Miracle-dz/UniFAR-FTUs huggingface dataset:
A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis

Single nucleotide polymorphisms (SNPs) in stable genome regions provide durable measurements of species evolution. We systematically identified each SNP in concatenations of all backbone ORFs in 7 newly or previously sequenced evolutionarily instructive pathogenic Escherichia coli O157:H7, O157:H−, and O55:H7. The 1,113 synonymous SNPs demonstrate emergence of the largest cluster of this pathogen only in the last millennium. Unexpectedly, shared SNPs within circumscribed clusters of organisms suggest severely restricted survival and limited effective population sizes of pathogenic O157:H7, tenuous survival of these organisms in nature, source-sink evolutionary dynamics, or, possibly, a limited number of mutations that confer selective advantage. A single large segment spanning the rfb-gnd gene cluster is the only backbone region convincingly acquired by recombination as O157 emerged from O55. This concatenomic analysis also supports using SNPs to differentiate closely related pathogens for infection control and forensic purposes. However, constrained radiations raise the possibility of making false associations between isolates.
A Microwave Resonant Sensor for Concentration Measurements of Liquid Solutions

This paper presents the design, fabrication, and characterization of a microwave resonator as a tool for concentration measurements of liquid compounds. The sensing device is a rectangular waveguide cavity tuned at 1.91 GHz, which exploits the fundamental TE101 mode in a transmission-type configuration. The coupling structure is optimized by means of a finite element code so as to achieve a high Q-factor. According to the type of substance inside the mixture, its concentration is conveniently related to changes of the S21 scattering parameter (transmission coefficient) in terms of: 1) resonance frequency; 2) 3-dB bandwidth; and 3) amplitude at the resonance frequency. Experimental tests on liquid solutions in controlled conditions are presented to evaluate the performance of the device.
Sperm function test

With absolute normal semen analysis parameters it may not be necessary to shift to specialized tests early but in cases with borderline parameters or with history of fertilization failure in past it becomes necessary to do a battery of tests to evaluate different parameters of spermatozoa. Various sperm function tests are proposed and endorsed by different researchers in addition to the routine evaluation of fertility. These tests detect function of a certain part of spermatozoon and give insight on the events in fertilization of the oocyte. The sperms need to get nutrition from the seminal plasma in the form of fructose and citrate (this can be assessed by fructose qualitative and quantitative estimation, citrate estimation). They should be protected from the bad effects of pus cells and reactive oxygen species (ROS) (leukocyte detection test, ROS estimation). Their number should be in sufficient in terms of (count), structure normal to be able to fertilize eggs (semen morphology). Sperms should have intact and functioning membrane to survive harsh environment of vagina and uterine fluids (vitality and hypo-osmotic swelling test), should have good mitochondrial function to be able to provide energy (mitochondrial activity index test). They should also have satisfactory acrosome function to be able to burrow a hole in zona pellucida (acrosome intactness test, zona penetration test). Finally, they should have properly packed DNA in the nucleus to be able to transfer the male genes (nuclear chromatic decondensation test) to the oocyte during fertilization.
Retinoblastoma‐independent regulation of cell proliferation and senescence by the p53–p21 axis in lamin A /C‐depleted cells

The expression of A‐type lamin is downregulated in several cancers, and lamin defects are the cause of several diseases including a form of accelerated aging. We report that depletion of lamin A/C expression in normal human cells leads to a dramatic downregulation of the Rb family of tumor suppressors and a defect in cell proliferation. Lamin A/C‐depleted cells exhibited a flat morphology and accumulated markers of cellular senescence. This senescent phenotype was accompanied by engagement of the p53 tumor suppressor and induction of the p53 target gene p21 and was prevented by small hairpin RNAs against p53, p21, or by the oncoprotein Mdm2. The expression of E2F target genes, normally required for cell cycle progression, was downregulated after lamin A/C depletion but restored after the inactivation of p53. A similar senescence response was observed in myoblasts from a patient with a lamin A mutation causing muscular dystrophy. We thus reveal a previously unnoticed mechanism of controlling cell cycle genes expression, which depends on p53 but does not require the retinoblastoma family of tumor suppressors and that can be relevant to understand the pathogenesis of laminopathies and perhaps aging.
The Most Basic Missing Instrument in Financial Markets: The Case for Bonds for Financial Security

