gebhart/patrepeval huggingface dataset:
Rodent Heart and Brain Tissue Preparation for Digital Macro Photography after Ischemia-reperfusion (2022)

Macro photography is applicable for imaging various tissue samples at high magnification to perform qualitative and quantitative analyses. Tissue preparation and subsequent image capture are steps performed immediately after the ischemia-reperfusion (IR) experiment and must be performed in a timely manner and with appropriate care. For the evaluation of IR-induced damage in the heart and brain, this paper describes 2,3,5-triphenyl-2H-tetrazolium chloride (TTC)-based staining followed by macro photography. Scientific macro photography requires controlled lighting and an appropriate imaging setup. The standardized methodology ensures high-quality, detailed digital images even if a combination of an inexpensive up-to-date digital camera and macro lens is used. Proper techniques and potential mistakes in sample preparation and image acquisition are discussed, and examples of the influence of correct and incorrect setups on image quality are provided. Specific tips are provided on how to avoid common mistakes, such as overstaining, improper sample storage, and suboptimal lighting conditions. This paper shows the appropriate methodology for rat heart and brain tissue slicing and staining and provides guidelines for establishing lighting and camera setups and photography techniques for high-resolution image acquisition.
Bioreactors for Bone Tissue Engineering (2011)

Bone tissue engineering is a promising solution for patients with bone defects that require reconstruction. This regenerative therapy consists in culturing osteogenic cells on a biodegradable substrate to obtain a bio-hybrid construct that will stimulate bone healing after implantation. This multidisciplinary technology nevertheless requires further development before it can become routine clinical practice. One challenge is to achieve three-dimensional seeding and osteogenic commitment of mesenchymal stem cells on biomaterials under sterile and reproducible conditions. For this purpose, different dynamic culture systems have been developed. This paper reviews recent advances in the field of bioreactors for bone tissue engineering. The purpose of such systems is to improve nutrient delivery to the cells and generate shear stress that may promote cell differentiation into osteoblastic phenotypes. A brief overview of the value of computational fluid dynamics for understanding the cell environment is also provided. Finally, some proposals are made regarding the use of bioreactors as safe and controllable devices that will help commit cells and biomaterials for the regeneration of bone tissue.
Optimal step size of the adaptive multichannel LMS algorithm for blind SIMO identification (2005)

Adaptive algorithms for blindly identifying single-input multiple-output (SIMO) systems are appealing because of their computational efficiency and capability of continuously tracking a time-varying system. Adaptive multichannel least-mean-square (MCLMS) algorithms (with and without the unit-norm constraint) are analyzed, and the optimal step size is derived. A simple yet effective variable step-size MCLMS algorithm is proposed, and its performance is evaluated with simulations.
Nanocrystalline Fe–Fe2O3 particle-deposited N-doped graphene as an activity-modulated Pt-free electrocatalyst for oxygen reduction reaction (2015)

Correction for 'Nanocrystalline Fe-Fe<sub>2</sub>O<sub>3</sub> particle-deposited N-doped graphene as an activity-modulated Pt-free electrocatalyst for oxygen reduction reaction' by Vishal M. Dhavale et al., Nanoscale, 2015, 7, 20117-20125.
HER2/neu overexpression in the development of muscle-invasive transitional cell carcinoma of the bladder (2003)

