Miracle-dz/UniFAR-FTUs huggingface dataset:
Flow Cytometry Pulse Width Data Enables Rapid and Sensitive Estimation of Biomass Dry Weight in the Microalgae Chlamydomonas reinhardtii and Chlorella vulgaris

Dry weight biomass is an important parameter in algaculture. Direct measurement requires weighing milligram quantities of dried biomass, which is problematic for small volume systems containing few cells, such as laboratory studies and high throughput assays in microwell plates. In these cases indirect methods must be used, inducing measurement artefacts which vary in severity with the cell type and conditions employed. Here, we utilise flow cytometry pulse width data for the estimation of cell density and biomass, using Chlorella vulgaris and Chlamydomonas reinhardtii as model algae and compare it to optical density methods. Measurement of cell concentration by flow cytometry was shown to be more sensitive than optical density at 750 nm (OD750) for monitoring culture growth. However, neither cell concentration nor optical density correlates well to biomass when growth conditions vary. Compared to the growth of C. vulgaris in TAP (tris-acetate-phosphate) medium, cells grown in TAP + glucose displayed a slowed cell division rate and a 2-fold increased dry biomass accumulation compared to growth without glucose. This was accompanied by increased cellular volume. Laser scattering characteristics during flow cytometry were used to estimate cell diameters and it was shown that an empirical but nonlinear relationship could be shown between flow cytometric pulse width and dry weight biomass per cell. This relationship could be linearised by the use of hypertonic conditions (1 M NaCl) to dehydrate the cells, as shown by density gradient centrifugation. Flow cytometry for biomass estimation is easy to perform, sensitive and offers more comprehensive information than optical density measurements. In addition, periodic flow cytometry measurements can be used to calibrate OD750 measurements for both convenience and accuracy. This approach is particularly useful for small samples and where cellular characteristics, especially cell size, are expected to vary during growth.
Purchases of ready-to-eat cereals vary across US household sociodemographic categories according to nutritional value and advertising targets

Abstract Objective To describe ready-to-eat (RTE) cereal purchases in 2008 in the USA according to cereal nutritional quality and marketing strategy and household sociodemographic characteristics. Design Cross-sectional study of purchases in one year. Each type of cereal was assigned to one of four nutrition quality categories (based on Nutrient Profile Index, NPI) and one of four advertising categories based on television exposure and analysis of packaging (child-targeted, family-targeted, adult-targeted and no television advertising). Medians and distributions of purchase indicators were calculated for the cereal categories and the distributions were compared across sociodemographic groups. Setting RTE cereals (n 249) with complete label and nutritional content. Subjects RTE cereal purchases according to household sociodemographic characteristics obtained from Nielsen Homescan, a nationally representative panel of households. Results Purchases of RTE cereals were highest in households with one or more child and lowest in African-American and Asian households, as well as those earning <$US 30 000 per annum. The lowest-quality products were purchased by four times as many households as the highest-quality cereals, but loyalty to these products was lower. Purchases of cereals by households with children and in African-American and Hispanic households increased as cereal nutritional quality declined. Compared with non-advertised products, advertised child-targeted cereals were purchased thirteen times more frequently; family-targeted brand purchases were ten times higher; and adult-targeted cereals were purchased four times more frequently. Conclusions Our findings suggest that improving the nutritional quality of RTE cereals with advertising targeted to children could also lead to increased consumption of healthier products by young people.
What Determines the Shape of an EQ-5D Index Distribution?

