Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic and Pathotypic Characterization of Newcastle Disease Viruses Circulating in South China and Transmission in Different Birds

Although Newcastle disease virus (NDV) with high pathogenicity has frequently been isolated in poultry in China since 1948, the mode of its transmission among avian species remains largely unknown. Given that various wild bird species have been implicated as sources of transmission, in this study we genotypically and pathotypically characterized 23 NDV isolates collected from chickens, ducks, and pigeons in live bird markets (LBMs) in South China as part of an H7N9 surveillance program during December 2013–February 2014. To simulate the natural transmission of different kinds of animals in LBMs, we selected three representative NDVs—namely, GM, YF18, and GZ289—isolated from different birds to evaluate the pathogenicity and transmission of the indicated viruses in chickens, ducks, and pigeons. Furthermore, to investigate the replication and shedding of NDV in poultry, we inoculated the chickens, ducks, and pigeons with 106 EID50 of each virus via intraocular and intranasal routes. Eight hour after infection, the naïve contact groups were housed with those inoculated with each of the viruses as a means to monitor contact transmission. Our results indicated that genetically diverse viruses circulate in LBMs in South China's Guangdong Province and that NDV from different birds have different tissue tropisms and host ranges when transmitted in different birds. We therefore propose the continuous epidemiological surveillance of LBMs to support the prevention of the spread of these viruses in different birds, especially chickens, and highlight the need for studies of the virus–host relationship.
Elastic-Plastic Model of Adhesive-Bonded Single-Lap Composite Joints

An analytical model for determining adhesive stress distributions within the adhesive-bonded single-lap composite joints was developed. ASTM D3165 ‘‘Strength Properties of Adhesives in Shear by Tension Loading of Single-Lap-Joint Laminated Assemblies’’ test specimen geometry was followed in the model derivation. In the model derivation, the composite adherends were assumed linear elastic while the adhesive was assumed elastic-perfectly plastic following von Mises yield criterion. Laminated Anisotropic Plate Theory was applied in the derivation of the governing equations of the bonded laminates. The adhesive was assumed to be very thin and the adhesive stresses are assumed constant through the bondline thickness. The entire coupled system of equations was determined through the kinematics relations and force equilibrium of the adhesive and the adherends. The overall system of governing equations was solved analytically with appropriate boundary conditions. Computer software Maple V was used as the solution tool. The developed stress model was verified with finite element analysis using ABAQUS by comparing the adhesive stress distributions.
Stimulus-specific adaptation in a recurrent network model of primary auditory cortex

Stimulus-specific adaptation (SSA) occurs when neurons decrease their responses to frequently-presented (standard) stimuli but not, or not as much, to other, rare (deviant) stimuli. SSA is present in all mammalian species in which it has been tested as well as in birds. SSA confers short-term memory to neuronal responses, and may lie upstream of the generation of mismatch negativity (MMN), an important human event-related potential. Previously published models of SSA mostly rely on synaptic depression of the feedforward, thalamocortical input. Here we study SSA in a recurrent neural network model of primary auditory cortex. When the recurrent, intracortical synapses display synaptic depression, the network generates population spikes (PSs). SSA occurs in this network when deviants elicit a PS but standards do not, and we demarcate the regions in parameter space that allow SSA. While SSA based on PSs does not require feedforward depression, we identify feedforward depression as a mechanism for expanding the range of parameters that support SSA. We provide predictions for experiments that could help differentiate between SSA due to synaptic depression of feedforward connections and SSA due to synaptic depression of recurrent connections. Similar to experimental data, the magnitude of SSA in the model depends on the frequency difference between deviant and standard, probability of the deviant, inter-stimulus interval and input amplitude. In contrast to models based on feedforward depression, our model shows true deviance sensitivity as found in experiments.
Building and Evolving Data Warehousing and Business Intelligence artefacts: the Case of Sysco