There is a looming retirement crisis globally with the three pillars of retirement threatened because of insufficient funding, improper investment decisions, and transferring risk to individuals who are least capable of bearing such risk. This paper argues that the introduction of a unique financial instrument, basically an inflation linked bond which pays coupons when you need it, might help ameliorate this crisis. The Life Cycle Hypothesis (LCH) demonstrated why people save; namely, they try to set aside resources during their working lives, to be able to tap into them to ensure retirement income when labor income stops. Modern Portfolio Theory (MPT) attempted to help individuals make optimal investment decisions on these savings by investing in stocks, bonds and other assets to ensure sufficient retirement wealth. There are three problems with using MPT approaches for retirement planning: (a) MPT ignores the uses of funds; (b) focuses on wealth as opposed to retirement income maximization; and (b) none of these assets is an ideal hedge for a desired retirement income. As a result, seemingly safe MPT assets are risky from a retirement income perspective (because the Capital Asset Pricing Model (CAPM) is a specific case of a more general Relative Asset Pricing Model (RAPM)). The need for our bond is simple: the riskless retirement asset is an inflation-indexed, coupon-only bond that defers payment until retirement and pays till death. All attempts to recreate this profile through traditional stocks and bonds, or purchase such a profile through annuities are sub-optimal, risky, complex or expensive thereby threatening retirement security. The paper goes further to demonstrate that there is a potentially willing supplier of such bonds, and that this bond offers the perfect offsetting cash flow profile to infrastructure projects, thereby completing the market. It also addresses challenges, issues and opportunities surrounding such an instrument and examines issues relating to the creation of a market for FSBs.
A reconfigurable printed monopole antenna for MIMO application

The new reconfigurable antenna array is demonstrated for multiple input multiple output (MIMO) communication systems. The antenna system consists of an array of two printed monopole antenna separated by a distance of 10.2 mm (of the lowest frequency band). Each of the dipoles can be reconfigured in length using PIN diode switches. This has been done by changing the switch state to either on or off mode. With the switch closed, the antenna operated at a lower frequency of 2.3 GHz, and to switch opened, the antenna operated at 3.5 GHz. The preference of reconfigurable antenna is that, the radiation characteristics are certain, since the resonance frequency is changed. Invasive Weed optimization(IWO) algorithm is used for the design and optimization of the single printed monopole antenna, to operate at these frequencies. This algorithm is then applied to design two channel MIMO antenna arrays for high degree of isolation. It is shown that good MIMO performance can be achieved even for small element spacing. The simulation results are presented.
The discrete nature and distinguishing molecular features of pancreatic intraductal tubulopapillary neoplasms and intraductal papillary mucinous neoplasms of the gastric type, pyloric gland variant

Intraductal tubulopapillary neoplasms (ITPNs) are composed of tubulopapillary glands with high‐grade dysplasia in the pancreatic duct. Intraductal papillary mucinous neoplasms of the gastric type, pyloric gland variant (IPMN‐PGs) are composed of tubular glands mimicking pyloric glands with low‐grade dysplasia and were formerly called intraductal tubular adenomas. Because of their apparent common tubular morphology, IPMN‐PGs and ITPNs could be associated. While the former might progress to the latter, this has not been fully assessed. In this study, we compared the molecular features of ITPNs and IPMN‐PGs to determine their association using formalin‐fixed, paraffin‐embedded tissues of 14 ITPNs and 15 IPMN‐PGs. Somatic mutations in PIK3CA, GNAS, KRAS, and BRAF were determined by Sanger sequencing. Expression of phosphorylated AKT was examined by immunohistochemistry. Somatic PIK3CA mutations were found in 3 of 14 ITPNs (21.4%) but in none of the IPMN‐PGs (p = 0.0996). In contrast, GNAS mutations were found in none of the ITPNs but in 9 of 15 IPMN‐PGs (60.0%; p < 0.001). KRAS mutations were detected in 1 of 14 ITPNs (7.1%) and 12 of 15 IPMN‐PGs (80.0%; p < 0.001). BRAF mutation was found in one ITPN but in none of the IPMN‐PGs. Phosphorylated AKT expression in ITPNs was significantly more evident than that in IPMN‐PGs (p = 0.0401). These results indicate that ITPNs and IPMN‐PGs are molecularly distinct, suggesting that IPMN‐PG does not progress to ITPN. Furthermore, the molecular features of IPMN‐PGs are confirmed to be identical to those of IPMNs reported elsewhere. These results validate the current World Health Organization system that classifies pancreatic intraductal neoplasms into IPMN and ITPN and confirm that IPMN‐PG is not a benign counterpart of ITPN. The term ‘intraductal tubular adenoma’ should be eliminated and replaced with IPMN‐PG. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Distributed and Multilayer UAV Networks for Next-Generation Wireless Communication and Power Transfer: A Feasibility Study