Background. EQ-5D-3L index scores in patient and general populations typically have a nonnormal distribution, divided into 2 distinct groups. It is important to understand to what extent this is determined by the way that the EQ-5D-3L index is constructed rather than by the true distribution of ill health. Objective. This paper examines the determinants of the “2 groups” distribution pattern and the extent to which this pattern is attributable either to the EQ-5D-3L classification system used to create health state profiles or to the weights applied to profiles. Methods. Data from the English NHS PROMs program (hip and knee replacements and varicose vein and hernia repairs) and from a study of 2 chronic conditions (asthma and angina) were used to compare the distributions of EQ-5D-3L index scores with distributions from which weights have been stripped; profile data decomposed into their constituent dimensions and levels; a condition-specific index; and using weights from different countries, based on both time tradeoff and visual analogue scale. Results. The EQ-5D-3L classification system generates differences between patients with the same condition in respect of dimensions that are mainly observed at level 2 or 3. The weights commonly used to calculate the index exacerbate this grouping by placing a larger weight on level 3 observations, generating a noticeable gap in index scores between the groups. Conclusions. Analyzing EQ-5D profile data enables a better understanding of the resulting distribution of EQ-5D scores. The distinctive shape observed for these distributions is the result of both the classification system and the weights applied to it.
Steady State Auditory Evoked Potentials in Normal Hearing Subjects: Evaluation of Threshold and Testing Time

Background: Steady state responses (SSRs), between 75 and 110 Hz, evoked by auditory amplitude modulated single or multiple tone stimuli, may be used to estimate objective hearing threshold. Methods: The aim of this study was to compare SSRs and click-evoked auditory brainstem responses (ABRs) in both ears of 20 adults (10 males and 10 females, aged between 24 and 36 years) with normal hearing threshold. Results: Mean ABR threshold was found at 21.25 (±5.9) dB nHL. Mean SSR threshold was found at 15.6 (±9.6) dB nHL after a single frequency stimulus (1 kHz); at 10.5 (±18.2) dB nHL and at 7.1 (±12.4) dB nHL after bifrequency stimulation (0.5 and 2 kHz). SSR thresholds after multifrequency stimulation (0.5, 1, 2 and 4 kHz) were found, respectively, at 12.1 (±12.9) dB nHL, 12.2 (±12.8) dB nHL, 12.3 (±8.3) dB nHL and 18.9 (±17.2) dB nHL. Mean duration of the recording session was 6 min in the case of ABRs, while it was 25 min in the single frequency condition and 29 min in the multifrequency condition in the case of SSRs. Conclusion: SSRs can be used for frequency-specific objective audiometry. The multifrequency stimulation greatly reduces the whole testing time.
Hydrophobicity of fluorocarbon-finished electrospun poly (acrylonitrile) nanofibrous webs

Abstract This article reports the hydrophobicity of fluorocarbon-finished nanofibrous webs composed of electrospun poly (acrylonitrile) nanofibers with fiber diameter in the range of about 100–3000 nm. The results obtained from sliding angle and contact angle measurements tests are reported. It was found that the contact angle of unfinished samples with average fiber diameters of about 700, 980 , and 3050 nm lies between 132° and 134°, indicating a rather high and at the same time not much different hydrophobicity for the webs. However, after finishing the electrospun nano- and microfibrous webs, the contact angle increased by a considerable amount to 138°–157° for the webs with average fiber diameter in the range of about 100–3050 nm, respectively. Sliding angle test of the finished nanofibrous webs showed a minimum angle of about 3° for the web with average fiber diameter of 3055 nm. To the best of authors’ knowledge, the rolling angle of 3° is the smallest rolling angle ever reported in the literature. The result of this work showed also that sliding angle test may be more sensitive than contact angle test. It was also ascertained that none of the Wenzel model and Cassie–Baxter model can represent the superhydrophobicity of the fluorocarbon-finished nano- and microfibrous webs.
A Two-Stage Reconstruction Processor for Human Detection in Compressive Sensing CMOS Radar

