large vibronic wave functions of real molecules. We demonstrate how ab initio modelling, machine learning and entanglement analysis can enable simulations which provide real-time insight and direct visualisation of dissipative photophysics, and illustrate this with an example based on the ultrafast process known as singlet fission.
Intracellular hydrogelation preserves fluid and functional cell membrane interfaces for biological interactions
Authors: Lin Jung-Chen , Chien Chen-Ying , Lin Chi-Long , Yao Bing-Yu , Chen Yuan-I , Liu Yu-Han , Fang Zih-Syun , Chen Jui-Yi , Chen Wei-ya , Lee No-No , Chen Hui-Wen , Hu Che-Ming J.
Published: March 2019

Cell membranes are an intricate yet fragile interface that requires substrate support for stabilization. Upon cell death, disassembly of the cytoskeletal network deprives plasma membranes of mechanical support and leads to membrane rupture and disintegration. By assembling a network of synthetic hydrogel polymers inside the intracellular compartment using photo-activated crosslinking chemistry, we show that the fluid cell membrane can be preserved, resulting in intracellularly gelated cells with robust stability. Upon assessing several types of adherent and suspension cells over a range of hydrogel crosslinking densities, we validate retention of surface properties, membrane lipid fluidity, lipid order, and protein mobility on the gelated cells. Preservation of cell surface functions is further demonstrated with gelated antigen presenting cells, which engage with antigen-specific T lymphocytes and effectively promote cell expansion ex vivo and in vivo. The intracellular hydrogelation technique presents a versatile cell fixation approach adaptable for biomembrane studies and biomedical device construction.
Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)
Authors: Asgari Ehsaneddin , McHardy Alice C. , Mofrad Mohammad R. K.
Published: March 2019

In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic segmentation of protein sequences into commonly occurring variable-length sub-sequences. The idea of PPE segmentation is inspired by the byte-pair encoding (BPE) text compression algorithm, which has recently gained popularity in subword neural machine translation. We modify this algorithm by adding a sampling framework allowing for multiple ways of segmenting a sequence. PPE segmentation steps can be learned over a large set of protein sequences (Swiss-Prot) or even a domain-specific dataset and then applied to a set of unseen sequences. This representation can be widely used as the input to any downstream machine learning tasks in protein bioinformatics. In particular, here, we introduce this representation through protein motif discovery and protein sequence embedding. (i) DiMotif: we present DiMotif as an alignment-free discriminative motif discovery method and evaluate the method for finding protein motifs in three different settings: (1) comparison of DiMotif with two existing approaches on 20 distinct motif discovery problems which are experimentally verified, (2) classification-based approach for the motifs extracted for integrins, integrin-binding proteins, and biofilm formation, and (3) in sequence pattern searching for nuclear localization signal. The DiMotif, in general, obtained high recall scores, while having a comparable F1 score with other methods in the discovery of experimentally verified motifs. Having high recall suggests that the DiMotif can be used for short-list creation for further experimental investigations on motifs. In the classification-based evaluation, the extracted motifs could reliably detect the integrins, integrin-binding, and biofilm formation-related proteins on a reserved set of sequences with high F1 scores. (ii) ProtVecX: we extend k-mer based protein vector (ProtVec) embedding to variablelength protein embedding using PPE sub-sequences. We show that the new method of embedding can marginally outperform ProtVec in enzyme prediction as well as toxin prediction tasks. In addition, we conclude that the embeddings are beneficial in protein classification tasks when they are combined with raw amino acids k-mer features.
Vertical disc tilt and features of the optic nerve head anatomy are related to visual field defect in myopic eyes
Authors: Park Hae-Young Lopilly , Kim Yong Chan , Jung Younhea , Park Chan Kee
Published: March 2019

