gebhart/patrepeval huggingface dataset:
The Laser Photocoagulating Dielectric Waveguide Scalpel (1981)

This paper presents the physical theory and engineering development of a new hemostatic scalpel, the photocoagulating dielectric waveguide scalpel. (laser blade). This device has demonstrated a marked reduction in blood loss during surgery of organs where bleeding is normally a major problem, such as the debridement of third-degree burns. The scalpel utilizes an argon laser for optical power (25 W) and a fiber-optic waveguide to flexibly transport the laser radiation to a fused silica scalpel blade. The blade is a dielectric waveguide which carries the laser radiation to a tapered cutting edge which is used for the mechanical incision of tissue and provides the means by which the laser radiation couples (tapered waveguide coupling) into the surrounding tissue for photocoagulation. The optical characteristics of the blade are analyzed and experimentally verified.
Spritz: A Proteogenomic Database Engine (2020)

Abstract Proteoforms are the workhorses of the cell, and subtle differences between their amino acid sequence or post-translational modifications (PTMs) can change their biological function. To most effectively identify and quantify proteoforms in genetically diverse samples by mass spectrometry (MS), it is advantageous to search the MS data against a sample-specific protein database that is tailored to the sample being analyzed, in that it contains the correct amino acid sequences and relevant PTMs for that sample. To this end, we have developed Spritz ( https://smith-chem-wisc.github.io/Spritz/ ), an open-source software tool for generating protein databases annotated with sequence variations and PTMs. We provide a simple graphical user interface (GUI) for Windows and scripts that can be run on any operating system. Spritz automatically sets up and executes approximately 20 tools, which enable construction of a proteogenomic database from only raw RNA sequencing data. Sequence variations that are discovered in RNA sequencing data upon comparison to the Ensembl reference genome are annotated on proteins in these databases, and PTM annotations are transferred from UniProt. Modifications can also be discovered and added to the database using bottom-up mass spectrometry data and global PTM discovery in MetaMorpheus. We demonstrate that such sample-specific databases allow the identification of variant peptides, modified variant peptides, and variant proteoforms by searching bottom-up and top-down proteomic data from the Jurkat human T lymphocyte cell line and demonstrate the identification of phosphorylated variant sites with phosphoproteomic data from the U2OS human osteosarcoma cell line.
Assessment of polymerase chain reaction and serology for detection of chlamydia pneumoniae in patients with acute respiratory tract infection. (2002)

Chlamydia pneumoniae is an important pathogen that causes infection of the human respiratory tract and attention should be drawn to this special illness.
<i>In-situ</i>high-resolution electron microscopy study on a surface reconstruction of Au-deposited Si at very high temperatures (1997)

Abstract In-situ high-temperature high-resolution electron microscopy was applied to a study of the surface modification of Au-deposited Si. The experiment was carried out above the melting points of small particles of Au (approximately several nanometres in diameter) in a 300 kV high-resolution analytical transmission electron microscope equipped with a direct-heating-type specimen-heating holder in a vacuum of 4–6 × 10−6 Pa. Facet-unfacet transformation and reconstruction of the Si{111}, {001}, {211} and {311} surfaces induced by wetting of molten Au atoms have been observed at near-atomic resolution. It is concluded that molten Au atoms remove a surface amorphous layer on the Si surface, making the surface clean even in a non ultra-high vacuum.
Piezoelectric ceramic transformer operating in thickness extensional vibration mode for power supply (2003)

A new kind of multilayer piezoelectric ceramic transformer for switching regulated power supplies is described. This transformer operates in the second thickness extensional vibration mode. Its resonant frequency is higher than 1 MHz. Theoretical calculations are implemented using a distributed constant electromechanical equivalent circuit method. It is calculated that this transformer can operate with higher than 90% efficiency. A fabricated transformer is examined. PbTiO/sub 3/ family ceramics are used because of the large anisotropy between electromechanical coupling factors. Results indicate that the piezoelectric transformer has good resonant characteristics, with little spurious vibration, and exhibits 16 W/cm/sup 3/ power density with high efficiency at 2 MHz. A switching regulated power supply, applying the piezoelectric transformer, is built and examined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Cyst Fluid Carcinoembryonic Antigen Is an Accurate Diagnostic Marker of Pancreatic Mucinous Cysts (2011)

