gebhart/patrepeval huggingface dataset:
Identification of a Glypican‐3‐Binding Peptide for In Vivo Non‐Invasive Human Hepatocellular Carcinoma Detection (2016)

Early and accurate detection of hepatocellular carcinoma (HCC) is essential to improve the prognosis of patients and reduce the morbidity of surgical therapy. Glypican-3 (GPC3) is a protein abnormally expressed in HCC that has been identified as a serological and histochemical HCC marker. A novel peptide that specifically recognizes GPC3 will facilitate early detection of HCC and guide the treatment strategy. Herein, phage display screening technology is utilized to obtain a GPC3 binding peptide (GBP) using HCC cells expressing GPC3 in varying abundances. After seven rounds of panning, a peptide with sequence of THVSPNQGGLPS is identified with 735.2 ± 53.6 × 10<sup>-9</sup> m affinity to GPC3. The ability to target GPC3 in vivo is evaluated by intravenous injection of GBP labeled with a near-infrared dye, Cy5.5, into a HCC tumor-bearing mouse model. Significant high tumor accumulation (tumor/muscle ratio: 6.49 ± 0.55) of Cy5.5-GBP in HepG2 tumors is observed compared with that of the low GPC3 expressing prostate cancer cell line, PC3 (tumor/muscle ratio: 1.15 ± 0.32). By targeting GPC3, GBP differentiates tumor tissues from normal liver tissues in patients, suggesting a great clinical translation potency of GBP. Collectively, GBP demonstrates great potential for HCC detection via fluorescent imaging or histological staining.
The Cytochrome c Gene from the Green Alga Chlamydomonas reinhardtii. Structure and Expression in Wild-Type Cells and in Obligate Photoautotrophic (dk) Mutants (2000)

The expression of the Chlamydomonas reinhardtii cytochrome c gene was studied at the steady-state mRNA level. The inclusion of acetate under illumination produced a marked increase in cytochrome c transcripts. This effect was not affected by two inhibitors of mitochondrial energy metabolism. Three different obligate photoautotrophic mutants with defective mitochondria showed normal levels of induction, suggesting that utilization of acetate for respiration is not required for this process. Light, in the presence or absence of acetate, also promoted an increase in cytochrome c transcript levels. This effect could be abolished by treatment of the cells with an inhibitor of the photosynthetic electron transport chain, suggesting that light acts through photosynthesis to promote the induction. In addition, a genomic clone encompassing the Chlamydomonas cytochrome c gene has been isolated and analyzed. The gene contains three introns, two of which are located at positions similar to those in the rice and Arabidopsis cytochrome c genes, indicating the existence of an evolutionary link. It is concluded that the cytochrome c gene from C. reinhardtii is subject to metabolic regulation through a mechanism that responds to the intracellular level of either acetate or a compound derived from its metabolization through a pathway different from mitochondrial respiration.
MEIS-WNT5A axis regulates development of fourth ventricle choroid plexus (2021)

The choroid plexus (ChP) produces cerebrospinal fluid and forms an essential brain barrier. ChP tissues form in each brain ventricle, each one adopting a distinct shape, but remarkably little is known about the mechanisms underlying ChP development. Here, we show that epithelial WNT5A is crucial for determining fourth ventricle (4V) ChP morphogenesis and size in mouse. Systemic Wnt5a knockout, or forced Wnt5a overexpression beginning at embryonic day 10.5, profoundly reduced ChP size and development. However, Wnt5a expression was enriched in Foxj1-positive epithelial cells of 4V ChP plexus, and its conditional deletion in these cells affected the branched, villous morphology of the 4V ChP. We found that WNT5A was enriched in epithelial cells localized to the distal tips of 4V ChP villi, where WNT5A acted locally to activate non-canonical WNT signaling via ROR1 and ROR2 receptors. During 4V ChP development, MEIS1 bound to the proximal Wnt5a promoter, and gain- and loss-of-function approaches demonstrated that MEIS1 regulated Wnt5a expression. Collectively, our findings demonstrate a dual function of WNT5A in ChP development and identify MEIS transcription factors as upstream regulators of Wnt5a in the 4V ChP epithelium.
Development of a multi-functional scarifier dislodger with an integral pneumatic conveyance retrieval system for single-shell tank remediation. FY93 summary report (1994)

