bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying challenges in crowdfunded product development: a review of Kickstarter projects
Authors: Jensen Lasse Skovgaard , Özkil Ali Gürcan
Published: October 2018

This paper provides an empirical review of the reward-based crowdfunding platformKickstarter.com, with the aim to explore and identify challenges in crowdfunded product development, which consequently can lead to failure of the crowdfunding campaign. The review was based on the analysis of a total of 144 successfully funded ‘technology’ campaigns, which all concerned the creation of physical consumer hardware preordered by campaign backers. The analysis was built around a failure mode model, which was established through a pre-study. The study reveals that (i) no more than 32% of the campaigns managed to deliver the crowdfunded products on time, and, if campaigns are delayed, (ii) there is a significantly higher probability that the delivered products might lack expected attributes. The causes for delay have many reasons, but (iii) a set of particular product development issues were identified as the main challenges. A better understanding of crowdfunded product development can help researchers and practitioners to better understand and utilize the opportunities of this new product development paradigm.
Embeddings of interval exchange transformations into planar piecewise isometries
Authors: ASHWIN PETER , GOETZ AREK , PERES PEDRO , RODRIGUES ANA
Published: October 2018

Althoughpiecewise isometries(PWIs) are higher-dimensional generalizations of one-dimensionalinterval exchange transformations(IETs), their generic dynamical properties seem to be quite different. In this paper, we consider embeddings of IET dynamics into PWI with a view to better understanding their similarities and differences. We derive some necessary conditions for existence of such embeddings using combinatorial, topological and measure-theoretic properties of IETs. In particular, we prove that continuous embeddings of minimal 2-IETs into orientation-preserving PWIs are necessarily trivial and that any 3-PWI has at most one non-trivially continuously embedded minimal 3-IET with the same underlying permutation. Finally, we introduce a family of 4-PWIs, with an apparent abundance of invariant non-smooth fractal curves supporting IETs, that limit to a trivial embedding of an IET.
Suppression of amplitude modulation induced by polarization mode dispersion using a multi-degree-of-freedom fiber filter
Authors: Li Rao , Jiang Youen , Qiao Zhi , Huang Canhong , Fan Wei , Li Xuechun , Lin Zunqi
Published: October 2018

Polarization mode dispersion (PMD) in fibers for high-power lasers can induce significant frequency modulation to amplitude modulation (FM-to-AM) conversion. However, existing techniques are not sufficiently flexible to achieve efficient compensation for such FM-to-AM conversion. By analyzing the nonuniform transmission spectrum caused by PMD, we found that the large-scale envelope of the transmission spectrum has more serious impacts on the amount of AM. In order to suppress the PMD-induced FM-to-AM conversion, we propose a novel tunable spectral filter with multiple degrees of freedom based on a half-wave plate, a nematic liquid crystal, and an axis-rotated polarization-maintaining fiber. Peak wavelength, free spectral range (FSR), and modulation depth of the filter are decoupled and can be controlled independently, which is verified through both simulations and experiments. The filter is utilized to compensate for the PMD-induced FM-to-AM conversion in the front end of a high-power laser facility. The results indicate that, for a pulse with phase-modulation frequency of 22.82 GHz, the FM-to-AM conversion could be reduced from 18% to 3.2% within a short time and maintained below 6.5% for 3 h. The proposed filter is also promising for other applications that require flexible spectral control such as high-speed channel selection in optical communication networks.
TOWERS IN FILTERS, CARDINAL INVARIANTS, AND LUZIN TYPE FAMILIES
Authors: BRENDLE JÖRG , FARKAS BARNABÁS , VERNER JONATHAN
Published: October 2018

We investigate which filters onωcan contain towers, that is, a modulo finite descending sequence without any pseudointersection (in${[\omega ]^\omega }$). We prove the following results:

(1)

Many classical examples of nice tall filters contain no towers (in ZFC).

(2)

It is consistent that tall analytic P-filters contain towers of arbitrary regular height (simultaneously for many regular cardinals as well).

(3)

It is consistent that all towers generate nonmeager filters (this answers a question of P. Borodulin-Nadzieja and D. Chodounský), in particular (consistently) Borel filters do not contain towers.

(4)

The statement “Every ultrafilter contains towers.” is independent of ZFC (this improves an older result of K. Kunen, J. van Mill, and C. F. Mills).

Furthermore, we study many possible logical (non)implications between the existence of towers in filters, inequalities between cardinal invariants of filters (${\rm{ad}}{{\rm{d}}^{\rm{*}}}\left( {\cal F} \right)$,${\rm{co}}{{\rm{f}}^{\rm{*}}}\left( {\cal F} \right)$,${\rm{no}}{{\rm{n}}^{\rm{*}}}\left( {\cal F} \right)$, and${\rm{co}}{{\rm{v}}^{\rm{*}}}\left( {\cal F} \right)$), and the existence of Luzin type families (of size$\ge {\omega _2}$), that is, if${\cal F}$is a filter then${\cal X} \subseteq {[\omega ]^\omega }$is an${\cal F}$-Luzin family if$\left\{ {X \in {\cal X}:|X \setminus F| = \omega } \right\}$is countable for every$F \in {\cal F}$.
SIMPLE GROUPS OF MORLEY RANK 5 ARE BAD
Authors: DELORO ADRIEN , WISCONS JOSHUA
Published: October 2018

