gebhart/patrepeval huggingface dataset:
Genetic variants in epigenetic genes and breast cancer risk (2006)

Epigenetic events, resulting changes in gene expression capacity, are important in tumour progression, and variation in genes involved in epigenetic mechanisms might therefore be important in cancer susceptibility. To evaluate this hypothesis, we examined common variants in 12 genes coding for DNA methyltransferases (DNMT), histone acetyltransferases, histone deacetyltransferases, histone methyltrasferases and methyl-CpG binding domain proteins, for association with breast cancer in a large case-control study (N cases = 4474 and N controls = 4580). We identified 63 single nucleotide polymorphisms (SNPs) that efficiently tag all the known common variants in these genes, and are also expected to tag any unknown SNP in each gene. We found some evidence for association for six SNPs: DNMT3b-c31721t [P (2 df) = 0.007], PRDM2-c99243 t [P (2 df) = 0.03] and t105413c [P-recessive = 0.05], EHMT1-g-9441a [P (2df) = 0.05] and g41451t (P-trend = 0.04), and EHMT2-S237S [P (2df) = 0.04]. The most significant result was for DNMT3b-c31721t (P-trend = 0.124 after adjusting for multiple testing). However, there were three other results with P < 0.05. The permutation-based probability of this occurring by chance was 0.335. These significant SNPs were genotyped in 75 human cancer cell lines from different tumour types to assess if there was an association between them and six epigenetic measures. No statistically significant association was found. However, a trend was observed: homozygotes for the rare alleles of the EHMT1, EHMT2 and PRDM2 had a mean value for both trimethylation of K9 and K27 of histone H3 remarkably different to the homozygotes for the common alleles. Thus, these preliminary observations suggest the possible existence of a functional consequence of harbouring these genetic variants in histone methyltransferases, and warrant the design of larger epidemiological and biochemical studies to establish the true meaning of these findings.
Online machine learning for cloud resource provisioning of microservice backend systems (2017)

Microservices are bundled and generating traffic on the backend systems that need to scale on demand. When microservices generate variant and unexpected, the challenge is to classify the workload on the backend systems and adjust the scaling policy to reflect the resource demand timely and accurately. In this paper, we propose a microservice architecture that encapsulates functions of monitoring metrics and learning workload pattern. Then this service architecture is used to predict the future workload for decision making on resource provisioning. We deploy two machine learning algorithms and predict the resource demand of the backend systems of microservices emulated by a Netflix workload benchmark application. This service architecture presents an integrated solution of implementing self-managing cloud data services under variant workload.
Polarity reversal correction for elastic reverse time migration (2012)

ABSTRACT Polarity reversals in PS and SP images of elastic reverse time migration will cause destructive interference in the final stacked results, which may lead to an erroneous interpretation. We derive a polarity reversal correction based on an analysis of the polarity distribution of PS and SP images. The key aspect for a polarity reversal correction is the polarity distribution of the S-wave component. Polarity reversal correction methods can be performed according to the actual patterns of the polarity distribution in gathers. For the 2D isotropic case, a sign factor is introduced to represent the polarity distribution of the S-wave component; this sign factor can be computed using the energy flux density vector. We present a procedure to correct the polarity reversal for elastic reverse time migration in the common-shot domain. First, the sign factor is computed during the wavefield reconstruction for every imaging point. Then, the polarity reversal is corrected by multiplying the PS and SP images with the sign factor at every time step when an elastic imaging condition is applied. We also design a filter algorithm for the sign factor to improve its consistency along an event and thereby to diminish the impact of the inaccuracy of the energy flux density vector and to improve the imaging results. Numerical examples have shown that the polarity reversal correction procedure works and that the sign filter algorithm successfully eliminates the consequences of the inaccuracy of the energy flux density vector. The quality of the migration events is effectively improved.
Design and Concept of an Energy System Based on Renewable Sources for Greenhouse Sustainable Agriculture (2018)

