Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the eighth TNM classification on p16-positive oropharyngeal squamous cell carcinomas in the Netherlands and the importance of additional HPV DNA testing

Background Oropharyngeal squamous cell carcinomas (OPSCCs) are traditionally caused by smoking and excessive alcohol consumption. However, in the last decades high-risk human papillomavirus (HPV) infections play an increasingly important role in tumorigenesis. HPV-driven OPSCCs are known to have a more favorable prognosis, which has led to important and marked changes in the recently released TNM-8. In this 8th edition, OPSCCs are divided based on p16 immunostaining, with p16 overexpression as surrogate marker for the presence of HPV. The aims of this study are to evaluate TNM-8 on a Dutch consecutive cohort of patients with p16-positive OPSCC and to determine the relevance of additional HPV DNA testing. Patients and methods All OPSCC patients without distant metastases at diagnosis and treated with curative intent at VU University Medical Center (2000-2015) and Erasmus Medical Center (2000-2006) were included (N = 1204). HPV status was determined by p16 immunostaining followed by HPV DNA PCR on the p16-immunopositive cases. We compared TNM-7 and TNM-8 using the Harrell's C index. Results In total, 388 of 1204 (32.2%) patients were p16-immunopositive. In these patients, TNM-8 had a markedly better predictive prognostic power than TNM-7 (Harrell's C index 0.63 versus 0.53). Of the 388 p16-positive OPSCCs, 48 tumors (12.4%) were HPV DNA-negative. This subgroup had distinct demographic, clinical and morphologic characteristics and showed a significantly worse five-year overall survival compared with the HPV DNA-positive tumors (P < 0.001). Conclusions TNM-8 has a better predictive prognostic power than TNM-7 in patients with p16-positive OPSCC. However, within p16-positive OPSCCs, there is an HPV DNA-negative subgroup with distinct features and a worse overall survival, indicating the importance to perform additional HPV DNA testing when predicting prognosis and particularly for selecting patients for de-intensified treatment regimens.
Rheological measurement of redispersibility and settling to analyze the effect of surfactants on MR particles

The smart materials such as magnetorheological (MR) fluids are gaining wide popularity due to their superior control abilities. These abilities are strongly dependent about the stability of the MR fluid which needs to be sustained for the useful life of the system. In the present research work, experimental studies focusing on aggregation, redispersibility and settling of carbonyl iron-based MR fluids have been conducted to analyze the effect of surfactants on controlling settling and redispersibility. The experimental investigations were conducted by preparation of nine MR fluids samples using three types of surfactants (oleic acid, citric acid and tetramethylammonium hydroxide) and three different carrier fluids (water, silicone oil and DTE light mineral oil). The samples were prepared by mixing on rotational machine for 24 h and the homogeneity of the samples was visually inspected. The shear stress and viscosity variation of the homogenous mixture with respect to shear rate was obtained using magnetic rheometer. A new method is presented for measuring the settling of homogenous mixtures by measurement of the change in the magnetic field strength due to settlement of particles. The effect of surfactant type and its quantity on the stability of MR fluid is explored and the results of settling and redispersibility have been presented.
Gastrointestinal Tolerance and Glycemic Response of Isomaltooligosaccharides in Healthy Adults

Ingredients delivering functional and nutritional benefits are of interest to food manufacturers. Isomaltooligosaccharides (IMOs) which serve as alternate sweeteners fit into this category. IMOs are a mixture of α-(1 → 6) and α-(1 → 4)-linked glucose oligomers, synthesized by an enzymatic reaction from starch (corn, tapioca). The aim of this study was to evaluate the fermentability and glycemic response of IMO in a healthy population. Two randomized, double-blind, placebo-controlled, cross-over human studies were conducted. In the first study (n = 26), participants’ breath hydrogen over 24 h, gastrointestinal tolerance, and glycemic and insulinemic response to BIOLIGOTM IL5040 isomaltooligosaccharide were measured. In another study (n = 10), participants’ two-hour post-prandial glycemic response to BIOLIGOTM IL5040 isomaltooligosaccharide and BIOLIGOTM IL7010 isomaltooligosaccharide was measured compared to dextrose (control). The IMOs differed in the composition of mono and di-saccharide sugars. IMO syrup dose was matched for 50 g of total carbohydrates and was consumed by mixing in water (237 mL/8 oz.). Mean composite gastrointestinal score was not significantly different (p = 0.322) between the control (1.42) and IMO (1.38). Lack of difference in glycemic response (p = 0.662), with no impact on breath hydrogen (24 h; p = 0.319) and intestinal tolerance, demonstrates that IMO is digestible and can be used to replace sugars in product formulations.
Sharing Ontology in Complex Scenario using a Peer-To-Peer Approach ∗

