gebhart/patrepeval huggingface dataset:
Distinct methylation profiles of glioma subtypes (2003)

Gliomas are tumors of the central nervous system with a wide spectrum of different tumor types. They range from pilocytic astrocytoma, with a generally good prognosis, to the extremely aggressive malignant glioblastoma. In addition to these 2 types of contrasting neoplasms, several other subtypes can be distinguished, each characterized by specific phenotypic, as well as genotypic features. Recently, the epigenotype, as evident from differentially methylated DNA loci, has been proposed to be useful as a further criterion to distinguish between tumor types. In our study, we screened 139 tissue samples, including 33 pilocytic astrocytomas, 46 astrocytomas of different grades, 7 oligoastrocytomas, 10 oligodendrogliomas, 10 glioblastoma multiforme samples and 33 control tissues, for methylation at CpG islands of 15 different gene loci. We used the semiquantitative high throughput method MethyLight to analyze a gene panel comprising ARF, CDKN2B, RB1, APC, CDH1, ESR1, GSTP1, TGFBR2, THBS1, TIMP3, PTGS2, CTNNB1, CALCA, MYOD1 and HIC1. Seven of these loci showed tumor specific methylation changes. We found tissue as well as grade specific methylation profiles. Interestingly, pilocytic astrocytomas showed no evidence of CpG island hypermethylation, but were significantly hypomethylated, relative to control tissues, at MYOD1. Our results show that glioma subtypes have characteristic methylation profiles and, with the exception of pilocytic astrocytomas, show both locus specific hyper- as well as hypomethylation.
Identification and Functional Expression of the Mitochondrial Pyruvate Carrier (2012)

The transport of pyruvate, the end product of glycolysis, into mitochondria is an essential process that provides the organelle with a major oxidative fuel. Although the existence of a specific mitochondrial pyruvate carrier (MPC) has been anticipated, its molecular identity remained unknown. We report that MPC is a heterocomplex formed by two members of a family of previously uncharacterized membrane proteins that are conserved from yeast to mammals. Members of the MPC family were found in the inner mitochondrial membrane, and yeast mutants lacking MPC proteins showed severe defects in mitochondrial pyruvate uptake. Coexpression of mouse MPC1 and MPC2 in Lactococcus lactis promoted transport of pyruvate across the membrane. These observations firmly establish these proteins as essential components of the MPC.
[Histydyl-proline diketopiperazine (HPD), a metabolite of thyrotropin-releasing hormone (TRH), improves the ataxic gait in 3-acetylpyridine (3-AP) treated rats]. (1986)

Histidyl-proline diketopiperazine (HPD) is the active metabolite deriving from thyrotropin-releasing hormone (TRH). However, its regional distribution in the central nervous system is quite different from TRH. Above all, it is to be noted that cerebellum is one of the richest region of HPD. In rat cerebellum, for example, the concentration of HPD is 20 times higher than that of TRH. This indicates the probable action of HPD within cerebellar system. Recently, a fascinating hypothesis has been proposed by Prasad et al that some activities of TRH are based on its conversion to HPD. The purpose of this experiment is to clarify whether the hypothesis may also be appropriate for the action in the cerebellar system. Twenty four Wistar rats treated with 3-acetylpyridin (3-AP) intraperitoneally were used in our experiment. Before 3-AP administration, those rats were conditioned by electric stimulation to run forward. The 3-AP treated rat is established so as to make an ataxic rat along with a selective degeneration of the inferior olive nucleus. Those ataxic rats were divided into 3 groups according to the test drugs, that is, the group of HPD, TRH (5 mumole/kg each), and saline [the same volume (3.6 ml/kg)] control. Eight rats of each group received an intraperitoneal injection once a day from 5th to 9th day after 3-AP treatment. The behavioral tests were carried out at the 5th, 7th, and 9th day after 3-AP treatment. The ataxic gaits were observed every 30 minutes over 4 hours in succession.(ABSTRACT TRUNCATED AT 250 WORDS)
Improved techniques for 4 transmit and 4 receive antenna MIMO-OFDM for wireless communications (2002)

