Miracle-dz/UniFAR-FTUs huggingface dataset:
Epidermal Growth Factor Receptor Expression in Pancreatic Carcinoma Using Tissue Microarray Technique

Background: The effect of overexpression of epidermal growth factor receptor (EGFR) in pancreatic carcinoma is not clear. Utilizing tissue microarrays, we evaluated EGFR expression in pancreatic cancer to determine the association of EGFR expression with histopathologic characteristics and patient outcome. Methods: 71 cases of pancreatic adenocarcinoma and 18 cases of chronic pancreatitis were retrieved from archival files. Tissue cores from donor blocks were arrayed to create a tissue microarray. Sections were stained with EGFR and the intensity of membranous staining and percentage of tumor cells showing immunoreactivity were determined. At least 1% membranous staining and 1+ intensity were considered positive. Results: EGFR was present in 49 of 71 (69%) cases of pancreatic adenocarcinoma and 7 of 18 (39%) cases of chronic pancreatitis (p = 0.03). There was no statistically significant correlation between intensity or extent of EGFR expression and tumor grade, size, or lymph node status. While median survival was nearly twice as long when EGFR was expressed (15.2 vs. 8.3 months), this did not reach statistical significance. Conclusions: EGFR is overexpressed in pancreatic cancers independent of histopathologic characteristics and does not predict survival. Immunohistochemical analysis of EGFR staining may help in identifying candidates for EGFR inhibitor therapy.
Health Related Quality of Life among Patients with Tuberculosis and HIV in Thailand

Introduction Health utilities of tuberculosis (TB) patients may be diminished by side effects from medication, prolonged treatment duration, physical effects of the disease itself, and social stigma attached to the disease. Methods We collected health utility data from Thai patients who were on TB treatment or had been successfully treated for TB for the purpose of economic modeling. Structured questionnaire and EuroQol (EQ-5D) and EuroQol visual analog scale (EQ-VAS) instruments were used as data collection tools. We compared utility of patients with two co-morbidities calculated using multiplicative model (UCAL) with the direct measures and fitted Tobit regression models to examine factors predictive of health utility and to assess difference in health utilities of patients in various medical conditions. Results Of 222 patients analyzed, 138 (62%) were male; median age at enrollment was 40 years (interquartile range [IQR], 35–47). Median monthly household income was 6,000 Baht (187 US$; IQR, 4,000–15,000 Baht [125–469 US$]). Concordance correlation coefficient between utilities measured using EQ-5D and EQ-VAS (UEQ-5D and UVAS, respectively) was 0.6. UCAL for HIV-infected TB patients was statistically different from the measured UEQ-5D (p-value<0.01) and UVAS (p-value<0.01). In tobit regression analysis, factors independently predictive of UEQ-5D included age and monthly household income. Patients aged ≥40 years old rated UEQ-5D significantly lower than younger persons. Higher UEQ-5D was significantly associated with higher monthly household income in a dose response fashion. The median UEQ-5D was highest among patients who had been successfully treated for TB and lowest among multi-drug resistant TB (MDR-TB) patients who were on treatment. Conclusions UCAL of patients with two co-morbidities overestimated the measured utilities, warranting further research of how best to estimate utilities of patients with such conditions. TB and MDR-TB treatments impacted on patients' self perceived health status. This effect diminished after successful treatment.
Unlike ASXL1 and ASXL2 mutations, ASXL3 mutations are rare events in acute myeloid leukemia with t(8;21)

Unlike ASXL1 and ASXL2 mutations, ASXL3 mutations are rare events in acute myeloid leukemia with t(8;21) Nicolas Duployez, Jean-Baptiste Micol, Nicolas Boissel, Arnaud Petit, Sandrine Geffroy, Maxime Bucci, Helene Lapillonne, Aline Renneville, Guy Leverger, Norbert Ifrah, Herve Dombret, Omar Abdel-Wahab, Eric Jourdan & Claude Preudhomme a Laboratory of Hematology and Tumor Bank, INSERM U837 Team 3, Cancer Research Institute of Lille, Centre Hospitalier Regional Universitaire of Lille, University Lille Nord de France, Lille b Hematology Department, INSERM Unite Mixte de Recherche 1009, Gustave Roussy Cancer Campus Grand Paris, Villejuif, Paris-Sud University, Orsay, France c Human Oncology and Pathogenesis Program and Leukemia Service, Memorial SloanKettering Cancer Center and Weill Cornell Medical College, New York, NY, USA d Department of Hematology and EA3518, Hopital Saint-Louis (Assistance Publique-Hopitaux de Paris), University Paris Diderot, Paris, France e Department of Pediatric Hematology, Paris, France f Laboratory of Hematology, Hopital Armand Trousseau (Assistance Publique-Hopitaux de Paris), Paris, France g Department of Hematology, INSERM U892, Centre Hospitalier Universitaire d’Angers, Angers, France h Department of Hematology and Oncology, Centre Hospitalier Universitaire of Nimes, University Montpellier-Nimes, Nimes, France Published online: 06 Jul 2015.
Detection of cough signals in continuous audio recordings using hidden Markov models