The Underground Storage Tank Integrated Demonstration (UST-ID) is evaluating several hydraulic dislodger concepts and retrieval technologies to develop specifications for system that can retrieve wastes from single-shell tanks. Each of the dislodgers will be evaluated sequentially to determine its ability to fracture and dislodge various waste simulants such as salt cake, sludge, and viscous liquid. The retrieval methods will be evaluated to determine their ability to convey this dislodged material from the tank. This report describes on-going research that commenced in FY93 to develop specifications for a scarifier dislodger coupled with a pneumatic conveyance retrieval system. The scarifier development is described in Section 3; pneumatic conveyance development is described in Section 4. Preliminary system specifications are listed in Section 5. FY94 plans are summarized in Section 6.
Anatomic changes during head and neck radiotherapy observed with automated MRI tracking (2023)

Longitudinal MRI is an ideal tool for tracking anatomic changes that occur during head and neck radiotherapy. We have implemented an image tracking system that monitors volumetric changes in gross tumor volumes (GTV) and parotid glands to identify and alert of major changes early in treatment. In a cohort of 91 patients, this system identified systematic shrinkage of GTVs (9.2&amp;plusmn;8.3% per week) and parotids (3.1&amp;plusmn;3.7% per week) during treatment. Importantly, GTV changes observed in the first week of treatment were strongly predictive of larger changes that would occur later in the course (P&amp;lt;1x10 -5 , two-tailed t-test).
Fast methods for testing quantified relational calculus assertions (1982)

Semantic integrity assertions are predicates that define consistent states. A database system enforces assertions by ensuring that consistency is maintained as the database is updated.Most research on the efficient enforcement of assertions has concentrated on assertion simplification algorithms --- algorithms that produce simplified assertions that can be evaluated before the update is executed. This paper describes a strategy for further improving the efficiency of assertion enforcement.We develop an efficient algorithm for evaluating an assertion produced by an assertion simplification algorithm. We characterize a class of assertions that can be evaluated using a simple two-step procedure. The first step defines and evaluates simple selection queries on each relation. The second step applies set emptiness tests to the results of these selections. We also show how these techniques may be used to improve the efficiency of evaluating assertions outside our class.
PELVIC TILT AND ACETABULAR ORIENTATION: CAN THE EFFECT BE QUANTIFIED? (2013)

The position of the pelvis influences acetabular orientation. In particular, pelvic tilt in the sagittal plane may lead to inaccurate interpretation of plain pelvic radiographs. We therefore quantified the relationship between this pelvic tilt and acetabular orientation in native hips, and determined whether pelvic tilt affects femoral head cover.

We analysed computed tomography scans of 93 hips (36 normal, 31 dysplastic, 26 with acetabular retroversion) and measured acetabular anteversion, inclination, and femoral head cover at pelvic tilt angles ranging from −20° to 20° in relation to the anterior pelvic plane using 5° increments.

The effect of pelvic tilt on version was similar in the normal, dysplastic, and retroverted groups, with a drop in anteversion ranging from 2.5° to 5° for every 5° of forward tilt.

There was a tendency for the inclination angle to decrease when the pelvis was tilted forward from a position of extension, and in normal hips, this produced a reduction in inclination of about 4° for every 8° of pelvic tilt; but once neutral pelvic tilt was reached, further forward rotation of the acetabulum had rather a small effect on the inclination angle.

In normal and dysplastic hips pelvic tilt increased apparent femoral head cover; in the retroverted group the effect was less marked and tended to be negligible at higher tilt angles. Anterior cover increased with increasing forward tilt in all three groups of hips. Posterior cover, on the other hand, decreased by just 2% for the dysplastic hips, 3.5% for the normal hips, and 6% for the retroverted hips over the whole range of tilt from −20° to 20°.

