Miracle-dz/UniFAR-FTUs huggingface dataset:
Managing information well: Toward an ontology-driven informatics platform for data sharing and secondary use in epilepsy self-management research centers

Epilepsy is a chronic neurological condition that requires active self-management to reduce personal and population burden. The Managing Epilepsy Well Network, funded by the US Centers for Disease Control and Prevention, conducts research on epilepsy self-management. There is an urgent need to develop an integrated informatics platform to maximize the secondary use of existing Managing Epilepsy Well Network data. We have implemented multiple steps to develop an informatics platform, including: (a) a survey of existing outcome data, (b) identification of common data elements, and (c) an integrated database using an epilepsy domain ontology to reconcile data heterogeneity. The informatics platform enables assessment of epilepsy self-management samples by site and in aggregate to support data interpretations for clinical care and ongoing epilepsy self-management research. The Managing Epilepsy Well informatics platform is expected to help advance epilepsy self-management, improve health outcomes, and has potential application in other thematic research networks.
Transcription factor and microRNA co-regulatory loops: important regulatory motifs in biological processes and diseases

Transcription factors (TFs) and microRNAs (miRNAs) can jointly regulate target gene expression in the forms of feed-forward loops (FFLs) or feedback loops (FBLs). These regulatory loops serve as important motifs in gene regulatory networks and play critical roles in multiple biological processes and different diseases. Major progress has been made in bioinformatics and experimental study for the TF and miRNA co-regulation in recent years. To further speed up its identification and functional study, it is indispensable to make a comprehensive review. In this article, we summarize the types of FFLs and FBLs and their identified methods. Then, we review the behaviors and functions for the experimentally identified loops according to biological processes and diseases. Future improvements and challenges are also discussed, which includes more powerful bioinformatics approaches and high-throughput technologies in TF and miRNA target prediction, and the integration of networks of multiple levels.
Efficacy, safety, and patient preference of monoamine oxidase B inhibitors in the treatment of Parkinson’s disease

Parkinson’s disease (PD) is the second most common neurodegenerative disease and the most treatable. Treatment of PD is symptomatic and generally focuses on the replacement or augmentation of levodopa. A number of options are available for treatment, both in monotherapy of early PD and to treat complications of advanced PD. This review focuses on rasagiline and selegiline, two medications that belong to a class of antiparkinsonian drugs called monoamine oxidase B (MAO-B) inhibitors. Topics covered in the review include mechanism of action, efficacy in early and advanced PD, effects on disability, the controversy regarding disease modification, safety, and patient preference for MAO-B inhibitors.
Exploiting NVM in large-scale graph analytics

Data center applications like graph analytics require servers with ever larger memory capacities. DRAM scaling, however, is not able to match the increasing demands for capacity. Emerging byte-addressable, non-volatile memory technologies (NVM) offer a more scalable alternative, with memory that is directly addressable to software, but at a higher latency and lower bandwidth. Using an NVM hardware emulator, we study the suitability of NVM in meeting the memory demands of four state of the art graph analytics frameworks, namely Graphlab, Galois, X-Stream and Graphmat. We evaluate their performance with popular algorithms (Pagerank, BFS, Triangle Counting and Collaborative filtering) by allocating memory exclusive from DRAM (DRAM-only) or emulated NVM (NVM-only). While all of these applications are sensitive to higher latency or lower bandwidth of NVM, resulting in performance degradation of up to 4x with NVM-only (compared to DRAM-only), we show that the performance impact is somewhat mitigated in the frameworks that exploit CPU memory-level parallelism and hardware prefetchers. Further, we demonstrate that, in a hybrid memory system with NVM and DRAM, intelligent placement of application data based on their relative importance may help offset the overheads of the NVM-only solution in a cost-effective manner (i.e., using only a small amount of DRAM). Specifically, we show that, depending on the algorithm, Graphmat can achieve close to DRAM-only performance (within 1.2x) by placing only 6.7% to 31.5% of its total memory footprint in DRAM.
Attended Polysomnography for Evaluation of Sleep Disorders

