gebhart/patrepeval huggingface dataset:
Integrative Analysis Identifies Genetic Variants Associated With Autoimmune Diseases Affecting Putative MicroRNA Binding Sites (2018)

Genome-wide and fine mapping studies have shown that more than 90% of genetic variants associated with autoimmune diseases (AID) are located in non-coding regions of the human genome and especially in regulatory sequences, including microRNAs (miRNA) target sites. MiRNAs are small endogenous noncoding RNAs that modulate gene expression at the post-transcriptional level. Single nucleotide polymorphisms (SNPs) located within the 3' untranslated region of their target mRNAs (miRSNP) can alter miRNA binding sites. Yet, little is known about their effect on regulation by miRNA and the consequences for AID. Conversely, it is well known that two or more AID may share part of their genetic background. Here, we hypothesized that miRSNPs could be associated with more than one AID. To identify miRSNPs associated with AID, we integrated results from three different prediction tools (Polymirts, miRSNP, and miRSNPscore) using a naïve Bayes classifier approach to identify miRSNPs predicted to affect binding sites of miRNAs. Further, to detect miRSNPs associated with two or more AID, we integrated predictions with summary statistics from 12 AID studies. In addition, to prioritize miRSNPs, miRNAs and AID-associated target genes, we used public expression quantitative trait locus (eQTL) data and mRNA-seq and small RNA-seq data. We identified 34 miRNSPs associated with at least two AID. Furthermore, we found 86 miRNAs predicted to target 18 of the associated gene's mRNAs. Our integrative approach revealed new insights into miRNAs and AID associated target genes. Thus, it helped to prioritize AID noncoding risk SNPs that might be involved in the causal mechanisms, providing valuable information for further functional studies.
Elucidating the Sole Contribution from Electromagnetic Near‐Fields in Plasmon‐Enhanced Cu<sub>2</sub>O Photocathodes (2015)

Despite many promising reports of plasmon‐enhanced photocatalysis, the inability to identify the individual contributions from multiple enhancement mechanisms has delayed the development of general design rules for engineering efficient plasmonic photocatalysts. Herein, a plasmonic photocathode comprised of Au@SiO 2 (core@shell) nanoparticles embedded within a Cu 2 O nanowire network is constructed to exclusively examine the contribution from one such mechanism: electromagnetic near‐field enhancement. The influence of the local electromagnetic field intensity is correlated with the overall light‐harvesting efficiency of the device through variation of the SiO 2 shell thickness (5–22 nm) to systematically tailor the distance between the plasmonic Au nanoparticles and the Cu 2 O nanowires. A threefold increase in device photocurrent is achieved upon integrating the Au@SiO 2 nanoparticles into the Cu 2 O nanowire network, further enabling a 40% reduction in semiconductor film thickness while maintaining photocathode performance. Photoelectrochemical results are further correlated with photoluminescence studies and optical simulations to confirm that the near‐field enhancement is the sole mechanism responsible for increased light absorption in the plasmonic photocathode.
Electrochemical Intercalation of Tetraethylammonium Tetrafluoroborate into KOH-Treated Carbon Consisting of Multi-Graphene Sheets for an Electric Double Layer Capacitor (1998)

Carbons produced by calcination at700-850of the materials derived from petroleum cokes and pitches consist of we11-grown graphite-like layers with an average intcr-layer distance of doo2 035-0365nm Additional heat treatment of the carbon with KOH at800can provide the expansion of inter-laycr distance up to036-0385nm and the latent ability of electrhemical intercalation of Et4Nand BE in PC into the multi-graphenc laycrsUsing the KOH-treated carbons as electrodes of EDLCa high-density cnergy storc such as25-30Fcm30f dry total electrodes operatng at35-4O V is available when the depth of the ccll is rigidly restricted
Greenbottle (<i>Lucilia sericata</i>) Larval Secretions Delivered from a Prototype Hydrogel Wound Dressing Accelerate the Closure of Model Wounds (2006)