A greater understanding of the influence of pelvic tilt may allow improvements in the radiological diagnosis and surgical treatment of acetabular abnormalities, particularly in relation to acetabular reorientation procedures and femoroacetabular impingement.
Reversibility of scattered fields(Conference Presentation) (2016)

In recent years, tremendous efforts have been spent on deep tissue imaging using phase conjugation, a technique used to undo the effects of light scattering in a thick tissue. Despite the early debates between Yariv and Wolf, it is still not well understood physically how deep can a field propagate into biological tissue and still be phase conjugated. In order to answer this question, we developed a light scattering theory to describe the evolution of the phase associated with a field scattered by a thick tissue block. The multiple scattering through the sample is simplified to a series of single scattering through consecutive thin tissue slices. With this theory, we identify the limits of the phase conjugation operation and recover the previous results by Yariv and Wolf, which asserts that phase conjugation is rooted in small angle approximation. Importantly, we discover the fundamental principle that rules phase conjugation: the mean axial wavenumber of a field progressively decreases to zero as it scatters multiple times. At this point, phase becomes a spatially random variable and phase conjugation becomes impossible. This result describes a fundamental phenomenon: the interaction between a deterministic object and a deterministic field can result in a random scattered field. We show that this phenomenon is rooted into Heisenberg’s uncertainty principle.
Effect of in vitro fermentation using human faecal inoculum on the water-holding capacity of dietary fibre (1985)

The water-holding capacities (WHC) of four sources of fibre were measured using dialysis membranes and osmotic-suction pressures of 45, 89 and 178 mosmol/1 (1, 2 and 4 atm). At all pressures, pectin had the highest WHC, followed by cabbage (Brassica oleracea) and lucerne (Medicago sativa) and then cellulose. A suction pressure of 89 mosmol/1 (2 atm) was used in the subsequent fermentation study since it had the lowest standard error of the mean and most closely approximated physiological conditions. The four fibres were anaerobically fermented in vitro with human faecal inoculum for 24 h. The WHC of the fermentation residues were measured. The potential water-holding capacity (PWHC), a function of the extent of fermentability and the WHC of the fermentation residues, was highest for lucerne, followed by cellulose, then cabbage and, finally, pectin. Only the PWHC values ranked the four fibres in the same order as in vivo values. It was concluded that the ethanol-insoluble residues containing unfermented fibre organic matter and microbial organic matter, both of which hold water, should be used to calculate PWHC and to predict the effect of fibre on rate of passage and faecal mass in humans.
Automatic Categorization of Email into Folders: Benchmark Experiments on Enron and SRI Corpora (2005)

Office workers everywhere are drowning in email---not only spam, but also large quantities of legitimate email to be read and organized for browsing. Although there have been extensive investigations of automatic document categorization, email gives rise to a number of unique challenges, and there has been relatively little study of classifying email into folders. This paper presents an extensive benchmark study of email foldering using two large corpora of real-world email messages and foldering schemes: one from former Enron employees, another from participants in an SRI research project. We discuss the challenges that arise from differences between email foldering and traditional document classification. We show experimental results from an array of automated classification methods and evaluation methodologies, including a new evaluation method of foldering results based on the email timeline, and including enhancements to the exponential gradient method Winnow, providing top-tier accuracy with a fraction the training time of alternative methods. We also establish that classification accuracy in many cases is relatively low, confirming the challenges of email data, and pointing toward email foldering as an important area for further research.
Steroid replacement education: are we getting it right? (2016)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Changes in facial profile during orthodontic treatment with extraction of four first premolars (2008)

The present study was designed to evaluate soft tissue profile changes after the orthodontic treatment of class I bimaxillary dentoalveolar protrusion in adult cases. Pre- and post-treatment cephalograms of 20 Caucasian female class I bimaxillary dentoalveolar protrusion patients were selected from private practice. All of them were treated by extraction of four first premolars, and banded and bonded by 022 × 028 standard edgewise technique. t-Test was used to analyze pre- and post-treatment cephalograms. This study showed that upper and lower lip protrusions were decreased respectively 2.7 ± 2.9 mm (p < 0.001) and 2.8 ± 2.8 mm (p < 0.001). The mean changes of upper and lower lip thickness and length, as well as nasolabial and labiomental angles were not significant. Significant positive correlation was found between changes of maxillary and mandibular incisors with changes in upper lip (rUI = 0.70, p < 0.001, rLI = 0.59, p < 0.006) and the lower lip positions (rUI = 0.64, p < 0.002, rLI = 0.72, p < 0.001). By using stepwise regression it was found that a ratio of 0.63:1 was obtained between upper lip retraction and maxillary incisor retraction and a ratio of 0.62:1 was obtained between lower lip retraction and mandibular incisor changes. This study concluded that, a strong correlation exists between anterior tooth retraction and the position of both lips.
The Reduced Release of GH by GHRH in 8 Subjects Aged 65–69 Years Is Augmented Considerably by Rivastigmine, a Drug for Alzheimer’s Disease (2003)

