gebhart/patrepeval huggingface dataset:
The mechanisms involved in formation of deletions and duplications of 15q11-q13. (1998)

Haplotype analysis was undertaken in 20 cases of 15q11-q13 deletion associated with Prader-Willi syndrome (PWS) or Angelman syndrome (AS) to determine if these deletions arose through unequal meiotic crossing over between homologous chromosomes. Of these, six cases of PWS and three of AS were informative for markers on both sides of the deletion. For four of six cases of paternal 15q11-q13 deletion (PWS), markers on both sides of the deletion breakpoints were inferred to be of the same grandparental origin, implying an intrachromosomal origin of the deletion. Although the remaining two PWS cases showed evidence of crossing over between markers flanking the deletion, this was not more frequent than expected by chance given the genetic distance between proximal and distal markers. It is therefore possible that all PWS deletions were intrachromosomal in origin with the deletion event occurring after normal meiosis I recombination. Alternatively, both sister chromatid and homologous chromosome unequal exchange during meiosis may contribute to these deletions. In contrast, all three cases of maternal 15q11-q13 deletion (AS) were associated with crossing over between flanking markers, which suggests significantly more recombination than expected by chance (p = 0.002). Therefore, there appears to be more than one mechanism which may lead to PWS/AS deletions or the resolution of recombination intermediates may differ depending on the parental origin of the deletion. Furthermore, 13 of 15 cases of 15q11-q13 duplication, triplication, or inversion duplication had a distal duplication breakpoint which differed from the common distal deletion breakpoint. The presence of at least four distal breakpoint sites in duplications indicates that the mechanisms of rearrangement may be complex and multiple repeat sequences may be involved.
An E2F dominant negative mutant blocks E1A induced cell cycle progression. (1994)

E2F is a cellular transcription factor that is regulated during the cell cycle through interactions with the product of the retinoblastoma susceptibility gene (RB1) and the pRb-like p107 and p130 proteins. Analysis of mutations within both adenovirus E1A and pRb, which affected their ability to regulate cellular proliferation and alter E2F activity, suggested that E2F may play a role in cell cycle progression. Microinjection of a GST-E2F-1 fusion protein into quiescent Balb/c 3T3 cells induced DNA synthesis whereas co-injection of GST-E2F-1 and GST-E2F(95-191) protein, encoding only the DNA binding domain of E2F-1, blocked the induction of S-phase. While E1A likely targets multiple cellular pathways, co-injection of the GST-E2F(95-191) dominant inhibitory protein with 12S E1A protein blocked E1A-mediated induction of DNA synthesis, suggesting that the E2F-dependent pathway is dominant. Analysis of the interval required for microinjected quiescent cells to enter S-phase indicated that E2F-1 acted faster than either E1A or serum.
Mechanical and Fracture Properties of Bamboo (2006)

The microstructure, mechanical, impact and fracture properties of Australian bamboo have been investigated. The graded composition and property has been confirmed by depth-profiles obtained by synchrotron radiation diffraction and Vickers indentation. The mechanical performance of bamboo is stronly dependent on age. Results showed that young bamboo has higher strength, elastic stiffness and fracture toughness than its old counterpart. Both crack-deflection and crackbridging are the major energy dissipative processes for imparting a high toughness in bamboo.
Fast Coding Unit size decision algorithm for intra coding in HEVC (2013)

The recursive quad-tree structure of Coding Unit (CU) in HEVC can improve coding efficiency while the encoding complexity is increased significantly. In this paper, a fast CU size decision algorithm to reduce the complexity of HEVC intra coding is proposed. It introduces the early termination method based on the statistics of rate-distortion costs in CU splitting process. Experimental results show the encoding time can be reduced by 24% on average without significant loss of BD-rate.
Synthesis and Characterization of Oligonucleotides Containing 2′-Deoxyxanthosine Using Phosphoramidite Chemistry (2000)

