Miracle-dz/UniFAR-FTUs huggingface dataset:
Fungi and the Rise of Mammals

Here are two indisputable facts: we are living in the age of mammals [1], and immunologically intact mammals are highly resistant to fungal diseases, such that most human systemic fungal are considered ‘‘opportunistic’’ [2]. Could these two facts be connected? The mammalian lifestyle is characterized by endothermy, homeothermy, and care for the young, including nourishment via lactation, all of which are energetically costly activities. In contrast, reptiles, which are ectotherms, require about one-tenth of the daily mammalian energy needs [3], and reptilian development is faster and requires less parental involvement. Given this energy handicap, how did mammals replace reptiles as the dominant land animals? This essay further develops the hypothesis originally proposed seven years ago that fungi contributed to the emergence of mammals by creating a fungal filter at the end of the Cretaceous that selected for the mammalian lifestyle and against reptiles [4].
Transaction time indexing with version compression

Immortal DB is a transaction time database system designed to enable high performance for temporal applications. It is built into a commercial database engine, Microsoft SQL Server. This paper describes how we integrated a temporal indexing technique, the TSB-tree, into Immortal DB to serve as the core access method. The TSB-tree provides high performance access and update for both current and historical data. A main challenge was integrating TSB-tree functionality while preserving original B+tree functionality, including concurrency control and recovery. We discuss the overall architecture, including our unique treatment of index terms, and practical issues such as uncommitted data and log management. Performance is a primary concern. To increase performance, versions are locally delta compressed, exploiting the commonality between adjacent versions of the same record. This technique is also applied to index terms in index pages. There is a tradeoff between query performance and storage space. We discuss optimizing performance regarding this tradeoff throughout the paper. The result of our efforts is a high-performance transaction time database system built into an RDBMS engine, which has not been achieved before. We include a thorough experimental study and analysis that confirms the very good performance that it achieves.
High temperature solid lubricants - When and where to use them.

The state of the art of solid lubrication for moderate to extremely high temperature lubrication (to 1600 F) is reviewed. Lubricating characteristics, stability in various environments, and relevant machine design considerations are discussed. Lubricating materials discussed include the layer lattice compounds: MoS2, WS2, graphite and graphite fluoride, the high temperature polyimide polymer, and calcium fluoride based coating and composites. The scope of the information includes results from wear testers, ball bearing, and journal bearings.
Modeling and Computer simulation of 3D object Grasping and Manipulation by dual fingers under nonholonomic constraints

Construction of a numerical simulator for 3-D object pinching and manipulation by a pair of robot fingers is described on the basis of mathematical modeling of physical interactions between the object and fingers under rolling constraints. The simulator consists of a set of Lagrange's equations of motion of the fingers and object under holonomic constrains and differential equations of nonholonomic constraints expressing rotational motion of the rigid object. By using this simulator, numerical simulation results of 3-D object pinching and manipulation under the gravity effect based on the control law rendering "blind grasping" without use of any object kinematics or any external sensing is carried out in a case that the fingers have excess joints. Numerical results show the validity of mathematical modeling and the control method
Learning Sparse Metrics, One Feature at a Time

Learning distance metrics from data is a fundamental problem in machine learning and useful way to extract data-driven features by using the matrix root of a distance matrix. Finding a proper metric amounts to optimization over the cone of positive definite (PD) matrices. This optimization is difficult since restricting optimization to remain within the PD cone or repeatedly projecting to the cone is prohibitively costly. Here we describe COMET, a block-coordinate descent procedure, which efficiently keeps the search within the PD cone, avoiding both costly projections and unnecessary computation of full gradients. COMET also continuously maintains the Cholesky root of the matrix, providing feature extraction and embedding of samples in a metric space. We further develop a structurally sparse variant of COMET, where only a small number of features interacts with other features. SparseCOMET significantly accelerates both training and inference while improving interpretability. As a block-coordinate descent procedure, COMET has fast convergence bounds showing linear convergence with high probability. When tested on benchmark datasets in a task of retrieving similar images and similar text documents, COMET has significantly better precision than competing projection-free methods. Furthermore, sparse-COMET achieves almost identical precision as dense-COMET in document classification, while running◊4.5 faster, maintaining a 0.5% sparsity level, and outperforming competing methods both in precision and in run time.
Managing the Internet of Things

The Internet of Things (IoT) offers many interesting solutions to problems encountered in a range of application areas. The potentially huge number and the diversity of things that may be part of such an infrastructure can pose prominent issues for their systemic management. This paper explores such issues and proposes a management platform that partially addresses them. More specifically, our proposed IoT Management Platform (IoT-MP) takes into account the fact that things, in general, have limited power, computation, and communication resources available to them. The proposed platform supports fundamental management functions, including those needed for proper operation, monitoring and communications. After introducing the architecture and the major components of the platform, we show the advantages of our proposed approach through some simulation studies.
Molecular Characterization, Tissue Distribution, Subcellular Localization and Actin-Sequestering Function of a Thymosin Protein from Silkworm

