Miracle-dz/UniFAR-FTUs huggingface dataset:
Indirect effects of red imported fire ants on Attwater's prairie‐chicken brood survival

ABSTRACT The invasive red imported fire ant (Solenopsis invicta) has negatively affected a host of taxonomic groups throughout its acquired North American range. Many studies have hypothesized indirect trophic impacts, but few documented those impacts. We evaluated invertebrate abundance as a factor limiting juvenile survival of the endangered Attwater's prairie‐chicken (Tympanuchus cupido attwateri), and whether fire ants reduce invertebrate numbers and biomass. From 2009–2013, we monitored survival of Attwater's prairie‐chicken broods (n = 63) with radio telemetry during the first 2 weeks post‐hatch and collected daily invertebrate samples at brood sites. Broods located in areas with the highest median invertebrate count (338 invertebrates/25 sweeps) had a survival probability of 0.83 at 2 weeks post‐hatch compared to 0.07 for broods located in areas with the lowest median invertebrate count (18 invertebrates/25 sweeps). During 2011–2012, we evaluated the reduction of fire ants on invertebrate numbers and biomass by aerially treating areas with Extinguish Plus™ in an impact‐reference study design. Treated fields had 27% more individual invertebrates and 26% higher invertebrate biomass than reference fields. Our results clearly document that invertebrate abundance affects Attwater's prairie‐chicken brood survival and that fire ants may indirectly contribute to low brood survival by suppressing invertebrate abundance. We posit that within the fire ant's acquired North American range, fire ants are likely contributing to declines of other insectivorous species. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.
Alterations of the p16ink4a gene in resected nonsmall cell lung tumors and exfoliated cells within sputum

Recently, we reported that p16 protein expression was nondetectable in 49.5% of 107 resected nonsmall cell lung cancers (NSCLCs), suggesting that the p16INK4a gene is frequently inactivated in primary NSCLC. To identify the molecular basis for this p16 immunohistochemical negativity further, we performed a genetic and epigenetic study of p16INK4a status in a series of 115 NSCLC samples parallel to the clinicopathologic and prognostic analyses. Microdissected tumor DNA samples were screened for homozygous deletion using comparative multiplex‐polymerase chain reaction (PCR), for intragenic mutation using direct sequencing and for loss of heterozygosity (LOH) using an intragenic microsatellite marker, D9S942. Of these samples, 67 were further analyzed by SmaI‐based PCR methylation assay to evaluate aberrant methylation at the gene. To examine the correlation of aberrant methylation in tumor and sputum samples, sputum samples from 12 matched patients were assessed for this change. We found that methylation of the p16INK4a gene was present in 38 of the 67 (56.7%) tumors and was significantly associated with negative p16 protein expression (p = 0.029). A 92% (11/12) concordance of sputum samples with matched resected tumors was found. The survival rates among adenocarcinoma patients with p16INK4a methylation were lower, but at a level of borderline significance compared with those patients without methylation (p = 0.071). In addition, 29.4% of the informative cases were found to harbor LOH at D9S942. None of the 115 microdissected tumors exhibited homozygous deletion in the p16INK4a gene. Only 1 patient exhibited a complex mutation at the fourth ankyrin repeat consensus sequence and concordantly demonstrated p16 immunohistochemical negativity. Overall, 69% (79/115) of NSCLC tumors had at least 1 type of p16INK4a alteration. Our data provide compelling evidence that p16INK4a alterations are involved in NSCLC tumorigenesis and that promoter methylation is the predominant mechanism in p16INK4a deregulation. © 2002 Wiley‐Liss, Inc.
Dynamic noise aware training for speech enhancement based on deep neural networks

