gebhart/patrepeval huggingface dataset:
Pilot study of irreversible electroporation for intracranial surgery (2009)

Irreversible electroporation (IRE) is a new minimally invasive technique to treat cancer using intense but short electric pulses. This technique is unique because of its non-thermal mechanism of tissue ablation. Furthermore it can be predicted with numerical models and can be confirmed with ultrasound and MRI. We present some preliminary results on the safety of using irreversible electroporation for canine brain surgery. We also present the electric field (460 V/cm - 560 V/cm) necessary for focal ablation of canine brain tissue and provide some guidelines for treatment planning and execution. This preliminary study is the first step towards using irreversible electroporation as a brain cancer treatment.
MicroRNAs in Parkinson's disease and emerging therapeutic targets (2017)

Parkinson's disease (PD) is the second most common age-related neurodegenerative disorder, with the clinical main symptoms caused by a loss of dopaminergic neurons in the substantia nigra, corpus striatum and brain cortex. Over 90% of patients with PD have sporadic PD and occur in people with no known family history of the disorder. Currently there is no cure for PD. Treatment with medications to increase dopamine relieves the symptoms but does not slow down or reverse the damage to neurons in the brain. Increasing evidence points to inflammation as a chief mediator of PD with inflammatory response mechanisms, involving microglia and leukocytes, activated following loss of dopaminergic neurons. Oxidative stress is also recognized as one of the main causes of PD, and excessive reactive oxygen species (ROS) and reactive nitrogen species can lead to dopaminergic neuron vulnerability and eventual death. MicroRNAs control a range of physiological and pathological functions, and may serve as potential targets for intervention against PD to mitigate damage to the brain. Several studies have demonstrated that microRNAs can regulate oxidative stress and prevent ROS-mediated damage to dopaminergic neurons, suggesting that specific microRNAs may be putative targets for novel therapeutic strategies in PD. Recent human and animal studies have identified a large number of dysregulated microRNAs in PD brain tissue samples, many of which were downregulated. The dysregulated microRNAs affect downstream targets such as SNCA, PARK2, LRRK2, TNFSF13B, LTA, SLC5A3, PSMB2, GSR, GBA, LAMP-2A, HSC. Apart from one study, none of the studies reviewed had used agomirs or antagomirs to reverse the levels of downregulated or upregulated microRNAs, respectively, in mouse models of PD or with isolated human or mouse dopaminergic cells. Further large-scale studies of brain tissue samples collected with short postmortem interval from human PD patients are warranted to provide more information on the microRNA profiles in different brain regions and to test for gender differences.
Treatment of Infected Tibial Nonunions with Debridement, Antibiotic Beads, and the Ilizarov Method (2004)

This study of 10 patients presents the early results of a protocol of debridement, antibiotic bead placement, and use of the Ilizarov method with a circular external fixator for treatment of infected nonunions of the tibia in a military population. The nonunions resulted from high-energy fractures in nine cases and an osteotomy in one. The Ilizarov techniques used were transport (five cases), shortening and secondary lengthening (two cases), minimal resection with compression (one case), and resection with bone grafting (two cases). Flap coverage was required for five patients. There were two recurrences of infection (20%) among patients with the most compromised soft tissue. Only 50% of patients were able to perform limited duties while wearing the external fixator. Only four patients returned to active duty; however, three patients from special operations units were able to return to jump status. Six patients underwent medical retirement because of insufficient function, resulting from decreased ankle or knee range of motion and arthrosis or muscle weakness.
A Broad Diversity of Volatile Carboxylic Acids, Released by a Bacterial Aminoacylase from Axilla Secretions, as Candidate Molecules for the Determination of Human-Body Odor Type (2006)

