gebhart/patrepeval huggingface dataset:
An Improved Method to Extract DNA from 1 ml of Uncultured Amniotic Fluid from Patients at Less than 16 Weeks’ Gestation (2013)

The aim of this study was to develop an improved technique for DNA extraction from 1 ml of uncultured AF from patients with a gestational age less than 16 weeks and to allow the use of array-CGH without DNA amplification. The DNA extraction protocol was tested in a series of 90 samples including 41 of uncultured AF at less than 16 weeks of gestation. Statistical analyses were performed using linear regression. To evaluate the sensitivity and the specificity of array-CGH on 1 ml of uncultured AF, five samples with an abnormal karyotype (three with aneuploidy, two with structural abnormalities) and five with a normal karyotype were studied. This protocol was reproducible and we were able to show a great improvement with higher yield of DNA obtained from all patients, including those with a gestational age less than 16 weeks (p = 0.003). All chromosomal abnormalities were detected and characterized by array-CGH and normal samples showed normal profiles. This new DNA extraction protocol associated with array-CGH analysis could be used in prenatal testing even when gestational age is less than 16 weeks, especially in cases with abnormal ultrasound findings.
Development of barcode and proteome profiling of glioblastoma (2014)

High grade glioma (glioblastoma) is the most common brain tumor. Its malignancy makes it the fourth biggest cause of cancer death. In our experiments we used several glioblastoma cell lines generated in our laboratory to obtain proteomics information specific for this disease. This study starts our developing the complete 2DE map of glioblastoma proteins. 2DE separation with following imaging, immunochemistry, spot picking, and mass-spectrometry allowed us detecting and identifying more than 100 proteins. Several of them have prominent differences in their level between norm and cancer. Among them are alpha-enolase (ENOA_HUMAN), pyruvate kinase isozymes M1/M2 (KPYM_HUMAN), cofilin 1 (COF1_HUMAN), translationally-controlled tumor protein TCTP_HUMAN, annexin 1 (ANXA1_HUMAN), PCNA (PCNA_HUMAN), p53 (TP53_HUMAN) and others. Most interesting results were obtained with protein p53. In all glioblastoma cell lines, its level was dramatically up regulated and enriched by multiple additional isoforms. This distribution is well correlated with presence of these proteins inside of cells themselves. At this initial step we suggest the panel of specific brain tumor markers (signature) to help creating noninvasive techniques to diagnose disease. These preliminary data point to these proteins as promising markers of glioblastoma.
THE EFFECT OF THALIDOMIDE AND ITS DERIVATIVES ON THYROXINE-INDUCED METAMORPHOSIS OF TADPOLE (1965)

Thalidomide and its derivatives are inhibitory to both morphological and biochemical changes occurring during thyroxine-accelerated metamorphosis of the tadpole. In general, the morphological changes are more affected than the biochemical differentiation. Thyroxine treatment increases the amount of the liver glucosamine, while simultaneous treatment with thalidomide has no effect on the content of this compound. Treatment of the tadpoles with thyroxine alone or thyroxine and thalidomide does not affect the adrenaline and noradrenaline contents of kidney and brain. Thus, the effect of thalidomide on the metamorphosis of tadpole induced by thyroxine is quite selective. These changes were brought about at a thalidomide concentration of 1 × 10 −4 M, which is the lowest ever reported to be effective in biological systems.
From Peptide Precursors to Oxazole and Thiazole-Containing Peptide Antibiotics: Microcin B17 Synthase (1996)

Esherichia coli microcin B17 is a posttranslationally modified peptide that inhibits bacterial DNA gyrase. It contains four oxazole and four thiazole rings and is representative of a broad class of pharmaceutically important natural products with five-membered heterocycles derived from peptide precursors. An in vitro assay was developed to detect heterocycle formation, and an enzyme complex, microcin B17 synthase, was purified and found to contain three proteins, McbB, McbC, and McbD, that convert 14 residues into the eight mono- and bisheterocyclic moieties in vitro that confer antibiotic activity on mature microcin B17. These enzymatic reactions alter the peptide backbone connectivity. The propeptide region of premicrocin is the major recognition determinant for binding and downstream heterocycle formation by microcin B17 synthase. A general pathway for the enzymatic biosynthesis of these heterocycles is formulated.
Guam, the Brown Tree Snake Invasion, and Suicide Prevention (2011)