We propose and analyze improved MIMO-OFDM techniques for wireless systems using QPSK modulation for four transmit and four receive antennas. Cases with frequency selective fading channels are considered. We first consider such a system, employing two 16-state, 2-antenna space-time codes with successive interference cancellation and channel estimation, which was previously proposed to reduce the complexity of a 4-antenna space-time code system. We. show that our previously proposed space-time code has a 2 dB improvement over a previously published code at 5 Hz fading. Furthermore, we propose a 4-antenna, 16-state code that achieves an additional 2 dB improvement with lower complexity and a 256-state code that achieves an additional 2 dB gain. The 256-state code performs within 3 dB of the outage capacity (and within 2 dB with perfect channel estimation), which is better than any other published result, yet does not use complex iterative decoding.
Low-Density Lipoprotein, Non-High-Density Lipoprotein, and Apolipoprotein B as Targets of Lipid-Lowering Therapy (2002)

lthough low-density lipoprotein (LDL) is widely recognized as the major atherogenic lipoprotein and the primary target of lipid-lowering therapy, 1 other lipoprotein species nonetheless appear to be involved in atherogenesis.These include very low-density lipoproteins (VLDL), intermediate-density lipoproteins (IDL), and highdensity lipoproteins (HDL).Both VLDL and IDL are triglyceride-rich lipoproteins (TGRLP).Thus, in the aftermath of unequivocal evidence that LDL lowering reduces risk for major coronary events and stroke, 2 the field of lipid study is turning more of its attention to the other lipoproteins that appear to be involved in atherosclerosis.The recent Adult Treatment Panel III (ATP III) report 1 of the National Cholesterol Education Program has summarized our current understanding of the relationship between other lipoprotein species and risk for coronary heart disease (CHD).
Full-waveform inversion of ground-penetrating radar (GPR) data using pest (FWI-pest method) applied to utility detection (2016)

Utility detection, UXO investigations and archeological studies can be heavily dependent on the results of ground penetrating radar data. Obtaining desired information about the depth, position and physical characteristics of the buried targets also requires an image of the soil properties. In cases of rebar or pipe detection, precise estimations of the location and depth can be critical. However, the highly nonlinearity of this problem makes the inversion for target position and target dimensions more complex and computationally expensive. We have recently established a new method for inverting GPR data using two freely available well-known software packages, gprMax for forward modeling of radar wave propagation and PEST for the inversion procedure. The combination of these packages enables retrieval of target location, dimensions, and constraints on the soil permittivity structure. Inversion results are presented in this paper for both synthetic and real cases of buried pipes. For the case of synthetic data, the structure of soil permittivity, the location, depth and the diameter of a pipe have been considered as unknowns. For the case of real data, parameters of the source wavelet are also considered as unkonwn. Pipe dimension radius and position are retrieved with errors of 10% in the synthetic case and 13% with the real field data. Presentation Date: Wednesday, October 19, 2016 Start Time: 9:15:00 AM Location: Lobby D/C Presentation Type: POSTER
Phase II study of weekly intravenous trastuzumab (Herceptin) in patients with HER2/neu-overexpressing metastatic breast cancer. (1999)

The HER2/neu proto-oncogene is overexpressed in 25% to 30% of patients with breast cancer. Trastuzumab (Herceptin; Genentech, San Francisco, CA), a recombinant humanized monoclonal antibody with high affinity for the HER2 protein, inhibits the growth of breast cancer cells overexpressing HER2. In this phase II study the efficacy and toxicity of weekly administration of trastuzumab was evaluated in 46 patients with metastatic breast cancer whose tumors overexpressed HER2. A loading dose of 250 mg trastuzumab was administered intravenously, which was followed by 10 weekly doses of 100 mg each. Upon completion of this treatment period, patients with no disease progression could receive a weekly maintenance dose of 100 mg. Patients in this trial had extensive metastatic disease, and most had received prior anticancer therapy. Ninety percent of patients achieved adequate serum levels of trastuzumab. Toxicity was minimal, and no antibodies against trastuzumab could be detected. Objective responses were observed in 5 of the 43 evaluable patients, which included 1 complete remission and 4 partial remissions, for an overall response rate of 11.6%. Responses were seen in mediastinum, lymph nodes, liver, and chest wall lesions. Minor responses (seen in 2 patients) and stable disease (14 patients) lasted for a median of 5.1 months. These results demonstrate that trastuzumab is well tolerated and clinically active in patients with HER2-overexpressing metastatic breast cancers who have received extensive prior therapy. The regression of human cancer through the targeting of putative growth factor receptors such as HER2 warrants further evaluation of trastuzumab in the treatment of breast cancer.
Hepatitis B Virus Infection (1997)