Complementary metal-oxide-semiconductor (CMOS) radar has recently gained much research attraction because small and low-power CMOS devices are very suitable for deploying sensing nodes in a low-power wireless sensing system. This study focuses on the signal processing of a wireless CMOS impulse radar system that can detect humans and objects in the home-care internet-of-things sensing system. The challenges of low-power CMOS radar systems are the weakness of human signals and the high computational complexity of the target detection algorithm. The compressive sensing-based detection algorithm can relax the computational costs by avoiding the utilization of matched filters and reducing the analog-to-digital converter bandwidth requirement. The orthogonal matching pursuit (OMP) is one of the popular signal reconstruction algorithms for compressive sensing radar; however, the complexity is still very high because the high resolution of human respiration leads to high-dimension signal reconstruction. Thus, this paper proposes a two-stage reconstruction algorithm for compressive sensing radar. The proposed algorithm not only has lower complexity than the OMP algorithm by 75% but also achieves better positioning performance than the OMP algorithm especially in noisy environments. This study also designed and implemented the algorithm by using Vertex-7 FPGA chip (Xilinx, San Jose, CA, USA). The proposed reconstruction processor can support the 256×13 real-time radar image display with a throughput of 28.2 frames per second.
Serglycin as a potential biomarker for glioma: association of serglycin expression, extent of mast cell recruitment and glioblastoma progression

Serglycin is an intracellular proteoglycan with a unique ability to adopt highly divergent structures by glycosylation with variable types of glycosaminoglycans (GAGs) when expressed by different cell types. Serglycin is overexpressed in aggressive cancers suggesting its protumorigenic role. In this study, we explored the expression of serglycin in human glioma and its correlation with survival and immune cell infiltration. We demonstrate that serglycin is expressed in glioma and that increased expression predicts poor survival of patients. Analysis of serglycin expression in a large cohort of low- and high-grade human glioma samples reveals that its expression is grade dependent and is positively correlated with mast cell (MC) infiltration. Moreover, serglycin expression in patient-derived glioma cells is significantly increased upon MC co-culture. This is also accompanied by increased expression of CXCL12, CXCL10, as well as markers of cancer progression, including CD44, ZEB1 and vimentin. In conclusion, these findings indicate the importance of infiltrating MCs in glioma by modulating signaling cascades involving serglycin, CD44 and ZEB1. The present investigation reveals serglycin as a potential prognostic marker for glioma and demonstrates an association with the extent of MC recruitment and glioma progression, uncovering potential future therapeutic opportunities for patients.
Base Cases for Assessing Risk in Transmission System Planning

This paper discusses probabilistic methodology for Transmission System Planning. Recent NESCOE memo suggested that current transmission planning procedure at ISO-NE might create inconsistency within the region and between the development plans of various transmission owners. The proposed methodology establishes base cases and contingency testing as means for consistent probabilistic assessment of reliability for a proposed transmission system plan. The system stress is computed through consistent probabilistic modeling and the base cases established by systematically sampling corresponding probability distributions. The methodology is illustrated for a simplified two-zone model of the power system.
Computer simulations of reentrant activity in the rabbit sinoatrial node

With the aid of detailed computer simulations, we have estimated distributions of membrane potential and ionic currents in the core region of a sinoatrial node reentry. We observe reduced amplitudes of the measured quantities in the core; the core sizes for potential and currents did not always coincide. Simulations revealed that acetylcholine, when applied in the vicinity of unstable reentry, attracted the reentry to become the core and to stabilize its rotation. Anatomically detailed simulations of sinoatrial node and surrounding atrial tissue revealed that reentry always rotated around small strips of connective tissue. Acetylcholine superfusion over superior part of the sinoatrial node resulted in a drift of reentry in the cranial direction. Under the latter conditions, reentry may coexist with the pacemaker in the caudal part of the sinoatrial node. Copyright © 2016 John Wiley & Sons, Ltd.
Entropy of Spatial Network Ensembles

