gebhart/patrepeval huggingface dataset:
Femtosecond laser pulse filamentation characterized by polymer gel dosimetry and Fricke dosimetry (2010)

A femtosecond laser pulse that can generate water radiolysis species was studied in view of its potential medical and biological applications. Intense ultra-short laser pulses can propagate in liquid water, leading to self-focusing and filamentation. Briefly, electrons produced by either multiphoton or tunnel ionization are further accelerated by the electric field of the pulse in an inverse Bremsstrahlung effect. If the electrons acquire enough kinetic energy, they will give rise to a second generation of electrons by impact ionization of other molecules in an avalanche-like process. The geometry and trajectory of femtosecond filaments were captured within a polymer gel dosimeter and imaged by magnetic resonance imaging (MRI) at high resolution. The results revealed that changing pulse duration modifies the penetration of the filament track in the medium. In addition, we used Fricke dosimetry to measure the absorbed dose and dose rate of the femtosecond laser pulse filamentation. A very high dose rate of 5.3 × 1012 Gy/s was calculated in filaments having a diameter of ∼600 μm.
GLC3 and GHA1 of Saccharomyces cerevisiae Are Allelic and Encode the Glycogen Branching Enzyme (1992)

In the yeast Saccharomyces cerevisiae, glycogen serves as a major storage carbohydrate. In a previous study, mutants with altered glycogen metabolism were isolated on the basis of the altered iodine-staining properties of colonies. We found that when glycogen produced by strains carrying the glc-1p (previously called gha1-1) mutation is stained with iodine, the absorption spectrum resembles that of starch rather than that of glycogen, suggesting that this mutation might reduce the level of branching in the glycogen particles. Indeed, glycogen branching activity was undetectable in extracts from a glc3-1p strain but was elevated in strains which expressed GLC3 from a high-copy-number plasmid. These observations suggest that GLC3 encodes the glycogen branching enzyme. In contrast to glc3-1p, the glc3-4 mutation greatly reduces the ability of yeast to accumulate glycogen. These mutations appear to be allelic despite the striking difference in the phenotypes which they produce. The GLC3 clone complemented both glc3-1p and glc3-4. Deletions and transposon insertions in this clone had parallel effects on its ability to complement glc3-1p and glc3-4. Finally, a fragment of the cloned gene was able to direct the repair of both glc3-1p and glc3-4. Disruption of GLC3 yielded the glycogen-deficient phenotype, indicating that glycogen deficiency is the null phenotype. The glc3-1p allele appears to encode a partially functional product, since it is dominant over glc3-4 but recessive to GLC3. These observations suggest that the ability to introduce branches into glycogen greatly increases the ability of the cell to accumulate that polysaccharide. Northern (RNA) blot analysis identified a single mRNA of 2,300 nucleotides that increased in abundance ca. 20-fold as the culture approached stationary phase. It thus appears that the expression of GLC3 is regulated, probably at the level of transcription.
Functional MRI Mapping of Human Meniscus Functionality and its Relation to Degeneration (2020)

Meniscus pathology may promote early osteoarthritis. This study assessed human meniscus functionality (i.e. its response to loading) ex vivo based on quantitative T1, T1ρ, and T2 mapping as a function of histological degeneration and loading. Forty-five meniscus samples of variable degeneration were harvested from the lateral meniscus body region of 45 patients during total knee arthroplasties. Samples underwent serial mapping on a 3.0-T MRI scanner (Achieva, Philips) using a force-controlled and torque-inducing compressive loading device. Samples were measured at three loading positions, i.e. unloaded, loaded to 2 bar (compression force 37 N) and 4 bar (69 N). Histology (Pauli classification) and biomechanics (Elastic Modulus) served as references. Based on histology, samples were trichotomized as grossly intact (n = 14), mildly degenerative (n = 16), and moderate-to-severely degenerative (n = 15) and analyzed using appropriate parametric and non-parametric tests. For T1, we found loading-induced decreases in all samples, irrespective of degeneration. For T1ρ, zonal increases in intact (apex) and decreases in degenerative samples (base) were found, while for T2, changes were ambiguous. In conclusion, force-controlled loading and serial MR imaging reveal response-to-loading patterns in meniscus. Zonal T1ρ response-to-loading patterns are most promising in differentiating degeneration, while T1 and T2 aren't clearly related to degeneration.and may provide an imaging-based indication of functional tissue properties.
100 GHz Plasmonic Photodetector (2018)

