bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classical Imaging with Undetected Photons
Authors: Shapiro Jeffrey H. , Venkatraman Dheera , Wong Franco N. C. 
Published: May 2015

AbstractBarreto Lemos et al. [Nature512, 409–412 (2014)] reported an experiment in which a non-degenerate parametric downconverter and a non-degenerate optical parametric amplifier—used as a wavelength-converting phase conjugator—were employed to image object transparencies in a manner akin to ghost imaging. Their experiment, however, relied on single-photon detection, rather than the photon-coincidence measurements employed in ghost imaging with a parametric downconverter source. More importantly, their system formed images despite the photons that passed through the object never being detected. Barreto Lemos et al. interpreted their experiment as a quantum imager, as assuredly it is, owing to its downconverter’s emitting entangled signal and idler beams. We show, however, that virtually all the features of their setup can be realized in a quantum-mimetic fashion using classical-state light, specifically a pair of bright pseudothermal beams possessing a phase-sensitive cross correlation. Owing to its much higher signal-to-noise ratio, our bright-source classical imager could greatly reduce image-acquisition time compared to that of Barreto Lemos et al.‘s quantum system, while retaining the latter’s ability to image with undetected photons.
The cytochrome bd-type quinol oxidase is important for survival of Mycobacterium smegmatis under peroxide and antibiotic-induced stress
Authors: Lu Ping , Heineke Marieke H. , Koul Anil , Andries Koen , Cook Gregory M. , Lill Holger , van Spanning Rob , Bald Dirk 
Published: May 2015

AbstractTargeting respiration and ATP synthesis has received strong interest as a new strategy for combatting drug-resistant Mycobacterium tuberculosis. Mycobacteria employ a respiratory chain terminating with two branches. One of the branches includes a cytochrome bc1 complex and an aa3-type cytochrome c oxidase while the other branch terminates with a cytochrome bd-type quinol oxidase. In this communication we show that genetic inactivation of cytochrome bd, but not of cytochrome bc1, enhances the susceptibility of Mycobacterium smegmatis to hydrogen peroxide and antibiotic-induced stress. The type-II NADH dehydrogenase effector clofazimine and the ATP synthase inhibitor bedaquiline were bacteriostatic against wild-type M. smegmatis, but strongly bactericidal against a cytochrome bd mutant. We also demonstrated that the quinone-analog aurachin D inhibited mycobacterial cytochrome bd at sub-micromolar concentrations. Our results identify cytochrome bd as a key survival factor in M. smegmatis during antibiotic stress. Targeting the cytochrome bd respiratory branch therefore appears to be a promising strategy that may enhance the bactericidal activity of existing tuberculosis drugs.
Salt stains from evaporating droplets
Authors: Shahidzadeh Noushine , Schut Marthe F. L. , Desarnaud Julie , Prat Marc , Bonn Daniel 
Published: May 2015

AbstractThe study of the behavior of sessile droplets on solid substrates is not only associated with common everyday phenomena, such as the coffee stain effect, limescale deposits on our bathroom walls , but also very important in many applications such as purification of pharmaceuticals, de-icing of airplanes, inkjet printing and coating applications. In many of these processes, a phase change happens within the drop because of solvent evaporation, temperature changes or chemical reactions, which consequently lead to liquid to solid transitions in the droplets. Here we show that crystallization patterns of evaporating of water drops containing dissolved salts are different from the stains reported for evaporating colloidal suspensions. This happens because during the solvent evaporation, the salts crystallize and grow during the drying. Our results show that the patterns of the resulting salt crystal stains are mainly governed by wetting properties of the emerging crystal as well as the pathway of nucleation and growth and are independent of the evaporation rate and thermal conductivity of the substrates.
Detection of Composite Communities in Multiplex Biological Networks
Authors: Bennett Laura , Kittas Aristotelis , Muirhead Gareth , Papageorgiou Lazaros G. , Tsoka Sophia 
Published: May 2015

