Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Analysis of Plasmodium falciparum Apical Membrane Antigen 1 Utilizing Interspecies Domains

ABSTRACT Plasmodium falciparum apical membrane antigen 1 (AMA1) is a leading malaria vaccine candidate whose function has not been unequivocally defined. Partial complementation of function can be achieved by exchanging the AMA1 of P. falciparum (PfAMA1) with that of P. chabaudi (PcAMA1). In this study, parasites expressing chimeric AMA1 proteins were created to identify domains of PfAMA1 critical in erythrocyte invasion and which are important immune targets. We report that specific chimeric AMA1 proteins containing domains I to III from PfAMA1 and PcAMA1 were able to complement PfAMA1 function in erythrocyte invasion. We demonstrate that domain III does not contain dominant epitope targets of antibodies raised against Escherichia coli expressed and refolded PfAMA1 ectodomain. Furthermore, we generated a parasite line in which the N-terminal pro region of PfAMA1 does not undergo proteolytic cleavage and show that its removal is necessary for PfAMA1 function.
Factors influencing quantitative isolation of varicella-zoster virus

Optimal conditions are described for the recovery of cell culture-derived varicella-zoster virus (VZV). Of the cells tested, human embryonic lung fibroblasts were the most sensitive. Storage and handling procedures were examined to determine the stability of VZV in viral transport medium. When the initial VZV titer was high (2 X 10(4) PFU/ml) 40% of the VZV survived room temperature for 24 h and 75% of the VZV remained viable for this long at 4 degrees C. Recovery was 5- to 10-fold less at lower initial VZV titers (less than 2 X 10(3) PFU/ml). Other factors which influenced VZV recovery included freezing at -20 degrees C, the use of cotton or calcium alginate swabs, and filtration to remove bacterial contaminants. The tissue culture methods described were used in a reconstruction experiment to demonstrate that VZV could be recovered from a laboratory coat or human skin (0.1 to 0.3% of input VZV) or from a stethoscope (19% of input VZV) as late as 30 min after inoculation. During a clinical trial using optimal VZV recovery procedures, 76% of the patients with herpes zoster yielded VZV when first cultured, and 60% remained culture positive for an additional 48 h.
Neural Network Bottleneck Features for Language Identification

This paper presents the application of Neural Network Bottleneck (BN) features in Language Identification (LID). BN f eatures are generally used for Large Vocabulary Speech Recognition in conjunction with conventional acoustic features, s uch as MFCC or PLP. We compare the BN features to several common types of acoustic features used in the state-of-the-art LID systems. The test set is from DARPA RATS (Robust Automatic Transcription of Speech) program, which seeks to advance state-of-the-art detection capabilities on audio from hig hly degraded radio communication channels. On this type of noisy data, we show that in average, the BN features provide a 45% relative improvement in the Cavgor Equal Error Rate (EER) metrics across several test duration conditions, with resp ect to our single best acoustic features. Index Terms: language identification, noisy speech, robust feature extraction
The impact of Massachusetts health care reform on access, quality, and costs of care for the already-insured.

OBJECTIVE To assess the impact of Massachusetts Health Reform (MHR) on access, quality, and costs of outpatient care for the already-insured. DATA SOURCES/STUDY SETTING Medicare data from before (2006) and after (2009) MHR implementation. STUDY DESIGN We performed a retrospective difference-in-differences analysis of quantity of outpatient visits, proportion of outpatient quality metrics met, and costs of care for Medicare patients with ≥ 1 chronic disease in 2006 versus 2009. We used the remaining states in New England as controls. DATA COLLECTION/EXTRACTION METHODS We used existing Medicare claims data provided by the Centers for Medicare and Medicaid Services. PRINCIPAL FINDINGS MHR was not associated with a decrease in outpatient visits per year compared to controls (9.4 prereform to 9.6 postreform in MA vs. 9.4-9.5 in controls, p = .32). Quality of care in MA improved more than controls for hemoglobin A1c monitoring, mammography, and influenza vaccination, and similarly to controls for diabetic eye examination, colon cancer screening, and pneumococcal vaccination. Average costs for patients in Massachusetts increased from $9,389 to $10,668, versus $8,375 to $9,114 in control states (p < .001). CONCLUSIONS MHR was not associated with worsening in access or quality of outpatient care for the already-insured, and it had modest effects on costs. This has implications for other states expanding insurance coverage under the Affordable Care Act.
Etude de la dynamique hydro-sédimentaire de fleuves tropicaux par mesures in situ et de télédétection : le cas du Maroni, de l'Oyapock et de l'Orénoque

