Miracle-dz/UniFAR-FTUs huggingface dataset:
Computationally designed libraries for rapid enzyme stabilization

The ability to engineer enzymes and other proteins to any desired stability would have wide-ranging applications. Here, we demonstrate that computational design of a library with chemically diverse stabilizing mutations allows the engineering of drastically stabilized and fully functional variants of the mesostable enzyme limonene epoxide hydrolase. First, point mutations were selected if they significantly improved the predicted free energy of protein folding. Disulfide bonds were designed using sampling of backbone conformational space, which tripled the number of experimentally stabilizing disulfide bridges. Next, orthogonal in silico screening steps were used to remove chemically unreasonable mutations and mutations that are predicted to increase protein flexibility. The resulting library of 64 variants was experimentally screened, which revealed 21 (pairs of) stabilizing mutations located both in relatively rigid and in flexible areas of the enzyme. Finally, combining 10–12 of these confirmed mutations resulted in multi-site mutants with an increase in apparent melting temperature from 50 to 85°C, enhanced catalytic activity, preserved regioselectivity and a >250-fold longer half-life. The developed Framework for Rapid Enzyme Stabilization by Computational libraries (FRESCO) requires far less screening than conventional directed evolution.
Segmentation of confocal microscopic image of insect brain

Accurate analysis of insect brain structures in digital confocal microscopic images is valuable and important to biology research needs. The first step is to segment meaningful structures from images. Active contour model, known as snakes, is widely used for segmentation of medical images. A new class of active contour model called gradient vector flow snake has been introduced in 1998 to overcome some critical problems encountered in the traditional snake. In this paper, we use gradient vector flow snake to segment the mushroom body and the central body from the confocal microscopic insect brain images. First, an edge map is created from images by some edge filters. Second, a gradient vector flow field is calculated from the edge map using a computational diffusion process. Finally, a traditional snake deformation process starts until it reaches a stable configuration. User interface is also provided here, allowing users to edit the snake during deformation process, if desired. Using the gradient vector flow snake as the main segmentation method and assist with user interface, we can properly segment the confocal microscopic insect brain image for most of the cases. The identified mushroom and central body can then be used as the preliminary results toward a 3-D reconstruction process for further biology researches.
Continuous analytic I-V model for surrounding-gate MOSFETs

We present a continuous analytic current-voltage (I-V) model for cylindrical undoped (lightly doped) surrounding gate (SGT) MOSFETs. It is based on the exact solution of the Poisson's equation, and the current continuity equation without the charge-sheet approximation, allowing the inversion charge distribution in the silicon film to be adequately described. It is valid for all the operation regions (linear, saturation, subthreshold) and traces the transition between them without fitting parameters, being ideal for the kernel of SGT MOSFETs compact models. We have demonstrated that the I-V characteristics obtained by this model agree with three-dimensional numerical simulations for all ranges of gate and drain voltages.
The Moisture Relations of Textile Fibres at Elevated Temperatures

The moisture contents of ten kinds of textile fibres in the form of specially prepared yarns were determined when the fibres were in equilibrium with air for a series of relative humidities and tem peratures. Data were obtained for both "desorption. " and "ad sorption," the yarns being brought to equilibrium from a wet condition and a dry condition, respectively. The fibres studied were raw cotton, "purified" cotton, mercerized cotton, clothing wool, carpet wool, viscose rayon, cuprammonium rayon, raw silk, degummed silk and cellulose acetate. The temperatures ranged from 96° F. to 302° F. and the relative humidities ranged from 5% to 90% for temperatures below 212° F. and up to the maximum obtainable at atmospheric pressure above 212° F. The results are given in the form of graphs showing moisture content against relative humidity and also in the form of graphs in which the logarithms of the moisture contents at given relative humidities are plotted against the reciprocals of the corresponding absolute temperatures. The last show straight line relationships with changes in the slopes of the lines between 200° F. and 220° F.
Context-Based Energy Saving Strategies for Continuous Determination of Position on iOS Devices