We propose three algorithms to address the mismatch problem in deep neural network (DNN) based speech enhancement. First, we investigate noise aware training by incorporating noise informationin the testutterance with anideal binary maskbased dynamic noise estimation approach to improve DNN’s speech separation ability from the noisy signal. Next, a set of more than 100 noise types is adopted to enrich the generalization capabilities of the DNN to unseen and non-stationary noise conditions. Finally, the quality of the enhanced speech can further be improved by global variance equalization. Empirical results show that each of the three proposed techniques contributes to the performance improvement. Compared to the conventional logarithmic minimum mean squared error speech enhancement method, our DNN system achieves 0.32 PESQ (perceptual evaluation of speech quality) improvement across six signal-tonoise ratio levels ranging from -5dB to 20dB on a test set with unknown noise types. We also observe that the combined strategies can well suppress highly non-stationary noise better than all the competing state-of-the-art techniques we have evaluated. Index Terms: Speech enhancement, deep neural networks, noise aware training, ideal binary mask, non-stationary noise
Combination of Multiplex PCRs for Staphylococcal Cassette Chromosome mec Type Assignment: Rapid Identification System for mec, ccr, and Major Differences in Junkyard Regions

ABSTRACT Staphylococcal cassette chromosome mec (SCCmec) typing, in combination with genotyping of the Staphylococcus aureus chromosome, has become essential for defining methicillin-resistant S. aureus (MRSA) clones in epidemiological studies. We have developed a convenient system for SCCmec type assignment. The system consists of six multiplex PCRs (M-PCRs) for identifying the ccr gene complex (ccr), the mec gene complex (mec), and specific structures in the junkyard (J) regions: M-PCR with primer set 1 (M-PCR 1) identified five types of ccr genes; M-PCR 2 identified class A to class C mec; M-PCRs 3 and 4 identified specific open reading frames in the J1 regions of type I and IV and of type II, III, and V SCCmec elements, respectively; M-PCR 5 identified the transposons Tn554 and ΨTn554 integrated into the J2 regions of type II and III SCCmec elements; and M-PCR 6 identified plasmids pT181 and pUB110 integrated into J3 regions. The system was validated with 99 MRSA strains carrying SCCmec elements of different types. The SCCmec types of 93 out of the 99 MRSA strains could be assigned. The SCCmec type assignments were identical to those made with a PCR system that uses numerous primer pairs to identify genes or gene alleles. Our system of six M-PCRs is thus a convenient and reliable method for typing SCCmec elements.
Determination of age at death using combined morphology and histology of the femur

Bone is characterised by age‐related morphological and histological changes. We have previously established an automated method of recording bone morphometry and histology from entire transverse sections of cortical bone. Our aim was to determine whether data acquired using this automated system were useful in the prediction of age. Ninety‐six specimens of human femoral middiaphysis were studied from subjects aged 21–92 y. Equations predicting specimen age were constructed using macroscopic data (total subperiosteal area (TSPA), periosteal perimeter (PP), endosteal perimeter (EP), cortical bone area (CA) and moments of area) and microscopic data (the number, size and diversity of pores and intracortical porosity) together with sex, height and weight. Both TSPA and PP were independent predictors of age but the number of pores was not a significant predictor of age in any equation. The age predicted by these equations was inaccurate by more than 8 y in over half the subjects. We conclude that we could not predict age at a clinically acceptable level using data from our automated system. This most likely reflects an insensitivity to regional age‐related changes in bone histology because we recorded data from each entire cortex. Automated bone measurement according to cortical region might be more useful in the prediction of age. The inclusion of TSPA together with PP as independent predictors of age raises the possibility that a future measure of periosteal shape at the femoral diaphysis could also be helpful in the prediction of age. The accuracy reached with the relatively simple methods described here is sufficient to encourage the development of image‐analysis systems for the automatic detection of more complex features.
Extensions of the Penalized Spline of Propensity Prediction Method of Imputation

Summary Little and An (2004, Statistica Sinica 14, 949–968) proposed a penalized spline of propensity prediction (PSPP) method of imputation of missing values that yields robust model‐based inference under the missing at random assumption. The propensity score for a missing variable is estimated and a regression model is fitted that includes the spline of the estimated logit propensity score as a covariate. The predicted unconditional mean of the missing variable has a double robustness (DR) property under misspecification of the imputation model. We show that a simplified version of PSPP, which does not center other regressors prior to including them in the prediction model, also has the DR property. We also propose two extensions of PSPP, namely, stratified PSPP and bivariate PSPP, that extend the DR property to inferences about conditional means. These extended PSPP methods are compared with the PSPP method and simple alternatives in a simulation study and applied to an online weight loss study conducted by Kaiser Permanente.
A system and mathematical framework to model shear flow effects in biomedical DW‐imaging and spectroscopy