We show that any simple group of Morley rank 5 is a bad group all of whose proper definable connected subgroups are nilpotent of rank at most 2. The main result is then used to catalog the nonsoluble connected groups of Morley rank 5.
PROVABILITY LOGICS RELATIVE TO A FIXED EXTENSION OF PEANO ARITHMETIC
Authors: KURAHASHI TAISHI
Published: October 2018

Let T and U be any consistent theories of arithmetic. If T is computably enumerable, then the provability predicate $P{r_\tau }\left( x \right)$ of T is naturally obtained from each ${{\rm{\Sigma }}_1}$ definition $\tau \left( v \right)$ of T. The provability logic $P{L_\tau }\left( U \right)$ of τ relative to U is the set of all modal formulas which are provable in U under all arithmetical interpretations where □ is interpreted by $P{r_\tau }\left( x \right)$. It was proved by Beklemishev based on the previous studies by Artemov, Visser, and Japaridze that every $P{L_\tau }\left( U \right)$ coincides with one of the logics $G{L_\alpha }$, ${D_\beta }$, ${S_\beta }$, and $GL_\beta ^ -$, where α and β are subsets of ω and β is cofinite.

We prove that if U is a computably enumerable consistent extension of Peano Arithmetic and L is one of $G{L_\alpha }$, ${D_\beta }$, ${S_\beta }$, and $GL_\beta ^ -$, where α is computably enumerable and β is cofinite, then there exists a ${{\rm{\Sigma }}_1}$ definition $\tau \left( v \right)$ of some extension of $I{{\rm{\Sigma }}_1}$ such that $P{L_\tau }\left( U \right)$ is exactly L.
AN ALGEBRAIC APPROACH TO MSO-DEFINABILITY ON COUNTABLE LINEAR ORDERINGS
Authors: CARTON OLIVIER , COLCOMBET THOMAS , PUPPIS GABRIELE
Published: October 2018

We develop an algebraic notion of recognizability for languages of words indexed by countable linear orderings. We prove that this notion is effectively equivalent to definability in monadic second-order (MSO) logic. We also provide three logical applications. First, we establish the first known collapse result for the quantifier alternation of MSO logic over countable linear orderings. Second, we solve an open problem posed by Gurevich and Rabinovich, concerning the MSO-definability of sets of rational numbers using the reals in the background. Third, we establish the MSO-definability of the set of yields induced by an MSO-definable set of trees, confirming a conjecture posed by Bruyère, Carton, and Sénizergues.
Anticipating emerging biotechnology threats
Authors: Vogel Kathleen M. , Ouagrham-Gormley Sonia Ben
Published: October 2018

This article discusses the contingencies and complexities of CRISPR. It outlines key problems regarding off-target effects and replication of experimental work that are important to consider in light of CRISPR’s touted ease of use and diffusion. In light of literature on the sociotechnical dimensions of the life sciences and biotechnology and literature on former bioweapons programs, this article argues that we need more detailed empirical case studies of the social and technical factors shaping CRISPR and related gene-editing techniques in order to better understand how they may be different from other advances in biotechnology — or whether similar features remain. This information will be critical to better inform intelligence practitioners and policymakers about the security implications of new gene-editing techniques.
Carbon-14 release and speciation from carbon steel in highly alkaline conditions
Authors: Druyts Frank , Caes Sébastien , Thomas Peter
Published: October 2018

The release and the speciation of carbon species from irradiated JRQ carbon steel samples, representative of the reactor pressure vessel of Belgian nuclear power plants, were studied in a saturated portlandite aqueous solution, relevant for the Belgian Supercontainer design, as perceived for the geological disposal of high-level nuclear waste. To achieve this, we performed simple immersion and potentiostatic corrosion tests. In addition, the corrosion rate (which determines the 14C release) was estimated by measuring the release of 60Co. Gas chromatography showed that during the static corrosion test, the carbonaceous species methane, carbon dioxide, ethene, and ethane were produced. Under the hypothesis that all the carbon released from the JRQ steel was transformed into carbon-base gaseous compounds, this corresponds to a corrosion rate of approximately 100 nm/yr, which is in good agreement with literature data.
Stigma as a barrier to family planning use among married youth in Ethiopia
Authors: Jain Aparna , Ismail Hussein , Tobey Elizabeth , Erulkar Annabel
Published: October 2018

Nearly 33 million female youths have an unmet need for voluntary family planning (FP), meaning they are sexually active and do not want to become pregnant. In Ethiopia, age at marriage remains low: 40% and 14% of young women aged 20–24 were married by the ages of 18 and 15, respectively. Despite increases in FP use by married 15- to 24-year-olds from 5% in 2000 to 37% in 2016, unmet need remains high at 19%. Supply-and-demand factors have been shown to limit FP use, yet little is known about how stigma influences FP use among youth. This study validates an anticipated stigma (expectation of discrimination from others) index and explores its effect on unmet need. A cross-sectional survey was implemented with 15- to 24-year-old female youth in Ethiopia in 2016. The analytic sample included married respondents with a demand (met and unmet need) for FP (n=371). A five-item anticipated stigma index (Cronbach’sα=0.66) was developed using principal component factor analysis. These items related to fear, worry and embarrassment when accessing FP. The findings showed that 30% agreed with at least one anticipated stigma question; 44% had an unmet need; 58% were married before age 18; and 100% could name an FP method and knew where to obtain FP. In multivariate regression models, youth who experienced anticipated stigma were significantly more likely to have an unmet need, and those who lived close to a youth-friendly service (YFS) site were significantly less likely to have an unmet need. Interventions should address anticipated stigma while focusing on social norms that restrict married youth from accessing FP; unmet need may be mitigated in the presence of a YFS; and the anticipated stigma index appears valid and reliable but should be tested in other countries and among different adolescent groups.
MULTI-CRITERIA DECISION ANALYSIS AS A DECISION-SUPPORT TOOL FOR DRUG EVALUATION: A PILOT STUDY IN A PHARMACY AND THERAPEUTICS COMMITTEE SETTING
Authors: Roldán Úrsula Baños , Badia Xavier , Marcos-Rodríguez Jose Antonio , de la Cruz-Merino Luis , Gómez-González Jaime , Melcón-de Dios Ana , Caraballo-Camacho María de la O , Cordero-Ramos Jaime , Alvarado-Fernández María Dolores , Galiana-Auchel José Manuel , Calleja-Hernández Miguel Ángel
Published: October 2018