Photodetectors compatible with CMOS technology have shown great potential in implementing active silicon photonics circuits, yet current technologies are facing fundamental bandwidth limitations. Here, we propose and experimentally demonstrate for the first time a plasmonic photodetector achieving simultaneously record-high bandwidth beyond 100 GHz, an internal quantum efficiency of 36% and low footprint. High-speed data reception at 72 Gbit/s is demonstrated. Such superior performance is attributed to the subwavelength confinement of the optical energy in a photoconductive based plasmonic-germanium waveguide detector that enables shortest drift paths for photogenerated carriers and a very small resistance-capacitance product. In addition, the combination of plasmonic structures with absorbing semiconductors enables efficient and highest-speed photodetection. The proposed scheme may pave the way for a cost-efficient CMOS compatible and low temperature fabricated photodetector solution for photodetection beyond 100 Gbit/s, with versatile applications in fields such as communications, microwave photonics, and THz technologies.
Robust Tolerance Design Applied on Robot Concept Development (2010)

A robust tolerance design concept based on locating schemes (for example, used in the car industry for sheet metal parts) and the methods and tools connected to that concept are applied on a new robot development. A case study of a robot assembly is performed in a new robot development project. The robot is mainly designed using machined parts, and traditionally these parts are toleranced using feature-to-feature based tolerances and linear dimensioning. The goal of this case study is to see if there are any advantages to using a new approach when designing robots to enable high geometric quality at a low cost. With limitations, the study shows that it seems possible to effectively use the tolerance design concept in robot development with assemblies consisting of machined parts.
Transversus Abdominis Plane Infiltration and Quality of Recovery After Laparoscopic Hysterectomy (2011)

I.
Optimal Antenna Pattern Design For Synthetic Aperture Radar Using Particle Swarm Intelligence (2007)

Active phased array SAR(Synthetic Aperture Radar) system requires a variety of operational modes based on the mission requirements. According to the complex system operation concepts, SAR requires the various antenna patterns in order to meet the system performance such as range ambiguity. An antenna pattern optimization method for improvement of the range ambiguity in the synthetic aperture radar is presented. To determine the amplitude and phase excitations of the active phased array SAR antenna, the particle swarm method is applied to the antenna elevation pattern optimization based on the cost functions, which are derived from the system configuration, operation concept and requirements. In this paper, we propose a novel beam synthesis technique using the particle swarm optimization in order to obtain the optimal range ambiguity ratio with the shaped antenna pattern.
Aboveground Net Primary Productivity in a Riparian Wetland Following Restoration of Hydrology (2016)

This research presents the initial results of the effects of hydrological restoration on forested wetlands in the Mississippi alluvial plain near Memphis, Tennessee. Measurements were carried out in a secondary channel, the Loosahatchie Chute, in which rock dikes were constructed in the 1960s to keep most flow in the main navigation channel. In 2008-2009, the dikes were notched to allow more flow into the secondary channel. Study sites were established based on relative distance downstream of the notched dikes. Additionally, a reference site was established north of the Loosahatchie Chute where the dikes remained unnotched. We compared various components of vegetation composition and productivity at sites in the riparian wetlands for two years. Salix nigra had the highest Importance Value at every site. Species with minor Importance Values were Celtis laevigata, Acer rubrum, and Plantanus occidentalis. Productivity increased more following the introduction of river water in affected sites compared to the reference. Aboveground net primary productivity was highest at the reference site (2926 ± 458.1 g·m(-2)·year(-1)), the intact site; however, there were greater increase at the sites in the Loosahatchie Chute, where measurements ranged from 1197.7 ± 160.0 g m(-2)·year(-1)·to 2874.2 ± 794.0 g·m(-2)·year(-1). The site furthest from the notching was the most affected. Pulsed inputs into these wetlands may enhance forested wetland productivity. Continued monitoring will quantify impacts of restored channel hydrology along the Mississippi River.
Insulin Production in a Neuroectodermal Tumor that Expresses Islet Factor-1, But Not Pancreatic-Duodenal Homeobox 1 (2001)