The pulsed‐field gradient (PFG) MR experiment enables one to measure particle displacements, velocities, and even higher moments of complex fluid motions. In diffusion‐weighted MRI (DWI) in living tissue, where the PFG MRI experiment is used to measure diffusion, Brownian motion is assumed to dominate the displacements causing the observed signal loss. However, motions of water molecules caused by various active biological processes occurring at different length and time scales may also cause additional dephasing of magnetization and signal loss. To help understand their relative effects on the DWI signal attenuation, we used an integrated experimental and theoretical framework: a Rheo‐NMR, which served as an experimental model system to precisely prescribe a microscopic velocity distribution; and a mathematical model that relates the DW signal intensity in the Rheo‐NMR to experimental parameters that characterize the impressed velocity field. A technical innovation reported here is our use of ‘natural’ (in this case, polar) coordinates both to simplify the description the fluid motion within the Couette cell of the Rheo‐NMR, as well as to acquire and reconstruct magnitude and phase MR images obtained within it. We use this integrated model system to demonstrate how shear flows appears as pseudo‐diffusion in magnitude DW MR signals obtained using PFG spin‐echo (PGSE) NMR and MRI sequences. Our results lead us to reinterpret the possible causes of signal loss in DWI in vivo, in particular to revise and generalize the previous notion of intra‐voxel incoherent motion (IVIM) in order to describe activity driven flows that appear as pseudo‐diffusion over multiple length and time scales in living tissues. Copyright © 2010 John Wiley & Sons, Ltd.
Modeling Microwave Propagation in Natural Caves Passages

An approach for modeling the attenuation of radio signals at microwave frequencies in natural cave passages has been developed. The method involves sequentially modeling sections of uniform characteristics including straight segments, perhaps of differing cross-sectional shapes and sizes, curved segments, and sharp bends. Reasonably good correlation with experimental measurements has been demonstrated in a variety of cave passages although a few areas of discrepancy have been noted. The circumstances in which the theoretical results deviate from practice are discussed with a view to identifying the limitations of the technique for predicting performance.
Balancing the Energy Budget in Free-Ranging Male Myotis daubentonii Bats

Mammals use five main, mutually nonexclusive mechanisms to balance energy budgets: torpor, metabolic compensation, change in activity patterns, change in ingested energy, and/or variability in digestive efficiency. Bats, as small and actively flying mammals, have a high mass-specific energy demand; therefore, balancing mechanisms should be pronounced in this group. We found that male Myotis daubentonii exhibited marked variation in the relative importance of these different mechanisms during their period of seasonal activity in response to extrinsic (ambient temperature, insect abundance) and intrinsic (reproduction, body condition) factors. Cold ambient temperatures in spring facilitated long and frequent daily torpor bouts, whereas in early summer, increased energy intake was the dominant factor in energy balancing. Intake was further increased in late summer, when insect abundance was highest, and daily torpor bouts were shorter and less frequent than in early summer. In autumn, males used metabolic compensation to reduce their resting metabolic rate in addition to daily torpor. Metabolic compensation might be one of the mechanisms that allow males to maintain high body temperature during the day while decreasing the need for foraging time at night, thus maximizing their opportunities to mate.
Influence of the Implant Prosthetic Restorations Components on the StressValues and Distribution in Surrounding Bone - Finite Element Analysis Study