The resurgence of larval biotherapy as a debridement tool in wound management has been accompanied by several clinical reports highlighting concomitant tissue regeneration. Studies employing in vitro cell motility assays have found that purified excretory/secretory (ES) products from Greenbottle larvae (blowfly, Lucilia sericata) are motogenic for human dermal fibroblasts when used as a supplement in culture media. The objective of the present study was to determine whether ES delivered using a prototype hydrogel wound dressing induced similar motogenic effects on fibroblastic (3T3) and epithelial cells (HaCaTs) comprising a scratched-monolayer wound model. Quantitative analysis by MTT assay failed to detect significant mitogenic effects of ES on either cell type. Quantitative image analysis revealed that ES exposure markedly accelerated wound closure through a motogenic effect on both fibroblasts and keratinocytes. Quantitative histochemical analysis detected significantly higher phosphotyrosine (pTyr) expression in ES-exposed cell cultures than in controls; moreover immunocytochemistry revealed conspicuously raised levels of pTyr expression in cells located at the wound margin. By attenuation with a panel of enzyme inhibitors these effects were attributed to the protease components of ES. The present results suggest that controlled delivery of ES as a follow-up to maggot debridement therapy may be an effective therapeutic option for stimulation of tissue regeneration in wound management.
Ultra-localized single cell electroporation using silicon nanowires (2012)

Analysis of cell-to-cell variation can further the understanding of intracellular processes and the role of individual cell function within a larger cell population. The ability to precisely lyse single cells can be used to release cellular components to resolve cellular heterogeneity that might be obscured when whole populations are examined. We report a method to position and lyse individual cells on silicon nanowire and nanoribbon biological field effect transistors. In this study, HT-29 cancer cells were positioned on top of transistors by manipulating magnetic beads using external magnetic fields. Ultra-rapid cell lysis was subsequently performed by applying 600-900 mV(pp) at 10 MHz for as little as 2 ms across the transistor channel and the bulk substrate. We show that the fringing electric field at the device surface disrupts the cell membrane, leading to lysis from irreversible electroporation. This methodology allows rapid and simple single cell lysis and analysis with potential applications in medical diagnostics, proteome analysis and developmental biology studies.
Effects of diets enriched in n−6 or n−3 fatty acids on cholesterol metabolism in older rats chronically fed a cholesterol‐enriched diet (2001)

Hypocholesterolemic effects in older animals after long-term feeding are unknown. Therefore, aged rats (24 wk of age) fed a conventional diet were shifted to diets containing 10% perilla oil [PEO; oleic acid + linoleic acid + alpha-linolenic acid; n-6/n-3, 0.3; polyunsaturated fatty acid/saturated fatty acid (P/S), 9.6], borage oil [oleic acid + linoleic acid + alpha-linolenic acid; n-6/n-3, 15.1; P/S, 5.3], evening primrose oil (EPO; linoleic acid + gamma-linolenic acid; P/S, 10.5), mixed oil (MIO; oleic acid + linoleic acid + gamma-linolenic acid + alpha-linolenic acid; n-6/n-3, 1.7; P/S, 6.7), or palm oil (PLO; palmitic acid + oleic acid + linoleic acid; n-6/n-3, 25.3; P/S, 0.2) with 0.5% cholesterol for 15 wk in this experiment. There were no significant differences in the food intake and body weight gain among the groups. The liver weight in the PEO (n-6/n-3, 0.3) group was significantly higher than those of other groups in aged rats. The serum total cholesterol and very low density lipoprotein (VLDL) + intermediate density lipoprotein (IDL) + low density lipoprotein (LDL)-cholesterol concentrations of the PLO (25.3) group were consistently higher than those in the other groups. The serum high density lipoprotein cholesterol concentrations of the PEO (0.3) and EPO groups were significantly lower than in the other groups at the end of the 15-wk feeding period. The liver cholesterol concentration of the PLO (25.3) group was significantly higher than those of other groups. There were no significant differences in the hepatic LDL receptor mRNA level among the groups. Hepatic apolipoprotein (apo) B mRNA levels were not affected by the experimental conditions. The fecal neutral steroid excretion of the PLO (25.3) group tended to be low compared to the other groups. The results of this study demonstrate that both n-6 fatty acid and n-3 fatty acids such as gamma-linolenic acid and alpha-linolenic acid inhibit the increase of serum total cholesterol and VLDL + IDL + LDL-cholesterol concentrations of aged rats in the presence of excess cholesterol in the diet compared with dietary saturated fatty acid.
Las huellas de Mutis y Humboldt en la Ciencia y Educación Colombianas. (1999)

Es un estudio de las ideas cientificas y educativas, alrededor de! pensamiento y la accion de los cientificos JOSE CELESTINO MUTIS, fundador y director de la Expedicion Botanica en el Nuevo Reino de Granada, y de las observaciones y estudios que realizo el cientifico ALEJANDRO DE HUMBOLDT en su viaje que realizo a esta region en el ano 1801. Corresponde a los anos de penetracion de la Ilustracion, el Racionalismo y el Naturalismo; y ios cambios en la educacion neogranadina, de gran influencia en la generacion que planeo y realizo ia revolucion de Independencia.

