Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic Ice thickness estimation in radar imagery based on charged particles concept

Accelerated loss of ice from Greenland and Antarctica has been observed in recent decades. Ice thickness is a key factor in making predictions about the future of massive ice reservoirs and can be estimated by calculating the exact location of the ice surface and bottom in radar imagery. Identifying the locations of ice boundaries is typically performed manually which is a very time consuming procedure. Here we propose a novel approach which automatically detects the complex topology of ice surface and bottom boundaries based on charged particle concept. Here we first applied anisotropic diffusion to remove the noise and enhance the image. At the second step, we detected the contours in the image based on Coulomb's electrostatic law and the assumption that each pixel is an electrically charged particle. The final ice surface and bottom are detected based on the projection profile of the contours. The results are evaluated on a large dataset of airborne radar imagery collected during IceBridge mission over Antarctica and show promising results with respect to hand-labeled ground truth.
Novel Secondary Ig VH Gene Rearrangement and In-Frame Ig Heavy Chain Complementarity-Determining Region III Insertion/Deletion Variants in De Novo Follicular Lymphoma1

Human germinal center B cell tumors retain the ability of their nontransformed counterparts to somatically hypermutate Ig V genes by nucleotide substitution. Among a survey of 60 primary previously untreated, clonal, follicular lymphomas we have identified a rare VH rearrangement variant and two other in-frame nucleotide insertion/deletion variants within complementarity-determining region III of the Ig heavy chain. The neoplastic origin of the VH rearrangement variant was directly demonstrated in cells isolated by microdissection from malignant follicles. In all three cases a common clonal origin for the variants was demonstrated by complementarity-determining region III nucleotide sequence homology and shared somatic mutations in germline encoded positions in framework region IV. The monoclonal nature of the tumors was independently confirmed by demonstrating a single t(14;18) translocation breakpoint in the two cases with a detectable translocation. All the variants occurred in functional VH rearrangements, which in two cases were directly shown to encode functional Ab molecules. Both recombination-activating genes 1 and 2 were expressed in lymph node tumor cells containing the VH rearrangement variant, although recombination-activating gene expression among a panel of lymphomas was not limited to this variant.
Mammalian Endothermy Optimally Restricts Fungi and Metabolic Costs

ABSTRACT Endothermy and homeothermy are mammalian characteristics whose evolutionary origins are poorly understood. Given that fungal species rapidly lose their capacity for growth above ambient temperatures, we have proposed that mammalian endothermy enhances fitness by creating exclusionary thermal zones that protect against fungal disease. According to this view, the relative paucity of invasive fungal diseases in immunologically intact mammals relative to other infectious diseases would reflect an inability of most fungal species to establish themselves in a mammalian host. In this study, that hypothesis was tested by modeling the fitness increase with temperature versus its metabolic costs. We analyzed the tradeoff involved between the costs of the excess metabolic rates required to maintain a body temperature and the benefit gained by creating a thermal exclusion zone that protects against environmental microbes such as fungi. The result yields an optimum at 36.7°C, which closely approximates mammalian body temperatures. This calculation is consistent with and supportive of the notion that an intrinsic thermally based resistance against fungal diseases could have contributed to the success of mammals in the Tertiary relative to that of other vertebrates. IMPORTANCE Mammals are characterized by both maintaining and closely regulating high body temperatures, processes that are known as endothermy and homeothermy, respectively. The mammalian lifestyle is energy intensive and costly. The evolutionary mechanisms responsible for the emergence and success of these mammalian characteristics are not understood. This work suggests that high mammalian temperatures represent optima in the tradeoff between metabolic costs and the increased fitness that comes with resistance to fungal diseases. Mammals are characterized by both maintaining and closely regulating high body temperatures, processes that are known as endothermy and homeothermy, respectively. The mammalian lifestyle is energy intensive and costly. The evolutionary mechanisms responsible for the emergence and success of these mammalian characteristics are not understood. This work suggests that high mammalian temperatures represent optima in the tradeoff between metabolic costs and the increased fitness that comes with resistance to fungal diseases.
Does 30-day readmission affect long-term outcome among glioblastoma patients?

