gebhart/patrepeval huggingface dataset:
COUP-TFII Regulates Human Endometrial Stromal Genes Involved in Inflammation (2013)

Chicken ovalbumin upstream promoter-transcription factor II (COUP-TFII; NR2F2) is an orphan nuclear receptor involved in cell-fate specification, organogenesis, angiogenesis, and metabolism. Ablation of COUP-TFII in the mouse uterus causes infertility due to defects in embryo attachment and impaired uterine stromal cell decidualization. Although the function of COUP-TFII in uterine decidualization has been described in mice, its role in the human uterus remains unknown. We observed that, as in mice, COUP-TFII is robustly expressed in the endometrial stroma of healthy women, and its expression is reduced in the ectopic lesions of women with endometriosis. To interrogate the role of COUP-TFII in human endometrial function, we used a small interfering RNA-mediated loss of function approach in primary human endometrial stromal cells. Attenuation of COUP-TFII expression did not completely block decidualization; rather it had a selective effect on gene expression. To better elucidate the role of COUP-TFII in endometrial stroma cell biology, the COUP-TFII transcriptome was defined by pairing microarray comparison with chromatin immunoprecipitation followed by deep sequencing. Gene ontology analysis demonstrates that COUP-TFII regulates a subset of genes in endometrial stroma cell decidualization such as those involved in cell adhesion, angiogenesis, and inflammation. Importantly this analysis shows that COUP-TFII plays a role in controlling the expression of inflammatory cytokines. The determination that COUP-TFII plays a role in inflammation may add insight into the role of COUP-TFII in embryo implantation and in endometrial diseases such as endometriosis.
Abstract B26: OIP5-Antisense 1, a long noncoding RNA deregulated in non-small cell lung cancer (2016)

Abstract Background: Lung cancer represents an enormous health burden, representing the most common cause of cancer death worldwide. The poor therapeutic outcome is largely due to a complex molecular background as well as late stage diagnosis, with most patients presenting unresectable local tumors, or metastatic disease. While mutations of driver genes is a well-known mechanism, approximately half of all non-small cell lung cancer (NSCLC) tumors harbor no known clinically relevant oncogenic drivers, emphasizing the need to explore alternative mechanisms such as non-coding RNAs (ncRNAs). Natural antisense transcripts (NATS) are ncRNAs that are expressed from the opposite strand of coding mRNAs. These genes overlap with, and are often involved in the regulation of their sense counterparts. NATs can recruit regulatory complexes to their transcriptional locus, leading to silencing of transcription and have recently been described in cancer to silence tumor suppressor genes. NATs are quite prevalent as it is estimated that 25-40% of genes display overlapping transcription, however only a few NATs have been characterized, emphasizing the need to explore these ncRNAs in the context of NSCLC. Hypothesis: We hypothesize NATs of NSCLC-related genes are deregulated in NSCLC. Methods: We performed RNAseq and miRNAseq on a set of 65 NSCLC tumors including 36 adenocarcinomas and 29 squamous cell carcinomas as well as matched non-malignant lung tissue. A sign rank test was used to identify NATs with significantly altered expression between tumor and matched normal. Survival analysis was done using a Cox Proportional hazard model, as well as the Kaplan-Meier method. Results: We have identified a NAT of OIP5, a lung cancer oncogene required for chromatin segregation, to be significantly underexpressed, while its sense counterpart, OIP5 mRNA, is significantly overexpressed. We also find that expression of both OIP5 and OIP5-AS1 has a significant impact on 5 year survival. These findings suggest that deregulation of OIP5 through its antisense RNA may represent a novel mechanism regulating tumor phenotypes in NSCLC. Citation Format: Greg L. Stewart, Katey SS Enfield, David A. Rowbotham, Roland Hubaux, Victor Martinez, Stephen Lam, Wan Lam. OIP5-Antisense 1, a long noncoding RNA deregulated in non-small cell lung cancer. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr B26.
Synthesis and ion transport activity of oligoesters containing an environment-sensitive fluorophore (2011)

