gebhart/patrepeval huggingface dataset:
Genome-wide Hypomethylation in Human Glioblastomas Associated with Specific Copy Number Alteration, Methylenetetrahydrofolate Reductase Allele Status, and Increased Proliferation (2006)

Genome-wide reduction in 5-methylcytosine is an epigenetic hallmark of human tumorigenesis. Experimentally induced hypomethylation in mice promotes genomic instability and is sufficient to initiate tumorigenesis. Here, we report that global hypomethylation is common in primary human glioblastomas [glioblastoma multiforme (GBM)] and can affect up to an estimated 10 million CpG dinucleotides per haploid tumor genome. Demethylation involves satellite 2 (Sat2) pericentromeric DNA at chromosomes 1 and 16, the subtelomeric repeat sequence D4Z4 at chromosomes 4q and 10q, and interspersed Alu elements. Severe hypomethylation of Sat2 sequences is associated with copy number alterations of the adjacent euchromatin, suggesting that hypomethylation may be one factor predisposing to specific genetic alterations commonly occurring in GBMs. An additional apparent consequence of global hypomethylation is reactivation of the cancer-testis antigen MAGEA1 via promoter demethylation, but only in GBMs and GBM cell lines exhibiting a 5-methylcytosine content below a threshold of approximately 50%. Primary GBMs with significant hypomethylation tended to be heterozygous or homozygous for the low-functioning Val allele of the rate-limiting methyl group metabolism gene methylenetetrahydrofolate reductase (MTHFR), or had a deletion encompassing this gene at 1p36. Tumors with severe genomic hypomethylation also had an elevated proliferation index and deletion of the MTHFR gene. These data suggest a model whereby either excessive cell proliferation in the context of inadequate methyl donor production from MTHFR deficiency promotes genomic hypomethylation and further genomic instability, or that MTHFR deficiency-associated demethylation leads to increased proliferative activity in GBM.
A New Look at Colorimetry (1955)

This is a report on the proceedings of the International Commission on Illumination (CIE) which met in Zürich, Switzerland, from June 13 to June 22. The status of the revision of the standard data for colorimetry is explained and discussed. The present FCC standards for color television are specified in terms of colorimetric data adopted by the CIE in 1931. Most quantitative work on color, during the past 24 years, has been based on the CIE data. The significance of the proposed revisions in relation to that work and to future work and specifications is discussed.
RESOURCE ASSESSMENT & PRODUCTION TESTING FOR COAL BED METHANE IN THE ILLINOIS BASIN (2004)

The geological surveys of Illinois, Indiana and Kentucky have completed the initial geologic assessment of their respective parts of the Illinois Basin. Cumulative thickness maps have been generated and target areas for drilling have been selected. The first well in the Illinois area of the Illinois Basin coal bed methane project was drilled in White County, Illinois in October 2003. This well was cored in the major coal interval from the Danville to the Davis Coals and provided a broad spectrum of samples for further analyses. Sixteen coal samples and three black shale samples were taken from these cores for canister desorption tests and were the subject of analyses that were completed over the following months, including desorbed gas volume, gas chemical and isotope composition, coal proximate, calorific content and sulfur analyses. Drilling programs in Indiana and Kentucky are expected to begin shortly.
Quantitative structure-activity relationships (1979)

Designing of biologically active molecules on a rational basis is of utmost importance to medicinal chemists. Until about the late 1950’s most of the structure-activity correlations were emperical and qualitative. Although attempts have been made to apply quantitative methods to biological activity since last century, a major effort in this field has been made only very recently based on physical organic chemistry using regression analysis and computer technology.
Industry’s Giant Leap Into Cellular Therapy: Catalyzing Chimeric Antigen Receptor T Cell (CAR-T) Immunotherapy (2019)