Objectives:

The aim of this study was to develop and to assess a specific Multi-Criteria Decision Analysis (MCDA) framework to evaluate new drugs in an hospital pharmacy and therapeutics committee (P&TC) setting.

Methods:

A pilot criteria framework was developed based on the EVIDEM (Evidence and Value: Impact on DEcisionMaking) framework, together with other relevant criteria, and assessed by a group of P&TC's members. The weighting of included criteria was done using a 5-point weighting technique. Two drugs were chosen by evaluation: an orphan-drug for Gaucher disease, and a nonorphan drug for the treatment of inflammatory bowel disease. Evidence matrices were developed, and value contribution of each drug was evaluated by P&TC's members. An agreed final framework was obtained through a discussion between the P&TC's members.

Results:

After criteria assessment, the pilot framework included eight quantitative criteria: “disease severity,” “unmet needs,” “comparative efficacy/effectiveness,” “comparative safety/tolerability,” “comparative patient-reported outcomes,” “comparative cost consequences-cost of treatment,” “comparative cost consequences-other medical costs,” and “quality of evidence”; and one contextual criterion: “opportunity costs and affordability.” The most valued criteria were: “comparative safety/tolerability,” “disease severity,” and “comparative efficacy/effectiveness.” When assessing the drugs most valued characteristics of the MCDA were the possibility that all team may contribute to drug assessment by means of scoring the matrices and the discussion to reach a consensus in drug positioning and value decision making.

Conclusions:

The reflective MCDA would integrate quantitative and qualitative criteria relevant for a P&TC setting, allowing reflective discussions based on the criteria weighting score.
A group version of stable regularity
Authors: CONANT G. , PILLAY A. , TERRY C.
Published: October 2018

We prove that, given ε > 0 and k ≥ 1, there is an integer n such that the following holds. Suppose G is a finite group and A ⊆ G is k-stable. Then there is a normal subgroup H ≤ G of index at most n, and a set Y ⊆ G, which is a union of cosets of H, such that |A △ Y| ≤ε|H|. It follows that, for any coset C of H, either |C ∩ A|≤ ε|H| or |C \ A| ≤ ε |H|. This qualitatively generalises recent work of Terry and Wolf on vector spaces over $\mathbb{F}_p$.
Comparative study in the control of bovine viral diarrhea
Authors: Larghi Mauro
Published: October 2018

Bovine viral diarrhea virus (BVDV) is an important infectious agent affecting herd productivity and reproduction, and leading to massive economic losses. As such, BVD is the subject of a number of control and eradication schemes globally. The key elements of such schemes are: diagnosis and removal of persistently infected animals from herds; implementation of biosecurity practices aimed at preventing the introduction or re-introduction of BVDV in free herds; and ongoing surveillance to monitor the progress of the program and to detect new infections. The objective of this review is to examine the impact of BVD and the management of the disease in three countries: Scotland, Spain, and Argentina, where BVD control programs are in distinct phases: established, developing, and yet to be initiated. This work also sets out to highlight potential difficulties and formulate recommendations for successful BVD control. It concludes that a systematic, countrywide approach is needed to achieve a sustainable decrease in BVD prevalence. The role of vaccines in control programs is concluded to be a valuable additional biosecurity measure. This study also concludes that there are potential wider benefits to a systematic BVD control program, such as a reduction in antimicrobial use and increases in the competitiveness of the cattle industry.
Cautious Optimism and Incremental Goals Toward Stabilizing Atmospheric CO2
Authors: Ballantyne A. P. , Ciais P. , Miller J. B.
Published: October 2018

Fossil fuel emissions of CO2 to the atmosphere appear to have leveled off in recent years; however, atmospheric CO2 concentrations continue to rise. Our simple analysis shows that peaks in the growth rates of human population and fossil fuel emissions have been observed, but the growth rate of atmospheric CO2 has reached record levels and shows no indication of peaking. Before atmospheric CO2 concentrations can be stabilized at safe levels, a peak in the CO2 growth rate must be achieved.
USP7 deubiquitinates and stabilizes NOTCH1 in T-cell acute lymphoblastic leukemia
Authors: Shan Huizhuang , Li Xiangyun , Xiao Xinhua , Dai Yuting , Huang Jinyan , Song Junjun , Liu Meng , Yang Li , Lei Hu , Tong Yin , Zhou Li , Xu Hanzhang , Wu Yingli
Published: October 2018