BACKGROUND Research on readmissions has focused mainly on the economic and resource burden it places on hospitals. OBJECTIVE To evaluate the effect of 30-day readmission on overall survival among newly diagnosed glioblastoma multiforme (GBM) patients. METHODS A nationwide cohort of GBM patients diagnosed between 1991 and 2007 was studied using the Surveillance, Epidemiology and End Results Medicare database. Multivariate models were used to determine factors associated with readmission and overall survival. Odds ratio, hazard ratio, 95% confidence interval, and P values were reported. Complete case and multiple imputation analyses were performed. RESULTS Among the 2774 newly diagnosed GBM patients undergoing surgery at 442 hospitals nationwide, 437 (15.8%) were readmitted within 30 days of the index hospitalization. Although 63% of readmitted patients returned to the index hospital where surgery was performed, a significant portion (37%) were readmitted to nonindex hospitals. The median overall survival for readmitted patients (6.0 months) was significantly shorter than for nonreadmitted (7.6 months; P < .001). In a confounder-adjusted imputed model, 30-day readmission increased the hazard of mortality by 30% (hazard ratio, 1.3; P < .001). Neurological symptoms (30.2%), thromboembolic complications (19.7%), and infections (17.6%) were the leading reasons for readmission. CONCLUSION Prior studies that have reported only the readmissions back to index hospitals are likely underestimating the true 30-day readmission rate. GBM patients who were readmitted within 30 days had significantly shorter survival than nonreadmitted patients. Future studies that attempt to decrease readmissions and evaluate the impact of reducing readmissions on patient outcomes are needed.
Heterogeneity at Work

The Clinical and Translational Science Award (CTSA) program is an ambitious multibillion dollar initiative sponsored by the National Institutes of Health (NIH) organized around the mission of facilitating the improved quality, efficiency, and effectiveness of translational health sciences research across the country. Although the NIH explicitly requires internal evaluation, funded CTSA institutions are given wide latitude to choose the structure and methods for evaluating their local CTSA program. The National Evaluators Survey was developed by a peer-led group of local CTSA evaluators as a voluntary effort to understand emerging differences and commonalities in evaluation teams and techniques across the 61 CTSA institutions funded nationwide. This article presents the results of the 2012 National Evaluators Survey, finding significant heterogeneity in evaluation staffing, organization, and methods across the 58 CTSAs institutions responding. The variety reflected in these findings represents both a liability and strength. A lack of standardization may impair the ability to make use of common metrics, but variation is also a successful evolutionary response to complexity. Additionally, the peer-led approach and simple design demonstrated by the questionnaire itself has value as an example of an evaluation technique with potential for replication in other areas across the CTSA institutions or any large-scale investment where multiple related teams across a wide geographic area are given the latitude to develop specialized approaches to fulfilling a common mission.
Distinct Mechanisms Direct SCL/tal-1 Expression in Erythroid Cells and CD34 Positive Primitive Myeloid Cells*

The SCL/tal-1 gene (hereafter designated SCL) encodes a basic helix-loop-helix transcription factor which is pivotal for the normal development of all hematopoietic lineages and which is expressed in committed erythroid, mast, and megakaryocytic cells as well as in hematopoietic stem cells. The molecular basis for expression of SCL in stem cells and its subsequent modulation during lineage commitment is of fundamental importance for understanding how early “decisions” are made during hematopoiesis. We now compare the activity of SCL promoters 1a and 1b in erythroid cells and in CD34 positive primitive myeloid cells. SCL mRNA expression in CD34 positive myeloid cells did not require GATA-1. Promoter 1a activity was weak or absent in CD34 positive myeloid cells and appeared to correlate with the presence or absence of low levels of GATA-1. However, promoter 1b, which was silent in committed erythroid cells, was strongly active in transient assays using CD34 positive myeloid cells, and functioned in a GATA-independent manner. Interestingly, RNase protection assays demonstrated that endogenous promoter 1b was active in both erythroid and CD34 positive myeloid cells. These results demonstrate that fundamentally different mechanisms regulate the SCL promoter region in committed erythroid cells and in CD34 positive myeloid cells. Moreover these observations suggest that in erythroid, but not in CD34 positive myeloid cells, promoter 1b required integration in chromatin and/or additional sequences for its activity. Stable transfection experiments showed that both core promoters were silent following integration in erythroid or CD34 positive myeloid cells. Our data therefore indicate that additional regulatory elements were necessary for both SCL promoters to overcome chromatin-mediated repression.
Identification and molecular characterization of numerous Histomonas meleagridis proteins using a cDNA library

