Miracle-dz/UniFAR-FTUs huggingface dataset:
Amino acid residues involved in ligand preference of the Snf3 transporter‐like sensor in Saccharomyces cerevisiae

Snf3 is a plasma membrane protein in Saccharomyces cerevisiae able to sense the presence of glucose. Although the Snf3 protein does not transport sugars, it shares sequence similarity with various glucose transporters from other organisms. We investigated the sugar specificity/preferences of Snf3. The ability of cells to sense sugars in vivo was monitored by following the degradation of the Mth1 protein, an early event in the signal pathway. Our study reveals that Snf3, in addition to glucose, also senses fructose and mannose, as well as the glucose analogues 2‐deoxyglucose, 3‐O‐methylglucoside and 6‐deoxyglucose. The signalling proficiency of a non‐phosphorylatable analogue strongly supports the notion that sensing through Snf3 does not require sugar phosphorylation. Sequence comparisons of Snf3 to glucose transporters indicated amino acid residues possibly involved in sensing of sugars other than glucose. By site‐specific mutagenesis of the structural gene, roles of specific residues in Snf3 could be established. Change of isoleucine‐374 to valine in transmembrane segment 7 of Snf3 partially abolished sensing of fructose and mannose, while mutagenesis causing a change of phenylalanine‐462 to tyrosine in transmembrane segment 10 of Snf3 abolished sensing of fructose. Neither of these amino acid changes affected the ability of Snf3 to sense glucose, nor did they permit Snf3 to sense galactose. These data indicate a similarity between a ligand binding site of the sensor Snf3 and binding sites used for facilitated hexose transport in the GLUT proteins. Copyright © 2009 John Wiley & Sons, Ltd.
Mass spectrometric analysis of the secretome of Candida albicans

The pathogenic fungus Candida albicans secretes a considerable number of hydrolases and other proteins. In‐depth studies of the C. albicans secretome could thus provide new candidates for diagnostic markers and vaccine development. We compared various growth conditions differing in pH, temperature and the presence of the hyphal inducer N‐acetylglucosamine. The polypeptide content of the growth media was ca. 0.1–0.2% of the total biomass. Using LC–tandem mass spectrometry, we identified 44 secretory proteins, the transmembrane protein Msb2, six secretory pathway‐associated proteins and 28 predicted cytosolic proteins. Many secretory proteins are wall‐related, suggesting that their presence in the growth medium is at least partially due to accidental release from the walls. Als3, Csa2, Rbt4, Sap4 and Sap6 were enriched in the medium of hyphal cultures; Bgl2, Cht3, Dag7, Eng1, Pir1, Rbe1, Scw11, Sim1/Sun42, Xog1 and Ywp1 in the medium of yeast cells; and Plb4.5 in pH 4 medium. Seven proteins (Cht3, Mp65, Orf19.5063/Coi1, Scw11, Sim1, Sun41 and Tos1) were consistently present under all conditions tested. These observations indicate that C. albicans tightly regulates its secretome. Mp65, Sun41, and Tos1 were each predicted to contain at least one highly immunogenic peptide. In total, we identified 29 highly immunogenic peptides originating from 18 proteins, including two members of the family of secreted aspartyl proteases. Fifty‐six peptides were identified as proteotypic and will be useful for quantification purposes. In summary, the number of identified secretory proteins in the growth medium has been substantially extended, and growth conditions strongly affect the composition of the secretome. Copyright © 2010 John Wiley & Sons, Ltd.
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

The genomic origins of rape oilseed Many domesticated plants arose through the meeting of multiple genomes through hybridization and genome doubling, known as polyploidy. Chalhoub et al. sequenced the polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed (canola), kale, and rutabaga. B. napus has undergone multiple events affecting differently sized genetic regions where a gene from one progenitor species has been converted to the copy from a second progenitor species. Some of these gene conversion events appear to have been selected by humans as part of the process of domestication and crop improvement. Science, this issue p. 950 The polyploid genome of oilseed rape exhibits evolution through homologous gene conversion. Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
The Neurological Patient in History

“Every generation rewrites its history. ” This is one of the statements of the Dutch historian Johan Huizinga. Applying this to today's medicine, the title of the present book is of no surprise. In an era in which health care has become organized around the patient, it is to be expected that historians of medicine look at history from the perspective of the patient.
A photoinduced metal-like phase of monoclinic VO2 revealed by ultrafast electron diffraction

