Miracle-dz/UniFAR-FTUs huggingface dataset:
Colocalization of a CD1d-Binding Glycolipid with a Radiation-Attenuated Sporozoite Vaccine in Lymph Node–Resident Dendritic Cells for a Robust Adjuvant Effect

A CD1d-binding glycolipid, α-Galactosylceramide (αGalCer), activates invariant NK T cells and acts as an adjuvant. We previously identified a fluorinated phenyl ring-modified αGalCer analog, 7DW8-5, displaying nearly 100-fold stronger CD1d binding affinity. In the current study, 7DW8-5 was found to exert a more potent adjuvant effect than αGalCer for a vaccine based on radiation-attenuated sporozoites of a rodent malaria parasite, Plasmodium yoelii, also referred to as irradiated P. yoelii sporozoites (IrPySpz). 7DW8-5 had a superb adjuvant effect only when the glycolipid and IrPySpz were conjointly administered i.m. Therefore, we evaluated the effect of distinctly different biodistribution patterns of αGalCer and 7DW8-5 on their respective adjuvant activities. Although both glycolipids induce a similar cytokine response in sera of mice injected i.v. , after i.m. injection, αGalCer induces a systemic cytokine response, whereas 7DW8-5 is locally trapped by CD1d expressed by dendritic cells (DCs) in draining lymph nodes (dLNs). Moreover, the i.m. coadministration of 7DW8-5 with IrPySpz results in the recruitment of DCs to dLNs and the activation and maturation of DCs. These events cause the potent adjuvant effect of 7DW8-5, resulting in the enhancement of the CD8+ T cell response induced by IrPySpz and, ultimately, improved protection against malaria. Our study is the first to show that the colocalization of a CD1d-binding invariant NK T cell–stimulatory glycolipid and a vaccine, like radiation-attenuated sporozoites, in dLN-resident DCs upon i.m. conjoint administration governs the potency of the adjuvant effect of the glycolipid.
3D Imaging of Greenhouse Plants with an Inexpensive Binocular Stereo Vision System

Nowadays, 3D imaging of plants not only contributes to monitoring and managing plant growth, but is also becoming an essential part of high-throughput plant phenotyping. In this paper, an inexpensive (less than 70 USD) and portable platform with binocular stereo vision is established, which can be controlled by a laptop. In the stereo matching step, an efficient cost calculating measure—AD-Census—is integrated with the adaptive support-weight (ASW) approach to improve the ASW’s performance on real plant images. In the quantitative assessment, our stereo algorithm reaches an average error rate of 6.63% on the Middlebury datasets, which is lower than the error rates of the original ASW approach and several other popular algorithms. The imaging experiments using the proposed stereo system are carried out in three different environments including an indoor lab, an open field with grass, and a multi-span glass greenhouse. Six types of greenhouse plants are used in experiments; half of them are ornamentals and the others are greenhouse crops. The imaging accuracy of the proposed method at different baseline settings is investigated, and the results show that the optimal length of the baseline (distance between the two cameras of the stereo system) is around 80 mm for reaching a good trade-off between the depth accuracy and the mismatch rate for a plant that is placed within 1 m of the cameras. Error analysis from both theoretical and experimental sides show that for an object that is approximately 800 mm away from the stereo platform, the measured depth error of a single point is no higher than 5 mm, which is tolerable considering the dimensions of greenhouse plants. By applying disparity refinement, the proposed methodology generates dense and accurate point clouds of crops in different environments including an indoor lab, an outdoor field, and a greenhouse. Our approach also shows invariance against changing illumination in a real greenhouse, as well as the capability of recovering 3D surfaces of highlighted leaf regions. The method not only works on a binocular stereo system, but is also potentially applicable to a SFM-MVS (structure-from-motion and multiple-view stereo) system or any multi-view imaging system that uses stereo matching.
A frequency-based gene selection method to identify robust biomarkers for radiation dose prediction

Purpose: A fast, radiation-specific and highly accurate prediction of the radiation dose of accidentally exposed individuals is essential for medical decision-making. The aim of the present study is to identify small gene signatures allowing the discrimination between low and medium dose exposure of low linear energy transfer (LET)-radiation. Material and methods: We developed a framework for dose prediction using a frequency-based gene selection approach, based on a p-value and fold-change criterion applied to microarray expression data. A repeated cross-validated classification guarantees unbiased performance results. Human blood from six healthy donors was irradiated ex vivo with 0.5, 1, 2 and 4 Gy (Cs-137 γ-rays). Expression levels of isolated blood lymphocytes were measured at 6, 24 and 48 h after irradiation. Results: We identified radiation-responsive genes, most of them functionally linked to apoptosis, DNA-damage or cell-cycle regulation. We extracted small subsets of genes, with which 95.7% of all samples can be correctly predicted, regardless of the time post irradiation. Seven of these genes were used for validation by Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). Conclusion: The genes identified are potential robust biomarkers, which are particularly suitable for dose level discrimination at a window of time that would be appropriate for life-saving medical triage.
A vision based online motion planning of robot manipulators