This paper investigates use of data warehouse and business intelligence capabilities to integrate with customers in the supply chain and improve insights into customer sales. By making internal data warehouse sales information available to customers, additional value to those customers is created, eliminating asymmetries of information in the supply chain. In addition, the evolution of data warehousing into business intelligence is investigated, expanding sales information to include marketing associate performance analysis generated for internal use. Further, a methodology that was used for building a business intelligence system is also examined. Finally, what appears to be a business-intelligence-driven focus on enterprise resource planning systems is analyzed. These issues are illustrated using real-world data warehousing and business intelligence artefacts developed at SYSCO. Copyright © 2012 John Wiley & Sons, Ltd.
Attacking NTP's Authenticated Broadcast Mode

We identify two attacks on the Network Time Protocol (NTP)'s cryptographically-authenticated broadcast mode. First, we present a replay attack that allows an on-path attacker to indefinitely stick a broadcast client to a specific time. Second, we present a denial-of-service (DoS) attack that allows an off-path attacker to prevent a broadcast client from ever updating its system clock; to do this, the attacker sends the client a single malformed broadcast packet per query interval. Our DoS attack also applies to all other NTP modes that are `ephemeral' or `preemptable' (including manycast, pool, etc). We then use network measurements to give evidence that NTP's broadcast and other ephemeral/preemptable modes are being used in the wild. We conclude by discussing why NTP's current implementation of symmetric-key cryptographic authentication does not provide security in broadcast mode, and make some recommendations to improve the current state of affairs.
History of silence affects auditory evoked fields regardless of intervening sounds: a magnetoencephalographic study

The amplitudes of auditory evoked N1 m responses are known to depend on the length of the pre‐stimulus silent interval. However, it remains unknown whether pre‐penultimate silent intervals affect the auditory evoked responses elicited by test stimuli. In the present study, we investigated the N1 m responses elicited by a train of four successive tones with a silent interval of 1 s subsequent to that with a 0.25‐, 0.5‐, 2‐ or 4‐s silent interval using magnetoencephalography. The results obtained demonstrated that the N1 m source strength decreased as the pre‐penultimate silent interval became shorter. A history of silences had a significant impact on the N1 m source strength. Human brain activity that is modulated by silence history may play an important role in encoding a series of sound streams that include silences, such as speech and music.
Unique Endemicity of Cryptosporidiosis in Children in Kuwait

ABSTRACT To understand the transmission of Cryptosporidium infection in children, fecal specimens from 62 Kuwaiti children with gastrointestinal symptoms found to be positive by microscopy were genotyped and subtyped with a small subunit rRNA-based PCR-restriction fragment length polymorphism analysis and a 60-kDa glycoprotein-based DNA sequencing tool. The median age of infected children was 4.5 years, and 77% of infections occurred during the cool season of November to April. Fifty-eight of the children (94%) had Cryptosporidium parvum, three (5%) had Cryptosporidium hominis, and one (1%) had both C. parvum and C. hominis. Altogether, 13 subtypes of C. parvum (belonging to four subtype allele families) and C. hominis (belonging to three subtype allele families) were observed, with 92% of specimens belonging to the common allele family IIa and the unusual allele family IId. Thus, the transmission of cryptosporidiosis in Kuwaiti children differed significantly from other tropical countries.
Influence of CYP3A5 6986A > G and ABCB1 3435C > T Polymorphisms on Adverse Events Associated With Tacrolimus in Jordanian Pediatric Renal Transplant Patients

The aim of the study is to investigate the influence of ABCB1(3435) and CYP3A5(6986) polymorphisms, tacrolimus troughs and clinical factors on the time of adverse events associated with tacrolimus in pediatric kidney transplant patients. Clinical data, adverse events, tacrolimus troughs, corresponding doses, ABCB1 3435C > T and CYP3A5 6986A > G genotypes were collected from 38 pediatric kidney transplant patients in a retrospective study for over 2 years post‐transplant. We used a marginal Cox proportional hazard model to evaluate the influence of clinical factors and single nucleotide polymorphisms (SNPs) on tacrolimus‐associated adverse events. CYP3A5 genotype, the Bayesian predicted tacrolimus concentrations, hematocrit and mean corpuscular volume are significant risk factors of adverse events over a 2‐year‐period. CYP3A5*1 genotype was associated with 36% relative risk of CYP3A5*3/*3 genotype. In the 9‐month period, the additional factor, ABCB1 3435TT genotype, was shown to be associated with 38% relative risk of the CC and CT genotypes. For graft loss, acute and chronic rejection, only tacrolimus concentration and hematocrit, but not CYP3A5 or ABCB1 polymorphisms, are important factors influencing their occurrences.
Patch-based Object Recognition Using Discriminatively Trained Gaussian Mixtures