Tisagenlecleucel was the first CAR-T therapy and the first gene therapy to receive US Food and Drug Administration approval in 2017, with an initial indication for pediatric and young adult patients with relapsed or refractory (r/r) acute lymphoblastic leukemia, followed by approval in May 2018 for a second indication in adult patients with r/r diffuse large B cell lymphoma. Subsequent approvals in the European Union, Switzerland, and Canada soon followed. The tisagenlecleucel success story represents the development and commercialization of a first-of-its-kind personalized cellular therapy with a manufacturing process that supports commercial production and ongoing global clinical trials in a growing number of countries.
Double‐stranded DNA can be translocated across a planar membrane containing purified mitochondrial porin (1998)

The transport of genetic material across biomembranes is a process of great relevance for several fields of study. However, much remains to be learned about the mechanisms underlying transport, one of which implies the involvement of proteic DNA-conducting pores. Entry of genetic material into mitochondria has been observed under both physiological and pathological conditions. We report here that double-stranded DNA can move through a planar bilayer membrane containing isolated mitochondrial porin (voltage-dependent anion channel). The transport is driven by the applied electrical field, and the presence of DNA is associated with a decrease of current conduction by the pores. The passage of DNA does not take place if the bilayer has not been doped with any protein or in the presence of both reconstituted porin and anti-porin antibody. Translocation does not occur if the bilayer contains Shigella sonnei maltoporin, gramicidin A channels, or a 30 pS anion-selective channel plus other proteins. These results show that mitochondrial porin is capable of mediating the transport of genetic material, revealing a new property of this molecule and further confirming the idea that DNA can move through proteic pores.
Chapter 1: Human Papillomavirus and Cervical Cancer--Burden and Assessment of Causality (2003)

Cervical cancer remains the second most common cancer in women worldwide and the most frequent in developing countries. Pre-neoplasic cervical lesions represent an additional burden in countries where screening is widespread. The human papillomavirus (HPV) prevalence and type distribution in normal smears and in cancer specimens are being described and show relatively small international variation. State-of-the-art detection techniques have unequivocally shown that HPV-DNA can be detected in 95% to 100% of adequate specimens of cervical cancer, supporting the claim that HPV is the necessary cause. The odds ratios for cervical cancer related to a cross sectional detection of HPV-DNA range from 50 to several hundred in all studies. The risk for any of 15 high-risk types is not statistically different from the risk reported for HPV16. The estimates of the attributable fraction range from 90% to 98%. Additional work should be done in providing information on incidence of cervical cancer and on HPV infection in areas where the disease is common. Theoretical work including modeling of the incidence could be of potential use in the evaluation of the existing and novel preventive strategies. Research is currently being conducted on the mechanisms of HPV carcinogenesis. These include the determinants of the systemic and cellular immune response to the viral infection, the interaction between the host and the virus and the relevance of the different strains and variants of the HPV viral types. Technology developments in this area suitable for epidemiological studies are needed.
PDS Cloud: Long Term Digital Preservation in the Cloud (2013)

The emergence of the cloud and advanced object-based storage services provides opportunities to support novel models for long term preservation of digital assets. Among the benefits of this approach is leveraging the cloud's inherent scalability and redundancy to dynamically adapt to evolving needs of digital preservation. PDS Cloud is an OAIS-based preservation-aware storage service employing multiple heterogeneous cloud providers. It materializes the logical concept of a preservation information-object into physical cloud storage objects. Preserved information can be interpreted by deploying virtual appliances in the compute cloud provisioned with cloud storage data objects together with their designated rendering software. PDS Cloud has a hierarchical data model supporting independent tenants whose assets are organized in multiple aggregations based on content and value. Continuous changes to data objects, life-cycle activities, virtual appliances and cloud providers are applied in a manner transparent to the client. PDS Cloud is being developed as an infrastructure component of the European Union ENSURE project, where it is used for preservation of medical and financial data.
Biodegradation of 2,4,5-trichlorophenoxyacetic acid by a pure culture of Pseudomonas cepacia (1982)

A pure culture of Pseudomonas cepacia, designated AC1100, that can utilize 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) as its sole source of carbon and energy was isolated. An actively growing culture of AC1100 was able to degrade more than 97% of 2,4,5-T, present at 1 mg/ml, within 6 days as determined by chloride release, gas chromatographic, and spectrophotometric analyses. The ability of AC1100 to oxidize a variety of chlorophenols and related compounds is also reported.
PROMISE - A Procedure for Multimodal Interactive System Evaluation (2002)