The mortality from transitional cell carcinoma (TCC) of the urinary bladder increases significantly with the progression of superficial or locally invasive disease (pTa/pT1) to detrusor muscle-invasive disease (pT2+). The most common prognostic markers in clinical use are tumour stage and grade, which are subject to considerable intra- and interobserver variation. Polysomy 17 and HER2/neu gene amplification and protein overexpression have been associated with more advanced disease. Standardised techniques of fluorescence in situ hybridisation and immunohistochemistry, which are currently applied to other cancers with a view to offering anti-HER2/neu therapies, were applied to tumour pairs comprising pre- and postinvasive disease from 25 patients undergoing treatment for bladder cancer. In the preinvasive tumours, increased HER2/neu copy number was observed in 76% of cases and increased chromosome 17 copy number in 88% of cases, and in the postinvasive group these values were 92 and 96%, respectively (not significantly different P=0.09 and 0.07, respectively). HER2 gene amplification rates were 8% in both groups. Protein overexpression rates were 76 and 52%, respectively, in the pre- and postinvasive groups (P=0.06). These results suggest that HER2/neu abnormalities occur prior to and persist with the onset of muscle-invasive disease. Gene amplification is uncommon and other molecular mechanisms must account for the high rates of protein overexpression. Anti-HER2/neu therapy might be of use in the treatment of TCC.
Some Evidence of Subsidization: the U.S. Trucking Industry, 1900–1920 (1973)

This paper is concerned with the rapid growth of the trucking industry during the period 1900 to 1920. Our purpose is to examine the frequently asserted proposition that motor trucking was able to grow rapidly in competition with a well-established railroad industry because of the hidden subsidy provided by public expenditures on highways. Though this is a popularly held notion there has been little empirical evidence presented to support or refute it.
Nonlinear RF and space-charge induced emittance growth in a thermionic injector accelerating cavity (2010)

The performance of a high-power free-electron laser depends crucially on the attainment of low beam emittances and short pulse lengths from the injector. One potential injector design involves generating a beam from an rf-gated thermionic cathode that is located within a 700 MHz accelerating cavity. The proposed RF cavity design is modeled using the field-solver Poisson Superfish. Particle energies in the cavity range from a few hundred eV at the cathode up to 1 MeV at the cavity exit. At these low energies, space-charge effects play a crucial role in determining the phase-space evolution and emittance growth of the beam. To examine these effects, the accelerating cavity region is modeled using the 3-d particle-in-cell code PARMELA. We explore the use of an additional 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> -harmonic 2.1 GHz accelerating structure to minimize RF-induced curvature in the longitudinal phase space and to improve the longitudinal bunching of the beam.
A Cost Model of Screening and Treatment for Anal HPV, Anal Dysplasia, and Anal Cancer with Attention to Woman Undergoing Screening Colonoscopy (2014)

Introduction: Chronic HPV infection is associated with cancer and dysplasia of the cervix and anus. Screening for anal cancer is cost effective in HIV infected men having sex with men (MSM). Data in other high-risk groups is lacking. We estimate the cost of screening woman 50 years of age or older with a prior history of cervical HPV infection, a group undergoing screening colonoscopy. Methods: A dynamic model was created using STELLA (isee software, Hanover New Hampshire). Populations are represented on STELLA as “stocks” that fill and empty according to rates within the model. The total U.S. female population over age 50 years eligible for screening colonoscopy with a 50% compliance was 128,000; 4% are estimated to have cervical HPV infection. Frequency of low-grade (LGD) and high-grade dysplasia (HGD), with progression to cancer and regression were estimated from cervical infection literature and anal infection in HIV-negative MSM. Costs for anal high-risk HPV testing ($50.27) and anal cytology ($37.94) were obtained from billing rates at NorthShore. Treatment costs for HGD and cancer including ongoing screening were also obtained. Simulations of cost and clinical outcomes were performed in a hypothetical screened and treated versus non-screened population over a 10-year period. Results: The estimated annual cost for screening for anal high-risk HPV and performing anal cytology in the female U.S. population coming for colonoscopy with known cervical HPV was ˜$16 million. HGD was reduced in the screened group at 10 years (from 31,219 women to 8,904 women respectively); 4,667 cases of anal cancer would be prevented over a 10-year period and that 1,144 lives would be saved. Figure 2 shows the prevalence of anal cancer cases in the screened and treated group and the unscreened group. Cost per life saved using screening was $4,474.65. Conclusion: Women older than age 50 years with a history of cervical HPV are at risk for anal HPV, dysplasia, and anal cancer. Our model suggests that testing for high-risk anal HPV and anal cytology results in significant reduction of the development of HGD and anal cancer on the group and that this approach is cost effective.Figure 1
Two Modes of Survival of Fission Yeast Without Telomerase (1998)