Myopia is significantly growing eye disease which accompanies various ocular pathologies including glaucoma. Understanding visual field (VF) and retinal nerve fiber layer (RNFL) damage observed in myopic eyes is important. Therefore, we evaluated optic disc margin anatomy using spectral-domain (SD) optical coherence tomography (OCT). We enrolled 40 healthy myopic patients and 64 myopic patients with RNFL defects in the superonasal region of the optic disc on red-free photographs and OCT. Optic disc stereophotographs were co-localized to SD-OCT images, and we analyzed the frequency with which the disc margin identified in photographs coincided with Bruch’s membrane (BM) opening, BM/border tissue, or border tissue. For each scan, the presence of border tissue overhang beyond the clinical disc margin and the end of Bruch’s membrane was identified. Among 64 myopic eyes with RNFL defects, 42 had corresponding inferotemporal VF defects. Border tissue overhang was found from 25 to 60% of myopic eyes with RNFL defect at all clock positions. However, border tissue overhang was found from 86 to 97% at 1, 2, 11 and 12 o’clock position in myopic eyes with VF defects. This was significantly different from myopic healthy eyes. We suggest that the OCT structure at the disc margin might contribute to VF damage in myopic patients.
Characterization of Plaque-Sized Variants of Daniel’s (DA) Strain in Theiler’s Virus-Induced Epilepsy
Authors: Bijalwan M. , Young C. R. , Tingling J. , Zhou X. J. , Rimmelin A. R. , Leibowitz J. L. , Welsh C. J.
Published: March 2019

Epilepsy is a complex neurological disease characterized by recurrent seizures. Patients with viral encephalitis have a 16-fold increased risk of developing epilepsy, and this risk can persist for about 15 years after the occurrence of initial viral infection. Theiler’s murine encephalomyelitis virus (TMEV) infection induces a well-characterized experimental model of epilepsy in C57BL/6 mice. In response to intracerebral (I.C.) injection of Daniel’s (DA) strain of TMEV, there is vigorous immune response, which is detrimental to neurons and contributes to acute seizures, rendering mice susceptible to epilepsy. A comparativein vivochallenge study with either one of the two variants of the DA strain, small (DA-DS) or large (DA-CL) plaque forming variants, revealed differences in the diseases they induced in C57BL/6 mice. Compared to DA-CL-, DA-DS-infected mice exhibited significantly more seizures, higher clinical scores, neuroinflammation, and neuronal damage (mainly in the CA1-CA2 regions of hippocampus). Moreover, the brains of DA-DSinfected mice contained approximately five-fold higher virus than those of DA-CLinfected mice. A sequence comparison of the DA-CLand DA-DSgenome sequences showed mutations in the leader (L) and L* proteins of DA-CLvariant, which may be the cause of attenuating phenotype of DA-CLvariant in the C57BL/6 mouse model of epilepsy.
Long Non-coding RNAs Coordinate Developmental Transitions and Other Key Biological Processes in Grapevine
Authors: Bhatia Garima , Sharma Shailesh , Upadhyay Santosh Kumar , Singh Kashmir
Published: March 2019

Long non-coding RNAs (lncRNAs) are transcripts >200 nucleotides that have prominently surfaced as dynamic regulatory molecules. Using computational approaches, we identified and characterized 56,441 lncRNAs in grapevine (Vitis vinifera) by harnessing RNA-seq data from 10 developmental stages of leaf, inflorescence, and berry tissues. We conducted differential expression analysis and determined tissue- and developmental stage-specificity of lncRNAs in grapevine, which indicated their spatiotemporal regulation. Functional annotation using co-expression analysis revealed their involvement in regulation of developmental transitions in sync with transcription factors (TFs). Further, pathway enrichment analysis revealed lncRNAs associated with biosynthetic and secondary metabolic pathways. Additionally, we identified 115, 560, and 133 lncRNAs as putative miRNA precursors, targets, and endogenous target mimics, respectively, which provided an insight into the interplay of regulatory RNAs. We also explored lncRNA-mediated regulation of extra-chromosomal genes–i.e., mitochondrial and chloroplast coding sequences and observed their involvement in key biological processes like ‘photosynthesis’ and ‘oxidative phosphorylation’. In brief, these transcripts coordinate important biological functions via interactions with both coding and non-coding RNAs as well as TFs in grapevine. Our study would facilitate future experiments in unraveling regulatory mechanisms of development in this fruit crop of economic importance.
Continuously Frequency-Tuneable Plasmonic Structures for Terahertz Bio-sensing and Spectroscopy
Authors: Deng Xiangying , Li Leyang , Enomoto Mitsuhiro , Kawano Yukio
Published: March 2019

