Miracle-dz/UniFAR-FTUs huggingface dataset:
Heligmosomoides polygyrus Elicits a Dominant Nonprotective Antibody Response Directed against Restricted Glycan and Peptide Epitopes

Heligmosomoides polygyrus is a widely used gastrointestinal helminth model of long-term chronic infection in mice, which has not been well-characterized at the antigenic level. We now identify the major targets of the murine primary Ab response as a subset of the secreted products in H. polygyrus excretory–secretory (HES) Ag. An immunodominant epitope is an O-linked glycan (named glycan A) carried on three highly expressed HES glycoproteins (venom allergen Ancylostoma-secreted protein-like [VAL]-1, -2, and -5), which stimulates only IgM Abs, is exposed on the adult worm surface, and is poorly represented in somatic parasite extracts. A second carbohydrate epitope (glycan B), present on both a non-protein high molecular mass component and a 65-kDa molecule, is widely distributed in adult somatic tissues. Whereas the high molecular mass component and 65-kDa molecules bear phosphorylcholine, the glycan B epitope itself is not phosphorylcholine. Class-switched IgG1 Abs are found to glycan B, but the dominant primary IgG1 response is to the polypeptides of VAL proteins, including also VAL-3 and VAL-4. Secondary Ab responses include the same specificities while also recognizing VAL-7. Although vaccination with HES conferred complete protection against challenge H. polygyrus infection, mAbs raised against each of the glycan epitopes and against VAL-1, VAL-2, and VAL-4 proteins were unable to do so, even though these specificities (with the exception of VAL-2) are also secreted by tissue-phase L4 larvae. The primary immune response in susceptible mice is, therefore, dominated by nonprotective Abs against a small subset of antigenic epitopes, raising the possibility that these act as decoy specificities that generate ineffective humoral immunity.
Two-stage base station sleeping scheme for green cellular networks

In this paper, we propose a two-stage base station (BS) sleeping scheme to save energy consumption in cellular networks. The BS sleeping mode is divided into a light sleeping stage and a deep sleeping stage according to whether there is a user in the BS's coverage. In the light sleeping stage, a BS will retain its coverage and frequently switch between the on state and the doze state according to the service characteristics. While in the deep sleeping stage analysis, the BS will shut down its coverage, and neighbor BSs will patch the coverage hole. Several closed-form formulas are derived to demonstrate the power consumption in each sleeping stage and the stage switching conditions are discussed to minimize the average power consumption. The average traffic delay caused by BS sleeping and the average deep sleeping rate under a given traffic load have also been studied. In addition, it is shown that BS sleeping is not always possible because of the limited quality of service (QoS) requirements. Simulation results show that the proposed scheme can effectively reduce the average BS power consumption, at the cost of some extra traffic delay. In summary, our proposed framework provides an essential understanding of the design of future green networks that aim to take full advantage of different stages of BS sleeping to obtain the best energy efficiency.
Effect of irradiation on DNA synthesis, NBN gene expression and chromosomal stability in cells with NBN mutations

Introduction The NBN gene product is part of the MRE11/RAD50/NBN complex, which plays an essential role in genomic stability. In the study we try to answer the question what is the effect of irradiation on DNA synthesis, NBN gene expression and chromosomal stability in cells with homozygous c.657-661del, and heterozygous c.657-661del, p.I171V and p.R215W NBN gene mutations. Material and methods Immortalized B-lymphocytes with NBN gene mutations were X-ray irradiated at doses of 1, 2, 5 and 8 Gy/min. Radioresistant DNA synthesis rate and the percentage of cells in phase S was analyzed by 3H thymidine and BrdU incorporation assays. NBN gene expression was quantified by real-time PCR with TaqMan fluorescent probe. Results Increasing the irradiation dose resulted in gradual decrease of 3H thymidine incorporation in all cells, but significantly only in homo- and heterozygous c.657-661del cells (p-values < 0.0001). After irradiation the relative expression of NBN was significantly higher in homozygous c.657-661del and heterozygous p.R215W cells as compared to heterozygous c.657-661del, p.I171V and control cells (p < 0.01). All cells with NBN gene mutations showed significantly higher total number of chromosomal aberrations per metaphase as compared to control cells, with the highest number of aberrations in homozygous c.657-661del cells (p < 0.001). Conclusions The results obtained indicate that homozygous c.657-661del mutation affects cell sensitivity to irradiation. Moreover, homozygous variant is associated with disturbance in the activation of cell cycle checkpoints and with defects in DNA repair. In turn, heterozygous c.657-661del, p.R215W and p.I171V mutations do not substantially alter the radiosensitivity.
A Research on the Sequential Pattern Similarity of Time Series

