gebhart/patrepeval huggingface dataset:
Calix[4]pyrrole-Based Ion Pair Receptors (2014)

Ion pair receptors, which are able to bind concurrently both a cation and an anion, often display higher selectivity and affinity for specific ion pairs than simple ion receptors capable of recognizing primarily either a cation or an anion. This enhancement in recognition function is attributable to direct or indirect cooperative interactions between cobound ions via electrostatic attractions between oppositely charged ions, as well as to positive allosteric effects. In addition, by virtue of binding the counterions of the targeted ion, ion pair receptors can minimize the solvation of the counterions, which can otherwise have a negative effect on the interactions between the receptors and the targeted ions. As a result of their more favorable interactions, ion pair receptors are attractive for use in applications, such as extraction and sensing, where control of the binding interactions is advantageous. In this Account, we illustrate this potential in the context of ion pair receptors based on the calix[4]pyrrole scaffold. Both simple ditopic ion pair receptors, containing sites for the recognition of a single anion and single cation, and so-called multitopic ion pair receptors will be discussed. The latter systems differ from conventional, so-called ditopic ion pair receptors in that they contain more than one binding site for a given targeted ion (e.g., a cation). This permits a level of selectivity and control over binding function not normally seen for simple ion or ion pair receptors containing one or two binding sites, respectively. Calix[4]pyrroles are macrocyclic compounds consisting of four pyrrole units linked via fully substituted sp(3) hybridized meso carbon atoms. They are effective receptors for Lewis basic anions (e.g., halides) in typical organic media and under certain conditions will recognize ion pairs containing charge diffuse cations, such as a small alkylammonium, imidazolium, or cesium cations. The calix[4]pyrrole framework is further attractive in that it is relatively easy to modify. In particular, functionalization of the β-pyrrolic carbon and meso-carbon atoms with simple crown ethers or calix[4]arene crown ethers can produce heteromultitopic ion pair receptors containing more than two cation binding sites. This allows the interactions between receptors and ions to be manipulated on a higher level than can be achieved using simple ion receptors or heteroditopic ion pair receptors and has made these systems attractive for use in ion transport, recognition, and extraction. Recent progress in developing calix[4]pyrroles as both multitopic and more conventional ion pair receptors is summarized in this Account. The emphasis will be on our own work.
A Conversation about Assisted Suicide (2006)

The following is a discussion between two doctors: one who advocates for physician assisted suicide and another opposed to the idea. Both are Christians, and will be talking respectfully in an attempt to convince the other. They will not go into great detail, only using points that they believe significant in an attempt to make their case that assisted suicide is either morally wrong or morally acceptable. There will be no conclusions drawn; this is, after all, a debate. Doctor Lang and Doctor Munson are on their lunch break one day, and the topic comes up in their conversation. They are not close friends, only acquaintances. They have always known they think differently on the issue, but have never taken the time to discuss it in length. The setting is at a bagel shop down the road from the hospital. Dr. Lang: I am glad that we have this chance to eat together and discuss this issue. First, I just wanted to let you know that I greatly respect your clinical work. Dr. Munson: Well, thank you Dr. Lang, I think the same of you. I am going to get another cup of coffee and a bagel. Would you like anything? Dr. Lang: No thank you. Dr. Munson (a few minutes later): OK Doctor, my first question is: Where do you stand on the sanctity of
Challenges and opportunities in electronic textiles modeling and optimization (2002)

This paper addresses an emerging new field of research that combines the strengths and capabilities of electronics and textiles in one: electronic textiles, or e-textiles. E-textiles, also called Smart Fabrics, have not only "wearable" capabilities like any other garment, but also local monitoring and computation, as well as wireless communication capabilities. Sensors and simple computational elements are embedded in e-textiles, as well as built into yarns, with the goal of gathering sensitive information, monitoring vital statistics and sending them remotely (possibly over a wireless channel) for further processing. Possible applications include medical (infant or patient) monitoring, personal information processing systems, or remote monitoring of deployed personnel in military or space applications. We illustrate the challenges imposed by the dual textile/electronics technology on their modeling and optimization methodology.
HGF inhibits BMP-induced osteoblastogenesis: possible implications for the bone disease of multiple myeloma (2006)