A series of oligoesters based on a rigid triphenyl-diyne core is described. The molecules were readily synthesized from key intermediates, and retained good solubility properties. One of the compounds displayed modest ion transport activity in vesicles, was capable of forming highly conducting single channels in planar bilayers and exhibited an irregular non-linear current-voltage response. All the reported molecules had minimal aqueous fluorescence while being highly fluorescent in less-polar media including lipid vesicles; their partitioning into the membrane could be monitored by a significant blue-shift and increase in fluorescence intensity, as well as a decreased extent of quenching in vesicles over that in water. The combined data indicated that the compounds are highly aggregated in aqueous solution, which limits their membrane partitioning and ion transport activity, in agreement with mechanisms proposed for other 'simple' oligoester channels.
Definition and assignment of complex data-paths suited for high throughput applications (2003)

A novel methodology is proposed for the data-path definition and assignment for high-throughput front-end audio, image, and video applications. The technique is based on the concept of the identification of application-specific units that can solve the computational bottlenecks of an algorithm in an efficient way. An algorithm for the automatic assignment of operations on these specific units is presented. A test vehicle taken from the video field demonstrates the proposed method.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Coronary artery constriction in rats affects the activation of 1 adrenergic receptors in cardiac myocytes (1994)

Objective: To determine whether α1 adrenergic receptor mediated myocyte contractility and growth are depressed acutely after non-occlusive coronary artery narrowing, the left coronary artery was constricted in rats and mechanical behaviour, cytosolic calcium, and regulation of α1 adrenergic receptors were examined in myocytes seven days later. Methods: Coronary artery stenosis was surgically induced in rats and following the estimation of global cardiac performance myocytes were enzymatically dissociated and radioligand binding studies were performed. In addition, the isotonic contractile performance, cytosolic calcium transients and noradrenaline stimulated inositol phosphate generation in myocytes were measured in the presence of WB 4101 or after chlorethylclonidine treatment. Results: Estimations of cell mechanics in vitro established that peak shortening was decreased by 36% and 18% in left and right ventricular myocytes of coronary stenosed rats. Time to peak shortening was prolonged by 29% in left and 20% in right myocytes, whereas velocity of shortening was decreased by 27% in left myocytes. These alterations were associated with increases in cell length and width, indicative of myocyte hypertrophy. In addition, coronary stenosis was accompanied by reductions in the expression of α1a and α1b receptor subtypes in myocytes α1 Adrenergic receptor density and noradrenaline stimulated phosphoinositol turnover were decreased by 30% and 34% in left myocytes. α1 Adrenergic receptor subtype mediated cytosolic calcium concentration and myocyte mechanical performance were also impaired in left myocytes only. The α1a adrenergic receptor subtype antagonist WB 4101 abolished noradrenaline stimulated inositol phosphate generation in myocytes, whereas chlorethylclonidine at large doses only partially inhibited this response. Conclusions: In conclusion, coronary narrowing leads to defects in the regulation of α1 adrenergic receptors on myocytes which are coupled with attenuation in the transmission of signals, possibly affecting mvocyte cell function and ongoing reactive cellular hypertrophy. Cardiovascular Research 1994;28:1070-1082
1.3 qm tunable quantum dot lasers (2020)

We report the first directly modulated single-mode tunable quantum dot lasers at 1.3 pm. 27-channel wavelength switching was achieved with side-mode-suppression-ratio of around 35 dB without requiring nonuniform gratings or epitaxial regrowth.
Lectin precipitation using phytohemagglutinin‐L 4 coupled to avidin–agarose for serological biomarker discovery in colorectal cancer (2008)

N-acetylglucosaminyltransferase V (GnT-V) has been reported to be upregulated in malignant cancer cells, and its targets have been sought after with regard to biomarker identification. The low capacity and high false positive rates of 2-DE gel-based lectin blots using phytohemagglutinin-L(4) (L-PHA) prompted us to develop a novel protocol for identifying GnT-V targets, in which serum proteins were subjected to immunodepletion, alkylation, and lectin precipitation using L-PHA coupled to avidin-agarose bead complexes, and tryptic digestion. Proteins captured by L-PHA conjugates were analyzed by a nano-LC-FT-ICR/LTQ MS. Here, we report 26 candidate biomarkers for colorectal cancer (CRC) that show 100% specificity and sensitivities of greater than 50%. Not only can these candidate proteins be used as analytes for validation, but the novel protocol described herein can be applied to biomarker discovery in nonCRCs.
Data from Targeted Deletion of <i>Prkar1a</i> Reveals a Role for Protein Kinase A in Mesenchymal-to-Epithelial Transition (2023)