Plasmon-based devices are powerful for use in highly sensitive evanescent-field detection and analysis, but they exhibit the problem of limited frequency tunability for fixed structures. This feature causes problems in the multi-frequency investigations required for materials characterization, bio-related research, etc. Here, we propose and fabricate a spiral-shaped plasmonic structure that enables a continuous frequency-tuneable evanescent-field concentration in the terahertz (THz) region with simple operation. The device also increases the electric field intensity at the subwavelength aperture, thus significantly amplifying the transmission. Highly tuneable transmission bands are observed by simply rotating the spiral plasmonic structure, which are in good agreement with the behaviour expected from electromagnetic simulation. Medical examinations are performed by measuring the interactions between the frequency-tuneable plasmons and bio-samples, which enables observing distinct tissue-dependent transmission spectra and images. The developed device simultaneously offers the advantages of both plasmonic devices and frequency-tuneable devices, which can increase the availability and versatility of evanescent-field THz sensing and analysis. The mechanism presented will shed light on THz plasmonics and motivate the implementation of a variety of applications based on plasmon-mediated THz technologies.
Speed tuning properties of mirror symmetry detection mechanisms
Authors: Sharman Rebecca J. , Gheorghiu Elena
Published: March 2019

The human visual system is often tasked with extracting image properties such as symmetry from rapidly moving objects and scenes. The extent to which motion speed and symmetry processing mechanisms interact is not known. Here we examine speed-tuning properties of symmetry detection mechanisms using dynamic dot-patterns containing varying amounts of position and local motion-direction symmetry. We measured symmetry detection thresholds for stimuli in which symmetric and noise elements either drifted with different relative speeds, were relocated at different relative temporal frequencies or were static. We also measured percentage correct responses under two stimulus conditions: a segregated condition in which symmetric and noise elements drifted at different speeds, and a non-segregated condition in which the symmetric elements drifted at two different speeds in equal proportions, as did the noise elements. We found that performance (i) improved gradually with increasing the difference in relative speed between symmetric and noise elements, but was invariant across relative temporal frequencies/lifetime duration differences between symmetric and noise elements, (ii) was higher in the segregated compared to non-segregated conditions, and in the moving compared to the static conditions. We conclude that symmetry detection mechanisms are broadly tuned to speed, with speed-selective symmetry channels combining their outputs by probability summation.
A thin layer of sucrose octasulfate protects the oesophageal mucosal epithelium in reflux oesophagitis
Authors: Hayakawa Takuya , Kawasaki Shizuka , Hirayama Yutaka , Tsutsui Takuya , Sugiyama Eiji , Adachi Kiyo , Kon Ryo , Suematsu Makoto , Sugiura Yuki
Published: March 2019

Sucralfate is effective for the treatment of gastric and duodenal ulcers owing to its protective gel-forming ability. However, the mechanism by which sucralfate protects the oesophageal mucosa against reflux oesophagitis has not been clarified. We aimed to investigate the mechanisms of action of sucralfate and sucrose octasulfate (SOS), a component of sucralfate. SOS and sucralfate were administered to oesophagitis-induced rats, and the ulcer lesion size was macroscopically examined and scored. Effective pepsin activity in the gastric juices obtained from the animal model was evaluated by a casein digestion test. Sucralfate and SOS improved the pathology scores in a dose-dependent manner, whereas gastric juice pepsin activity was not impaired by therapeutic doses of SOS. As SOS lacks the ability to form a thick gel layer by polymerisation, we examined the distribution of SOS in the mucosal lumen by imaging mass spectrometry (IMS) to determine whether SOS directly adheres to the mucosal surface. A clear homogeneous thin-layer SOS film (>100 μm thick) was visualized on the oesophageal mucosal surface. Moreover, this SOS film formation was enhanced at ulcer lesion sites. Taken together, SOS appears to protect oesophageal mucosa against reflux oesophagitis via thin-layer formation on the mucosal surface.
A retinal model of cerebral malaria
Authors: Paquet-Durand François , Beck Susanne C. , Das Soumyaparna , Huber Gesine , Le Chang  , Schubert Timm , Tanimoto Naoyuki , Garcia-Garrido Marina , Mühlfriedel Regine , Bolz Sylvia , Hoffmann Wolfgang , Schraermeyer Ulrich , Mordmüller Benjamin , Seeliger Mathias W.
Published: March 2019