Cyst fluid CEA concentration provides a highly accurate test for the diagnosis of a mucinous cyst, but does not distinguish benign from malignant cysts. Cytology is the most accurate test for the diagnosis of a malignant cyst.
Bone regeneration in orthodontically produced alveolar bone dehiscences (1982)

Orthodontic appliances, designed to tip the maxillary second and third incisors in facial direction, were inserted in 3 dogs. During a 5 month period, the incisors on the left side of the jaw were tipped to a facially displaced position. During a further 5 month period these teeth were moved back to their original position while the two incisors on the right side of the jaw were moved to a position corresponding to that previously reached by the incisors of the left side. The orthodontic appliances were then used to retain the teeth In these positions for 5 months. Teeth in three non‐treated dogs served as controls. During the study, the animals were subjected to meticulous plaque control. The animals were sacrificed 15 months after the start of the study. The jaws were removed and buccolingually oriented histological sections of the experimental and control teeth were produced. The study has shown (1) that dehiscences can be produced in the alveolar bone by tipping teeth in facial direction and that bone will reform in such defects when the teeth are moved back to their original position and (2) that such tooth movements are not necessarily accompanied by loss of connective tissue attachment.
Cystathionine ?-synthase mutations in homocystinuria (1999)

The major cause of homocystinuria is mutation of the gene encoding the enzyme cystathionine beta-synthase (CBS). Deficiency of CBS activity results in elevated levels of homocysteine as well as methionine in plasma and urine and decreased levels of cystathionine and cysteine. Ninety-two different disease-associated mutations have been identified in the CBS gene in 310 examined homocystinuric alleles in more than a dozen laboratories around the world. Most of these mutations are missense, and the vast majority of these are private mutations. The two most frequently encountered of these mutations are the pyridoxine-responsive I278T and the pyridoxine-nonresponsive G307S. Mutations due to deaminations of methylcytosines represent 53% of all point substitutions in the coding region of the CBS gene.
Effects of Metal Chelator, Sodium Azide, and Superoxide Dismutase on the Oxidative Stability in Riboflavin-Photosensitized Oil-in-Water Emulsion Systems (2011)

The effects of riboflavin photosensitization on the oxidative stability of oil-in-water (O/W) emulsions were determined using lipid hydroperoxides and headspace volatile analyses. The influences of a metal chelator, sodium azide, and superoxide dismutase (SOD) on oxidation pathways were tested to gain a better understanding of the role of transition metals, singlet oxygen, and superoxide anion, respectively. Emulsions with riboflavin and visible light irradiation had significantly higher lipid hydroperoxides and volatiles (p < 0.05) as compared to samples without light irradiation or riboflavin. The addition of ethylenediammetetraacetic acid (EDTA) decreased the formation of lipid hydroperoxides, hexanal, 2-heptenal, and 1-octen-3-ol in a concentration-dependent manner. Sodium azide, a singlet oxygen physical quencher, only inhibited the formation of 2-heptenal and 1-octen-3-ol. Overall, photosensitized riboflavin participated in both type I and type II pathways in O/W emulsions, and these pathways enhance the prooxidant activity of metals through their ability to produce lipid hydroperoxides and superoxide anion.
[Effect of recombinant human erythropoietin on hepcidin mRNA expression in patients with multiple myeloma]. (2011)