Background: This FEA study aims to help the dentists in choosing the most appropriate implant-prosthetic components for predictable results in cases of deficient bone quality and quantity; this type of analysis can be made without biological implications. Methods: we used 3.75 mm diameter implants, in molar mandibular area, with 8, 10, 11.5 and 13 mm lengths, straight, angled 15° and 25° abutments and a two mesio-distal dimensions metal-ceramic crown (12 and 7.6 mm). The von Mises stress distribution in bone was analyzed using IBM Autodesk Inventor 2014 software. Results: maximum von Mises stress decreases in cortical bone from 40.3 MPa for the 8 mm implant to 35.03 MPa for the 13 mm implant and in trabecular bone from 5.073 MPa to 4.214 MPa; in cortical bone is rising from 39.07 MPa in the straight abutment to 56.2 MPa in the 25° angled abutment, while in trabecular bone from 4.78 MPa to 5.371 MPa; in cortical bone is rising from 40.3 MPa for the 12 mm crown to 46.76 MPa for 7.6 mm crown, while in trabecular bone from 5.073 MPa to 5.932 MPa. Conclusions: using longer implants reduces the maximum stress’values in the implant-prosthetic restoration and also in bone. The stress distribution is independent to the implant’s length. Using angled abutments and also reduced mesio-distal dimension crowns raises the stress, especially in cortical bone.
Comparing morphological plasticity of root orders in slow- and fast-growing citrus rootstocks supplied with different nitrate levels.

BACKGROUND AND AIMS Studies of the plasticity of functional root traits involved in resource acquisition have focused mainly on root length without considering such 'morphological components' as biomass allocation, specific root length, root fineness, and tissue density that affect root length. The plasticity of the above components in response to nitrate supply was studied in each root order of two co-generic citrus rootstocks, namely the fast-growing Citrus jambhiri 'Rough Lemon' (RL) and the slow-growing Citrus reshni 'Cleopatra Mandarin' (CM). METHODS Morphological traits of individual root orders of CM and RL, grown at different nitrate levels (NO(3)-N at 0.1, 0.5, 1 and 10 mm) were examined by using an image-specific analysis system. KEY RESULTS At high nitrate levels, the root length ratio, root mass ratio and, to a lesser degree, specific root length, root fineness and tissue density of tap and 1st-order laterals in both CM and RL were reduced. In 2nd-order laterals, however, the same treatment led to increased values of each morphological trait in CM but decreased values of the same traits in RL. At low nitrate supply, CM exhibited longer tap roots whereas RL developed longer 2nd-order laterals. These effects were due to root mass ratio and, to a lesser extent, specific root length. CONCLUSIONS Biomass allocation was the main component of nitrate-induced changes in root length ratio. The 2nd-order laterals were more sensitive to nitrate availability than the tap root and 1st-order laterals. At low nitrate availability, RL displayed longer 2nd-order lateral roots and lower root plasticity than CM. This suggests a different root growth strategy among citrus rootstocks for adapting to nitrate availability: RL invests in 2nd-order laterals, the preferred zone for acquiring the nutrient, whereas CM responds with longer tap roots.
Irisin immunohistochemistry in gastrointestinal system cancers

Cancer is the leading cause of morbidity and mortality worldwide. Some studies have shown that high heat kills cancer cells. Irisin is a protein involved in heat production by converting white into brown adipose tissue, but there is no information about how its expression changes in cancerous tissues. We used irisin antibody immunohistochemistry to investigate changes in irisin expression in gastrointestinal cancers compared to normal tissues. Irisin was found in human brain neuroglial cells, esophageal epithelial cells, esophageal epidermoid carcinoma, esophageal adenocarcinoma and neuroendocrine esophageal carcinoma, gastric glands, gastric adenosquamous carcinoma, gastric neuroendocrine carcinoma, gastric signet ring cell carcinoma, neutrophils in vascular tissues, intestinal glands of colon, colon adenocarcinoma, mucinous colon adenocarcinoma, hepatocytes, hepatocellular carcinoma, islets of Langerhans, exocrine pancreas, acinar cells and interlobular and interlobular ducts of normal pancreas, pancreatic ductal adenocarcinoma, and intra- and interlobular ducts of cancerous pancreatic tissue. Histoscores (area × intensity) indicated that irisin was increased significantly in gastrointestinal cancer tissues, except liver cancers. Our findings suggest that the relation of irisin to cancer warrants further investigation.
The Effects of Image Compression on Automated DTM Generation