Oligodeoxynucleotides containing 2′-deoxyxanthosine (Xd) were synthesized in good yield from a O2,O6-bis[2-(4-nitrophenyl)ethyl](NPE)-protected phosphoramidite of Xd. Attempts to synthesize a O6-monoNPE-protected phosphoramidite resulted in formation of a major by-product. The NPE protecting groups were removed by treatment with oximate ion after other protecting groups were removed with aqueous NH4OH solution. The composition of the synthetic oligonucleotides was verified by enzymatic degradation and MALDI-TOF mass spectrometry. The efficacy of this procedure allowed isolation of oligodeoxynucleotides containing multiple Xd residues.
Intersubband relaxation in GaAs-AlxGa1−xAs quantum well structures observed directly by an infrared bleaching technique (1987)

Direct intersubband excitations in narrow, modulation doped GaAs-${\mathrm{Al}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As quantum well structures are studied by picosecond infrared spectroscopy. The bleaching of the intersubband absorption induced by a high-intensity picosecond pump pulse, is studied by a delayed probe pulse. Typical intersubband relaxation times are of the order of 10 ps at 300 K for a subband splitting of about 150 meV. Polar LO-phonon scattering is discussed as the most relevant relaxation mechanism.
Placenta-Derived Soluble MHC Class I Chain-Related Molecules Down-Regulate NKG2D Receptor on Peripheral Blood Mononuclear Cells during Human Pregnancy: A Possible Novel Immune Escape Mechanism for Fetal Survival (2006)

Mammalian pregnancy is an intriguing immunological phenomenon where the semiallogeneic fetus is not rejected. Tolerance toward the fetus involves a number of mechanisms associated with modifications of the immune status of the mother. In this study, we strongly suggest a novel mechanism for fetal evasion of maternal immune attack, based on the engagement and down-regulation of the activating NK cell receptor NKG2D on PBMC by soluble MHC class I chain-related proteins A and B (collectively termed MIC). A similar immune escape pathway was previously described in tumors. We found that MIC mRNA was constitutively expressed by human placenta and could be up-regulated upon heat shock treatment. Our immunomorphologic studies showed that the MIC expression in placenta was restricted to the syncytiotrophoblast. Immunoelectron microscopy revealed a dual MIC expression in the syncytiotrophoblast: on the apical and basal cell membrane and in cytoplasmic vacuoles as MIC-loaded microvesicles/exosomes. Soluble MIC molecules were present at elevated levels in maternal blood throughout normal pregnancy and were released by placental explants in vitro. Simultaneously, the cell surface NKG2D expression on maternal PBMC was down-regulated compared with nonpregnant controls. The soluble MIC molecules in pregnancy serum were able to interact with NKG2D and down-regulate the receptor on PBMC from healthy donors, with the consequent inhibition of the NKG2D-dependent cytotoxic response. These findings suggest a new physiological mechanism of silencing the maternal immune system that promotes fetal allograft immune escape and supports the view of the placenta as an immunoregulatory organ.
Secretion of annexin A3 from ovarian cancer cells and its association with platinum resistance in ovarian cancer patients (2011)

Early detection of resistance to platinum-based therapy is critical for improving the treatment of ovarian cancers. We have previously found that increased expression of annexin A3 is a mechanism for platinum resistance in ovarian cancer cells. Here we demonstrate that annexin A3 can be detected in the culture medium of ovarian cancer cells, particularly these cells that express high levels of annexin A3. Levels of annexin A3 were then determined in sera from ovarian cancer patients using an enzyme-linked immunosorbent assay. Compared with those from normal donors, sera from ovarian cancer patients contain significantly higher levels of annexin A3. Furthermore, serum levels of annexin A3 were significantly higher in platinum-resistant patients than in platinum-sensitive patients. To gain insight into the mechanism of secretion, the ovarian cancer cell lines were examined using both transmission electron microscopy and immunoelectron microscopy. Compared with parent cells, there are significantly more vesicles in the cytoplasm of ovarian cancer cells that express high levels of annexin A3, and at least some vesicles are annexin A3-positive. Moreover, some vesicles appear to be fused with the cell membrane, suggesting that annexin A3 secretion may be associated with exocytosis and the release of exosomes. This is supported by our observation that ovarian cancer cells expressing higher levels of annexin A3 released increased numbers of exosomes. Furthermore, annexin A3 can be detected in exosomes released from cisplatin-resistant cells (SKOV3/Cis) by immunoblotting and immunoelectron microscopy.
A Review of the Development of a Vehicle for Localized and Controlled Drug Delivery for Implantable Biosensors (2008)

