gebhart/patrepeval huggingface dataset:
Reflections on the nature of measurement in language-based automated assessments of patients' mental state and cognitive function (2022)

Modern advances in computational language processing methods have enabled new approaches to the measurement of mental processes. However, the field has primarily focused on model accuracy in predicting performance on a task or a diagnostic category. Instead the field should be more focused on determining which computational analyses align best with the targeted neurocognitive/psychological functions that we want to assess. In this paper we reflect on two decades of experience with the application of language-based assessment to patients' mental state and cognitive function by addressing the questions of what we are measuring, how it should be measured and why we are measuring the phenomena. We address the questions by advocating for a principled framework for aligning computational models to the constructs being assessed and the tasks being used, as well as defining how those constructs relate to patient clinical states. We further examine the assumptions that go into the computational models and the effects that model design decisions may have on the accuracy, bias and generalizability of models for assessing clinical states. Finally, we describe how this principled approach can further the goal of transitioning language-based computational assessments to part of clinical practice while gaining the trust of critical stakeholders.
Integrative genomic analysis reveals widespread enhancer regulation by p53 in response to DNA damage (2015)

The tumor suppressor p53 has been studied extensively as a direct transcriptional activator of protein-coding genes. Recent studies, however, have shed light on novel regulatory functions of p53 within noncoding regions of the genome. Here, we use a systematic approach that integrates transcriptome-wide expression analysis, genome-wide p53 binding profiles and chromatin state maps to characterize the global regulatory roles of p53 in response to DNA damage. Notably, our approach identified conserved features of the p53 network in both human and mouse primary fibroblast models. In addition to known p53 targets, we identify many previously unappreciated mRNAs and long noncoding RNAs that are regulated by p53. Moreover, we find that p53 binding occurs predominantly within enhancers in both human and mouse model systems. The ability to modulate enhancer activity offers an additional layer of complexity to the p53 network and greatly expands the diversity of genomic elements directly regulated by p53.
Tyrosine Phosphorylation Regulates Alpha II Spectrin Cleavage by Calpain (2002)

Spectrins, components of the membrane skeleton, are implicated in various cellular functions. Understanding the diversity of these functions requires better characterization of the interacting domains of spectrins, such as the SH3 domain. Yeast two-hybrid screening of a kidney cDNA library revealed that the SH3 domain of alpha II-spectrin binds specifically isoform A of low-molecular-weight phosphotyrosine phosphatase (LMW-PTP). The alpha II-spectrin SH3 domain does not interact with LMW-PTP B or C nor does LMW-PTP A interact with the alpha I-spectrin SH3 domain. The interaction of spectrin with LMW-PTP A led us to look for a tyrosine-phosphorylated residue in alpha II-spectrin. Western blotting showed that alpha II-spectrin is tyrosine phosphorylated in vivo. Using mutagenesis on recombinant peptides, we identified the residue Y1176 located in the calpain cleavage site of alpha II-spectrin, near the SH3 domain, as an in vitro substrate for Src kinase and LMW-PTP A. This Y1176 residue is also an in vivo target for kinases and phosphatases in COS cells. Phosphorylation of this residue decreases spectrin sensitivity to calpain in vitro. Similarly, the presence of phosphatase inhibitors in cell culture is associated with the absence of spectrin cleavage products. This suggests that the Y1176 phosphorylation state could modulate spectrin cleavage by calpain and may play an important role during membrane skeleton remodeling.
Development of Moving Bed Temperature Swing Adsorption (MBTSA) Process for Post-combustion CO2 Capture: Initial Benchmarking in a NGCC Context (2017)