Cough is a common symptom of many respiratory diseases. The evaluation of its intensity and frequency of occurrence could provide valuable clinical information in the assessment of patients with chronic cough. In this paper we propose the use of hidden Markov models (HMMs) to automatically detect cough sounds from continuous ambulatory recordings. The recording system consists of a digital sound recorder and a microphone attached to the patient's chest. The recognition algorithm follows a keyword-spotting approach, with cough sounds representing the keywords. It was trained on 821 min selected from 10 ambulatory recordings, including 2473 manually labeled cough events, and tested on a database of nine recordings from separate patients with a total recording time of 3060 min and comprising 2155 cough events. The average detection rate was 82% at a false alarm rate of seven events/h, when considering only events above an energy threshold relative to each recording's average energy. These results suggest that HMMs can be applied to the detection of cough sounds from ambulatory patients. A postprocessing stage to perform a more detailed analysis on the detected events is under development, and could allow the rejection of some of the incorrectly detected events.
Sensory neurons in the spinal cord of nominal female embryos in the marine turtle Lepidochelys olivacea respond to shifts in incubation temperature: implications for temperature dependent sex determination

Gonadal determination in marine turtles depends on incubation temperature. The mechanisms that spark off this process remain unclear. Previously, we proposed that sensory nerves reaching the gonadal primordium in nominal female embryos of Lepidochelys (L) olivacea may sense and signal incubation temperature. These nerves could later trigger ovarian determination by releasing neurotransmitters in a code constructed based on the thermal information (Gutierrez-Ospina et al., Acetylcholinesterase-positive innervation is present at the undifferentiated stages of the sea turtle Lepidochelys olivacea embryo gonads: implications for temperature-dependent sex determination, J. Comp. Neurol. 410 (1999) 90-98). The hypothesis briefly described, however, has been recently refuted under weak theoretical grounds and experimental misinterpretations (see introduction). Here, we present preliminary results that show that nominal female embryos have sensory neurons located in the dorsal horn laminae I and II of the lumbar spinal cord that display increased c-Fos-like immuno-staining after being incubated either at 15°C or 50°C. Because these spinal neurons are the primary central target of dorsal root ganglion neurons that innervate the urogential crest, these observations keep open the possibility that gonadal sensory nerves indeed signal thermal information that could later be used to trigger or instruct ovarian specification in marine turtles.
Elevated White Blood Cell Count and Carotid Plaque Thickness: The Northern Manhattan Stroke Study

Background and Purpose— Elevated leukocyte count has been associated with cardiovascular and cerebrovascular disease in several epidemiological studies. We sought to determine whether white blood cell count (WBC) is associated with carotid plaque thickness in a stroke-free, multiethnic cohort. Methods— For this cross-sectional analysis, WBC was measured in stroke-free community subjects undergoing carotid duplex Doppler ultrasound. Maximal internal carotid plaque thickness (MICPT) was measured for each subject. Demographic and potential medical confounding factors were analyzed with linear and logistic regression to calculate the effect of quartile of WBC on MICPT. Odds ratios (ORs) and 95% confidence intervals (CIs) for the effect of quartile of WBC on MICPT ≥75th percentile were calculated. All analyses were stratified by race-ethnicity. Results— The mean age of the 1422 subjects was 68.6±10.2 years; 40.0% were men; 24.4% were white, 46.9% Hispanic, and 26.7% black. Among Hispanics, compared with the lowest quartile of WBC, those in the highest quartile had significantly increased MICPT (mean difference=0.30 mm, P =0.0086) after adjustment for age, sex, and other atherosclerotic risk factors. There was no significant increase for blacks or whites. The OR for MICPT ≥75th percentile (1.9 mm) was significantly increased for Hispanics (OR, 2.8; 95% CI, 1.4 to 5.6), marginally elevated for black non-Hispanics (OR, 1.6; 95% CI, 0.8 to 3.2), and not increased for white non-Hispanics (OR, 0.5; 95% CI, 0.2 to 1.1). Conclusions— Relative elevation in WBC is associated with carotid atherosclerosis, but this relationship differs by race-ethnicity. The association is strongest in Hispanics, intermediate in black non-Hispanics, and not present in white non-Hispanics in this population. Chronic subclinical infection or inflammation may account for this association.
Improving the acquisition time of a PLL-based, integer-N frequency synthesizer