Deletion of the telomerase catalytic subunit gene trt1+ in Schizosaccharomyces pombe results in death for the majority of cells, but a subpopulation survives. Here it is shown that most survivors have circularized all of their chromosomes, whereas a smaller number maintain their telomeres presumably through recombination. When the telomeric DNA-binding gene taz1+ is also deleted, trt1- taz1- survivors use the recombinational mode more frequently. Moreover, the massive elongation of telomeres in taz1- cells is absent in the double mutant. Thus, Taz1p appears to regulate telomeric recombination as well as telomerase activity in fission yeast.
Wholly thermoplastic composites from woven preforms based on nylon‐11 fibers reinforced in situ with a hydroquinone‐based liquid crystalline polyester (1997)

Abstract This work concerns a novel means to generate wholly thermoplastic composites based on low‐melting thermoplastics reinforced with high‐melting thermotropic liquid crystalline polymers (TLCPs). A novel dual extrusion process was employed to generate nylon‐11 fibers that are reinforced with continuous fibrils of a hydroquinone‐based liquid crystalline polyester (DuPont TLCP, HX8000). These composite fibers display tensile properties significantly higher than those predicted by composite theory. These fibers were subsequently woven into a fabric, which in turn serves as a composite preform. Several layers of the fabric preform were stacked and consolidated to yield a composite plaque. The consolidation was carried out at temperatures just high enough for nylon‐11 to melt, but well below the melting temperature of HX8000. Fabric preform composites based on the composite fibers with ∼35 wt% HX8000 gave modulus values close to five and one half times that of nylon‐11, and strength values approximately two and one half times that of nylon‐11. The tensile and flexural properties of these composites are superior to continuous glass‐fiber reinforced composites at comparable loadings on a volume basis. Moreover, as the reinforcing fibrils are already encapsulated by the matrix, fiber wetting and fabric impregnation issues that are critical in the fabrication of continuous glass and carbon fiber composites are eliminated.
Nuclear entry and export of FIH are mediated by HIF1α and exportin1, respectively (2018)

Hypoxia plays a crucial role at cellular and physiological levels in all animals. The responses to chronic hypoxia are, at least substantially, orchestrated by activation of the hypoxia inducible transcription factors (HIFs), whose stability and subsequent transcriptional activation are regulated by HIF hydroxylases. Factor inhibiting HIF (FIH), initially isolated as a HIFα interacting protein following a yeast two-hybrid screen, is an asparaginyl hydroxylase that negatively regulates transcriptional activation by HIF. This study aimed to define the mechanisms that govern transitions of FIH between the nucleus and cytoplasm. We report that FIH accumulates in the nucleus within a short time window during hypoxia treatment. We provide evidence, based on the application of genetic interventions and small molecule inhibition of the HIF hydroxylases, that the nuclear localization of FIH is governed by two opposing processes: nuclear entry by 'coupling' with HIF1α for importin β1-mediated nuclear import and active export via a Leptomycin B-sensitive exportin1-dependent pathway.This article has an associated First Person interview with the first author of the paper.
Solar Control Tunable Lippmann Holowindows (1985)

Tunable Lippmann Holowindows have been developed by NTS as a particular application for Broad-Band Lippmann Holograms investigated within Super High Efficiency (SHE) Holographic Technology. Those holograms can be tuned to be highly reflective (above 99%) in any part of the near UV, Visible and near IR. In particular, they can reflect all direct solar heat radiation and additionally, the near UV part of the solar spectrum that cannot be blocked by glass or acrylic. Additionally, they can be combined with conductive adhesives to create ideal cooling mirrors, with parameters much better than those of existing products. Therefore, they can create a new generation of high efficiency solar heat control windows whose rejection of adjusted parts of the solar spectrum still preserve high visible transmission (up to 87% for single glazing), and the near perfect (close to 100%) reflection of IR direct solar component. In the case of Tunable Lippmann Holowindows, it is possible to adjust independently the U-value, emittance and shading coefficient by the number of glazings, conductive adhesive thickness and hologram reflection, respectively. In other words, SHE Holographic Technology introduces to heat mirror engineering a new degree of freedom - separate near IR reflection coefficient.
Synchronization of speech frames based on phase data with application to concatenative speech synthesis (1999)