Unmanned aerial vehicles (UAVs) for wireless communications have rapidly grown into a research hotspot as the mass production of high-performance, low-cost, and intelligent UAVs becomes practical. In the meantime, the fifth generation (5G) wireless communication and Internet-of-Things (IoT) technologies are being standardized and planned for global deployment. During this process, UAVs are becoming an important part of 5G and IoT, and expected to play a crucial role in enabling more functional diversity for wireless communications. In this paper, we first present a summary of mainstream UAVs and their use in wireless communications. Then, we propose a hierarchical architecture of UAVs with multilayer and distributed features to facilitate the integration of different UAVs into the next-generation wireless communication networks. Finally, we unveil the design tradeoffs with the consideration of power transfer, wireless communication, and aerodynamic principles. In particular, empirical models and published measurement data are used to analyze power transfer efficiency, and meteorological impacts on UAVs enabled next-generation wireless communications.
Machine learning for disruption warnings on Alcator C-Mod, DIII-D, and EAST

This paper reports on disruption prediction using a shallow machine learning method known as a random forest, trained on large databases containing only plasma parameters that are available in real-time on Alcator C-Mod, DIII-D, and EAST. The database for each tokamak contains parameters sampled ∼106 times throughout ∼104 discharges (disruptive and non-disruptive) over the last four years of operation. It is found that a number of parameters (e.g. , , , ) exhibit changes in aggregate as a disruption is approached on one or more of these tokamaks. However, for each machine, the most useful parameters, as well as the details of their precursor behaviors, are markedly different. When the prediction problem is framed using a binary classification scheme to discriminate between time slices ‘close to disruption’ and ‘far from disruption’, it is found that the prediction algorithms differ substantially in performance among the three machines on a time slice-by-time slice basis, but have similar disruption detection rates (∼80%–90%) on a shot-by-shot basis after appropriate optimisation. This could have important implications for disruption prediction and avoidance on ITER, for which development of a training database of disruptions may be infeasible. The algorithm’s output is interpretable using a method that identifies the most strongly contributing input signals, which may have implications for avoiding disruptive scenarios. To further support its real-time capability, successful applications in inter-shot and real-time environments on EAST and DIII-D are also discussed.
Blood transfusion safety; current status and challenges in Nigeria

The attainment of blood transfusion safety in Nigeria (and probably the rest of Sub-Saharan Africa) remains an uphill task due to a number of factors, ranging from shortage of blood, poor implementation of blood transfusion guidelines, infrastructural deficits to high prevalence of transfusion-transmissible infections (TTIs), particularly hepatitis and human immune deficiency viruses. We reviewed available data on blood transfusion practices and safety in Nigeria using the PubMed, PubMed Central, Google Scholar, and African Index Medicus search engines, through a combination of word and phrases relevant to the subject. The World Health Organization has been in the forefront of efforts to establish safe, available, and affordable blood transfusion services in most parts of Africa through encouraging adequate blood donor recruitment, donor blood testing, and collection as well developing strategies for the rational use of blood. Even though modest improvement has been recorded, particularly with regards to donor blood screening for common TTIs, considerable efforts are needed in the form of robust public enlightenment campaigns (on blood donation) and continuous system improvement to drive the current transfusion practices in the country toward safety and self-sustenance.
Innovative platform technologies for stabilization and controlled release of proteins from polymer depots