AbstractThe detection of community structure is a widely accepted means of investigating the principles governing biological systems. Recent efforts are exploring ways in which multiple data sources can be integrated to generate a more comprehensive model of cellular interactions, leading to the detection of more biologically relevant communities. In this work, we propose a mathematical programming model to cluster multiplex biological networks, i.e. multiple network slices, each with a different interaction type, to determine a single representative partition of composite communities. Our method, known as SimMod, is evaluated through its application to yeast networks of physical, genetic and co-expression interactions. A comparative analysis involving partitions of the individual networks, partitions of aggregated networks and partitions generated by similar methods from the literature highlights the ability of SimMod to identify functionally enriched modules. It is further shown that SimMod offers enhanced results when compared to existing approaches without the need to train on known cellular interactions.
Refugial isolation and range expansions drive the genetic structure of Oxyria sinensis (Polygonaceae) in the Himalaya-Hengduan Mountains
Authors: Meng Lihua , Chen Gang , Li Zhonghu , Yang Yongping , Wang Zhengkun , Wang Liuyang 
Published: May 2015

AbstractThe formation of the Mekong-Salween Divide and climatic oscillations in Pleistocene were the main drivers for the contemporary diversity and genetic structure of plants in the Himalaya-Hengduan Mountains (HHM). To identify the relative roles of the two historical events in shaping population history of plants in HHM, we investigated the phylogeographic pattern of Oxyria sinensis, a perennial plant endemic to the HHM. Sixteen chloroplast haplotypes were identified and were clustered into three phylogenetic clades. The age of the major clades was estimated to be in the Pleistocene, falling into several Pleistocene glacial stages and postdating the formation of the Mekong-Salween Divide. Range expansions occurred at least twice in the early and middle Pleistocene, but the spatial genetic distribution rarely changed since the Last Glacial Maximum. Our results suggest that temporary mountain glaciers may act as barriers in promoting the lineage divergence in O. sinensis and that subsequential range expansions and secondary contacts might reshape the genetic distribution in geography and blur the boundary of population differentiation created in the earlier glacial stages. This study demonstrates that Pleistocene climatic change and mountain glaciers, rather than the Mekong-Salween Divide, play the primary role in shaping the spatial genetic structure of O. sinensis.
Changes in the composition of intestinal fungi and their role in mice with dextran sulfate sodium-induced colitis
Authors: Qiu Xinyun , Zhang Feng , Yang Xi , Wu Na , Jiang Weiwei , Li Xia , Li Xiaoxue , Liu Yulan 
Published: May 2015

AbstractIntestinal fungi are increasingly believed to greatly influence gut health. However, the effects of fungi on intestinal inflammation and on gut bacterial constitution are not clear. Here, based on pyrosequencing method, we reveal that fungal compositions vary in different intestinal segments (ileum, cecum and colon), prefer different colonization locations (mucosa and feces) and are remarkably changed during intestinal inflammation in dextran sulfate sodium (DSS)-colitis mouse models compare to normal controls: Penicillium, Wickerhamomyces, Alternaria, and Candida are increased while Cryptococcus, Phialemonium, Wallemia and an unidentified Saccharomycetales genus are decreased in the guts of DSS-colitis mice. Fungi-depleted mice exhibited aggravated acute DSS-colitis associated with gain of Hallella, Barnesiella, Bacteroides, Alistipes, and Lactobacillus and loss of butyrate-producing Clostridium XIVa and Anaerostipes compare with normal control. In contrast, bacteria-depleted mice show attenuated acute DSS-colitis. Mice with severely chronic recurrent DSS-colitis show increased plasma (1,3)-β-D-glucan level and fungal translocation into the colonic mucosa, mesenteric lymph nodes and spleen. This work demonstrate the different roles of fungi in acute and chronic recurrent colitis: They are important counterbalance to bacteria in maintaining intestinal micro-ecological homeostasis and health in acutely inflamed intestines, but can harmfully translocate into abnormal sites and could aggravate disease severity in chronic recurrent colitis.
Unique somatic and malignant expression patterns implicate PIWI-interacting RNAs in cancer-type specific biology
Authors: Martinez Victor D. , Vucic Emily A. , Thu Kelsie L. , Hubaux Roland , Enfield Katey S.S. , Pikor Larissa A. , Becker-Santos Daiana D. , Brown Carolyn J. , Lam Stephen , Lam Wan L. 
Published: May 2015