Continuous determination of position on modern smartphones, in particular permanent utilization of GPS, considerably reduces operating times of batteries. However, incessant exploitation of power for determining the current location is avoidable, e.g., while the device is not being moved. This basic idea of considering the kinetic context of a device for localization enables the development of advanced localization techniques positively impacting energy consumption. This paper outlines the fundamental concept and the architecture for context-based energy saving strategies for continuous location determination on mobile devices, practically implemented on iOS. It proves their potentials in terms of energy consumption by a series of conducted tests, reflects on accuracy issues, and discusses reutilization for other platforms.
Adaptive Lookup of Open WiFi Using Crowdsensing

Open WiFi access points (APs) are demonstrating that they can provide opportunistic data services to moving vehicles. We present CrowdWiFi, a novel system to look up roadside WiFi APs located outdoors or inside buildings. CrowdWiFi consists of two components: online compressive sensing (CS) and offline crowdsourcing. Online CS presents an efficient framework for the coarse-grained estimation of nearby APs along the driving route, where received signal strength (RSS) values are recorded at runtime, and the number and location of the APs are recovered immediately based on limited RSS readings and adaptive CS operations. Offline crowdsourcing assigns the online CS tasks to crowd-vehicles and aggregates answers on a bipartite graphical model. Crowd-server also iteratively infers the reliability of each crowd-vehicle from the aggregated sensing results, and then refines the estimation of the APs using weighted centroid processing. Extensive simulation results and real testbed experiments confirm that CrowdWiFi can successfully reduce the computation cost and energy consumption of roadside WiFi lookup, while maintaining satisfactory localization accuracy.
Short proofs are narrow—resolution made simple

The widthof a Resolution proof is defined to be the maximal number of literals in any clause of the proof. In this paper, we relate proof width to proof length (=size), in both general Resolution, and its tree-like variant. The following consequences of these relations reveal width as a crucial “resource” of Resolution proofs. In one direction, the relations allow us to give simple, unified proofs for almost all known exponential lower bounds on size of resolution proofs, as well as several interesting new ones. They all follow from width lower bounds, and we show how these follow from natural expansion property of clauses of the input tautology. In the other direction, the width-size relations naturally suggest a simple dynamic programming procedure for automated theorem proving—one which simply searches for small width proofs. This relation guarantees that the runnuing time (and thus the size of the produced proof) is at most quasi-polynomial in the smallest tree-like proof. This algorithm is never much worse than any of the recursive automated provers (such as DLL) used in practice. In contrast, we present a family of tautologies on which it is exponentially faster.
Automatic generation of synthesis units for trainable text-to-speech systems

The Whistler text-to-speech engine was designed so that we can automatically construct the model parameters from training data. This paper describes in detail the design issues of constructing the synthesis unit inventory automatically from speech databases. The automatic process includes (1) determining the scaleable synthesis unit which can reflect spectral variations of different allophones; (2) segmenting the recording sentences into phonetic segments; (3) select good instances for each synthesis unit to generate best synthesis sentence during the run time. These processes are all derived through the use of probabilistic learning methods which are aimed at the same optimization criteria. Through this automatic unit generation, Whistler can automatically produce synthetic speech that sounds very natural and resembles the acoustic characteristics of the original speaker.
Whole Genome Sequencing of a Methicillin-Resistant Staphylococcus aureus Pseudo-Outbreak in a Professional Football Team

Two American football players on the same team were diagnosed with methicillin-resistant Staphylococcus aureus (MRSA) skin and soft tissue infections on the same day. Our investigation, including whole genome sequencing, confirmed that players did not transmit MRSA to one another nor did they acquire the MRSA from a single source within the training facility.
Biochemical and immunologic analysis of hereditary myeloperoxidase deficiency.