A major obstacle to the development of implantable biosensors is the foreign body response (FBR) that results from tissue trauma during implantation and the continuous presence of the implant in the body. The in vivo stability and functionality of biosensors are compromised by damage to sensor components and decreased analyte transport to the sensor. This paper summarizes research undertaken by our group since 2001 to control the FBR toward implanted sensors. Localized and sustained delivery of the anti-inflammatory drug, dexamethasone, and the angiogenic growth factor, vascular endothelial growth factor (VEGF), was utilized to inhibit inflammation as well as fibrosis and provide a stable tissue-device interface without producing systemic adverse effects. The drug-loaded polylactic-co-glycolic acid (PLGA) microspheres were embedded in a polyvinyl alcohol (PVA) hydrogel composite to fabricate a drug-eluting, permeable external coating for implantable devices. The composites were fabricated using the freeze-thaw cycle method and had mechanical properties similar to soft body tissue. Dexamethasone-loaded microsphere/hydrogel composites were able to provide anti-inflammatory protection, preventing the FBR. Moreover, concurrent release of dexamethasone with VEGF induced neoangiogenesis in addition to providing anti-inflammatory protection. Sustained release of dexamethasone is required for the entire sensor lifetime, as a delayed inflammatory response developed after depletion of the drug from the composites. These studies have shown the potential of PLGA microsphere/PVA hydrogel-based composites as drug-eluting external coatings for implantable biosensors.
The translocation (6;9) (p23;q34) shows consistent rearrangement of two genes and defines a myeloproliferative disorder with specific clinical features (1992)

Translocation (6;9)(p23;q34) is a cytogenetic aberration that can be found in specific subtypes of both acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). This translocation is associated with an unfavourable prognosis. Recently, the genes involved in the t(6;9) were isolated and characterized. Breakpoints in both the dek gene on chromosome 6 and the can gene on chromosome 9 appear to occur in defined regions, which allows us to diagnose this type of leukemia at the molecular level. Moreover, because of the translocation a chimeric dek-can mRNA is formed which, as we show here, is an additional target for diagnosis via cDNA-preparation and the polymerase chain reaction (PCR). We studied 17 patients whose blood cells and/or bone marrow cells showed a t(6;9) with karyotypic analysis. Fourteen patients suffered from AML, one patient had a refractory anemia with excess of blasts in transformation (RAEBt), one patient had an acute myelofibrosis (AMF), and one patient a chronic myeloid leukemia (CML). In nine cases studies at the DNA and RNA levels were possible while in seven cases only the DNA could be analyzed. In one case only RNA was available. Conventional Southern blot analysis showed the presence of rearrangements of both the dek gene and the can gene. In both genes, breakpoints cluster in one intron in the patients investigated. The presence of a consistent chimeric dek-can product after cDNA preparation followed by the PCR was demonstrated. We conclude from our data that the t(6;9) is found in myeloproliferative disorders with typical clinical characteristics. This translocation results in highly consistent abnormalities at the molecular level.
Data distribution support on distributed shared memory multiprocessors (1997)

Cache-coherent multiprocessors with distributed shared memory are becoming increasingly popular for parallel computing. However, obtaining high performance on these machines mquires that an application execute with good data locality. In addition to making efiective use of caches, it is often necessary to distribute data structures across the local memories of the processing nodes, thereby reducing the latency of cache misses.We have designed a set of abstractions for performing data distribution in the context of explicitly parallel programs and implemented them within the SGI MIPSpro compiler system. Our system incorporates many unique features to enhance both programmability and performance. We address the former by providing a very simple programmming model with extensive support for error detection. Regarding performance, we carefully design the user abstractions with the underlying compiler optimizations in mind, we incorporate several optimization techniques to generate efficient code for accessing distributed data, and we provide a tight integration of these techniques with other optimizations within the compiler Our initial experience suggests that the directives are easy to use and can yield substantial performance gains, in some cases by as much as a factor of 3 over the same codes without distribution.
In vivo transformation of human skin with human papillomavirus type 11 from condylomata acuminata (1986)

