Miracle-dz/UniFAR-FTUs huggingface dataset:
Conformal mapping of nuclei in 3D tomographic cell images to assess shape heterogeneity

Nuclear shape and its heterogeneity are diagnostically important criteria used by pathologists in cancer diagnosis. Pathology assessment is currently qualitative and is based on 2D brightfield microscopy images. We propose an imaging informatics framework to quantify nuclear pleomorphism by statistical characterization of 3D nuclear shape. We applied optical projection tomographic microscopy (OPTM) to image individual hematoxylin and eosin-stained cells with isotropic, sub-micron spatial resolution. We used adaptive thresholding schemes to segment cells and nuclei, and applied spherical conformal mapping methods on the 3D nuclear masks to compute 256 rotation invariant coefficients as shape descriptors for each nucleus. As a first application, we tested our methods on normal and cancerous epithelial cell lines derived from human esophagus and breast, analyzing 10 cell images per class. We applied ANOVA techniques to assess variations in nuclear shape within each cell type and among the four cell types. The automated segmentation was 96% accurate compared to manual tracing of the volumes of interest. Statistical analysis of shape coefficients revealed that cancer cell nuclei from both organs exhibited considerably larger variance in their coefficients relative to the corresponding normal cell nuclei. Our results demonstrate the promise of our methodology for the development of quantitative pathological assessments.
Studying the experience of mobile applications used in different contexts of daily life

Mobile applications and services increasingly assist us in our daily life situations, fulfilling our needs for information, communication, entertainment or leisure. However, user acceptance of a mobile application depends on at least two conditions; the application's perceived Quality of Experience (QoE) and the appropriateness of the application to the user's situation and context. Yet, there is generally a weak understanding of a mobile user's QoE and the factors influencing it. The mobile user's experience is related to the Quality of Service (QoS) provided by the underlying service and network infrastructures, which provides a starting point for our work. We present "work-in-progress" results from an ongoing study of Android phone users. In this study, we aim to derive and improve understanding of their QoE in different situations and daily life environments. In particular, we evaluate the user's qualitative QoE for a set of widely used mobile applications in the users' natural environments and different contexts, and we analyze this experience and its relation to the underlying quantitative QoS. In our approach we collect both QoE and QoS measures through a combination of user, application and network input from mobile phones. We present initial data acquired in the study and derived from that, a set of preliminary implications for mobile applications design.
The effect of tap water, carbonated water, sodium bicarbonate, and calcium chloride on blood acid-base balance in cockerels subjected to heat stress.

Twenty Hubbard cockerels each weighing 2.4 kg were surgically fitted with plastic cannulae in the carotid artery and crop. A solution of either tap water (TW), carbonated water (CW), 2% sodium bicarbonate (HCO3-), or 3.5% calcium chloride (CaCl2) with pH of 7.8, 5.2, 8.0, and 7.4, respectively, was infused into the crop at . 41 ml X min-1 X kg body weight (BW)-1. Blood pH, carbon dioxide partial pressure (PCO2), and respiratory rate (RR) were measured at 15-min intervals during a 90-min thermoneutral period (25 C) followed by a 90-min heat stress (37 C). Polypnea occurred in all treatments in the 37 C environment. Infusion of HCO3- increased blood pH throughout the thermoneutral and heat stress periods, and CaCl2 infusion decreased blood pH throughout the experimental periods. At thermoneutral temperature, TW and CW infusions did not affect blood pH or PCO2. During heat stress, blood pH increased in TW and CW treatments; change and final pH were significantly lower (P less than .05) for CW- compared with TW-infused birds. Although blood PCO2 decreased in all treatments with the imposition of heat stress, blood PCO2 was significantly greater (P less than .05) in birds infused with HCO3- at the end of the heat-stress period. The results demonstrate that CW treatment produced a more favorable acid-base balance during acute heat stress than TW by reducing blood pH change during thermal polypnea. Also, high levels of NaHCO3 and CaCl2 intake can produce abnormal acid-base equilibrium conditions during the heat stress-induced respiratory alkalosis.
Mining Health Examination Records—A Graph-Based Approach