The hepatitis B virus (HBV), discovered in 1966, infects more than 350 million people worldwide.1 Hepatitis B is a leading cause of chronic hepatitis, cirrhosis, and hepatocellular carcinoma, accounting for 1 million deaths annually. Knowledge of the intricacies of viral infection and of the molecular biology of this fascinating virus has led to the successful development of a vaccine and to treatment sometimes capable of eradicating chronic infection. This review addresses many aspects of HBV infection, including the role of the immune system in determining the outcome of clinical infection, recent developments in molecular studies of the virus, and new . . .
Expression of an activated Notch4(int-3) oncoprotein disrupts morphogenesis and induces an invasive phenotype in mammary epithelial cellsin vitro (2000)

The protein encoded by the Notch4 gene is a member of the Notch/lin-12 family of transmembrane receptor proteins, which have been shown to control cell fate determination and cell differentiation in a wide variety of organisms. Expression of Notch4(int-3), a truncated form of Notch4 having most of its extracellular domain deleted, as a transgene in mice induces the formation of poorly differentiated mammary carcinomas. To establish whether Notch4(int-3) has the capacity of subverting normal epithelial architecture, we assessed the effect of Notch4(int-3) expression on the in vitro morphogenetic properties of TAC-2 mammary epithelial cells. When grown in three-dimensional collagen gels in the presence of hydrocortisone, both wild-type and LacZ-transfected TAC-2 cells formed alveolar-like structures composed of polarized epithelial cells surrounding a central lumen. In contrast, TAC-2 cells programmed to express Notch4(int-3) formed compact cell aggregates devoid of tissue-specific organization. In addition, when grown on the surface of a collagen gel, Notch4(int-3)-expressing TAC-2 cells invaded the underlying matrix, whereas TAC-2 LacZ cells remained strictly confined to the gel surface. Expression of Notch4(int-3) in TAC-2 cells also disrupted contact-inhibition of cell proliferation, resulting in cell multilayering. Our results suggest that the ability of Notch4(int-3) to subvert normal epithelial morphogenesis and to promote invasion of the extracellular matrix contributes significantly to its tumorigenic potential.
Chapter 20 Strategies for Rare Cell Detection and Isolation (1994)

This chapter discusses a fairly nontechnical, practical, and pragmatic way what one can do with conventional flow cytometry and cell sorting instrumentation to analyze and sort rare cells. It also attempts to point out some of the methodological pitfalls. Most flow cytometers use cell light scatter as a default system trigger for obvious reasons. All cells should have a light scatter signal, whereas only some cells will be fluorescent. Light scatter can also be used to eliminate debris at the analog level prior to digital signal processing, which can greatly reduce the effective dead time of the instrument. The chapter demonstrates that with sensitivity to the problems of rare cell analysis and sorting, it is possible to analyze rare and, in some cases, ultrarare cells. Impure sorts may suffice for many situations. The theoretical discussions in this chapter are designed to enable experimenters to determine whether their experiments are at all feasible. Each biological application should be approached pragmatically; the analysis or sort may not need to be perfect, only good enough to answer the question at hand.
Common breast cancer susceptibility alleles are associated with tumour subtypes in BRCA1 and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCA1/2 (2011)

The associations of the 12 SNPs with risk for BRCA1 and BRCA2 carriers differ by ER-positive or ER-negative breast cancer status. The apparent differences in SNP associations between BRCA1 and BRCA2 carriers, and non-carriers, may be explicable by differences in the prevalence of tumour subtypes. As more risk modifying variants are identified, incorporating these associations into breast cancer subtype-specific risk models may improve clinical management for mutation carriers.
InGaN-Based Near-Ultraviolet and Blue-Light-Emitting Diodes with High External Quantum Efficiency Using a Patterned Sapphire Substrate and a Mesh Electrode (2002)