The problem of defining efficient techniques for knowledge representation (KR) is becoming more and more a challenging topic in both academic and industrial community. The Semantic Web needs of formal knowledge representations for implementing useful services and put in common the different views between man and machines. In this framework, we assume that new approaches for knowledge definition and representation may be useful, in particular the ones based on the concept of ontology. We chose the issue of landscape planning as a case study, particularly focusing on cultural landscape. This choice was motivated by cultural and scientific innovations, which led in recent years to a completely new interpretation of landscape making it a high complex scenario. Based on these considerations, we propose a suitable ontology-based model and implement it in a system designed to manage ontologies using a peer-to-peer (P2P) paradigm to share general and domain knowledge. The network knowledge is exposed using a Web Service and it can be used by intelligent Web agents.
Phrase-Based Statistical Model for Korean Morpheme Segmentation and POS Tagging

In this paper, we propose a novel phrase-based model for Korean morphological analysis by considering a phrase as the basic processing unit, which generalizes all the other existing processing units. The impetus for using phrases this way is largely motivated by the success of phrase-based statistical machine translation (SMT), which convincingly shows that the larger the processing unit, the better the performance. Experimental results using the SEJONG dataset show that the proposed phrasebased models outperform the morpheme-based models used as baselines. In particular, when combined with the conditional random field (CRF) model, our model leads to statistically significant improvements over the state-of-the-art CRF method. key words: phrase-based model, segmentation, tagging, morphological analysis, Korean morphological analysis
Fast, Sample-Efficient Algorithms for Structured Phase Retrieval

We consider the problem of recovering a signal x in R^n, from magnitude-only measurements, y_i = |a_i^T x| for i={1,2.m}. Also known as the phase retrieval problem, it is a fundamental challenge in nano-, bio- and astronomical imaging systems, astronomical imaging, and speech processing. The problem is ill-posed, and therefore additional assumptions on the signal and/or the measurements are necessary. In this paper, we first study the case where the underlying signal x is s-sparse. We develop a novel recovery algorithm that we call Compressive Phase Retrieval with Alternating Minimization, or CoPRAM. Our algorithm is simple and can be obtained via a natural combination of the classical alternating minimization approach for phase retrieval, with the CoSaMP algorithm for sparse recovery. Despite its simplicity, we prove that our algorithm achieves a sample complexity of O(s^2 log n) with Gaussian samples, which matches the best known existing results. It also demonstrates linear convergence in theory and practice and requires no extra tuning parameters other than the signal sparsity level s. We then consider the case where the underlying signal x arises from to structured sparsity models. We specifically examine the case of block-sparse signals with uniform block size of b and block sparsity k=s/b. For this problem, we design a recovery algorithm that we call Block CoPRAM that further reduces the sample complexity to O(ks log n). For sufficiently large block lengths of b=Theta(s), this bound equates to O(s log n). To our knowledge, this constitutes the first end-to-end linearly convergent family of algorithms for phase retrieval where the Gaussian sample complexity has a sub-quadratic dependence on the sparsity level of the signal.
Integrating 5hmC and gene expression data to infer regulatory mechanisms