In general, the distance measuring method could only measure the pattern similarities of the time series with the same length. Through introducing the concept of dynamic time warping distance, this work proposed a way to define the dynamic time warping distance of the sequential patterns and finally carry out simulation experiments based on the defining the similarities of meta patterns.
Embedded Multilayer Thin Film Stacks as Polarizing Beam Splitters and Wave Retarders Operating under Condition of Frustrated Total Internal Reflection

The polarization properties of embedded centro-symmetric and periodic multilayer stacks under conditions of frustrated total internal reflection (FTIR) are considered. The centrosymmetric multilayer stack consists of a high-index center layer sandwiched between two identical low-index films and high-index – low-index bilayers repeated on both sides of the central trilayer maintaining the symmetry of the entire stack. The periodic multilayer consists of periodically repeated low-index – high-index bilayers. Each multilayer stack is embedded in a high-index prism. Embedded centro-symmetric multilayer stacks are designed to function as efficient polarizers or polarizing beam splitters (PBSs) under conditions of FTIR over an extended range of incidence angles. For a given set of refractive indices, all possible solutions for the thicknesses of the layers that suppress the reflection of p-polarized light at a specified angle, and the associated reflectance of the system for the orthogonal s polarization, are determined. The angular and spectral sensitivities of polarizing multilayer stacks employing 3, 7, 11, 15 and 19 layers of BaF2 and PbTe thin films embedded in a ZnS prism, operating at λ = 10.6 μm, are presented. Embedded centro-symmetric multilayer stacks are also designed to function as completetransmission quarter-wave or half-wave retardation (QWR or HWR) devices under conditions of FTIR. QWR and HWR designs at λ =1.55 m μ are presented that employ 11 and 7 layers of Si and SiO2 thin films embedded in GaP and Si cube prisms, respectively. The angular and spectral sensitivities of these devices are also considered. Embedded centro-symmetric multilayer stacks under FTIR conditions are also designed to produce various 50%-50% beam splitters.
Pregnancy diagnosis in cattle

DETECTION of the non-pregnant cow or heifer, as soon as possible after an unsuccessful insemination, is important to ensure good reproductive performance in dairy and beef herds. Pregnancy diagnosis is still the most common procedure carried out during routine visits conducted as part of a fertility control programme. In herds that are not part of such a scheme, pregnancy diagnosis is often one of the few routine procedures performed by veterinary surgeons. This article describes the relative advantages, disadvantages and reliability of the various methods used to detect pregnancy in cattle.
Delay Minimization in Vertical Handoff algorithm in 4 G network with reduced call drop rate Miss

Fourth generation of wireless network is expected to include heterogeneous wireless network that uses a common IP network that uses a diverse range of high data rate multimedia service to end users . So 4G is the wireless networks is envisioned as a convergence of different wireless access technologies providing the user with the best connection anywhere, anytime and improving the system resource utilization. Vertical handover is a network that automatically changes its connection type by using to accessing a supporting infrastructure. When a computing device could be connect to a Internet into two different network technologies, it is automatically connected to the available network. Vertical handoff can be used by various parameters like RSS, bandwidth, data rate, cost etc. The proposed algorithm shows the cross-layer notifications regarding the changes in the access link characteristics. In this paper we propose an enhancement to the TCP sender algorithm to combat packet reordering that may be occur due to a vertical handoff from a slow to a fast access link.
Tailoring Wideband Signals With a Photonic Hardware Accelerator

