Miracle-dz/UniFAR-FTUs huggingface dataset:
Constrained cyclic coordinate descent for cryo-EM images at medium resolutions: beyond the protein loop closure problem

SUMMARY The cyclic coordinate descent (CCD) method is a popular loop closure method in protein structure modeling. It is a robotics algorithm originally developed for inverse kinematic applications. We demonstrate an effective method of building the backbone of protein structure models using the principle of CCD and a guiding trace. For medium-resolution 3-dimensional (3D) images derived using cryo-electron microscopy (cryo-EM), it is possible to obtain guiding traces of secondary structures and their skeleton connections. Our new method, constrained cyclic coordinate descent (CCCD), builds α-helices, β-strands, and loops quickly and fairly accurately along predefined traces. We show that it is possible to build the entire backbone of a protein fairly accurately when the guiding traces are accurate. In a test of 10 proteins, the models constructed using CCCD show an average of 3.91 Å of backbone root mean square deviation (RMSD). When the CCCD method is incorporated in a simulated annealing framework to sample possible shift, translation, and rotation freedom, the models built with the true topology were ranked high on the list, with an average backbone RMSD100 of 3.76 Å. CCCD is an effective method for modeling atomic structures after secondary structure traces and skeletons are extracted from 3D cryo-EM images.
Characterization of Vertex-Centric Breadth First Search for Lattice Graphs

Google's Pregel vertex-centric programming model has led to a class of component-centric abstractions that are widely used for designing and executing distributed graph algorithms in a Bulk Synchronous Parallel (BSP) manner on commodity clusters. There has, however, been little effort to formally understand the behavior of such programming models to allow analytical comparison of graph algorithms with narrow bounds. Graphs and graph algorithms have asymmetry that make them challenging to model effectively. Lattice (or grid) graphs, commonly used in scientific computing, offer a simpler structure to tackle this novel problem. Here, we propose analytical models with tight bounds on the coordination, computation and communication costs for performing a vertex-centric Breadth First Search (BFS) on uniform lattice graphs. We validate these further with empirical results. Our results hold for lattice graphs of arbitrary dimension and uniform odd-valued length, but can be extended to non-uniform lengths as well. These results offer a formal understanding of the behavior of vertex-centric BFS for a lattice structure, and lays the foundation for further analysis and exploration of component-centric algorithms.
Extraction of genomic DNA from Pseudomonas aeruginosa: a comparison of three methods

17 Diggle MA, Edwards GFS, Clarke SC. Developments in the diagnosis of meningococcal disease and the characterisation of Neisseria meningitidis. Rev Med Microbiol 2001; 12: 211-7 18 Dingle KE, Colles FM, Ure R et al. Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation. Emerg Infect Dis 2002; 8: 949-55. 19 Maggi Solca N, Bernasconi MV, Valsangiacomo C, Van Doorn LJ, Piffaretti JC. Population genetics of Helicobacter pylori in the southern part of Switzerland analysed by sequencing of four housekeeping genes (atpD, glnA, scoB and recA), and by vacA, cagA, iceA and IS605 genotyping. Microbiology 2001; 147: 1693-707.
Thresholding based on sequential Monte-Carlo for DCT speech enhancement

This paper deals with speech enhancement achieved by thresholding the Discrete Cosine Transform coefficients of noisy speech. The sequential Monte-Carlo algorithm is used to approximate the a posteriori threshold distribution, thus the minimum mean square error estimate of the thresholded speech samples over each frequency bin are deduced. The a priori distribution of the time-frequency varying threshold is adopted as the importance density and the Gaussian random walk is used to model the threshold particle mutation. Experiences with additive white Gaussian and car noises shown the improved performance of the proposed method, compared to current speech enhancement algorithms.
Accurate identification of layer number for few-layer WS2 and WSe2 via spectroscopic study