Rivastigmine is a powerful drug to enhance GH release to repeated GHRH stimulation in healthy elderly human subjects. Future investigations are necessary to find out whether rivastigmine can restore the senile decline of the circadian GH secretion in the long term and, therefore, has new implications for patient treatment.
Multiple metastasized extramammary Paget's disease cured with bisphosphonate risedronate sodium after CyberKnife radiosurgery and docetaxel chemotherapy (2016)

Invasive extramammary Paget's disease (EMPD) is highly metastatic to lymph nodes and other organs, including bone, and when metastatic lesions have expanded beyond the inguinal lymph node, it is difficult to cure. In this report, we present a case of multiple metastasized, receptor activator of nuclear factor kappa-B ligand-expressing EMPD in the pelvic lymph nodes successfully cured with continuous administration of bisphosphonate risedronate sodium after intensive CyberKnife radiotherapy and docetaxel monochemotherapy. Our present case suggested the usefulness of bisphosphonates as a maintenance therapy for metastatic invasive EMPD after the intensive chemoradiotherapy.
Silk Layering As Studied with Neutron Reflectivity (2012)

Neutron reflectivity (NR) measurements of ultrathin surface films (below 30 nm) composed of Bombyx mori silk fibroin protein in combination with atomic force microscopy and ellipsometry were used to reveal the internal structural organization in both dry and swollen states. Reconstituted aqueous silk solution deposited on a silicon substrate using the spin-assisted layer-by-layer (SA-LbL) technique resulted in a monolayer silk film composed of random nanofibrils with constant scattering length density (SLD). However, a vertically segregated ordering with two different regions has been observed in dry, thicker, seven-layer SA-LbL silk films. The vertical segregation of silk multilayer films indicates the presence of a different secondary structure of silk in direct contact with the silicon oxide surface (first 6 nm). The layered structure can be attributed to interfacial β-sheet crystallization and the formation of well-developed nanofibrillar nanoporous morphology for the initially deposited silk surface layers with the preservation of less dense, random coil secondary structure for the layers that follow. This segregated structure of solid silk films defines their complex nonuniform behavior in the D(2)O environment with thicker silk films undergoing delamination during swelling. For a silk monolayer with an initial thickness of 6 nm, we observed the increase in the effective thickness by 60% combined with surprising decrease in density. Considering the nanoporous morphology of the hydrophobic silk layer, we suggested that the apparent increase in its thickness in liquid environment is caused by the air nanobubble trapping phenomenon at the liquid-solid interface.
Tetanus and Diphtheria Immunization Coverage in Ecuadorian Children after a National Vaccination Campaign (1993)

Between October 1985 and June 1986, a national vaccination campaign was launched in Ecuador. Between March and November 1986, 7798 Ecuadorian children < 5 years old were enrolled in a representative health survey. According to their vaccination cards, 65% of children had a complete series of three doses of diphtheria-tetanus-pertussis (DTP) vaccination. Serum samples were obtained from a subset of 1400 children; by ELISA, 80% had serologic evidence of recent DTP vaccination and > 80% of the newborns had tetanus antitoxin titers, indicating recent tetanus vaccination of their mothers. For all 1400 children, median tetanus and diphtheria antitoxin titers were 1.0 and 0.6 IU/mL, respectively. These data indicate the possibility of success of such vaccination campaigns if supported by the government.
Resolving sub-clonal heterogeneity within cell-line growths by single cell sequencing genomic DNA (2019)