improvement of AHI and somnolence, change in sleep quality and the acceptance and compliance of CPAP treatment compared to manual titration. Ten randomized controlled trials (849 patients) met the inclusion criteria. Studies were pooled to yield odds ratios (OR) or mean differences (MD) with 95% confidence intervals (CI). Automatic titration improved the AHI (MD=0.03/h, 95% CI=4.48-4.53) and ESS (SMD=0.02, 95% CI=0.34-0.31) as effectively as manual titration. There was no difference in sleep architecture between auto titration and manual titration. There was also no difference in acceptance of CPAP treatment or compliance with treatment. The authors concluded that automatic titration is as effective as standard manual titration in terms of improvement in AHI, somnolence and sleep quality, as well as acceptance and adherence to CPAP. Among 39 patients completing the PAP-Nap, 90% completed overnight titrations, compared with 63% in the historical control group. Eight-five percent of the nap-tested group filled PAP therapy prescriptions for home use compared with 35% of controls. Sixty-seven percent of the nap-tested group maintained regular use of PAP therapy compared with 23% of the control group. Using standards from the field of sleep medicine, the nap-tested group demonstrated objective adherence of 49% to 56% compared to 12% to 17% among controls. Further results from large, prospective studies are needed to assess the clinical value of this test.
A 120–145 GHz Heterodyne Receiver Chipset Utilizing the 140 GHz Atmospheric Window for Passive Millimeter-Wave Imaging Applications

For passive mm-wave imaging applications, broadband mm-wave receivers functioning within atmospheric windows are highly desired. Within this paper, a heterodyne receiver chipset utilizing the 140 GHz atmospheric window is presented. The heterodyne chipset is based on two different millimeter-wave monolithic integrated circuits (MIMICs). One is the receiver MIMIC including a low-noise amplifier, a down-conversion mixer, a frequency multiplier and a local oscillator buffer amplifier together with a local oscillator distribution network. The other is a voltage-controlled oscillator (VCO) working in the 35 GHz frequency range to generate the local oscillator signal for the receiver (down-converter) chip. The process technology chosen to realize the chipset is a 100 nm gatelength metamorphic InAlAs/InGaAs high electron mobility transistor (HEMT) technology on 50 μm thick and 4 inch diameter GaAs substrates. The chips are utilizing a grounded coplanar waveguide (GCPW) technology. For an operation frequency band from 120 to 145 GHz, the receiver demonstrates a flat conversion gain between -1 and +2 dB with a power consumption of 120 mW. The VCO is tuneable from 31 to 37 GHz with associated output power levels from -2 to +1 dBm. Detailed descriptions of the individual building blocks are given and measured results are presented for the building blocks as well as for the receiver.
Imaging Spreading Depression and Associated Intracellular Calcium Waves in Brain Slices

Spreading depression (SD) was analyzed in hippocampal and neocortical brain slices by imaging intrinsic optical signals in combination with either simultaneous electrophysiological recordings or imaging of intracellular calcium dynamics. The goal was to determine the roles of intracellular calcium (Ca2+int) waves in the generation and propagation of SD. Imaging of intrinsic optical signals in the hippocampus showed that ouabain consistently induced SD, which characteristically started in the CA1 region, propagated at 15–35 μm/sec, and traversed across the hippocampal fissure to the dentate gyrus. In the dendritic regions of both CA1 and the dentate gyrus, SD caused a transient increase in light transmittance, characterized by both a rapid onset and a rapid recovery. In contrast, in the cell body regions the transmittance increase was prolonged. Simultaneous imaging of intracellular calcium and intrinsic optical signals revealed that a slow Ca2+int increase preceded any change in transmittance. Additionally, a wave of increased Ca2+int typically propagated many seconds ahead of the change in transmittance. These calcium increases were also observed in individual astrocytes injected with calcium orange, indicating that Ca2+int waves were normally associated with SD. However, when hippocampal slices were incubated in calcium-free/EGTA external solutions, SD was still observed, although Ca2+int waves were completely abolished. Under these conditions SD had a comparable peak increase in transmittance but a slower onset and a faster recovery. These results demonstrate that although there are calcium dynamics associated with SD, these increases are not necessary for the initiation or propagation of spreading depression.
Kick It Like Özil ? Second Generation Migrants ’ Initial Disadvantage and the Failure of the Education System ∗