A moving-bed temperature-swing adsorption (MBTSA) process has been evaluated for post-combustion CO 2 capture in a natural-gas combined cycle (NGCC) context using Zeolite 13X as adsorbent. The performance of the different sections of the reactor (adsorption, regeneration and heat exchange) were modelled in gPROMS using real equilibrium and kinetic adsorption data and typical heat transfer parameters. As a consequence of the internal heat transfer between the hot adsorbent powder leaving the regenerator with the cold powder entering the regenerator, a low specific heat requirement for regeneration of 2.3 GJ th /ton CO 2 captured is estimated. When also including the electrical energy needed (also compression of CO 2 ) a total energy penalty of 6.5%-points is obtained. For regeneration, flue gas at 222 °C was used for heating and it was assumed that the flue gas was heated after the power plant by using saturated steam condensing at 230 °C. A major reduction in the heat requirement for the process can be gained if the heat required for regeneration is provided from more optimal integration with the steam cycle of the power plant.
Activity Analysis Using Spatio-Temporal Trajectory Volumes in Surveillance Applications (2007)

In this paper, we present a system to analyze activities and detect anomalies in a surveillance application, which exploits the intuition and experience of security and surveillance experts through an easy- to-use visual feedback loop. The multi-scale and location specific nature of behavior patterns in space and time is captured using a wavelet-based feature descriptor. The system learns the fundamental descriptions of the behavior patterns in a semi-supervised fashion by the higher order singular value decomposition of the space described by the training data. This training process is guided and refined by the users in an intuitive fashion. Anomalies are detected by projecting the test data into this multi-linear space and are visualized by the system to direct the attention of the user to potential problem spots. We tested our system on real-world surveillance data, and it satisfied the security concerns of the environment.
Identification ofAnaplasma phagocytophila(FormerlyEhrlichia phagocytophila) Variants in Blood from Sheep in Norway (2002)

A total of 41 blood samples were collected from 40 Anaplasma phagocytophila-infected sheep in 11 sheep flocks from four different counties of southern Norway. The presence and nature of the Anaplasma species were identified by microscopic detection of morulae, PCR, reverse line blot hybridization, and 16S rRNA gene sequencing. A. phagocytophila was identified in all of the samples, and sequencing of the 16S rRNA gene revealed the presence of four variants of A. phagocytophila. Two of these variants have been described before, but two were newly identified 16S rRNA variants of this species. A. phagocytophila variant 1 was found in nine flocks, A. phagocytophila variant 2 was found in four flocks, the A. phagocytophila prototype was found in two flocks, and A. phagocytophila variant 5 was found in one flock. In two flocks, some sheep were infected with A. phagocytophila variant 1, whereas others were infected with A. phagocytophila variant 2, and in three animals a double infection with two variants was registered. Analyses of the blood samples revealed that blood from sheep infected with A. phagocytophila variant 2 contained nearly twice as many neutrophils and eight times as many Anaplasma-infected neutrophils as blood from sheep infected with the A. phagocytophila variant 1. Furthermore, only 43% of the A. phagocytophila variant 2-infected sheep displayed antibody responses in an immune fluorescence assay, whereas 93% of the sheep with the A. phagocytophila variant 1-infected sheep were seropositive.
Reflexiones nerviosas: la importancia de la ropa (I) pacientes y médicos. (2011)

Sin resumen.
IC‐P‐036: Preliminary analysis of copy number variation in the ADNI cohort (2010)

Copy number variations (CNVs) are segments of DNA, ranging from 1 kilobase (kb) to several megabases (Mb), for which copy number differences (deletions or duplications) have been revealed by comparison of two or more genomes. CNVs have been implicated in neuropsychiatric disorders such as autism and schizophrenia [1], but to our knowledge the role of CNVs has been examined in only one study in Alzheimer's disease (AD) [2] and has not yet been investigated in amnestic mild cognitive impairment (MCI) compared to healthy controls (HC). CNV calls for 655 non-Hispanic Caucasian ADNI participants (Current diagnosis: AD = 285, MCI = 187, HC = 183), whose DNA were derived from peripheral blood (genotyped on the Illumina Human610-Quad BeadChip), were generated using Log R Ratio (LRR) and B allele frequency (BAF) as computed by PennCNV. Quality control (QC) procedures followed [2]. CNV burden, mean size of deletions and duplications and variation in gene regions were compared by current diagnosis. 440 samples (AD = 193, MCI = 116, HC = 131) passed all QC. No differences were seen in overall CNV burden or average length of segments when comparing the 3 diagnosis groups (Table 1). No excess of very large (>1Mb) deletions or duplications in AD or MCI subjects were found relative to controls. Preliminary analysis of case/control associations for CNVs partially overlapping or disrupting genes (PLINK gene list: hg18 coordinates), identified several genes of potential interest including TP53TG3, CSMD1, ANKRD36 and SLC35F2, although none reached significance (p < 0.05) after permutation. Cook and Scherer. Nature, 2008. Heinzen et al. J Alzheimers Dis, 2010.
Light extraction mechanisms in surface-textured light-emitting diodes (2001)