T-cell acute lymphoblastic leukemia (T-ALL) is a highly aggressive leukemia that is primarily caused by aberrant activation of the NOTCH1 signaling pathway. Recent studies have revealed that posttranslational modifications, such as ubiquitination, regulate NOTCH1 stability, activity, and localization. However, the specific deubiquitinase that affects NOTCH1 protein stability remains unestablished. Here, we report that ubiquitin-specific protease 7 (USP7) can stabilize NOTCH1. USP7 deubiquitinated NOTCH1 in vivo and in vitro, whereas knockdown of USP7 increased the ubiquitination of NOTCH1. USP7 interacted with NOTCH1 protein in T-ALL cells, and the MATH and UBL domains of USP7 were responsible for this interaction. Depletion of USP7 significantly suppressed the proliferation of T-ALL cells in vitro and in vivo, accompanied by downregulation of the NOTCH1 protein level. Similarly, pharmacologic inhibition of USP7 led to apoptosis of T-ALL cells. More importantly, we found that USP7 was significantly upregulated in human T-ALL cell lines and patient samples, and a USP7 inhibitor exhibited cell cytotoxicity toward primary T-ALL cells, indicating the clinical relevance of these findings. Overall, our results demonstrate that USP7 is a novel deubiquitinase that stabilizes NOTCH1. Therefore, USP7 may be a promising therapeutic target in the currently incurable T-ALL.
Oligodendrocyte differentiation of induced pluripotent stem cells derived from subjects with schizophrenias implicate abnormalities in development
Authors: McPhie Donna L. , Nehme Ralda , Ravichandran Caitlin , Babb Suzann M. , Ghosh Sulagna Dia , Staskus Alexandra , Kalinowski Amy , Kaur Rupinderjit , Douvaras Panagiotis , Du Fei , Ongur Dost , Fossati Valentina , Eggan Kevin , Cohen Bruce M.
Published: October 2018

Abnormalities of brain connectivity and signal transduction are consistently observed in individuals with schizophrenias (SZ). Underlying these anomalies, convergent in vivo, post mortem, and genomic evidence suggest abnormal oligodendrocyte (OL) development and function and lower myelination in SZ. Our primary hypothesis was that there would be abnormalities in the number of induced pluripotent stem (iPS) cell-derived OLs from subjects with SZ. Our secondary hypothesis was that these in vitro abnormalities would correlate with measures of white matter (WM) integrity and myelination in the same subjects in vivo, estimated from magnetic resonance imaging. Six healthy control (HC) and six SZ iPS cell lines, derived from skin fibroblasts from well-characterized subjects, were differentiated into OLs. FACS analysis of the oligodendrocyte-specific surface, glycoprotein O4, was performed at three time points of development (days 65, 75, and 85) to quantify the number of late oligodendrocyte progenitor cells (OPCs) and OLs in each line. Significantly fewer O4-positive cells developed from SZ versus HC lines (95% CI 1.0: 8.6, F1,10 = 8.06, p = 0.02). The difference was greater when corrected for age (95% CI 5.4:10.4, F1,8 = 53.6, p < 0.001). A correlation between myelin content in WM in vivo, estimated by magnetization transfer ratio (MTR) and number of O4-positive cells in vitro was also observed across all time points (F1,9 = 4.3, p = 0.07), reaching significance for mature OLs at day 85 in culture (r = 0.70, p < 0.02). Low production of OPCs may be a contributing mechanism underlying WM reduction in SZ.
Oncolysis with DTT-205 and DTT-304 generates immunological memory in cured animals
Authors: Zhou Heng , Mondragón Laura , Xie Wei , Mauseth Brynjar , Leduc Marion , Sauvat Allan , Gomes-da-Silva Lígia C. , Forveille Sabrina , Iribarren Kristina , Souquere Sylvie , Bezu Lucillia , Liu Peng , Zhao Liwei , Zitvogel Laurence , Sveinbjørnsson Baldur , Eksteen J. Johannes , Rekdal Øystein , Kepp Oliver , Kroemer Guido
Published: October 2018

Oncolytic peptides and peptidomimetics are being optimized for the treatment of cancer by selecting agents with high cytotoxic potential to kill a maximum of tumor cells as well as the capacity to trigger anticancer immune responses and hence to achieve long-term effects beyond therapeutic discontinuation. Here, we report on the characterization of two novel oncolytic peptides, DTT-205 and DTT-304 that both selectively enrich in the lysosomal compartment of cancer cells yet differ to some extent in their cytotoxic mode of action. While DTT-304 can trigger the aggregation of RIP3 in ripoptosomes, coupled to the phosphorylation of MLKL by RIP3, DTT-205 fails to activate RIP3. Accordingly, knockout of either RIP3 or MLKL caused partial resistance against cell killing by DTT-304 but not DTT-205. In contrast, both agents shared common features in other aspects of pro-death signaling in the sense that their cytotoxic effects were strongly inhibited by both serum and antioxidants, partially reduced by lysosomal inhibition with bafilomycin A1 or double knockout of Bax and Bak, yet totally refractory to caspase inhibition. Both DTT-304 and DTT-205 caused the exposure of calreticulin at the cell surface, as well as the release of HMGB1 from the cells. Mice bearing established subcutaneous cancers could be cured by local injection of DTT-205 or DTT-304, and this effect depended on T lymphocytes, as it led to the establishment of a long-term memory response against tumor-associated antigens. Thus, mice that had been cured from cancer by the administration of DTT compounds were refractory against rechallenge with the same cancer type several months after the disappearance of the primary lesion. In summary, DTT-205 and DTT-304 both have the capacity to induce immunotherapeutic oncolysis.
Ultrafast carbon monoxide photolysis and heme spin-crossover in myoglobin via nonadiabatic quantum dynamics
Authors: Falahati Konstantin , Tamura Hiroyuki , Burghardt Irene , Huix-Rotllant Miquel
Published: October 2018