We investigate second generation migrants and natives in Germany’s education system. We determine at what stage the persistent native-migrant gap in labor market and schooling outcomes emerges. Controlling for family background and other characteristics, we employ a matching approach in order to account for the fact that migrants and natives are different. We find that second generation migrants are initially disadvantaged due to both their socioeconomic family background and the education system. We also find that comparable natives, in terms of family background, face similar difficulties. Thus, Germany’s education system fails to provide equal opportunities for all initially disadvantaged individuals.
A Location Service Mechanism for Position-Based Multicasting in Wireless Mobile Ad hoc Networks

In this paper we propose a novel location management scheme tailored for multicasting in Mobile Ad-hoc Networks (MANETs). We furthermore propose AMDLM, a location-based multicast algorithm relying on the location management service. Such an approach avoids fragile data structures such as trees or DAGs to manage multicast groups, without reverting to more reliable, yet overhead-prone mesh-based algorithms. AMDLM additionally enables us to derive analytical bounds due to its location-based nature.
How to prove existence in shape optimization

This paper deals with the existence question in opti- mal design. We present a general variational technique for proving existence, and give several examples concerning functionals of eigen- values and of energy type. In particular, we show how the isoperi- metric problem for the Dirichlet eigenvalues of an elliptic operator of general order fits into this frame.
A comparative population pharmacokinetic analysis for methylprednisolone following multiple dosing of two prodrugs in patients with acute asthma.

AIMS To conduct a randomized, parallel group comparison of the population pharmacokinetics of the two methylprednisolone (MP) prodrugs Promedrol (MP suleptanate) and Solu-Medrol (MP succinate) in patients hospitalized with acute asthma. METHODS Ninety volunteers were included in the pharmacokinetic analysis. Each volunteer received a dosage regimen of 40 mg (MP equivalents) i.v. 6 hourly for 48 h. The bio-conversion and disposition of a 40 mg (MP equivalent) i.v. dose of either MP suleptanate or MP succinate to MP was modelled as a first order input, and a mono-exponential elimination phase. RESULTS Population modelling indicated that the only difference in MP pharmacokinetics between MP suleptanate and MP succinate was in the input rate constant (66.0 h-1 vs 5.5 h-1 respectively). Based on individual Bayesian estimates, the exposure of patients to MP was marginally lower for MP suleptanate although the parameter estimates were not significantly different for half-life (2.7 h vs 3.0 h), steady-state AUC (2007.0 ng ml-1 h vs 2321.0 ng ml-1 h) and steady-state Cmax (698.4 ng ml-1 vs 647.8 ng ml-1) for MP suleptanate and MP succinate respectively. CONCLUSIONS It was concluded that for the multiple dosage regimen used in patients with acute asthma the systemic exposure to MP following dosing with MP suleptanate is similar to that arising from MP succinate. In addition the differences in the pharmacokinetics for the prodrugs resulted in only a small difference in the relative bioavailability of MP for MP suleptanate (0.94) compared with MP succinate.
Delayed cutaneous reactions in the rat.