How to make vanadium dioxide metallic At about 70°C, the material vanadium dioxide (VO2) switches from being a semiconductor to a metal. The switch happens so fast that it may be useful in electronic devices, but it is not clear whether the switch is primarily caused by enhanced interactions between electrons or by a change in the crystal structure. Morrison et al. shone laser light on a sample of VO2, initially in a semiconducting state. They used electron diffraction to monitor the changes in the material's crystal structure and simultaneously measured its optical properties to monitor the electronic state. For certain laser powers, VO2 switched to a long-lived metallic state even though it preserved its initial crystal structure. Science, this issue p. 445 Simultaneous measurements of structural and optical properties are used to study optically excited vanadium dioxide. The complex interplay among several active degrees of freedom (charge, lattice, orbital, and spin) is thought to determine the electronic properties of many oxides. We report on combined ultrafast electron diffraction and infrared transmissivity experiments in which we directly monitored and separated the lattice and charge density reorganizations that are associated with the optically induced semiconductor-metal transition in vanadium dioxide (VO2). By photoexciting the monoclinic semiconducting phase, we were able to induce a transition to a metastable state that retained the periodic lattice distortion characteristic of the semiconductor but also acquired metal-like mid-infrared optical properties. Our results demonstrate that ultrafast electron diffraction is capable of following details of both lattice and electronic structural dynamics on the ultrafast time scale.
Optimizing dynamic binary translation for SIMD instructions

Dynamic binary translation technology allows a program written for one architecture to be executed on a second architecture without recompiling the source code. Effective dynamic binary translation of SIMD (single instruction multiple data) instructions has become more and more important as SIMD extensions have gained popularity among general-purpose CPUs within the last decade. Many SIMD extensions allow an SIMD register to hold data of different types at different times. Supporting multiple data types within the same register complicates the task of a dynamic translator, which may or may not be able to determine the type of the register at translation time. We propose the SIMD data type tracking algorithm to translate the SIMD instructions and three algorithms to further optimize the translation. Our results show that the three optimizing algorithms give overall 3.89% performance improvement for SPEC2K INT benchmarks and 6.61%for SPEC2KFP benchmarks.
Dosimetry of two new interstitial brachytherapy sources

Dosimetry of two new interstitial brachytherapy sources With increased demand for low 103Pd (palladium) seed sources, to treat prostate and eye cancers, new sources have been designed and introduced. This article presents the two new palladium brachytherapy sources, IR03-103Pd and IR04-103Pd that have been developed at Nuclear Science and Technology Research Institute. The dosimetry parameters such as the dose rate constant Λ, the radial dose function g(r), and the anisotropy function F(r,θ), around the sources have been characterized using Version 5 Monte Carlo radiation transport code in accordance with the update AAPM Task Group No. 43 report (TG-43U1). The results indicated the dose rate constant of 0.689±0.02 and 0.667±0.02 cGy h-1 U-1 for the IR03-103Pd and IR04-103Pd sources respectively, which are in acceptable agreement with other commercial seeds. The calculated results were compared with published results for those of other source manufacturers. However, they show an acceptable dose distribution, using for clinical applications is pending experimental dosimetry.
The environmental controls that govern the end product of bacterial nitrate respiration

How microbes compete for nitrate Much of the ammonia fertilizer we use ends up in surface or coastal waters as nitrate. This runoff lowers water quality and damages ecosystems. Although microbial nitrogen respiration influences the fate of nitrate, it is unclear which environmental factors exert the most control. Kraft et al. performed multiple long-term incubation studies of microbial communities from marine sediments. The relative supply of nitrate and nitrite, as well as total carbon and nitrogen, provided selective pressures that drove communities toward denitrification or ammonification. The average generation time of the community also strongly influenced which respiration pathway dominated. Science, this issue p. 676 Denitrification and ammonification compete for nitrate based on environmental pressures. In the biogeochemical nitrogen cycle, microbial respiration processes compete for nitrate as an electron acceptor. Denitrification converts nitrate into nitrogenous gas and thus removes fixed nitrogen from the biosphere, whereas ammonification converts nitrate into ammonium, which is directly reusable by primary producers. We combined multiple parallel long-term incubations of marine microbial nitrate-respiring communities with isotope labeling and metagenomics to unravel how specific environmental conditions select for either process. Microbial generation time, supply of nitrite relative to nitrate, and the carbon/nitrogen ratio were identified as key environmental controls that determine whether nitrite will be reduced to nitrogenous gas or ammonium. Our results define the microbial ecophysiology of a biogeochemical feedback loop that is key to global change, eutrophication, and wastewater treatment.
Optimal next hop selection for VANET routing