We studied a 60-yr-old female with a brain tumor who showed severe symptoms of hypoglycemia (plasma glucose, 2.2 mmol/L) and hyperinsulinemia (1.28 nmol/L) after radiotherapy. The cystic brain tumor contained proinsulin and insulin at concentrations of 13.6 and 1.22 nmol/L, respectively. Immunohistochemical studies showed the tumor cells were ectodermal in origin but not endodermal, based on three diagnostic features of neuroectodermal tumors 1) pseudorosette formation noted under light microscopy, 2) finding of a small number of dense core neurosecretory granules on electron microscopy, and 3) positive immunostaining for both neuronal specific enolase and protein gene product 9.5. These cells also expressed the transcription factor, neurogenin-3, NeuroD/beta 2, and islet factor I, which are believed to be transcription factors in neuroectoderm as well as in pancreatic islet cells, but not pancreatic-duodenal homeobox 1, Pax4, or Nkx2.2. In addition, they did not express glucagon, somatostatin, or glucagon-like peptide-1. Our results show the presence of proinsulin in an ectoderm cell brain tumor that does not express the homeobox gene, pancreatic-duodenal homeobox 1, but expresses other transcription factors, i.e. neurogenin3, NeuroD/beta 2, and islet factor-1, which are related to insulin gene expression in the brain tumor.
Site-specific chelation therapy with EDTA-loaded albumin nanoparticles reverses arterial calcification in a rat model of chronic kidney disease (2019)

Medial arterial calcification (MAC) is a common outcome in diabetes and chronic kidney disease (CKD). It occurs as linear mineral deposits along the degraded elastin lamellae and is responsible for increased aortic stiffness and subsequent cardiovascular events. Current treatments for calcification, particularly in CKD, are predominantly focused on regulating the mineral disturbance and other risk factors. Ethylene diamine tetraacetic acid (EDTA), a chelating agent, can resorb mineral deposits, but the systemic delivery of EDTA may cause side effects such as hypocalcemia and bone resorption. We have developed elastin antibody conjugated albumin nanoparticles that target only degraded elastin in vasculature while sparing healthy tissues. In this study, we tested a targeted nanoparticle-based EDTA chelation therapy to reverse CKD-associated MAC. Renal failure was induced in Sprague-Dawley rats by a high adenine diet supplemented by high P and Ca for 28 days that led to MAC. Intravenous delivery of DiR dye-loaded nanoparticles confirmed targeting to vascular degraded elastin and calcification sites within 24 hours. Next, EDTA-loaded albumin nanoparticles conjugated with an anti-elastin antibody were intravenously injected twice a week for two weeks. The targeted nanoparticles delivered EDTA at the site of vascular calcification and reversed mineral deposits without any untoward effects. Systemic EDTA injections or blank nanoparticles were ineffective in reversing MAC. Reversal of calcification seems to be stable as it did not return after the treatment was stopped for an additional four weeks. Targeted EDTA chelation therapy successfully reversed calcification in this adenine rat model of CKD. We consider that targeted NP therapy will provide an attractive option to reverse calcification and has a high potential for clinical translation.
A Collision Check Program for the IBM Sedab Two-Arm Robot (1991)

Abstract This paper proposes an algorithm to check for collision between the two arms of the IBM SEDAB robot The collision check is based on static interference checks at discrete points along the selected trajectory. The points are equidistant and chosen such that the motion of all joints involved does not exceed given limits. The robot arms are modeled by a series of boxes, with each box representing a link. A collision check is performed by testing critical pairs of boxes for interference. The box - box interference tests involve excessive computation and are therefore time consuming. To reduce the number of necessary box interference tests, a quick test based on a rough model of the arms is used to determine the critical box pairs. This model consists of a series of spheres with one or two spheres circumscribing a box completely. Tools or parts fixed to the grippers can be included into the collision check.
Abstract 838: Mdm2 and oncogenic mutant p53 as biomarkers for potential drug targets in estrogen receptor positive and triple negative breast cancer (2010)