Typical delayed skin reactions to tuberculin were elicited in rats sensitized by footpad injection of killed tubercle bacilli in oil. Their similarity to classical delayed reactions in guinea pig or rabbit is demonstrated by their identical time course, characteristic histologic appearance and passive transfer with sensitized lymph node cells. Similar reactions were obtained after sensitization with Nocardia asteroides in oil, OT in incomplete Freund's adjuvant or BSA in complete adjuvant. These were indurated reactions made up largely of mononuclear infiltrates in the deep dermis and subcutaneous tissues, maximal at 24 to 48 hr. This location of the lesions is correlated with the distribution of vessels of venous type.
How Good Is a Security Policy against Real Breaches? A HIPAA Case Study

Policy design is an important part of software development. As security breaches increase in variety, designing a security policy that addresses all potential breaches becomes a nontrivial task. A complete security policy would specify rules to prevent breaches. Systematically determining which, if any, policy clause has been violated by a reported breach is a means for identifying gaps in a policy. Our research goal is to help analysts measure the gaps between security policies and reported breaches by developing a systematic process based on semantic reasoning. We propose SEMAVER, a framework for determining coverage of breaches by policies via comparison of individual policy clauses and breach descriptions. We represent a security policy as a set of norms. Norms (commitments, authorizations, and prohibitions) describe expected behaviors of users, and formalize who is accountable to whom and for what. A breach corresponds to a norm violation. We develop a semantic similarity metric for pairwise comparison between the norm that represents a policy clause and the norm that has been violated by a reported breach. We use the US Health Insurance Portability and Accountability Act (HIPAA) as a case study. Our investigation of a subset of the breaches reported by the US Department of Health and Human Services (HHS) reveals the gaps between HIPAA and reported breaches, leading to a coverage of 65%. Additionally, our classification of the 1,577 HHS breaches shows that 44% of the breaches are accidental misuses and 56% are malicious misuses. We find that HIPAA's gaps regarding accidental misuses are significantly larger than its gaps regarding malicious misuses.
Melanoma Prognosis: A REMARK-Based Systematic Review and Bioinformatic Analysis of Immunohistochemical and Gene Microarray Studies

Despite intensive research efforts, within-stage survival rates for melanoma vary widely. Pursuit of molecular biomarkers with improved prognostic significance over clinicohistological measures has produced extensive literature. Reviews have synthesized these data, but none have systematically partitioned high-quality studies from the remainder across different molecular methods nor examined system properties of that output. Databases were searched for studies analyzing protein expression by immunohistochemistry (n = 617, extending the only systematic review to date by 102 studies) or for gene expression microarray studies (n = 45) in melanoma in relation to outcome. REMARK-derived criteria were applied to identify high-quality studies. Biomarkers and pathways were functionally assessed by using gene ontology software. Most manuscripts did not meet REMARK-based criteria, an ongoing trend that can impede translational research. Across REMARK-compliant literature, 41 proteins were significantly associated with outcome. Multimarker tests consistently emerged among the most promising potential biomarkers, indicating a need to continue assessing candidates in that composite setting. Twenty-one canonical pathways were populated by outcome-related proteins but not by those that failed to show such an association; we propose that this set of pathways warrants closer investigation to understand drivers of poor outcome in melanoma. Two-gene expression microarray studies met REMARK-based criteria reflecting a genuine paucity of literature in the area. The 254 outcome-related genes were examined for correspondences with the systematically identified protein signature. This analysis highlighted proliferating cell nuclear antigen and survivin as priorities for further examination as biomarkers in melanoma prognosis, and illustrated ongoing need to integrate alternative approaches to biomarker discovery in melanoma translational research. Mol Cancer Ther; 10(8); 1520–8. ©2011 AACR.
An evaluation of text-to-speech synthesizers in the foreign language classroom: learners’ perceptions