SUMMARY Histomonas meleagridis is a protozoan parasite of various galliform birds causing a type of enterohepatitis termed histomonosis or ‘blackhead disease’. Due to the ban of chemotherapeutic substances and an increase in free-range poultry production, histomonosis is currently a re-emerging disease. So far limited molecular knowledge is available. In the present work, mRNAs coding for antigenic proteins of H. meleagridis were identified. For this purpose, a cDNA expression library was constructed from a mono-eukaryotic culture of H. meleagridis. The library was screened with polyclonal rabbit serum raised against purified H. meleagridis trophozoites. Polyclonal rabbit serum specifically recognized the same major H. meleagridis antigens as chicken and turkey sera originating from animal trials, but displayed a significantly lower bacteria-dependent background signal. After 2 rounds of screening, a total of 95 positive clones were sequenced. Bioinformatics analyses were performed on nucleotide and deduced amino acid sequences, identifying 37 unique clones. Based on the homology to other protozoan parasites, mostly Trichomonas vaginalis, the clones were grouped according to functional aspects: structural proteins, possible surface proteins, oxygen reducing proteins, ribosomal proteins, protein kinases and various other intracellular proteins.
The order of genetic events associated with colorectal cancer progression inferred from meta‐analysis of copy number changes

To identify chromosomal aberrations that differentiate among the Dukes' stages of colorectal cancer (CRC) as well as those that are responsible for the progression into liver metastases, we performed a meta‐analysis of data obtained from 31 comparative genomic hybridization (CGH) studies comprising a total of 859 CRCs. Individual copy number profiles for 373 primary tumors and 102 liver metastases were recorded and several statistical analyses, such as frequency, multivariate logistic regression, and trend tests, were performed. In addition, time of occurrence analysis was applied for the first time to copy number changes identified by CGH, and each genomic imbalance was thereby classified as an early or late event in colorectal tumorigenesis. By combining data from the different statistical tests, we present a novel genetic pathway for CRC progression that distinguishes the Dukes' stages and identifies early and late events in both primary carcinomas and liver metastases. Results from the combined analyses suggest that losses at 17p and 18 and gains of 8q, 13q, and 20 occur early in the establishment of primary CRCs, whereas loss of 4p is associated with the transition from Dukes' A to B–D. Deletion of 8p and gains of 7p and 17q are correlated with the transition from primary tumor to liver metastasis, whereas losses of 14q and gains of 1q, 11, 12p, and 19 are late events. We supplement these findings with a list of potential target genes for the specific alterations from a publicly available microarray expression dataset of CRC. This article contains Supplementary Material available at http://www.interscience. wiley.com/jpages/1045‐2257/suppmat. © 2005 Wiley‐Liss, Inc.
Indoor molds, bacteria, microbial volatile organic compounds and plasticizers in schools--associations with asthma and respiratory symptoms in pupils.