This article presents a vision based online system for the robust trajectory planning of robot manipulators. It uses a 3D vision system to determine the relative position of the objects to be engaged and the obstacle to avoid, and a novel obstacle avoidance procedure for manipulator motion planning. From intensity images acquired by a CCD camera mounted on the robot arm, the salient features are first accurately and robustly detected and then grouped. Through the correspondences between the feature groupings and the model features, the 3D poses of the objects and the obstacles are determined and confirmed by back-projection. Once these poses are determined, an online procedure, based on redundancy resolution, is used to achieve obstacle avoidance. The approach utilizes a null space vector to set properly the robot configuration, and a potential field method to guide the end-effector. By pseudoinverse perturbation it also prevents singular configurations and local minima. The feasibility and effectiveness of the system is demonstrated by an experiment with online engagement and transportation of objects posed inside an aluminium frame.
Molecular characterization of tropical sweet corn inbred lines using microsatellite markers

Genetic variability among 13 tropical sweet corn inbred lines derived from source populations originating from five tropical countries was investigated using 95 polymorphic microsatellite markers. It was found that 92.9% of total molecular variance was due to variations among the inbred lines. This was further supported by the presence of high values of DST, FST, GST and FIT, indicating high genetic variation among the inbred lines. The average number of alleles and effective number of alleles were both close to one allele per locus per inbred line. Departure from Hardy-Weinberg equilibrium was observed with a drastic reduction of the observed heterozygosity, resulting in a lower index of genotypic diversity than expected for each of the inbred lines. The inbred lines were further assigned into six main heterotic groups based on their molecular characteristics using Fitch-Margoliash algorithm. High genetic variations among the inbred lines indicates the presence of different heterotic groups, while low level of genetic variability within the inbred lines indicates that they met the assumption of homozygosity of their loci to enable further diallel crosses to be made for analysis of their combining ability. It is therefore expected that high heterosis in yield and its components could be obtained from crosses among those inbred lines belonging to different heterotic groups.
Proteinase activity in Ascaris suum eggs, hatching fluid, and excretions-secretions.

Hatching fluid and the excretions and secretions (E.S.) of hatched larvae of Ascaris suum revealed proteinase activity when assayed by 2 different procedures employing collagen or casein as substrates. Both assays apparently detected similar levels of proteinase activity in hatching fluid and E.S. of hatched larvae. The Anson (casein substrate) assay worked best in 0.05 M phosphate buffer, pH 8.0. The Azocoll (collagen substrate) assay worked best in 0.05 M borate buffer at pH 8.8. Azocoll assays done at temperatures ranging from 25 to 65 C revealed maximal proteinase activity at 55 C. Analysis of hatching fluid from 18-, 21-, and 28-day-old embryos and of extracts from sonicated 0- to 28-day-old developmental stages showed that proteinase activity increased markedly 18 days after embryonation had begun. Prior to the 18th day of embryonation proteinase levels were relatively low.
Risk-limiting Audits and the Margin of Victory in Nonplurality Elections

Abstract Post-election audits are an important method for verifying the outcome of an election. Recent work on risk-limiting, post-election audits has focused almost exclusively on plurality elections. Several organization and municipalities use nonplurality methods such as range voting, the Borda count, and instant-runoff voting (IRV). We believe that it is crucial to develop effective methods of performing risk-limiting, post-election audits for these methods. We define a general notion of the margin of victory and develop risk-limiting auditing procedures for these nonplurality methods. For scored systems, we show how to adapt methods from plurality auditing. For IRV, the situation is markedly different. We provide a risk-limiting method for auditing the candidate elimination order. We provide a more efficient audit for the elections in which the margin of the IRV election can be efficiently calculated or bounded. We provide efficiently computable upper and lower bounds on the margin and, where possible, compare them to the exact margins for a large number of real elections.
Bullying and Internalizing Problems

Bullying is a widespread problem facing American adolescents. A better understanding of factors that may moderate the impact of bullying is important given its negative consequences for well-being. This study examines the association between bullying experiences and internalizing problems among a nationally representative sample of young adolescents. Additionally, we consider the ease of parental communication as a potential moderating factor in these associations. Using a structural equation modeling technique, results suggest that bullying is characteristically different for adolescent boys and girls and that its association with internalizing problems is stronger for adolescent females. Results also indicate that parental communication moderates the association between bullying and internalizing problems; higher levels of parental communication buffer adolescents against the negative influence of bullying.
Longitudinal Analysis of Airways using Registration