We identified a novel gene encoding a Bombyx mori thymosin (BmTHY) protein from a cDNA library of silkworm pupae, which has an open reading frame (ORF) of 399 bp encoding 132 amino acids. It was found by bioinformatics that BmTHY gene consisted of three exons and two introns and BmTHY was highly homologous to thymosin betas (Tβ). BmTHY has a conserved motif LKHTET with only one amino acid difference from LKKTET, which is involved in Tβ binding to actin. A His-tagged BmTHY fusion protein (rBmTHY) with a molecular weight of approximately 18.4 kDa was expressed and purified to homogeneity. The purified fusion protein was used to produce anti-rBmTHY polyclonal antibodies in a New Zealand rabbit. Subcellular localization revealed that BmTHY can be found in both Bm5 cell (a silkworm ovary cell line) nucleus and cytoplasm but is primarily located in the nucleus. Western blotting and real-time RT-PCR showed that during silkworm developmental stages, BmTHY expression levels are highest in moth, followed by instar larvae, and are lowest in pupa and egg. BmTHY mRNA was universally distributed in most of fifth-instar larvae tissues (except testis). However, BmTHY was expressed in the head, ovary and epidermis during the larvae stage. BmTHY formed complexes with actin monomer, inhibited actin polymerization and cross-linked to actin. All the results indicated BmTHY might be an actin-sequestering protein and participate in silkworm development.
The dextranase along sugar-making industry

In sugar production, dextrans are undesirable compounds synthesized by contaminant microorganisms from sucrose, increasing the viscosity of the flow and reducing industrial recovery, bringing about significant losses. The use of the dextranase enzyme is the most efficient method for hydrolyzing the dextrans at sugar mills. Some bacterial strains, filamentous fungi and a small number of yeasts have been shown to produce dextranase. The fungal dextranases showed the highest reaction rate at low Brix, with pH and temperature close to 5.0 and 50 oC, respectively, that is, conditions existing in juice extraction. Some of these dextranases formulated in enzymatic preparations have been efficiently used for hydrolyzing dextrans in sugar mill juices. In more advanced points of the process, where the dextrans have already caused losses, the conditions of temperature and Brix are high. However, although the volumes are smaller, the treatment with these enzymes in syrup showed the need to increase the dose, equaling dextranase consumption. Some thermo tolerant bacterial dextranases identified up to now showed a much reduced specific activity that makes their industrial use unfeasible. The fungal dextranases from Chaetomium sp. have shown the best results on dextrans treatment both in juices and syrups. Any attempt to obtain a new natural or recombinant dextranase enzyme, must be comparable with to the Chaetomium enzyme.
Generic Darwinian selection in catalytic protocell assemblies

To satisfy the minimal requirements for life, an information carrying molecular structure must be able to convert resources into building blocks and also be able to adapt to or modify its environment to enhance its own proliferation. Furthermore, new copies of itself must have variable fitness such that evolution is possible. In practical terms, a minimal protocell should be characterized by a strong coupling between its metabolism and genetic subsystem, which is made possible by the container. There is still no general agreement on how such a complex system might have been naturally selected for in a prebiotic environment. However, the historical details are not important for our investigations as they are related to assembling and evolution of protocells in the laboratory. Here, we study three different minimal protocell models of increasing complexity, all of them incorporating the coupling between a ‘genetic template’, a container and, eventually, a toy metabolism. We show that for any local growth law associated with template self-replication, the overall temporal evolution of all protocell's components follows an exponential growth (efficient or uninhibited autocatalysis). Thus, such a system attains exponential growth through coordinated catalytic growth of its component subsystems, independent of the replication efficiency of the involved subsystems. As exponential growth implies the survival of the fittest in a competitive environment, these results suggest that protocell assemblies could be efficient vehicles in terms of evolving through Darwinian selection.
Nonlocal variational method application for image denoising

Combining of nonlocal means and variational models can extend the ability of image processing such as texture image processing. In this paper, an implementation scheme of nonlocal variational models is proposed, which contains discretization, coordinate transformation, and dimension expansion. Firstly, continuous models are transferred to discrete model. Then we transform absolute coordinate to relative coordinate. Because relative coordinate can limit to patch area instead of whole image area, it enormously reduces the data storage. Finally we expand dimension of some array, so it is easy to calculate directly in MATLAB because arrays become same dimension. In experiment, we add noises such as Possion, Gaussian, Salt&Pepper, and Speckle to original image. The results show the proposed scheme is validated for all kind noises and is quite efficient.
The Significance of Type II and PrxQ Peroxiredoxins for Antioxidative Stress Response in the Purple Bacterium Rhodobacter sphaeroides*