AbstractHuman PIWI-interacting RNAs (piRNAs) are known to be expressed in germline cells, functionally silencing LINEs and SINEs. Their expression patterns in somatic tissues are largely uncharted. We analyzed 6,260 human piRNA transcriptomes derived from non-malignant and tumour tissues from 11 organs. We discovered that only 273 of the 20,831 known piRNAs are expressed in somatic non-malignant tissues. However, expression patterns of these piRNAs were able to distinguish tissue-of-origin. A total of 522 piRNAs are expressed in corresponding tumour tissues, largely distinguishing tumour from non-malignant tissues in a cancer-type specific manner. Most expressed piRNAs mapped to known transcripts, contrary to “piRNA clusters” reported in germline cells. We showed that piRNA expression can delineate clinical features, such as histological subgroups, disease stages and survival. PiRNAs common to many cancer types might represent a core gene-set that facilitates cancer growth, while piRNAs unique to individual cancer types likely contribute to cancer-specific biology.
Deep ultraviolet laser direct write for patterning sol-gel InGaZnO semiconducting micro/nanowires and improving field-effect mobility
Authors: Lin Hung-Cheng , Stehlin Fabrice , Soppera Olivier , Zan Hsiao-Wen , Li Chang-Hung , Wieder Fernand , Ponche Arnaud , Berling Dominique , Yeh Bo-Hung , Wang Kuan-Hsun 
Published: May 2015

AbstractDeep-UV (DUV) laser was used to directly write indium-gallium-zinc-oxide (IGZO) precursor solution and form micro and nanoscale patterns. The directional DUV laser beam avoids the substrate heating and suppresses the diffraction effect. A IGZO precursor solution was also developed to fulfill the requirements for direct photopatterning and for achieving semi-conducting properties with thermal annealing at moderate temperature. The DUV-induced crosslinking of the starting material allows direct write of semi-conducting channels in thin-film transistors but also it improves the field-effect mobility and surface roughness. Material analysis has been carried out by XPS, FTIR, spectroscopic ellipsometry and AFM and the effect of DUV on the final material structure is discussed. The DUV irradiation step results in photolysis and a partial condensation of the inorganic network that freezes the sol-gel layer in a homogeneous distribution, lowering possibilities of thermally induced reorganization at the atomic scale. Laser irradiation allows high-resolution photopatterning and high-enough field-effect mobility, which enables the easy fabrication of oxide nanowires for applications in solar cell, display, flexible electronics and biomedical sensors.
iMSRC: converting a standard automated microscope into an intelligent screening platform
Authors: Carro Angel , Perez-Martinez Manuel , Soriano Joaquim , Pisano David G. , Megias Diego 
Published: May 2015

AbstractMicroscopy in the context of biomedical research is demanding new tools to automatically detect and capture objects of interest. The few extant packages addressing this need, however, have enjoyed limited uptake due to complexity of use and installation. To overcome these drawbacks, we developed iMSRC, which combines ease of use and installation with high flexibility and enables applications such as rare event detection and high-resolution tissue sample screening, saving time and resources.
Enthalpy-entropy compensation at play in human copper ion transfer
Authors: Niemiec Moritz S. , Dingeldein Artur P. G. , Wittung-Stafshede Pernilla 
Published: May 2015

AbstractCopper (Cu) is an essential trace element but toxic in free form. After cell uptake, Cu is transferred, via direct protein-protein interactions, from the chaperone Atox1 to the Wilson disease protein (WD) for incorporation into Cu-dependent enzymes. Cu binds to a conserved C1XXC2 motif in the chaperone as well as in each of the cytoplasmic metal-binding domains of WD. Here, we dissect mechanism and thermodynamics of Cu transfer from Atox1 to the fourth metal binding domain of WD. Using chromatography and calorimetry together with single Cys-to-Ala variants, we demonstrate that Cu-dependent protein heterocomplexes require the presence of C1 but not C2. Comparison of thermodynamic parameters for mutant versus wild type reactions reveals that the wild type reaction involves strong entropy-enthalpy compensation. This property is explained by a dynamic inter-conversion of Cu-Cys coordinations in the wild type ensemble and may provide functional advantage by protecting against Cu mis-ligation and bypassing enthalpic traps.
Multiple MoS2 Transistors for Sensing Molecule Interaction Kinetics
Authors: Nam Hongsuk , Oh Bo-Ram , Chen Pengyu , Chen Mikai , Wi Sungjin , Wan Wenjie , Kurabayashi Katsuo , Liang Xiaogan 
Published: May 2015

