Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracting Information for Generating A Diabetes Report Card from Free Text in Physicians Notes

Achieving guideline-based targets in patients with diabetes is crucial for improving clinical outcomes and preventing long-term complications. Using electronic heath records (EHRs) to identify high-risk patients for further intervention by screening large populations is limited because many EHRs store clinical information as dictated and transcribed free text notes that are not amenable to statistical analysis. This paper presents the process of extracting elements needed for generating a diabetes report card from free text notes written in English. Numerical measurements, representing lab values and physical examinations results are extracted from free text documents and then stored in a structured database. Extracting diagnosis information and medication lists are work in progress. The complete dataset for this project is comprised of 81,932 documents from 30,459 patients collected over a period of 5 years. The patient population is considered high risk for diabetes as they have existing cardiovascular complications. Experimental results validate our method, demonstrating high precision (88.8--100%).
Dual energy X-ray absorptiometry body composition reference values of limbs and trunk from NHANES 1999–2004 with additional visualization methods

Body Mass Index has traditionally been used as a measure of health, but Fat Mass Index (FMI) and Lean Mass Index (LMI) have been shown to be more predictive of mortality and health risk. Total body FMI and LMI reference curves have particularly been useful in quantifying sarcopenia and sarcopenic obesity. Research has shown regional composition has significant associations to health outcomes. We derived FMI and LMI reference curves of the regions of the body (leg, arm, and trunk) for 15,908 individuals in the 1999–2004 National Health and Nutrition Examination Survey data for each sex and ethnicity using the Lambda-Mu-Sigma (LMS) method and developed software to visualize this regional composition. These reference curves displayed differentiation between males and females during puberty and sharper limb LMI declines during late adulthood for males. For adults ages 30–50, females had 39%, 83%, and 47% larger arm, leg, and trunk FMI values than males, respectively. Males had 49%, 20%, and 15% higher regional LMI values than females for the arms, legs, and trunk respectively. The leg FMI and LMI of black females were 14% and 15% higher respectively than those of Hispanic and white females. White and Hispanic males had 37% higher trunk FMI values than black males. Hispanic females had 20% higher trunk FMI than white and black females. These data underscore the importance of accounting for sex and ethnicity in studies of regional composition. This study is the first to produce regional LMI and FMI reference tables and curves from the NHANES dataset. These reference curves provide a framework useful in studies and research involving sarcopenia, obesity, sarcopenic obesity, and other studies of compositional phenotypes. Further, the software tool we provide for visualizing regional composition will prove useful in monitoring progress in physical therapy, diets, or other attempts to attain healthier compositions.
Analysis of p16 Gene Mutation, Deletion and Methylation in Patients with Arseniasis Produced by Indoor Unventilated-Stove Coal Usage in Guizhou, China

The aim of this study was to determine p16 gene mutation, deletion, and promoter 5′ CpG island hypermethylation in peripheral blood mononuclear leukocyte of patients with arseniasis as attributed to exposure to indoor unventilated coal stove. The role of the aberrant change of p16 gene in the induction and development of carcinogenesis in endemic arsenisiasis region in China was also examined. Polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP), multiplex PCR (mPCR), methylation-specific PCR (MSP), and sequencing techniques were performed to detect (1) mutation of the p16 gene exon 2, (2) homozygous deletion of the p16 gene exon 1 and exon 2, and (3) hypermethylation of the promoter CpG island in peripheral blood mononuclear leukocyte of patients with arseniasis. Results showed no mutation was found in exon 2 of p16 gene. The homozygous deletion frequency of p16 gene was 5 and 15% in control and arseniasis patients, respectively. The homozygous deletion occurred mainly in exon 2, with significant deletion frequencies of 9, 13, and 20% in mild, intermediate, and severe arseniasis groups. The significant homozygous deletion frequency was 9 and 39% in noncarcinoma and carcinoma individuals. The positive rate of p16 gene promoter CpG island hyermethylation was 42 and 2% in the exposed group and the control group, respectively. The positive rate was 26, 42, and 50% in mild, intermediate, and severe arseniasis. The marked different positive rate was 22 and 56% in noncarcinoma and carcinoma individuals, respectively. In conclusion, homozygous deletion and hypermethylation of p16 gene may play an important role in the initiation and development of manifestations seen in endemic arseniasis including carcinogenesis.
On the scaling of shear-driven entrainment: a DNS study