A sample of vignettes from past and present psychological applications in tropical Guam with an assist from contemporary Singapore. An emphasis on cultural adaptation to an invasion of brown tree snakes is followed by antidotes to teen suicide subsequent a high profile suicidal event. A chaos theory perspective is suggested.
Wafer chuck for magnification correction in x-ray lithography (1998)

Magnification correction has emerged as a critical issue in x-ray lithography for very large scale integrated circuits. We have developed a simple and robust method to correct the magnification, which is suitable for use in a collimated x-ray beam from a storage ring. In our technique the wafer is bent to conform to a chuck whose surface is a portion of a sphere of adjustable radius. Both increases and decreases in the pattern size may be accommodated by using convex and concave spherical surfaces, respectively. The radius of the chuck can be set to achieve desired corrections of up to several parts per million. The maximum attainable correction is determined by the permissible out of plane distortion which accompanies the wafer bending, and is dependent upon the wafer thickness and the field size. The change in the wafer pattern is expected to be very nearly an isotropic magnification; however a limited one-dimensional magnification correction may also be added by differentially scanning the mask and wafer.
mTOR Inhibition Alleviates Mitochondrial Disease in a Mouse Model of Leigh Syndrome (2013)

Mitochondrial dysfunction contributes to numerous health problems, including neurological and muscular degeneration, cardiomyopathies, cancer, diabetes, and pathologies of aging. Severe mitochondrial defects can result in childhood disorders such as Leigh syndrome, for which there are no effective therapies. We found that rapamycin, a specific inhibitor of the mechanistic target of rapamycin (mTOR) signaling pathway, robustly enhances survival and attenuates disease progression in a mouse model of Leigh syndrome. Administration of rapamycin to these mice, which are deficient in the mitochondrial respiratory chain subunit Ndufs4 [NADH dehydrogenase (ubiquinone) Fe-S protein 4], delays onset of neurological symptoms, reduces neuroinflammation, and prevents brain lesions. Although the precise mechanism of rescue remains to be determined, rapamycin induces a metabolic shift toward amino acid catabolism and away from glycolysis, alleviating the buildup of glycolytic intermediates. This therapeutic strategy may prove relevant for a broad range of mitochondrial diseases.
StVEC: A Vector Instruction Extension for High Performance Stencil Computation (2011)

Stencil computations comprise the compute-intensive core of many scientific applications. The data access pattern of stencil computations often requires several adjacent data elements of arrays to be accessed in innermost parallel loops. Although such loops are vectorized by current compilers like GCC and ICC that target short-vector SIMD instruction sets, a number of redundant loads or additional intra-register data shuffle operations are required, reducing the achievable performance. Thus, even when all arrays are cache resident, the peak performance achieved with stencil computations is considerably lower than machine peak. In this paper, we present a hardware-based solution for this problem. We propose an extension to the standard addressing mode of vector floating-point instructions in ISAs such as SSE, AVX, VMX etc. We propose an extended mode of paired-register addressing and its hardware implementation, to overcome the performance limitation of current short-vector SIMD ISA's for stencil computations. Further, we present a code generation approach that can be used by a vectorizing compiler for processors with such an instructions set. Using an optimistic as well as a pessimistic emulation of the proposed instruction extension, we demonstrate the effectiveness of the proposed approach on top of SSE and AVX capable processors. We also synthesize parts of the proposed design using a 45nm CMOS library and show minimal impact on processor cycle time.
Inhibition of nitric oxide synthesis increases blood pressure in healthy humans (1993)

Basal generation of nitric oxide influences total peripheral resistance and blood pressure in healthy humans. The natriuresis induced by L-NMMA may be related to the increase in blood pressure, or arise from inhibition of the intrarenal actions of nitric oxide. Any decrease in nitric oxide generation, as has been postulated to occur in essential hypertension, could have substantial effects on blood pressure and tissue blood flow.
Efficient indexing for large scale visual search (2009)

