Miracle-dz/UniFAR-FTUs huggingface dataset:
In Silico Identification of Gene Amplification Targets for Improvement of Lycopene Production

ABSTRACT The identification of genes to be deleted or amplified is an essential step in metabolic engineering for strain improvement toward the enhanced production of desired bioproducts. In the past, several methods based on flux analysis of genome-scale metabolic models have been developed for identifying gene targets for deletion. Genome-wide identification of gene targets for amplification, on the other hand, has been rather difficult. Here, we report a strategy called flux scanning based on enforced objective flux (FSEOF) to identify gene amplification targets. FSEOF scans all the metabolic fluxes in the metabolic model and selects fluxes that increase when the flux toward product formation is enforced as an additional constraint during flux analysis. This strategy was successfully employed for the identification of gene amplification targets for the enhanced production of the red-colored antioxidant lycopene. Additional metabolic engineering based on gene knockout simulation resulted in further synergistic enhancement of lycopene production. Thus, FSEOF can be used as a general strategy for selecting genome-wide gene amplification targets in silico.
Distinct Roles of Kv1 and Kv3 Potassium Channels at the Calyx of Held Presynaptic Terminal

Despite identification of >100 potassium channel subunits, relatively little is known about their roles in synaptic transmission. To address this issue we recorded presynaptic potassium currents (IPK) directly from the calyx of Held terminal in brainstem slices of rats. IPK was composed of a 4-aminopyridine (4-AP)-sensitive component and a smaller 4-AP-insensitive component composed of an iberiotoxin-sensitive current and an unidentified slowly activating potassium current. IPK could also be separated into a tetraethylammonium (TEA; 1 mm)-sensitive high-voltage-activated component and a margatoxin (10 nm)-sensitive low-voltage-activated component, which was also blocked by dendrotoxin-I (200 nm) and tityustoxin-Kα (100 nm). In outside-out patches excised from calyceal terminals, TEA (1 mm) consistently and to a large extent attenuated IPK, whereas margatoxin attenuated IPK only in a subset of patches (three of seven). Immunocytochemical examination using Kv subtype-specific antibodies indicated that multiple Kv1 and Kv3 subtypes were present at the calyceal terminal. In paired presynaptic and postsynaptic whole-cell recordings, TEA (1 mm) increased both the duration and peak amplitude of presynaptic action potentials and simultaneously potentiated EPSCs. Margatoxin alone had no such effect but reduced the amount of depolarization required for action potential generation, thereby inducing a burst of spikes when the nerve terminal was depolarized for a prolonged period. Thus, at the calyx of Held terminal, Kv3 channels directly regulate evoked transmitter release, whereas Kv1 channels reduce nerve terminal excitability, thereby preventing aberrant transmitter release. We conclude that both Kv3 and Kv1 channels contribute differentially to maintaining the fidelity of synaptic transmission at the calyx of Held.
Colloido-polymersomes: Capsules consisting of a composite layer of particles and polymer

We present an approach to fabricate capsules consisting of a composite layer of particles and block copolymers . The capsules are fabricated by directed assembly of block copolymers at the interfaces of a double emulsion template and electrostatic adsorption of particles onto the copolymers. The double emulsion drops are prepared using capillary-based microfluidics. The solvent phase of the double emulsion is then evaporated to yield polymersomes. The particles are locked together on the surface of the polymersomes. The resultant structures, which we call “colloido-polymersomes”, are hollow shells of particlecoated thin polymer films. Our approach provides a simple strategy for fabricating vesicles with a complex structure for encapsulation-related applications; by tuning the characteristics of the particles attached, the final vesicles can be used for attaching biomolecules such as proteins and DNA, and thus are useful for biomedical applications such
Persistent homology theory-the heart of Topological Data Analysis