Malaria is a causative factor in about 500.000 deaths each year world-wide. Cerebral malaria is a particularly severe complication of this disease and thus associated with an exceedingly high mortality. Malaria retinopathy is an ocular manifestation often associated with cerebral malaria, and presumably shares a substantial part of its pathophysiology. Here, we describe that indeed murine malaria retinopathy reproduced the main hallmarks of the corresponding human disease. In the living animal, we were able to follow the circulation and cellular localization of malaria parasites transgenically labelled with GFP via non-invasive in vivo retinal imaging. We found that malaria parasites cross the blood-retinal-barrier and infiltrate the neuroretina, concomitant with an extensive, irreversible, and long-lasting retinal neurodegeneration. Furthermore, anti-malarial treatment with dihydroartemisinin strongly diminished the load of circulating parasites but resolved the symptoms of the retinopathy only in part. In summary, we introduce here a novel preclinical model for human cerebral malaria that is much more directly accessible for studies into disease pathophysiology and development of novel treatment approaches. In vivo retinal imaging may furthermore serve as a valuable tool for the early diagnosis of the human disease.
Quantum Oscillations from Nontrivial States in Quasi-Two-Dimensional Dirac Semimetal ZrTe5 Nanowires
Authors: Yang Pei , Wang Wei , Zhang Xiaoqian , Wang Kejie , He Liang , Liu Wenqing , Xu Yongbing
Published: March 2019

Recently discovered Dirac semimetal ZrTe5 bulk crystal, exhibits nontrivial conducting states in each individual layer, holding great potential for novel spintronic applications. Here, to reveal the transport properties of ZrTe5, we fabricated ZrTe5 nanowires (NWs) devices, with much larger surface-to-volume ratio than bulk materials. Quantum oscillations induced by the two-dimensional (2D) nontrivial conducting states have been observed from these NWs and a finite Berry phase of ~π is obtained by the analysis of Landau-level fan diagram. More importantly, the absence of the Aharonov-Bohm (A-B) oscillations, along with the SdH oscillations, suggests that the electrons only conduct inside each layer. And the intralayer conducting is suppressed because of the weak connection between adjacent layers. Our results demonstrate that ZrTe5 NWs can serve as a suitable quasi-2D Dirac semimetal with high mobility (~85000 cm2V−1s−1) and large nontrivial conductance contribution (up to 8.68%).
Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation
Authors: Viiri Leena E. , Rantapero Tommi , Kiamehr Mostafa , Alexanova Anna , Oittinen Mikko , Viiri Keijo , Niskanen Henri , Nykter Matti , Kaikkonen Minna U. , Aalto-Setälä Katriina
Published: March 2019

Hepatocyte-like cells (HLCs) derived from induced pluripotent stem cells (iPSCs) provide a renewable source of cells for drug discovery, disease modelling and cell-based therapies. Here, by using GRO-Seq we provide the first genome-wide analysis of the nascent RNAs in iPSCs, HLCs and primary hepatocytes to extend our understanding of the transcriptional changes occurring during hepatic differentiation process. We demonstrate that a large fraction of hepatocyte-specific genes are regulated at transcriptional level and identify hundreds of differentially expressed non-coding RNAs (ncRNAs), including primary miRNAs (pri-miRNAs) and long non-coding RNAs (lncRNAs). Differentiation induced alternative transcription start site (TSS) usage between the cell types as evidenced for miR-221/222 and miR-3613/15a/16-1 clusters. We demonstrate that lncRNAs and coding genes are tightly co-expressed and could thus be co-regulated. Finally, we identified sets of transcriptional regulators that might drive transcriptional changes during hepatocyte differentiation. These included RARG, E2F1, SP1 and FOXH1, which were associated with the down-regulated transcripts, and hepatocyte-specific TFs such as FOXA1, FOXA2, HNF1B, HNF4A and CEBPA, as well as RXR, PPAR, AP-1, JUNB, JUND and BATF, which were associated with up-regulated transcripts. In summary, this study clarifies the role of regulatory ncRNAs and TFs in differentiation of HLCs from iPSCs.
Neural correlates of early adversity among Bangladeshi infants
Authors: Jensen Sarah K. G. , Kumar Swapna , Xie Wanze , Tofail Fahmida , Haque Rashidul , Petri William A. , Nelson Charles A.
Published: March 2019