Abstract The deepening of a shear-driven turbulent layer penetrating into a stably stratified quiescent layer is studied using direct numerical simulation (DNS). The simulation design mimics the classical laboratory experiments by Kato & Phillips (J. Fluid Mech., vol. 37, 1969, pp. 643–655) in that it starts with linear stratification and applies a constant shear stress at the lower boundary, but avoids sidewall and rotation effects inherent in the original experiment. It is found that the layers universally deepen as a function of the square root of time, independent of the initial stratification and the Reynolds number of the simulations, provided that the Reynolds number is large enough. Consistent with this finding, the dimensionless entrainment velocity varies with the bulk Richardson number as $R{i}^{- 1/ 2} $ . In addition, it is observed that all cases evolve in a self-similar fashion. A self-similarity analysis of the conservation equations shows that only a square root growth law is consistent with self-similar behaviour.
Numerical Hydrodynamics in Special Relativity

This review is concerned with a discussion of numerical methods for the solution of the equations of special relativistic hydrodynamics (SRHD). Particular emphasis is put on a comprehensive review of the application of high-resolution shock-capturing methods in SRHD. Results obtained with different numerical SRHD methods are compared, and two astrophysical applications of SRHD flows are discussed. An evaluation of the various numerical methods is given and future developments are analyzed.
Recommendations in taste related domains: collaborative filtering vs. social filtering

We investigate how social networks can be used in recommendation generation in taste related domains. Social Filtering (using social networks for neighborhood generation) is compared to Collaborative Filtering with respect to prediction accuracy in the domain of rating clubs. After reviewing background and related work, we present an extensive empirical study where over thousand participants from a social networking community where asked to provide ratings for clubs in Munich. We then compare a typical traditional CF-approach to a social recommender / social filtering approach where friends from the underlying social network are used as rating neighborhood and analyze the experiments statistically. Surprisingly, the social filtering approach outperforms the CF approach in all variants of the experiment. The implications of the experiment for professional and private-life collaborative environments and services where recommendations play a role are discussed. We conclude with future perspectives on social recommender systems, especially in upcoming mobile environments.
Cellular signaling by neural cell adhesion molecules of the immunoglobulin superfamily

Neural cell adhesion molecules (CAMs) of the immunoglobulin superfamily nucleate and maintain groups of cells at key sites during early development and in the adult. In addition to their adhesive properties, binding of CAMs can affect intracellular signaling. Their ability to influence developmental events, including cell migration, proliferation, and differentiation can therefore result both from their adhesive as well as their signaling properties. This review focuses on the two CAMs for which the most information is known, the neural CAM, N‐CAM, and L1. N‐CAM was the first CAM to be characterized and, therefore, has been studied extensively. The binding of N‐CAM to cells leads to a number of signaling events, some of which result in changes in gene expression. Interest in L1 derives from the fact that mutations in its gene lead to human genetic diseases including mental retardation. Much is known about modifications of the L1 cytoplasmic domain and its interaction with cytoskeletal molecules. The study of CAM signaling mechanisms has been assay‐dependent rather than molecule‐dependent, with particular emphasis on assays of neurite outgrowth and gene expression, an emphasis that is maintained throughout the review. The signals generated following CAM binding that lead to alterations in cell morphology and gene expression have been linked directly in only a few cases. We also review information on other CAMs, giving special consideration to those that are anchored in the membrane by a phospholipid anchor. These proteins, including a form of N‐CAM, are presumed to be localized in lipid rafts, membrane substructures that include distinctive subsets of cytoplasmic signaling molecules such as members of the src‐family of nonreceptor protein tyrosine kinases. In the end, these studies may reveal that what CAMs do after they bind cells together may have as profound consequences for the cells as the adhesive interactions themselves. This area will therefore remain a rich ground for future studies. Dev Dyn;218:260–279. © 2000 Wiley‐Liss, Inc.
A new twist to the emerging functions of ceramides in cancer: novel role for platelet acid sphingomyelinase in cancer metastasis