Light-emitting diodes (LEDs) with high efficiencies can be fabricated by a combination of surface texturing and the application of a rear reflector. We demonstrate an external quantum efficiency of 43% for unencapsulated surface-textured thin-film LEDs, which increases to 54% after encapsulation. At low temperatures, the efficiency of unencapsulated devices increases up to 68%. We investigate the light extraction mechanism from such LEDs employing a Monte Carlo simulation of the light propagation inside the LED structure. One essential input parameter for the simulation are the light scattering properties of the textured surface, which have been investigated experimentally. For light incidence below the critical angle of total internal reflection, the transmission through a textured surface is reduced compared to a flat surface. However, due to surface texturing, transmission becomes possible for incident angles above the critical angle. As a result, the internal scattering during internal reflection at the textured surface is not necessary for an efficient extraction of the light generated inside the LED structure. In addition, the Monte Carlo simulation also explains the strong increase of the LED efficiency at low temperatures quantitatively by photon recycling effects. Photon recycling is also demonstrated to be partially responsible for the shift of the emission wavelength in thin- film LEDs, as compared to conventional LEDs.
Electrodynamic Containment of Charged Particles (1959)

Electrically charged iron and aluminum particles having diameters of a few microns have been contained in a confined region of space by means of alternating and static electric fields. The theory is essentially that of alternating gradient focusing; here the motion is governed by Mathieu's equation. Under certain circumstances when many particles are confined the three dimensional focusing force and the Coulomb repulsion results in a ``crystaline'' array which can be ``melted'' and reformed.
Effect of encapsulant film properties on PV module performance (2012)

Field test results show that: Modules with Dow prototype films show stable power output while module with EVA film shows decline in power output after half year in field; Modules with Dow prototype films show lower current leakage during the test compared to module with EVA film.
Nano‐ and Microparticles of Organic Fluorescent Dyes (2008)

Organic nanostructured materials are of increasing interest for applications in the fields of bioanalysis, photocatalysis, photonics, and organic light-emitting diodes. However, their preparation is still difficult to control and their optical properties are inadequately known. A solvent-exchange process called the "reprecipitation method" was used here to prepare nano- and microcrystals from fluorescent dyes belonging, for example, to the coumarin and nitrobenzoxadiazole (NBD) series. Typically, the dyes were dissolved in a hydrophilic organic solvent and then suddenly placed in an aqueous environment, where they spontaneously produce molecular assemblies. According to the self-association properties of the dyes and to the experimental conditions used, the nano- and microcrystals obtained exhibited different sizes and shapes, as observed by fluorescence and electron microscopy. In some cases, the crystal habit was controlled by adding some additives to the reprecipitation medium. The overall optical properties of the free-standing particles in suspension were generally quite close to those of the dissolved dyes. However, strong distortions of the absorption and emission spectra were observed for crystals grown in the presence of ionic additives. Under the fluorescence microscope, individual microcrystals may show peculiar emission characteristics, displaying bright and dark zones, or behaving like tiny optical fibers.
THE FORMATION OF AN ORIENTED STRUCTURE DURING THE RADIATION POLYMERIZATION OF A VINYL MONOMER ON A FIBER (1962)