This paper describes a general framework for evaluating and comparing the performance of multimodal dialogue systems: PROMISE (Procedure for Multimodal Interactive System Evaluation). PROMISE is a possible extention to multimodality of the PARADISE framework ([1, 2] used for the evaluation of spoken dialogue systems), where we aimed to solve the problems of scoring multimodal inputs and outputs, weighting the different recognition modalities and of how to deal with not directed (non-directed) task definitions and the resulting, potentially uncompleted tasks by the users.
[Control of postoperative pain in heart surgery. Comparison of analgesics]. (2001)

Tramadol in continuous infusion (dose 12 mg/h) proved to be effective for the control of postoperative pain after cardiac surgery. The proposed dose represents a good compromise between analgesic efficacy and interference with the vital functions of operated patients.
An in vitro comparison of commonly used topical glucocorticoid preparations (1999)

These data, combined with information on pharmacodynamics of these drugs in vivo, may be useful in estimating GC local anti-inflammatory effects.
Molecular analysis of the A322D mutation in the GABA<sub>A</sub> receptor α<sub>1</sub>‐subunit causing juvenile myoclonic epilepsy (2005)

Juvenile myoclonic epilepsy (JME) belongs to the most common forms of hereditary epilepsy, the idiopathic generalized epilepsies. Although the mode of inheritance is usually complex, mutations in single genes have been shown to cause the disease in some families with autosomal dominant inheritance. The first mutation in a multigeneration JME family has been recently found in the alpha1-subunit of the GABAA receptor (GABRA1), predicting the single amino acid substitution A322D. We further characterized the functional consequences of this mutation by coexpressing alpha1-, beta2- and gamma2-subunits in human embryonic kidney (HEK293) cells. By using an ultrafast application system, mutant receptors have shown reduced macroscopic current amplitudes at saturating GABA concentrations and a highly reduced affinity to GABA compared to the wild-type (WT). Dose-response curves for current amplitudes, activation kinetics, and GABA-dependent desensitization parameters showed a parallel shift towards 30- to 40-fold higher GABA concentrations. Both deactivation and resensitization kinetics were considerably accelerated in mutant channels. In addition, mutant receptors labelled with enhanced green fluorescent protein (EGFP) were not integrated in the cell membrane, in contrast to WT receptors. Therefore, the A322D mutation leads to a severe loss-of-function of the human GABAA receptor by several mechanisms, including reduced surface expression, reduced GABA-sensitivity, and accelerated deactivation. These molecular defects could decrease and shorten the resulting inhibitory postsynaptic currents (IPSCs) in vivo, which can induce a hyperexcitability of the postsynaptic membrane and explain the occurrence of epileptic seizures.
Excited-State Properties of C<sub>60</sub> Fullerene Derivatives (2000)

This Account reviews our main achievements in the field of excited-state properties of fullerene derivatives. The photosensitizing and electron-acceptor features of some relevant classes of functionalized fullerene materials are highlighted, considering the impact of functionalization on fullerene characteristics. In addition, the unique optimization in terms of redox potentials, water-solubility, and singlet oxygen generation is presented for several novel fullerene-based materials.
Pathology (2004)

Objectives: To characterize minute prostate cancer seen at radical prostatectomy. With aggressive screening and more extensive biopsy sampling, we have increasingly seen these cancers at radical prostatectomy.
Development and Characterization of A Recombinant Truncated Type VII Collagen “Minigene” (2000)