A Phase-Locked Loop-based frequency synthesizer switches between channels as the feedback division ratio is changed. For a given spectral purity, the acquisition time is often the bottleneck in the design of integer-N synthesizers. This paper presents a review of the three major phases of the total acquisition time from control systems theory and PLL literature. These are the pull-in time, the settling-time and the lock-time. An implementation example in a 0.25 /spl mu/m CMOS process illustrates the process of reduction of the acquisition time by a factor of 3.5 for an integer-N synthesizer.
Differential Effects of B and T Lymphocyte Attenuator and Programmed Death-1 on Acceptance of Partially versus Fully MHC-Mismatched Cardiac Allografts1

Although fully MHC-mismatched murine cardiac allografts are rapidly rejected, allografts mismatched at only MHC class I or class II alleles survive long term; the immunologic basis for the long-term survival of MHC class I- or II-mismatched allografts is unknown. We examined the roles of two recently described inhibitory receptors, B and T lymphocyte attenuator (BTLA) and programmed death-1 (PD-1), in the survival of partially or fully MHC-mismatched allografts using gene-deficient recipients as well as through use of blocking mAbs in wild-type hosts. Partially MHC-mismatched allografts showed strong induction of BTLA, but not PD-1 mRNA and survived long term in wild-type recipients, whereas targeting of BTLA or its ligand, herpesvirus entry mediator, but not PD-1, prompted their rapid rejection. By contrast, fully MHC-mismatched cardiac allografts were acutely rejected in wild-type recipients despite the induction of both BTLA and PD-1. Targeting of PD-1 in several fully MHC-mismatched models accelerated rejection, whereas targeting of BTLA unexpectedly enhanced PD-1 induction by alloreactive CD4 and CD8 T cells and prolonged allograft survival. In vitro studies using allogeneic dendritic cells and T cells showed that at low levels of T cell activation, BTLA expression was primarily induced, but that with increasing degrees of T cell activation, the expression of PD-1 was strongly up-regulated. These data suggest that BTLA and PD-1 exert distinct inhibitory actions in vivo, with the BTLA/herpesvirus entry mediator pathway appearing to dominate in regulating responses against a restricted degree of allogeneic mismatch.
Global Chemical Composition of Ambient Fine Particulate Matter for Exposure Assessment

Epidemiologic and health impact studies are inhibited by the paucity of global, long-term measurements of the chemical composition of fine particulate matter. We inferred PM2.5 chemical composition at 0.1° × 0.1° spatial resolution for 2004–2008 by combining aerosol optical depth retrieved from the MODIS and MISR satellite instruments, with coincident profile and composition information from the GEOS-Chem global chemical transport model. Evaluation of the satellite-model PM2.5 composition data set with North American in situ measurements indicated significant spatial agreement for secondary inorganic aerosol, particulate organic mass, black carbon, mineral dust, and sea salt. We found that global population-weighted PM2.5 concentrations were dominated by particulate organic mass (11.9 ± 7.3 μg/m3), secondary inorganic aerosol (11.1 ± 5.0 μg/m3), and mineral dust (11.1 ± 7.9 μg/m3). Secondary inorganic PM2.5 concentrations exceeded 30 μg/m3 over East China. Sensitivity simulations suggested that population-weighted ambient PM2.5 from biofuel burning (11 μg/m3) could be almost as large as from fossil fuel combustion sources (17 μg/m3). These estimates offer information about global population exposure to the chemical components and sources of PM2.5.
Tensile Strength of Carbon–Carbon Composites: II – Effect of Heat Treatment Temperature