This study was purposed to investigate the effect of multiple myeloma patients' sera on hepcidin mRNA expression of Hep-3b hepatoma cell line and effect of human interleukin-6 (IL-6) antibody or recombinant human erythropoietin (rhEPO) on hepcidin mRNA expression. The clinical information and serum of multiple myeloma patients were collected. Their sera of a final concentration of 10% were added into Hep-3b cell medium. The mRNA from Hep-3b cells was extracted, and hepcidin mRNA expression was detected by semi-quantitative reverse transcription polymerase chain reaction (RT-PCR). A final concentration of 10 ng/ml human IL-6 antibody and 2 U/ml rhEPO were added into the medium respectively. The results showed that the sera of untreated multiple myeloma patients elevated hepcidin mRNA expression of Hep-3b cells, compared with healthy controls and iron deficiency anemia patients. This effect was fully neutralized by human IL-6 antibody or rhEPO. The hemoglobin (Hb) level was stable during the follow up of regularly treated multiple myeloma patients and the effect of MM patient serum on Hep-3b cell hepcidin mRNA expression was reduced. It is concluded that the hepcidin mRNA expression of Hep-3b cell can be increased by untreated multiple myeloma patient serum. This promotive effect can be antagonised by IL-6, which suggests that IL-6 may be possible to elevate expression level of hepcidin in Hep-3b cells and results in anemia of chronic disease (ACD). The above mentioned promotive effects also can be suppressed by rhEPO, which indicates that the rhEPO may possess curative effect for ACD disease. During short-term follow-up of treated patients with multiple myeloma the Hb level is stable, the influence of patients serum on hepcidin mRNA of Hep-3b cells decreases, which shows the stabilization of disease and amelioration of ACD patient status.
Flexible use of Spectrum and Photonic Grooming (2010)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text O. Gerstel, "Flexible use of Spectrum and Photonic Grooming," in Integrated Photonics Research, Silicon and Nanophotonics and Photonics in Switching, OSA Technical Digest (CD) (Optica Publishing Group, 2010), paper PMD3. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
The Association between Mushroom Consumption and Mild Cognitive Impairment: A Community-Based Cross-Sectional Study in Singapore (2019)

We examined the cross-sectional association between mushroom intake and mild cognitive impairment (MCI) using data from 663 participants aged 60 and above from the Diet and Healthy Aging (DaHA) study in Singapore. Compared with participants who consumed mushrooms less than once per week, participants who consumed mushrooms >2 portions per week had reduced odds of having MCI (odds ratio = 0.43, 95% CI 0.23-0.78, p = 0.006) and this association was independent of age, gender, education, cigarette smoking, alcohol consumption, hypertension, diabetes, heart disease, stroke, physical activities, and social activities. Our cross-sectional data support the potential role of mushrooms and their bioactive compounds in delaying neurodegeneration.
Midinfrared Optical Properties of Petroleum Oil Aerosols (1994)

The mass normalized absorption and extinction coefficients were measured for fog oil aerosol at 3.4 micrometers with a combined photoacoustic and transmissometer system. An extinction spectral profile was determined over a range of infrared (IR) wavelengths from 2.7 to 4.0 micrometers by an IR scanning transmissometer. The extinction spectrum was mass normalized by referencing it to the photoacoustic portion of the experiment. A corresponding Mie calculation was conducted and compared with the above measurements. Agreement is good for the most recent optical coefficients. An extrapolation of this data to other similar petroleum products such as kerosene or diesel fuel that exhibit similar bulk absorption characteristics were briefly examined.
B lymphocytes are impaired in mice lacking the transcriptional co‐activator Bob1/OCA‐B/OBF1 (1996)

The protein Bob1 (also called OCA-B or OBF-1) is a B lymphocyte-specific transcriptional co-activator which can stimulate transcription by interaction with Oct-1 or Oct-2 and the octamer sequence found in the promoter and most enhancer regions of the immunoglobulin genes. The role that Bob1 plays in the maturation and function of B cells was investigated in mice deficient for Bob1. Although early stages of B cell development in the bone marrow do not appear to be affected, these mice show reduced numbers of B cells in peripheral lymphoid organs. Based on staining for B220, heat-stable antigen, and IgD, this reduction is particularly strong in those cells representing the more mature B cell stages. Probably as a consequence of this reduction in mature B cells, Bob1-deficient mice show reduced serum titers of the immunoglobulin isotypes IgG1, IgG2a, IgG2b and IgA, but not IgM. Histological examination of sections from spleen and lymph nodes reveal that while Bob-1-deficient mice have primary follicles, they lack well-developed germinal centers. Interestingly, B1 (Ly1) B cells in the peritoneum do not appear to be affected by the lack of Bob1. Taken together, these results suggest that, at least in conventional B cells, Bob1 plays in important role in the antigen-driven stages of B cell activation and maturation.
Deferring design pattern decisions and automating structural pattern changes using a design-pattern-based programming system (2009)