Dystrophic epidermolysis bullosa (DEB) is an inherited mechano-bullous disorder of skin caused by mutations in the type VII collagen gene. The lack of therapy for DEB provides an impetus to develop gene therapy strategies. However, the full-length 9-kilobase type VII collagen cDNA exceeds the cloning capacity of current viral delivery vectors. In this study, we produced a recombinant type VII minicollagen containing the intact noncollagenous domains, NC1 and NC2, and part of the central collagenous domain using stably transfected human 293 cell clones and purified large quantities of the recombinant minicollagen VII from culture media. Minicollagen VII was secreted as correctly-folded, disulfide-bonded, helical trimers resistant to protease degradation. Purified minicollagen VII bound to fibronectin, laminin-5, type I collagen, and type IV collagen. Furthermore, retroviral-mediated transduction of the minigene construct into DEB keratinocytes (in which type VII collagen was absent) resulted in persistent synthesis and secretion of a 230-kDa recombinant minicollagen VII. In comparison with parent DEB keratinocytes, the gene-corrected DEB keratinocytes demonstrated enhanced cell-substratum adhesion, increased proliferative potential, and reduced cell motility, features that reversed the DEB phenotype toward normal. We conclude that the use of the minicollagen VII may provide a strategy to correct the cellular manifestations of gene defects in DEB.
Low-cost three-dimensional vision system based on a low-power semiconductor laser rangefinder and a single scanning mirror (2001)

Machine vision systems based on direct laser rangefinders are an interesting option for applications demanding high lateral and radial resolution, along with the capability to operate under varying illu- mination conditions. Furthermore, as outdoor applications such as colli- sion avoidance or smart highways automated navigation appear, the in- terest of direct laser rangefinders for machine vision will rise, since they do not present the limitations commonly found in intensity based vision systems. We present a 3-D vision system designed around a direct laser rangefinder (which we also developed). Although initially conceived for short-range indoor applications, the system is designed so that it can be easily adapted to longer range outdoor operation. The main features of this system are its high-speed optomechanical scanner, based in a single scanning mirror, and its direct interface to the industry standard architecture (ISA) bus, which enables the system to operate in any PC- based application. © 2001 Society of Photo-Optical Instrumentation Engineers.
Methylation of <i>p16</i> and <i>Ras Association Domain Family Protein 1a</i> during Colorectal Malignant Transformation (2006)

Accurate assessment of gene methylation in formalin-fixed, paraffin-embedded archived tissue (FF-PEAT) by microdissection remains challenging because the tissue volume is small and DNA is damaged. In addition, methods for methylation assessment, such as methylation-specific PCR (MSP), require sodium bisulfite modification (SBM) on purified DNA, which causes major loss of DNA. On-slide SBM, in which DNA is modified in situ before isolation of tumor cells, eliminates DNA purification steps and allows histology-oriented assessment of gene methylation. This study describes a protocol and use of on-slide SBM using 20 FF-PEAT of colorectal cancers with intratumoral adenoma components to detect accumulation of gene methylation during colorectal malignant transformation. Deparaffinized tissue sections were incubated in sodium bisulfite solution for 8 hours at 60 degrees C, stained with hematoxylin, and then microdissected. Proteinase K lysate was directly used as a template in subsequent PCR. Using on-slide SBM, 282-bp-long bisulfite direct sequencing was possible. Yield of modified DNA was 2.6-fold greater than standard SBM on average. The mean conversion rate was 97%, and false-positive or false-negative results were not observed in subsequent MSP. Intratumoral heterogeneity by accumulation of p16 and Ras association domain family protein 1a methylation during malignant transformation were shown by MSP comparing cancer with adenoma parts within a single section. On-slide SBM is applicable in most methylation studies using FF-PEAT. It allows detailed, intratumoral analysis of methylation heterogeneity within solid tumors. On-slide SBM will significantly improve our approach and understanding of epigenetic events in minimal disease and the carcinogenic process.
An efficient implementation of trie structures (1992)

Abstract A new internal array structure, called a double‐array , implementing a trie structure is presented. The double‐array combines the fast access of a matrix form with the compactness of a list form. The algorithms for retrieval, insertion and deletion are introduced through examples. Although insertion is rather slow, it is still practical, and both the deletion and the retrieval time can be improved from the list form. From the comparison with the list for various large sets of keys, it is shown that the size of the double‐array can be about 17 per cent smaller than that of the list, and that the retrieval speed of the double‐array can be from 3–1 to 5–1 times faster than that of the list.
The ORL active floor [sensor system] (1997)