In de laatste decennia is er groeiende interesse voor de toepassing van therapeutische eiwitten voor de behandeling van ziekten. Injecteerbare depotpreparaten op basis van een polymeer waaruit een eiwit over een langere tijd wordt afgegeven vormen een aantrekkelijk alternatief voor de injecties die nu vaak frequent toegediend moeten worden. Smelt-extrusie (hot melt extrusion, HME) is een technologie die vaak toegepast wordt voor de bereiding van polymeermatrices met gereguleerde afgifte van geneesmiddelen. Deze technologie is echter nog nauwelijks onderzocht voor de gereguleerde afgifte van eiwitten. Vanwege de gevoeligheid van deze macromoleculen kan HME leiden tot degradatie . Het doel van deze studie was de stabilisatie van eiwitten te onderzoeken tijdens en na incorporatie in polymeermatrices door middel van HME en tijdens de daarop volgende afgifte van de eiwitten uit deze matrices. Suikerglastechnologie werd toegepast om de eiwitten stabiliseren en het mechanisme van stabilisatie werd onderzocht. Diverse suikerglas gestabiliseerde eiwitten werden ingebouwd in nieuwe, biologisch afbreekbare polymeren door middel van HME, hetgeen kon worden gedaan bij relatief lage temperaturen. Vanwege de pre-stabilisatie met behulp van suikerglazen en de lage procestemperatuur bleven eiwitten volledig intact tijdens het HME-proces. De afgifte van eiwitten uit polymeermatrices kon worden beinvloed door co-incorporatie van porie-vormende hulpstoffen en door de grootte van het eiwit en de polymeersamenstelling te varieren. Ook de afbraaksnelheid van het polymeer zelf bleek een belangrijke factor bij het ontwerpen van de juiste depotformuleringen. Een te snelle afbraak leidde echter tot ongewenste polymeer-eiwit interacties die de eiwitafgifte belemmerde. Samengevat wordt in dit proefschrift het samenspel beschreven tussen eigenschappen van polymeren en eiwitten die belangrijk zijn voor de ontwikkeling van een platformtechnologie voor een succesvolle stabilisatie, incorporatie en gereguleerde afgifte van eiwitten.
Adaptive maneuvering target tracking with 2-HFSWR multisensor surveillance system

The high frequency surface wave radar (HFSWR) with detection capability of hundreds of kilometers plays an important role in marine surveillance [1]–[8]. Nevertheless, HFSWR has low azimuth measurement accuracy, which causes great deviation of target location and tracking [9]. Meanwhile, the miniaturization of radar arrays leads to the limitation of antenna length, which further causes severe decline of azimuth accuracy. Moreover, the interference from external environment also decreases the azimuth accuracy, making the accurate tracking of vessels difficult. In recent years, the 2-HFSWR multisensor surveillance system has become a hot spot, because it only requires parameters of distance and velocity without using the azimuth measurement when tracking vessels. The 2-HFSWR multisensor surveillance system consists of two independent radars implementing the target location and tracking task by detecting the radial distance and velocity, respectively. The 2-HFSWR multisensor surveillance system can ensure the detection accuracy without azimuth measurement, which is advantageous to the miniaturization of HFSWR. However, there are still certain complicated cases to be solved for continuous tracking of vessels, for example sudden change in motion state, an inaccurate model, and unknown priori statistical properties of noise.
An information retrieval scheme for Delay and Tolerance Networks

Delay and Tolerant Network (DTN) techniques are designed to address data communication challenges in network scenarios, which suffer from intermittent connectivity and frequent partitions. A lot of work about routing has been done, but there is little to provide an efficient information retrieval scheme. A content based information retrieval system for DTNs is studied in this paper. Differing from the denounced information access pattern of Internet, destination host of a request is not required. Content replication and indexing is adopted to accelerate response speed. Each node caches its data to the nodes which is more active, and some nodes stores the indexes to help determining the destination of the queries. Simulation results show that the mechanism of caching and indexing can acquire performance improvement.
Effect of the tumor promoter phenobarbital on the pattern of global gene expression in liver of connexin32‐wild‐type and connexin32‐deficient mice