In this paper we explore the relationship between the Visual Evoked Potential (VEP), a component of the electroencephalogram elicited by visual stimuli, and cognitive functions in children growing up in an urban slum in Bangladesh. VEPs in response to pattern-reversing checkerboards were collected in 6 month-old-infants (n = 91) and 36-month-old children (n = 112). We examine variation in the amplitude and latency of the first positive component, the P1, of the VEP in relation to cognitive scores on the Mullen Scales of Early Learning and the Wechsler Preschool and Primary Scale of Intelligence. We also examine whether children’s caregiving experiences prior to the neuro-cognitive assessment explain variation in the P1 of the VEP. We find that the P1 amplitude of the VEP is related to concurrent cognitive performance in each respective cohort. We also find that the P1 amplitude at 6 months is prospectively associated with cognitive outcomes at 27 months, and the P1 amplitude at 36 months is prospectively associated with children’s IQ at 60 months. We find no associations between caregiving experiences and variation in the P1 of the VEP at 6 months, yet caregiving experience do explain variation in the P1 amplitude at 36 months. Caregiving experiences also explain variation in children’s concurrent and prospective cognitive functioning. The VEP may be used as a biomarker to index the neurobiological embedding of early adversity, which in turn may impact children’s cognitive functions.
Trimethylation of Elongation Factor-Tu by the Dual Thermoregulated Methyltransferase EftM Does Not Impact Its Canonical Function in Translation
Authors: Prezioso Samantha M. , Duong Duc M. , Kuiper Emily G. , Deng Qiudong , Albertí Sebastián , Conn Graeme L. , Goldberg Joanna B.
Published: March 2019

The Pseudomonas aeruginosa methyltransferase EftM trimethylates elongation factor-Tu (EF-Tu) on lysine 5 to form a post-translational modification important for initial bacterial adherence to host epithelial cells. EftM methyltransferase activity is directly temperature regulated. The protein stability of EftM is tuned with a melting temperature (Tm) around 37 °C such that the enzyme is stable and active at 25 °C, but is completely inactivated by protein unfolding at higher temperatures. This leads to higher observable levels of EF-Tu trimethylation at the lower temperature. Here we report an additional layer of thermoregulation resulting in lower eftM mRNA transcript level at 37 °C compared to 25 °C and show that this regulation occurs at the level of transcription initiation. To begin to define the impact of this system on P. aeruginosa physiology, we demonstrate that EF-Tu is the only observable substrate for EftM. Further, we interrogated the proteome of three different wild-type P. aeruginosa strains, their eftM mutants, and these mutants complemented with eftM and conclude that trimethylation of EF-Tu by EftM does not impact EF-Tu’s canonical function in translation. In addition to furthering our knowledge of this Pseudomonas virulence factor, this study provides an intriguing example of a protein with multiple layers of thermoregulation.
Effect of various concentrations of superabsorbent polymers on soil particle-size distribution and evaporation with sand mulching
Authors: Zhao Wenju , Cao Taohong , Dou Pinxin , Sheng Jie , Luo Minqiang
Published: March 2019

Superabsorbent polymers (SAPs) are type of hydrogels capable to swell and absorb a large amount of water, but easily decomposed and oxidized by the air. We used electron-microscopic imaging in an indoor simulation with sand mulching to test the effects of various SAP concentrations on controlling evaporation and salt formation. The treatments were sand-mulched columns containing 0, 0.1, 0.2, 0.5 and 1.0% SAP. The soil particle pores were from dense to sparse and the corresponding fractal dimension decreased as SAP concentration increased. SAP concentration was correlated negatively with fractal dimension, clay-particle fraction and silt-volume fraction. And it showed a positive correlation with sand volume fraction. SAP concentration significantly affected the particle-size distribution. Water-storage capacity increased in each column layer (five 8-cm layers) at the same infiltration depth. Evaporation decreased the water content of each layer. Sand mulching combined with the SAP decreased evaporation in each layer relative to the control, which retained more water and decreased the accumulation of surface salt in the order 1.0% > 0.5% > 0.2% > 0.1% > 0. Salt migrated at 0–30 cm with sand mulching but 0–25 cm with sand mulching and SAP amendment. The decrease in salt accumulation was most effective at a SAP concentration of 0.2%.
A note on retrograde gene transfer efficiency and inflammatory response of lentiviral vectors pseudotyped with FuG-E vs. FuG-B2 glycoproteins
Authors: Tanabe Soshi , Uezono Shiori , Tsuge Hitomi , Fujiwara Maki , Miwa Miki , Kato Shigeki , Nakamura Katsuki , Kobayashi Kazuto , Inoue Ken-ichi , Takada Masahiko
Published: March 2019