Se estudian los cambios en la educacion neogranadina con el Plan de Estudios de Moreno y Escanden; las polemicas entre los partidarios de la Tradicion y los pensadores de la Ilustracion; la obra cientifica de Mutis y la Expedicion Botanica; las ideas europeas sobre ia inferioridad de America y las Expediciones Cientificas; y los aportes de los Viajeros, entre ellos el sabio Humboldt. Se estudian las maravillas neogranadinas; los volcanes de aire de Turbaco, el salto del Tequendama, el Puente natura! de Icononzo, el paso por el Quindio y otros.

Con sus estudios. Mutis y Humboldt se convirtieron en los descubridores cientificos de las tierras americanas. Sus ideas repercutieron en ia Educacion, con una nueva filosofia de nacionalidad, libertad e identidad nacional.

Fuentes: presenta documentos historicos de Mutis y la Expedicion Botanica y los estudios y correspondencia del Sabio Humboldt sobre el Nuevo Reino de Granada.
CARBON ASSIMILATION BY <i>PSEUDOMONAS OXALATICUS</i> (OX 1). 7. DECARBOXYLATION OF OXALYL-COENZYME A TO FORMYL-COENZYME A (1963)

Oxalyl-coenzyme A has been implicated in the decarboxylation of oxalate in an oxalate-grown bacterium by Jakoby, Ohmura & Hayaishi (1956), who suggested this series of reactions:Quayle, Keech & Taylor (1961) concluded that de- carboxylation of oxalate by crude extracts of oxalate-grown Pseudomonas oxalaticus followed reactions (1)-( 3) except that acetyl-CoA is replaced in (1) by succinyl-CoA and, in addition, a trans- ferase is present capable of transferring the CoA grouping from formyl-CoA to either succinate or oxalate.Koch & Jaenicke (1962) also refer to decarboxylation of oxalate by extracts of a species of Pseudomonas in which phosphate, CoA and thiamine pyrophosphate were cofactors for the reaction.This paper records a study of the decarboxylation of oxalyl-CoA and oxalate in crude extracts of P. oxalaticus, and the purification from such extracts of an enzyme that catalyses reaction (2).Part of this work has been communicated to The Biochemical Society (Quayle, 1963b). MATERIALS AND METHODSAbbreviation.TPP, Thiamine pyrophosphate.Special chemicals.Oxalyl-CoA was prepared by thiol ester interchange between CoA and thiocresyl hydrogen oxalate and was assayed by the use of oxalyl-CoA reductase (Quayle, 1963a).[14C2]0xalyl-[12C]CoA was prepared by a similar method from thiocresyl hydrogen [l"C2]oxalate.The latter compound was prepared from [14C2]oxalyl chloride according to the method of Stolle (1914).Succinyl-CoA was prepared by the reaction of CoA with succinic anhydride (Simon, 1957).Malonyl-CoAwasgivenbyProfessorF.Lynen (Max Planck
The relationship among persecutory ideation, other-consciousness, and self-consciousness. (1999)

本研究では,一般青年に見られる被害妄想的心性を検討するため,被害妄想的心性を測定する尺度を新たに作成した.被験者は85名の大学生と176名の専門学校生(男子70名,女子190名,不明1名)であった.被害妄想的心性,他者意識,および自己意識からなる質問紙に回答を求めた.被害妄想的心性尺度の因子分析を行った結果,自己関連づけと猜疑心の2因子が抽出された.重回帰分析の結果では,猜疑心は私的自己意識との関連が示されたのに対し,自己関連づけは他者意識および公的自己意識との関連が示された.これらの結果から,被害妄想的心性は自己関連づけと猜疑心の質的に異なる2側面からとらえられることが示された.また,自己関連づけについては,他者に対する関心のあらわれであることが示唆された.
Interim PET-CT in the management of diffuse large B-cell lymphoma. (2012)