Human papillomaviruses (HPVs) have been implicated in the development of a number of human malignancies, but direct tests of their involvement have not been possible. We describe a system in which human skin from various sites was infected with HPV type 11 (HPV-11) extracted from vulvar condylomata and was grafted beneath the renal capsule of athymic mice. Most of the skin grafts so treated underwent morphological transformation, resulting in the development of condylomata identical to those which occur spontaneously in patients. Foreskins responded with the most vigorous proliferative response to HPV-11. The lesions produced the characteristic intranuclear group-specific antigen of papillomaviruses. Both dot blot and Southern blot analysis of DNA from the lesions revealed the presence of HPV-11 DNA in the transformed grafts. These results demonstrate the first laboratory system for the study of the interaction of human skin with an HPV. The method may be useful in understanding the mechanisms of HPV transformation and replication and is free of the ethical restraints which have impeded study. This system will allow the direct study of factors which permit neoplastic progression of HPV-induced cutaneous lesions in human tissues.
Role of CXCR5 and CCR7 in Follicular Th Cell Positioning and Appearance of a Programmed Cell Death Gene-1High Germinal Center-Associated Subpopulation (2007)

Th cell access to primary B cell follicles is dependent on CXCR5. However, whether CXCR5 induction on T cells is sufficient in determining their follicular positioning has been unclear. In this study, we find that transgenic CXCR5 overexpression is not sufficient to promote follicular entry of naive T cells unless the counterbalancing influence of CCR7 ligands is removed. In contrast, the positioning of Ag-engaged T cells at the B/T boundary could occur in the absence of CXCR5. The germinal center (GC) response was 2-fold reduced when T cells lacked CXCR5, although these T cells were able to access the GC. Finally, CXCR5(high)CCR7(low) T cells were found to have elevated IL-4 transcript and programmed cell death gene-1 (PD-1) expression, and PD-1(high) cells were reduced in the absence of T cell CXCR5 or in mice compromised in GC formation. Overall, these findings provide further understanding of how the changes in CXCR5 and CCR7 expression regulate Th cell positioning during Ab responses, and they suggest that development and/or maintenance of a PD-1(high) follicular Th cell subset is dependent on appropriate interaction with GC B cells.
Photoradiation Therapy. II. Cure of Animal Tumors With Hematoporphyrin and Light23 (1975)

Exposure of mouse and rat tumors of various types to more than 600 nm light 24 or 48 hours after an injection of hematoporphyrin resulted in a substantial number of long-term cures. Since hematoporphyrin is preferentially retained in tumor tissue, selective tumor destruction could be obtained. Light penetration studies and the high efficiency of this technique indicated its applicability even to certain deep-seated human tumors.
Molecular cloning and characterization of drimenol synthase from valerian plant (Valeriana officinalis) (2014)

Drimenol, a sesquiterpene alcohol, and its derivatives display diverse bio-activities in nature. However, a drimenol synthase gene has yet to be identified. We identified a new sesquiterpene synthase cDNA (VoTPS3) in valerian plant (Valeriana officinalis). Purification and NMR analyses of the VoTPS3-produced terpene, and characterization of the VoTPS3 enzyme confirmed that VoTPS3 synthesizes (-)-drimenol. In feeding assays, possible reaction intermediates, farnesol and drimenyl diphosphate, could not be converted to drimenol, suggesting that the intermediate remains tightly bound to VoTPS3 during catalysis. A mechanistic consideration of (-)-drimenol synthesis suggests that drimenol synthase is likely to use a protonation-initiated cyclization, which is rare for sesquiterpene synthases. VoTPS3 can be used to produce (-)-drimenol, from which useful drimane-type terpenes can be synthesized.
The Effects of Arcing Ground Faults on Low-Voltage System Design (1972)

Recurring reports of arcing ground fault burndowns have generated a considerable amount of interest in the subject on the part of those individuals who are responsible for the design of power systems. In fact the interest is so widespread that as one consequence, article 230-95 of the 1972 edition of the National Electrical Code requires that service entrance devices of specific types be equipped with additional ground fault protection.
The long-wavelength limit of the structure factor of amorphous silicon and vitreous silica (2009)