Human body odor is to a large part determined by secretions of glands in the axillary regions. Two key odoriferous principles, 3-methylhex-2-enoic acid (3MH2; 4/5) and 3-hydroxy-3-methylhexanoic acid (HMHA; 6) have been shown to be released from glutamine conjugates secreted in the axilla by a specific N(alpha)-acyl-glutamine aminoacylase (N-AGA) obtained from axilla isolates of Corynebacteria sp. However, the low number of different odorants reported in humans stands in contrast to the observed high inter-individual variability in body odors. Axilla secretions of individual donors were, therefore, analyzed in detail. The secretions were treated with N-AGA, analyzed by GC/MS, and compared to undigested controls. Over 28 different carboxylic acids were released by this enzyme from odorless axilla secretions (Table 1). Many of these body odorants have not been reported before from a natural source, and they include several aliphatic 3-hydroxy acids with 4-Me branches, 3,4-unsaturated, 4-Et-branched aliphatic acids, and a variety of degradation products of amino acids. The odor threshold of some of the acids was found to be in the range of 1 ng. Most of these compounds were present in all donors tested, but in highly variable relative amounts, and they are, thus, candidate molecules as key components of a 'compound odor' determining the individual types of human body odor.
PCAP: A Whole-Genome Assembly Program (2003)

We describe a whole-genome assembly program named PCAP for processing tens of millions of reads. The PCAP program has several features to address efficiency and accuracy issues in assembly. Multiple processors are used to perform most time-consuming computations in assembly. A more sensitive method is used to avoid missing overlaps caused by sequencing errors. Repetitive regions of reads are detected on the basis of many overlaps with other reads, instead of many shorter word matches with other reads. Contaminated end regions of reads are identified and removed. Generation of a consensus sequence for a contig is based on an alignment of reads in the contig, in which both base quality values and coverage information are used to determine every consensus base. The PCAP program was tested on a mouse whole-genome data set of 30 million reads and a human Chromosome 20 data set of 1.7 million reads. The program is freely available for academic use.
Therapeutic Applications of the PhiC31 Integrase System (2011)

The potential use of the ΦC31 integrase system in gene therapy opens up the possibilities of new treatments for old diseases. ΦC31 integrase mediates the integration of plasmid DNA into the chromsomes of mammalian cells in a sequence-specific manner, resulting in robust, long-term transgene expression. In this article, we review how ΦC31 integrase mediates transgene integration into the genomes of target cells and summarize the recent preclinical applications of the system to gene therapy. These applications encompass in vivo studies in liver and lung, as well as increasing ex vivo uses of the system, including in neural and muscle stem cells, in cord-lining epithelial cells, and for the production of induced pluripotent stem cells. The safety of the ΦC31 integrase system for gene therapy is evaluated, and its ability to provide treatments for hemophilia is discussed. We conclude that gene therapy strategies utilizing ΦC31 integrase offer great promise for the development of treatments in the future.
Hierarchical file systems are dead (2009)

For over forty years, we have assumed hierarchical file system namespaces. These namespaces were a rudimentary attempt at simple organization. As users have begun to interact with increasing amounts of data and are increasingly demanding search capability, such a simple hierarchical model has outlasted its usefulness. For this reason, we should design file systems whose organizations map to the ways we access and manipulate data now. We present a new file system architecture in which we replace the hierarchical namespace with a tagged, search-based one. 1
Molecular biology techniques for loss of heterozygosity detection: the glioma example (2015)

ABSTRACT In recent years, many oncology institutions have implemented the use of molecular approaches to assess and manage cancer patients. One commonly observed type of genetic alteration in cancer is the loss of heterozygosity (LOH). In the clinical setting, this molecular genetic marker is an important tool for disease prognosis, diagnosis and treatment. For example, the loss of 1p/19q is a classical molecular marker for oligodendroglioma assessment. In addition, this marker is associated with a favorable prognosis and chemosensitivity in oligodendroglial tumors. Interpretation of the clinical significance of molecular markers requires that health professionals and biomedical scientists understand the basic theoretical fundamentals of molecular diagnostic techniques. Although there are different methodologies to assess LOH, including high-performance techniques, this review aims to describe the polymerase chain reaction (PCR)-based LOH assays and fluorescence in situ hybridization (FISH), which are the molecular techniques most used for evaluation of 1p/19q status in pathology laboratories.
The importance of theSMNgenes in the genetics of sporadic ALS (2009)

The human genome contains two SMN (survival motor neuron) genes: SMN1, the telomeric gene whose homozygous deletion causes spinal muscular atrophy (SMA), and SMN2, the centromeric version whose copy number modulates the phenotype of SMA. We performed a Medline search and reviewed all of the publications that focus on SMN1 and SMN2 in amyotrophic lateral sclerosis (ALS) to analyse whether these genes also act as risk factors or phenotypic modulators in ALS. While homozygous deletion of SMN1 was not associated in ALS, abnormal SMN1 copy numbers significantly increased the risk of ALS. The role of the SMN2 gene in ALS needs further clarification. The existence of abnormal SMN1 copy numbers in ALS provides additional evidence that gene copy number variants may contribute to neurodegeneration and might open new approaches to treatment.
Towards nuclear magnetic resonance μ-spectroscopy and μ-imaging (2004)