L'eau des fleuves, des rivieres, des lacs et des reservoirs ne represente que 0,26 % des 2,5 % (35 millions de km3) d'eau douce disponibles a l’etat liquide sur Terre, or sa qualite et quantite ont fortement diminue ces dernieres annees. Sa degradation a des consequences sur l'agriculture, la sante, l'environnement et l'economie des territoires et est aujourd'hui au centre des preoccupations societales. Les objectifs de la presente these sont pour trois fleuves localises dans le Bouclier des Guyanes, au nord de l'Amerique du Sud (le Maroni, l'Oyapock, l'Orenoque): (i) d'utiliser et d'adapter des outils novateurs de teledetection pour suivre et quantifier, sur du long terme, leurs charges sedimentaires en suspension, (ii) d'evaluer l'existence de tendances spatio-temporelles, ainsi que de ruptures dans les chroniques de donnees, (iii) de quantifier la part organique et minerale de ces charges, (iv) d'apprecier le role des facteurs naturels (debits et precipitations) et anthropiques (surfaces urbaines, agricoles et minieres) sur les tendances observees et enfin, (v) de discuter de seuils de charges pour le suivi de la qualite de l'eau. Les resultats ont montre qu'il est possible de suivre les concentrations de matieres en suspension, pour les fleuves Orenoque et Maroni avec une erreur relative de 32 et 25% respectivement. Sur la periode 2000-2016, des tendances spatio-temporelles regulieres ont ete observees pour l'Orenoque, alors qu'elles sont en augmentation pour le Maroni avec une rupture en 2009 et en diminution pour l'Oyapock depuis 2008 (donnees in situ). Un lien fort avec l'augmentation de la deforestation pour les surfaces minieres et les precipitations est observe pour le Maroni alors que pour l'Oyapock les tendances sont liees aux debits.Pour les deux annees d'etudes (2014-2016), les charges minerales ont represente la plus forte fraction des particules transportees dans les eaux du Maroni au Saut Hermina (en moyenne 93 %) et de l'Oyapock au Saut Maripa (en moyenne 82 %) avec une grande variabilite selon les mois de la teneur en carbone dans les matieres transportees et pour les deux fleuves. Enfin, les rapports C/N et C/Chl-a ont devoile des matieres organiques d'origine principalement endogene avec une forte biomasse chlorophyllienne surtout durant les basses eaux.
Arteries of the insula.

OBJECT The insula is located at the base of the sylvian fissure and is a potential site for pathological processes such as tumors and vascular malformations. Knowledge of insular anatomy and vascularization is essential to perform accurate microsurgical procedures in this region. METHODS Arterial vascularization of the insula was studied in 20 human cadaver brains (40 hemispheres). The cerebral arteries were perfused with red latex to enhance their visibility, and they were dissected with the aid of an operating microscope. Arteries supplying the insula numbered an average of 96 (range 77-112). Their mean diameter measured 0.23 mm (range 0.1-0.8 mm), and the origin of each artery could be traced to the middle cerebral artery (MCA), predominantly the M2 segment. In 22 hemispheres (55%), one to six insular arteries arose from the M1 segment of the MCA and supplied the region of the limen insulae. In an additional 10 hemispheres (25%), one or two insular arteries arose from the M3 segment of the MCA and supplied the region of either the superior or inferior periinsular sulcus. The insular arteries primarily supply the insular cortex, extreme capsule, and, occasionally, the claustrum and external capsule, but not the putamen, globus pallidus, or internal capsule, which are vascularized by the lateral lenticulostriate arteries (LLAs). However, an average of 9.9 (range four-14) insular arteries in each hemisphere, mostly in the posterior insular region, were similar to perforating arteries and some of these supplied the corona radiata. Larger, more prominent insular arteries (insuloopercular arteries) were also observed (an average of 3.5 per hemisphere, range one-seven). These coursed across the surface of the insula and then looped laterally, extending branches to the medial surfaces of the opercula. CONCLUSIONS Complete comprehension of the intricate vascularization patterns associated with the insula, as well as proficiency in insular anatomy, are prerequisites to accomplishing appropriate surgical planning and, ultimately, to completing successful exploration and removal of pathological lesions in this region.
Intestinal marginal zone B‐cell lymphoma of MALT type: clinical manifestation and outcome of a rare disease

