gebhart/patrepeval huggingface dataset:
Neuropathologic Findings in an Aged Albino Gorilla (2008)

Pallido-nigral spheroids associated with iron deposition have been observed in some aged clinically normal nonhuman primates. In humans, similar findings are observed in neurodegeneration with brain iron accumulation diseases, which, in some cases, show associated mutations in pantothenate kinase 2 gene (PANK2). Here we present an aged gorilla, 40 years old, suffering during the last 2 years of life from progressive tetraparesis, nystagmus, and dyskinesia of the arms, hands, and neck, with accompanying abnormal behavior. The postmortem neuropathologic examination revealed, in addition to aging-associated changes in the brain, numerous corpora amylacea in some brain areas, especially the substantia nigra, and large numbers of axonal spheroids associated with iron accumulation in the internal globus pallidus. Sequencing of the gorilla PANK2 gene failed to detect any mutation. The clinical, neuropathologic, and genetic findings in this gorilla point to an age-related pallido-nigral degeneration that presented PKAN-like neurologic deficits.
The serine/threonine kinase PknB of Mycobacterium tuberculosis phosphorylates PBPA, a penicillin-binding protein required for cell division (2006)

The authors would like to retract the article as the published versions of Figs. 3b, 6a, b, d, 7a, b(lower panel) were modified prior to publication. The authors would like to apologise to thereaders, reviewers and editors of Microbiology for this error.
Simulated Small‐Channel Bed Scour and Head Cut Erosion Rates Compared (1995)

Abstract Concentrated‐flow erosion is often a major part of cropland erosion. The concentrated‐flow processes of bed scour and head cut need improved characterization to better predict and prevent erosion. This study was conducted to compare the erosion rates due to simulated small‐scale bed‐scour ( D b ) and head‐cut ( D h ) processes. A 6.4‐m‐long by 0.15‐m‐wide hydraulic flume was used to simulate concentrated‐flow erosion on five Midwestern soils: Barnes (fine‐loamy, mixed Udic Haploboroll), Forman (fine‐loamy, mixed Udic Argiboroll), Mexico (fine, montmorillonitic, mesic Udollic Ochraqualf), Sharpsburg (fine, montmorillonitic, mesic Typic Argiudoll), and Sverdrup (sandy, mixed Udic Haploboroll). For slopes of 1.5, 3.5, and 5.0%, flow rates of 3.78, 5.67, 7.65, 11.34, and 15.12 L min −1 were used to provide a range from low (0.5 Pa) to moderate (2.5 Pa) shear stresses (τ). Soil detachment rates are functions of slope, flow rate, and shear stress. Slope, flow, their squares, and the slope × flow interaction were highly significant predictors of D b . Only flow, its square, and its interaction with slope were significant predictors of D b . Nonlinear power regressions using τ as an independent variable were better predictors of detachment than simple linear regressions. Erodibility for the soils from this study does not relate well with soil erodibility calculated using the Universal Soil Loss Equation. Differences in the slope and intercept of detachment vs. τ exist among soils. The value of D b was at least four times greater than D b for all soils at equal slope and flow rate, indicating that head cutting is the main process of detachment for the conditions tested.
1320. The preparation of tetrahydrofurfuryl esters of certain mono- and di-basic carboxylic acids (1965)

R. T. Wragg, J. Chem. Soc., 1965, 7162 DOI: 10.1039/JR9650007162
Parameterization of cloud droplet formation for global and regional models: including adsorption activation from insoluble CCN (2009)