Bio-organic greenhouses that are based on alternative resources for producing heat and electricity stand out as an efficient option for the sustainable development of agriculture, thus ensuring good growth and development of plants in all seasons, especially during the cold season. Greenhouses can be used with maximum efficiency in various agricultural lands, providing ideal conditions of temperature and humidity for short-term plant growing, thereby increasing the local production of fruit and vegetables. This paper presents the development of a durable greenhouse concept that is based on complex energy system integrating fuel cells and solar panels. Approaching this innovative concept encountered a major problem in terms of local implementation of this type of greenhouses because of the difficulty in providing electrical and thermal energy from conventional sources to ensure an optimal climate for plant growing. The project result consists in the design and implementation of a sustainable greenhouse energy system that is based on fuel cells and solar panels.
Kinesin superfamily protein-derived peptides with the ability to induce glioma-reactive cytotoxic T lymphocytes in human leukocyte antigen-A24+ glioma patients (2007)

One promising modality in the treatment of malignant glioma is specific immunotherapy. However, this modality requires information about target antigens and their epitope peptides that are recognized by T cells. In this study, we searched for new target candidates in specific immunotherapy for malignant glioma by utilizing cDNA microarray technology to compare gene expressions in malignant glioma tissues to those in benign glioma and a panel of normal tissues. The selected genes included three members of the kinesin superfamily proteins (KIFs): KIF1C, KIF3C, and KIF21B. RT-PCR showed that these three genes were expressed in the majority of glioma cell lines. These antigen-derived 25 peptides, which had the ability to bind to human leukocyte antigen (HLA)-A24 molecules, were first screened for their ability to be recognized by the immunoglobulin G of glioma patients, and then tested for their potential to induce peptide-specific and glioma-reactive cytotoxic T lymphocytes (CTLs) from the peripheral blood mononuclear cells of HLA-A24+ glioma patients. The results showed that the KIF1C149-158 and KIF3C512-520 peptides efficiently induced HLA-A24-restricted and glioma-reactive CD8+ T cells. These results suggest the existence of KIF-reactive CTL precursors in glioma patients, and should facilitate the development of specific immunotherapies for malignant glioma.
Cyclic Vector Multiplication Algorithm Based on a Special Class of Gauss Period Normal Basis (2007)

This paper proposes a multiplication algorithm for , which can be efficiently applied to many pairs of characteristic p and extension degree m except for the case that 8p divides m(p–1). It uses a special class of type-⟨k, m⟩ Gauss period normal bases. This algorithm has several advantages: it is easily parallelized; Frobenius mapping is easily carried out since its basis is a normal basis; its calculation cost is clearly given; and it is sufficiently practical and useful when parameters k and m are small.
Retinoic acid induces cholinergic differentiation of cultured newborn rat sympathetic neurons (1993)

Many studies provide evidence that retinoic acid (RA), an endogenous derivative of vitamin A, plays a role in the development of the nervous system. We now report that RA controls the neurotransmitter phenotype of post-mitotic rat sympathetic neurons in cell culture. RA added to the culture medium increased the specific activity of choline acetyltransferase (ChAT) and the level of acetylcholine (ACh). Concomitantly, RA reduced the specific activities of two catecholamine synthetic enzymes, tyrosine hydroxylase (TH) and dopamine beta-hydroxylase (DBH) and the level of norepinephrine (NE). After a 2 week treatment with 5 microM RA, ChAT was increased by 5-10 fold, whereas TH and DBH were decreased by 10-15 fold and 2-3 fold, respectively, as compared to sympathetic neurons grown in the absence of RA. The modulation of the activity of the three enzymes was dose-dependent and followed a similar time course. The decrease of TH expression was demonstrated to be due to a decreased number of TH molecules.
siRNA-Like Double-Stranded RNAs Are Specifically Protected Against Degradation in Human Cell Extract (2011)

RNA interference (RNAi) is a set of intracellular pathways in eukaryotes that controls both exogenous and endogenous gene expression. The power of RNAi to knock down (silence) any gene of interest by the introduction of synthetic small-interfering (si)RNAs has afforded powerful insight into biological function through reverse genetic approaches and has borne a new field of gene therapeutics. A number of questions are outstanding concerning the potency of siRNAs, necessitating an understanding of how short double-stranded RNAs are processed by the cell. Recent work suggests unmodified siRNAs are protected in the intracellular environment, although the mechanism of protection still remains unclear. We have developed a set of doubly-fluorophore labeled RNAs (more precisely, RNA/DNA chimeras) to probe in real-time the stability of siRNAs and related molecules by fluorescence resonance energy transfer (FRET). We find that these RNA probes are substrates for relevant cellular degradative processes, including the RNase H1 mediated degradation of an DNA/RNA hybrid and Dicer-mediated cleavage of a 24-nucleotide (per strand) double-stranded RNA. In addition, we find that 21- and 24-nucleotide double-stranded RNAs are relatively protected in human cytosolic cell extract, but less so in blood serum, whereas an 18-nucleotide double-stranded RNA is less protected in both fluids. These results suggest that RNAi effector RNAs are specifically protected in the cellular environment and may provide an explanation for recent results showing that unmodified siRNAs in cells persist intact for extended periods of time.
Failure of Translation of Human Adenovirus mRNA in Murine Cancer Cells Can be Partially Overcome by L4-100K Expression In Vitro and In Vivo (2012)