Pseudotyped lentiviral vectors give access to pathway-selective gene manipulation via retrograde transfer. Two types of such lentiviral vectors have been developed. One is the so-called NeuRet vector pseudotyped with fusion glycoprotein type E, which preferentially transduces neurons. The other is the so-called HiRet vector pseudotyped with fusion glycoprotein type B2, which permits gene transfer into both neurons and glial cells at the injection site. Although these vectors have been applied in many studies investigating neural network functions, it remains unclear which vector is more appropriate for retrograde gene delivery in the brain. To compare the gene transfer efficiency and inflammatory response of the NeuRet vs. HiRet vectors, each vector was injected into the striatum in macaque monkeys, common marmosets, and rats. It was revealed that retrograde gene delivery of the NeuRet vector was equal to or greater than that of the HiRet vector. Furthermore, inflammation characterized by microglial and lymphocytic infiltration occurred when the HiRet vector, but not the NeuRet vector, was injected into the primate brain. The present results indicate that the NeuRet vector is more suitable than the HiRet vector for retrograde gene transfer in the primate and rodent brains.
A permeability-increasing drug synergizes with bacterial efflux pump inhibitors and restores susceptibility to antibiotics in multi-drug resistant Pseudomonas aeruginosa strains
Authors: Ferrer-Espada Raquel , Shahrour Hawraa , Pitts Betsey , Stewart Philip S. , Sánchez-Gómez Susana , Martínez-de-Tejada Guillermo
Published: March 2019

Resistance to antibiotics poses a major global threat according to the World Health Organization. Restoring the activity of existing drugs is an attractive alternative to address this challenge. One of the most efficient mechanisms of bacterial resistance involves the expression of efflux pump systems capable of expelling antibiotics from the cell. Although there are efflux pump inhibitors (EPIs) available, these molecules are toxic for humans. We hypothesized that permeability-increasing antimicrobial peptides (AMPs) could lower the amount of EPI necessary to sensitize bacteria to antibiotics that are efflux substrates. To test this hypothesis, we measured the ability of polymyxin B nonapeptide (PMBN), to synergize with antibiotics in the presence of EPIs. Assays were performed using planktonic and biofilm-forming cells of Pseudomonas aeruginosa strains overexpressing the MexAB-OprM efflux system. Synergy between PMBN and EPIs boosted azithromycin activity by a factor of 2,133 and sensitized P. aeruginosa to all tested antibiotics. This reduced several orders of magnitude the amount of inhibitor needed for antibiotic sensitization. The selected antibiotic-EPI-PMBN combination caused a 10 million-fold reduction in the viability of biofilm forming cells. We proved that AMPs can synergize with EPIs and that this phenomenon can be exploited to sensitize bacteria to antibiotics.
Two-year observation of the occlusal vertical dimension after bite raising via cone-beam computerized tomography: A preliminary study
Authors: Liu Chuanzi , Huang Dan , Zhou Lizhi , Liu Guochen , Wang Yining , Jiang Tao
Published: March 2019