Abstract. Dust and black carbon aerosol have long been known to exert potentially important and diverse impacts on cloud droplet formation. Most studies to date focus on the soluble fraction of these particles, and overlook interactions of the insoluble fraction with water vapor (even if known to be hydrophilic). To address this gap, we developed a new parameterization that considers cloud droplet formation within an ascending air parcel containing insoluble (but wettable) particles externally mixed with aerosol containing an appreciable soluble fraction. Activation of particles with a soluble fraction is described through well-established Köhler theory, while the activation of hydrophilic insoluble particles is treated by "adsorption-activation" theory. In the latter, water vapor is adsorbed onto insoluble particles, the activity of which is described by a multilayer Frenkel-Halsey-Hill (FHH) adsorption isotherm modified to account for particle curvature. We further develop FHH activation theory to i) find combinations of the adsorption parameters AFHH, BFHH which yield atmospherically-relevant behavior, and, ii) express activation properties (critical supersaturation) that follow a simple power law with respect to dry particle diameter. The new parameterization is tested by comparing the parameterized cloud droplet number concentration against predictions with a detailed numerical cloud model, considering a wide range of particle populations, cloud updraft conditions, water vapor condensation coefficient and FHH adsorption isotherm characteristics. The agreement between parameterization and parcel model is excellent, with an average error of 10% and R2~0.98. A preliminary sensitivity study suggests that the sublinear response of droplet number to Köhler particle concentration is not as strong for FHH particles.
Reconfigurable delay cell for area-efficient implementation of on-chip MOSFET monitor schemes (2013)

To measure target MOSFET variation, specific monitor schemes are required. With device scaling, developing each monitor scheme is costly. This paper proposes a universal delay monitor cell which enables measurements of various types of variations with single monitor scheme. The monitor cell is reconfigurable and standard cell compatible; thus it can be used in the conventional place and route flow. An area-efficient monitor scheme to monitor global, local, and dynamic variations is developed. Measurement results from a 65-nm test chip shows the validity of the proposed monitor cell. The proposed cell enables area-efficient and low cost implementation of monitor schemes which can be integrated with application such as testing and adaptive voltage scaling.
Device-Based Approaches to Modulate the Autonomic Nervous System and Cardiac Electrophysiology (2014)

Alterations in resting autonomic tone can be pathogenic in many cardiovascular disease states, such as heart failure and hypertension. Indeed, autonomic modulation by way of beta-blockade is a standard treatment of these conditions. There is a significant interest in developing non-pharmacological methods of autonomic modulation as well. For instance, clinical trials of vagal stimulation and spinal cord stimulation in the treatment of heart failure are currently underway, and renal denervation has been studied recently in the treatment of resistant hypertension. Notably, autonomic stimulation is also a potent modulator of cardiac electrophysiology. Manipulating the autonomic nervous system in studies designed to treat heart failure and hypertension have revealed that autonomic modulation may have a role in the treatment of common atrial and ventricular arrhythmias as well. Experimental data on vagal nerve and spinal cord stimulation suggest that each technique may reduce ventricular arrhythmias. Similarly, renal denervation may play a role in the treatment of atrial fibrillation, as well as in controlling refractory ventricular arrhythmias. In this review, we present the current experimental and clinical data on the effect of these therapeutic modalities on cardiac electrophysiology and their potential role in arrhythmia management.
Molecularly imprinted polymers (MIP): From the bulk synthesis to hybrid material to classic and new applications (2017)

Molecular imprinting has become one of the most effective techniques in developing biomimetic material and, within these approaches, molecularly imprinted polymers (MIP) have proven their potential in synthetic recognition. Their advantages, when compared to biological material (like enzymes and antibodies), include high chemical and thermal stability, easy preparation, low cost and proven stability in long-term storage. Additionally, MIP present many uses, from the preparation of samples, to Solid Phase Extraction (SPE), High Performance Liquid Chromatography (HPLC) and layer recognition in sensors. Therefore, because of the great potential of biomimetic polymers, this chapter will undertake the history of its development and synthesis methods, structural modifications that enable the formation of new MIP and its various uses. The scope of this chapter aims to highlight some of the examples of MIP synthesis and use, without covering the extensive literature available and providing a broad view of the field.
Construction of Local Vertebral Coordinate Systems Using a Digitizing Probe (1997)

The described technique quickly, easily, and accurately relates anatomic landmarks to optical markers and constructs local coordinate axes, two steps that are necessary before monitoring the kinematics of individual motion segments during multilevel spine testing.
Enhancing Spatial Attention and Working Memory in Younger and Older Adults (2017)