UNLABELLED We investigated asthma and atopy in relation to microbial and plasticizer exposure. Pupils in eight primary schools in Uppsala (Sweden) answered a questionnaire, 1014 (68%) participated. Totally, 7.7% reported doctor-diagnosed asthma, 5.9% current asthma, and 12.2% allergy to pollen/pets. Wheeze was reported by 7.8%, 4.5% reported daytime breathlessness, and 2.0% nocturnal breathlessness. Measurements were performed in 23 classrooms (May-June), 74% had <1000 ppm CO(2) indoors. None had visible mold growth or dampness. Mean total microbial volatile organic compound (MVOC) concentration was 423 ng/m(3) indoors and 123 ng/m(3) outdoors. Indoor concentration of TMPD-MIB (2,2,4-trimethyl-1,3-pentanediol monoisobutyrate, Texanol) and TMPD-DIB (2,2,4-trimethyl-1,3-pentanediol diisobutyrate, TXIB), two common plasticizers, were 0.89 and 1.64 microg/m(3), respectively. MVOC and plasticizer concentration were correlated (r = 0.5; P < 0.01). Mold concentration was 360 cfu/m(3) indoors and 980 cfu/m(3) outdoors. At higher indoor concentrations of total MVOC, nocturnal breathlessness (P < 0.01) and doctor-diagnosed asthma (P < 0.05) were more common. Moreover, there were positive associations between nocturnal breathlessness and 3-methylfuran (P < 0.01), 3-methyl-1-butanol (P < 0.05), dimethyldisulfide (P < 0.01), 2-heptanone (P < 0.01), 1-octen-3-ol (P < 0.05), 3-octanone (P < 0.05), TMPD-MIB (P < 0.05), and TMPD-DIB (P < 0.01). TMPD-DIB was positively associated with wheeze (P < 0.05), daytime breathlessness (P < 0.05), doctor-diagnosed asthma (P < 0.05), and current asthma (P < 0.05). In conclusion, exposure to MVOC and plasticizers at school may be a risk factor for asthmatic symptoms in children. PRACTICAL IMPLICATIONS Despite generally good ventilation and lack of visible signs of mold growth, we found an association between respiratory symptoms and indoor MVOC concentration. In addition, we found associations between asthmatic symptoms and two common plasticizers. The highest levels of MVOC, TMPD-MIB, and TMPD-DIB were found in two new buildings, suggesting that material emissions should be better controlled. As MVOC and plasticizers concentrations were positively correlated, while indoor viable molds and bacteria were negatively correlated, it is unclear if indoor MVOC is an indicator of microbial exposure. Further studies focusing on health effects of chemical emissions from indoor plastic materials, including PVC-floor coatings, are needed.
Second-order consensus for multi-agent systems with limited communication range

This paper studies the second-order consensus problem for multi-agent systems with a limited communication range where two agents can communicate with each other only when they are within a certain distance. Second-order consensus means that the agents asymptotically gather to a point and move in the same velocity. Different form most existing works where the change of network topology is independent of the system evolution, we construct a Cuker-Smale type model to formulate the relation between the network topology and the system state. The main result of this paper provides a sufficient condition on the initial velocities, positions and the communication range which can guarantee the multi-agent system to asymptotically achieve the second-order consensus. We prove it using the Lyapunov functional approach. Finally, simulation examples are given to verify the theorem.
Adaptive Convergence Rates of a Dirichlet Process Mixture of Multivariate Normals

It is shown that a simple Dirichlet process mixture of multivariate normals offers Bayesian density estimation with adaptive posterior convergence rates. Toward this, a novel sieve for non-parametric mixture densities is explored, and its rate adaptability to various smoothness classes of densities in arbitrary dimension is demonstrated. This sieve construction is expected to offer a substantial technical advancement in studying Bayesian non-parametric mixture models based on stick-breaking priors.
Need and impressions of communication robots for seniors with slight physical and cognitive disabilities: Evaluation using system usability scale

Various types of communication robots have emerged for supporting elderly people with impairments or frailties. However, the need of the robots for healthy elderly persons with decreasing physical and cognitive abilities remains unclear. Knowledge about these needs can help determine the guidelines or implications of the introduction of communication robots for healthy seniors. The objective of this study is to clarify the needs and the impressions of various communication robots for seniors with slight physical or cognitive problems. The scores on the system usability scale (SUS) and interview results indicated that, with increasing participant age, mammal-like communication robots were more preferable than other types. In addition, elderly persons with minor physical problems tended not to prefer manually operated robots.
Is STAPLE algorithm confident to assess segmentation methods in PET imaging?