We analyze complexity in spatial network ensembles through the lens of graph entropy. Mathematically, we model a spatial network as a soft random geometric graph, i.e., a graph with two sources of randomness, namely nodes located randomly in space and links formed independently between pairs of nodes with probability given by a specified function (the "pair connection function") of their mutual distance. We consider the general case where randomness arises in node positions as well as pairwise connections (i.e., for a given pair distance, the corresponding edge state is a random variable). Classical random geometric graph and exponential graph models can be recovered in certain limits. We derive a simple bound for the entropy of a spatial network ensemble and calculate the conditional entropy of an ensemble given the node location distribution for hard and soft (probabilistic) pair connection functions. Under this formalism, we derive the connection function that yields maximum entropy under general constraints. Finally, we apply our analytical framework to study two practical examples: ad hoc wireless networks and the US flight network. Through the study of these examples, we illustrate that both exhibit properties that are indicative of nearly maximally entropic ensembles.
Mutation analysis in primary immunodeficiency diseases: case studies

Purpose of review The application of mutation analysis is becoming an integral part of the complete evaluation of patients with primary immunodeficiencies, and as such, clinicians caring for these patients must develop a better understanding of the utility and challenges of this important laboratory technology. Recent findings Genomic DNA sequencing is currently the standard approach used to characterize a possible gene mutation causing a specific primary immunodeficiency. There are clinical situations in which this approach is revealing of a genetic defect and other circumstances in which this generates a false-positive or false-negative result. One case study is presented that reviews a straightforward analysis that clarifies the genetic basis of a primary immunodeficiency, and four cases are presented that required additional studies to clarify the underlying basis of the immunodeficiency. In the latter circumstances, the rationale for additional studies is outlined and the outcome of these is presented. Summary The identification of a gene mutation as the underlying basis of a primary immunodeficiency begins with the evaluation of the clinical presentation focusing on the infection history so as to develop a differential diagnosis including potential genetic causes. The next step is to obtain specific laboratory studies, including immunologic function evaluation, and, based on these findings, to proceed with DNA sequencing of one or several selected candidate genes. Genomic DNA sequencing has certain limitations, and alternative follow-up approaches may be necessary to establish the molecular basis of the primary immunodeficiency in a given patient.
The Devil is in the Middle: Exploiting Mid-level Representations for Cross-Domain Instance Matching

Many vision problems require matching images of object instances across different domains. These include fine-grained sketch-based image retrieval (FG-SBIR) and Person Re-identification (person ReID). Existing approaches attempt to learn a joint embedding space where images from different domains can be directly compared. In most cases, this space is defined by the output of the final layer of a deep neural network (DNN), which primarily contains features of a high semantic level. In this paper, we argue that both high and mid-level features are relevant for cross-domain instance matching (CDIM). Importantly, mid-level features already exist in earlier layers of the DNN. They just need to be extracted, represented, and fused properly with the final layer. Based on this simple but powerful idea, we propose a unified framework for CDIM. Instantiating our framework for FG-SBIR and ReID, we show that our simple models can easily beat the state-of-the-art models, which are often equipped with much more elaborate architectures.
ImmunoFISH Is a Reliable Technique for the Assessment of 1p and 19q Status in Oligodendrogliomas

Objective To develop a new ImmunoFISH technique for the study of oligodendrogliomas by combining a standard immunohistochemical stain using MIB-1 antibody with a standard FISH technique using commercial 1p36 and 19q13 chromosomal probes. Methods Validation was performed by two observers on a series of 36 pre-selected oligodendrogliomas and compared to the results previously determined by FISH alone. Results The ImFISH technique is easy to perform and to analyze and is no more time-consuming than the usual FISH technique. Our results show that the inter-observer reliability of ImFISH is high (κ = 0.86 and 0.95 respectively for 1p and 19q). Compared to FISH, the ImFISH exhibits a very high sensitivity (∼100%) and specificity (∼90%) for 1p and/or 19q deleted cases. The sensitivity is high for normal cases (∼85%) and imbalanced cases (∼90%) with a specificity ranging between 50 and 85%. Finally, there were no significant differences between FISH and ImFISH results calculated on 60, 40 or 20 cells. Conclusion Our study demonstrates the reliability of the ImFISH technique in oligodendrogliomas and emphasizes its advantage in poorly cellular tumoral specimen.
The Effect of Dopaminergic Medication on Joint Kinematics during Haptic Movements in Individuals with Parkinson's Disease