In the design phase of software development, the designer must make many fundamental design decisions concerning the architecture of the system. Incorrect decisions are relatively easy and inexpensive to fix if caught during the design process, but the difficulty and cost rise significantly if problems are not found until after coding begins. Unfortunately, it is not always possible to find incorrect design decisions during the design phase. To reduce the cost of expensive corrections, it would be useful to have the ability to defer some design decisions as long as possible, even into the coding stage. Failing that, tool support for automating design changes would give more freedom to revisit and change these decisions when needed. This article shows how a design-pattern-based programming system based on generative design patterns can support the deferral of design decisions where possible, and automate changes where necessary. A generative design pattern is a parameterized pattern form that is capable of generating code for different versions of the underlying design pattern. We demonstrate these ideas in the context of a parallel application written with the CO 2 P 3 S pattern-based parallel programming system. We show that CO 2 P 3 S can defer the choice of execution architecture (shared-memory or distributed-memory), and can automate several changes to the application structure that would normally be daunting to tackle late in the development cycle. Although we have done this work with a pattern-based parallel programming system, it can be generalized to other domains.
Thyroid Hormone Analogue Stimulates Keratinocyte Proliferation but Inhibits Cell Differentiation in Epidermis (2012)

Gross clinical manifestations of thyroid hormone (TH) imbalance are often first seen in the skin where TH plays an integral role in sustaining natural function. Although mounting evidence suggests that TH plays an important role in epidermal proliferation and wound healing, the physiologic role of thyroid hormone in skin is not well understood. In the current study, we investigated the effect of a natural thyroid hormone analogue-3, 3', 5-triiodo-thyroacetic acid (TRIAC) on regulating proliferation and differentiation and its possible molecular mechanism in normal human epidermal keratinocytes and C57BL/6 mice. We determined that TRIAC could stimulate epidermal thickening in mice and promote human keratinocyte proliferation by activating Cyclin D1 expression and promoting entrance into S phase. Moreover, TRIAC might inhibit cell differentiation through repressing the expression of Casein Kinase 1 (CK1), which is a key regulatory protein involved in the control of cell differentiation. Taken together, our data explored the physiologic effect of TRIAC on skin and the possible molecular mechanism of TRIAC, which might be an interesting compound for the treatment of hyperkeratotic skin disorders.
Probabilistic robot navigation in partially observable environments (1995)

Autonomous mobile robots need very reliable navigation capabilities in order to operate unattended for long periods of time. This paper reports on first results of a research program that uses partially observable Markov models to robustly track a robot&apos;s location in office environments and to direct its goal-oriented actions. The approach explicitly maintains a probability distribution over the possible locations of the robot, taking into account various sources of uncertainty, including approximate knowledge of the environment, and actuator and sensor uncertainty. A novel feature of our approach is its integration of topological map information with approximate metric information. We demonstrate the robustness of this approach in controlling an actual indoor mobile robot navigating corridors. 1 Introduction We are interested in the task of long-term autonomous navigation in an office environment (with corridors, foyers, and rooms). While the state of the art in autonomous office nav...
736. Physical changes in milk caused by the action of rennet: III. Effects of separation, homogenization and pasteurization and of varying calcium content on the rigidity moduli and viscosities of curd (1958)