The bone disease in multiple myeloma is caused by an uncoupling of bone formation from bone resorption. A key difference between patients with and patients without osteolytic lesion is that the latter have fewer and less active osteoblasts. Hepatocyte growth factor (HGF) is often produced by myeloma cells and is found at high concentrations in the bone marrow of patients with multiple myeloma. Here we show that HGF inhibited bone morphogenetic protein (BMP)-induced in vitro osteoblastogenesis. Thus, HGF inhibited BMP-induced expression of alkaline phosphatase in human mesenchymal stem cells (hMSCs) and the murine myoid cell line C2C12, as well as mineralization by hMSCs. Furthermore, the expression of the osteoblast-specific transcription factors Runx2 and Osterix was reduced by HGF treatment. HGF promoted proliferation of hMSCs, and the BMP-induced halt in proliferation was overridden by HGF, keeping the cells in a proliferative, undifferentiating state. BMP-induced nuclear translocation of receptor-activated Smads was inhibited by HGF, providing a possible explanation of how HGF inhibits BMP signaling. The in vitro data were supported by the observation of a negative correlation between HGF and a marker of osteoblast activity, bone-specific alkaline phosphatase (rho = -0.45, P = .008), in sera from 34 patients with myeloma. These observations suggest that HGF inhibits bone formation in multiple myeloma.
A Study of Seismoelectric Signals in Measurement While Drilling (M.S. Thesis) (2005)

An LWD acoustic wave can move the excess charge in the electric double layer along the borehole wall to generate a streaming electric field. This thesis is an experimental and theoretical investigation of the electric field induced by the multipole LWD acoustic wave. The main goal of this thesis is to understand the mechanism in the seismoelectric conversion under the LWD geometry and prove the absence of the tool mode in the LWD-acoustic-wave induced electric signals. In this experimental study, we measured the seismoelectric signals excited by an acoustic multipole source in the scaled logging-while-drilling model. We put the scaled tool in a sandstone borehole to perform LWD seismoelectric and acoustic measurements. Monopole and dipole acoustic and the induced electric signals were recorded separately under exactly the same settings. The recorded acoustic and seismoelectric signals were analyzed in both time and frequency domains using a semblance method. We found no tool mode components in the electric signals by examining both the waveforms and the time and frequency domain semblances. The underlying mechanism is the electric double layer (EDL) at the steel water interface is much weaker than the one at the formation water interface. Thus, in the LWD seismoelectric signal, there should be no component with an apparent velocity of tool mode. Since only formation acoustic modes have their corresponding components in the electric signal, we calculated the coherence of the two kinds of signals in the frequency domain. By applying the coherence curve to filter the acoustic signals, we can eliminate the tool modes and pick out the formation acoustic modes. In the theoretical study, we developed a Pride-theory-based model for the LWD-acoustic-wave induced electric field. The electric field strength is calculated at the electrode positions along the borehole wall, analogous to what was done in the experiment. The electric boundary conditions, which are the continuity of the electric field at the borehole wall and disappearance at the LWD tool surface, reveal the underlying mechanism in the LWD sismoelectric conversion which is also the basis of our lab experiment. The absence of the tool modes in the synthetic waveforms of the electric field coincides with what we have observed in the experimental study. Both the experiment and the theoretical results confirm that measuring the seismoelectric signal generated by an acoustic multipole source during the LWD process can be an effective way to eliminate the tool wave contamination on the LWD acoustic measurements. This thesis research shows that seismoelectric logging-while-drilling may be a potential new method in formation property evaluation.
A low loss, dielectric substrate in ZnAl2O4–TiO2 system for microelectronic applications (2005)

A temperature stable low loss substrate based on 0.83ZnAl2O4–0.17TiO2 (ZAT) was developed as a substitute to Al2O3 for possible applications in microelectronic industry as substrates and packaging materials. The thermal conductivity of ZAT is 59Wm−1K−1 which is more than twice as that of Al2O3. The thermal-expansion coefficient of this dielectric is 6.3ppm∕°C which is comparable to that of silicon used in microelectronic circuitry. Furthermore, 0.83ZnAl2O4–0.17TiO2 dielectric is chemically inert with silicon, which increases its applicability in microelectronic packages.
A inclusão escolar nas aulas de educação física: dificuldades dos professores (2015)