Abstract The study of Mdm2 and oncogenic p53 as biomarkers for potential drug targets in breast cancers has not been developed. Triple negative breast cancers often have gain-of-function oncogenic mutant p53 while estrogen receptor positive breast cancers retain wild-type p53 and over-express Mdm2. We are investigating how to inhibit the growth of various types of breast cancer cell lines when p53 function is compromised. Here we report two approaches. The first approach utilizes the nucleoside analogue 8-aminoadenosine (8-amino-Ado) and the second approach utilizes inducible RNA interference for oncogenic mdm2 or p53. 8-amino-Ado is under pre-clinical investigation for the treatment of hematological malignancies. We investigated if 8-amino-Ado could inhibit breast cancer cell growth and promote cell death in a manner that did not require functional p53 protein and compared this to gemcitabine (a nucleoside analogue used to treat breast cancer). We used the triple negative breast cancer cell lines MDA-MB-231 and MDA-MB-468 as well as the estrogen receptor positive breast cancer cell line MCF-7. 8-amino-Ado promoted death of the triple negative mutant p53 breast cancers as well, or better, than it did for the estrogen receptor positive wild-type p53 breast cancer and in all cases was superior to gemcitabine. For the second approach we constructed cell lines using an inducible shRNA vector that contained a naturally occurring miR sequence. We previously showed that mutant p53 is required for the survival of MDA-MB-231 cells in the absence of serum. Using an inducible p53 shRNA we see that the mutant p53 found in MDA-MB-231 and MDA-MB-468 gives these cells a survival advantage in the absence of serum and when p53 is knocked down the cells die without PARP cleavage, suggesting non-apoptotic cell death. Estrogen increases the expression of Mdm2 in MCF-7 cells and therefore we investigated if the growth activation feature of estrogen in MCF-7 cells required Mdm2 protein. Induction of mdm2 shRNA reduced the Mdm2 protein level and increased the p21 protein level without a detectable change in p53. Induction of mdm2 shRNA caused a corresponding decrease in estrogen-activated MCF-7 cell growth. Inducible expression of shRNA to p53 or the control construct had no effect on the growth of MCF-7 cells. Our data suggest that 8-amino-Ado induced death occurs via a p53-independent pathway and thus might be beneficial for the treatment of all breast cancers. Additionally Mdm2 and oncogenic mutant p53 are biomarkers that can be used to screen for interfering RNA based and 8-amino-Ado therapeutic approaches for estrogen receptor positive and triple negative breast cancers. This work was supported by The Breast Cancer Research Foundation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 838.
Bar induction: The good, the bad, and the ugly (2017)

We present an extension of the computation system and logic of the Nuprl proof assistant with intuitionistic principles, namely versions of Brouwer's bar induction principle, which is equivalent to transfinite induction. We have substantially extended the formalization of Nuprl's type theory within the Coq proof assistant to show that two such bar induction principles are valid w.r.t. Nuprl's semantics (the Good): one for sequences of numbers that involved only minor changes to the system, and a more general one for sequences of name-free (the Ugly) closed terms that involved adding a limit constructor to Nuprl's term syntax in our model of Nuprl's logic. We have proved that these additions preserve Nuprl's key metatheoretical properties such as consistency. Finally, we show some new insights regarding bar induction, such as the non-truncated version of bar induction on monotone bars is intuitionistically false (the Bad).
Early Stage Cancer in Older Adults (2017)

The diagnosis of prostate cancer in elderly men is likely to increase over the next several decades, owing to changing demographics and a rising population of men older than 65 years. Given the heterogeneity and well-documented challenges in screening, diagnosing, and managing indolent versus aggressive prostate cancer, the geriatric patient population is particularly vulnerable to prostate cancer treatment nuances. Clinicians must become familiar with geriatric assessment tools to better answer life-expectancy questions prior to counseling patients on treatment options. The preferences and values of patients and their families must always be considered when making screening and treatment decisions. Careful selection of patients following a holistic evaluation will not only minimize overtreatment and undertreatment of prostate cancer, but may also allow for the early identification of unique geriatric vulnerabilities and permit quicker interventions to improve the quality of life of these men during their elderly years.
Thymidine kinase from Tetrahymena thermophila (1991)