We markedly improved the extraction efficiency of emission light from the InGaN-based light-emitting diode (LED) chips grown on sapphire substrates. Two new techniques were adopted in the fabrication of these LEDs. One is to grow nitride films on the patterned sapphire substrate (PSS) in order to scatter emission light. Another is to use the Rh mesh electrode for p-GaN contact instead of Ni/Au translucent electrode in order to reduce the optical absorption by the p-contact electrode. We fabricated near-ultraviolet (n-UV) and blue LEDs using the above-mentioned techniques. When the n-UV (400 nm) LED was operated at a forward current of 20 mA at room temperature, the output power and the external quantum efficiency were estimated to be 22.0 mW and 35.5%, respectively. When the blue (460 nm) LED was operated at a forward current of 20 mA at room temperature, the output power and the external quantum efficiency were estimated to be 18.8 mW and 34.9%, respectively.
Design of a Protein Surface Antagonist Based on α-Helix Mimicry: Inhibition of gp41 Assembly and Viral Fusion We thank the National Institutes of Health for support of this work and the Deutsche Forschungsgemeinschaft (DFG) for a research fellowship to O.K. (2002)

Low micromolar inhibition of HIV-1 fusion into host cells has been achieved by using a small molecule antagonist for the disruption of the gp41 core that was designed by mimicry of the α-helical 4-3 hydrophobic repeat regions (see schematic representation). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2002/z17509_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
AACR/SNMMI State-of-the-Art Molecular Imaging in Cancer Biology and Therapy: Abstracts (2015)

AACR) have reconvened to cosponsor State-of-the-Art Molecular Imaging in Cancer Biology and Therapy, a conference to be held February 11-14, 2015, at the Hard Rock Hotel San Diego. The focus of the conference will be to educate, promote, and support the application and use of molecular imaging in cancer biology. This joint meeting will bring together imaging scientists with biologists in basic, translational, and clinical cancer research to explore how new fi ndings in molecular imaging can improve cancer diagnostics, treatment, and patient outcomes.
Melanoma brain metastasis: overview of current management and emerging targeted therapies (2012)

The high rate of brain metastasis in patients with advanced melanoma has been a clinical challenge for oncologists. Despite considerable progress made in the management of advanced melanoma over the past two decades, improvement in overall survival has been elusive. This is due to the high incidence of CNS metastases, which progress relentlessly and which are only anecdotally responsive to systemic therapies. Surgery, stereotactic radiosurgery and whole-brain radiotherapy with or without cytotoxic chemotherapy remain the mainstay of treatment. However, new drugs have been developed based on our improved understanding of the molecular signaling mechanisms responsible for host immune tolerance and for melanoma growth. In 2011, the US FDA approved two agents, one antagonizing each of these processes, for the treatment of advanced melanoma. The first is ipilimumab, an anti-CTLA-4 monoclonal antibody that enhances cellular immunity and reduces tolerance to tumor-associated antigens. The second is vemurafenib, an inhibitor that blocks the abnormal signaling for melanoma cellular growth in tumors that carry the BRAF(V600E) mutation. Both drugs have anecdotal clinical activity for brain metastasis and are being evaluated in clinical trial settings. Additional clinical trials of newer agents involving these pathways are also showing promise. Therefore, targeted therapies must be incorporated into the multimodality management of melanoma brain metastasis.
15N CIDNP investigations of the peroxynitric acid nitration of l-tyrosine and of related compounds (2006)

Peroxynitric acid (O2NOOH) nitrates L-tyrosine and related compounds at pH 2-5. During reaction with O2(15)NOOH in the probe of a 15N NMR spectrometer, the NMR signals of the nitration products of L-tyrosine, N-acetyl-L-tyrosine, 4-fluorophenol and 4-methoxyphenylacetic acid appear in emission indicating a nitration via free radicals. Nuclear polarizations are built up in radical pairs [15NO2* , PhO*]F or [15NO2* , ArH*+]F formed by diffusive encounters of 15NO2 with phenoxyl-type radicals PhO or with aromatic radical cations ArH*+. Quantitative 15N CIDNP investigations with N-acetyl-L-tyrosine and 4-fluorophenol show that the radical-dependent nitration is the only reaction pathway. During the nitration reaction, the 15N NMR signal of 15NO3- also appears in emission. This is explained by singlet-triplet transitions in radical pairs [15NO2* , 15NO3*]S generated by electron transfer between O2(15)NOOH and H15NO2 formed as a reaction intermediate. During reaction of peroxynitric acid with ascorbic acid, 15N CIDNP is again observed in the 15N NMR signal of 15NO3- showing that ascorbic acid is oxidized by free radicals. In contrast to this, O2(15)NOOH reacts with glutathione and cysteine without the appearance of 15N CIDNP, indicating a direct oxidation without participation of free radicals.
Ultrasound biomicroscopy of the peripheral retina and the ciliary body in degenerative retinoschisis associated with pars plana cysts (2001)