Intestinal marginal zone B‐cell lymphoma of the MALT type (I‐MZL) is a relatively uncommon form of lymphoma. Twenty‐seven patients with histologically‐confirmed I‐MZL were analyzed. The patients initially presented with abdominal pain (62.9%), and diarrhea (22.2%). The most common involved site was the ileo‐caecal area (40.7%). Musshoff’s stage IE, IIE1, IIE2, IIIE and IV were present in 44%, 15%, 11%, 7.4% and 22% respectively. Sixty‐three percent were in the low‐risk group according to the Follicular Lymphoma International Prognostic Index. Complete response and partial response were achieved in 82% and 4% patients. The estimated 5‐year overall survival (OS) and progression‐free survival (PFS) rates were 86% and 54%. Stage ≥ IIE2 was determined to be a poor prognostic factor for PFS and OS. I‐MZL commonly manifests in an early‐stage, low‐risk state and tends to respond well to local and systemic treatment with favorable prognosis. I‐MZL tends to be an indolent disease – characterized by prolonged survival with frequent relapses, similarly to other site MZLs.
Towards 3D-imaging with low-cost SiGe-Technology at 160GHz

This paper presents a compact, low-weight and flexible continuous wave (CW) millimeter-wave (mmWave) active imaging system implemented in low-cost SiGe-Technology. It is based on a receiver (RX) chip with zero-intermediate frequency (IF) quadrature mixing covering the 158-to-165 GHz band. This heterodyne imaging system provides dynamic range of 110 dB and yields high imaging contrast. Using this mmWave imaging system it is possible to exploit both the magnitude and the phase information of the transmitted wave. The available bandwidth of 8 GHz can be employed for swept sources in radar sensing applications offering the capability of 3D image reconstruction.
Severe, chronic proliferative kidney disease (PKD) induced in rainbow trout Oncorhynchus mykiss held at a constant 18°C

Proliferative kidney disease (PKD), caused by the myxozoan parasite Tetracapsuloides bryosalmonae, is well documented as a seasonal disease of rainbow trout Oncorhynchus mykiss. Water temperatures influence the course of the infection both within the fish and the invertebrate host, the recovery of fish from the disease being accelerated with decreasing water temperatures. During this study, groups of rainbow trout were held at a constant temperature (18°C) for a sustained period of time following initial exposure to T. bryosalmonae. While the majority of these fish had recovered from the clinical disease after 9 mo, 10% remained infected, showing clinical signs of dis- ease. A histological study revealed that the majority exhibited very high parasite loads and unusually severe symptoms of PKD. This demonstrates that while most rainbow trout can recover from PKD independent of water temperature, there exists a sub-population that cannot.
PHENOLOGICAL PATTERNS OF WOODY VEGETATION AT TINIGUA PARK , COLOMBIA : METHODOLOGICAL COMPARISONS WITH EMPHASIS ON FRUIT PRODUCTION

Phenological patterns have a great influence on community ecology. I have quantified fruit abundance using fruit traps, phenological transects, and observations on marked trees of selected species. All methods showed the main peaks of fleshy fruit production between the dry period and the middle of the rainy season. Wind, water, and mechanically dispersed seeds showed a peak of production at the dry period. According to the number of individuals on transects, flower abundance showed predominantly two peaks, one at the end of the rainy period and one in the dry period. This pattern was positively correlated with solar irradiance estimates and differences between maximum and minimum temperatures, which tend to occur on dry days when the activity and abundance of pollinating insects seemed to be high. There was also a good correlation between relative day length and the density of flowering individuals, which suggest that this variable could trigger flowering patterns. Although many species lose their leaves in the dry period, the production of new leaves does not seem to be associated with any particular season. I used a new method to quantify fruit production for each species (in kg/ha), based on phenological transects, corrected visual estimates, and dry fruit weights. The mature forest produced more fruits than the other forests, and the flooded forest showed less fruit production during the dry season and the beginning of the rainy period. In contrast, average density of fruiting trees was similar or slightly greater in the flooded forests than in terra-firme forests during the middle part of the rainy period. Finally, I estimated how long the transects should be in order to get adequate estimates of fruit production, and I found that in general at least 7 km are necessary to get good estimates for terra firme forests at Tinigua.
QUANTUM THEORY OF DISPERSIVE ELECTROMAGNETIC MODES