General health examination is an integral part of healthcare in many countries. Identifying the participants at risk is important for early warning and preventive intervention. The fundamental challenge of learning a classification model for risk prediction lies in the unlabeled data that constitutes the majority of the collected dataset. Particularly, the unlabeled data describes the participants in health examinations whose health conditions can vary greatly from healthy to very-ill. There is no ground truth for differentiating their states of health. In this paper, we propose a graph-based, semi-supervised learning algorithm called SHG-Health (Semi-supervised Heterogeneous Graph on Health) for risk predictions to classify a progressively developing situation with the majority of the data unlabeled. An efficient iterative algorithm is designed and the proof of convergence is given. Extensive experiments based on both real health examination datasets and synthetic datasets are performed to show the effectiveness and efficiency of our method.
Conceptual Models of Disability and Their Role in the Daily Routine of Clinical Rehabilitation

The aim of this paper is to analyse how the different conceptual models of disability can help daily work of rehabilitation clinicians. Previous papers described the usefulness in rehabilitation psychology of the International classification of Functioning, Disability and Health (ICF) a worldwide-known conceptual model of disability [1-6] In this paper, we describe how other conceptual models could be useful for rehabilitation clinicians [7-8]. A Narrative review of the literature on conceptual models of disability was undertaken. Based on a previous history of Conceptual models of disability in the 20° century, we describe four groups of models and their impact on rehabilitation: models that analysed the role of pathology, models that analysed the relationship between pathology and its consequences, models that emphasized the role of the environment, and models that analysed the relationship between person and environment. In the daily routine of rehabilitation psychology and in general in rehabilitation sciences, as in the theoretical analysis, one can choose one or another of these options, although the history of the conceptual models of disability shows that the fourth option is the most advanced and the most worldwide-recognized (thanks to the ICF). As for rehabilitation clinicians, the awareness of the chosen option can help in understanding the focus of intervention and to modify it. The main aims of this process is to transform the disablement process into a positive one by which the person can be enabled.
Prestin as an Otologic Biomarker of Cisplatin Ototoxicity in a Guinea Pig Model

Objective To evaluate (1) whether changes in serum prestin aid in early detection of cisplatin ototoxicity, (2) the role of diltiazem as an otoprotectant, and (3) whether prestin levels are sensitive to effects of diltiazem. Study Design Experimental animal study. Setting Translational research laboratory. Subjects Twenty female guinea pigs. Methods Two groups of 10 guinea pigs were used. The relationship between serum prestin levels and auditory brainstem response (ABR) thresholds was compared between the groups. All animals had baseline blood draws and ABR thresholds recorded prior to cisplatin administration. Intraperitoneal cisplatin bolus (8 mg/kg) was administered followed by 5 consecutive days of intratympanic (IT) diltiazem (2 mg/kg) or sham IT-saline injection. Serum prestin levels and ABR thresholds were measured at days 1, 2, 3, 7, and 14 postcisplatin. Results In sham, IT-saline–treated animals, mean prestin levels were elevated above baseline on days 1 to 7. The prestin levels were significantly elevated from baseline on day 1 (P < .001), while significant ABR threshold elevations did not occur until day 2 (P = .028) for click-evoked ABRs and day 3 (P = .041) for tones. In diltiazem-treated animals, prestin levels were not elevated above baseline but ABR thresholds were elevated on days 1 to 3. However, the thresholds returned toward baseline on days 7 and 14. Conclusion Changes in serum prestin levels were detectable prior to shifts in ABR thresholds in a guinea pig cisplatin ototoxicity model. These changes did not occur in diltiazem-treated animals. Prestin may serve as a biomarker of cochlear injury that is sensitive to therapeutic interventions in cisplatin ototoxicity.
Speciation of “brown” carbon in cloud water impacted by agricultural biomass burning in eastern China