As stated in Cardoso, Smith, and Garcia Fuentes (2015), second language researchers and practitioners have explored the pedagogical capabilities of Text-ToSpeech synthesizers (TTS) for their potential to enhance the acquisition of writing (e.g. Kirstein, 2006), vocabulary and reading (e.g. Proctor, Dalton, & Grisham, 2007), and pronunciation (e.g. Cardoso, Collins, & White, 2012). Despite their demonstrated effectiveness, there is a need for up-to-date formal evaluations of TTS systems, specifically for their potential to promote the ideal conditions under which languages are acquired, particularly in an English as a Foreign Language (EFL) environment, as suggested by Cardoso, Smith, and Garcia Fuentes (2015). This study evaluated a modern English TTS system in an EFL context in Brazil, at a number of levels, including speech quality, opportunity to focus on form, and learners’ cognitive processing of TTS-generated texts. Fifteen Brazilian EFL learners participated in the study in which they listened to both human and TTSproduced speech samples while performing the abovementioned tasks. Semistructured interviews were used to collect data about participants’ perceptions of the technology. We report an analysis of these interviews, which indicate that EFL learners have overall positive attitudes towards the pedagogical use of TTS, and that they would like to use the technology as a learning tool.
Discovery of the Galaxy Proximity Effect and Implications for Measurements of the Ionizing Background Radiation at Low Redshifts

We present an analysis of galaxy and quasi-stellar object (QSO) absorption line pairs toward 24 QSOs at redshifts between z ≈ 0.2 and 1 in an effort to establish the relationship between galaxies and absorption lines in physical proximity to QSOs. We demonstrate the existence of a galaxy proximity effect, in that galaxies in the vicinities of QSOs do not show the same incidence and extent of gaseous envelopes as galaxies far from QSOs. We show that the galaxy proximity effect exists to galaxy-QSO velocity separations of ≃3000 km s-1, much larger than the size of a typical cluster (≃1000 km s-1); i.e., it is more comparable to the scale of the sphere of influence of QSO ionizing radiation rather than the scale of galaxy-QSO clustering. This indicates that the QSO ionizing radiation rather than some dynamical effect from the cluster environment is responsible for the galaxy proximity effect. We combine previous findings that (1) many or most Lyα absorption lines arise in extended galaxy envelopes, and (2) galaxies cluster around QSOs to show that the magnitude of the Lyα forest proximity effect is underestimated. Consequently, determinations of the UV ionizing background intensity using the proximity effect are likely overestimated. We use the galaxy-QSO cross-correlation function measured from our data to estimate the magnitude of this overestimate and find that it could be as high as a factor of 20 at z ≲ 1. This can have strong implications for models of the origin and evolution of the ionizing background and may indicate that QSOs produce sufficient ionizing flux at all redshifts to account for the entire background radiation field.
Results of latest paleontological, stratigraphic and geoarchaeological research of the Volchia Griva mammoth fauna site

The Volchia Griva is the largest site in Asia where the mammoth fauna remains are buried in situ. It is located in the Baraba forest-steppe (Western Siberia). In the 20th century, remains of at least 70 mammoths, 5 horses, 3 bisons and 1 wolf, as well as 37 stone artifacts were found here. The latest excavations of 2015–2017 on ~30 m2 revealed over 1500 bones and teeth, 95% of which belong to mammoths (at least 14 individuals), and the rest are from horses (3), bison, wolf, red fox, arctic fox, and rodents; associated artifacts – 23 items. With an average thickness of the bonebearing lens ~ 0.3–0.5 m, the local remain concentration exceeded 130/m2. The forty five crossed 14C dates were obtained from these materials, which reveal a burial period of ~20–10 ka BP. Obviously, there was the southernmost and one of the youngest mammoth refugia of Eurasia on this territory. The favorable Ca-Na geochemical landscape of the beast solonetz was the main reason for mammoth to visit the Volchia Griva. During the mineral starvation, the site attracted hundreds of large mammals, the remains of which were buried in mud baths and erosion forms. The main levels of the bone-bearing horizon have been forming for several thousand years, and that matched two waves of the megafauna’s geochemical stress in the Last Glacial Maximum and Late Glacial. Typical bone pathologies, such as exostoses, osteoporosis, erosion of articular surfaces, etc., characterize this process. These facts, together with the lack of strong evidence of hunting and butchering, indicate that the Volchia Griva was the natural mammoth death site, which was well known and used by Palaeolithic humans.