This study examined whether altered joint angular motion during haptic exploration could account for a decline in haptic sensitivity in individuals with PD by analyzing joint position data during haptic exploration of a curved contour. Each participant's hand was passively moved by a robotic arm along the edges of a virtual box (5 cm × 15 cm) with a curved left wall. After each trial, participants indicated whether the contour was curved or straight. Visual, auditory, and tactile cues were occluded, and an electrogoniometer recorded shoulder and elbow joint angles during each trial. The PD group in the OFF state had a higher mean detection threshold (4.67 m−1) than the control group (3.06 m−1). Individuals with PD in the OFF state also had a significantly greater magnitude of shoulder abduction than those in the ON state (p = 0.003) and a smaller magnitude of elbow flexion than those in the ON state or compared to the control group (both p < 0.001). These findings suggest that individuals with PD employ joint configurations that may contribute to haptic insensitivity. Dopamine replacement therapy improved joint configurations during haptic exploration in patients with PD, suggesting a role for dopaminergic dysfunction in PD-related haptic insensitivity.
Second cancer risk in childhood cancer survivors treated with intensity‐modulated radiation therapy (IMRT)

Treatment with radiotherapy (RT) is associated with an increased risk of second malignant neoplasms (SMNs) in childhood cancer survivors; it is unclear how treatment with intensity‐modulated radiation therapy (IMRT) impacts this risk. We provide the first report of SMN risk in a cohort of childhood cancer survivors treated with IMRT.
A bi-level text classification approach for sms spam filtering and identifying priority messages

Short Message Service (SMS) traffic is increasing day by day and trillions of sms are sent and received by billions of users every day. Spam messages are also increasing in same proportionate. Numbers of recent advancements are taking place in the field of sms spam detection and filtering. The objective of this work is twofold, first is to identify and classify spam messages from the collection of sms messages and second is to identify the priority or important sms messages from the filtered non-spam messages. The objective of the work is to categorize the sms messages for effective management and handling of sms messages. the work is planned in two level of binary classification wherein at the first level of classification the sms messages are categorized into the two classes spam and non-spam using popular binary classifiers, and then at the second level of classification non-spam sms messages are further categorized into the priority and normal sms messages. four state of the art popular text classification techniques namely, Naïve Bayes (NB), Support Vector Machine (SVM), Latent Dirichlet Allocation (LDA) and Non-negative Matrix Factorization (NMF) are used to categorize the sms text message at different levels of classification. The proposed bi-level classification model is also evaluated using the performance measures accuracy and fmeasure. Combinations of classifiers at both levels are compared and it is shown from the experiments that SVM algorithm performs better for filtering the spam messages and categorizing the priority messages.
Human Adipose-Derived Mesenchymal Stem/Stromal Cells Handling Protocols. Lipid Droplets and Proteins Double-Staining

Human Adipose-derived mesenchymal stem/stromal cells (hASCs) are of great interest because of their potential for therapeutic approaches. The method described here covers every single step necessary for hASCs isolation from subcutaneous abdominal adipose tissue, multicolor phenotyping by flow cytometry, and quantitative determination of adipogenic differentiation status by means of lipid droplets (LDs) accumulation, and Western blot analysis. Moreover, to simultaneously analyze both LDs accumulation and cellular proteins localization by fluorescence microscopy, we combined Oil Red O (ORO) staining with immunofluorescence detection. For LDs quantification we wrote a program for automatic ORO-stained digital image processing implemented in Octave, a freely available software package. Our method is based on the use of the traditional low cost neutral lipids dye ORO, which can be imaged both by bright-field and fluorescence microscopy. The utilization of ORO instead of other more expensive lipid-specific dyes, together with the fact that the whole method has been designed employing cost-effective culture reagents (standard culture medium and serum), makes it affordable for tight-budget research laboratories. These may be replaced, if necessary or desired, by defined xeno-free reagents for clinical research and applications.