Longitudinal investigations of airway abnormalities associated with Chronic Obstructive Pulmonary Disease (COPD) has been very limited so far, partly due to the difficulties in obtaining reproducible measures. We propose to improve on this by limiting measurements to corresponding branches found using image registration. The results obtained from scans of 237 subjects show increased intrasubject correlation when measurements are conducted in branches found in each scan compared to similar measurements not limited to corresponding branches. This indicates the method could be useful for longitudinal analysis. Yearly changes in CT measures showed that airways increase in size and decrease in density with time. Changes were in general not found to be significantly correlated with changes in lung function and neither were there any significant differences between COPD GOLD stages.
Gender‐based issues in interventional cardiology: A consensus statement from the Women in Innovations (WIN) Initiative

Cardiovascular disease (CVD) is the leading cause of mortality in women, yet studies have suggested that it is often under‐recognized. Of particular concern is the apparent suboptimal treatment of women in comparison to men, with less revascularization and use of evidence‐based medications. The Women in Innovations group of cardiologists aims to highlight these issues and change perceptions to optimize the treatment of female patients with CVD, to support future research, and to encourage and guide the training of female interventional cardiologists. © 2010 Wiley‐Liss, Inc.
Intra- and interspecific facilitation in mangroves may increase resilience to climate change threats

Mangroves are intertidal ecosystems that are particularly vulnerable to climate change. At the low tidal limits of their range, they face swamping by rising sea levels; at the high tidal limits, they face increasing stress from desiccation and high salinity. Facilitation theory may help guide mangrove management and restoration in the face of these threats by suggesting how and when positive intra- and interspecific effects may occur: such effects are predicted in stressed environments such as the intertidal, but have yet to be shown among mangroves. Here, we report the results of a series of experiments at low and high tidal sites examining the effects of mangrove density and species mix on seedling survival and recruitment, and on the ability of mangroves to trap sediment and cause surface elevation change. Increasing density significantly increased the survival of seedlings of two different species at both high and low tidal sites, and enhanced sediment accretion and elevation at the low tidal site. Including Avicennia marina in species mixes enhanced total biomass at a degraded high tidal site. Increasing biomass led to changed microenvironments that allowed the recruitment and survival of different mangrove species, particularly Ceriops tagal.
Mass Spectrometric Detection of Carcinogen Adducts

Genotoxic carcinogens interact with nucleic acids and proteins to yield covalently bound products (adducts), the quantitative determination of which has been proposed as a biomonitor of human exposure to carcinogens. Mass spectrometry is playing a leading role both in the structural characterisation and in the quantitative determination of these carcinogen adducts. In particular electrospray ionisation and matrix assisted laser desorption ionisation are being increasingly used in nucleotide and protein adduct detection and in sequencing of carcinogen-modiÐed oligonucleotides and peptides. Quantitative determination of carcinogen-modiÐed nucleic acid bases and protein amino acids is generally carried out by GC/MS or GC/MS/MS, the highest sensitivity being achieved using negative ion chemical ionisation. These techniques are now being applied to samples from humans exposed to carcinogens from environmental, medicinal and occupational sources.
Modeling and simulation of fault detection methods for power electronic interfaced microgrids

Conventional protection schemes are unable to detect low fault current levels common in microgrids. A number of methods have been proposed in various research papers. Some of the recently proposed methods are the total harmonic distortion detection method, addition of a current source, abc-dq0 transformation method and the voltage constraint overcurrent method. Analysis of these methods is conducted in this paper and simulations run using Matlab Simulink.
Analysis of silica in bulk materials response.

Advance Access publication 21 May 2014 may be very difficult to go much <1%, even with the additional use of the Rietveld refinement in X-ray diffraction (LOQ = 0.76%). We are unaware of any method that has been published for the determination of crystalline silica in bulk materials that can measure down to 0.1%. If the laboratory used by Radnoff and Kutz has been able to modify NIOSH 7500 to achieve this goal, we would welcome publication of the details of the modification and methods validation as this would be of value to the occupational health community.
The antibody response to Dracunculus medinensis in an endemic human population of northern Ghana

Abstract The serum antibody response (total, and isotypes IgG1, IgG4, IgM, IgA and IgE) to Guinea worm infection was examined in humans from a highly endemic area of northern Ghana by ELISA and SDSPAGE/Western blot techniques using an adult D. medinensis antigen. Sera were obtained early and late in the peak transmission period, from persons with patent and postpatent infections, as well as from persons from the same endemic area who claimed never to have had Guinea worm infection. To observe for potential cross-reactions in the tests, sera were also obtained from areas with no transmission of Guinea worm from patients with hookworm. O. volvulus and W. bancrofti infections, and from non-infected controls. Sera from persons living in the Guinea worm endemic area reacted extensively with Guinea worm antigen in both tests, and large numbers of bands were produced in the Western blots (up to 35 identified for some sera). For most antibody isotypes, the ELISA absorbance values obtained with sera from the same individuals varied between the two transmission seasons, with the highest titres present towards the end of the peak transmission period. The mean antibody titres for persons in the patent and postpatent infection categories were not significantly different when sera were obtained at the same season of the year. Persons from the endemic area, who claimed never to experience patent infections, also had antibodies to Guinea worm, although at significantly lower mean levels than for the patent and postpatent categories. The highest specificity in the ELISA and the most homogenous Western blots were obtained when detecting for antibodies of the IgG4 isotype.
Monocytic leukemia cutis diagnosed simultaneously with refractory anemia with monocytosis: A case report