Motivation Epigenetic mechanisms are known to play a major role in breast cancer. However, the role of 5-hydroxymethylcytosine (5hmC) remains understudied. We hypothesize that 5hmC mediates redox regulation of gene expression in an aggressive subtype known as triple negative breast cancer (TNBC). To address this, our objective was to highlight genes that may be the target of this process by identifying redox-regulated, antioxidant-sensitive, gene-localized 5hmC changes associated with mRNA changes in TNBC cells. Results We proceeded to develop an approach to integrate novel Pvu-sequencing and RNA-sequencing data. The result of our approach to merge genome-wide, high-throughput TNBC cell line datasets to identify significant, concordant 5hmC and mRNA changes in response to antioxidant treatment produced a gene set with relevance to cancer stem cell function. Moreover, we have established a method that will be useful for continued research of 5hmC in TNBC cells and tissue samples. Availability and implementation Data are available at Gene Expression Omnibus (GEO) under accession number GSE103850. Contact bollig@karmanos.org.
Carbon sequestration by Chinese bamboo forests and their ecological benefits: assessment of potential, problems, and future challenges

Bamboo is widely distributed in Southeast Asia, Africa, and Latin America. As a major non-wood forest product and wood substitute, bamboo is of increasing interest to ecologists owing to its rapid growth and correspondingly high potential for mitigating climate change. With a long history of production and utilization of bamboo, China is one of the countries with the richest bamboo resources and largest area of bamboo forest, and has paid unprecedented attention in recent decades to management of its bamboo forests. This review summarizes the versatility of bamboo in terms of its ecological benefits including carbon sequestration, water and soil conservation, its benefits for socioeconomic development, and its potential to mitigate climate change. Current problems, and the future potential of and challenges to rapidly expanding bamboo forests under both wider use of intensive management and the effects of global warming, are also discussed.
Acetyl L‐carnitine targets adenosine triphosphate synthase in protecting zebrafish embryos from toxicities induced by verapamil and ketamine: An in vivo assessment

Verapamil is a Ca2+ channel blocker and is highly prescribed as an anti‐anginal, antiarrhythmic and antihypertensive drug. Ketamine, an antagonist of the Ca2+‐permeable N‐methyl‐d‐aspartate‐type glutamate receptors, is a pediatric anesthetic. Previously we have shown that acetyl l‐carnitine (ALCAR) reverses ketamine‐induced attenuation of heart rate and neurotoxicity in zebrafish embryos. Here, we used 48 h post‐fertilization zebrafish embryos that were exposed to relevant drugs for 2 or 4 h. Heart beat and overall development were monitored in vivo. In 48 h post‐fertilization embryos, 2 mm ketamine reduced heart rate in a 2 or 4 h exposure and 0.5 mm ALCAR neutralized this effect. ALCAR could reverse ketamine's effect, possibly through a compensatory mechanism involving extracellular Ca2+ entry through L‐type Ca2+ channels that ALCAR is known to activate. Hence, we used verapamil to block the L‐type Ca2+ channels. Verapamil was more potent in attenuating heart rate and inducing morphological defects in the embryos compared to ketamine at specific times of exposure. ALCAR reversed cardiotoxicity and developmental toxicity in the embryos exposed to verapamil or verapamil plus ketamine, even in the presence of 3,4,5‐trimethoxybenzoic acid 8‐(diethylamino)octyl ester, an inhibitor of intracellular Ca2+ release suggesting that ALCAR acts via effectors downstream of Ca2+. In fact, ALCAR's protective effect was blunted by oligomycin A, an inhibitor of adenosine triphosphate synthase that acts downstream of Ca2+ during adenosine triphosphate generation. We have identified, for the first time, using in vivo studies, a downstream effector of ALCAR that is critical in abrogating ketamine‐ and verapamil‐induced developmental toxicities. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.
Efficiently Validating Aggregated IoT Data Integrity

We address the problem of validating the integrity of data aggregated in applications that run on the Internet of Things (IoT). When data from multiple sources is sent to a single receiver, the receiver needs to efficiently verify the authenticity and integrity of data. For example, sensors from multiple IoT devices would send the measurements to a gateway for data aggregation and/or processing. The gateway needs to verify the authenticity and integrity of the readings from sensors. To address this need, we propose a lightweight homomorphic signature scheme that supports the execution of aggregation operations. Our approach collects digital signatures from multiple sources and provides an efficient aggregated signature verification mechanism for the end receiver. The aggregation and verification mechanism preserves the privacy of intermediate nodes. We discuss how our homomorphic signature scheme resists forgery and replay attacks.
Bias from restricting to live births when estimating effects of prescription drug use on pregnancy complications: A simulation

Administrative claim databases are increasingly being used to study the safety of medication exposures during pregnancy. These studies are restricted to live births due to a reliance on algorithms for estimating gestational age that are based on codes associated with live delivery. Conditioning on live birth may induce selection bias when studying the effect of a drug on a pregnancy complication if fetal death is a competing risk for the complication or is caused by the complication.
Inhibiting p21-Activated Kinase Induces Cell Death in Vestibular Schwannoma and Meningioma via Mitotic Catastrophe.