EnglishThe survey is titled: School Inclusion in physical education classes: problems of teachers, which aimed to analyze the main difficulties of the physical education teachers about the participation of students with disabilities in special physical education classes. The methodology was qualitative approach, with the object of research a semi­structured interview conducted with 03 teachers working in schools in the city of Treviso­SC. So there is a school inclusion, not just simply the willingness of teachers, but more of a range, from the school board to the physical space. This process requires very careful because we must include the student to the fullest adapting our classes so that they feel valued. All students have the right and need of physical education classes, with this, teachers need to be prepared to work with disabled students, adjusting activities according to the capabilities and limitations of each student. portuguesA pesquisa tem como titulo: a inclusao escolar nas aulas de educacao fisica: dificuldades dos professores, na qual teve como objetivo principal analisar as principais dificuldades dos professores de educacao fisica sobre a participacao do aluno com deficiencias especiais em aulas de educacao fisica. A metodologia utilizada foi abordagem qualitativa, tendo como objeto de pesquisa uma entrevista semi­estruturada realizadas com 03 professores que atuam nas escolas do municipio de Treviso­SC. Para que haja a inclusao escolar, nao basta apenas a vontade dos professores, mais sim de todo um conjunto, desde a direcao da escola ate do espaco fisico. Esse processo exige muito cuidado, pois devemos incluir o aluno ao maximo adaptando nossas aulas para que se sintam valorizados. Todos os alunos tem direito e precisam das aulas de Educacao Fisica, com isso, os professores precisam estar preparados para atuar com alunos deficientes, adaptando as atividades de acordo com a capacidade e limitacoes de cada aluno.
Achromatization in Optical Reconstruction of Computer Generated Color Holograms (2015)

In optical reconstruction of time-multiplexed color holography, three types of chromatic aberrations exist: magnification chromatic aberration (MCA), lateral chromatic aberration (LCA), and axial chromatic aberration (ACA). MCA is due to wavelength change of light source for reconstruction of different color components. In order to compensate for MCA, a different number of pixels for each color component is suggested and demonstrated. LCA causes mismatch of image centers for the three-color components. The use of digital blazed gratings superposed on the computer-generated hologram (CGH) is demonstrated as an effective way to correct for LCA. The error due to non-integer period is analyzed, and the maximum red wavelength is deduced in use based on the critical value of resolving power of human eyes. For ACA, where the images of the three reconstructing wavelengths focus at different planes, adding specific phase values for digital achromatization is proposed. The image quality is numerically evaluated by the mean square error. The techniques summarized in this paper are used during generation of the CGH and thus avoids mechanical complexity.
The theory of quantum-dot infrared phototransistors (1996)

A novel device - the quantum-dot infrared phototransistor (QDIP) - is proposed and considered theoretically. The QDIP utilizes intersubband electron transitions from the bound states. The dark current and sensitivity are calculated using a proposed analytical model of the QDIP. It is shown that the QDIP can exhibit low dark current, high photoelectric gain and sensitivity surpassing the characteristics of other intersubband photodetectors.
Visualizing Deep Neural Network Decisions: Prediction Difference Analysis (2017)

This article presents the prediction difference analysis method for visualizing the response of a deep neural network to a specific input. When classifying images, the method highlights areas in a given input image that provide evidence for or against a certain class. It overcomes several shortcoming of previous methods and provides great additional insight into the decision making process of classifiers. Making neural network decisions interpretable through visualization is important both to improve models and to accelerate the adoption of black-box classifiers in application areas such as medicine. We illustrate the method in experiments on natural images (ImageNet data), as well as medical images (MRI brain scans).
A Study of Antidiabetic and Antioxidant Effects of <i>Helichrysum graveolens</i> Capitulums in Streptozotocin-Induced Diabetic Rats (2007)