Liquids are in thermal equilibrium and have a non-zero structure factor S(Q --> 0) = [<N(2)>-<N>(2)]/<N> = rho(0)k(B)Tchi(T) in the long-wavelength limit where rho(0) is the number density, T is the temperature, Q is the scattering vector and chi(T) is the isothermal compressibility. The first part of this result involving the number N (or density) fluctuations is a purely geometrical result and does not involve any assumptions about thermal equilibrium or ergodicity, so is obeyed by all materials. From a large computer model of amorphous silicon, local number fluctuations extrapolate to give S(0) = 0.035 +/- 0.001. The same computation on a large model of vitreous silica using only the silicon atoms and rescaling the distances gives S(0) = 0.039 +/- 0.001, which suggests that this numerical result is robust and perhaps similar for all amorphous tetrahedral networks. For vitreous silica, it is found that S(0) = 0.116 +/- 0.003, close to the experimental value of S(0) = 0.0900 +/- 0.0048 obtained recently by small-angle neutron scattering. Further experimental and modeling studies are needed to determine the relationship between the fictive temperature and structure.
Radioautographic and cytochemical ultrastructural studies of axoplasmic transport in the monkey optic nerve head. (1978)

Radioautographic and cytochemical studies were performed at the ultrastructural level on the optic nerve heads of 21 Macaca fascicularis eyes with normal, elevated, or decreased intraocular pressures (IOP). Orthograde axoplasmic transport was labeled in all eyes by intravitreal injec- tions of a tritiated amino acid (leucine or proline) from 4 hr to 6 days before sacrifice. Retro- grade axoplasmic transport was labeled in most of the same eyes by injection of horseradish peroxidase (HRP) into one or both optic tracts and/or dorsal lateral geniculate nuclei (dLGN) from 12 to 24 hr before sacrifice. Electron microscopic studies were concentrated in the lamina scleralis (LS). Tritiated leucine was confined to axons in the nerve head in both normal and pathologic eyes. In hypertensive eyes both orthograde and retrograde transport appeared blocked initially in the posterior LS, then with increasing severity of injury appeared blocked and intermixed throughout the LS. In hypertensive eyes, collections of HRP were especially prominent within peripherally lying axons in bundles in the LS and on the posterior side of glial-scleral trabeculae in the LS. Hypotensive eyes (with papilledema) had similar, but much less severe, intra-axonal alterations of morphology and also demonstrated accumulations' of HRP in the LS. The morphologic alterations and blockage of axoplasmic transport within the LS in both hypertensive and hypotensive eyes appear to have resulted from mechanical com- pression of axonal bundles.
A Functional Yeast Survival Screen of Tumor-Derived cDNA Libraries Designed to Identify Anti-Apoptotic Mammalian Oncogenes (2013)

Yeast cells can be killed upon expression of pro-apoptotic mammalian proteins. We have established a functional yeast survival screen that was used to isolate novel human anti-apoptotic genes overexpressed in treatment-resistant tumors. The screening of three different cDNA libraries prepared from metastatic melanoma, glioblastomas and leukemic blasts allowed for the identification of many yeast cell death-repressing cDNAs, including 28% of genes that are already known to inhibit apoptosis, 35% of genes upregulated in at least one tumor entity and 16% of genes described as both anti-apoptotic in function and upregulated in tumors. These results confirm the great potential of this screening tool to identify novel anti-apoptotic and tumor-relevant molecules. Three of the isolated candidate genes were further analyzed regarding their anti-apoptotic function in cell culture and their potential as a therapeutic target for molecular therapy. PAICS, an enzyme required for de novo purine biosynthesis, the long non-coding RNA MALAT1 and the MAST2 kinase are overexpressed in certain tumor entities and capable of suppressing apoptosis in human cells. Using a subcutaneous xenograft mouse model, we also demonstrated that glioblastoma tumor growth requires MAST2 expression. An additional advantage of the yeast survival screen is its universal applicability. By using various inducible pro-apoptotic killer proteins and screening the appropriate cDNA library prepared from normal or pathologic tissue of interest, the survival screen can be used to identify apoptosis inhibitors in many different systems.