HYPOTHESIS p21-activated kinase (PAK) regulates signaling pathways that promote cell survival and proliferation; therefore, pharmacological inhibition of PAK will induce cell death in vestibular schwannomas (VS) and meningiomas. BACKGROUND All VS and many meningiomas result from loss of the neurofibromatosis type 2 (NF2) gene product merlin, with ensuing PAK hyperactivation and increased cell proliferation/survival. METHODS The novel small molecule PAK inhibitors PI-8 and PI-15-tested in schwannoma and meningioma cells-perturb molecular signaling and induce cell death. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, flow cytometry, and terminal deoxynucleotidyl transferase dUTP nick end labeling assay analyzed PAK inhibitors' effect on cell viability, cell cycle, and cell death, respectively. Western blots evaluated activation and expression of cell proliferation, apoptotic, and mitotic catastrophe markers. Light microscopy evaluated cell morphology, and immunocytochemistry analyzed cellular localization of phospho-Merlin and autophagy-related protein. RESULTS Treatment with PI-8 and PI-15 decreased cell viability at 0.65 to 3.7 μM 50% inhibitory concentration (IC50) in schwannoma and meningioma cells. Terminal deoxynucleotidyl transferase dUTP nick end labeling and immunocytochemistry studies show that PI-8 and PI-15 induce mitotic catastrophe but not apoptosis in HEI193 cells while in BenMen1 cells, PI-8 induces autophagy and mitotic catastrophe. PI-15 induces apoptosis in BenMen1 cells. PAK inhibitor treated cells show phospho-Merlin localized to over-duplicated centrosomes of dividing cells, multiple enlarged nuclei, and misaligned/missegregated chromosomes-markers for mitotic catastrophe. Increased autophagy-related protein levels in the nucleus confirmed this cell death type. PI-8 and PI-15 inhibits PAK in both cell lines. However, only PI-15 inhibits v-akt murine thymoma viral oncogene homolog in BenMen1 cells. CONCLUSION PAK inhibitors induce cell death in schwannoma and meningioma cells, at least in part, by mitotic catastrophe.
Abnormal P-Wave Axis and Ischemic Stroke: The ARIC Study (Atherosclerosis Risk In Communities)

Background and Purpose— Abnormal P-wave axis (aPWA) has been linked to incident atrial fibrillation and mortality; however, the relationship between aPWA and stroke has not been reported. We hypothesized that aPWA is associated with ischemic stroke independent of atrial fibrillation and other stroke risk factors and tested our hypothesis in the ARIC study (Atherosclerosis Risk In Communities), a community-based prospective cohort study. Methods— We included 15 102 participants (aged 54.2±5.7 years; 55.2% women; 26.5% blacks) who attended the baseline examination (1987–1989) and without prevalent stroke. We defined aPWA as any value outside 0 to 75° using 12-lead ECGs obtained during study visits. Each case of incident ischemic stroke was classified in accordance with criteria from the National Survey of Stroke by a computer algorithm and adjudicated by physician review. Multivariable Cox regression was used to estimate hazard ratios and 95% confidence intervals for the association of aPWA with stroke. Results— During a mean follow-up of 20.2 years, there were 657 incident ischemic stroke cases. aPWA was independently associated with a 1.50-fold (95% confidence interval, 1.22–1.85) increased risk of ischemic stroke in the multivariable model that included atrial fibrillation. When subtyped, aPWA was associated with a 2.04-fold (95% confidence interval, 1.42–2.95) increased risk of cardioembolic stroke and a 1.32-fold (95% confidence interval, 1.03–1.71) increased risk of thrombotic stroke. Conclusions— aPWA is independently associated with ischemic stroke. This association seems to be stronger for cardioembolic strokes. Collectively, our findings suggest that alterations in atrial electric activation may predispose to cardiac thromboembolism independent of atrial fibrillation.
A Randomized Controlled Trial of a CPR Decision Support Video for Patients Admitted to the General Medicine Service