Light absorption of myoglobin triggers diatomic ligand photolysis and a spin crossover transition of iron(II) that initiate protein conformational change. The photolysis and spin crossover reactions happen concurrently on a femtosecond timescale. The microscopic origin of these reactions remains controversial. Here, we apply quantum wavepacket dynamics to elucidate the ultrafast photochemical mechanism for a heme–carbon monoxide (heme–CO) complex. We observe coherent oscillations of the Fe–CO bond distance with a period of 42 fs and an amplitude of ∼1 Å. These nuclear motions induce pronounced geometric reorganization, which makes the CO dissociation irreversible. The reaction is initially dominated by symmetry breaking vibrations inducing an electron transfer from porphyrin to iron. Subsequently, the wavepacket relaxes to the triplet manifold in ∼75 fs and to the quintet manifold in ∼430 fs. Our results highlight the central role of nuclear vibrations at the origin of the ultrafast photodynamics of organometallic complexes.
Line excitation array detection fluorescence microscopy at 0.8 million frames per second
Authors: Martin Chris , Li Tianqi , Hegarty Evan , Zhao Peisen , Mondal Sudip , Ben-Yakar Adela
Published: October 2018

Three-dimensional, fluorescence imaging methods with ~1 MHz frame rates are needed for high-speed, blur-free flow cytometry and capturing volumetric neuronal activity. The frame rates of current imaging methods are limited to kHz by the photon budget, slow camera readout, and/or slow laser beam scanners. Here, we present line excitation array detection (LEAD) fluorescence microscopy, a high-speed imaging method capable of providing 0.8 million frames per second. The method performs 0.8 MHz line-scanning of an excitation laser beam using a chirped signal-driven longitudinal acousto-optic deflector to create a virtual light-sheet, and images the field-of-view with a linear photomultiplier tube array to generate a 66 × 14 pixel frame each scan cycle. We implement LEAD microscopy as a blur-free flow cytometer for Caenorhabditis elegans moving at 1 m s−1 with 3.5-µm resolution and signal-to-background ratios >200. Signal-to-noise measurements indicate future LEAD fluorescence microscopes can reach higher resolutions and pixels per frame without compromising frame rates.
A diverse suite of pharmaceuticals contaminates stream and riparian food webs
Authors: Richmond Erinn K. , Rosi Emma J. , Walters David M. , Fick Jerker , Hamilton Stephen K. , Brodin Tomas , Sundelin Anna , Grace Michael R.
Published: October 2018

A multitude of biologically active pharmaceuticals contaminate surface waters globally, yet their presence in aquatic food webs remain largely unknown. Here, we show that over 60 pharmaceutical compounds can be detected in aquatic invertebrates and riparian spiders in six streams near Melbourne, Australia. Similar concentrations in aquatic invertebrate larvae and riparian predators suggest direct trophic transfer via emerging adult insects to riparian predators that consume them. As representative vertebrate predators feeding on aquatic invertebrates, platypus and brown trout could consume some drug classes such as antidepressants at as much as one-half of a recommended therapeutic dose for humans based on their estimated prey consumption rates, yet the consequences for fish and wildlife of this chronic exposure are unknown. Overall, this work highlights the potential exposure of aquatic and riparian biota to a diverse array of pharmaceuticals, resulting in exposures to some drugs that are comparable to human dosages.
Candida albicans gains azole resistance by altering sphingolipid composition
Authors: Gao Jiaxin , Wang Haitao , Li Zeyao , Wong Ada Hang-Heng , Wang Yi-Zheng , Guo Yahui , Lin Xin , Zeng Guisheng , Liu Haoping , Wang Yue , Wang Jianbin
Published: October 2018

Fungal infections by drug-resistant Candida albicans pose a global public health threat. However, the pathogen’s diploid genome greatly hinders genome-wide investigations of resistance mechanisms. Here, we develop an efficient piggyBac transposon-mediated mutagenesis system using stable haploid C. albicans to conduct genome-wide genetic screens. We find that null mutants in either gene FEN1 or FEN12 (encoding enzymes for the synthesis of very-long-chain fatty acids as precursors of sphingolipids) exhibit resistance to fluconazole, a first-line antifungal drug. Mass-spectrometry analyses demonstrate changes in cellular sphingolipid composition in both mutants, including substantially increased levels of several mannosylinositolphosphoceramides with shorter fatty-acid chains. Treatment with fluconazole induces similar changes in wild-type cells, suggesting a natural response mechanism. Furthermore, the resistance relies on a robust upregulation of sphingolipid biosynthesis genes. Our results shed light into the mechanisms underlying azole resistance, and the new transposon-mediated mutagenesis system should facilitate future genome-wide studies of C. albicans.
Direct observation of selective autophagy induction in cells and tissues by self-assembled chiral nanodevice
Authors: Sun Maozhong , Hao Tiantian , Li Xiaoyun , Qu Aihua , Xu Liguang , Hao Changlong , Xu Chuanlai , Kuang Hua
Published: October 2018