AbstractAtomically layered transition metal dichalcogenides (TMDCs) exhibit a significant potential to enable next-generation low-cost transistor biosensors that permit single-molecule-level quantification of biomolecules. To realize such potential biosensing capability, device-oriented research is needed for calibrating the sensor responses to enable the quantification of the affinities/kinetics of biomolecule interactions. In this work, we demonstrated MoS2-based transistor biosensors capable of detecting tumor necrosis factor – alpha (TNF-α) with a detection limit as low as 60 fM. Such a detection limit was achieved in both linear and subthreshold regimes of MoS2 transistors. In both regimes, all sets of transistors exhibited consistent calibrated responses with respect to TNF-α concentration and they resulted in a standard curve, from which the equilibrium constant of the antibody-(TNF-α) pair was extracted to be KD = 369 ± 48 fM. Based on this calibrated sensor model, the time-dependent binding kinetics was also measured and the association/dissociation rates of the antibody-(TNF-α) pair were extracted to be (5.03 ± 0.16) × 108 M−1s−1 and (1.97 ± 0.08) × 10−4 s−1, respectively. This work advanced the critical device physics for leveraging the excellent electronic/structural properties of TMDCs in biosensing applications as well as the research capability in analyzing the biomolecule interactions with fM-level sensitivities.
Decreased LKB1 predicts poor prognosis in Pancreatic Ductal Adenocarcinoma
Authors: Yang Jian-Yu , Jiang Shu-Heng , Liu De-Jun , Yang Xiao-Mei , Huo Yan-Miao , Li Jiao , Hua Rong , Zhang Zhi-Gang , Sun Yong-Wei 
Published: May 2015

AbstractLiver kinase B1 (LKB1) has been identified as a critical modulator involved in cell proliferation and polarity. The purpose of the current study was to characterize the expression pattern of LKB1 and assess the clinical significance of LKB1 expression in pancreatic ductal adenocarcinoma (PDAC) patients. LKB1 mRNA expression which was analyzed in 32 PDAC lesions and matched non-tumor tissues, was downregulated in 50% (16/32) of PDAC lesions. Similar results were also obtained by analyzing three independent datasets from Oncomine. Protein expression of LKB1 was significantly reduced in 6 PDAC cell lines and downregulated in 31.3% (10/32) of PDAC lesions compared to matched non-tumorous tissues, as determined by Western blot analysis. Additionally, tissue microarray containing 205 PDAC specimens was evaluated for LKB1 expression by IHC and demonstrated that reduced expression of LKB1 in 17.6% (36/205) of PDAC tissues was significantly correlated with clinical stage, T classification, N classification, liver metastasis and vascular invasion. Importantly, Kaplan-Meier survival and Cox regression analyses were executed to evaluate the prognosis of PDAC and found that LKB1 protein expression was one of the independent prognostic factors for overall survival of PDAC patients.
A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data
Authors: Lu Qiongshi , Hu Yiming , Sun Jiehuan , Cheng Yuwei , Cheung Kei-Hoi , Zhao Hongyu 
Published: May 2015

AbstractIdentifying functional regions in the human genome is a major goal in human genetics. Great efforts have been made to functionally annotate the human genome either through computational predictions, such as genomic conservation, or high-throughput experiments, such as the ENCODE project. These efforts have resulted in a rich collection of functional annotation data of diverse types that need to be jointly analyzed for integrated interpretation and annotation. Here we present GenoCanyon, a whole-genome annotation method that performs unsupervised statistical learning using 22 computational and experimental annotations thereby inferring the functional potential of each position in the human genome. With GenoCanyon, we are able to predict many of the known functional regions. The ability of predicting functional regions as well as its generalizable statistical framework makes GenoCanyon a unique and powerful tool for whole-genome annotation. The GenoCanyon web server is available at http://genocanyon.med.yale.edu
Depsipeptide Intermediates Interrogate Proposed Biosynthesis of Cereulide, the Emetic Toxin of Bacillus cereus
Authors: Marxen Sandra , Stark Timo D. , Rütschle Andrea , Lücking Genia , Frenzel Elrike , Scherer Siegfried , Ehling-Schulz Monika , Hofmann Thomas 
Published: May 2015