The era of Big Data has brought forward complex and high volume of data and along with it the demand for development of efficient and innovative methods to process and analyze them. Today, Data are often noisy, high dimensional and incomplete making the task of ‘Analyzing’ them challenging. Along with the ‘Traditional’ Quantitative Data Analysis methods from Machine Learning and Statistics, recently developed areas like Topogical data Analysis (TDA) has provided new perspective in the study of data in an increasingly diverse set of applications, for instance, Analysis of Complex Network [4], Analysis of Breast Cancer Data [6], Viral Evolution [1], Contagion spread on Network [7] etc. TDA is a field where we study the shape of the data, we develop tools to understand qualitative features of the data using ideas developed from several branch of Mathematics Topology, Algebraic Homology etc. How qualitative features of data can be defined, how to compute them efficiently and how we can visualize those features all these questions has been answered in a more general problem settings in Persistent Homology [9] [10] [2] and can be applied to specific application areas.
Folding and Activity of the Hammerhead Ribozyme

The hammerhead is the smallest of the nucleolytic ribozymes, that undergo backbone cleavage by a transesterification reaction in the presence of magnesium ions. The RNA is induced to fold into its active conformation by the binding of metal ions in two stages. These generate domain 2, the scaffold on which the ribozyme is built, and domain 1, the active centre of the ribozyme. Further local structural rearrangement during the activation of the ribozyme is suggested by a number of crystal structures. The 105‐fold rate enhancement is probably brought about by a combination of metal‐ion participation and stereochemical factors in the environment of the folded RNA structure.
Hypothetical gene C18orf42 encodes a novel protein kinase A‐binding protein

The substrate specificity of cAMP‐dependent protein kinase A (PKA) is controlled by its interaction with the A‐kinase anchoring protein (AKAP) family. Individual AKAP members are localized to particular intracellular sites and tether PKA specifically to the subcellular compartments where target substrates exist. Here, we report that the human hypothetical gene C18orf42 encodes a novel PKA‐binding protein that potentially regulates PKA–AKAP interactions. C18orf42 is expressed preferentially in neural tissues. Functional motif searching predicted that C18orf42 may encode a short protein that contains a putative PKA‐binding motif. To confirm this possibility, we applied the CRISPR/Cas9 genome‐editing system to incorporate the FLAG tag into the C‐terminus of the endogenous C18orf42 protein in the mouse neural cell line Neuro2a. Immunoprecipitation and immunoblotting using anti‐FLAG antibody showed translation of the endogenous C18orf42 protein and the physical interaction of the C18orf42 protein with PKA subunits. Immunoprecipitation and pull‐down assays showed that C18orf42 binds specifically to the type II regulatory subunits of PKA. Unlike the expression of many AKAPs, that of C18orf42 could block the AKAP‐mediated subcellular localization of PKA. These findings suggest that C18orf42 may be a novel PKA signaling gene that serves as an endogenous disruptor peptide for PKA–AKAP interactions.
[Toxicological assessment of 2,5,2',5'-tetrachlorobiphenyl and its major metabolite, 3-hydroxy-2,5,2',5'-tetrachlorobiphenyl in rats].

We observed previously that polychlorinated biphenyl (PCB) could be classified to two groups, 3-methylcholanthrene (MC)-type and phenobarbital (PB)-type, in term of inducibility of the hepatic enzymes. MC-type PCBs such as 3,4,3',4'-tetrachlorobiphenyl (TCB), 3,4,5,3',4'-pentachlorobiphenyl (PenCB) and 3,4,5,3',4',5'-hexachlorobiphenyl (HexCB) exhibited high acute toxicity in parallel with their induction ability of microsomal benzo[a]pyrene 3-hydroxylase and cytosolic DT-diaphorase. On the contrary, PB-type PCBs such as 2,5,2',5'-TCB and 2,4,5,2',4',5'-HexCB which induce microsomal benzphetamine N-demethylase and NADPH-cytochrome P-450 reductase activities showed virtually no or very low toxicity. In the present study, we examined effects of 2,5,2',5'-TCB and its major metabolite 3-hydroxy-2,5,2',5'-TCB on body weight gain, organ weights and activities of hepatic enzymes in rats and assessed acute toxicity of these compounds. As the results, in both 2,5,2',5'-TCB and 3-hydroxy-2,5,2',5'-TCB groups, the body weights were increased during the experiment, but the rate of growth was significantly suppressed after 3 days. Significant hypertrophy of the liver and decrease of total liver lipid content were observed in 2,5,2',5'-TCB group, but the atrophy of spleen and thymus was not affected in both groups. On the other hand, in 2,5,2',5'-TCB group, benzo[a]pyrene 3-hydroxylase and benzphetamine N-demethylase activities were increased to 2. 4-fold and 1.5-fold, respectively, but were not increased in 3-hydroxy-2,5,2',5'-TCB group. After injection of 2,5,2',5'-TCB, 45% of the dose was excreted as 3-hydroxy-2,5,2',5'-TCB in feces for 5 days. (ABSTRACT TRUNCATED AT 250 WORDS)
Microbial Isotopic Fractionation of Perchlorate Chlorine