Vehicular ad hoc network (VANET) applications become increasingly popular. Particular characteristics of VANETs profoundly impede the deployment of the VANET applications. Therefore, the merits of routing significantly affect the accomplishments of the VANETs. Though myriads of efforts have been made, the problems are partially solved. Quality of Service (QoS) requirements should be satisfied for various applications. Existing routing protocols are incapable of well satisfying distinct QoS needs. To remedy this problem, a next-hop selection scheme is proposed in this paper; which is able to select the next-hop node for various applications with diverse QoS requirements. Aspects including QoS type classification, link lifetime prediction, bandwidth evaluation, and next-hop node selection; are elaborately addressed in the proposed scheme. The simulation results show that the proposed next-hop selection scheme promotes packet delivery rate, shortens end-to-end delay, and decreases signaling overhead in VANETs.
Remote control of base station antenna systems based on two-dimensional electrically adjustable technology

The adjustments of vertical angle and horizontal azimuth angle of base station antenna are the most frequent and most enormous workload in the operation and maintenance of base station. Based on two-dimensional electrically adjustable technology, RCU with AISG2.0 protocol can remote control vertical beam and horizontal coverage area of the entire base station network. With the automated optimization software, the rational allocation of each base station antenna can be done smartly. Compared with the traditional base station systems, this one has the advantages such as smart remote to adjust, the two-dimensional electrical adjustment, and work around the clock.
CPRI compression transport for LTE and LTE-A signal in C-RAN

C-RAN is the next-generation clean wireless access network architecture, which is based on centralized processing, the Collaborative Radio and Real-time Cloud Infrastructure. In C-RAN architecture, different access technology (eg.GSM / TD-SCDMA / WCDMA / LTE) can be support on the same hardware platform in baseband pool system; C-RAN can be applied to reduce the consumption of operators. LTE (Long Term Evolution) and LTE-A, which are based on OFDM and MIMO technologies, are regarded as the main wireless access technology in the evolution from 3G to 4G. LTE introduces variety of novel technologies to improve the system performance, especially in C-RAN architecture, such as Multi antennas MIMO, Carrier Aggregation, CoMP. However, C -RAN architecture also brings about lager data transmission in the optical fiber. In this paper a low-latency baseband signal compression algorithm used in ALU is introduced to reduce the data rate. Based on the Characteristics of LTE signal data, the algorithm removal redundancies in the spectral domain firstly, and then the block scaling, which is combined with non-linear (nonuniform) quantizer, is designed to minimize quantization error. This algorithm can effectively reduce the amount of data transferred between BBU and RUU in LTE system, to facilitate the deployment of LTE in the CRan architecture. Simulation analysis is given out in the paper; meanwhile TD-LTE system demo verification is also implemented. The results indicate that the scheme introduced can get good performance under a certain compression rate in the real system. Further research is also in progress.
Improving Range Query Performance on Historic Web Page Data

This paper is about the performance of range queries on historic web page data set, i.e. requests into a data set of web pages that keeps record of historic versions of HTML data of URLs on the web for a subset of data, the URLs and the timestamps of which satisfy the query conditions. To keep track of all versions of every web URL, the data set could easily scale up to terabytes. Hence, systems providing query services to such a data set would require much computing resource. We show that in this scenario data storage layout has significant impact on query performance and propose storage design principles for performance improvement through quantitative approaches.
Web API Creation for Enterprise Mashup

It is desirable for web applications to be reusable, for example in case a vendor wants to deliver new valuable services by using and combining existing applications quickly. One of the well-known ways of reusing web applications, Mashup, has become popular in the web development community and applied to many open web sites, as we can just combine the data retrieved from Web pages or APIs of the web applications. But in the case of the Mashup of enterprise web applications, or Enterprise Mashup, it is quite difficult since these applications are often not intended to be reusable and have no Web APIs. That means we have to create the Web APIs for the applications, which takes much work. In this paper, we describe a light-weight Web API creation methodology in order to create Web APIs for enterprise web applications much more easily than we can by extending the source code. The created Web API can connect to the web application just as a client who has an account does. So we can create a Web API for Enterprise Mashup without modifying the application at all and we can call the Web API securely using the user account information of the application. We developed the implementation of our methodology and applied it to actual applications to evaluate its effectiveness.
The Medical Messiahs: A Social History of Health Quackery in Twentieth-Century America

Medical quackery represents a big business—with an annual gross of over $2 billion. In a previous volume, James Harvey Young, professor of history at Emory University, traced the earliest stages of medical quackery in this country, up through 1906, the year that the first significant regulatory legislation was enacted. The present volume begins where The Toadstool Millionaire left off. In the six decades elapsing since 1906, there has been enormous progress in medical science and education, but there has also been analogous progress in quackery promotion. In 20 well-written chapters, including one that sketches the earlier background, Young discusses in considerable detail a variety of nostrums, gadgets, and fraudulent claims. The book opens with a discussion of "Cuforhedake Braine Fude" (containing 24% alcohol), the first case tried under the 1906 Pure Food and Drug Act. The promoter made $2 million. He was fined $700. But the government gained an important
Economic and social implications of aging societies