Helichrysum graveolens (Bieb.) Sweet (Asteraceae) grows widely in Turkey. Capitulums of H. graveolens are used in the treatment of many diseases such as jaundice and wound healing and as a diuretic in the rural areas of Anatolia. The decoction from the capitulums of the plant is consumed for the symptoms of diabetes mellitus in folk medicine. In the present study, the hypoglycemic, antihyperglycemic, and antioxidant potentials of water and ethanol extracts of H. graveolens were evaluated by using in vivo methods in normal and streptozotocin-induced diabetic rats. Blood glucose levels of animals were measured by the glucose oxidase method. The antioxidant activity of these extracts was also studied in liver, kidney, and heart tissues. In order to determine antioxidant activity, tissue malondialdehyde and reduced glutathione levels were measured by using spectrophotometric methods. The experimental data obtained from water and ethanol extracts of capitulums confirmed the folkloric utilization. In order to discuss the role of polyphenolic components in the relevant activity, total phenol and flavonoid contents of each extract were also determined using the Folin-Ciocalteu reagent, and a positive correlation was observed.
Carcinogenesis in human skin grafted to SCID mice. (1996)

To directly examine a multistage carcinogenesis model and the role of UV light in human tissues, we grafted human skin onto mice with severe combined immunodeficiency disease. We found that the maximum dose of UV radiation in the B range (UVB; 280-320 nm) tolerated by these grafts was 500 J/m2 three times weekly. One hundred fifty-one grafted mice were then randomized and observed for a median of 9 months in five groups: no treatment, chemical initiation alone, UVB as a complete carcinogen, initiation plus UVB promotion, and initiation plus UVB and phorbol ester promotion. Actinic damage and squamous atypia were found in grafts of all groups receiving UV treatment; unequivocal human squamous carcinomas developed in two of these. Species origin was verified by human-specific bisbenzimide staining and in situ hybridization for human-specific Alu segment. Overall basal proliferation, measured immunohistologically, was reduced in UV-treated grafts, but foci of hyperproliferation were seen in conjunction with the dedifferentiated expression of cytokeratins 1, 10 and 5, 8. Murine tumors also developed frequently, confirming the biological relevance of the carcinogenic strategies tested. These findings demonstrate that development of malignant human tumors can be experimentally accelerated in human tissue.
Rolling Circle Amplification, a Powerful Tool for Genetic and Functional Studies of Complete Hepatitis B Virus Genomes from Low-Level Infections and for Directly Probing Covalently Closed Circular DNA (2008)

Complete characterization of the biological properties of hepatitis B virus (HBV) variants requires the generation of full-length genomes. The aim of this study was to develop new tools for the efficient full-length genome amplification of virus from samples with low viral loads. Rolling circle amplification (RCA) was used to amplify full-length HBV genomes from both sera and liver biopsy samples from chronic HBV carriers. Serum-derived relaxed circular HBV DNA could be amplified only after completion and ligation of plus-strand DNA. Covalently closed circular DNA (cccDNA) from liver biopsies could be amplified directly from as few as 13 copies, using RCA, followed by a full-length HBV PCR. Three serial liver biopsy samples were obtained from a lamivudine-resistant patient who cleared detectable serum HBV after adefovir dipivoxil was added to the lamivudine therapy and then seroconverted to anti-HBs. Only the genomes from the last biopsy specimen obtained after the emergence of lamivudine resistance contained the lamivudine resistance-associated mutations rtL180M and rtM204V ("rt" indicates reverse transcriptase domain). Defective genomes were also found in this biopsy sample. Genomes cloned from the liver biopsy specimens were transfected into HuH7 cells to study their replication competence and their susceptibility to lamivudine. RCA is a powerful tool for amplifying full-length HBV genomes and will be especially useful for the study of occult or inactive HBV infections and patients undergoing antiviral treatment. It can also be used to probe HBV cccDNA, the crucial intermediate in viral persistence and the archive of resistance mutations.
A Rapid and Simple PCR Analysis Indicates There Are Two Subgroups of <i>Vibrio vulnificus</i> Which Correlate with Clinical or Environmental Isolation (2005)