Myeloperoxidase (MPO), a heme enzyme present in the azurophilic granules of human polymorphonuclear neutrophils (PMN), is important in the oxygen-dependent microbicidal activity of PMN. MPO deficiency, defined as the lack of PMN peroxidative activity, is a common genetic defect of human PMN. The purpose of our study was to characterize the structural basis for this loss of enzymatic activity, using protein biochemical and immunochemical techniques to examine PMN from three subjects with partial MPO deficiency and from five subjects with complete MPO deficiency.We purified MPO from normal PMN and defined its electrophoretic mobility after two-dimensional electrophoretic separation, using nondenaturing acidic polyacrylamide gel electrophoresis (PAGE) followed by sodium dodecyl sulfate (SDS) denaturation and SDS-PAGE separation of MPO subunit peptides. In agreement with previous studies, we found that normal MPO had subunits of 59,000 and 13,500 mol wt when subjected to SDS-PAGE under reducing conditions. Granule protein extracts of normal PMN, partially MPO-deficient PMN, and completely MPO-deficient PMN were analyzed with two-dimensional PAGE. Partially MPO-deficient PMN granules contained electrophoretically normal MPO in less than normal amounts, whereas completely MPO-deficient PMN granules contain no protein with the electrophoretic mobility of normal MPO. Using rabbit antiserum against purified MPO, we used immunoautoradiographic analysis to examine whole PMN for peptides immunochemically related to MPO. PMN from normal, partially MPO-deficient, and completely MPO-deficient subjects were solubilized in SDS and component peptides separated by SDS-PAGE. The peptides were electroblotted onto nitrocellulose paper that was exposed sequentially to rabbit anti-MPO and (125)I-protein A before autoradiography. Radiolabeled bands were identical when partially purified MPO or normal PMN were compared except that whole PMN contained a small amount of an immunologically cross-reactive membrane associated material of 75,000-90,000 mol wt. Using a modification of this immunoautoradiographic analysis, we quantitated the relative amounts of MPO peptides in PMN. PMN from MPO-deficient subjects contain 41.0-52.3% the amount of MPO peptides present in normal PMN. Similar analysis showed that completely MPO-deficient PMN lacked any peptides corresponding to MPO peptides.We conclude that partial MPO deficiency is characterized by the presence of electrophoretically and immunologically normal MPO in amounts approximately one-half that seen in PMN from normal subjects. Completely MPO-deficient PMN lack any normal MPO peptides. No MPO-deficient subject studied had an immunologically cross-reacting variant of MPO. Since this deficiency is associated with the absence of more than one peptide, it is possible that the underlying genetic defect may involve: (a) failure to synthesize a single precursor peptide; (b) abnormal regulation of the synthesis of two separate peptides; or (c) an aberration in postsynthetic processing or packaging into azurophilic granules.
The transcription factor mohawk homeobox regulates homeostasis of the periodontal ligament

ABSTRACT The periodontal ligament (PDL), which connects the teeth to the alveolar bone, is essential for periodontal tissue homeostasis. Although the significance of the PDL is recognized, molecular mechanisms underlying PDL function are not well known. We report that mohawk homeobox (Mkx), a tendon-specific transcription factor, regulates PDL homeostasis by preventing its degeneration. Mkx is expressed in the mouse PDL at the age of 10 weeks and expression remained at similar levels at 12 months. In Mkx−/− mice, age-dependent expansion of the PDL at the maxillary first molar (M1) furcation area was observed. Transmission electron microscopy (TEM) revealed that Mkx−/− mice presented collagen fibril degeneration in PDL with age, while the collagen fibril diameter gradually increased in Mkx+/+ mice. PDL cells lost their shape in Mkx−/− mice, suggesting changes in PDL properties. Microarray and quantitative polymerase chain reaction (qPCR) analyses of Mkx−/− PDL revealed an increase in osteogenic gene expression and no change in PDL- and inflammatory-related gene expression. Additionally, COL1A1 and COL1A2 were upregulated in Mkx-overexpressing human PDL fibroblasts, whereas osteogenic genes were downregulated. Our results indicate that Mkx prevents PDL degeneration by regulating osteogenesis. Summary: Analyses of knockout mice indicate that the transcription factor mohawk regulates osteogenic changes associated with age and is essential for homeostasis of the periodontal ligament.
lp-norm support vector machine with CCCP