Transition metal dichalcogenides (TMDs) with a typical layered structure are highly sensitive to their layer number in optical and electronic properties. Seeking a simple and effective method for layer number identification is very important to low-dimensional TMD samples. Herein, a rapid and accurate layer number identification of few-layer WS2 and WSe2 is proposed via locking their photoluminescence (PL) peak-positions. As the layer number of WS2/WSe2 increases, it is found that indirect transition emission is more thickness-sensitive than direct transition emission, and the PL peak-position differences between the indirect and direct transitions can be regarded as fingerprints to identify their layer number. Theoretical calculation confirms that the notable thickness-sensitivity of indirect transition derives from the variations of electron density of states of W atom d-orbitals and chalcogen atom p-orbitals. Besides, the PL peak-position differences between the indirect and direct transitions are almost independent of different insulating substrates. This work not only proposes a new method for layer number identification via PL studies, but also provides a valuable insight into the thickness-dependent optical and electronic properties of W-based TMDs.
Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea

The deep‐sea brines of the Red Sea are remote and unexplored environments characterized by high temperatures, anoxic water, and elevated concentrations of salt and heavy metals. This environment provides a rare system to study the interplay between halophilic and thermophilic adaptation in biologic macromolecules. The present article reports the first DNA polymerase with halophilic and thermophilic features. Biochemical and structural analysis by Raman and circular dichroism spectroscopy showed that the charge distribution on the protein's surface mediates the structural balance between stability for thermal adaptation and flexibility for counteracting the salt‐induced rigid and nonfunctional hydrophobic packing. Salt bridge interactions via increased negative and positive charges contribute to structural stability. Salt tolerance, conversely, is mediated by a dynamic structure that becomes more fixed and functional with increasing salt concentration. We propose that repulsive forces among excess negative charges, in addition to a high percentage of negatively charged random coils, mediate this structural dynamism. This knowledge enabled us to engineer a halophilic version of Thermococcus kodakarensis DNA polymerase. —Takahashi M. , Takahashi, E. , Joudeh, L. I. , Marini, M. , Das, G. , Elshenawy, M. M. , Akal, A. , Sakashita, K. , Alam, I. , Tehseen, M. , Sobhy, M. A. , Stingl, U. , Merzaban, J. S. , Di Fabrizio E. , Hamdan S. M. , Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep‐sea brines of the Red Sea. FASEB J. 32, 3346–3360 (2018). www.fasebj. org
Protecting Privacy in Shared Photos via Adversarial Examples Based Stealth

Online image sharing in social platforms can lead to undesired privacy disclosure. For example, some enterprises may detect these large volumes of uploaded images to do users’ in-depth preference analysis for commercial purposes. And their technology might be today’s most powerful learning model, deep neural network (DNN). To just elude these automatic DNN detectors without affecting visual quality of human eyes, we design and implement a novel Stealth algorithm, which makes the automatic detector blind to the existence of objects in an image, by crafting a kind of adversarial examples. It is just like all objects disappear after wearing an “invisible cloak” from the view of the detector. Then we evaluate the effectiveness of Stealth algorithm through our newly defined measurement, named privacy insurance. The results indicate that our scheme has considerable success rate to guarantee privacy compared with other methods, such as mosaic, blur, and noise. Better still, Stealth algorithm has the smallest impact on image visual quality. Meanwhile, we set a user adjustable parameter called cloak thickness for regulating the perturbation intensity. Furthermore, we find that the processed images have transferability property; that is, the adversarial images generated for one particular DNN will influence the others as well.
Inhibition of the proteasome activity by graphene oxide contributes to its cytotoxicity

Abstract Due to its hydrophobicity and other unique physicochemical properties, graphene oxide (GO) has been extensively utilized in various biological applications. However, introducing nanomaterials into the biological environment may raise serious risk in terms of nanotoxicity, leading to some unintended changes to the structure and the function of other biomolecules. This study investigates the interaction of GO with the ubiquitin–proteasome system, one of the essential machineries in the cellular metabolism, using a combination of experimental and computational approaches. The experimental results show that GO could adsorb the 20S proteasome, causing a dose-dependent suppression of the proteolytic activity of proteasome. This adverse effect eventually disturbed other important cellular activities relevant to cell cycle and survival. Meanwhile, the molecular dynamics simulations revealed that when 20S proteasome was adsorbed onto the graphene surface, the central gate in the outer ring (α-subunit) for the entry and the exit of the peptide ligand to the protease active site was effectively blocked. These findings of GO induced functional disturbance of 20S proteasome provides a novel perspective to understand the molecular mechanism of GO’s cytotoxicity, which might further promote applications of GO in potential therapies for various cancers due to the abnormal elevation of the relevant proteasome activities.
A bioreactor with an electro-responsive elastomeric membrane for mimicking intestinal peristalsis