Digital hardware accelerators are increasingly employed to speed up computation and reduce power dissipation, enabling real-time operation. Inspired by this paradigm, we propose the concept of the photonic hardware accelerator-an analog optical processing engine that precedes optical-to-electrical conversion and alleviates the burden on subsequent electronics. We propose one specific class of photonic hardware accelerators designed to assist in acquisition, feature extraction, and storage of wideband waveforms. This fundamental unit reshapes, in real time, the spectrotemporal evolution of a wideband streaming signal based on signal's sparsity. Functioning as an information gearbox, the accelerator transforms the signal according to the nonuniform entropy of its spectrum. Nonlinear group delay dispersion modes are introduced as primitive building blocks for such transformations. Representing spectrotemporal basis functions, these modes and their corresponding time-stretch wavelets have distinct and useful properties that depend on their symmetry. We focus on polynomial basis functions, but also discuss their limitations and alternatives such as spline functions that offer more efficient representation of group delay spectra with localized features. They are used to synthesize complex warped spectrotemporal operations that are reconfigurable and can be implemented in both analog optical and digital (computational) domains. We show how these dispersion-based computational primitives reshape the wideband signal to enable nonuniform sampling, compression, and pattern recognition in real time. Additional applications including coding, signal classification, and enhancement of signal-to-noise ratio during ultrafast analog-to-digital conversion are discussed.
End-to-End Evaluation of Multimodal Dialogue Systems – can we Transfer Established Methods?

The goal of this paper is to define a methodology for the end-to-end evaluation of the multimodal dialogue system SmartKom along the lines of the DARPA guidelines for spoken dialogue systems. The methodology consists of an extended framework for the evaluation of a multimodal dialogue system, evaluation metrics for its various components, and an approach to compare the user satisfaction with the system’s technical performance.
A viral activator of gene expression functions via the ubiquitin–proteasome pathway

The ability of herpes simplex virus type 1 (HSV‐1) to attain a latent state in sensory neurones and reactivate periodically is crucial for its biological and clinical properties. The active transcription of the entire 152 kb viral genome during lytic replication contrasts with the latent state, which is characterized by the production of a single set of nuclear‐retained transcripts. Reactivation of latent genomes to re‐initiate the lytic cycle therefore involves a profound change in viral transcriptional activity, but the mechanisms by which this fundamentally important process occurs are yet to be well understood. In this report we show that the stimulation of the onset of viral lytic infection mediated by the viral immediate‐early (IE) protein Vmw110 is strikingly inhibited by inactivation of the ubiquitin–proteasome pathway. Similarly, the Vmw110‐dependent reactivation of quiescent viral genomes in cultured cells is also dependent on proteasome activity. These results constitute the first demonstration that the transcriptional activity of a viral genome can be regulated by protein stability control pathways.
Why the Prone Position Is a Risk Factor for Sudden Infant Death Syndrome

Introduction. The laryngeal chemoreflex may explain why prone sleeping increases the risk of sudden infant death syndrome (SIDS). Swallowing and arousal are crucial to prevent laryngeal chemoreflex stimulation. Our aim was to examine these reflexes and breathing responses in healthy neonates after pharyngeal infusion of water in the supine versus the prone position, controlling for sleep state. Methods. A total of 10 term infants were recruited after parental consent and ethics approval. Polygraphic recordings included sleep state (active and quiet sleep by electroencephalogram, eye movements, breathing, and behavior), cardiorespiratory measurements (nasal airflow, chest wall movements, heart rate, and oxygen saturation), swallowing, and esophageal activity (solid state pressure catheter). Initial sleeping position was assigned randomly. Measurements were made for 1 minute before and after 0.4 mL of water was instilled into the oropharynx. To detect a 30% decrease in swallowing, power analysis indicated that ≥10 babies were required. Analysis, blinded to position, was made using nonparametric statistics. Results. Of the 164 infusions, the most commonly evoked airway protective responses to pharyngeal infusion were swallowing (95%) and arousal (54%). After infusion in active sleep, there was a significant reduction in swallowing and breathing when the prone position was compared with the supine position (prone: 21.3 [1.0] swallows/min and −9.6 [2.1] breaths/min; and supine: 32 (2.2) and −2.9 (1.5), respectively). However, there was no difference in the occurrence of arousal after water infusion. Conclusion. These data suggest that airway protection is compromised in the prone sleeping position during active sleep, even in healthy infants exposed to minute pharyngeal fluid volumes of 0.4 mL. This is because swallowing rate is reduced significantly, and there is no compensatory increase in arousal. The reduction in airway protective reflexes when in the prone position and in active sleep may be the mechanism for the increased risk of SIDS in the prone position.
Longitudinal Noninvasive Imaging of Progesterone Receptor as a Predictive Biomarker of Tumor Responsiveness to Estrogen Deprivation Therapy