ABSTRACT We performed shallow single-cell sequencing of genomic DNA across 1,475 cells from a well-studied cell-line, COLO829, to resolve overall tumor complexity and clonality. This melanoma tumor-line has been previously characterized by multiple technologies and provides a benchmark for evaluating somatic alterations, though has exhibited conflicting and indeterminate copy number states. We identified at least four major sub-clones by discriminant analysis of principal components (DAPC) of single cell copy number data. Break-point and loss of heterozygosity (LOH) analysis of aggregated data from sub-clones revealed a complex rearrangement of chromosomes 1, 10 and 18 that was maintained in all but two sub-clones. Likewise, two of the sub-clones were distinguished by loss of 1 copy of chromosome 8. Re-analysis of previous spectral karyotyping data and bulk sequencing data recapitulated these sub-clone hallmark features and explains why the original bulk sequencing experiments generated conflicting copy number results. Overall, our results demonstrate how shallow copy number profiling together with clustering analysis of single cell sequencing can uncover significant hidden insights even in well studied cell-lines.
Oxidative Stress Relaxation of Natural Rubber Vulcanized with Di-Tertiary-Butyl Peroxide (1956)

Abstract It has been shown by Farmer and Moore that natural rubber can be vulcanized with di- tert. -butyl peroxide (DTBP), Presumably the free radicals formed by the unimolecular decomposition of the peroxide abstract some of the more labile (e.g., α-methylenic) hydrogen atoms, leading to direct C—C crosslinks between the rubber molecules, with tert. -butanol and acetone as the main reaction products. This preliminary communication presents some of the results of an investigation of the oxidative stress relaxation of the following types of DTBP vulcanizates. (A) First grade pale crepe, DTBP, and carbon black (MPC) mixed on the mill and vulcanized in a press. The carbon black was added to minimize the deleterious effect of impurities. (B) Purified rubber vulcanized: (1) in aqueous heating media; (2) in the press; (3) in DTBP vapor.
Humor in Collective Discourse: Unsupervised Funniness Detection in the New Yorker Cartoon Caption Contest (2015)

The New Yorker publishes a weekly captionless cartoon. More than 5,000 readers submit captions for it. The editors select three of them and ask the readers to pick the funniest one. We describe an experiment that compares a dozen automatic methods for selecting the funniest caption. We show that negative sentiment, human-centeredness, and lexical centrality most strongly match the funniest captions, followed by positive sentiment. These results are useful for understanding humor and also in the design of more engaging conversational agents in text and multimodal (vision+text) systems. As part of this work, a large set of cartoons and captions is being made available to the community.
Deposition of naphthalene and tetradecane vapors in models of the human respiratory system (2011)

Jet-propulsion fuel (particularly JP-8) is currently being used worldwide, exposing especially Air Force personnel and people living near airfields to JP-8 vapors and aerosols during aircraft fueling, maintenance operations, and/or cold starts. JP-8 is a complex mixture containing >200, mostly toxic, aliphatic and aromatic hydrocarbon compounds of which tetradecane and naphthalene were chosen as two representative chemical markers for computer simulations. Thus, transport and deposition of naphthalene and tetradecane vapors have been simulated in models of the human respiratory system. The inspiratory deposition data were analyzed in terms of regional deposition fractions (DFs) and deposition enhancement factors (DEF). The vapor depositions are affected by vapor properties (e.g. diffusivity), airway geometric features, breathing patterns, inspiratory flow rates, as well as airway-wall absorption parameter. Specifically, the respiratory uptake of vapors is greatly influenced by the degree of airway-wall absorption. For example, being an almost insoluble species in the mucus layer, the deposition of tetradecane vapor is nearly zero in the extrathoracic and tracheobronchial (TB) airways, that is, the DF is <1%. The remaining vapors may penetrate further and deposit in the alveolar airways. The DF of tetradecane vapors during inhalation in the alveolar region can range from 7% to 24%, depending on breathing waveform, inhalation rate, and thickness of the mucus layer. In contrast, naphthalene vapor almost completely deposits in the extrathoracic and TB airways and hardly moves downstream and deposits in the respiratory zone. The DFs of naphthalene vapor in the extrathoracic airways from nasal/oral to trachea under normal breathing conditions (Q = 15-60 L/min) are about 12-34%, although they are about 66-87% in the TB airways. In addition, the variation of breathing routes (say, from nasal breathing to oral breathing) may influence the vapor deposition in the regions of nasal and oral cavities, nasopharynx and oropharynx, but hardly affects the deposition at and beyond the larynx. The different deposition patterns of naphthalene and tetradecane vapors in the human respiratory system may indicate different toxic and hence health effects of these toxic jet-fuel components.