The effects of JPEG compression on automated DTM extraction via the approach of feature-based matching are investigated. JPEG lossy compression involves a truncation of higher spatial frequency data, a process which influences the accuracy of computation of grey-value gradients in the feature determination phases of image matching. Resulting accuracy effects on DTM heights obtained via the MATCH-T software system are investigated using a single stereomodel of 1:18,000 scale aerial photography at digital image resolutions of 15, 30, 45 and 60 µm. Heighting errors are computed for a range of compression ratios from 2:1 to about 40:1, illustrating that the impact of compression on DTM accuracy can be significant. It is concluded from this study that it is preferable to use the highest resolution available and to compress the image to the maximum extent allowed given the constraints of accuracy and image file size.
BORN AGAIN TREES

Tree predictors such as CART or C4.5 are often not as accurate as neural nets or use of multiple trees. But these latter methods lead to predictors whose structure is difficult to understand, whereas trees have a universal simplicity. Because of this, it is appealing to try and find tree representations of more complex predictors. We study tree representers of multiple tree predictors. These representers are larger, more stable and more accurate than trees grown the usual way. For this reason, we call them "born again" trees.
Similarity Metric Learning for Face Recognition

Recently, there is a considerable amount of efforts devoted to the problem of unconstrained face verification, where the task is to predict whether pairs of images are from the same person or not. This problem is challenging and difficult due to the large variations in face images. In this paper, we develop a novel regularization framework to learn similarity metrics for unconstrained face verification. We formulate its objective function by incorporating the robustness to the large intra-personal variations and the discriminative power of novel similarity metrics. In addition, our formulation is a convex optimization problem which guarantees the existence of its global solution. Experiments show that our proposed method achieves the state-of-the-art results on the challenging Labeled Faces in the Wild (LFW) database [10].
Neonatal isolation impairs neurogenesis in thedentate gyrus of the guinea pig

In the current study we examined the effects of early isolation rearing on cell proliferation, survival and differentiation in the dentate gyrus of the guinea pig. Animals were assigned to either a standard (control) or an isolated environment a few days after birth (P5–P6), taking advantage of the precocious independence from maternal care of the guinea pig. On P14–P17 animals received one daily bromodeoxyuridine injection, to label dividing cells, and were sacrificed either on P18, to evaluate cell proliferation or on P45, to evaluate cell survival and differentiation. In P18 isolated animals we found a reduced cell proliferation (−35%) compared to controls and a lower expression of brain‐derived neurotrophic factor (BDNF). Though in absolute terms P45 isolated animals had less surviving cells, they showed no differences in survival rate and phenotype percent distribution compared to controls. Looking at the location of the new neurons, we found that while in control animals 76% of them had migrated to the granule cell layer, in isolated animals only 55% of the new neurons had reached this layer. Examination of radial glia cells of P18 and P45 animals by vimentin immunohistochemistry showed that in isolated animals radial glia cells were reduced in density and had less and shorter processes. Granule cell count revealed that P45 isolated animals had less (−42%) granule cells than controls. Results show that isolation rearing reduces hippocampal cell proliferation, likely by reducing BDNF expression and hampers migration of the new neurons to the granule cell layer, likely by altering density/morphology of radial glia cells. The large reduction in granule cell number following isolation rearing emphasizes the role of environmental cues as relevant modulators of neurogenesis. © 2006 Wiley‐Liss, Inc.
Dynamic Cardiac PET Imaging: Extraction of Time-Activity Curves Using ICA and a Generalized Gaussian Distribution Model

Kinetic modeling of metabolic and physiologic cardiac processes in small animals requires an input function (IF) and a tissue time-activity curves (TACs). In this paper, we present a mathematical method based on independent component analysis (ICA) to extract the IF and the myocardium's TACs directly from dynamic positron emission tomography (PET) images. The method assumes a super-Gaussian distribution model for the blood activity, and a sub-Gaussian distribution model for the tissue activity. Our appreach was applied on 22 PET measurement sets of small animals, which were obtained from the three most frequently used cardiac radiotracers, namely: desoxy-fluoro-glucose (18F-FDG), [13 N]-ammonia, and [11C]-acetate. Our study was extended to PET human measurements obtained with the Rubidium-82 (82 Rb) radiotracer. The resolved mathematical IF values compare favorably to those derived from curves extracted from regions of interest (ROI), suggesting that the procedure presents a reliable alternative to serial blood sampling for small-animal cardiac PET studies.