A novel type of sensor system called the active floor is presented that allows the time-varying spatial weight distribution of the active office environment to be captured. The properties of the active floor are described, showing that it differs substantially from other commonly encountered sensor systems. Furthermore, classification of the footstep signature of a number of individuals is attempted by application of the hidden Markov model technique.
Talking about trees (1993)

In this paper we introduce a modal language LT for imposing constraints on trees, and an extension LT (LF) for imposing constraints on trees decorated with feature structures. The motivation for introducing these languages is to provide tools for formalising grammatical frameworks perspicuously, and the paper illustrates this by showing how the leading ideas of GPSG can be captured in LT (LF).In addition, the role of modal languages (and in particular, what we have called layered modal languages) as constraint formalisms for linguistic theorising is discussed in some detail.
Comment gérer la pénurie (2003)

Les exigences économiques ne sont pas incompatibles avec les préoccupations scientifiques. En dépit d'une conjoncture plutôt ingrate, les travaux des chercheurs restent plus que jamais nécessaires. Ainsi, bien qu'il soit principalement axé sur les sciences naturelles, l'Institut fédéral de recherches sur la forêt, la neige et le paysage (WSL) compte depuis avril 2000 déjà, une section <em>Economie</em>. Quelles sont ses attributions et à quoi sert-elle exactement? <em>Priska Baur, Anna Roschewitz</em> et <em>lrmi Seidl</em>, animatrices de cette unité de recherche, répondent ici aux questions que peuvent se poser nos lecteurs. <em>(réd.)</em>
Voltage-Dependent Sodium Channels in Spinal Cord Motor Neurons Display Rapid Recovery From Fast Inactivation in a Mouse Model of Amyotrophic Lateral Sclerosis (2006)

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by a substantial loss of motor neurons in the spinal cord, brain stem, and motor cortex. Previous evidence showed that in a mouse model of a familial form of ALS expressing high levels of the human mutated protein Cu,Zn superoxide dismutase (Gly(93)-->Ala, G93A), the firing properties of single motor neurons are altered to induce neuronal hyperexcitability. To determine whether the functionality of the macroscopic voltage-dependent Na(+) currents is modified in G93A motor neurons, in the present work their physiological properties were examined. The voltage-dependent sodium channels were studied in dissociated motor neurons in culture from nontransgenic mice (Control), from transgenic mice expressing high levels of the human wild-type protein [superoxide dismutase 1 (SOD1)], and from G93A mice, using the whole cell configuration of the patch-clamp recording technique. The voltage dependency of activation and of steady-state inactivation, the kinetics of fast inactivation and slow inactivation of the voltage-dependent Na(+) channels were not modified in the mutated mice. Conversely, the recovery from fast inactivation was significantly faster in G93A motor neurons than that in Control and SOD1. The recovery from fast inactivation was still significantly faster in G93A motor neurons exposed for different times (3-48 h) and concentrations (5-500 microM) to edaravone, a free-radical scavenger. Clarification of the importance of these changes in membrane ion channel functionality may have diagnostic and therapeutic implications in the pathogenesis of ALS.
Nanoprocessors: Configurable Hardware Accelerators for Embedded Systems (2003)

Today’s consumer market is driven by technology innovations. Many technologies that were not available a few years ago are quickly being adopted into common use. Equipment for these services requires micropro-cessors inside and can be regarded as embedded systems. Embedded sys-tems are designed to serve a particular functionality at a minimal cost. To improve efficiency and throughput, embedded systems uses hardware peripherals to perform sub-functionality in hardware. Because there are many vendors of embedded systems and each system is designed for a spe-cific purpose, the peripherals differ widely across systems. Applications developed for a particular system is not portable to another system. As a result, many embedded systems incorporate programmable hardware to provide flexibility. One popular use of the programmable hardware is for I/ O devices. In this work, we propose and discuss other uses for the program-mable hardware. Specifically, we have identified an I/O controller and a hardware scheduler that can be incorporated into programmable logic. Our result shows that these hardware components improve the system perfor-mance significantly at a nominal cost.