Variation of the occlusal vertical dimension (OVD) has been discussed empirically for decades, but it has not been thoroughly explored with experimental data. In the present study, cone-beam computerized tomography (CBCT) of six selected patients was conducted to evaluate the bones of the lower facial structures. The anterior lower facial heights (ALFHs), alveolar process heights (APHs), vertical facial pattern (VFP), occluding dentition height (ODH) and condyle space (CS), which were evaluated by three-dimensional (3D) and two-dimensional (2D) lateral cephalometry derived from CBCT, were compared before and two years after the OVD increased full mouth rehabilitation. Consistent significant increases in ALFHs and the VFP indicated the OVD increase, while a significant decrease in the ΔODH indicated compressed dentition. In addition, 55 of the 56 sites (98.21%) of APH measurement illustrated no significant difference before and after treatment. The findings indicated that the increased OVD did not relapse to baseline and was sufficiently tolerated, with mostly constant APHs and an altered ODH after two years of observation in the six patients.
CRISPR/Cas9 targeted CAPTURE of mammalian genomic regions for characterization by NGS
Authors: Slesarev Alexei , Viswanathan Lakshmi , Tang Yitao , Borgschulte Trissa , Achtien Katherine , Razafsky David , Onions David , Chang Audrey , Cote Colette
Published: March 2019

The robust detection of structural variants in mammalian genomes remains a challenge. It is particularly difficult in the case of genetically unstable Chinese hamster ovary (CHO) cell lines with only draft genome assemblies available. We explore the potential of the CRISPR/Cas9 system for the targeted capture of genomic loci containing integrated vectors in CHO-K1-based cell lines followed by next generation sequencing (NGS), and compare it to popular target-enrichment sequencing methods and to whole genome sequencing (WGS). Three different CRISPR/Cas9-based techniques were evaluated; all of them allow for amplification-free enrichment of target genomic regions in the range from 5 to 60 fold, and for recovery of ~15 kb-long sequences with no sequencing artifacts introduced. The utility of these protocols has been proven by the identification of transgene integration sites and flanking sequences in three CHO cell lines. The long enriched fragments helped to identify Escherichia coli genome sequences co-integrated with vectors, and were further characterized by Whole Genome Sequencing (WGS). Other advantages of CRISPR/Cas9-based methods are the ease of bioinformatics analysis, potential for multiplexing, and the production of long target templates for real-time sequencing.
Inhibition of avian-origin influenza A(H7N9) virus by the novel cap-dependent endonuclease inhibitor baloxavir marboxil
Authors: Taniguchi Keiichi , Ando Yoshinori , Nobori Haruaki , Toba Shinsuke , Noshi Takeshi , Kobayashi Masanori , Kawai Makoto , Yoshida Ryu , Sato Akihiko , Shishido Takao , Naito Akira , Matsuno Keita , Okamatsu Masatoshi , Sakoda Yoshihiro , Kida Hiroshi
Published: March 2019

Human infections with avian-origin influenza A(H7N9) virus represent a serious threat to global health; however, treatment options are limited. Here, we show the inhibitory effects of baloxavir acid (BXA) and its prodrug baloxavir marboxil (BXM), a first-in-class cap-dependent endonuclease inhibitor, against A(H7N9), in vitro and in vivo. In cell culture, BXA at four nanomolar concentration achieved a 1.5–2.8 log reduction in virus titers of A(H7N9), including the NA-R292K mutant virus and highly pathogenic avian influenza viruses, whereas NA inhibitors or favipiravir required approximately 20-fold or higher concentrations to achieve the same levels of reduction. A(H7N9)-specific amino acid polymorphism at position 37, implicated in BXA binding to the PA endonuclease domain, did not impact on BXA susceptibility. In mice, oral administration of BXM at 5 and 50 mg/kg twice a day for 5 days completely protected from a lethal A/Anhui/1/2013 (H7N9) challenge, and reduced virus titers more than 2–3 log in the lungs. Furthermore, the potent therapeutic effects of BXM in mice were still observed when a higher virus dose was administered or treatment was delayed up to 48 hours post infection. These findings support further investigation of BXM for A(H7N9) treatment in humans.
Interpretation of EBV infection in pan-cancer genome considering viral life cycle: LiEB (Life cycle of Epstein-Barr virus)
Authors: Song Hyojin , Lim Yoojoo , Im Hogune , Bae Jeong Mo , Kang Gyeong Hoon , Ahn Junhak , Baek Daehyun , Kim Tae-You , Yoon Sung-Soo , Koh Youngil
Published: March 2019