The interactions between chiral nanomaterials and organisms are still challenging and mysterious. Here, a chiral nanodevice made of yolk–shell nanoparticles tetrahedron (UYTe), centralized with upconversion nanoparticles (UCNPs), was fabricated to induce autophagy in vivo. The proposed chiral nanodevice displayed a tunable circular dichroism (CD) signal when modified with different enantiomers of glutathione (GSH). Notably, UYTe showed significant chirality-dependent autophagy-inducing ability afterd-GSH-modification because the enhanced oxidative stress and accumulation in living cell. The activation of autophagy resulted in the reduced intracellular CD intensity from the disassembly of the structure. The intracellular ATP concentration was simultaneously enhanced in response to autophagy activity, which was quantitatively bio-imaged with the upconversion luminescence (UCL) signal of the UCNP that escaped from UYTe. The autophagy effect induced in vivo by the chiral UYTe was also visualized with UCL imaging, demonstrating the great potential utility of the chiral nanostructure for cellular biological applications.
Locking loop movement in the ubiquinone pocket of complex I disengages the proton pumps
Authors: Cabrera-Orefice Alfredo , Yoga Etienne Galemou , Wirth Christophe , Siegmund Karin , Zwicker Klaus , Guerrero-Castillo Sergio , Zickermann Volker , Hunte Carola , Brandt Ulrich
Published: October 2018

Complex I (proton-pumping NADH:ubiquinone oxidoreductase) is the largest enzyme of the mitochondrial respiratory chain and a significant source of reactive oxygen species (ROS). We hypothesized that during energy conversion by complex I, electron transfer onto ubiquinone triggers the concerted rearrangement of three protein loops of subunits ND1, ND3, and 49-kDa thereby generating the power-stoke driving proton pumping. Here we show that fixing loop TMH1-2ND3 to the nearby subunit PSST via a disulfide bridge introduced by site-directed mutagenesis reversibly disengages proton pumping without impairing ubiquinone reduction, inhibitor binding or the Active/Deactive transition. The X-ray structure of mutant complex I indicates that the disulfide bridge immobilizes but does not displace the tip of loop TMH1-2ND3. We conclude that movement of loop TMH1-2ND3 located at the ubiquinone-binding pocket is required to drive proton pumping corroborating one of the central predictions of our model for the mechanism of energy conversion by complex I proposed earlier.
Chemical shifts in molecular solids by machine learning
Authors: Paruzzo Federico M. , Hofstetter Albert , Musil Félix , De Sandip , Ceriotti Michele , Emsley Lyndon
Published: October 2018

Due to their strong dependence on local atonic environments, NMR chemical shifts are among the most powerful tools for strucutre elucidation of powdered solids or amorphous materials. Unfortunately, using them for structure determination depends on the ability to calculate them, which  comes at the cost of high accuracy first-principles calculations. Machine learning has recently emerged as a way to overcome the need for quantum chemical calculations, but for chemical shifts in solids it is hindered by the chemical and combinatorial space spanned by molecular solids, the strong dependency of chemical shifts on their environment, and the lack of an experimental database of shifts. We propose a machine learning method based on local environments to accurately predict chemical shifts of molecular solids and their polymorphs to within DFT accuracy. We also demonstrate that the trained model is able to determine, based on the match between experimentally measured and ML-predicted shifts, the structures of cocaine and the drug 4-[4-(2-adamantylcarbamoyl)-5-tert-butylpyrazol-1-yl]benzoic acid.
Sequence based prediction of enhancer regions from DNA random walk
Authors: Singh Anand Pratap , Mishra Sarthak , Jabin Suraiya
Published: October 2018

Regulatory elements play a critical role in development process of eukaryotic organisms by controlling the spatio-temporal pattern of gene expression. Enhancer is one of these elements which contributes to the regulation of gene expression through chromatin loop or eRNA expression. Experimental identification of a novel enhancer is a costly exercise, due to which there is an interest in computational approaches to predict enhancer regions in a genome. Existing computational approaches to achieve this goal have primarily been based on training of high-throughput data such as transcription factor binding sites (TFBS), DNA methylation, and histone modification marks etc. On the other hand, purely sequence based approaches to predict enhancer regions are promising as they are not biased by the complexity or context specificity of such datasets. In sequence based approaches, machine learning models are either directly trained on sequences or sequence features, to classify sequences as enhancers or non-enhancers. In this paper, we derived statistical and nonlinear dynamic features along with k-mer features from experimentally validated sequences taken from Vista Enhancer Browser through random walk model and applied different machine learning based methods to predict whether an input test sequence is enhancer or not. Experimental results demonstrate the success of proposed model based on Ensemble method with area under curve (AUC) 0.86, 0.89, and 0.87 in B cells, T cells, and Natural killer cells for histone marks dataset.
Comparative genomics of the Erwinia and Enterobacter olive fly endosymbionts
Authors: Estes Anne M. , Hearn David J. , Agrawal Sonia , Pierson Elizabeth A. , Dunning Hotopp Julie C.
Published: October 2018