A case of leukemia cutis (LC) of monocytic lineage in a patient with myelodysplastic syndrome (MDS) is presented. Cutaneous infiltrates were recognized concurrent with diagnosis of refractory anemia (RA) with monocytosis. Skin infiltrates subsequently spontaneously regressed although MDS progressed with increasing monocytosis, anemia, and thrombocytopenia. Death occurred 6 months after diagnosis with evolution of acute monoblastic leukemia complicated by sepsis. This case supports previous observations of poor prognosis associated with leukemia cutis. LC associated with MDS is reviewed including the role of monocytes. Am. J. Hematol. 66:120–122, 2001. © 2001 Wiley‐Liss, Inc.
The human papillomavirus type 16 E7 protein complements adenovirus type 5 E1A amino-terminus-dependent transactivation of adenovirus type 5 early genes and increases ATF and Oct-1 DNA binding activity

We have previously shown that conserved region 1 (CR1) of the adenovirus type 5 (Ad5) E1A protein synergizes with CR3 in the transactivation of Ad5 early genes (H.K. Wong and E. B. Ziff, J. Virol. 68:4910-4920, 1994). CR1 lies within the E1A amino terminus and binds host regulatory proteins such as the RB protein, p107, p130, and p300. Since simian virus 40 (SV40) large T antigen and human papillomavirus type 16 (HPV16) E7 protein also bind host regulatory factors, we investigated whether these viral proteins can complement E1A mutants which are defective in early gene activation. We show that the HPV16 E7 protein but not SV40 T antigen can complement mutations in the Ad5 E1A CR1 in the transactivation of viral early promoters. The inability of SV40 T antigen to complement suggests that RB binding on its own is not sufficient for early promoter transactivation by the E1A amino terminus. Nuclear runoff assays show that complementation by HPV16 E7 restores the ability of the E1A mutants to stimulate early gene expression at the level of transcription. Furthermore, nuclear extracts from the E7-transformed cells show increased binding activity of ATF and Oct-1, factors that can recognize the elements of Ad5 early genes, consistent with gene activation by E1A and E7 at the transcriptional level.
Electrospray ionization mass spectrometry: How it all began.

Malcolm Dole’s now famous paper that led to electrospray ionization was published in 1968.1 That was the year after I had left the faculty of mechanical engineering at Princeton to join the faculty of chemical engineering at Yale where I continued my ten-year affair with big leaks in vacuum systems. Those leaks had turned out to be very powerful and versatile research tools because they could produce molecular beams with much higher energies and intensities than could the effusive sources with which Otto Stern and his disciples had earned half a dozen Nobel prizes in physics. Moreover, the supersonic free jets issuing from these leaks introduced their component gases to nonequilibrium steady states having combinations of temperature and density not previously dreamt of, let alone encountered. Those supersonic free jets subsequently ushered in the era of electrospray ionization (ESI) in mass spectrometry (MS) and are thus responsible for my being here today. (Jets also powered my transport on this trip to Austin but those jets were neither supersonic nor free! ) When I was told that I would have the honor of receiving the 2002 award from the ABRF, I realized that once again I was following in the footsteps of Csaba Horvath who received this award in 2001. Csaba had also preceded me by a year or two in becoming a chemical engineer at Yale. That sequence, together with subsequent events, lends credence to the notion that the loom of Fate might be weaving some preordained pattern! When I arrived at New Haven in 1967 Csaba was spending half his time in the medical school, working with Professor Seymour “Sandy” Lipsky on HPLC, then known as “high pressure liquid chromatography. ” The success of their efforts changed the meaning of “P” from pressure to performance, an achievement honored by Csaba’s receiving this ABRF award last year. The subject of this year’s award—electrospray ionization—has become a hyphen of choice in the practice of LC-MS. Because detection follows separation in that practice, it seems entirely appropriate, and consistent with classic Presbyterian Predestination, that today’s award for an LC detection method should follow last year’s award for LC separation itself! Moreover, the notion of an intervention by Fate is given still more credence by the fact that, unbeknownst to the Award Committee, REVIEWS Journal of Biomolecular Techniques 13:101–118 © 2002 ABRF