1. Preliminary experiments show that homogenization, separation and pasteurization all tended to delay the onset of rigidity in renneted milk, though it must be borne in mind that the first two of these treatments were accompanied by some heating of the milk. 2. Once setting had started, homogenized and separated samples set more quickly, and pasteurized (especially over-heated) milk more slowly, than did raw milk. 3. Homogenization would seem to increase, and separation perhaps to decrease the proportion of elastic recovery of the gel which is immediate. The torsiometer, which gives an over-all measure of general consistency, agrees well with the -tube gelometer but when the latter shows an unusual ratio of immediate to slow recovery, the torsiometer follows the former modulus. 4. Increasing quantities of CaCl 2 added to reconstituted dried fat-free milk progressively reduce the time needed for rigidity to make its appearance but do not greatly alter the final setting rates. All setting curves approximate to the law that, once rigidity is well established, rate of setting is proportional to the percentage of casein still unset. When the amount of added lactic acid is adjusted so as to prevent the addition of various quantities of CaCl 2 from altering the pH appreciably, no great difference is found in the setting curves. 5. The relaxation times, retardation times and their ratio, called ‘the springiness number’, are not greatly affected by the treatments to which the milk samples, either whole or dried, were subjected. 6. Appreciably syneresis usually occurs in the -tube gelometer only when the curd has been strained, though very small strains are sufficient to produce it. The site of its occurrence depends on the hydrodynamic distribution of the larger fat globules. In fat-free or homogenized milk, such syneretic phenomena are either absent or very slight.
SPARKLING: variable‐density k‐space filling curves for accelerated T<sub>2</sub><sup>*</sup>‐weighted MRI (2019)

The proposed optimization-driven design of k-space trajectories is a versatile framework that is able to enhance MR sampling performance in the context of compressed sensing.
Determining the Structure of Decision Directed Acyclic Graphs for Multiclass Classification Problems (2016)

An usual strategy to solve multiclass classification problems in Machine Learning is to decompose them into multiple binary sub-problems. The final multiclass prediction is obtained by a proper combination of the outputs of the binary classifiers induced in their solution. Decision directed acyclic graphs (DDAG) can be used to organize and to aggregate the outputs of the pairwise classifiers from the one-versus-one (OVO) decomposition. Nonetheless, there are various possible DDAG structures for problems with many classes. In this paper evolutionary algorithms are employed to heuristically find the positions of the OVO binary classifiers in a DDAG. The objective is to place easier sub-problems at higher levels of the DDAG hierarchical structure, in order to minimize the occurrence of cumulative errors. For estimating the complexity of the binary sub-problems, we employ two indexes which measure the separability of the classes. The proposed approach presented sound results in a set of experiments on benchmark datasets, although random DDAGs also performed quite well.
The effective microwave surface impedance of high <i>T</i> <i>c</i> thin films (1990)

The dependence of the effective surface impedance Zeff=Reff+iXeff of superconducting thin films on the film thickness d, on the magnetic field penetration depth λ, and on the dielectric properties of the substrate material is investigated theoretically by means of impedance transformations. It was found that the effective surface resistance Reff can be expressed by RSf(d/λ)+Rtrans where RS is the intrinsic surface resistance of the superconductor. The function f(d/λ) describes the altered current density distribution in the film. Rtrans arises from power transmission through the film. It depends on d and λ as well as on the dielectric properties of the substrate material and is significantly altered in the case of a resonant background. The effective surface reactance Xeff of a superconducting thin film can be expressed by XS cosh(d/λ) where XS=ωμ0λ is the intrinsic surface reactance. Measurements of Zeff at 87 GHz have been performed for YBa2Cu3O7−δ thin films grown epitaxially by laser ablation on SrTiO3, MgO, and LaAlO3. With the best films, Reff (77 K) values of 21 mΩ and RS (77 K) values of 8 mΩ were achieved. The temperature dependence of λ was found to be in good agreement to both weak-coupling BCS theory in the clean limit and the empirical two-fluid model relation with λ (0 K) values ranging from 140 to 170 nm and 205 to 250 nm, respectively.
Magnetic domain pinning in patterned magneto-optical material (1999)

Pinning magnetic domains with defined shapes have been made for magneto-optical thin film material. The pinning array of holes on the substrate was fabricated using electron beam lithography. The domain pinning behaviors were studied by applying an external magnetic field perpendicular to the film plane and imaged by atomic force microscopy in their remanent state. Magnetic domains were found to be pinned inside the hole arrays and reproduced the shapes of the holes. The coercivity in the patterned region is larger than in the nonpatterned region. Moreover, the coercivity inside the hole sites is larger than the land sites.