AbstractCereulide and isocereulides A-G are biosynthesized as emetic toxins by Bacillus cereus via a non-ribosomal peptide synthetase (NRPS) called Ces. Although a thiotemplate mechanisms involving cyclo-trimerization of ready-made D-O-Leu-D-Ala-L-O-Val-L-Val via a thioesterase (TE) domain is proposed for cereulide biosynthesis, the exact mechanism is far from being understood. UPLC-TOF MS analysis of B. cereus strains in combination with 13C-labeling experiments now revealed tetra-, octa- and dodecapeptides of a different sequence, namely (L-O-Val-L-Val-D-O-Leu-D-Ala)1-3, as intermediates of cereulide biosynthesis. Surprisingly, also di-, hexa- and decadepsipeptides were identified which, together with the structures of the previously reported isocereulides E, F and G, do not correlate to the currently proposed mechanism for cereulide biosynthesis and violate the canonical NRPS biosynthetic logic. UPLC-TOF MS metabolite analysis and bioinformatic gene cluster analysis highlighted dipeptides rather than single amino or hydroxy acids as the basic modules in tetradepsipeptide assembly and proposed the CesA C-terminal C* domain and the CesB C-terminal TE domain to function as a cooperative esterification and depsipeptide elongation center repeatedly recruiting the action of the C* domain to oligomerize tetradepsipeptides prior to the release of cereulide from the TE domain by macrocyclization.
Starvation-induced collective behavior in C. elegans
Authors: Artyukhin Alexander B. , Yim Joshua J. , Cheong Cheong Mi , Avery Leon 
Published: May 2015

AbstractWe describe a new type of collective behavior in C. elegans nematodes, aggregation of starved L1 larvae. Shortly after hatching in the absence of food, L1 larvae arrest their development and disperse in search for food. In contrast, after two or more days without food, the worms change their behavior—they start to aggregate. The aggregation requires a small amount of ethanol or acetate in the environment. In the case of ethanol, it has to be metabolized, which requires functional alcohol dehydrogenase sodh-1. The resulting acetate is used in de novo fatty acid synthesis and some of the newly made fatty acids are then derivatized to glycerophosphoethanolamides and released into the surrounding medium. We examined several other Caenorhabditis species and found an apparent correlation between propensity of starved L1s to aggregate and density dependence of their survival in starvation. Aggregation locally concentrates worms and may help the larvae to survive long starvation. This work demonstrates how presence of ethanol or acetate, relatively abundant small molecules in the environment, induces collective behavior in C. elegans associated with different survival strategies.
BCL-2 family member BOK promotes apoptosis in response to endoplasmic reticulum stress
Authors: Carpio Marcos A. , Michaud Michael , Zhou Wenping , Fisher Jill K. , Walensky Loren D. , Katz Samuel G. 
Published: May 2015

SignificanceThe role of B-cell lymphoma-2 (BCL-2) ovarian killer (BOK) in apoptosis regulation has been a long-standing enigma. Despite the homology to BAX and BAK, BOK has yet to be linked to a definitive physiologic function in the classical apoptotic pathway. Here, we report a selective role for BOK in promoting mitochondrial apoptosis in response to endoplasmic reticulum stress.
Classification images reveal decision variables and strategies in forced choice tasks
Authors: Pritchett Lisa M. , Murray Richard F. 
Published: May 2015

Significance
Signal detection theory is a classic theory of perceptual decision making. This theory states that when people make a decision based on visual or auditory information, they calculate a “decision variable” that encodes their estimate of the probability of each possible response being correct. Until now, there has been no way to measure decision variables behaviorally. We describe a method of estimating decision variables, and we show that it is a highly effective way of revealing peoples’ decision strategies. This creates a new approach to answering long-standing questions about perception and decision making.
Dissecting enzyme function with microfluidic-based deep mutational scanning
Authors: Romero Philip A. , Tran Tuan M. , Abate Adam R. 
Published: May 2015

Significance
As powerful biological catalysts, enzymes can solve challenging problems that range from the industrial production of chemicals to the treatment of human disease. The ability to design new enzymes with tailor-made chemical functions would have a far-reaching impact. However, this important capability has been limited by our cursory understanding of enzyme catalysis. Here, we report a method that uses unbiased empirical analysis to dissect the molecular basis of enzyme function. By comprehensively mapping how changes in an enzyme’s amino acid sequence affect its activity, we obtain a detailed view of the interactions that shape the enzyme function landscape. Large, unbiased analyses of enzyme function allow the discovery of new biochemical mechanisms that will improve our ability to engineer custom biocatalysts.