Daily experiences demand both focused and broad allocation of attention for us to interact efficiently with our complex environments. Many types of attention have shown age-related decline, although there is also evidence that such deficits may be remediated with cognitive training. However, spatial attention abilities have shown inconsistent age-related differences, and the extent of potential enhancement of these abilities remains unknown. Here, we assessed spatial attention in both healthy younger and older adults and trained this ability in both age groups for 5 hr over the course of 2 weeks using a custom-made, computerized mobile training application. We compared training-related gains on a spatial attention assessment and spatial working memory task to age-matched controls who engaged in expectancy-matched, active placebo computerized training. Age-related declines in spatial attention abilities were observed regardless of task difficulty. Spatial attention training led to improved focused and distributed attention abilities as well as improved spatial working memory in both younger and older participants. No such improvements were observed in either of the age-matched control groups. Note that these findings were not a function of improvements in simple response time, as basic motoric function did not change after training. Furthermore, when using change in simple response time as a covariate, all findings remained significant. These results suggest that spatial attention training can lead to enhancements in spatial working memory regardless of age.
COVID-19 and the fear of other unknowns: challenges and lessons learned from a digital contact tracing activity in the Rohingya camps in Cox’s Bazar, Bangladesh (2022)

Contact tracing can play an important role in controlling infectious disease outbreaks such as the COVID-19 pandemic. Containing the spread of COVID-19 is crucial in humanitarian settings such as in the Rohingya camps in Cox’s Bazar, Bangladesh. This manuscript describes the COVID-19 contact tracing activities undertaken by a group of researchers and implementers in Cox’s Bazar, Bangladesh. The paper details the design and development of the Commcare ‘Contact tracing and case monitoring app’, subsequent implementation of the contact tracing activity, challenges faced during the implementation process, and the strategies adopted by the research team to overcome these challenges. The research team leveraged the suite of template applications for COVID-19 response developed by Dimagi in response to the COVID-19 pandemic. Research partners organized a series of brainstorming meetings and workshops with relevant stakeholders to finalize the ‘COVID- 19 contact tracing and case monitoring app’ for final implementation. This app was implemented in 10 Rohingya camps from Ukhiya and Teknaf sub-districts of Cox’s Bazar for 4.5 months from 1st January 2021 to 15th May 2021. Due to a restriction on internet availability in the Rohingya camps by the government of the host country, the research team had to adopt a manual approach to implement the contact tracing activity. During these 4.5 months, 249,452 individuals from 10 Rohingya camps were screened for COVID-19 case registration. Of all the screened individuals, 431 were identified as COVID suspected cases, and 77 were identified as confirmed cases. The research team experienced several implementation challenges such as inexperience of contact tracers with the nature of the work, convincing the community to register in a digital system, obtaining information around COVID-19 symptoms, and many cultural, linguistic, gender, and other social barriers. The team adopted challenge-specific mitigation strategies for the effective implementation of the activity. The modalities of operation adopted by the team engaged with this present intervention to overcome the difficulties experienced in its conduction can hopefully provide some guidance to future parties attempting to conduct similar activities in complex humanitarian settings.
Pharmacokinetics and Pharmacodynamics of Vecuronium (ORG NC45) and Pancuronium in Anesthetized Humans (1984)

CRONNELLY, R.; FISHER, D. M.; MILLER, R. D.; GENCARELLI, P.; NGUYEN-GRUENKE, L.; CASTAGNOLI, N. JR.; Adams, Anthony P. M.B., B.S., PhD., FFARCS Author Information
Review: Bioresorbable polymeric stents: current status and future promise (2003)

Metal stents and, more recently, polymer-coated metal stents are used to stabilize dissections, eliminate vessel recoil, and guide remodeling after balloon angioplasty and other treatments for arterial disease. Bioresorbable polymeric stents are being developed to improve the biocompatibility and the drug reservoir capacity of metal stents, and to offer a transient alternative to the permanent metallic stent implant. Following a brief review of metal stent technology, the emerging class of expandable, bioresorbable polymeric stents is described, with emphasis on developments in the authors' laboratory.
Comparison of Different Methods for Extraction of Mitochondrial DNA from Human Pathogenic Yeasts (2002)