The first successful experiments demonstrating Nuclear Magnetic Resonance (NMR) were a spin-off from the development of electromagnetic technology and its introduction into civilian life in the late forties. It was soon discovered that NMR spectra held chemically relevant information making it useful as an analytical tool. By introducing a new way of detection, moving away from continuous wave spectroscopy, Fourier Transform NMR helped to overcome sensitivity problems and subsequently opened the way for multi-dimensional spectroscopy. As a result NMR has developed into one of the most powerful analysis techniques with widespread applications. Still sensitivity is a limiting factor in the applicability of NMR. Therefore we witness a renaissance of technique development in magnetic resonance striving to improve its receptiveness. This tutorial review introduces the efforts currently made in miniaturizing inductive detection by designing optimal radio-frequency microcoils. A second approach is to introduce a new way of detecting magnetic resonance signals by means of very sensitive micromechanical force detectors. This shows that the detection limits in terms of absolute sensitivity or imaging resolution are still open to significant improvements.
Wavelength shifting in GaAs quantum well lasers by proton irradiation (1997)

Proton irradiation followed by rapid thermal annealing was used to selectively induce layer intermixing and thus shift the emission wavelengths of GaAs–AlGaAs graded-index separate-confinement-heterostructure quantum well lasers. Up to 40 nm shifts were observed in 4 μm ridge waveguide devices irradiated to a dose of 1.5×1016 cm−2. Although the wavelength shifts were accompanied by some degradation in the lasing threshold current and differential quantum efficiency, they were still quite acceptable at moderate wavelength shifts. This technique provides a simple and promising postgrowth process of integrating lasers of different wavelengths for wavelength-division-multiplexing applications.
VEGFR-3 and CD133 identify a population of CD34+ lymphatic/vascular endothelial precursor cells (2002)

Human CD133 (AC133)(+)CD34(+) stem and progenitor cells derived from fetal liver and from bone marrow and blood incorporate a functional population of circulating endothelial precursor cells. Vascular endothelial growth factor receptor 3 (VEGFR-3) regulates cardiovascular development and physiological and pathological lymphangiogenesis and angiogenesis. However, the origin of VEGFR-3(+) endothelial cells (ECs) and the mechanisms by which these cells contribute to postnatal physiological processes are not known, and the possible existence of VEGFR-3(+) lymphatic or vascular EC progenitors has not been studied. Using monoclonal antibodies to the extracellular domain of VEGFR-3, we show that 11% +/- 1% of CD34(+) cells isolated from human fetal liver, 1.9% +/- 0.8% CD34(+) cells from human cord blood, and 0.2% +/- 0.1% of CD34(+) cells from healthy adult blood donors are positive for VEGFR-3. CD34(+)VEGFR-3(+) cells from fetal liver coexpress the stem/precursor cell marker CD133 (AC133). Because mature ECs do not express CD133, coexpression of VEGFR-3 and CD133 on CD34(+) cells identifies a unique population of stem and progenitor cells. Incubation of isolated CD34(+)VEGFR-3(+) cells in EC growth medium resulted in a strong proliferation (40-fold in 2 weeks) of nonadherent VEGFR-3(+) cells. Plating of these cells resulted in the formation of adherent VEGFR-3(+)Ac-LDL(+) (Ac-LDL = acetylated low-density lipoprotein) EC monolayers expressing various vascular and lymphatic endothelial-specific surface markers, including CD34, VE-cadherin, CD51/61, CD105, LYVE-1, and podoplanin. These data demonstrate that human CD34(+)CD133(+) cells expressing VEGFR-3 constitute a phenotypically and functionally distinct population of endothelial stem and precursor cells that may play a role in postnatal lymphangiogenesis and/or angiogenesis.
Isolation of Hammerhead Ribozymes with Altered Core Sequences by in Vitro Selection (1997)