BACKGROUND: Patient preferences regarding cardiopulmonary resuscitation (CPR) are important, especially during hospitalization when a patient's health is changing. Yet many patients are not adequately informed or involved in the decision‐making process. OBJECTIVES: We examined the effect of an informational video about CPR on hospitalized patients' code status choices. DESIGN: This was a prospective, randomized trial conducted at the Minneapolis Veterans Affairs Health Care System in Minnesota. PARTICIPANTS: We enrolled 119 patients, hospitalized on the general medicine service, and at least 65 years old. The majority were men (97%) with a mean age of 75. INTERVENTION: A video described code status choices: full code (CPR and intubation if required), do not resuscitate (DNR), and do not resuscitate/do not intubate (DNR/DNI). Participants were randomized to watch the video (n = 59) or usual care (n = 60). MEASUREMENTS: The primary outcome was participants' code status preferences. Secondary outcomes included a questionnaire designed to evaluate participants' trust in their healthcare team and knowledge and perceptions about CPR. RESULTS: Participants who viewed the video were less likely to choose full code (37%) compared to participants in the usual care group (71%) and more likely to choose DNR/DNI (56% in the video group vs. 17% in the control group) (P < 0.00001). We did not see a difference in trust in their healthcare team or knowledge and perceptions about CPR as assessed by our questionnaire. CONCLUSIONS: Hospitalized patients who watched a video about CPR and code status choices were less likely to choose full code and more likely to choose DNR/DNI.
Preparation of chitosan-coated liposomes as a novel carrier system for the antiviral drug Triazavirin

Abstract Novel method for the coating of positively charged liposomes with modified chitosan was elaborated. Liposomes were prepared by stepwise extrusion through inorganic membranes (Anotop) of 0.2 and 0.1 μm pore sizes. Chitosan derivatives were synthesized via the Ugi multicomponent reaction. Several series of liposomal compositions were produced and their properties were compared in terms of particle size, polydispersity index (PDI), zeta potential and stability. The effect of various additives was investigated and the optimal composition of the lipid film was determined. The addition of the uncharged fatty esters allowed the diameter of the liposomes obtained by extrusion to be reduced to 145–150 nm with a PDI of 0.13–0.15. The prepared liposomes were loaded with the novel antiviral drug Triazavirin and used to determine the release profile. Triazavirin was included into liposome layer as a salt with biocompatible choline derivatives of limiting fatty acids. The appropriate lipid composition was used for the preparation of a larger quantity of liposomes coated by modified chitosan. It was shown that an appropriate combination of liposomes and polysaccharide layer potentially extended colloidal stability by up to 3 months and exhibited broad functional capabilities for surface modification.
Rewriting Guarded Existential Rules into Small Datalog Programs

The goal of this paper is to understand the relative expressiveness of the query language in which queries are specified by a set of guarded (disjunctive) tuple-generating dependencies (TGDs) and an output (or 'answer') predicate. Our main result is to show that every such query can be translated into a polynomially-sized (disjunctive) Datalog program if the maximal number of variables in the (disjunctive) TGDs is bounded by a constant. To overcome the challenge that Datalog has no direct means to express the existential quantification present in TGDs, we define a two-player game that characterizes the satisfaction of the dependencies, and design a Datalog query that can decide the existence of a winning strategy for the game. For guarded disjunctive TGDs, we can obtain Datalog rules with disjunction in the heads. However, the use of disjunction is limited, and the resulting rules fall into a fragment that can be evaluated in deterministic single exponential time. We proceed quite differently for the case when the TGDs are not disjunctive and we show that we can obtain a plain Datalog query. Notably, unlike previous translations for related fragments, our translation requires only polynomial time if the maximal number of variables in the (disjunctive) TGDs is bounded by a constant.