Vibrio vulnificus is an estuarine bacterium which is the causative agent of both food-borne disease and wound infection. Although V. vulnificus is commonly found in molluscan shellfish at high numbers, the incidence of disease is relatively low, leading to the hypothesis that not all strains of V. vulnificus are equally virulent. Unfortunately, there is currently no easy test to identify virulent strains of this species. We have previously identified a 200 bp randomly amplified polymorphic DNA (RAPD) PCR amplicon associated with clinical isolates. DNA sequence data from this locus in six clinical and four environmental isolates showed that the strains could be divided into two groups, which we termed C-type (correlates with clinical origin) and E-type (correlates with environmental origin). We designed PCR primers that could distinguish between the two groups, and typed 55 randomly selected strains. We found that 90% of the C-type strains were clinical isolates, while 93% of environmental isolates were classified as E-type. The region directly downstream of this locus contained a heptanucleotide sequence repeated various times depending on the strain. Using a PCR-based assay to detect the repeat number present in a given strain, we found a statistically significant correlation with the C/E type classification and the number of repeats. The data reported here are consistent with the existence of two genotypes of V. vulnificus, with the C-type being a strong indicator of potential virulence.
Thrombopoietin Requires Additional Megakaryocyte-Active Cytokines for Optimal Ex Vivo Expansion of Megakaryocyte Precursor Cells (1998)

Little is known concerning the interaction of thrombopoietin (TPO) with other megakaryocyte-active cytokines in directing the early events of megakaryocyte development. Culture of CD34(+) cells in interleukins (IL) -1, -6, -11, plus stem cell factor (SCF; S) results in a 10- to 12-fold expansion in total cell numbers, whereas total CD41(+) megakaryocytes are expanded approximately 120-fold over input levels. Addition of TPO to IL-1, -6, -11, S generates a biphasic proliferation of CD41(+) cells, accelerates their rate of production, and results in an ex vivo expansion of more than 200-fold. The addition of Flt-3 ligand (FL) increases CD41+ cell expansion to approximately 380-fold over input levels. In the absence of TPO, approximately 95% of the expanded cells show the phenotype of promegakaryoblasts; TPO and/or FL addition increases CD41 antigen density and ploidy in a subpopulation of promegakaryoblasts. A moderate (approximately sevenfold) expansion of megakaryocyte progenitor cells (colony-forming unit-megakaryocyte) occurs in the presence of IL-1, -6, -11, S, and the addition of TPO to this cocktail yields an approximately 17-fold expansion. We conclude that early proliferative events in megakaryocyte development in vitro are regulated by multiple cytokines, and that TPO markedly affects these early developmental steps. However, by itself, TPO is neither necessary nor sufficient to generate a full proliferative/maturational in vitro response within the megakaryocyte compartment. TPO clearly affects terminal differentiation and the development of (some) high-ploidy human megakaryocytes. However, its limited in vitro actions on human cell polyploidization suggest that additional megakaryocyte-active cytokines or other signals are essential for the maximal development of human megakaryocytes.
Selective Processing of Chromogranin A in the Different Islet Cells in Human Pancreas (2001)

We studied the immunoreactivity of 12 different region-specific antibodies to the chromogranin A (CgA) molecule in the four major neuroendocrine cell types of the human pancreas by using double immunofluorescence techniques. The antibodies raised to the N-terminal and midportions of CgA showed, on the whole, stronger immunoreactivity than did the C-terminal antibodies, with a few exceptions. Often the immunoreactivity was stronger in glucagon cells. Insulin cells expressed immunoreactivity to all region-specific antibodies, but glucagon cells were nonreactive to two antibodies. Somatostatin cells reacted only with the C-terminal antibodies (amino acid sequences CgA 411-424), while PP cells were stained with four CgA region-specific antibodies between amino acid sequences 63-195. The cause of these differences may be that the CgA molecule is cleaved, partly masked, or partly translated from CgA mRNA. Microwave treatment improved only the staining with the CgA 361-372 antibodies, which indicates that masking is not the sole or entire cause. Our findings may indicate that the CgA molecule is cleaved in different ways in the various pancreatic endocrine cell types, giving rise to a variety of biologically functional fragments.