The hammerhead ribozyme has an invariant nucleotide sequence in the core region. In order to search for alternative sequences which can support the cleavage after the triplet GUC, the core region of 10 nucleotides was randomized and subjected to in vitro selection by repeated cycles of transcription, reverse transcription, and PCR. Active sequences were isolated after each transcription by denaturing PAGE, and after nine cycles of selection, two sequences dominated the pool. Both sequences conformed broadly to the consensus core region except that in one sequence a single A9U mutation was observed while in the other two mutations at A9U and U7A were seen. The catalytic efficiencies of these ribozymes were 6.4 and 14.1 microM(-1) min(-1), respectively, as compared to 163 microM(-1) min(-1) for the consensus sequence. Interestingly, the consensus was not found in any of the selected sequences. This discrimination against the consensus sequence was attributed to the specificity of the enzymes used in the selection procedure.
A Familial Mutation Renders Atrial Natriuretic Peptide Resistant to Proteolytic Degradation (2009)

A heterozygous frameshift mutation causing a 12-amino acid extension to the C terminus of atrial natriuretic peptide (ANP) was recently genetically linked to patients with familial atrial fibrillation (Hodgson-Zingman, D. M., Karst, M. L., Zingman, L. V., Heublein, D. M., Darbar, D., Herron, K. J., Ballew, J. D., de Andrade, M., Burnett, J. C., Jr., and Olson, T. M. (2008) N. Engl. J. Med. 359, 158-165). The frameshift product (fsANP), but not wild-type ANP (wtANP), was elevated in the serum of affected patients, but the molecular basis for the elevated peptide concentrations was not determined. Here, we measured the ability of fsANP to interact with natriuretic peptide receptors and to be proteolytically degraded. fsANP and wtANP bound and activated human NPR-A and NPR-C similarly, whereas fsANP had a slightly increased efficacy for human NPR-B. Proteolytic susceptibility was addressed with novel bioassays that measure the time required for kidney membranes or purified neutral endopeptidase to abolish ANP-dependent activation of NPR-A. The half-life of fsANP was markedly greater than that of wtANP in both assays. Additional membrane proteolysis studies indicated that wtANP and fsANP are preferentially degraded by neutral endopeptidase and serine peptidases, respectively. These data indicate that the familial ANP mutation associated with atrial fibrillation has only minor effects on natriuretic peptide receptor interactions but markedly modifies peptide proteolysis.
Immunogenicity negatively influences the outcome of adalimumab treatment in Crohn’s disease (2008)

Immunogenicity plays a role in adalimumab treatment because of the development of ATAs.
A multibit test trigger circuit for megabit SRAMs (1990)

A multibit test (MBT) trigger circuit for megabit SRAM packages with no unused pins is discussed. The features of the MBT trigger circuit are a logic trigger mode without using any additional pins and practical use of counter circuits. The essence of trigger mode selection is that two pulses are for MBT set and three pulses are for MBT reset. In this way, a logic trigger mode that does not use NC pins is especially effective as a 4-Mb SRAM. In addition, the proposed scheme is able to act as a logic trigger for an MBT circuit. The scheme is simple and effective. The logic trigger mode is proposed for future standardization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Fully Integrated RF-Powered Contact Lens With a Single Element Display (2010)

We present progress toward a wirelessly-powered active contact lens comprised of a transparent polymer substrate, loop antenna, power harvesting IC, and micro-LED. The fully integrated radio power harvesting and power management system was fabricated in a 0.13 μm CMOS process with a total die area of 0.2 mm(2). It utilizes a small on-chip capacitor for energy storage to light up a micro-LED pixel. We have demonstrated wireless power transfer at 10 cm distance using the custom IC and on-lens antenna.
Ezrin regulates cell-cell and cell-matrix adhesion, a possible role with E-cadherin/β-catenin (1999)