The pestivorous tephritid olive fly has long been known as a frequent host of the obligately host-associated bacterial endosymbiont, Erwinia dacicola, as well as other facultative endosymbionts. The genomes of Erwinia dacicola and Enterobacter sp. OLF, isolated from a California olive fly, encode the ability to supplement amino acids and vitamins missing from the olive fruit on which the larvae feed. The Enterobacter sp. OLF genome encodes both uricase and ureases, and the Er. dacicola genome encodes an allantoate transport pathway, suggesting that bird feces or recycling the fly’s waste products may be important sources of nitrogen. No homologs to known nitrogenases were identified in either bacterial genome, despite suggestions of their presence from experiments with antibiotic-treated flies. Comparisons between the olive fly endosymbionts and their free-living relatives revealed similar GC composition and genome size. The Er. dacicola genome has fewer genes for amino acid metabolism, cell motility, and carbohydrate transport and metabolism than free-living Erwinia spp. while having more genes for cell division, nucleotide metabolism and replication as well as mobile elements. A 6,696 bp potential lateral gene transfer composed primarily of amino acid synthesis and transport genes was identified that is also observed in Pseudomonas savastanoii pv savastanoii, the causative agent of olive knot disease.
NDVI dynamics under changing meteorological factors in a shallow lake in future metropolitan, semiarid area in North China
Authors: Zhang Yunlong , Wang Xuan , Li Chunhui , Cai Yanpeng , Yang Zhifeng , Yi Yujun
Published: October 2018

Three meteorological parameters, including one parameter representing water conditions (i.e., precipitation) and two parameters representing energy conditions (i.e., net radiation and air temperature), were used to make an in-depth analysis of the response of Normalized Difference Vegetation Index (NDVI) dynamics to climate change in Lake Baiyangdian, a shallow lake located in Xiong’an New Area (XNA), a future metropolitan in North China. The results showed that the vegetation coverage of the entire area remained at a medium level with average NDVI being 0.46 during 2000–2015. At a yearly scale, water was the key factor controlling the reed growth in Lake Baiyangdian. NDVI variations in each season had different water/energy driving factors. In spring, summer and autumn, vegetation growth was mainly affected by net radiation, air temperature and air temperature, respectively. Time-lags between NDVI and the meteorological parameters varied from parameters and seasons. Taken together, this research broadened our cognition about response characteristics of NDVI dynamics to water and energy variations through adding an important meteorological parameter (i.e., net radiation). With the rapid construction of XNA, it could be helpful for accurately understanding impacts of climate change on vegetation growth and be beneficial for effective ecosystem management in water shortage areas.
Complex Role of Capsaicin-Sensitive Afferents in the Collagen Antibody-Induced Autoimmune Arthritis of the Mouse
Authors: Borbély Éva , Kiss Tamás , Szabadfi Krisztina , Pintér Erika , Szolcsányi János , Helyes Zsuzsanna , Botz Bálint
Published: October 2018

Capsaicin-sensitive afferents have complex regulatory functions in the joints orchestrated via neuropeptides. This study aimed to determine their role in the collagen-antibody induced rheumatoid arthritis model. Capsaicin-sensitive nerves were defunctionalized by the capsaicin receptor agonist resiniferatoxin in C57Bl/6 mice. Arthritis was induced by the ArithroMab antibody cocktail and adjuvant. Arthritis was monitored by measuring body weight, joint edema by plethysmometry, arthritis severity by clinical scoring, mechanonociceptive threshold by plantar esthesiometry, thermonociceptive threshold by hot plate, cold tolerance by paw withdrawal latency from 0 °C water. Grasping ability was determined by the wire-grid grip test. Bone structure was evaluated byin vivomicro-CT and histology. Arthritic animals developed a modest joint edema, mechanical and cold hyperalgesia, weight loss, and a diminished grasping function, while thermal hyperalgesia is absent in the model. Desensitised mice displayed reduced arthritis severity, edema, and mechanical hyperalgesia, however, cold hyperalgesia was significantly greater in this group. Arthritic controls displayed a transient decrease of bone volume and an increased porosity, while bone density and trabecularity increased in desensitised mice. The activation of capsaicin-sensitive afferents increases joint inflammation and mechanical hyperalgesia, but decreases cold allodynia. It also affects inflammatory bone structural changes by promoting bone resorption.
Rapid pathogen identification using a novel microarray-based assay with purulent meningitis in cerebrospinal fluid
Authors: Hou Yuting , Zhang Xu , Hou Xiaolin , Wu Ruofen , Wang Yanbai , He Xuexian , Wang Libin , Wang Zhenhai
Published: October 2018

In order to improve the diagnosis of pathogenic bacteria in cerebrospinal fluid (CSF) with purulent meningitis, we developed a DNA microarray technique for simultaneous detection and identification of seven target bacterium. DNA were extracted from 24 CSF samples with purulent meningitis (or suspected purulent meningitis). The specific genes of each pathogen were chosen as the amplification target, performed the polymerase chain reaction (PCR), labeled with a fluorescence dye, and hybridized to the oligonucleotide probes on the microarray. There is no significant cross-hybridization fluorescent signal occurred in untargeted bacteria. There were 87.5% (21/24) positive results in DNA microarray compared with the 58.3% (14/24) of the CSF culture test. Of which 58.3% (14/24) of the patients with culture-confirmed purulent meningitis, 37.5% (9/24) patients who were not confirmed by culture test but were demonstrated by the clinical diagnosis and DNA microarray. Multiple bacterial infections were detected in 5 cases by the microarray. In addition, the number of gene copies was carried out to determine the sensitivity of this technique, which was shown to be 3.5 × 101 copies/μL. The results revealed that the microarray technique which target pathogens of the CSF specimen is better specificity, accuracy, and sensitivity than traditional culture method. The microarray method is an effective tool for rapidly detecting more target pathogens and identifying the subtypes of strains which can eliminate the impact of the different individuals with purulent meningitis for prompt diagnosis and treatment.
Synthesis of N-Bridged Pyrido[4,3-d]pyrimidines and Self-Assembly into Twin Rosette Cages and Nanotubes in Organic Media
Authors: Igci Cansu , Karaman Osman , Fan Yiwen , Gonzales Arthur A. , Fenniri Hicham , Gunbas Gorkem
Published: October 2018