It is now appreciated that sphingolipids constitute a rich class of bioactive molecules that include ceramide, sphingosine, and sphingosine 1‐phosphate whose formation is controlled by a network of highly regulated enzymes (Hannun & Obeid, ). Notably, several stress stimuli induce the production of ceramide, which, as a single entity, has been traditionally associated with apoptotic and growth suppressive functions. However, recent data clearly suggest that this simplistic formulation is no longer tenable.
A proof of Green's conjecture regarding the removal properties of sets of linear equations

A system of ℓ linear equations in p unknowns Mx = b is said to have the removal property if every set S ⊆ {1, …, n} that contains o(np−ℓ) solutions of Mx = b can be turned into a set S′ containing no solution of Mx = b by the removal of o(n) elements. Green (Geom. Funct. Anal. 15 (2005) 340–376) proved that a single homogenous linear equation always has the removal property, and conjectured that every set of homogenous linear equations has the removal property. In this paper we confirm Green's conjecture by showing that every set of linear equations (even non‐homogenous) has the removal property. We also discuss some applications of our result in theoretical computer science and, in particular, use it to resolve a conjecture of Bhattacharyya, Chen, Sudan and Xie related to algorithms for testing properties of boolean functions.
Molecular patterns in the evolution of serrated lesion of the colorectum

Colorectal cancer (CRC) mostly develops from a variety of polyps following mainly three different molecular pathways: chromosomal instability (CIN), microsatellite instability (MSI) and CpG island methylation (CIMP). Polyps are classified histologically as conventional adenomas, hyperplastic polyps, sessile serrated adenomas/polyps (SSA/P) and traditional serrated adenomas (TSA). However, the association of these polyps with the different types of CRCs and the underlying genetic and epigenetic aberrations has yet to be resolved. In order to address this question we analyzed 140 tumors and 20 matched mucosae by array comparative genomic hybridization, by sequence analysis of the oncogenes BRAF, KRAS, PI3K3CA and by methylation arrays. MSI was tested indirectly by immunohistochemistry (IHC) and a loss of MLH1, MSH2, MSH6 or PMS2 was assigned as high microsatellite instability (MSI‐H), while low microsatellite instability (MSI‐L) was defined as MGMT IHC negativity only. CIN was detected in 78% of all MSI‐H CRCs, most commonly as a gain of chromosome 8. Methylation data analyses allowed classification of samples into four groups and detected similar methylation profiles in SSA/P and MSI‐H CRC. TSA also revealed aberrant methylation pattern, but clustered more heterogeneously and closer to microsatellite stable (MSS) CRCs. SSA/P, TSA and MSI‐H CRCs had the highest degree of promotor methylation (CIMP pathway). Chromosomal instability, in contrast to the established doctrine, is a common phenomenon in MSI CRCs, yet to a lower extent and at later stages than in MSS CRCs. Methylation analyses suggest that SSA/P are precursors for MSI‐H CRCs and follow the CIMP pathway.
Detection of serum human epididymis secretory protein 4 in patients with ovarian cancer using a label-free biosensor based on localized surface plasmon resonance