An attempt was made to grow an oriented synthetic polymer by exposing a gaseous monomer (acrylonitrile) to a matrix'' of a caproic acid-amide fiber in the presence of radiation. The x-ray dose strength was 3 x 10/sup 15/ ev/cm/sup 3/-sec, and the time of irradiation was 3 to 6 hours. The temperature of the matrix fiber was 80 deg C during irradiation, and the temperature of the monomer was 40 deg C (vapor pressure of 200 mm Hg std). The increase in weight of the fiber was 15 to 33 wt.% after polymerization of the monomer. Infrared spectroscopy in polarized light showed up a perpendicular dichroism on the fiber. The magnitude of the dichroism (0.83 to 0.87) indicated a definite orientation. No dichroism, and consequently no orientation, could be detected, when the acrylonitrile monomer was polymerized on a non-orientated caproic fiber, or on an oriented fiber wetted with liquid monomer. The data indicate that polymerization of a monomer from the gaseous phase onto an orientated fiber in a high-level radiation field results in the directed growth of a new orientated polymer. (TTT).
Narrative Discourse Cohesion in Early Stage Parkinson’s Disease (2015)

These results support the conclusion that the BG in PD may have an executive role in expressive language use that can be disrupted without impacting language form.
Astrocytes fuel the fire of lymphocyte toxicity after stroke (2017)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
A compiler framework for speculative analysis and optimizations (2003)

Speculative execution, such as control speculation and data speculation, is an effective way to improve program performance. Using edge/path profile information or simple heuristic rules, existing compiler frameworks can adequately incorporate and exploit control speculation. However, very little has been done so far to allow existing compiler frameworks to incorporate and exploit data speculation effectively in various program transformations beyond instruction scheduling. This paper proposes a speculative SSA form to incorporate information from alias profiling and/or heuristic rules for data speculation, thus allowing existing program analysis frameworks to be easily extended to support both control and data speculation. Such a general framework is very useful for EPIC architectures that provide checking (such as advanced load address table (ALAT) [10]) on data speculation to guarantee the correctness of program execution. We use SSAPRE [21] as one example to illustrate how to incorporate data speculation in those important compiler optimizations such as partial redundancy elimination (PRE), register promotion, strength reduction and linear function test replacement. Our extended framework allows both control and data speculation to be performed on top of SSAPRE and, thus, enables more aggressive speculative optimizations. The proposed framework has been implemented on Intel's Open Research Compiler (ORC). We present experimental data on some SPEC2000 benchmark programs to demonstrate the usefulness of this framework and how data speculation benefits partial redundancy elimination.
BUTORPHANOL, AZAPERONE, AND MEDETOMIDINE ANESTHESIA IN FREE-RANGING WHITE-TAILED DEER (ODOCOILEUS VIRGINIANUS) USING RADIOTRANSMITTER DARTS (2009)

Fourteen free-ranging white-tailed deer (Odocoileus virginianus) were successfully anesthetized for a total of 15 anesthetic events using a combination of butorphanol (mean+/-SD, 0.58+/-0.1 mg/kg), azaperone (0.37+/-0.06 mg/kg), and medetomidine (0.19+/-0.03 mg/kg) (BAM) administered by radiotelemetry darts from hunting blinds between November 2006 and May 2007. Mean time to locate deer (mean+/-SD, 17. 3+/-7 min), to recumbency (21.4+/-5 min), to initiation of data acquisition (27.5+/-8 min), total down time (37+/-6 min), and average distance run (161+/-82 m) were recorded. Physiologic monitoring was done every 5 min for a total of 20 min. Arterial blood gases were collected every 10 min. Mild to moderate hypoxemia and mildly depressed ventilation occurred in some animals. Muscle relaxation and plane of anesthesia were adequate for completion of all procedures; two deer were administered intravenous butorphanol supplementation to achieve light anesthesia (mean+/-SD, 0.19 mg/kg; 0.12 mg/kg). Recovery following intramuscular administration of naltrexone (1.34+/-0.42 mg/kg; 2x butorphanol dose) and atipamezole (0.93+/-0.14 mg/kg; 5x medetomidine dose) was rapid, smooth, and complete. Mean+/-SD recovery time was 4.5+/-1.5 min. Overall efficacy of the Pneu-Dart radiotelemetry system was 65%. Negative attributes of this protocol included long induction time and dart failure. No known mortalities occurred as a result of the study. This drug combination provided safe, reliable, short-term anesthesia of free-ranging white-tailed deer. Further evaluation for use in field procedures in other cervids is warranted.
Risperidone long-acting injection: a review of its long term safety and efficacy (2008)