Two N-bridged pyrido[4,3-d]pyrimidine derivatives were synthesized toward realization of a self-assembled bis-rosette cage, in organic media. Starting from commercially available malononitrile dimer and dimethyl 5-aminoisophthalate, the target molecules were synthesized in 11 steps using a convergent approach. The final bridged compounds were characterized by nuclear magnetic resonance spectroscopy and high-resolution mass spectrometry. The hierarchical self-assembly of the nanocages into rosette nanotubes and nanobundles was established by electron microscopy and molecular modelling studies.
Reversal of cerebrovascular constriction in experimental cerebral malaria by L-arginine
Authors: Ong Peng Kai , Moreira Aline S. , Daniel-Ribeiro Cláudio T. , Frangos John A. , Carvalho Leonardo J. M.
Published: October 2018

Vascular dysfunction associated with low nitric oxide (NO) biavailability and low plasma L-arginine levels is observed in both human and experimental cerebral malaria (ECM). In ECM, cerebrovascular constriction results in decreased pial blood flow and hypoxia, and administration of NO donors reverses constriction and increases survival. Supplementation of L-arginine, the substrate for NO synthesis by NO synthases, has been considered as a strategy to improve vascular health and act as adjunctive therapy in human severe malaria. We investigated the effect of L-arginine supplementation on pial vascular tonus of mice with ECM after direct superfusion on the brain surface or systemic delivery. Pial arteriolar diameters ofPlasmodium berghei-infected mice with implanted cranial windows were measured using intravital microscopy methods, before and after L-arginine administration. Systemic delivery of L-arginine was performed intravenously, at 10, 50, 100 and 200 mg/kg, as bolus injection or slowly through osmotic pumps, combined or not with artesunate. Direct superfusion of L-arginine (10−7M, 10−5M and 10−3M) on the brain surface of mice with ECM resulted in immediate, consistent and dose-dependent dilation of pial arterioles. ECM mice showed marked cerebrovascular constriction that progressively worsened over a 24 h-period after subcutaneous saline bolus administration. L-arginine administration prevented the worsening in pial constriction at all the doses tested, and at 50 mg/kg and 100 mg/kg it induced temporary reversal of vasoconstriction. Slow, continuous delivery of L-arginine by osmotic pumps, or combined bolus administration of artesunate with L-arginine, also prevented worsening of pial constriction and resulted in improved survival of mice with ECM. L-arginine ameliorates pial vasoconstriction in mice with ECM.
Development and validation of an in vitro model system to study peripheral sensory neuron development and injury
Authors: Jones Iwan , Yelhekar Tushar Devanand , Wiberg Rebecca , Kingham Paul J. , Johansson Staffan , Wiberg Mikael , Carlsson Leif
Published: October 2018

The ability to discriminate between diverse types of sensation is mediated by heterogeneous populations of peripheral sensory neurons. Human peripheral sensory neurons are inaccessible for research and efforts to study their development and disease have been hampered by the availability of relevant model systems. Thein vitrodifferentiation of peripheral sensory neurons from human embryonic stem cells therefore provides an attractive alternative since an unlimited source of biological material can be generated for studies that specifically address development and injury. The work presented in this study describes the derivation of peripheral sensory neurons from human embryonic stem cells using small molecule inhibitors. The differentiated neurons express canonical- and modality-specific peripheral sensory neuron markers with subsets exhibiting functional properties of human nociceptive neurons that include tetrodotoxin-resistant sodium currents and repetitive action potentials. Moreover, the derived cells associate with human donor Schwann cells and can be used as a model system to investigate the molecular mechanisms underlying neuronal death following peripheral nerve injury. The quick and efficient derivation of genetically diverse peripheral sensory neurons from human embryonic stem cells offers unlimited access to these specialised cell types and provides an invaluablein vitromodel system for future studies.
L10-FeNi films on Au-Cu-Ni buffer-layer: a high-throughput combinatorial study
Authors: Giannopoulos G. , Barucca G. , Kaidatzis A. , Psycharis V. , Salikhov R. , Farle M. , Koutsouflakis E. , Niarchos D. , Mehta A. , Scuderi M. , Nicotra G. , Spinella C. , Laureti S. , Varvaro G.
Published: October 2018

The fct L10-FeNi alloy is a promising candidate for the development of high performance critical-elements-free magnetic materials. Among the different materials, the Au-Cu-Ni alloy has resulted very promising; however, a detailed investigation of the effect of the buffer-layer composition on the formation of the hard FeNi phase is still missing. To accelerate the search of the best Au-Cu-Ni composition, a combinatorial approach based on High-Throughput (HT) experimental methods has been exploited in this paper. HT magnetic characterization methods revealed the presence of a hard magnetic phase with an out-of-plane easy-axis, whose coercivity increases from 0.49 kOe up to 1.30 kOe as the Au content of the Cu-Au-Ni buffer-layer decreases. Similarly, the out-of-plane magneto-crystalline anisotropy energy density increases from 0.12 to 0.35 MJ/m3. This anisotropy is attributed to the partial formation of the L10FeNi phase induced by the buffer-layer. In the range of compositions we investigated, the buffer-layer structure does not change significantly and the modulation of the magnetic properties with the Au content in the combinatorial layer is mainly related to the different nature and extent of interlayer diffusion processes, which have a great impact on the formation and order degree of the L10FeNi phase.