This study describes an actuated bioreactor which mimics the pulsatile contractile motion of the intestinal barrier using electro-responsive elastomers as smart materials that undergo deformation upon electrical stimulation. The device consists of an annular dielectric elastomer actuator working as a radial artificial muscle able to rhythmically contract and relax a central cell culture well. The bioreactor maintained up to 4 h of actuation at a frequency of 0.15 Hz and a strain of 8%–10%, to those of the cyclic contraction and relaxation of the small intestine. In vitro tests demonstrated that the device was biocompatible and cell-adhesive for Caco-2 cells, which formed a confluent monolayer following 21 days of culture in the central well. In addition, cellular adhesion and cohesion were maintained after 4 h of continuous cyclic strain. These preliminary results encourage further investigations on the use of dielectric elastomer actuation as a versatile technology that might overcome the limitations of commercially available pneumatic driving systems to obtain bioreactors that can cyclically deform cell cultures in a biomimetic fashion.
Morphology, Mechanical and Thermal Properties of Thermoplastic Polyurethane Containing Reduced Graphene Oxide and Graphene Nanoplatelets

Polyurethane/graphene nanocomposites were synthesized using commercial thermoplastic polyurethane (TPU, Apilon 52DE55), and two types of graphene derivatives: graphene nanoplatelets (GNP) and reduced graphene oxide (RGO). Fourier Transformation Infrared Spectroscopy Fourier Transformation Infrared Spectroscopy (FTIR) spectroscopy, TEM, and SEM microscopy and XRD techniques were used to chemically and structurally characterize GNP and RGO nanofillers. The properties of the new TPU nanocomposite materials were studied using thermal analysis techniques (Dynamical Mechanical Analysis (DMA), Differential Scanning Calorimetry (DSC), Thermogravimetric Analysis (TG)) to describe the influence of graphene nanofillers on polyurethane matrix. Our investigation describes the comparison of two types of graphene derivatives, commercial one (GNP) and synthesized (RGO) on thermoplastic polyurethanes. These nanofillers provides opportunities to achieve compatibility with the TPU matrix. The property enhancements are attributed commonly to high aspect ratio of graphene nanoplatelets and filler–polymer interactions at the interface. The obtained nanocomposites exhibit higher thermal and mechanical properties due to the good dispersion of both nanofillers into TPU matrix. It was found that the addition of 2 wt % of the nanofiller could lead to a significant reinforcement effect on the TPU matrix. Also, with high content of nanofiller (GNP and RGO), the Payne effect was observed.
Safety assessment of 16 sweeteners for the Korean population using dietary intake monitoring and poundage method

ABSTRACT A sweetener is a food additive that imparts a sweet taste to food products. Sweeteners have been increasingly used in Korea since the approval of sodium saccharin and d-sorbitol in 1962. Unlike food contaminants, humans are exposed to food additives only through the consumption of processed food products. For exposure assessments of sweeteners, the dietary intakes of food products containing acesulfame-K, aspartame, saccharin-Na, and sucralose were determined, and the resulting calculated estimated daily intake (EDI) values were compared directly with each additive’s ADI. The poundage method was used to calculate the daily intake per capita for 12 additional sweeteners, such as lactitol, for which appropriate analytical methods for food products do not exist. The risk, as evaluated by comparing the EDI with the ADI, was determined to be 2.9% for acesulfame-K, 0.8% for aspartame, 3.6% for saccharin-Na, 4.3% for steviol glycosides, and 2.1% for sucralose. No hazardous effect was predicted for the other 11 sweeteners, including lactitol.
Research on Clustream Algorithm Based on Spark