In this paper we successfully apply the MCE/GPD method to train speaker cluster HMM. The essential concept of our approach is to adjust all the parameters of the speaker cluster HMM simultaneously using each utterance of the whole training set. In other words, the parameters of each cluster-dependent HMM are no longer independently estimated by using only the training data of the speakers who belong to its corresponding cluster. To achieve this purpose, the discriminant function used in the MCE/GPD method need to be defined by the parameter set of the entire speaker cluster HMM. In our implementation, we define it as a function of the log-likelihood scores given the cluster-dependent HMMs. The proposed discriminative training procedure would increase the cluster separability and then improve the recognition rate.
Impaired Heart Rate Recovery and Chronotropic Incompetence in Patients With Heart Failure With Preserved Ejection Fraction (2009)

Background— This study assessed the chronotropic response to exercise and heart rate (HR) recovery after exercise in a carefully phenotyped group of patients with heart failure with preserved left ventricular ejection fraction (HfpEF) and a control group of similar age and gender distribution.

Methods and Results— We studied 41 patients with HfpEF, 41 healthy controls, and 16 hypertensive controls. None were taking HR-limiting medications. All study participants had clinical examination, 12-lead ECG, pulmonary function test, echocardiogram, and metabolic exercise test with HR monitoring throughout exercise. Chronotropic response was measured by the percentage of the HR reserve used during maximal exercise and the peak exercise HR as a percentage of predicted maximal HR. Patients with HfpEF were generally women (70%), overweight, aged 69±8 years. Controls were of similar gender (63%) and age (67±6 years). Patients with HfpEF had significantly reduced peak VO2 compared with controls (20±4 mL · kg−1 · min−1 versus 31±6 mL · kg−1 · min−1, P <0.001) and greater minute ventilation-carbon dioxide production relationship (Ve/Vco2 slope) (33±6 versus 29±4, P <0.001). Chronotropic incompetence was significantly more common in patients with HfpEF compared with matched healthy controls as measured by the percentage of the HR reserve used during maximal exercise (63% versus 2%, <0.001) and percentage of predicted maximal HR (34% versus 2%, <0.001). In addition, abnormal HR recovery 1-minute after exercise (defined as the reduction in the HR from peak exercise 1-minute after exercise) was also significantly more common in patients with HfpEF compared with controls (23% versus 2%, P =0.01). Hypertensive controls showed similar chronotropic response to peak exercise and HR recovery after exercise as healthy controls.

Conclusions— Patients with HfpEF have impaired chronotropic incompetence during maximal exercise and abnormal HR recovery after exercise.

Received May 5, 2009; accepted August 21, 2009.
Assessment of Respiration- and Cardiac-Related Flow Patterns of Cerebro-Spinal Fluid Using Balanced Steady-State Free Precession and Breathing-ECG Synchronization (2007)

The aim of this study was to measure Cere bro-Spinal Fluid (CSF) velocities and flow patterns caused by heartbeat and respirator y phase. An optimized flow-sensitive double-gated cine balanced Steady-State Free Precession (bSSFP) sequence was designed and implemented, together with a computerized system that provided visual feedback to the scanned subject in order to synchronize breathing phases and eartbeats. The high signal intensity given by CSF using this sequence allowed accurate measurement of velocities, and the dependence of flow patterns on cardiac and respiratory phase was confirmed and quantified.
Passive Haptic Rehearsal for Accelerated Piano Skill Acquisition (2022)