Despite growing interest in the visible light‐absorbing organic component of atmospheric aerosols, referred to as “brown” carbon, our knowledge of its chemical composition remains limited. It is well accepted that biomass burning is one important source of “brown” carbon in the atmosphere. In this study, cloud water samples heavily affected by biomass burning were collected at Mount Tai (1534 m, ASL), located in Shandong province in the North China Plain in summer 2008. The samples were analyzed with high performance liquid chromatography equipped with a UV/Vis absorbance detector immediately followed by electrospray ionization and analysis using a time‐of‐flight (ToF) mass spectrometer. The high mass resolution and accuracy provided by the ToF mass spectrometer allow determination of the elemental composition of detected ions. Using this approach, the elemental compositions of 16 major light‐absorbing compounds, which together accounted for approximately half of measured sample absorption between 300 and 400 nm, were determined. The most important classes of light‐absorbing compounds were found to be nitrophenols and aromatic carbonyls. Light absorption over this wavelength range by reduced nitrogen compounds was insignificant in these samples.
Necrotizing pancreatitis: Diagnose, treat, consult

Necrosis significantly increases rates of morbidity and mortality in acute pancreatitis. Hospitalists and general internists are on the front lines in identifying severe cases and consulting the appropriate specialists for optimal multidisciplinary care. Patients may need intensive care, nutritional support, antibiotics, and radiologic, endoscopic, or surgical interventions.
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

MOTIVATION Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10 kb in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long reads have an error rate as high as 10-15%. Complex and computationally intensive pipelines are required to assemble such reads. RESULTS We present a new mapper, minimap and a de novo assembler, miniasm, for efficiently mapping and assembling SMRT and ONT reads without an error correction stage. They can often assemble a sequencing run of bacterial data into a single contig in a few minutes, and assemble 45-fold Caenorhabditis elegans data in 9 min, orders of magnitude faster than the existing pipelines, though the consensus sequence error rate is as high as raw reads. We also introduce a pairwise read mapping format and a graphical fragment assembly format, and demonstrate the interoperability between ours and current tools. AVAILABILITY AND IMPLEMENTATION https://github.com/lh3/minimap and https://github.com/lh3/miniasm CONTACT hengli@broadinstitute.org SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
The genetic basis of the birchen pattern of the domestic fowl.

Abstract The primary plumage pattern of the gold-barred Fayoumi fowl is determined in part by the birchen (ER) allele at the E pigment locus. The ER allele is similar to E in its effect on the chick and adult female patterns. The chick down is black and the adult plumage is black with dark brown pigment in the lateral margin of feathers in the mid-hackle region. The adult male is wild type with black secondaries, similar to the birchen phenotype. The birchen allele (ER) is dominant to eWhe+ and eb, and interacts wit h the columbian-like factor, Db, in a manner distinct from the more dominant allele, E.
Reading Wikipedia to Answer Open-Domain Questions

This paper proposes to tackle open-domain question answering using Wikipedia as the unique knowledge source: the answer to any factoid question is a text span in a Wikipedia article. This task of machine reading at scale combines the challenges of document retrieval (finding the relevant articles) with that of machine comprehension of text (identifying the answer spans from those articles). Our approach combines a search component based on bigram hashing and TF-IDF matching with a multi-layer recurrent neural network model trained to detect answers in Wikipedia paragraphs. Our experiments on multiple existing QA datasets indicate that (1) both modules are highly competitive with respect to existing counterparts and (2) multitask learning using distant supervision on their combination is an effective complete system on this challenging task.
Crushed Hydrated Fly Ash as a Construction Aggregate

Hydrated fly ash (HFA) is being produced in Texas by first adding water to Class C fly ash and allowing it to hydrate in curing pits for several weeks. HFA typically attain unconfined compressive strengths as high as 15 MPa. Once the HFA gains an acceptable level of strength, it is crushed using specialized equipment to produce an aggregate material with characteristics very similar to those of conventional granular materials such as crushed limestone. In certain regions of Texas, where quality aggregate base materials are in short supply, this synthetic aggregate material has been used in the construction of road bases on an experimental basis. Experience from the use of HFA ash in these different regions has been quite variable. This paper provides an overview of HFA as a construction aggregate, and documents the experience from its use as a road base material.
Adult executive functioning inventory (ADEXI): Validity, reliability, and relations to ADHD