Ezrin, radixin, moesin and merlin form a subfamily of conserved proteins in the band 4.1 superfamily. The function of these proteins is to link the plasma membrane to the actin cytoskeleton. Merlin is defective or absent in schwannomas and meningiomas and has been suggested to function as a tumour suppressor. In this study, we have examined the role of ezrin as a potential regulator of the adhesive and invasive behaviour of tumour cells. We have shown that following inhibition of ezrin expression in colo-rectal cancer cells using antisense oligonucleotides, these cells displayed a reduced cell-cell adhesiveness together with a gain in their motile and invasive behaviour. These cells also displayed increased spreading over matrix-coated surfaces. Immunofluorescence studies revealed that antisense-treated cells also displayed an increased staining of paxillin in areas representing focal adhesions. Furthermore, coprecipitation studies revealed an association of ezrin with E-cadherin and beta-catenin. Induction of the phosphorylation of ezrin by orthovanadate and hepatocyte growth factor/scatter factor resulted in changes similar to those seen with antisense treatment, together with a marked decrease in the association of ezrin with both beta-catenin and E-cadherin. It is concluded that ezrin regulates cell-cell and cell-matrix adhesion, by interacting with cell adhesion molecules E-cadherin and beta-catenin, and may thus play an important role in the control of adhesion and invasiveness of cancer cells.
Expression and transcriptional regulation of the PD-Ialpha/autotaxin gene in neuroblastoma. (1997)

Autotaxin (ATX) is a newly found autocrine tumor cell motility-stimulating factor. ATX is a member of the ecto-phosphodiesterase I (PD-I)/ nucleotide pyrophosphatase family. PD-Ialpha was found as a brain-type ecto-phosphodiesterase I/nucleotide pyrophosphatase. ATX and PD-Ialpha are alternative splicing products from one gene. ATX stimulates motility of A2058 melanoma cells in vitro; however, it has not been known if PD-Ialpha/ATX is expressed in naturally occurred human tumors. In this study, we examined the expression of the human PD-Ialpha/ATX gene in human neuroblastoma tumor tissues and the motility stimulating activity of recombinant ATX on neuroblastoma cells and investigated its transcriptional regulatory mechanism in a human neuroblastoma cell line. The PD-Ialpha/ATX gene was expressed in the primary tumor tissues from neuroblastoma patients to varying degrees. This gene is also expressed in the SMS-KAN neuroblastoma cell line. We identified both isoforms, PD-Ialpha and ATX, in these tumor tissues and SMS-KAN cells. The recombinant ATX stimulated the motility of SMS-KAN cells at low nanomolar concentration. We situated the promoter region, which is essential for its transcription in SMS-KAN cells, at -287 to -254 nucleotides by the promoter activity assay. The gel-shift assay revealed that there exists a nuclear protein in SMS-KAN cells that binds this region. These new insights about autocrine tumor cell motility-stimulating protein will help us to understand the metastatic mechanism of human neuroblastoma.
Controlled ribozyme targeting demonstrates an antiapoptotic effect of carcinoembryonic antigen in HT29 colon cancer cells. (2001)

Our study suggests that CEA has an important regulatory role in apoptosis, and we propose that CEA is a survival factor for colon cancer cells.
Analysis of improvement in individual rheumatoid arthritis patients treated with disease‐modifying antirheumatic drugs, based on the findings in patients treated with placebo (1990)

A composite index for estimating improvement in individual rheumatoid arthritis (RA) patients during trials of slow-acting, disease-modifying antirheumatic drugs (DMARDs) was developed by analyzing the responses of 130 placebo-treated participants in Cooperative Systematic Studies of Rheumatic Diseases studies. If responses in 4 of 6 selected measures were required for improvement (by greater than or equal to 20% for morning stiffness, Westergren erythrocyte sedimentation rate, joint pain/tenderness score, and joint swelling score, and by greater than or equal to 2 grades on a 5-grade scale, or from grade 2 to grade 1 for patient's and physician's overall assessments of current disease severity), few placebo-treated patients qualified as improved, whereas significantly more DMARD-treated patients demonstrated improvement. The proposed index appears to be useful in estimating the probability that an RA patient will improve if taking a placebo during a DMARD trial, and may be a useful tool for analysis of DMARD studies.
Transgenic expression of tpr-met oncogene leads to development of mammary hyperplasia and tumors. (1996)

Receptor tyrosine kinases are important in cell signal transduction and proliferation. Abnormal expression of tyrosine kinases often leads to malignant transformation. C-met is a tyrosine kinase receptor and its ligand is hepatocyte growth factor (HGF). HGF/c-met plays diverse role in regulation of cell growth, shape and movement. Constitutively activated met, such as tpr-met, is a potent oncogene in vitro, but its carcinogenic role in vivo remains unclear. Our study demonstrates that expression of tpr-met leads to development of mammary tumors and other malignancies in transgenic mice, and suggests that deregulated met expression may be involved in mammary carcinogenesis.