In recent years, with the development of information society, producing a steady stream of data in daily life. These large amounts of data need to be analyzed in real time in order to obtain the value. Based on the original Clustream algorithm, this paper proposes a CClustream clustering algorithm based on Spark Streaming, which is based on the parallel implementation, and its offline part has been improved. Experiments show that the algorithm has better efficiency and accuracy than the original algorithm.
Neural Substrate for Motor Control of Feeding in Amphibians

Descending pathways to premotor/motor centers and their cell groups of origin were studied by means of retrograde biocytin tracing experiments in the frog Discoglossus pictus and the plethodontid salamander Plethodon jordani, which differ remarkably in the structure and function of their feeding apparatus and their feeding strategy. Labeled neurons were found in 30 major cell groups located in the telencephalon, diencephalon, synencephalon, mesencephalon and rhombencephalon. The number and distribution of nuclei are very similar in both species. Furthermore, the descending pathways of these groups of neurons take the same courses inside the medulla oblongata. Axons of most nuclei descend either in the ventromedial or ventrolateral medulla oblongata, and it is concluded that the spatial arrangement of pathways is identical in the species studied. Bilateral electrical stimulation of the optic tectum of the plethodontid salamander Hydromantes italicus elicited strong discharges of short latencies in the hypoglossal nerve. In most hypoglossal motor neurons, excitatory postsynaptic potentials (EPSPs) of short latencies followed paired shocks applied at intervals as short as 3 ms, but showed temporal and spatial facilitation, suggesting that the EPSPs include mono- as well as polysynaptic components. In the ventral white matter, orthodromic single units were found that are candidates for excitatory reticular interneurons. These properties of tectal descending pathways in salamanders strongly differ from those found in toads. Differences in feeding behavior and its control by the premotor/motor networks between the species investigated do not appear to result from anatomically altered input or from a different organization of descending pathways to these premotor/motor centers, but rather from differences in local properties of reticular premotor networks as well as from different effects of neuromodulatory systems.
Network organization of coopetitive genetic influences on cortical morphologies

Brain can be represented as a network, where regions are the nodes and relations between the regions are edges. Within a network, co-existence of cooperative and competitive relationships between different nodes is called coopetition. Inter-regional genetic influences on morphological phenotypes (cortical thickness, surface area) of cortex display such coopetitive relationships. Here, we have represented these genetic influences as a network and shown that cooperative and competitive genetic influences on cortical morphological phenotypes follow distinct organization principles. Utilizing the theory of structural balance, we have shown that the pattern of collective regulation of cortical morphological phenotypes by cooperative and competitive genetic influences are overall bilaterally symmetric and such patterns of collective genetic regulation are similar to the principal modes of population variation of cortical morphological phenotypes. Finally, we have observed that the maximally and minimally imbalanced regions corresponding to the collective genetic regulation partially overlap with the cortical structural network hubs.
Interferon‐induced protein 35 inhibits endothelial cell proliferation, migration and re‐endothelialization of injured arteries by inhibiting the nuclear factor‐kappa B pathway

Endothelial recovery, or re‐endothelialization, plays an important role in intimal hyperplasia and atherosclerosis after endothelial injury. Studying the mechanisms of re‐endothelialization and strategies to promote efficient endothelial recovery are still needed. Interferon‐induced protein 35 (IFI35) is an IFN‐γ‐induced protein that plays important roles in the antivirus‐related immune‐inflammatory response. In this study, we tested whether overexpression IFI35 affects the proliferation and migration of endothelial cells (ECs) and re‐endothelialization.
Fowl Typhoid (Salmonella Gallinarum) Outbreak in Japanese Quail (Coturnix coturnix japonica)