Adaptive immune responses may be vital in the overall efficacy of oncolytic viruses in human malignancies. However, immune responses to oncolytic adenoviruses are poorly understood because these viruses lack activity in murine cells, which precludes evaluation in immunocompetent murine cancer models. We have evaluated human adenovirus activity in murine cells. We show that a panel of murine carcinoma cells, including CMT64, MOVCAR7, and MOSEC/ID8, can readily be infected with human adenovirus. These cells also support viral gene transcription, messenger RNA (mRNA) processing, and genome replication. However, there is a profound failure of adenovirus protein synthesis, especially late structural proteins, both in vitro and in vivo, with reduced loading of late mRNA onto ribosomes. Our data also show that in trans expression of the nonstructural late protein L4-100K increases both the amount of viral mRNA on ribosomes and the synthesis of late proteins, accompanied by reduced phosphorylation of eIF2α and improved anticancer efficacy. These results suggest that murine models that support human adenovirus replication could be generated, thus allowing evaluation of human adenoviruses in immunocompetent mice.
Are Mesenchymal Cells Indeed Pluripotent Stem Cells or Just Stromal Cells? OCT-4 and VSELs Biology Has Led to Better Understanding (2013)

Stem cells have excited researchers because of their potential to regenerate. However, which stem cells will be the best candidate for regenerative medicine remains an enigma. Compared to pluripotent stem cells with associated risks of immune rejection and teratoma formation, adult stem cells especially the mesenchymal stem cells (MSCs) are hyped to be a suitable alternate since they also exhibit pluripotent properties. This review shows that there is a subpopulation of pluripotent very small embryonic-like stem cells (VSELs) among MSCs culture. The two populations differ from each other in expression pattern of OCT-4. VSELs exhibit nuclear OCT-4A, whereas the MSCs have cytoplasmic OCT-4B, similar to our earlier findings in testis and ovary. Pluripotent VSELs with nuclear OCT-4A exist in various adult body organs, and the immediate progenitors express cytoplasmic OCT-4B which is eventually lost as the cell differentiates further. To conclude it is essential to discriminate between nuclear and cytoplasmic OCT-4 expression and also to acknowledge the presence of VSELs.
Copper-mediated C–H trifluoromethylation of quinones (2013)

Quinones undergo copper-mediated C-H trifluoromethylation reactions using a hypervalent iodine reagent. The reactions have a broad synthetic scope involving naphtho, alkyl, chloro and methoxy quinones.
Relation between genomic and capsid structures in RNA viruses (1986)

We described a new computer program for calculation of RNA secondary structure. Calculation of 20 viral RNAs with this program showed that genomes of the icosahedral capsid viruses had higher folding probabilities than those of the helical capsid viruses. As this explains virus assembly quite well, the information of capsid structure must be imprinted not only in the capsid protein structures but also in the base sequence of the whole genome. We compared folding probability of the original sequence with that of the random sequence in which base composition was the same as the original. All the actual genomes of RNA viruses were more folded than the corresponding random sequences, even though most transcripts of chromosomal genes tended to be less folded. The data can be related to encapsidation of viral genomes. It was thus suggested that there exists a relation between actual sequences and random sequences with the same base ratios, and that the base ratio itself has some evolutional meaning.
Perfect Latin squares and parallel array access (1989)