This study examined the psychometric properties of the Adult Executive Functioning Inventory (ADEXI). This new executive functioning (EF) rating instrument has the advantage of being brief (14 items) and focusing specifically on working memory and inhibitory control. Results showed that scores on the ADEXI had high internal consistency and adequate test–retest reliability, but low concurrence between self‐ratings and other ratings. High and statistically significant correlations were found between ADEXI scores and scores from another EF rating instrument, whereas the correlations between ADEXI scores and neuropsychological test scores were weak and often non‐significant. Furthermore, with regard to discriminant validity, individuals with attention deficit hyperactivity disorder (ADHD) had significantly higher scores on both the inhibition and working memory subscales compared to clinical as well as non‐clinical controls. The results showed high specificity, but relatively low sensitivity, when discriminating between adults with ADHD and non‐clinical controls. Conclusively, the ADEXI can be a valuable screening instrument for assessing deficits in working memory and inhibitory control. However, similarly to other EF ratings, the ADEXI should be used as a complement rather than as a replacement for neuropsychological tests, and the low interrater reliability suggests that ratings from multiple sources is preferable compared to relying solely on self‐ratings.
Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks

Linking synaptic connectivity to dynamics is key to understanding information processing in neocortex. Circuit dynamics emerge from complex interactions of interconnected neurons, necessitating that links between connectivity and dynamics be evaluated at the network level. Here we map propagating activity in large neuronal ensembles from mouse neocortex and compare it to a recurrent network model, where connectivity can be precisely measured and manipulated. We find that a dynamical feature dominates statistical descriptions of propagating activity for both neocortex and the model: convergent clusters comprised of fan-in triangle motifs, where two input neurons are themselves connected. Fan-in triangles coordinate the timing of presynaptic inputs during ongoing activity to effectively generate postsynaptic spiking. As a result, paradoxically, fan-in triangles dominate the statistics of spike propagation even in randomly connected recurrent networks. Interplay between higher-order synaptic connectivity and the integrative properties of neurons constrains the structure of network dynamics and shapes the routing of information in neocortex.
Efficacy of hydrated sodium calcium aluminosilicate to reduce the individual and combined toxicity of aflatoxin and ochratoxin A.

A 2 x 2 x 2 factorial arrangement of treatments consisting of dietary aflatoxin (3.5 micrograms/g), ochratoxin A (2.0 micrograms/g), and hydrated sodium calcium aluminosilicate (HSCAS, .5%) was used to evaluate the individual and combined effects of these treatments. There were six replicate pens of 10 broilers per pen for each of the eight treatments. The broilers were maintained on these treatments from 1 day to 3 wk of age with feed and water available for ad libitum intake. Aflatoxin and ochratoxin A each significantly decreased body weight, serum protein, albumin, and cholesterol and increased the relative weight of the liver, kidney, and proventriculus. Aflatoxin increased the relative weight of the heart and decreased serum aspartate aminotransferase activity and ochratoxin A increased serum uric acid. The toxicity resulting from the combination of aflatoxin and ochratoxin A was more severe than when either of these mycotoxins were present alone. Addition of HSCAS alone did not alter any of the parameters evaluated. The HSCAS reduced the toxicity of aflatoxin, but had little effect on either the toxicity of ochratoxin A alone or the toxicity resulting from the combination of aflatoxin and ochratoxin A.
Social Networking Sites in Romantic Relationships: Attachment, Uncertainty, and Partner Surveillance on Facebook

Social networking sites serve as both a source of information and a source of tension between romantic partners. Previous studies have investigated the use of Facebook for monitoring former and current romantic partners, but why certain individuals engage in this behavior has not been fully explained. College students (N=328) participated in an online survey that examined two potential explanatory variables for interpersonal electronic surveillance (IES) of romantic partners: attachment style and relational uncertainty. Attachment style predicted both uncertainty and IES, with preoccupieds and fearfuls reporting the highest levels. Uncertainty did not predict IES, however. Future directions for research on romantic relationships and online surveillance are explored.
Active Rheumatoid Arthritis in Central Africa: A Comparative Study Between Sudan and Sweden