Purpose: To investigate whether longitudinal functional PET imaging of mammary tumors using the radiopharmaceuticals [18F]FDG (to measure glucose uptake), [18F]FES [to measure estrogen receptor (ER) levels], or [18F]FFNP [to measure progesterone receptor (PgR) levels] is predictive of response to estrogen-deprivation therapy. Experimental Design: [18F]FDG, [18F]FES, and [18F]FFNP uptake in endocrine-sensitive and -resistant mammary tumors was quantified serially by PET before ovariectomy or estrogen withdrawal in mice, and on days 3 and 4 after estrogen-deprivation therapy. Specificity of [18F]FFNP uptake in ERα+ mammary tumors was determined by competition assay using unlabeled ligands for PgR or glucocorticoid receptor (GR). PgR expression was also assayed by immunohistochemistry (IHC). Results: The levels of [18F]FES and [18F]FDG tumor uptake remained unchanged in endocrine-sensitive tumors after estrogen-deprivation therapy compared with those at pretreatment. In contrast, estrogen-deprivation therapy led to a reduction in PgR expression and [18F]FFNP uptake in endocrine-sensitive tumors, but not in endocrine-resistant tumors, as early as 3 days after treatment; the changes in PgR levels were confirmed by IHC. Unlabeled PgR ligand R5020 but not GR ligand dexamethasone blocked [18F]FFNP tumor uptake, indicating that [18F]FFNP bound specifically to PgR. Therefore, a reduction in FFNP tumor to muscle ratio in mammary tumors predicts sensitivity to estrogen-deprivation therapy. Conclusions: Monitoring the acute changes in ERα activity by measuring [18F]FFNP uptake in mammary tumors predicts tumor response to estrogen-deprivation therapy. Longitudinal noninvasive PET imaging using [18F]FFNP is a robust and effective approach to predict tumor responsiveness to endocrine treatment. Clin Cancer Res; 21(5); 1063–70. ©2014 AACR.
A mobile trusted path system based on social network data

Social networks provide rich data sources for analyzing people journeys in urban environments. This paper introduces a trusted path system that helps users to find their routes based in two criteria: low crime rate and no theft report. These data are obtained from two complementary sources: geo-tagged tweets from the social network Twitter, and an official database given by the Police of Mexico City. Recommended paths are computed automatically from these data sources by a complementary application of social mining techniques, Bayes algorithm and an adaptation of the Dijkstra algorithm. This system can be also used to identify the probability that an event occurs in specific locations and times. A proof of concept of the system is illustrated through two example scenarios.
Depth-Dependent Survival of Escherichia coli and Enterococci in Soil after Manure Application and Simulated Rainfall

ABSTRACT Once released, manure-borne bacteria can enter runoff via interaction with the thin mixing layer near the soil surface. The objectives of this work were to document temporal changes in profile distributions of manure-borne Escherichia coli and enterococci in the near-surface soil layers after simulated rainfalls and to examine differences in survival of the two fecal indicator bacteria. Rainfall simulations were performed in triplicate on soil-filled boxes with grass cover and solid manure application for 1 h with rainfall depths of 30, 60, and 90 mm. Soil samples were collected weekly from depth ranges of 0 to 1, 1 to 2, 2 to 5, and 5 to 10 cm for 1 month. Rainfall intensity was found to have a significant impact on the initial concentrations of fecal indicator bacteria in the soil. While total numbers of enterococci rapidly declined over time, E. coli populations experienced initial growth with concentration increases of 4, 10, and 25 times the initial levels at rainfall treatment depths of 30, 60, and 90 mm, respectively. E. coli populations grew to the approximately the same level in all treatments. The 0- to 1-cm layer contained more indicator bacteria than the layers beneath it, and survival of indicator bacteria was better in this layer, with decimation times between 12 and 18 days after the first week of growth. The proportion of bacteria in the 0- to 1-cm layer grew with time as the total number of bacteria in the 0- to 10-cm layer declined. The results of this work indicate the need to revisit the bacterial survival patterns that are assumed in water quality models.
Mechanics of Electrodes in Lithium-ion Batteries