The study of peripheral degenerative retinoschisis and pars plana cysts is possible in vivo by means of UBM, showing the detailed morphology of the lesions (not otherwise evident through ophthalmoscopic examination) and the close relation between pars plana cysts, cystoid degeneration, and peripheral retinoschisis.
Single Low-Dose Administration of Human Recombinant Hepatocyte Growth Factor Attenuates Intimal Hyperplasia in a Balloon-Injured Rabbit Iliac Artery Model (2000)

Accelerated endothelialization after local delivery of hrHGF, a novel and potent endothelial cell mitogen, effectively attenuates neointimal proliferation even after single low-dose administration. This observation could have potential therapeutic implications in the prevention of restenosis after angioplasty.
A dipole antenna for interstitial microwave hyperthermia (1991)

An improved interstitial microwave antenna design was investigated in static phantom experiments at 915 MHz and different insertion depths. Compared with conventional interstitial antennas, the presented dipole microwave antenna shows heating patterns which are concentrated on the dipole irrespective of the insertion depth. By analogy to interstitial radiotherapy, the microwave antenna allows a high concentration of energy in the target volume with as little damage as possible to the healthy surrounding tissue. The undesired heating of healthy tissue along the feeding line observed with conventional interstitial antennas is avoided. A lambda /4 sleeve on the feeding line (which does not radiate microwave energy itself to the surrounding tissue) transforms an open end, i.e. a high impedance at the generator end of the dipole antenna. The current flowing back along the outside of the outer conductor of the feeding line in the direction of the generator is zero at this point. Both dipole sections have the same terminating impedance. Since the lambda /4 sleeve is mounted outside the antenna, its mechanical length is not restricted by the mechanical length of the antenna. It can be charged with dielectric materials of low dielectricity constants.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Collection and Culture Techniques for Gelatinous Zooplankton (2003)

Gelatinous zooplankton are the least understood of all planktonic animal groups. This is partly due to their fragility, which typically precludes the capture of intact specimens with nets or trawls. Specialized tools and techniques have been developed that allow researchers and aquarists to collect intact gelatinous animals at sea and to maintain many of these alive in the laboratory. This paper summarizes the scientific literature on the capture, collection, and culture of gelatinous zooplankton and incorporates many unpublished methods developed at the Monterey Bay Aquarium in the past 15 years.
The Carboxyl-terminal Domain of Phosphophoryn Contains Unique Extended Triplet Amino Acid Repeat Sequences Forming Ordered Carboxyl-Phosphate Interaction Ridges That May Be Essential in the Biomineralization Process (1996)

Phosphophoryns (PPs), a family of Asp and Ser(P)-rich dentin proteins, are considered to be archetypal regulators of several aspects of extracellular matrix (ECM) biomineralization. We have cloned a rat incisor PP gene, Dmp2, from our odontoblast cDNA library and localized it to mouse chromosome 5q21 within 2 centimorgans of Dmp1, another tooth-specific ECM protein. The carboxyl-terminal region of Dmp2 protein (60 residue % Ser, 31 residue % Asp) is divided into two domains, one with unique repetitive blocks of [DSS]n,3</=14, the other with [SD]m = 2,3. Conformational analysis shows the phosphorylated form of the [DS*S*]n repeats to have a unique structure with well defined ridges of phosphates and carboxyls available for counter ion binding. The [S*D]m domains have different phosphate and carboxylate interaction edges and thus different calcium ion and apatite surface binding properties. These two domains and the colocalization of Dmp1 and Dmp2 genes at a position equivalent to the dentinogenesis imperfecta type II location on human 4q21 all suggest that the PPs are indeed involved in some aspect of ECM mineralization.