The antiepileptic drug phenobarbital (PB) is used frequently as a model tumor promoter in rodent liver. It is believed to increase the probability of cancer by accelerating the clonal expansion of cells transformed during tumor initiation. The molecular mechanism underlying this process is only partly understood but seems to require the function of connexin32 (Cx32), one of the 2 gap junction proteins expressed in hepatocytes. PB mediates transcriptional activation of various genes in liver but which of these are relevant for tumor promotion is unknown. We have used oligonucleotide microarrays to identify genes differentially modulated in expression by PB in liver of Cx32‐wild‐type and Cx32‐null mice. Mice of both strains were kept on PB containing (0.05%) or control diet for 2 weeks. Total liver RNA was isolated from 3 mice per experimental group and reverse transcribed; cDNAs were hybridized to oligonucleotide microarrays and a gene‐by‐gene linear model was used for statistical analysis of data. Five genes were identified as induced or repressed in untreated Cx32‐null as compared to untreated Cx32‐wild‐type mice. PB affected the expression of 53 genes, of which 13 code for members of Phase‐I/II of drug metabolism, and 12 genes were differentially affected in expression by PB in Cx32‐null as compared to Cx32‐wild‐type mice. Among the differentially affected genes that could be verified by quantitative RT‐PCR or Western analysis were the insulin like growth factor binding protein‐1, retinol dehydrogenase‐6 and the Y‐chromosomally located gene Dby, among which may be a candidate of relevance for PB‐mediated tumor promotion. © 2005 Wiley‐Liss, Inc.
Soccer Offside Judgments in Laypersons with Different Types of Static Displays

Four experiments investigated offside decisions in laypersons with different types of static displays. Previous research neglected this group although the majority of assistant referees in soccer games at the amateur level are laypersons. The aims of our research were (a) to investigate the spatial resolution in laypersons’ perception of offside situations, (b) to search for biases in laypersons’ offside judgments, and (c) to develop useful displays for future research. The displays showed the moment when a midfielder passes the ball to a forward moving in the vicinity of a defender. We varied the spatial location of the forward around the defender in eleven steps and participants made their offside decision by pressing a key. Across experiments, displays varied in abstractness (simple shapes, clipart figures, photographs). There were two major findings. Firstly, both accuracy and speed of offside judgments deteriorated when the spatial distance between forward and defender decreased, approaching guessing rate at the smallest distances. Secondly, participants showed a consistent bias in favor of the non-offside response, in contrast to most studies on professional assistant referees. In sum, the results highlight the limited spatial resolution of the visual system and underscore the role of response bias in offside-judgment tasks.
Lung expansion in the premature rabbit fetus after tracheal deposition of surfactant.

Concentrated "surfactant" was obtained by centrifugation of alveolar wash from adult rabbits for 1 hour at 4°C, 1,000xG, and deposited in the trachea of premature rabbit fetuses, killed at the gestational age of 28 days, i.e., 1 day before appreciable amounts of surface active phospholipids are naturally present in the pulmonary fluid. Pressure-volume tracings revealed a mature pattern in the surfactant-treated animals, with wide hysteresis. Significantly less air entered the lungs of control fetuses from the same litters, and the pressure-volume tracings from these animals showed a premature pattern, with minimal hysteresis. The lungs of the fetuses were fixed in formalin under the endotracheal deflation pressure of 10 cm H20. Histological examination of the lungs revealed moderate or prominent air expansion of the parenchyma in surfactant-treated animals, whereas no or only slight air expansion characterized the controls. Tracheal deposition of surfactant prior to the first breath thus seems to enhance the air expansion of the premature lung, and might possibly be applied as a method for prophylaxis against the idiopathic respiratory distress syndrome, which is related to deficiency of surface active phospholipids in the pulmonary fluid.