A quantum theory of dispersion for an inhomogeneous solid is obtained, from a starting point of multipolar coupled atoms interacting with an electromagnetic field. The dispersion relations obtained are equivalent to the standard classical Sellmeir equations obtained from the Drude-Lorentz model. In the homogeneous (planewave) case, we obtain the detailed quantum mode structure of the coupled polariton fields, and show that the mode expansion in all branches of the dispersion relation is completely defined by the refractive index and the group velocity for the polaritons. We demonstrate a straightforward procedure for exactly diagonalizing the Hamiltonian in one-, two-, or three-dimensional environments, even in the presence of longitudinal phonon-exciton dispersion, and an arbitrary number of resonant transitions with different frequencies. This is essential, since it is necessary to include at least one phonon (IR) and one exciton (UV) mode, in order to represent dispersion in transparent solid media accurately. Our method of diagonalization does not require an explicit solution of the dispersion relation, but relies instead on the analytic properties of Cauchy contour integrals over all possible mode frequencies. When there is longitudinal-phonon dispersion, the relevant group-velocity term is modified so that it only includes the purely electromagnetic part of the group velocity. [S1050-2947(98)05811-9].
Homocysteine Exposure Affects Early Hemodynamic Parameters of Embryonic Chicken Heart Function

Maternal hyperhomocysteinemia has been associated with an increased risk of newborns with a congenital heart defect. This has been substantiated in the chicken embryo, as congenital heart defects have been induced after homocysteine treatment. Comparable heart defects are observed in venous clipping studies, a model of altered embryonic blood flow. Because of this overlap in heart defects, our aim was to test the hypothesis that homocysteine would cause alterations in embryonic heart function that precede the structural malformations previously described. Therefore, Doppler flow velocity waveforms were recorded in both primitive ventricles and the outflow tract of the embryonic heart of homocysteine treated and control chicken embryos at embryonic day 3.5. Homocysteine treatment consisted of 50 μL 0.05 M L‐homocysteine thiolactone at 24, 48, and 72 hr. Homocysteine‐treated embryos displayed significantly lower mean heart rates of 134 (SD 22) bpm, compared to 150 (14) bpm in control embryos. Homocysteine treatment caused an inhibiting effect on hemodynamic parameters, and altered heart function was presented by a shift in the proportions of the different wave times in percentage of total cycle time. Homocysteine induces changes in hemodynamic parameters of early embryonic chicken heart function. These changes may precede morphological changes and contribute to the development of CHD defects through alterations in shear stress and shear stress related genes, as seen before in venous clipping studies. Anat Rec,, 2012. © 2012 Wiley Periodicals, Inc.
Polynomial spline signal approximations: Filter design and asymptotic equivalence with Shannon's sampling theorem

The least-squares polynomial spline approximation of a signal g(t) in L/sub 2/(R) is obtained by projecting g(t) on S/sup n/(R) (the space of polynomial splines of order n). It is shown that this process can be linked to the classical problem of cardinal spline interpolation by first convolving g(t) with a B-spline of order n. More specifically, the coefficients of the B-spline interpolation of order 2n+1 of the sampled filtered sequence are identical to the coefficients of the least-squares approximation of g(t) of order n. It is shown that this approximation can be obtained from a succession of three basic operations: prefiltering, sampling, and postfiltering, which confirms the parallel with the classical sampling/reconstruction procedure for bandlimited signals. The frequency responses of these filters are determined for three equivalent spline representations using alternative sets of shift-invariant basis functions of S/sup n/(R): the standard expansion in terms of B-spline coefficients, a representation in terms of sampled signal values, and a representation using orthogonal basis functions. >
Painting Yosemite Valley: A Case Study of Rock Coatings Encountered at Half Dome