A new nonlinear skewing scheme is proposed for parallel array access. We introduce a new Latin square(perfect Latin square) which has several properties useful for parallel array access. A sufficient condition for the existence of perfect Latin squares and a simple construction method for perfect Latin squares are presented. The resulting skewing scheme provides conflict free access to various subsets of an N x N array using N memory modules. When the number of memory modules is an even power of two, address generation is performed in constant time using a simple circuit. This scheme is the first memory scheme that achieves constant time access to rows, columns, diagonals, and N1/2 x N1/2 subarrays of an N x N array using the minimum number of memory modules.
Photoageing: mechanism, prevention and therapy (2007)

Photoageing is the superposition of chronic ultraviolet (UV)-induced damage on intrinsic ageing and accounts for most age-associated changes in skin appearance. It is triggered by receptor-initiated signalling, mitochondrial damage, protein oxidation and telomere-based DNA damage responses. Photodamaged skin displays variable epidermal thickness, dermal elastosis, decreased/fragmented collagen, increased matrix-degrading metalloproteinases, inflammatory infiltrates and vessel ectasia. The development of cosmetically pleasing sunscreens that protect against both UVA and UVB irradiation as well as products such as tretinoin that antagonize the UV signalling pathways leading to photoageing are major steps forward in preventing and reversing photoageing. Improved understanding of the skin's innate UV protective mechanisms has also given rise to several novel treatment concepts that promise to revolutionize this field within the coming decade. Such advances should not only allow for the improved appearance of skin in middle age and beyond, but also greatly reduce the accompanying burden of skin cancer.
Live Migration of Virtual Machines in Cloud Environment using Prediction of CPU Usage (2015)

The virtualization gives the power of partitioning the physical host in to multiple virtual machines. We can manage the number of active host and their power consumption by migrating the virtual machines according to their resource requirement and current status on that particular host. Service level agreement is the main thing and essential one for giving the reliable quality of service between customers and the data centers. Live migration of the virtual machines managing the over load and under loaded host which gives the ability of dynamic resource allocation on another host. Dynamic virtual machine consolidation and switching off the idle host allow data centers to minimize the resource and power consumption. The proposed technique will provide the ability of dynamic virtual machine consolidation using adaptive utilization threshold based o CPU usage prediction which can easily manage the high level of SLA and reduces the number of VM migrations in between the host. The validation of the proposed technique on multiple workload traces of the Planet lab servers.
Different Sequences Show Similar Quaternary Interaction Stabilities in Prohead Viral RNA Self-assembly (2011)

Prohead RNA (pRNA) is an essential component of the self-assembling ϕ29 bacteriophage DNA packaging motor. Different related species of bacteriophage share only 12% similarity in pRNA sequences. The secondary structure for pRNA is conserved, however. In this study, we present evidence for self-assembly in different pRNA sequences and new measurements of the energetics for the quaternary interactions in pRNA dimers and trimers. The energetics for self-assembly in different pRNA sequences are similar despite very different sequences in the loop-loop interactions. The architecture surrounding the interlocking loops contributes to the stability of the pRNA quaternary interactions, and sequence variation outside the interlocking loops may counterbalance the changes in the loop sequences. Thus, the evolutionary divergence of pRNA sequences maintains not only conservation of function and secondary structure but also stabilities of quaternary interactions. The self-assembly of pRNA can be fine-tuned with variations in magnesium chloride, sodium chloride, temperature, and concentration. The ability to control pRNA self-assembly holds promise for the development of nanoparticle therapeutic applications for this biological molecule. The pRNA system is well suited for future studies to further understand the energetics of RNA tertiary and quaternary interactions, which can provide insight into larger biological assemblies such as viruses and biomolecular motors.
Direct Perfluorination of K<sub>2</sub>B<sub>12</sub>H<sub>12</sub> in Acetonitrile Occurs at the Gas Bubble−Solution Interface and Is Inhibited by HF. Experimental and DFT Study of Inhibition by Protic Acids and Soft, Polarizable Anions (2009)