We present an approach using Gaussian mixture models for part-based object recognition where spatial relationships of the parts are explicitly modeled and parameters of the generative model are tuned discriminatively. These extensions lead to great improvements of the classification accuracy. Furthermore we evaluate several improvements over our baseline system which incrementally improve the obtained results which compare favorable well to other published results for the three Caltech tasks and the PASCAL evaluation 05 tasks.
New enzyme for reductive cancer chemotherapy, YieF, and its improvement by directed evolution

Reductive prodrugs, mitomycin C and 5-aziridinyl-2,4-dinitrobenzamide (CB 1954), are nontoxic in their native form but become highly toxic upon reduction. Their effectiveness in cancer chemotherapy can be enhanced by delivering to tumors enzymes with improved prodrug reduction kinetics. We report the discovery of a new prodrug-reducing enzyme, YieF, from Escherichia coli, and the improvement of its kinetics for reducing mitomycin C and CB 1954. A YieF-derived enzyme, Y6, killed HeLa spinner cells with ≥5-fold efficiency than the wild-type enzymes, YieF and NfsA, at a variety of drug and enzyme concentrations and incubation times. With adhered HeLa cells and Salmonella typhimurium SL 7838 bacteria as enzyme delivery vehicle, at least an order of magnitude less of Y6-producing bacteria were required to kill >90% of tumor cells compared with bacteria expressing the wild-type enzymes, which at a comparable level killed <5% of the cells. Thus, Y6 is a promising enzyme for use in cancer chemotherapy, and Salmonella strain SL 7838, which specifically targets tumors, may be used to deliver the prodrug-activating enzymes to tumors. [Mol Cancer Ther 2006;5(1):97–103]
Identification of sublimation‐type thermal contraction crack polygons at the proposed NASA Phoenix landing site: Implications for substrate properties and climate‐driven morphological evolution

We identify a surface within the NASA Phoenix landing site Area D characterized by boulder‐topped, polygonally‐patterned mounds comparable in radius and cross‐sectional morphology to terrestrial sublimation polygons found in Antarctica. Both Martian and Antarctic polygons display topographic asymmetry, with shallow equator‐facing slopes and steep pole‐facing slopes, interpreted to indicate insolation‐dependent, differential sublimation of buried ice. On the basis of morphological similarities, we classify the Phoenix Box 1 polygons as sublimation polygons. Terrestrial sublimation polygons form where ice volumes exceeding available pore space occur in the shallow subsurface and where near‐surface conditions are too cold and dry to permit the development of saturated active layers: conditions comparable to those recently modeled for Mars in the Phoenix landing site Area D, Box 1. The identification of sublimation polygons on Mars would provide direct evidence for shallow, ground ice exceeding pore‐ice volumes and shed light on the emplacement mechanism of this ice.
Monadic Second-Order Logic Over Rectangular Pictures and Recognizability by Tiling Systems

Abstract It is shown that a set of pictures (rectangular arrays of symbols) is recognized by a finite tiling system iff it is definable in existential monadic second-order logic. As a consequence, finite tiling systems constitute a notion of recognizability over two-dimensional inputs which at the same time generalizes finite-state recognizability over strings and also matches a natural logic. The proof is based on the Ehrenfeucht–Fraisse technique for first-order logic and an implementation of “threshold counting” within tiling systems.
Incidence of Bladder Cancer in Sri Lanka: Analysis of the Cancer Registry Data and Review of the Incidence of Bladder Cancer in the South Asian Population