ABSTRACT Perchlorate contamination can be microbially respired to innocuous chloride and thus can be treated effectively. However, monitoring a bioremediative strategy is often difficult due to the complexities of environmental samples. Here we demonstrate that microbial respiration of perchlorate results in a significant fractionation (∼−15‰) of the chlorine stable isotope composition of perchlorate. This can be used to quantify the extent of biotic degradation and to separate biotic from abiotic attenuation of this contaminant.
DEGREE SUPERVALUATIONAL LOGIC

Supervaluationism is often described as the most popular semantic treatment of indeterminacy. There’s little consensus, however, about how to fill out the bare-bones idea to include a characterization of logical consequence. The paper explores one methodology for choosing between the logics: pick a logic that norms belief as classical consequence is standardly thought to do. The main focus of the paper considers a variant of standard supervaluational, on which we can characterize degrees of determinacy. It applies the methodology above to focus on degree logic. This is developed first in a basic, single-premise case; and then extended to the multipremise case, and to allow degrees of consequence. The metatheoretic properties of degree logic are set out. On the positive side, the logic is supraclassical—all classical valid sequents are degree logic valid. Strikingly, metarules such as cut and conjunction introduction fail.
Cardiovascular Responses of Women With Chronic Fatigue Syndrome to Stressful Cognitive Testing Before and After Strenuous Exercise

Objective The purpose of this study was to compare the cardiovascular responses of patients with chronic fatigue syndrome (CFS) to healthy control subjects when performing stressful cognitive tasks before and after strenuous exercise. Method Beat-by-beat blood pressure and electrocardiogram were recorded on 19 women with CFS and 20 healthy nonexercising (ie, sedentary) women while they performed cognitive tests before, immediately after, and 24 hours after incremental exercise to exhaustion. Results Diminished heart rate (p < .01) and systolic (p < .01) and diastolic (p < .01) blood pressure responses to stressful cognitive testing were seen in patients with CFS when compared with healthy, sedentary controls. This diminished stress response was seen consistently in patients with CFS across three separate cognitive testing sessions. Also, significant negative correlations between self-ratings of CFS symptom severity and cardiovascular responses were seen (r = −0.62, p < .01). Conclusions Women with CFS have a diminished cardiovascular response to cognitive stress; however, exercise did not magnify this effect. Also, the data showed that the patients with the lowest cardiovascular reactivity had the highest ratings of CFS symptom severity, which suggests that the individual response of the patient with CFS to stress plays a role in the common complaint of symptoms worsening after stress.
Influence of parasitization by Trichinella spiralis on the levels of heat shock proteins in rat liver and muscle

To examine levels of heat shock proteins (HSPs) in host responses to helminth infection, rats were infected with Trichinella spiralis. The kinetics of HSP25, HSP60, HSP70 and HSP90 production in the liver and muscle of infected rats was compared with that of non-infected controls. HSPs were detected using electrophoretic analysis of fixed amounts of proteins (0·02 mg) and then blotting and incubation of membranes with polyclonal anti-HSP25 antibody, or monoclonal antibody against HSP60, or HSP70 or HSP90. Quantitation of blotted separated polypeptides reactive with the specific anti-HSP antibodies was achieved using an image analyser. Enhancement of HSP25 production was observed in the liver of infected rats, whereas muscle from the same rats exhibited enhanced production of HSP25 and HSP60 one day after infection only. These data indicate that HSPs levels can be used successfully to measure stress injury brought about by helminth infection in organs and tissues of the host.
The Role of Sdf‐1α signaling in Xenopus laevis somite morphogenesis