This paper proposed an efficient model lp-support vector classification(lp-SVC) which combines C-SVC and feature selection strategy by introducing the lp-norm (0 < p < 1). Following a lower bound for the absolute value of nonzero entries in every local optimal solution of the model, we investigated the relationship between sparsity of the solution and the choice of the regularization parameter and p-norm. In order to solve the nonconvex problem in lp-SVC, we investigate an iteratively reweighted lq(q ≥ 1) convex relaxation scheme, in which the weighted problem solved by CCCP, and preliminary numerical experiments show the superior effectiveness of our model for identifying nonzero entries in numerical solutions and feature selection than standard l1 convex relatxation. We also apply it to a real-life credit dataset to prove its efficiency.
Electron Spin Resonance Analysis of Superoxide Anion Radical Scavenging Activity with Spin Trapping Agent, Diphenyl-PMPO

Recently, a novel electron spin resonance (ESR) spin-trapping agent, 2-(diphenylphosphinoyl)-2-methyl-3,4-dihydro-2 H -pyrrole N -oxide (Diphenyl-PMPO), was synthesized. Because it had some advantages in stability and reactivity over conventional spin-trapping agents, we applied it to the ESR analyses of superoxide anion radical scavenging activity (SOSA) of superoxide dismutase (SOD) and of well-known natural antioxidants (green tea, oolong tea, and red wine). At the same time, the results with Diphenyl-PMPO were compared with 5,5-dimethyl-1-pyrroline N -oxide (DMPO). Our results revealed that Diphenyl-PMPO showed higher detectability than DMPO in the SOSA assays of SOD and natural antioxidants, so it could be available for the ESR analyses as an alternative to conventional spin-trapping agents.
Influence of Disbond Defects on the Dispersion Properties of Adhesive Bonding Structures

With increasing application of adhesive bonding structures, the quality assessment of adhesive bonding became critical. Ultrasonic approach was an acknowledged promising method in many Nondestructive testing (NDT) techniques. The research object was to use analytical models to develop a quantitative understanding of the affections in different situations on the dispersion properties. An improved global matrix method was introduced to compute the dispersive curves, which can effectively eliminate the instability for thicker layers and higher frequencies. In order to evaluate the disbond defect, the cohesive strength degradation mode and the spring mode were then adopted to describe the cohesive failure and the interface failure, respectively. In the paper, cohesive failure, interface failure and mixed failure were analyzed for the steel/adhesive layer/insulation layered structure. Interface failure induced the modes of multilayer structure to regress to the modes of single layers, while the cohesive failure made the dispersive curves move to the lower frequency direction, and changing the relative position of spring layer led the dispersive curves shift to the higher frequency direction. Among all the factors, the interface failure was dominant. Finally, the variety of the dispersive modes in a special frequency band (1~1.5MHz) was found that can be regarded as parameters of the adhesive bonding quality.
14—THE EFFECT OF THE STRENGTH PROPERTIES OF WOOL STAPLES ON WORSTED PROCESSING PART I: THE LEVEL OF STAPLE STRENGTH

An account is given of an experimental study conducted specifically to examine the effects of large variations in the staple strength of greasy wool on subsequent performance in combing and spinning by means of pilot-scale processing techniques. Batches were processed for two levels of mean fibre diameter (20 and 22 μm), each at four levels of staple strength (nominally 20, 30, 45, and 60 N/ktex), and there was close control over other raw-wool properties. Three comb settings were used for each batch. Yarns were spun to five counts selected to include the normal commercial range and the limiting situation. The SAWTRI mean-spindle-speed test was employed to assess spinning performance. The resultant fibre length and its distribution for tops were found to be closely dependent on the staple strength and the comb setting. Differences in Hauteur of 11–14 mm were observed between the batches from the low- and high-staple-strength categories within each comb setting and fibre-diameter grouping. Differences in s.
Expressing Xylanases in Escherichia Coli by Cell Surface Display