SUMMARY A fowl typhoid (FT) outbreak is reported in a flock of 400 Japanese quail (Coturnix coturnix japonica) at 91 days of age. Of these, 222 died suddenly, and necropsy revealed swollen liver and spleen with off-white to yellowish granules and reddish small intestine mucosa. Histopathology showed severe multifocal necrosis of liver and spleen (5/5), pulmonary congestion with macrophage infiltration in air capillaries (5/5), discrete interstitial nephritis (2/2), superficial necrosis of the intestinal mucosa with large numbers of coccobacilli (2/2), moderate peritonitis (2/2), and discrete airsacculitis (1/1). Anti-Salmonella immunohistochemistry (IHC) stained the cytoplasm of macrophages or free in the liver (5/5), spleen (5/5), lungs (4/5), kidneys (2/2) small intestine mucosa (2/2), cecum (1/1), bone marrow (1/1), air sacs (1/1), and ovary (1/1). In the heart (5/5), brain (2/2), esophagus (2/2), pancreas (2/2), proventriculus (2/2), gizzard (1/1), bursa of Fabricius (1/1), oviduct (1/1), and skeletal muscle (1/1) staining was observed only in the lumen of blood vessels. Salmonella Gallinarum was isolated in pure cultures of liver, spleen, lung, intestine, and blood samples of two birds. RESUMEN Reporte de Caso—Brote de tifoidea aviar (Salmonella Gallinarum) en codornices japonesas (Coturnix coturnix japonica). Se describe un brote de tifoidea aviar en un lote de 400 codornices japonesas (Coturnix coturnix japonica) de 91 días de edad, de las cuales 222 murieron súbitamente. Se practicó la necropsia de cinco animales y se observó hígado aumentado de tamaño con puntos blanco amarillentos, bazo difusamente pálido de color blanco amarillento y la mucosa del intestino delgado se observó de un color rojizo. A la histopatología, se observó en el hígado y en el bazo marcada necrosis multifocal (5/5), congestión del pulmón asociada con infiltración de macrófagos en los capilares aéreos (5 /5), nefritis intersticial leve (2/2), necrosis superficial de la mucosa intestinal con gran cantidad de bacterias cocobacilares (2/2), peritonitis moderada (2/2) y aerosaculitis leve (1/1). El examen inmunohistoquímico para Salmonella demostró una fuerte tinción en el citoplasma de los macrófagos o de manera difusa en el hígado (5/5), bazo (5/5), pulmón (4/5), riñón (2/2) mucosa del intestino delgado (2/2) y el ciego (1/1), médula ósea (1/1), sacos aéreos (1/1) y ovario (1/1). Por otra parte, en el corazón (5/5), cerebro (2/2), esófago (2/2), páncreas (2/2), proventrículo (2/2), molleja (1/1), bolsa de Fabricio (1/1), oviducto (1/1) y músculo esquelético (1/1) se observó tinción positiva sólo en el lumen de los vasos sanguíneos. Se aisló Salmonella Gallinarum en cultivo puro de muestras de hígado, bazo, pulmón, intestino y de la sangre de dos aves.
Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data

Upstream open reading frames (uORFs), located in transcript leaders (5′ UTRs), are potent cis-acting regulators of translation and mRNA turnover. Recent genome-wide ribosome profiling studies suggest that thousands of uORFs initiate with non-AUG start codons. Although intriguing, these non-AUG uORF predictions have been made without statistical control or validation; thus, the importance of these elements remains to be demonstrated. To address this, we took a comparative genomics approach to study AUG and non-AUG uORFs. We mapped transcription leaders in multiple Saccharomyces yeast species and applied a novel machine learning algorithm (uORF-seqr) to ribosome profiling data to identify statistically significant uORFs. We found that AUG and non-AUG uORFs are both frequently found in Saccharomyces yeasts. Although most non-AUG uORFs are found in only one species, hundreds have either conserved sequence or position within Saccharomyces. uORFs initiating with UUG are particularly common and are shared between species at rates similar to that of AUG uORFs. However, non-AUG uORFs are translated less efficiently than AUG-uORFs and are less subject to removal via alternative transcription initiation under normal growth conditions. These results suggest that a subset of non-AUG uORFs may play important roles in regulating gene expression.