The effects of heat treatment temperature, HTT, on the tensile strength (u) of PAN-based carbon-fiber-reinforced carbon matrix composites (C–Cs) were examined. In order to understand the mechanisms yielding variation of the tensile strength, the distribution of fiber strength and the interfacial strength between the fiber and the matrix were also determined as a function of HTT. The us of the C–Cs and the PAN-based-fiber was found to decrease with increasing HTT. The degradations of the fiber strength proceeded with distortion of the fiber cross section and reduction of the fiber diameter. The interfacial strength slightly decreased with increasing HTT. The tensile strength of C–Cs is generally enhanced by the reduction of the interfacial bonding strength. Thus, the interfacial change is not a main source of the strength degradation. Finally, a comparison of u between two types of C–Cs, showed that the only difference was reinforcing fibers and led to the conclusion that the primary factor yielding the degradation of C–C strength by HTT was the fiber degradation.
Acute in vivo interactions of Helicobacter equorum with its equine host.

REASONS FOR PERFORMING STUDY A novel urease-negative Helicobacter species has been isolated from faecal samples of clinically healthy horses, but no information is available about the main sites of colonisation in the equine gastrointestinal tract nor is the pathogenic potential of this microorganism known. An experimental infection in horses was therefore carried out. METHODS Four horses were infected with H. equorum strain CCUG 52199T and subjected to euthanasia at 10 (n = 2) and 30 days (n = 2) post inoculation. A fifth animal was inoculated with phosphate buffered saline and used as control. Gastrointestinal samples were examined histologically and bacteriologically. These samples, as well as faecal material collected at regular intervals, were also subjected to PCR analysis. RESULTS All horses remained clinically healthy and no specific macroscopic lesions were identified, nor were there any microscopic changes. H. equorum-DNA was detected in the faeces during the whole experiment in all infected animals but not in the negative control. Sites of colonisation were caecum, colon and rectum. CONCLUSIONS H. equorum is able to colonise the equine lower bowel and is excreted in faeces without apparent pathology. No association between the presence of the organism and gastrointestinal disease was demonstrated.
Serum Biomarkers for Identifying Acute Chest Syndrome Among Patients Who Have Sickle Cell Disease and Present to the Emergency Department

Objective. To compare the accuracy of biomarkers for identifying acute chest syndrome (ACS) in patients with sickle cell disease presenting to a pediatric emergency department (ED). Methods. We conducted a 13-month-long (2002–2003) cohort study with nested case-control in patients with sickle cell disease presenting to the pediatric ED with vaso-occlusive crises or fever in which we compared levels of secretory phospholipase A2 (sPLA2), endothelin-1, interleukin-6 (IL-6), and peripheral white blood cell count (WBC) in cases that were complicated by ACS and in control subjects with uncomplicated illnesses. For diagnosis, a test was considered to be accurate when the area under its receiver operator characteristic curve (AUC) was >0.70. Laboratory tests with AUC values ≥0.70 were entered into a binary recursive partitioning model for diagnosis. Results. For the period of study, samples from 72 visits were obtained from 51 patients who presented with vaso-occlusive crises (range: 1–4 visits per patient; 15 were enrolled more than once). ACS complicated 19 of 72 visits (26%, 95% confidence interval: 17%–38%). At an AUC value of 0.79, only the sPLA2 test was accurate for diagnosing ACS. AUC values for peripheral WBC, endothelin-1, and IL-6 were 0.68, 0.51, and 0.52, respectively. Binary recursive partitioning retained only sPLA2 at a cutoff of 13.7 ng/mL to be accurate for diagnosis. This cutoff had a sensitivity of 74% (14 of 19), a specificity of 87% (46 of 53), a positive likelihood ratio of 5.6, and a negative likelihood ratio of 0.18. Conclusions. Secretory phospholipase A2 but not endothelin-1, IL-6, or WBC is an accurate test for identifying present or incipient ACS in young patients who present to the ED with sickle cell pain crises.
Focusing Narrowly or Broadly Attention When Judging Categorical and Coordinate Spatial Relations: A MEG Study