With the popularity of “bag of visual terms” representations of images, many text indexing techniques have been applied in large-scale image retrieval systems. However, due to a fundamental difference between an image query (e.g. 1500 visual terms) and a text query (e.g. 3-5 terms), the usages of some text indexing techniques, e.g. inverted list, are misleading. In this work, we develop a novel indexing technique for this problem. The basic idea is to decompose a document-like representation of an image into two components, one for dimension reduction and the other for residual information preservation. The computing of similarity of two images can be transferred to measuring similarities of their components. The decomposition has two major merits: (1) these components have good properties which enable them to be efficiently indexed and retrieved; (2) The decomposition has better generalization ability than other dimension reduction algorithms. The decomposition can be achieved by either a graphical model or a matrix factorization approach. Theoretic analysis and extensive experiments over a 2.3 million image database show that this framework is scalable to index large scale image database to support fast and accurate visual search.
Phase-Controlled One-Dimensional Shape Evolution of InSe Nanocrystals (2006)

Cubic-phase InSe nanowires were synthesized. Obtaining an appropriate high reaction temperature for formation of nanocrystals using poor solubility of Se powder in oleylamine induced the generation of unusual cubic phase of InSe to form nanowires. In comparison, hexagonal-phase nanoplates were formed by dissolving Se powder in oleylamine before increase of reaction temperature. The diameter of highly monodisperse wires was controlled by varying the amount of Se.
[Expression of human factor IX in retrovirus-transfected human umbilical cord tissue derived mesenchymal stem cells]. (2009)

The purpose of this study was to investigate the expression of human Factor IX (hFIX) in retrovirus-transfected human umbilical cord tissue derived mesenchymal stem cells (hUCT-MSCs). The pLEGFP-N1-hFIX vector was generated by cloning a 3.0 kb Bgl II-BamH I fragment from the pIRES2-EGFP-hFIX plasmid containing the hFIX cDNA and part of intron 1 of hFIX in pLEGFP-N1 vector. The retroviral supernatants were produced from the Phoenix packaging cell line and then infected the hUCT-MSCs. After selection with G418 for 10 day, the expression of FIX was detected by ELISA and Western blot. The biological activity of FIX was determined by the clotting assay employing human Factor IX-deficient plasma. The results showed that compared with the activity of pooled human normal plasma (100%), transduced cells produced biologically active hFIX with 100-130% activity in two-day culture supernatant and expressed hFIX at levels of 2.68 +/- 0.36 microg/10(6) cells/24 hours after G418 selection for 10 days. The secretion of hFIX into culture supernatant was also confirmed by Western blot analysis. It is concluded that genetically modified hUCT-MSCs can express biologically active hFIX and thus serve as an efficient drug delivery vehicle carrying hFIX used as a way of somatic gene therapy for hemophilia B.
Properties of chemically etched porous polycrystalline silicon deposited by r.f. sputtering (2002)

After the discovery of the luminescence phenomena in porous crystalline Si at room temperature, there has been tremendous research in the area of porous effects in Si due to its potential in optoelectronics applications. Recently, it was reported that similar photoluminescence (PL) was observed in porous CVD and cast Si formed by electrochemical anodization. Studies of porous polycrystalline Si films are attractive because it may be applied in large area devices. In this paper, we shall report the properties of porous polycrystalline silicon formed by chemically etching r.f. sputtered silicon films after furnace crystallization.
Influence of CD33 expression levels and ITIM-dependent internalization on gemtuzumab ozogamicin–induced cytotoxicity (2004)