Accurate tumor segmentation in [18F]-fluorodeoxyglucose positron emission tomography is crucial for tumor response assessment and target volume definition in radiation therapy. Evaluation of segmentation methods from clinical data without ground truth is usually based on physicians’ manual delineations. In this context, the simultaneous truth and performance level estimation (STAPLE) algorithm could be useful to manage the multi-observers variability. In this paper, we evaluated how this algorithm could accurately estimate the ground truth in PET imaging. Complete evaluation study using different criteria was performed on simulated data. The STAPLE algorithm was applied to manual and automatic segmentation results. A specific configuration of the implementation provided by the Computational Radiology Laboratory was used. Consensus obtained by the STAPLE algorithm from manual delineations appeared to be more accurate than manual delineations themselves (80% of overlap). An improvement of the accuracy was also observed when applying the STAPLE algorithm to automatic segmentations results. The STAPLE algorithm, with the configuration used in this paper, is more appropriate than manual delineations alone or automatic segmentations results alone to estimate the ground truth in PET imaging. Therefore, it might be preferred to assess the accuracy of tumor segmentation methods in PET imaging.
TLR4-Mediated Sensing of Campylobacter jejuni by Dendritic Cells Is Determined by Sialylation

In Guillain-Barré syndrome (GBS), ganglioside mimicry of Campylobacter jejuni lipo-oligosaccharide (LOS) drives the production of cross-reactive Abs to peripheral nerve gangliosides. We determined whether sialic acid residues in C. jejuni LOS modulate dendritic cell (DC) activation and subsequent B cell proliferation as a possible mechanism for the aberrant humoral immune response in GBS. Highly purified sialylated LOS of C. jejuni isolates from three GBS patients induced human DC maturation and secretion of inflammatory cytokines that were inhibited by anti-TLR4 neutralizing Abs. The extent of TLR4 signaling and DC activation was greater with LOS of the wild type isolates than with nonsialylated LOS of the corresponding sialyltransferase gene knockout (cst-II mutant) strains, indicating that sialylation boosts the DC response to C. jejuni LOS. Supernatants of LOS-activated DCs induced B cell proliferation after cross-linking of surface Igs in the absence of T cells. Lower B cell proliferation indices were found with DC supernatants after DC stimulation with cst-II mutant or neuraminidase desialylated LOS. This study showed that sialylation of C. jejuni LOS enhances human DC activation and subsequent B cell proliferation, which may contribute to the development of cross-reactive anti-ganglioside Abs found in GBS patients following C. jejuni infection.
Comparison of exposure estimates in the Finnish job-exposure matrix FINJEM with a JEM derived from expert assessments performed in Montreal

Context Retrospective exposure assessment in population-based case–control studies poses a major challenge due to the wide range of occupations and industries involved. The FINJEM is a generic job-exposure matrix (JEM) developed in Finland, which represents a potentially cost-effective exposure assessment tool. While FINJEM has been used in several studies outside Finland, little is known of its applicability in other countries. Methods We compared prevalence and intensity of exposure in FINJEM with a JEM developed from expert assessments of occupational histories obtained in a population-based case–control study in Montreal. Agreement for prevalence of exposure was measured by weighted κ coefficients between prevalence categories. Agreement for exposure intensity was measured by Spearman correlation coefficients between cells with non-null exposure. Results The comparison involved 27 chemicals, the time period 1945–1995 and included 4743 jobs initially assessed by the Montreal experts. 4293 combinations of agent, occupational title and period were available for comparison of prevalence. Agent-specific prevalence was consistently higher in the Montreal JEM (median difference 1.7%). Agent-specific κ values between prevalence categories varied from 0.89 (welding fumes) to 0.07 (flour dust). The comparison of exposure levels involved 14 agents and 198 cells with non-null exposure in both sources. Agent-specific Spearman correlation varied from 0.89 (flour dust) to −0.35 (benzo(a)pyrene). Conclusion Our observations suggest that information concerning several agents (eg, metals, welding fumes) can be successfully transported from Finland to Canada and probably other countries. However, for other agents, there was considerable disagreement, and hence, transportability of FINJEM cannot be assumed by default.