No prior research has documented the different types of rock coatings in Yosemite Valley, despite the evident black streaks down Yosemite Falls, the light granitic rock exposed by recent rock falls contrasting with dark rock coatings, and the millions of visitors who have photographed the coated rocks of Yosemite. This paper identifies the types of rock coatings found on Half Dome, in Yosemite Valley, assesses the hypothesis that the rock coatings of Yosemite are consistent with the landscape geochemical model of rock coating formation, and considers the relevance of equifinality. Eight types of rock coatings were identified: case-hardened surfaces, heavy metal skins, iron films, lithobiontic coatings, oxalate crusts, manganiferous rock varnish, silica glaze, and anthropogenic pigments. The landscape geochemical model of rock coating formation and the concept of equifinality both proved useful in this investigation.
V-Shaped Policies for Scheduling Deteriorating Jobs

A set of N jobs has to be processed on a single machine. Jobs have the same basic processing time, but the actual processing time of each job grows linearly with its starting time. A (possibly) different rate of growth is associated with each job. We show that the optimal sequence to minimize flow time is V-shaped: Jobs are arranged in descending order of growth rate if they are placed before the minimal growth rate job, and in ascending order if placed after it. Efficient (0(N log N)) asymptotically optimal heuristics are developed. Their average performance is shown to be extremely good: The average relative error over a set of 20-job problems is on the order of 10−5.
Addition of substitution of simian virus 40 enhancer sequences into the Moloney murine leukemia virus (M-MuLV) long terminal repeat yields infectious M-MuLV with altered biological properties

Moloney murine leukemia virus (M-MuLV) is a replication-competent retrovirus which induces T-cell lymphoma in mice. The enhancer sequences present within the M-MuLV long terminal repeat (LTR) region of the proviral genome have been shown to influence the disease specificity of the virus strongly. We examined the contribution of the M-MuLV enhancers to the transcriptional activity and pathogenesis of M-MuLV by constructing LTRs containing heterologous enhancer elements. The simian virus 40 enhancer region (72- and 21-base-pair repeats) was inserted into the U3 region (at -150 base pairs) of the M-MuLV LTR (Mo + SV) and also into a deleted form of the LTR which lacks the M-MuLV enhancer sequences (delta Mo + SV). These chimeric LTRs were used to generate infectious M-MuLVs by transfection of corresponding proviral plasmids into mouse fibroblasts. The relative infectivities of Mo + SV and delta Mo + SV recombinant viruses as determined by rat XC cell plaque assay and reverse transcriptase assay were 60 to 70% of wild-type M-MuLV levels. To study the pathogenicity of these two recombinant viruses, we inoculated newborn NIH Swiss mice with either Mo + SV or delta Mo + SV M-MuLV. Both viruses induced disease more slowly than M-MuLV, which induces disease 2 to 4 months postinoculation. Mo + SV M-MuLV-inoculated animals became moribund at 3 to 13 months postinoculation, whereas delta Mo + SV M-MuLV-inoculated animals became moribund at 6 to 24 months postinoculation. The tumors induced by the two viruses were characterized histologically and molecularly. Mo + SV M-MuLV-induced tumors were primarily T-cell-derived lymphoblastic lymphomas containing extensive rearrangements of the T-cell receptor beta gene. In contrast, delta Mo + SV M-MuLV induced pre-B- and B-cell lymphoblastic lymphomas, B-cell-derived follicular-center cell lymphomas, and acute myeloid leukemia. The delta Mo + SV tumor DNAs from B-lineage tumors were typically rearranged at the immunoglobulin gene loci and contained germ line configurations of the T-cell receptor beta gene. Southern blot hybridization confirmed that the tumor DNAs contained the predicted Mo + SV M-MuLV or delta Mo + SV M-MuLV provirus.
A Semi‐Parametric Shared Parameter Model to Handle Nonmonotone Nonignorable Missingness

Summary Longitudinal studies often generate incomplete response patterns according to a missing not at random mechanism. Shared parameter models provide an appealing framework for the joint modelling of the measurement and missingness processes, especially in the nonmonotone missingness case, and assume a set of random effects to induce the interdependence. Parametric assumptions are typically made for the random effects distribution, violation of which leads to model misspecification with a potential effect on the parameter estimates and standard errors. In this article we avoid any parametric assumption for the random effects distribution and leave it completely unspecified. The estimation of the model is then made using a semi‐parametric maximum likelihood method. Our proposal is illustrated on a randomized longitudinal study on patients with rheumatoid arthritis exhibiting nonmonotone missingness.