Passive haptic learning (PHL) uses vibrotactile stimulation to train piano songs using repetition, even when the recipient of stimulation is focused on other tasks. However, many of the benefits of playing piano cannot be acquired without actively playing the instrument. In this position paper, we posit that passive haptic rehearsal, where active piano practice is assisted by separate sessions of passive stimulation, is of greater everyday use than solely PHL. We propose a study to examine the effects of passive haptic rehearsal for self-paced piano learners and consider how to incorporate passive rehearsal into everyday practice.
Learning in the 21st century cyber-physical age (2017)

The learning tools necessary to prepare the next generation of students must be shaped by the socio-economic needs of the 21st century. The needs of the 21st century -from rebuilding city scale physical infrastructure to personalized healthcare -not only require learning from the wealth of global information available on the Internet, but also the building of a strong grounding in fundamentals. History has shown that the depth in fundamentals has been achieved through conventional books. Indeed, authoritative books in physical fundamentals have been penned in the 19th century and early 20th century. We present a 21st century cyber-physical learning platform that combines the best of physical books with information systems. The systemic instantiation of the platform combines modern optics and computing to view books, scan objects, and enable interactive learningwhile simultaneously benefitting from the vast pool of information on the Internet. The hybrid learning platform preserves the best of the past to pave the way for the future. It also enables future research such as meta-data and descriptive tagging of the large number of images available on the web.
The geometry of small fullerene cages: C20 to C70 (1992)

The ground-state structures of small fullerenes below C70 were determined by tight-binding molecular-dynamics total energy optimization. An efficient simulated annealing scheme was used to generate closed, hollow, spheroidal cage structures for all even-numbered carbon clusters from C20 to C70. As a general trend, fullerenes prefer geometries which separate the pentagonal rings as far apart as possible. Except for C60, C70, and C50, most fullerenes have relatively low symmetries.
Plasmodium falciparum Rab1A Localizes to Rhoptries in Schizonts (2016)

Over-expression of a GFP-PfRab1A fusion protein in Plasmodium falciparum schizonts produces a punctate pattern of fluorescence typical of rhoptries, secretory organelles involved in host cell invasion. The GFP-positive bodies were purified by a combination of differential and density gradient centrifugation and their protein content determined by MS/MS sequencing. Consistent with the GFP rhoptry-like pattern of transgenic parasites, four of the 19 proteins identified have been previously described to be rhoptry-associated and another four are ER or ER-associated proteins. Confirmation that GFP-PfRab1A decorates rhoptries was obtained by its co-localization with Rap1 and Ron4 in late phase schizonts. We conclude that PfRab1A potentially regulates vesicular traffic from the endoplasmic reticulum to the rhoptries in Apicomplexa parasites.
Estimation of the transmission time of stimulus-locked responses: modelling and stochastic phase resetting analysis (2005)

A model of two coupled phase oscillators is studied, where both oscillators are subject to random forces but only one oscillator is repetitively stimulated with a pulsatile stimulus. A pulse causes a reset, which is transmitted to the other oscillator via the coupling. The transmission time of the cross-trial (CT) averaged responses, i.e. the difference in time between the maxima of the CT averaged responses of both oscillators differs from the time difference between the maxima of the oscillators' resets. In fact, the transmission time of the CT averaged responses directly corresponds to the phase difference in the stable synchronized state with integer multiples of the oscillators' mean period added to it. With CT averaged responses it is impossible to reliably estimate the time elapsing, owing to the stimulus' action being transmitted between the two oscillators.
Recent Developments in Materials Synthesis and Processing Using Supercritical CO2 (2001)

The chemical and physical properties of carbon dioxide in the liquid or supercritical state differ quite strongly from those of conventional liquid organic solvents. These differences may be exploited in a wide variety of materials applications. Here we describe recent research involving the use of dense carbon dioxide in the areas of porous organic materials, coatings and lithography, metal nanoparticle synthesis, and biomaterials processing.