We measured activity in the dorsal system of the human cortex with magnetoencephalography (MEG) during a matching-to-sample plus cueing paradigm, where participants judged the occurrence of changes in either categorical or coordinate spatial relations (e.g., exchanges of left versus right positions or changes in the relative distances) between images of pairs of animals. The attention window was primed in each trial to be either small or large by using cues that immediately preceded the matching image. In this manner, we could assess the modulatory effects of the scope of attention on the activity of the dorsal system of the human cortex during spatial relations processing. The MEG measurements revealed that large spatial cues yielded greater activations and longer peak latencies in the right inferior parietal lobe for coordinate trials, whereas small cues yielded greater activations and longer peak latencies in the left inferior parietal lobe for categorical trials. The activity in the superior parietal lobe, middle frontal gyrus, and visual cortex, was also modulated by the size of the spatial cues and by the type of spatial relation change. The present results support the theory that the lateralization of each kind of spatial processing hinges on differences in the sizes of regions of space attended to by the two hemispheres. In addition, the present findings are inconsistent with the idea of a right-hemispheric dominance for all kinds of challenging spatial tasks, since response times and accuracy rates showed that the categorical spatial relation task was more difficult than the coordinate task and the cortical activations were overall greater in the left hemisphere than in the right hemisphere.
MRI in the evaluation of breast cancer patient response to neoadjuvant chemotherapy: predictive factors for breast conservative surgery.

PURPOSE We aimed to prospectively assess the role of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in the evaluation of predictive factors for breast conservative surgery during neoadjuvant chemotherapy. MATERIALS AND METHODS Sixty-six patients were evaluated before the first treatment cycle, after the second cycle, and upon the completion of neoadjuvant chemotherapy according to largest tumor diameter, tumor volume, postcontrast enhancement, and tumor regression pattern. The patients were divided into responders (pathologic complete and near complete response) and nonresponders. Each subgroup was re-evaluated according to morphokinetic criteria for identification of candidates for breast conservative surgery. RESULTS In responders (n=27), the lesion size upon the completion of neoadjuvant chemotherapy was significantly smaller compared to nonresponders (1.5 ± 0.6 vs. 3.2 ± 0.9 cm; P < 0.001), as was the volume (1.2 vs. 11.0 cm(3); P < 0.001). The measured lesion size did not differ from the histologic size (1.5 ± 0.6 vs. 1.2 ± 0.6 cm; P = 0.09) and had a high correlation (r=0.93). In responders, the following parameters were significantly different before and after neoadjuvant chemotherapy: size (3.6 ± 1.4 to 1.5 ± 0.6 cm; P < 0.001), volume (17.6 to 1.2 cm(3); P < 0.001), predominant concentric regression, plateau and continuous time-intensity curves (P < 0.001). DCE-MRI has the sensitivity of 87% and the accuracy of 77% to identify candidates for breast conservative surgery. CONCLUSION Selected morphokinetic DCE-MRI parameters may contribute to the multidisciplinary decision when considering the selection of candidates for breast conservative surgery.
CHROMOSOME NUMBER EVOLVES INDEPENDENTLY OF GENOME SIZE IN A CLADE WITH NONLOCALIZED CENTROMERES (CAREX: CYPERACEAE)

The effects of chromosome rearrangement on genome size are poorly understood. While chromosome duplications and deletions have predictable effects on genome size, chromosome fusion, fission, and translocation do not. In this study, we investigate genome size and chromosome number evolution in 87 species of Carex, one of the most species‐rich genera of flowering plants and one that has undergone an exceptionally high rate of chromosome rearrangement. Using phylogenetic generalized least‐squares regression, we find that the correlation between chromosome number and genome size in the genus grades from flat or weakly positive at fine phylogenetic scales to weakly negative at deeper phylogenetic scales. The rate of chromosome evolution exhibits a significant increase within a species‐rich clade that arose approximately 5 million years ago. Genome size evolution, however, demonstrates a nearly constant rate across the entire tree. We hypothesize that this decoupling of genome size from chromosome number helps explain the high lability of chromosome number in the genus, as it reduces indirect selection on chromosome number.
The Genetics of Axonal Transport and Axonal Transport Disorders

Neurons are specialized cells with a complex architecture that includes elaborate dendritic branches and a long, narrow axon that extends from the cell body to the synaptic terminal. The organized transport of essential biological materials throughout the neuron is required to support its growth, function, and viability. In this review, we focus on insights that have emerged from the genetic analysis of long-distance axonal transport between the cell body and the synaptic terminal. We also discuss recent genetic evidence that supports the hypothesis that disruptions in axonal transport may cause or dramatically contribute to neurodegenerative diseases.