We report a novel transcriptomic analysis workflow called LiEB (Life cycle of Epstein-Barr virus) to characterize distributions of oncogenic virus, Epstein-Barr virus (EBV) infection in human tumors. We analyzed 851 The Cancer Genome Atlas whole-transcriptome sequencing (WTS) data to investigate EBV infection by life cycle information using three-step LiEB workflow: 1) characterize virus infection generally; 2) align transcriptome sequences against a hybrid human-EBV genome, and 3) quantify EBV gene expression. Our results agreed with EBV infection status of public cell line data. Analysis in stomach adenocarcinoma identified EBV-positive cases involving PIK3CA mutations and/or CDKN2A silencing with biologically more determination, compared to previous reports. In this study, we found that a small number of colorectal adenocarcinoma cases involved with EBV lytic gene expression. Expression of EBV lytic genes was also observed in 3% of external colon cancer cohort upon WTS analysis. Gene set enrichment analysis showed elevated expression of genes related to E2F targeting and interferon-gamma responses in EBV-associated tumors. Finally, we suggest that interpretation of EBV life cycle is essential when analyzing its infection in tumors, and LiEB provides high capability of detecting EBV-positive tumors. Observation of EBV lytic gene expression in a subset of colon cancers warrants further research.
In-situ localization and biochemical analysis of bio-molecules reveals Pb-stress amelioration in Brassica juncea L. by co-application of 24-Epibrassinolide and Salicylic Acid
Authors: Kohli Sukhmeen Kaur , Bali Shagun , Tejpal Ruchi , Bhalla Vandana , Verma Vinod , Bhardwaj Renu , Alqarawi A. A. , Abd_Allah Elsayed Fathi , Ahmad Parvaiz
Published: March 2019

Lead (Pb) toxicity is a major environmental concern affirming the need of proper mitigation strategies. In the present work, potential of combined treatment of 24-Epibrassinolide (24-EBL) and Salicylic acid (SA) against Pb toxicity to Brassica juncea L. seedlings were evaluated. Seedlings pre-imbibed in EBL (0.1 mM) and SA (1 mM) individually and in combination, were sown in Pb supplemented petri-plates (0.25, 0.50 and 0.75 mM). Various microscopic observations and biochemical analysis were made on 10 days old seedlings of B. juncea. The toxic effects of Pb were evident with enhancement in in-situ accumulation of Pb, hydrogen peroxide (H2O2), malondialdehyde (MDA), nuclear damage, membrane damage, cell death and polyamine. Furthermore, free amino acid were lowered in response to Pb toxicity. The levels of osmoprotectants including total carbohydrate, reducing sugars, trehalose, proline and glycine betaine were elevated in response to Pb treatment. Soaking treatment with combination of 24-EBL and SA led to effective amelioration of toxic effects of Pb. Reduction in Pb accumulation, reactive oxygen content (ROS), cellular damage and GSH levels were noticed in response to treatment with 24-EBL and SA individual and combined levels. The contents of free amino acid, amino acid profiling as well as in-situ localization of polyamine (spermidine) was recorded to be enhanced by co-application of 24-EBLand SA. Binary treatment of 24-EBL and SA, further elevated the content of osmoprotectants. The study revealed that co-application of combined treatment of 24-EBL and SA led to dimination of toxic effects of Pb in B. juncea seedlings.
Consequences of delays and imperfect implementation of isolation in epidemic control
Authors: Young Lai-Sang , Ruschel Stefan , Yanchuk Serhiy , Pereira Tiago
Published: March 2019

For centuries isolation has been the main control strategy of unforeseen epidemic outbreaks. When implemented in full and without delay, isolation is very effective. However, flawless implementation is seldom feasible in practice. We present an epidemic model called SIQ with an isolation protocol, focusing on the consequences of delays and incomplete identification of infected hosts. The continuum limit of this model is a system of Delay Differential Equations, the analysis of which reveals clearly the dependence of epidemic evolution on model parameters including disease reproductive number, isolation probability, speed of identification of infected hosts and recovery rates. Our model offers estimates on minimum response capabilities needed to curb outbreaks, and predictions of endemic states when containment fails. Critical response capability is expressed explicitly in terms of parameters that are easy to obtain, to assist in the evaluation of funding priorities involving preparedness and epidemics management.