Gemtuzumab ozogamicin (GO; Mylotarg), a novel immunoconjugate used for treatment of acute myeloid leukemia (AML), contains the humanized anti-CD33 antibody (hP67.6) as a carrier to facilitate cellular uptake of the toxic calicheamicin-gamma(1) derivative. By use of lentivirus-mediated gene transfer to manipulate CD33 expression in myeloid cell lines that normally lack CD33 (murine 32D cells) or have very low levels of CD33 (human OCI-AML3 and KG-1a cells), we here show a quantitative relationship between CD33 expression and GO-induced cytotoxicity. The CD33 cytoplasmic immunoreceptor tyrosine-based inhibitory motifs (ITIMs) control internalization of antibody bound to CD33. Disruption of the ITIMs by introduction of point mutations not only prevented effective internalization of antibody-bound CD33 but also significantly reduced GO-induced cytotoxicity. Together, our data imply a pivotal role of both the number of CD33 molecules expressed on the cell surface and the amount of internalization of CD33 following antibody binding for GO-induced cytotoxicity and suggest novel therapeutic approaches for improvement of clinical outcome of patients treated with GO.
Preparation of Literally Two-Dimensional Magnets (1978)

The Langmuir-Blodgett technique was used to deposit manganese stearate in the form of monolayers. Because of the nature of the method, and a variety of supporting experiments, it is concluded that the Mn atoms are arrayed on a single surface, thus forming literally two-dimensional magnetic materials.
Treatment of lumbar disc herniation: Evidence-based practice (2010)

While surgery appears to provide more rapid relief, many patients will gradually get better with continued nonoperative management; thus, patient education and active participation in decision-making is vital.
<title>FBI wavelet/scalar quantization standard for gray-scale fingerprint image compression</title> (1993)

The FBI has recently adopted a standard for the compression of digitized 8-bit gray-scale fingerprint images. The standard is based on scalar quantization of a 64-subband discrete wavelet transform decomposition of the images, followed by Huffman coding. Novel features of the algorithm include the use of symmetric boundary conditions for transforming finite- length signals and a subband decomposition tailored for fingerprint images scanned at 500 dpi. The standard is intended for use in conjunction with ANSI/NBS-CLS 1-1993, American National Standard Data Format for the Interchange of Fingerprint Information, and the FBI's Integrated Automated Fingerprint Identification System.
The chemical composition and structure of the cell wall of Chlorella pyrenoidosa (1958)

Research Article| November 01 1958 The chemical composition and structure of the cell wall of Chlorella pyrenoidosa D. H. Northcote; D. H. Northcote 1Department of Biochemistry, University of Cambridge Search for other works by this author on: This Site PubMed Google Scholar K. J. Goulding; K. J. Goulding 1Department of Biochemistry, University of Cambridge Search for other works by this author on: This Site PubMed Google Scholar R. W. Horne R. W. Horne 2Cavendish Laboratory, University of Cambridge Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1958) 70 (3): 391–397. https://doi.org/10.1042/bj0700391 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation D. H. Northcote, K. J. Goulding, R. W. Horne; The chemical composition and structure of the cell wall of Chlorella pyrenoidosa. Biochem J 1 November 1958; 70 (3): 391–397. doi: https://doi.org/10.1042/bj0700391 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1958 CAMBRIDGE UNIVERSITY PRESS1958 Article PDF first page preview Close Modal You do not currently have access to this content.
Emerging drugs in multiple myeloma (2007)

The treatment of multiple myeloma has seen significant changes from the time of the initial use of cytotoxic agents such as melphalan, to the introduction of high-dose chemotherapy and stem cell transplantation, and most recently the era of novel targeted agents. These new drugs have rapidly become the mainstay of therapy of this disease and transformed the treatment paradigm, leading to improvements in survival and quality of life. Existing therapeutic options include agents such as thalidomide, bortezomib and lenalidomide, either used alone or in combination with standard agents, including glucocorticoids, and in conjunction with high-dose chemotherapy supported with stem cell transplantation. Several other targeted agents have demonstrated exciting preclinical activity, and are presently being tested in early Phase I and II clinical trials. This review summarizes the role of novel therapeutic agents in multiple myeloma, and the promising effect of multiple new agents in development.
Computer Predictions of Abnormal Test Results (1988)