Once the diagnosis of diffuse large B-cell lymphoma has been established, physicians and patients would like to know if a given treatment regimen is likely to succeed-if the patient can be cured or if at least a durable remission is achievable. This desire has lead to efforts to use interim positron emission tomography (PET) scanning as part of risk-adapted therapeutic clinical trials. In general, these studies use a variable number of doxorubicin-based induction cycles with rituximab, followed by the interim PET. If the test is negative, treatment is continued, but if it is positive, therapy is changed to treatment that concludes with autologous stem cell transplantation. Results of studies for interim PET have yielded mixed and confusing results, with high negative predictive value but positive predictive value ranging from 20%-80%. To use interim PET scanning effectively, clinicians need simple (positive or negative) criteria that are easy to interpret, reproducible, and have a high positive and negative predictive value so that we can be certain that by not changing therapy if the test is positive, we are not doing the patient a disservice.
Highly Efficient Electron‐Transporting/Injecting and Thermally Stable Naphthyridines for Organic Electrophosphorescent Devices (2012)

Abstract A series of 1,8‐naphthyridine derivatives is synthesized and their electron‐transporting/injecting (ET/EI) properties are investigated via a multilayered electrophosphorescent organic light‐emitting device (OLED) using fac ‐tris(2‐phenylpyridine)iridium [Ir(ppy) 3 ] as a green phosphorescent emitter doped into a 4,4′‐ N , N ′‐dicarbazolebiphenyl (CBP) host with 4,4′‐bis[ N ‐(1‐naphthyl)‐ N ‐phenylamino]biphenyl ( a ‐NPD) as the hole‐transporting layer, and poly(arylene ether sulfone) containing tetraphenylbenzidine (TPDPES) doped with tris(4‐bromophenyl)ammonium hexachloroantimonate (TBPAH) as the hole‐injecting layer. The turn‐on voltage of the device is 2.5 V using 2,7‐bis[3‐(2‐phenyl)‐1,8‐naphthyridinyl]‐9,9‐dimethylfluorene (DNPF), lower than that of 3.0 V for the device using a conventional ET material. The maximum current efficiency (CE) and power efficiency (PE) of the DNPF device are much higher than those of a conventional device. With the aid of a hole‐blocking (HB) and exciton‐blocking layer of bathocuproine (BCP), 13.2–13.7% of the maximum external quantum efficiency (EQE) and a maximum PE of 50.2–54.5 lm W −1 are obtained using the naphthyridine derivatives; these values are comparable with or even higher than the 13.6% for conventional ET material. The naphthyridine derivatives show high thermal stabilities, glass‐transition temperatures much higher than that of aluminum(III) bis(2‐methyl‐8‐quinolinato)‐4‐phenylphenolate (BAlq), and decomposition temperatures of 510–518 °C, comparable to or even higher than those of Alq 3 .
Phylogenetic analysis based on mitochondrial COI gene sequences in Thrips tabaci Lindeman (Thysanoptera: Thripidae) in relation to reproductive forms and geographic distribution (2007)

Thrips tabaci Lindeman is an extensively distributed pest insect that injures a wide range of crops. To investigate the intra-specific genetic diversity of this species, we analyzed an 810 bp region of the mitochondrial cytochrome oxidase gene subunit I (COI). Eight populations from six foreign countries and 18 Japanese populations were tested, and 17 different haplotypes were identified. Apparent differences were found between arrhenotokous and thelytokous strains in their COI sequences. A phylogenetic tree of the COI gene shows two distinct groups. We assume that these two groups correspond respectively to the arrhenotokous strain and the thelytokous strain. Japanese thelytokous types consisted of five haplotypes. Two haplotypes were identified from problematic populations in terms of the greater amount of damage they caused and the development of insecticide resistance. Both haplotypes were also found overseas, suggesting that some strains from overseas may have caused the above-mentioned problems in Japan.
Investigation of a Trimeric Hemagglutinin Stem Domain from Influenza B for a Universal Vaccine (2018)