A long-acting form of the second-generation antipsychotic drug risperidone is now broadly available for the treatment of schizophrenia and closely related psychiatric conditions. It combines the advantage of previously available depot formulations for first-generation drugs with the favorable characteristics of the modern "atypical" antipsychotics, namely higher efficacy in the treatment of the negative symptoms of schizophrenia and reduced motor disturbances. Published clinical studies show an objective clinical efficacy (as per psychiatric symptom scores and relapse data) that exceeds that of oral atypical antipsychotics when patients are switched to the long-acting injectable form, a low incidence of treatment-emergent extrapyramidal side effects, and very good acceptance by patients. Available data for maintenance treatment of bipolar disorder show equivalence with the oral form instead of superiority, but are still limited. As it seems likely that efficacy benefits are mostly due to the fact that the injectable form reduces the demand for patient compliance to one physician visit every 2 weeks instead of self-administration on a daily or twice-daily basis, additional potential could exist in other psychiatric disorders where atypical antipsychotic drugs are of benefit but where patient adherence to treatment schedules is typically low.
Reducing bend-induced loss and crosstalk in a two-mode ridge waveguide by steplike thickness structuring (2022)

This study demonstrated that two-step structuring of the waveguide thickness in a bent section significantly reduces bend-related inter-mode crosstalk, excess loss, and pure bending loss. A simple analytical formula was derived linking the thickness change required to compensate for bend-induced effects with geometrical parameters of the waveguide and bending radius. The effectiveness of the proposed approach was verified through rigorous numerical simulations of the loss and inter-mode crosstalk based on transformation optics formalism. The numerical results obtained for a <i>T</i><i>i</i><i>O</i><sub>2</sub>:<i>S</i><i>i</i><i>O</i><sub>2</sub> medium index contrast waveguide exhibited significant improvement of all relevant parameters for <i>T</i><i>E</i><sub>00</sub> and <i>T</i><i>E</i><sub>01</sub> modes.
Pay for Intersection Priority: A Free Market Mechanism for Connected Vehicles (2021)

The rapid development and deployment of vehicle technologies offer opportunities to re-think the way traffic is managed. This article capitalizes on vehicle connectivity and proposes an economic instrument and corresponding cooperative framework for allocating priority at intersections. The framework is compatible with a variety of existing intersection control approaches. Similar to free markets, our framework allows vehicles to trade their time based on their (disclosed) value of time. We design the framework based on transferable utility games, where winners (time buyers) pay losers (time sellers) in each game. We conduct simulation experiments of both isolated intersections and an arterial setting. The results show that the proposed approach benefits the majority of users when compared to other mechanisms both ones that employ an economic instrument and ones that do not. We also show that it drives travelers to estimate their value of time correctly, and it naturally dissuades travelers from attempting to cheat.
The effects of preservatives and temperatures on arachnid DNA (2005)

We tested the effects of different preservatives and temperatures on the yield of spider and scorpion DNA useable for PCR amplification. Our experiment was designed to simulate conditions in the field and laboratory over a six-week time period, testing the preservatives RNAlater®, propylene glycol, and various ethanol concentrations. Three replicates of each preservation treatment were stored at five different temperature treatments; –80°C, –20°C, 2–4°C, 19–24°C, and 40°C. DNA was extracted and quality was assessed by electrophoresis on mini-gels, and by PCR amplification of high copy mitochondrial DNA fragments (cytochrome oxidase subunit I) and low copy nuclear DNA fragments (actin). Results show that RNAlater® and propylene glycol are significantly better than the other preservatives for high quality DNA preservation and that tissue is best stored at –80°C or –20°C. Storage in 95% ethanol is appropriate if specimens are stored at –20°C or –80°C. We believe our results can help guide biologists in choosing preservatives and temperatures for DNA-based research on arachnids, other arthropods and invertebrates in general.