This thesis investigates the mechanical behavior of electrodes in Li-ion batteries. Each electrode in a Li-ion battery consists of host atoms and guest atoms (Li atoms). The host atoms form a framework, into which Li atoms are inserted via chemical reactions. During charge and discharge, the amount of Li in the electrode varies substantially, and the host framework deforms. The deformation induces in an electrode a field of stress, which may lead to fracture or morphological change. Such mechanical degradation over lithiation cycles can cause the capacity to fade substantially in a commercial battery. We study fracture of elastic electrodes caused by fast charging using a combination of diffusion kinetics and fracture mechanics. A theory is outlined to investigate how material properties, electrode particle size, and charging rate affect fracture of electrodes in Li-ion batteries. We model an inelastic host of Li by considering diffusion, elastic-plastic deformation, and fracture. The model shows that fracture is averted for a small and soft host—an inelastic host of a small feature size and low yield strength. We present a model of concurrent reaction and plasticity during lithiation of crystalline silicon electrodes. It accounts for observed lithiated silicon of anisotropic
Polynomial Heuristic Algorithms for Inconsistency Characterization in Firewall Rule Sets

Firewalls provide the first line of defence of nearly all networked institutions today. However, Firewall ACLs could have inconsistencies, allowing traffic that should be denied or vice versa. In this paper, we analyze the inconsistency characterization problem as a separate problem of the diagnosis one, and propose formal definitions in order to characterize one-to- many inconsistencies. We identify the combinatorial part of the problem that generates exponential complexities in combined diagnosis and characterization algorithms proposed by other authors. Then we propose a decomposition of the combinatorial problem in several smaller combinatorial ones, which can effectively reduce the complexity of the problem. Finally, we propose an approximate heuristic and algorithms to solve the problem in worst case polynomial time. Although many algorithms have been proposed to address this problem, all of them are combinatorial. The presented algorithms are an heuristic way to solve the problem with polynomial complexity. There are no constraints on how rule field ranges are expressed.
Is socioeconomic status a predictor of mortality in nonagenarians? The vitality 90+ study.

BACKGROUND socioeconomic inequalities in mortality are well-known in middle-aged and younger old adults, but the situation of the oldest old is less clear. The aim of this study was to investigate socioeconomic inequalities for all-cause, cardiovascular and dementia mortality among the people aged 90 or older. METHODS the data source was a mailed survey in the Vitality 90+ study (n = 1,276) in 2010. The whole cohort of people 90 years or over irrespective of health status or dwelling place in a geographical area was invited to participate. The participation rate was 79%. Socioeconomic status was measured by occupation and education, and health status by functioning and comorbidity. All-cause and cause-specific mortality was followed for 3 years. The Cox regression, with hazard ratios (HR) and 95% confidence intervals (CI), was applied. RESULTS the all-cause and dementia mortality differed by occupational class. Upper non-manuals had lower all-cause mortality than lower non-manuals (HR: 1.61; 95% CI: 1.11-2.32), skilled manual workers (HR: 1.56 95% CI: 1.09-2.25), unskilled manual workers (HR: 1.88; 95% CI: 1.20-2.94), housewives (HR: 1.77 95% CI: 1.15-2.71) and those with unknown occupation (HR: 2.33; 95% CI: 1.41-3.85). Inequalities in all-cause mortality were largely explained by the differences in functioning. The situation was similar according to education, but inequalities were not statistically significant. Socioeconomic differences in cardiovascular mortality were not significant. CONCLUSIONS socioeconomic inequalities persist in mortality for 90+-year-olds, but their magnitude varies depending on the cause of death and the indicator of socioeconomic status. Mainly, mortality differences are explained by differences in functional status.