Objective. To compare clinical characteristics and treatment between simultaneously investigated Sudanese and Swedish outpatients with rheumatoid arthritis (RA). Methods. Outpatients with RA from Sudan (n = 281) and Sweden (n = 542) diagnosed according to the 1987 American College of Rheumatology criteria were recruited between December 2008 and September 2010 and compared concerning clinical presentation, treatment, and laboratory findings, including immunoglobulin M with rheumatoid factor (IgM-RF). Results. Sudanese patients had lower inclusion age (median 49 vs 68 yrs), disease duration (48 vs 107 mos), and disease onset age (43 vs 56 yrs) as compared with Swedish patients (p < 0.0001 for all). When stratified concerning the age of inclusion, Swedish patients between 41–50 years had, however, a significantly lower age of onset, with a similar trend for all age groups above 30 years. The female preponderance was higher among Sudanese patients (89.3% vs 72.5%, p < 0.0001), and smoking was nonexistent among Sudanese female patients (p < 0.0001). Erythrocyte sedimentation rate levels and number of tender joints were significantly higher among Sudanese patients. The proportion of IgM-RF positivity was lower among Sudanese patients with RA (52.4% vs 75.5%, p < 0.0001). Higher proportions of Sudanese patients with RA were treated with methotrexate (MTX) and disease-modifying antirheumatic drug combinations, but none of them used biologics. Sudanese patients used lower doses of MTX and sulfasalazine (p < 0.0001) and higher doses of prednisolone (p < 0.0001) than Swedish patients. Conclusion. Sudanese patients with RA have significantly higher disease activity and are often IgM-RF–seronegative. Together with reports from Uganda and Cameroon, our data indicate a cluster of highly active and often seronegative RA in central Africa.
Ice algal bloom development on the surface of the Greenland Ice Sheet

ABSTRACT It is fundamental to understand the development of Zygnematophycean (Streptophyte) micro‐algal blooms within Greenland Ice Sheet (GrIS) supraglacial environments, given their potential to significantly impact both physical (melt) and chemical (carbon and nutrient cycling) surface characteristics. Here, we report on a space‐for‐time assessment of a GrIS ice algal bloom, achieved by sampling an ˜85 km transect spanning the south‐western GrIS bare ice zone during the 2016 ablation season. Cell abundances ranged from 0 to 1.6 × 104 cells ml−1, with algal biomass demonstrated to increase in surface ice with time since snow line retreat (R2 = 0.73, P < 0.05). A suite of light harvesting and photo‐protective pigments were quantified across transects (chlorophylls, carotenoids and phenols) and shown to increase in concert with algal biomass. Ice algal communities drove net autotrophy of surface ice, with maximal rates of net production averaging 0.52 ± 0.04 mg C l−1 d−1, and a total accumulation of 1.306 Gg C (15.82 ± 8.14 kg C km−2) predicted for the 2016 ablation season across an 8.24 × 104 km2 region of the GrIS. By advancing our understanding of ice algal bloom development, this study marks an important step toward projecting bloom occurrence and impacts into the future.
Magnetic Field Measurement Based on the Sagnac Interferometer With a Ferrofluid-Filled High-Birefringence Photonic Crystal Fiber

A compact optical fiber magnetic field sensor based on the principle of the Sagnac interferometer is proposed. Different from the conventional ones, a ferrofluid-filled high-birefringence photonic crystal fiber (HB-PCF) is inserted into the Sagnac as a magnetic field sensing element. The refractive index of the ferrofluid filled in the cladding air holes of the HB-PCF will change with respect to the applied magnetic field, and subsequently, the birefringence of the HB-PCF will change, which will affect the shifts of the output interference spectrum in Sagnac. Experiments are carried out to verify the simulation model and the results indicate that the interference spectrum exhibits a red shift with the increment in the magnetic field intensity. The sensitivity of the proposed sensor is up to 0.073 nm/mT for a magnetic field intensity ranging from 10 to 40 mT, while the resolution is 0.001 mT. The proposed magnetic field sensor is attractive due to its compact size, low cost, and immunity to electromagnetic interference beyond what conventional magnetic field sensors can offer.