Methods of rapidly extracting chromosomal DNA from human pathogenic yeasts were used in mitochondrial DNA (mtDNA) studies. This paper is concerned with rapid and reliable methods of extracting mtDNA for sequence analysis for species or strain identification, and epidemiological study of medically important fungi and fungal infections. To determine the optimal method of mtDNA extraction without isolating mitochondria, we examined three commonly used methods: 1). boiling, 2). glass bead disruption, and 3). a commercially available kit. We assessed the amount and quality of DNAs using a spectrophotometer and specific polymerase chain reaction (PCR). The DNA yield depended on the extraction method used and the yeast species. An adequate amount of mtDNA was obtained with both glass beads and a commercially available kit to amplify the mitochondrial gene using PCR without isolating the mitochondria. These techniques are convenient for extracting DNA from a variety of small-scale samples.
Degenerate layers in epitaxial ZnO films grown on sapphire substrates (2004)

ZnO films were grown on low-temperature (LT) buffer layers on sapphire a-plane (11–20) substrates by radical source molecular-beam epitaxy. The LT buffer layers were found to effect the electrical properties of subsequently grown undoped ZnO films, and their presence was found to be indispensable for the growth of films with low carrier concentrations and high mobilities. Temperature-dependent Hall measurements showed the existence of a degenerate region related to the LT buffer layers. It was found that the effects of degenerate layers could be reduced by using annealing treatments and nitrogen doping of the LT buffer layers. The dominant residual donor energy of 110 meV was found to be different than previously reported. The carrier concentration of a ZnO film fabricated using a nitrogen-doped buffer layer was 7.5×1016 cm−3 with a mobility of 132 cm2/V s at room temperature.
A flexible security model for using Internet content (2002)

Java applets, Netscape plug-ins and ActiveX controls have led to the popularization of a new paradigm: extensive downloading of executable code into applications to enhance the functionality of the desktop. One of the problems with this paradigm is the need to control the access rights of the downloaded content. In this paper, we describe a system for downloading content from the Internet and controlling its actions on a client machine. Our system generates a protection domain for the downloaded content dynamically rising the content's requested domain and a policy database that describes the user's trust in the content's manufacturer and type. Our system ensures that this protection domain is enforced throughout the execution of the content. We have modified the Java Virtual Machine to implement our security model. Our implementation, called Flexxguard, is freely available at http://www.alphaworks.ibm.com.
A Multivariate Timeseries Modeling Approach to Severity of Illness Assessment and Forecasting in ICU with Sparse, Heterogeneous Clinical Data (2015)

The ability to determine patient acuity (or severity of illness) has immediate practical use for clinicians. We evaluate the use of multivariate timeseries modeling with the multi-task Gaussian process (GP) models using noisy, incomplete, sparse, heterogeneous and unevenly-sampled clinical data, including both physiological signals and clinical notes. The learned multi-task GP (MTGP) hyperparameters are then used to assess and forecast patient acuity. Experiments were conducted with two real clinical data sets acquired from ICU patients: firstly, estimating cerebrovascular pressure reactivity, an important indicator of secondary damage for traumatic brain injury patients, by learning the interactions between intracranial pressure and mean arterial blood pressure signals, and secondly, mortality prediction using clinical progress notes. In both cases, MTGPs provided improved results: an MTGP model provided better results than single-task GP models for signal interpolation and forecasting (0.91 vs 0.69 RMSE), and the use of MTGP hyperparameters obtained improved results when used as additional classification features (0.812 vs 0.788 AUC).
Active diagnosis of discrete-event systems (1998)