Two peroxiredoxins, classified as Type II and PrxQ, were characterized in the purple non-sulfur photosynthetic bacterium Rhodobacter sphaeroides. Both recombinant proteins showed remarkable thioredoxin-dependent peroxidase activity with broad substrate specificity in vitro. Nevertheless, PrxQ of R. sphaeroides, unlike typical PrxQs studied to date, does not contain one of the two conserved catalytic Cys residues. We found that R. sphaeroides PrxQ and other PrxQ-like proteins from several organisms conserve a different second Cys residue, indicating that these proteins should be categorized into a novel PrxQ subfamily. Disruption of either the Type II or PrxQ gene in R. sphaeroides had a dramatic effect on cell viability when the cells were grown under aerobic light or oxidative stress conditions created by exogenous addition of reactive oxygen species to the medium. Growth rates of the mutants were significantly decreased compared with that of wild type under aerobic but not anaerobic conditions. These results indicate that the peroxiredoxins are crucial for antioxidative stress response in this bacterium. The gene disruptants also demonstrated reduced levels of photopigment synthesis, suggesting that the peroxiredoxins are directly or indirectly involved in regulated synthesis of the photosynthetic apparatus.
Transplantation of Allogeneic Peripheral Blood Stem Cells Mobilized by Recombinant Human Granulocyte Colony Stimulating Factor

Recombinant G‐CSF has been given to over 150 normal donors for the collection of allogeneic or syngeneic peripheral blood stem cells (PBSC). G‐CSF was found to be well‐tolerated with mild‐moderate bone pain, edema and mild thrombocytopenia being the observed side effects. To date, approximately 90 unmodified primary PBSC transplants from HLA‐identical related donors have been performed with engraftment that is, in general, considerably more rapid than marrow. Acute graft‐versus‐host‐disease (GVHD), grades II‐IV occurred in 47% of patients and grades III‐IV in 17%. Despite the infusion of one to two logs more T cells, these results are not remarkably different than would be expected with marrow transplantation. There have also been successful reports of using G‐CSF mobilized allogeneic PBSC following second transplants for graft rejection or relapse. Allogeneic PBSC have been infused without reconditioning for correction of graft failure and unmodified or CD34 selected PBSC have also been given with marrow to augment the dose of hematopoietic cells. Further studies are needed to define the role of allogeneic PBSC for transplantation, refine PBSC mobilization and collection techniques and to evaluate the long‐term effects of cytokines in normal donors.
Rigorous Measurement of IP-Level Neighborhood of Internet Core Routers

Many contributions use the degree distribution of IP-level internet topology. However, current knowledge of this property relies on biased and erroneous measurements, and so it is subject to much debate. We introduce here a new approach, dedicated to the core of the internet, which avoids the issues raised by classical measurements. It is based on the measurement of IP-level neighborhood of internet core routers, for which we design and implement a rigorous method. It consists in sending traceroute probes from many monitors distributed in the internet towards a given target router and carefully selecting the relevant information in collected data. Using simulations, we provide strong evidence of the accuracy of our approach. We then conduct real-world measurements illustrating the practical effectiveness of our method. This constitutes a significant step towards reliable knowledge of the IP-level degree distribution of the core of the internet.
Long-term research sites as refugia for threatened and over-harvested species

The presence of researchers, ecotourists or rangers inside protected areas is generally assumed to provide a protective effect for wildlife populations, mainly by reducing poaching pressure. However, this assumption has rarely been empirically tested. Here, we evaluate and quantify the conservation benefits of the presence of a long-term research area in Taï National Park, Côte d'Ivoire. A wildlife survey following 225 km of line transects revealed considerably higher primate and duiker encounter rates within the research area when compared with adjacent areas. This positive effect was particularly pronounced for threatened and over-harvested species, such as the endangered red colobus monkey (Procolobus badius). This pattern was clearly mirrored by a reversed gradient in signs of poaching, which decreased towards and inside the research area, a trend that was also supported with park-wide data. This study demonstrates that even relatively simple evidence-based analytical approaches can bridge the gap between conservation theory and practice. In addition, it emphasizes the value of establishing long-term research sites as an integral part of protected area management.
Enabling Accurate and Practical Online Flash Channel Modeling for Modern MLC NAND Flash Memory