Background Detection of the human epididymis secretory protein 4 (HE4) biomarker plays an important role in the early diagnosis of ovarian cancer. This study aimed to develop a novel localized surface plasmon resonance (LSPR) biosensor for detecting HE4 in blood samples from patients with ovarian cancer. Methods Silver nanoparticles were fabricated using a nanosphere lithography method. The anti-HE4 antibody as a probe, which can distinctly recognize HE4, was assembled onto the nanochip surface using an amine coupling method. Detection was based on the shift in the extinction maximum of the LSPR spectrum before and after the HE4-anti-HE4 antibody reaction. These nanobiosensors were applied to detect HE4 in human serum samples and compare them using an enzyme-linked immunosorbent assay. Results Tests relating to the detection of HE4 demonstrated that the LSPR-based biosensor featured a fast detection speed, good specificity, effective reproducibility, and long-term stability. The linear range for LSPR was between 10 pM and 10,000 pM, with a detection limit of 4 pM. An excellent correlation between LSPR and enzyme-linked immunosorbent assay results was observed in human serum. Conclusion This study is the first clinical diagnostic application of the LSPR biosensor in ovarian cancer. The LSPR biosensor, a rapid, low-cost, label-free and portable screening tool, can serve as a very effective alternative for the clinical serological diagnosis of ovarian cancer.
Shielding Google's language toxicity model against adversarial attacks

Lack of moderation in online communities enables participants to incur in personal aggression, harassment or cyberbullying, issues that have been accentuated by extremist radicalisation in the contemporary post-truth politics scenario. This kind of hostility is usually expressed by means of toxic language, profanity or abusive statements. Recently Google has developed a machine-learning-based toxicity model in an attempt to assess the hostility of a comment; unfortunately, it has been suggested that said model can be deceived by adversarial attacks that manipulate the text sequence of the comment. In this paper we firstly characterise such adversarial attacks as using obfuscation and polarity transformations. The former deceives by corrupting toxic trigger content with typographic edits, whereas the latter deceives by grammatical negation of the toxic content. Then, we propose a two--stage approach to counter--attack these anomalies, bulding upon a recently proposed text deobfuscation method and the toxicity scoring model. Lastly, we conducted an experiment with approximately 24000 distorted comments, showing how in this way it is feasible to restore toxicity of the adversarial variants, while incurring roughly on a twofold increase in processing time. Even though novel adversary challenges would keep coming up derived from the versatile nature of written language, we anticipate that techniques combining machine learning and text pattern recognition methods, each one targeting different layers of linguistic features, would be needed to achieve robust detection of toxic language, thus fostering aggression--free digital interaction.
Transmural Heterogeneity and Remodeling of Ventricular Excitation-Contraction Coupling in Human Heart Failure

Background— Excitation-contraction (EC) coupling is altered in end-stage heart failure. However, spatial heterogeneity of this remodeling has not been established at the tissue level in failing human heart. The objective of this article was to study functional remodeling of excitation-contraction coupling and calcium handling in failing and nonfailing human hearts. Methods and Results— We simultaneously optically mapped action potentials and calcium transients in coronary perfused left ventricular wedge preparations from nonfailing (n=6) and failing (n=5) human hearts. Our major findings are the following. First, calcium transient duration minus action potential duration was longer at subendocardium in failing compared with nonfailing hearts during bradycardia (40 bpm). Second, the transmural gradient of calcium transient duration was significantly smaller in failing hearts compared with nonfailing hearts at fast pacing rates (100 bpm). Third, calcium transient in failing hearts had a flattened plateau at the midmyocardium and exhibited a 2-component slow rise at the subendocardium in 3 failing hearts. Fourth, calcium transient relaxation was slower at the subendocardium than at the subepicardium in both groups. Protein expression of sarcoplasmic reticulum Ca2+-ATPase 2a was lower at the subendocardium than the subepicardium in both nonfailing and failing hearts. Sarcoplasmic reticulum Ca2+-ATPase 2a protein expression at subendocardium was lower in hearts with ischemic cardiomyopathy compared with those with nonischemic cardiomyopathy. Conclusions— For the first time, we present direct experimental evidence of transmural heterogeneity of excitation-contraction coupling and calcium handling in human hearts. End-stage heart failure is associated with the heterogeneous remodeling of excitation-contraction coupling and calcium handling.
Experimental methods to characterize the woven composite prepreg behavior during the preforming process