Influenza infection occurs in as much as 5–15% of the world population, resulting in 3–5 million cases of severe illness and up to 500,000 deaths annually. According to the CDC, on average 24% of all influenza positive respiratory samples during 2001 to 2011 tested positive for Influenza B. Influenza has two main surface glycoproteins, neuraminidase (NA) and hemagglutinin (HA), HA being responsible for the binding of the virus to the host cell. Currently, seasonal influenza vaccines are produced using two strains of Influenza A and one or two strains of Influenza B viruses recommended by the World Health Organization (WHO). These vaccines are mainly targeting the head domain of the HA protein, which mutates constantly, hence the need for annual vaccine updates. The goal of this research is to develop an experimental universal vaccine against influenza B and increase our knowledge to help pave the way for finding a one-time vaccination alternative, reducing the need for a yearly flu shot. To achieve the above, protection and toxicity studies were conducted in DBA/2 mice immunized with a designed HA2 adenoviral-vectored vaccine targeting the HA stem region of influenza B. Results showed that this designed vaccine was able to confer 100% survival protection, this was supported by lower viral titer in trachea and lung tissues. Additionally, we studied the influence of CD40L as a targeting adjuvant, by analyzing its effect on the humoral and cellular immune response, where results showed that it has a significant effect by inducing a higher TH1-bias response. This research is the first report that leads us to a better understanding of the potential use of a conserved consensus HA2 sequence to induce protection against influenza B virus.
In-Vehicle Networking - Serial Communication Requirements and Directions (1986)

<div class="htmlview paragraph">In recent years the functionality of automotive systems has been improved by the introduction of real time Electronic Control Units (ECUs) for engine management, anti-lock braking, and other applications. For customer comfort and convenience, body electronics options have also increased, including electronic windows, seat control, and others. Optimization of performance requires integrating the vehicle of the 90s as a system rather than a grouping of individual modules. As a result, inter - communication between real time ECUs as well as between body electronics modules is required. By linking vehicle electronics into a network or combination of networks, a cost-effective solution which guarantees required performance and maximum flexibility may be obtained.</div> <div class="htmlview paragraph">The following features are key requirements for distributed control and networking in automobiles:</div> <div class="htmlview paragraph"> <ul class="list disc"> <li class="list-item"><div class="htmlview paragraph">Open systems flexibility</div></li> <li class="list-item"><div class="htmlview paragraph">High reliability in a noisy environment</div></li> <li class="list-item"><div class="htmlview paragraph">Reduction of cost and manufacturing complexity</div></li> <li class="list-item"><div class="htmlview paragraph">Minimum CPU burden for communication</div></li> <li class="list-item"><div class="htmlview paragraph">Maximum programmer transparency</div></li> <li class="list-item"><div class="htmlview paragraph">Guaranteed data consistency</div></li> <li class="list-item"><div class="htmlview paragraph">Short transmission times</div></li> </ul> </div> <div class="htmlview paragraph">To date, no network system that meets all of these objectives has been available. This paper examines: in-vehicle networking applications; protocol features needed to meet requirements; the need for an automotive serial communication standard; and briefly shows how the protocol designed for in-vehicle communication, Inter-Controller Area Network, meets these needs.</div>
<i>Chlamydia pneumoniae</i> in vitro and in vivo: a critical evaluation of in situ detection methods (2000)

Because antigens with an inclusion-like staining were detected only together with DNA and 16S rRNA, this type of staining pattern suggested the presence of viable bacteria. Thus, the granular staining pattern of antigens in the absence of staining for DNA and 16S is most likely caused by non-viable bacteria. In conclusion, these methods are suitable for the in situ detection of C pneumoniae and the assessment of its viability.
Hearing impairment, hearing aids, and cues for self motion (2016)

When listeners make a head rotation, they compare the speed and direction of a signal with the speed and direction of their movement. Hearing impairment is frequently co-morbid with vestibular impairment, rendering access to self-motion cues less reliable. It is associated with an increase in the minimum audible movement angle, and is also typically associated with raised thresholds in the range of frequencies in which the filtering effects of the pinna are most spatially useful for resolving front/back localization ambiguities for example. Moving a sound source as a function of the position of the listener’s head creates a front/back illusion. This illusion has been used to demonstrate that listeners with hearing impairment rely more on self-motion cues than on high frequency information. The use of hearing aids had heterogeneous effects on the task, although in no case did they return a listener to normal performance. Recordings were made of the output of hearing aids driven with a noise sequence whose level transitions were statistically controlled. Results indicated that hearing aids affect spectral cues and interaural level and temporal envelope differences. Taken together with recordings made on a rotating KEMAR manikin, this study demonstrates that hearing aids may interfere with acoustical cues for self motion.
Understanding Written Words: Phonological, Lexical, and Contextual Effects in the Cerebral Hemispheres (2012)

This chapter contains sections titled: Introduction Alternative Proposal Experiments Demonstrating That Semantic Asymmetries are Modulated by Phonological Asymmetries Conclusions References