The need for accurate and timely diagnosis of system failures and the advantages of automated diagnostic systems are well appreciated. However, diagnosability considerations are often not explicitly taken into account in the system design. In particular, design of the controller and that of the diagnostic subsystem are decoupled, and this may significantly affect the diagnosability properties of a system. The authors present an integrated approach to control and diagnosis. More specifically, they present an approach for the design of diagnosable systems by appropriate design of the system controller. This problem, which they refer to as the active diagnosis problem, is studied in the framework of discrete-event systems (DESs); it is based on prior and new results on the theory of diagnosis for DESs and on existing results in supervisory control under partial observations. They formulate the active diagnosis problem as a supervisory control problem where the legal language is an "appropriate" regular sublanguage of the regular language generated by the system. They present an iterative procedure for determining the supremal controllable, observable, and diagnosable sublanguage of the legal language and for obtaining the supervisor that synthesizes this language. This procedure provides both a controller that ensures diagnosability of the closed-loop system and a diagnoser for online failure diagnosis. The procedure can be implemented using finite-state machines and is guaranteed to converge in a finite number of iterations. The authors illustrate their approach using a simple pump-valve system.
The spawning pheromone cysteine‐glutathione disulfide (‘nereithione’) arouses a multicomponent nuptial behavior and electrophysiological activity in Nereis succinea males (1999)

The pheromone nereithione (cysteine-glutathione disulfide), which is released by swimming females of the polychaete Nereis succinea to activate spawning behavior of N. succinea males, has recently been identified and synthesized. Nereithione activates sperm release at less than 10(-6) M, one to two orders of magnitude less than oxidized glutathione or any other glutathione derivative tested. The glutathione fragment gamma-glu-cys inhibited sperm release. Nereithione aroused three components of the male nuptial behavior: circling, sperm release, and accelerated swimming. Electrophysiological activity elicited by nereithione near the sperm release site consisted of initial large spikes, cyclic bursting activity, and small spikes lasting up to a minute and was dose dependent, rapid, reversible, and repeatable. This preparation is an excellent model system for characterizing the receptors and functions of a marine pheromone.
Avant-propos (2022)

sous le titre Samuel Beckett and the Arts: Music, Visual Arts, and Non-Print
High efficiency, large-active-area superconducting nanowire single-photon detectors (2015)

Niobium nitride superconducting nanowire single-photon detectors were fabricated on thermally oxidized silicon substrates with large active areas of 30 μm × 30 μm. To achieve non-constricted detectors, we improved the film growth and electron beam lithography process to fabricate uniform 100-nm wide NbN nanowires with a fill factor of 50%. The devices showed 72.4% system detection efficiency (SDE) at 100-Hz dark count rate (DCR) and 74-ps timing jitter, measured at the fiber communication wavelength of 1550 nm. The highest SDE which is 81.2% when the DCR is ~700 c/s appears at the wavelength of 1650 nm.
RNAseq Analysis of FFPE Radical Prostatectomy Specimens Identifies Predictors of Biochemical Recurrence (2013)

To identify effective predictors of recurrence following radical prostatectomy, RNAseq libraries were prepared from RNA derived from 71 Formalin Fixed Paraffin Embedded (FFPE) prostatectomy samples from two institutions, and high‐throughput sequencing was performed on an Illumina HiSeq2000 instrument. Subjects were divided into high and low risk groups based on the optimal predictive score cutoff from ROC analysis, and we performed log rank test to compare biochemical recurrence (BCR) between the two risk groups. For the 70 samples analyzed, clinical variables alone were highly predictive of recurrence (log‐rank test p=2.55e‐04); however the panel of 11 genes from the RNAseq analysis outperformed clinical variables alone (log rank test p=1.82e‐13). Prediction using this model achieved an ROC AUC of 0.959 with 85% sensitivity and 97% specificity. This set of RNA biomarkers may be useful in the prediction of BCR following radical prostatectomy, irrespective of stage, grade, race, or pre‐operative PSA. Patients with tumors having increased expression of these markers may benefit from close follow‐up after surgery. Research supported by DOD IDEA Award W81XWH‐010–1‐0090.