Purpose To investigate the incidence of bladder cancer (BC) in Sri Lanka and to compare risk factors and outcomes with those of other South Asian nations and South Asian migrants to the United Kingdom (UK) and the United States (US). Materials and Methods The incidence of BC in Sri Lanka was examined by using two separate cancer registry databases over a 5-year period. Smoking rates were compiled by using a population-based survey from 2001 to 2009 and the relative risk was calculated by using published data. Results A total of 637 new cases of BC were diagnosed over the 5-year period. Sri Lankan BC incidence increased from 1985 but remained low (1.36 and 0.3 per 100,000 in males and females) and was similar to the incidence in other South Asian countries. The incidence was lower, however, than in migrant populations in the US and the UK. In densely populated districts of Sri Lanka, these rates almost doubled. Urothelial carcinoma accounted for 72%. The prevalence of male smokers in Sri Lanka was 39%, whereas Pakistan had higher smoking rates with a 6-fold increase in BC. Conclusions Sri Lankan BC incidence was low, similar to other South Asian countries (apart from Pakistan), but the actual incidence is likely higher than the cancer registry rates. Smoking is likely to be the main risk factor for BC. Possible under-reporting in rural areas could account for the low rates of BC in Sri Lanka. Any genetic or environmental protective effects of BC in South Asians seem to be lost on migration to the UK or the US and with higher levels of smoking, as seen in Pakistan.
Mouse Gestation Length Is Genetically Determined

Background Preterm birth is an enormous public health problem, affecting over 12% of live births and costing over $26 billion in the United States alone. The causes are complex, but twin studies support the role of genetics in determining gestation length. Despite widespread use of the mouse in studies of the genetics of preterm birth, there have been few studies that actually address the precise natural gestation length of the mouse, and to what degree the timing of labor and birth is genetically determined. Methodology/Principal Findings To further develop the mouse as a genetic model of preterm birth, we developed a high-throughput monitoring system and measured the gestation length in 15 inbred strains. Our results show an unexpectedly wide variation in overall gestation length between strains that approaches two full days, while intra-strain variation is quite low. Although litter size shows a strong inverse correlation with gestation length, genetic difference alone accounts for a significant portion of the variation. In addition, ovarian transplant experiments support a primary role of maternal genetics in the determination of gestation length. Preliminary analysis of gestation length in the C57BL/6J-Chr#A/J/NaJ chromosome substitution strain (B.A CSS) panel suggests complex genetic control of gestation length. Conclusions/Significance Together, these data support the role of genetics in regulating gestation length and present the mouse as an important tool for the discovery of genes governing preterm birth.
The Thyroid Receptor Modulator KB3495 Reduces Atherosclerosis Independently of Total Cholesterol in the Circulation in ApoE Deficient Mice

Background Thyroid hormones (TH) regulate cholesterol metabolism but their use as lipid-lowering drugs is restricted due to negative cardiac effects. TH mimetic compounds modulating TH receptor β (THRβ) have been designed as potential drugs, reducing serum cholesterol levels while avoiding apparent deleterious cardiac effects. Objective Using ApoE deficient mice, we examined whether KB3495, a TH mimetic compound, reduces atherosclerosis and if there is a synergistic effect with atorvastatin. The effect of KB3495 was investigated after 10 and 25 weeks. Results KB3495 treatment reduced atherosclerotic plaque formation in aorta and decreased the cholesteryl ester (CE) content by 57%. Treatment with KB3495 was also associated with a reduction of macrophage content in the atherosclerotic plaques and reduced serum levels of IL-1β, TNFalpha, IL-6, Interferon γ, MCP-1 and M-CSF. Serum lipoprotein analysis showed no change in total cholesterol levels in ApoB-containing lipoproteins. KB3495 alone increased fecal BA excretion by 90%. The excretion of neutral sterols increased in all groups, with the largest increase in the combination group (350%). After 25 weeks, the animals treated with KB3495 showed 50% lower CE levels in the skin and even further reductions were observed in the combination group where the CE levels were reduced by almost 95% as compared to controls. Conclusion KB3495 treatment reduced atherosclerosis independently of total cholesterol levels in ApoB-containing lipoproteins likely by stimulation of sterol excretion from the body and by inhibition of the inflammatory response.
Sequence variant (CTAGGG)n in the human telomere favors a G-quadruplex structure containing a G·C·G·C tetrad