Thymidine kinase is an enzyme involved in DNA precursor metabolism and DNA replication. The synthesis of this enzyme is highly regulated during the cell cycle and the activity of the enzyme is also regulated by feedback inhibition. Genes encoding thymidine kinase have been extremely useful as selectable markers for introducing DNA into a number of cells. In order to study cell cycle regulation of thymidine kinase, the gene which encodes this enzyme, as well as aspects of DNA replication in the ciliated protozoan Tetrahymena thermophila, we have purified thymidine kinase from Tetrahymena. Two forms of thymidine kinase with native molecular masses of 59 kDa and 80 kDa have been identified and purified 6800- and 4600-fold, respectively. The 59-kDa enzyme, a homodimer of 30-kDa subunits, has been purified to near homogeneity and polyclonal antibodies have been raised against the 30-kDa subunit. Serological studies indicate that the two enzymes are antigenically distinct. The antibody against the Tetrahymena protein cross-reacts with a polypeptide in Chinese hamster ovary (CHO) cell extracts of 26 kDa which corresponds to the reported size of Chinese hamster thymidine kinase protein.
Gene expression profile comparison of Barrett's esophagus epithelial cell cultures and biopsies (2008)

Barrett's esophagus (BE) is a metaplastic process in which the normal squamous epithelium of the distal esophagus is replaced by columnar lined epithelium. The aim was to gain more insight in the process of metaplasia and to identify which genes are specifically expressed by the epithelial cells and the surrounding tissues in BE. Hereto, the gene expression profile of a BE epithelial primary cell culture was compared to that of a BE biopsy. To specifically obtain the epithelial cell layer, epithelial cells from biopsies of BE were cultured using a Barrett specific culturing medium. Serial analysis of gene expression was applied to obtain a transcription library of the primary epithelial cell culture. The transcriptome was analyzed and compared to a previously described transcriptome of a BE biopsy. Validation of results by reverse transcriptase-polymerase chain reaction was performed using tissues of 16 BE patients and 16 primary cell cultures. Over 43,000 tags were sequenced. Genes specifically expressed by the Barrett epithelial cells were for instance Lipocalin 2 and Cyclin D1, whereas annexin A10, trefoil factor (TFF)1 and TFF2 were specifically expressed in the BE biopsies. The comparison of the gene expression profiles of BE primary cultured epithelial cells with BE biopsy defines a subset of genes that are specifically expressed by the epithelial cells and another subset that most likely is expressed by the underlying stromal tissues in the BE biopsy specimens.
DEVELOPMENT OF DESIGN PROCEDURES FOR ESTIMATING CAPACITY AND DEFORMATION OF PILE GROUPS. VOLUME 4: A CENTRIFUGAL STUDY OF AXIALLY LOADED MODEL PILES AND PILE GROUPS IN REID-BEDFORD SAND. INTERIM REPORT (1989)

To obtain a better understanding of single pile and pile group behavior, 50 model pile and pile group tests were conducted in the centrifuge. The main objectives of this study were to provide load-deformation responses of single and group piles in sand and to determine the depth of influence below the pile tip for the model piles tested. Furthermore, two different methods of pile installation were tested to determine the influence on the load-deformation response of the models, and some preliminary tests were conducted using a miniature cone penetrometer. It was found that the depth of influence for single piles increases from 14 to 30 pile diameters, as the relative density increases from 30% to 75%. Based on tests conducted on two different model pile sizes, the depth of influence appears to be a function of pile diameter and soil density. The ultimate capacity of a modelled 10 in. diameter, 20 ft long steel pipe pile showed a strong dependency on the relative density of the test sand. The capacity increased threefold for an increase in relative density from 40% to 65%. The pile group efficiency was found to be less than one for a relative density greater than 40%. The method of pile installation, pushed incrementally or driven, does not seem to have any influence on the load-deformation response of the single model piles. Insufficient data were obtained to judge installation effects of pile groups. The load distribution between tip load and side friction of the piles appeared to be independent of soil density.