Background: Stromal derived factor‐1α (sdf‐1α), a chemoattractant chemokine, plays a major role in tumor growth, angiogenesis, metastasis, and in embryogenesis. The sdf‐1α signaling pathway has also been shown to be important for somite rotation in zebrafish (Hollway et al., 2007). Given the known similarities and differences between zebrafish and Xenopus laevis somitogenesis, we sought to determine whether the role of sdf‐1α is conserved in Xenopus laevis. Results: Using a morpholino approach, we demonstrate that knockdown of sdf‐1α or its receptor, cxcr4, leads to a significant disruption in somite rotation and myotome alignment. We further show that depletion of sdf‐1α or cxcr4 leads to the near absence of β‐dystroglycan and laminin expression at the intersomitic boundaries. Finally, knockdown of sdf‐1α decreases the level of activated RhoA, a small GTPase known to regulate cell shape and movement. Conclusion: Our results show that sdf‐1α signaling regulates somite cell migration, rotation, and myotome alignment by directly or indirectly regulating dystroglycan expression and RhoA activation. These findings support the conservation of sdf‐1α signaling in vertebrate somite morphogenesis; however, the precise mechanism by which this signaling pathway influences somite morphogenesis is different between the fish and the frog. Developmental Dynamics 243:509–526, 2014. © 2013 Wiley Periodicals, Inc.
On the Complexity of Scheduling in Wireless Networks

We consider the problem of throughput-optimal scheduling in wireless networks subject to interference constraints. We model the interference using a family of -hop interference models, under which no two links within a -hop distance can successfully transmit at the same time. For a given , we can obtain a throughput-optimal scheduling policy by solving the well-known maximum weighted matching problem. We show that for , the resulting problems are NP-Hard that cannot be approximated within a factor that grows polynomially with the number of nodes. Interestingly, for geometric unit-disk graphs that can be used to describe a wide range of wireless networks, the problems admit polynomial time approximation schemes within a factor arbitrarily close to 1. In these network settings, we also show that a simple greedy algorithm can provide a 49-approximation, and the maximal matching scheduling policy, which can be easily implemented in a distributed fashion, achieves a guaranteed fraction of the capacity region for "all . " The geometric constraints are crucial to obtain these throughput guarantees. These results are encouraging as they suggest that one can develop low-complexity distributed algorithms to achieve near-optimal throughput for a wide range of wireless networks.
Seven-color Fluorescence Imaging of Tissue Samples Based on Fourier Spectroscopy and Singular Value Decomposition

SUMMARY Seven-color analyses of immunofluorescence-stained tissue samples were accomplished using Fourier spectroscopy-based hyperspectral imaging and singular value decomposition. This system consists of a combination of seven fluorescent dyes, three filter-sets, an epifluorescence microscope, a spectral imaging system, a computer for data acquisition, and data analysis software. The spectra of all pixels in a multicolor image were taken simultaneously using a Sagnac type interferometer. The spectra were deconvolved to estimate the contribution of each component dye, and individual dye images were constructed based on the intensities of assigned signals. To obtain mixed spectra, three filter sets, i.e., Bl, Gr, and Rd for Alexa488 and Alexa532, for Alexa546, Alexa568, and Alexa594, and for Cy5 and Cy5.5, respectively, were used for simultaneous excitation of two or three dyes. These fluorophores have considerable spectral overlap which precludes their separation by conventional analysis. We resolved their relative contributions to the fluorescent signal by a method involving linear unmixing based on singular value decomposition of the matrices consisting of dye spectra. Analyses of mouse thymic tissues stained with seven different fluorescent dyes provided clear independent images, and any combination of two or three individual dye images could be used for constructing multicolor images.
Fusing 100’s of 3D Point Clouds of Objects