In this research, xylan was utilized by a recombinant whole cell biocatalyst, which was developed by expressing three xylanases — β-xylosidase, endoxylanase, and α-arabinofuranosidase — on the surface of the E. coli BL21 (DE3). The xylanases were displayed on the surface of the cells by fusing with anchor proteins, Blc. The assimilation of xylan by cell surface display was the first step in the consolidated bioprocessing (CBP). This result shows that the engineering strains could be endowed with the ability to assimilate xylan. The co-display engineering strains utilized xylan and expressed less metabolic burden than the engineering strains secreting extracellular xylanases.
Attention Trade-off between Two Types of User Contributions: Effects of Pinterest-Style Infinite Scroll Layouts on Creating Original Sharing and Appreciating Others' Sharing

User contributions are critical to social commerce sites. Prior studies mainly examined motivational factors influencing user contributions. In the current study, we examine effects of interface layouts on user contributions, from the perspective of attention allocation. We also distinguish between the two types of user contributions: creating original sharing and appreciating others’ sharing. Since attention is a limited resource, we argue that interface layouts may lead to attention trade-off between the two types of user contributions. Leveraging an opportunity of a popular social commerce site’s transformation to Pinterest-style infinite scrolling layouts, we collected panel data. Empirical findings show that the new layouts design has opposite effects on the two types of user contribution: a positive effect on users’ appreciation of others’ sharing, but a negative effect on users’ original sharing. Some user characteristics moderate the effects. The findings yield important implications for research and websites design practice.
Performance Analysis of Group Paging for Machine-Type Communications in LTE Networks

Machine-type communication (MTC) is a crucial service for next-generation cellular networks. Mass access to the network by MTC devices may result in the overload of radio access networks (RANs) and degrade the service quality of human-to-human communication. Group paging is one of the mechanisms proposed to alleviate the RAN-overload problem. This paper presents an analytical model based on a recursive contending-users estimation (RCE) method proposed in the literature to derive the performance metrics of collision probability, access success probability, average access delay, statistics of preamble transmissions, statistics of access delay, and utilization of random-access opportunities (RAOs) for group paging with various combinations of group sizes and reserved radio resources in a paging access interval. The optimal group size and required RAOs are subsequently derived based on the given target access success probability. Numerical results demonstrate that the proposed model can accurately estimate the performance of group paging.
Neuropeptide Y regulates the hematopoietic stem cell microenvironment and prevents nerve injury in the bone marrow

Many reports have revealed the importance of the sympathetic nervous system (SNS) in the control of the bone marrow environment. However, the specific role of neuropeptide Y (NPY) in this process has not been systematically studied. Here we show that NPY‐deficient mice have significantly reduced hematopoietic stem cell (HSC) numbers and impaired regeneration in bone marrow due to apoptotic destruction of SNS fibers and/or endothelial cells. Furthermore, pharmacological elevation of NPY prevented bone marrow impairments in a mouse model of chemotherapy‐induced SNS injury, while NPY injection into conditional knockout mice lacking the Y1 receptor in macrophages did not relieve bone marrow dysfunction. These results indicate that NPY promotes neuroprotection and restores bone marrow dysfunction from chemotherapy‐induced SNS injury through the Y1 receptor in macrophages. They also reveal a new role of NPY as a regulator of the bone marrow microenvironment and highlight the potential therapeutic value of this neuropeptide.
Joint Transmitter–Receiver Optimization in Multitarget MIMO Radar

Although a significant attention has been drawn to the concept of multiple-input multiple-output (MIMO) radar and in particular on the transmit beamforming design and multitarget localization, the cooperation between the transmitter (Tx) and the receiver (Rx) has been rarely investigated. In this paper, a novel joint Tx and Rx optimization approach for localization is proposed for MIMO radar, where the transmit beamforming design and the estimation of the target's complex path gain are jointly derived by solving an optimization problem that takes account various target parameters. Moreover, the proposed transmit beamforming design controls the power distribution per individual target. The performance of the proposed method is evaluated using computer simulation studies and compared with techniques which simply combine Tx beamforming design with multitarget localization methods.