During the optimization of the F(2) perfluorination of K(2)B(12)H(12) in acetonitrile with continuous bubbling of 20/80 F(2)/N(2), it was discovered that (i) HF and other protic acids inhibit each of the 12 fluorination steps (in contradiction to recently published findings) and (ii) the fluorinations appear to take place at the gas bubble-solution interface. Experimental results and DFT calculations suggest that these two phenomena are related by the relative propensities of the various B(12)H(12-x)F(x)(2-) anions to partition from bulk solution to the interface (i.e., their relative polarizabilities or softness; 0 <or= x <or= 12). Relative to the previously reported syntheses of K(2)B(12)F(12) or Cs(2)B(12)F(12), the new optimized procedure has the following advantages: (i) the scale was increased 10-fold without sacrificing yield (74% for K(2)B(12)F(12), 76% for Cs(2)B(12)F(12)) or purity (99.5+%); (ii) the reaction/purification time was decreased from ca. 1 week to 2 days; and (iii) the solvent was changed from anhydrous HF to acetonitrile, allowing ordinary glassware to be used. The anhydrous salt Cs(2)B(12)F(12) was found to be thermally stable up to 600 degrees C.
Remote execution of HAVi applications on Internet-enabled devices (2002)

This paper describes an approach for extending the HAVi home network beyond its IEEE1394 physical layer by allowing remote access to it from any Internet-enabled device.
Refactoring sequential Java code for concurrency via concurrent libraries (2009)

Parallelizing existing sequential programs to run efficiently on multicores is hard. The Java 5 package java.util.concurrent (j.u.c.) supports writing concurrent programs: much of the complexity of writing thread-safe and scalable programs is hidden in the library. To use this package, programmers still need to reengineer existing code. This is tedious because it requires changing many lines of code, is error-prone because programmers can use the wrong APIs, and is omission-prone because programmers can miss opportunities to use the enhanced APIs. This paper presents our tool, Concurrencer, that enables programmers to refactor sequential code into parallel code that uses three j.u.c. concurrent utilities. Concurrencer does not require any program annotations. Its transformations span multiple, non-adjacent, program statements. A find-and-replace tool can not perform such transformations, which require program analysis. Empirical evaluation shows that concurrencer refactors code effectively: concurrencer correctly identifies and applies transformations that some open-source developers overlooked, and the converted code exhibits good speedup.
A case report of pelvic lipomatosis with severe rectal stenosis. (1990)

Pelvic lipomatosisの1例を経験した. 症例: 32歳, 女性. 主訴: 便秘. 肛門縁より10cm口側に狭窄部下端を触知し狭窄部より口側への直腸鏡の挿入は不可能であった. 粘膜面に不整はなく, 生検では正常の直腸粘膜であった. 膀胱鏡検査では異常を認めなかった. 注腸造影でRa, Rsに長さ約10cmの全周性の高度狭窄を認めたが明かな偏位は認めなかった. Computed tomographyとmagneticresonaunce imageでは腫大した子宮と左卵巣に低吸収域を認め, 直腸周囲に厚さ約2cmの低吸収域を認めた. 腹部エコーにて子宮筋腫と両側卵巣嚢胞を認めたが直腸狭窄と関係ないと判断した. 手術所見: 直腸, 子宮, 卵巣は強く癒着しており直腸低位前方切除, 単純子宮全摘, 両側付属器摘除術を行った. 病理所見: 直腸粘膜に著変なく直腸周囲には厚い脂肪が認められた. この脂肪は正常の脂肪組織であり, 悪性所見はなく線維化や炎症所見は乏しかった.
Direct‐Write Fabrication of Pb(Nb,Zr,Ti)O <sub>3</sub> Devices: Influence of Paste Rheology on Print Morphology and Component Properties (2001)

Lead niobium zirconate titanate (PNZT) pastes with tailored rheological properties have been developed for direct‐write fabrication of thick‐film capacitor elements in highly integrated, multifunctional electroceramic devices. Such pastes exhibited pseudoplastic behavior with a low shear apparent viscosity of roughly 1 × 10 6 cP. On aging, the degree of shear thinning and the low shear apparent viscosity decreased. Pastes prepared from as‐received powders attained printable, steady‐state viscosities of ∼2 × 10 5 cP after 50 days of aging. In contrast, pastes prepared from dispersant‐coated powders showed no measurable rheological changes after 1 day of aging. Square elements were patterned on dense alumina substrates or Teflon sheets. Leveling behavior as a function of time for single line prints, and the resulting surface topographies of dried PNZT films were measured by laser profilometry. PNZT layers sintered at varying temperatures between 950° and 1050°C for 5 h in either air or a lead‐rich atmosphere yielded porous microstructures as revealed by scanning electron microscopy (SEM). Such layers exhibited dielectric constants ( K ) of 1400–1570 at 1 kHz with dissipation factors ( D ) of less than 4.1%.