This paper reports several characterization methods of the properties of the uncured woven prepreg during the preforming process. The uniaxial tension, biasextension, and bending tests are conducted to measure the in-plane properties of the material. The friction tests utilized to reveal the prepreg-prepreg and prepreg-forming tool interactions. All these tests are performed within the temperature range of the real manufacturing process. The results serve as the inputs to the numerical simulation for the product prediction and preforming process parameter optimization.
Frequencies of the pyrethroid resistance alleles of Vssc1 and CYP6D1 in house flies from the eastern United States

House flies were collected from four dairies in Maine, New York, North Carolina, and Florida, where high levels of resistance to permethrin have been documented. Regions of two genes, CYP6D1 and Vssc1, having alleles that confer resistance to permethrin (and other pyrethroids) were analysed from individuals at each collection site. The combinations of resistance alleles for Vssc1 and CYP6D1 were highly variable between each state. The resistance allele CYP6D1v1 was found at a high frequency (0.63–0.91) at all sites. Individuals homozygous susceptible for CYP6D1 were very rare and detected only at the dairy in Maine. In addition to the typical Vssc1 mutation responsible for resistance, kdr (L1014F), we also identified individuals with a L1014H mutation. Although house flies homozygous for the L1014H mutation had a lower level of resistance to permethrin, compared to L1014F, the H1014 resistance allele was frequently detected. No individuals with the super‐kdr allele (M918T + L1014F) were detected from the field collections. The intron 3 bp downstream of the kdr mutation was found to be extremely variable, providing an opportunity to reconstruct a phylogeny of Vssc1 alleles. Based on this analysis it appears the kdr‐his mutation had multiple evolutionary origins, but that the kdr mutation may have had a single origin. The impacts of these findings on resistance management are discussed.
Age-related effects of exercise training on diastolic function in heart failure with reduced ejection fraction: the Leipzig Exercise Intervention in Chronic Heart Failure and Aging (LEICA) Diastolic Dysfunction Study.

AIMS Diastolic dysfunction (DD) was identified as a predictor of adverse prognosis in heart failure with reduced ejection fraction (HFREF). It is, however, unknown if DD is improved by exercise training, which is known to induce reverse remodelling, and if the training effect is attenuated in elderly HFREF patients. We therefore assessed DD in a cohort of referent controls (RCs) and HFREF patients and studied the response of DD to endurance exercise in two age groups (≤55 years and ≥65 years). METHODS AND RESULTS Sixty RC (30 ≤ 55 years, mean age 50 ± 5 years; 30 ≥ 65 years, 72 ± 4 years) and 60 HFREF patients (30 ≤ 55 years, 46 ± 5 years; 30 ≥ 65 years, 72 ± 5 years, EF 28 ± 5%) were randomized to 4 weeks of supervised endurance training or to a control group. Exercise training was effective in reducing LV isovolumetric relaxation time by 29% in young and by 26% in old HFREF patients (P< 0.05 for both). As assessed by tissue Doppler, septal E' increased by 37% in young and by 39% among old HFREF patients (P< 0.005 for both) resulting in a significant decrease in the E/E' ratio from 13 ± 1 to 10 ± 1 in young and 14 ± 1 to 11 ± 1 in old HFREF patients (P< 0.05 for both). Serum levels of N-terminal pro brain natriuretic peptide were significantly reduced after endurance training in HFREF patients of all ages. CONCLUSION In HFREF, diastolic function is significantly impaired in all age groups. Endurance training is highly effective in improving left ventricular diastolic function in HFREF patients regardless of age. This study is registered at ClinicalTrials.gov (number: NCT00176319).
Learning to classify complex patterns using a VLSI network of spiking neurons

We propose a compact, low power VLSI network of spiking neurons which can learn to classify complex patterns of mean firing rates on-line and in real-time. The network of integrate-and-fire neurons is connected by bistable synapses that can change their weight using a local spike-based plasticity mechanism. Learning is supervised by a teacher which provides an extra input to the output neurons during training. The synaptic weights are updated only if the current generated by the plastic synapses does not match the output desired by the teacher (as in the perceptron learning rule). We present experimental results that demonstrate how this VLSI network is able to robustly classify uncorrelated linearly separable spatial patterns of mean firing rates.