Short contiguous arrays of variant CTAGGG repeats in the human telomere are unstable in the male germline and somatic cells, suggesting formation of unusual structures by this repeat type. Here, we report on the structure of an intramolecular G-quadruplex formed by DNA sequences containing four human telomeric variant CTAGGG repeats in potassium solution. Our results reveal a new robust antiparallel G-quadruplex fold involving two G-tetrads sandwiched between a G·C base pair and a G·C·G·C tetrad, which could represent a new platform for drug design targeted to human telomeric DNA.
Shiga Toxin Gene Loss and Transfer In Vitro and In Vivo during Enterohemorrhagic Escherichia coli O26 Infection in Humans

ABSTRACT Escherichia coli serogroup O26 consists of enterohemorrhagic E. coli (EHEC) and atypical enteropathogenic E. coli (aEPEC). The former produces Shiga toxins (Stx), major determinants of EHEC pathogenicity, encoded by bacteriophages; the latter is Stx negative. We have isolated EHEC O26 from patient stools early in illness and aEPEC O26 from stools later in illness, and vice versa. Intrapatient EHEC and aEPEC isolates had quite similar pulsed-field gel electrophoresis (PFGE) patterns, suggesting that they might have arisen by conversion between the EHEC and aEPEC pathotypes during infection. To test this hypothesis, we asked whether EHEC O26 can lose stx genes and whether aEPEC O26 can be lysogenized with Stx-encoding phages from EHEC O26 in vitro. The stx2 loss associated with the loss of Stx2-encoding phages occurred in 10% to 14% of colonies tested. Conversely, Stx2- and, to a lesser extent, Stx1-encoding bacteriophages from EHEC O26 lysogenized aEPEC O26 isolates, converting them to EHEC strains. In the lysogens and EHEC O26 donors, Stx2-converting bacteriophages integrated in yecE or wrbA. The loss and gain of Stx-converting bacteriophages diversifies PFGE patterns; this parallels findings of similar but not identical PFGE patterns in the intrapatient EHEC and aEPEC O26 isolates. EHEC O26 and aEPEC O26 thus exist as a dynamic system whose members undergo ephemeral interconversions via loss and gain of Stx-encoding phages to yield different pathotypes. The suggested occurrence of this process in the human intestine has diagnostic, clinical, epidemiological, and evolutionary implications.
Acoel development supports a simple planula-like urbilaterian

Molecular approaches to the study of development and evolution have had profound effects on our understanding of the nature of the evolutionary process. Developmental biologists became intoxicated with fanciful notions of reconstructing genetic pathways of morphogenesis while evolutionary biologists were sobered by the fallacy of reconstructing organismal relationships along increasing grades of morphological complexity. Increased taxon sampling and improvements in analytical techniques are providing a new approach and are forcing biologists to move past historical biases to allow more accurate mapping of morphological and developmental characters through evolutionary time. Here, we discuss the possible developmental and morphological features of the ‘urbilaterian’, the triploblastic animal with anterior-posterior and dorsoventral axes and predecessor of the protostome–deuterostome ancestor. We argue that this animal, with features resembling acoelomorph flatworms, was far simpler morphologically than the protostome–deuterostome ancestor despite possessing a nearly complete eubilaterian genome. We show that the deployment of some genes expected to pattern the protostome–deuterostome ancestor is not deployed in acoels in the predicted manner and thus might have been co-opted after the evolution of the urbilaterian. We also identify the developmental changes related to gastrulation that gave rise to the urbilaterian from a simpler cnidarian-like ancestor.
An Evidence-Based Approach to Nurses Week Celebrations

It is time to examine nurses week investments. With expenses increasingly scrutinized, healthcare leaders require data-driven decisions. Managing by instinct and intuition is both inadequate and reckless. This survey of 727 registered nurses identifies celebratory options for nurses week that nurses find meaningful. Knowing what registered nurses value will guide approaches to an effective nurses week activity planning.