We developed statistical equations to predict abnormalities on eight commonly ordered diagnostic tests and we gave the predictions to 112 physicians practicing in an academic internal medicine practice. Half of each physician's patients were randomized to intervention status. All diagnostic tests were ordered by microcomputer, and when a physician ordered one of the eight study tests for an intervention patient, the computer displayed the probability (0% to 100%) that the test would be positive for the main abnormality being tested for. The physician could then cancel the test if desired. During a six-month controlled trial, when there were more than 15,000 scheduled patient visits, patient charges for the eight study tests were 8.8% less for the intervention patients. The largest reductions (greater than 10%) were for serum electrolyte level tests and complete blood cell counts, the two most commonly ordered tests. Physicians ordered fewer low-probability tests for intervention patients than for controls, suggesting that with timely predictive information, physicians can target tests to higher-risk patients.
Selective Pairing of Polyfluorinated DNA Bases (2004)

Novel selective non-hydrogen-bonding DNA base pairs utilizing fluorinated nucleoside analogues have been investigated. Melting studies of DNA duplexes containing 2,3,4,5-tetrafluorobenzene and 4,5,6,7-tetrafluoroindole bases on opposite strands show greater stabilization of the duplex compared with nonfluorinated hydrocarbon controls. Overall, these hydrophobic analogues are destabilizing compared with natural base pairs but are stabilizing compared with natural base mismatches. Such selective pairing may be due to solvent avoidance of these hydrophobic structures, burying their surfaces within the duplex. Our findings suggest that polyfluoroaromatic bases might be employed as a new, selective base-pairing system orthogonal to the natural genetic system.
Heart Rate Variability in Complex Regional Pain Syndrome during Rest and Mental and Orthostatic Stress (2011)

The increased heart rate and decreased heart rate variability in CRPS suggest a general autonomic imbalance, which is an independent predictor for increased mortality and sudden death. The inability of the patients to protect their cardiac output during orthostatic stress was aggravated with the chronicity of the disease.
Molecular mechanism for silencing virally transduced genes involves histone deacetylation and chromatin condensation (2000)

Virally transduced genes are often silenced after integration into the host genome. Chromatin immunoprecipitation and nuclease sensitivity experiments now demonstrate that silencing of the transgene is characterized by deacetylation of histone H4 lysines and chromatin condensation. Trichostatin A treatment results in dramatic reactivation of gene expression that is preceded by histone acetylation and chromatin decondensation. Analysis of individual histone H4 lysines demonstrate that chromatin domain opening is coincident with rapid acetylation of histone H4 K5, K12, and K16 and that maintenance of the open domain is correlated with acetylation of histone H4 K8. Removal of trichostatin A results in rapid deacetylation of histone H4 K8, chromatin condensation, and transcription silencing. The results suggest that deacetylation of histone H4 lysines and coincident chromatin condensation are critically involved in the silencing of virally transduced genes.
Epidermal Growth Factor Receptor Serum Levels and Prognostic Value in Malignant Gliomas (2007)

Although a prospective study with large sample size is warranted, serum EGFR extracellular domain may be potentially useful as a biological marker of gliomas for prediction of prognosis and follow-up after treatment.
The consequences of meniscectomy (2006)

The menisci of the knee have an important role in load-bearing and shock absorption within the joint. They may also function as secondary stabilisers, have a proprioceptive role, and aid the lubrication and nutrition of the articular cartilage. Complete or partial loss of a meniscus can have damaging effects on a knee, leading to serious long-term sequelae. This paper reviews the consequences of meniscectomy and summarises the body of evidence in the literature regarding those factors most relevant to long-term outcome.
Properties of a non‐tumorigenic human cervical keratinocyte cell line (1989)

A human cervical keratinocyte cell line, W12, has been initiated from a low-grade cervical lesion histologically diagnosed as CIN I. This cell line has, to date, undergone over 300 generations in vitro with an average doubling time of 30 hr: an aneuploid karyotype has developed with progressive in vitro growth. W12 contains HPV16 DNA present at approximately 100 copies and the state of the viral DNA over a number of passages has been examined. The HPV16 DNA is stably maintained at high copy number over several passages and restriction enzyme analysis together with electrophoresis of uncleaved viral DNA indicate that it is present predominantly as the episomal molecule. W12 cells exhibit a typical keratinocyte morphology and, when transplanted into the flank of the nude mouse, form an epithelial lesion with the histological features of CIN I/II.