This abstract presents an approach to fusing hundreds of 3D point clouds to make complete models of 3D objects[1]. This topic first arose in the mid-1990s, but has now become particularly relevant because of the availability of consumer video-rate 3D sensors, such as the Kinect. These sensors can easily acquire hundreds or thousands of 3D images of objects or scenes in a few seconds, which has led researchers to ask again how to fuse the individual 3D datasets. This project focused on fusing hundreds of views of the exterior of an object, in contrast to hundreds of views of a scene, as in the KinectFusion [2] or SLAM approaches. The core motivating problem was how to manage registration error. For example, incremental image to image registration allows the registration errors to accumulate, and so the shape gradually distorts. The SLAM approach reduces the error by ‘loop closure’. The intuition was that one could create an alignment error minimization approach, whereby each individual scan minimized its registration error with all of the other scans. As each scan was attempting to do this independently, with the right registration error formulation, the scans would settle into a minimum error position. Previous approaches have incorporated similar alignment update schemes wherein transforms and point correspondences are alternatively optimized while keeping the other fixed ([3], [4], [5], [6]). By alternating the update of view transforms and error estimation, the two solutions tend to mutually improve one another during the process and converge to appropriate solutions.
A viable system structure for large‐scale software systems

A homogeneous system structure is proposed that enhances modularity and flexibility, and facilitates (further) development of large‐scale software systems in a major‐industry environment. In our opinion, it is an effective means of countering the inherent increase in software entropy when (further) developing existing large‐scale software systems, thereby substantially cutting down production costs. It can be applied generally both to new and existing systems, whether application programs or operating systems, promotes the parallel use of different programming paradigms and various implementation languages, and offers the option of either redesigning parts or introducing additional parts in stages based on a more modern technology. The proposed system structure is compared and contrasted with other architectures such as CORBA, and it is shown that it may be regarded as an embellishment of the CORBA architecture for the internal structuring or restructuring of possibly distributed software systems. So far it has been used in four releases of the BS2000/OSD operating system with very positive results. Dependencies between various entities – which we call ‘subsystems’ – in the course of the (further) development process, as well as during dynamic execution are minimized and well‐regulated. The subsystems may be loaded on demand during the session by a system authority. Every interface in the system is classified according to its permitted scope of use. For interfaces between subsystems, a uniform and standardized technique is introduced which uses the same format for all implementation languages at both the source‐ and binary‐code level. This technique exceeds the regulations in other architectures but actually achieves considerable rationalization. Copyright © 1999 John Wiley & Sons, Ltd.
Green fluorescent protein as a marker for gene expression and subcellular localization in budding yeast

The green fluorescent protein (GFP) from the jellyfish Aequorea victoria has attracted much attention as a tool to study a number of biological processes. This study describes the use of GFP as a vital reporter molecule for localization and expression studies in Saccharomyces cerevisiae. Construction of GFP expression vectors which allow N‐ or C‐terminal fusion of the gfp gene to a gene of interest allowed the generation of fusion proteins whose subcellular localization was followed by fluorescence microscopy in living yeast cells. Analysis of three unknown open reading frames obtained from the budding yeast chromosome XIV resulted in distinct staining patterns, allowing prediction of the cellular localization of these unknown proteins. Furthermore, GFP was used to construct a gene replacement cassette which, after homologous integration into the genomic locus, placed the gfp gene behind a promoter of interest. The amount of GFP produced from this promoter was then quantified in living yeast cells by flow cytometry. With this novel replacement cassette a gene of interest can be deleted and at the same time its expression level studied under various growth conditions. The experiments presented here suggest that GFP represents a convenient fluorescent marker for localization studies as well as gene expression studies in budding yeast. Systematic studies of a large number of genes should benefit from such assays.
Cognitive Wireless Sensor Network Platform for Cooperative Communications

Nowadays, Wireless Ad Hoc Sensor Networks (WAHSNs), specially limited in energy and resources, are subject to development constraints and difficulties such as the increasing RF spectrum saturation at the unlicensed bands. Cognitive Wireless Sensor Networks (CWSNs), leaning on a cooperative communication model, develop new strategies to mitigate the inefficient use of the spectrum that WAHSNs face. However, few and poorly featured platforms allow their study due to their early research stage. This paper presents a versatile platform that brings together cognitive properties into WAHSNs. It combines hardware and software modules as an entire instrument to investigate CWSNs. The hardware fits WAHSN requirements in terms of size, cost, features, and energy. It allows communication over three different RF bands, becoming the only cognitive platform for WAHSNs with this capability. In addition, its modular and scalable design is widely adaptable to almost any WAHSN application. Significant features such as radio interface (RI) agility or energy consumption have been proven throughout different performance tests.