NAND flash memory is a widely used storage medium that can be treated as a noisy channel. Each flash memory cell stores data as the threshold voltage of a floating gate transistor. The threshold voltage can shift as a result of various types of circuit-level noise, introducing errors when data are read from the channel and ultimately reducing flash lifetime. An accurate model of the threshold voltage distribution across flash cells can enable mechanisms within the flash controller that improve channel reliability and device lifetime. Unfortunately, existing threshold voltage distribution models are either not accurate enough or have high computational complexity, which makes them unsuitable for online implementation within the controller. We propose a new low-complexity flash memory model, built upon a modified version of the Student's t-distribution and the power law, which captures the threshold voltage distribution and predicts future distribution shifts as wear increases. Using our experimental characterization of the state-of-the-art 1X-nm (i.e., 15-19 nm) multi-level cell NAND flash chips, we show that our model is highly accurate (with an average modeling error of 0.68%), and also simple to compute within the flash controller (requiring 4.41 times less computation time than the most accurate prior model, with negligible decrease in accuracy). Our model also predicts future threshold voltage distribution shifts with a 2.72% modeling error. We demonstrate several example applications of our model in the flash controller, which improve flash channel reliability significantly, including a new mechanism to predict the remaining lifetime of a flash device. Our evaluations for two of these applications show that our model: 1) helps improve flash memory lifetime by 48.9% and/or (2) enables the flash device to safely sustain 69.9% more write operations than manufacturer specifications. We hope and believe that the analyses and models developed in this paper can inspire other novel approaches to flash memory reliability and modeling.
Comparative Study on Photosynthetic Characteristics of Two Ecotypes of Euhalophyte Suaeda salsa L. Grown Under Natural Saline Conditions

Suaeda salsa L. grown in the intertidal zone and those in high salinity soils of the Yellow River Delta were used to investigate the category and characteristic of photosynthesis and fluorescence. Results showed that the water content, Na+ and Cl- contents of the high salinity soils were lower. The temperature on the surface of soil and in the depth of 10 cm from the surface, the content of K+ and Ca2+ of the high salinity soils were significantly higher than those in the intertidal zone soils. Pn, Gs, Fv/Fm, ФPSII, the fresh weight and dry weight per plant of S. salsa grown in the high salinity soils were higher. However, Ci of S. salsa grown in the high salinity soils were lower. These suggested that S. salsa grown in the high salinity soils was mainly suffering from salt stress, while S. salsa in the intertidal zone soils was suffering from waterlogging, low temperature and salt stress together. S. salsa in the intertidal zone soils decreased light absorption and alleviated photoinhibition, but as a result the biomass was reduced.
An auto-input-offset removing floating gate pseudo-differential transconductor

A floating-gate pseudo-differential transconductor is presented, in which the differential input signal is allowed to have a dc offset. Normally such an offset would render a normal CMOS differential pair useless. The circuit inherently removes any dc offset from the floating gates by feedback mechanisms involving Fowler-Nordheim electron tunneling and hot-electron injection. This technique can enable direct cascading of several cells without amplifying and accumulating offsets, or can be used to generate differential current mode signals from a single voltage source that has a dc offset, as with an electret microphone.
A Proposed Hybrid Technique for Recognizing Arabic Characters

Optical character recognition systems improve human-machine interaction and are urgently required for many governmental and commercial departments. A considerable progress in the recognition techniques of Latin and Chinese characters has been achieved. By contrast, Arabic Optical Character Recognition (AOCR) is still lagging although the interest and research in this area is becoming more intensive than before. This is because the Arabic is a cursive language, written from right to left, each character has two to four different forms according to its position in the word, and most characters are associated with complementary parts above, below, or inside the character. The process of Arabic character recognition passes through several stages; the most serious and error-prone of which are segmentation, and feature extraction & classification. This research focuses on the feature extraction and classification stage, being as important as the segmentation stage. Features can be classified into two categories; Local features, which are usually geometric, and Global features, which are either topological or statistical. Four approaches related to the statistical category are to be investigated, namely: Moment Invariants, Gray Level Co-occurrence Matrix, Run Length Matrix, and Statistical Properties of Intensity Histogram. The paper aims at fusing the features of these methods to get the most representative feature vector that maximizes the recognition rate.
Realization of biped walking on uneven terrain by new foot mechanism capable of detecting ground surface

We have developed a new biped foot mechanism capable of detecting ground surface to realize stable walking on uneven terrain. The size of the foot mechanism is 160 mm × 277 mm and its weight is 1.5 kg. The foot system consists of four spikes each of which has an optical sensor to detect ground height. The foot makes a support polygon on uneven terrain by using three or four spikes. We have conducted several experiments on the outdoor ground surface that has a slope of 7.0 degrees and a maximum height of 15 mm bumps, and the effectiveness of the foot mechanism is confirmed.