The challenge of global population aging has been brought into sharper focus by the financial crisis of 2008. In particular, growing national debt has drawn government attention to two apparently conflicting priorities: the need to sustain public spending on pensions and health care versus the need to reduce budget deficits. A number of countries are consequently reconsidering their pension and health care provisions, which account for up to 40% of all government spending in advanced economies. Yet population aging is a global phenomenon that will continue to affect all regions of the world. By 2050 there will be the same number of old as young in the world, with 2 billion people aged 60 or over and another 2 billion under age 15, each group accounting for 21% of the world’s population.
Controllable Cost Search Strategy in Unstructured P2P

The search width and search depth is the key factor of unstructured Peer-to-Peer (P2P) network search algorithms in unstructured Peer-to-Peer (P2P) network. Existing guided search algorithms decreased search width by QoS or history search records, the TTL (time to live) can be used to constrain the search depth. However, there is a huge difference in the number of nodes searched by TTL-based algorithm even with the same search depth. And each search branch of the TTL-based algorithm can only search the same depth of the network, thus resulting in the unstable search efficiency. In this paper, a controllable cost search algorithms is presented, which would ensure more stable number of search nodes and achieve different search branches using different search depth, Experiments show that ours search algorithm based on budget in unstructured P2P network has more stable number of searched nodes, and greatly improved the utilization rate of search message, the successful rate of search and the search efficiency.
Genomic basis for the convergent evolution of electric organs

Only one way to make an electric organ? Electric fish have independently evolved electric organs that help them to communicate, navigate, hunt, and defend themselves. Gallant et al. analyzed the genome of the electric eel and the genes expressed in two other distantly related electric fish. The same genes were recruited within the different species to make evolutionarily new structures that function similarly. Science, this issue p. 1522 Multiple divergent fish lineages have used the same evolutionary toolkit to produce electric organs. Little is known about the genetic basis of convergent traits that originate repeatedly over broad taxonomic scales. The myogenic electric organ has evolved six times in fishes to produce electric fields used in communication, navigation, predation, or defense. We have examined the genomic basis of the convergent anatomical and physiological origins of these organs by assembling the genome of the electric eel (Electrophorus electricus) and sequencing electric organ and skeletal muscle transcriptomes from three lineages that have independently evolved electric organs. Our results indicate that, despite millions of years of evolution and large differences in the morphology of electric organ cells, independent lineages have leveraged similar transcription factors and developmental and cellular pathways in the evolution of electric organs.
Accuracy and Applications of Lung Ultrasound to Diagnose Ventilator-Associated Pneumonia: A Systematic Review

Background: Lung ultrasound (LUS) is an accurate tool to diagnose community-acquired pneumonia. However, it is not yet an established tool to diagnose ventilator-associated pneumonia (VAP). Purpose: To assess the evidence about LUS in the diagnosis of VAP, we conducted a systematic review of the literature. Methods: We searched PubMed, Embase, Scopus, Web of Science, and LILACS. Two researchers independently selected the studies that met the inclusion criteria. Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool was used to assess the quality of the studies. In a qualitative synthesis, 3 questions guided the review: Q1. What are the sonographic signs of VAP? Q2. How can LUS be combined with others tests or signs of VAP? Q3. What is the role of LUS in VAP screening? Main Results: Three studies (n = 377 patients) with different designs were included. In terms of Q1, the 3 studies assessed the accuracy of sonographic consolidations. In patients suspected for VAP, lobar or hemilobar consolidation alone was not sufficient to diagnose VAP but seems useful to exclude it. The most useful signs were small subpleural consolidations (sensitivity: 81%; specificity: 41%) and dynamic air bronchograms (sensitivity: 44%; specificity: 81%). Two studies were assessed for Q2, when the 2 signs above were included in a clinical score (Ventilator-associated Pneumonia Lung Ultrasound Score associated with quantitative culture of endotracheal aspirate—VPLUS-EAquant), the accuracy was amplified (sensitivity: 48% and specificity: 97% for score ≥4; sensitivity: 78% and specificity: 77% for score ≥3 points). Finally, regarding Q3, no studies have assessed the use of LUS in screening of VAP. Conclusion: Small subpleural consolidations and dynamic air bronchograms were the most useful sonographic signs to diagnose VAP in suspected patients. Clinical scores including LUS had better diagnosis accuracy than LUS alone. There are no data on LUS for VAP screening.