&lt;div&gt;Abstract&lt;p&gt;Dysregulation of protein kinase A (PKA) activity, caused by loss of function mutations in &lt;i&gt;PRKAR1A&lt;/i&gt;, is known to induce tumor formation in the inherited tumor syndrome Carney complex (CNC) and is also associated with sporadic tumors of the thyroid and adrenal. We have previously shown that &lt;i&gt;Prkar1a&lt;sup&gt;+/−&lt;/sup&gt;&lt;/i&gt; mice develop schwannomas reminiscent of those seen in CNC and that similar tumors are observed in tissue-specific knockouts (KO) of &lt;i&gt;Prkar1a&lt;/i&gt; targeted to the neural crest. Within these tumors, we have previously described the presence of epithelial islands, although the nature of these structures was unclear. In this article, we report that these epithelial structures are derived from KO cells originating in the neural crest. Analysis of the mesenchymal marker vimentin revealed that this protein was markedly down-regulated not only from the epithelial islands, but also from the tumor as a whole, consistent with mesenchymal-to-epithelial transition (MET). &lt;i&gt;In vitro, Prkar1a&lt;/i&gt; null primary mouse embryonic fibroblasts, which display constitutive PKA signaling, also showed evidence for MET, with a loss of vimentin and up-regulation of the epithelial marker E-cadherin. Reduction of vimentin protein occurred at the posttranslational level and was rescued by proteasomal inhibition. Finally, this down-regulation of vimentin was recapitulated in the adrenal nodules of CNC patients, confirming an unexpected and previously unrecognized role for PKA in MET. [Cancer Res 2008;68(8):2671–7]&lt;/p&gt;&lt;/div&gt;
At least two mutant alleles of ornithine delta-aminotransferase cause gyrate atrophy of the choroid and retina in Finns. (1989)

Gyrate atrophy of the choroid and retina (GA) is an inherited chorioretinal degeneration caused by deficiency of ornithine delta-aminotransferase (OAT; L-ornithine: 2-oxo-acid aminotransferase; EC 2.6.1.13). GA is one of the "Finnish genetic diseases," a group of several rare monogenic disorders that occur with increased frequency in the Finnish population. Using a combination of RNase A protection, genomic cloning, and polymerase chain reaction amplification of genomic DNA, we found one of two missense mutant OAT alleles to be present in each of 16 Finnish GA pedigrees. The first mutation R180T, in which arginine-180 is replaced by threonine, was present in homozygous form in patients from two pedigrees. The second mutation L402P, in which leucine-402 is replaced by proline, was present in homozygous form in patients from 14 pedigrees. Neither mutation was present in 19 Finnish controls. L402P was not present in 18 non-Finnish GA patients but R180T was found in an American GA patient. We constructed full-length mutant cDNAs by amplifying patient cDNA with the polymerase chain reaction and cloning a restriction fragment containing the mutation into an otherwise normal human OAT cDNA. These mutant cDNAs were then expressed in CHO-K1 cells, which lack endogenous OAT. Both R180T and L402P inactivate OAT. These results show molecular heterogeneity in GA alleles even in the Finnish population.
Targeting the perinatal diet to modulate the gut microbiota increases dietary variety and prebiotic and probiotic food intakes: results from a randomised controlled trial (2020)

A dietary intervention focused on 'eating for the gut microbiota' can improve aspects of perinatal diet quality during and after pregnancy.
The provenance of tills overlying the eastern part of the South Mountain Batholith, Nova Scotia (1988)

Happing of quarternary deposits on the South Mountain Batholitb (SMB) has resulted in a four-fold subdivision of tills, divided primarily on the basis of clast lithology, texture, stratigraphic position and morphology.&#x0D; &#x0D; Three tills have clast lithologies characterized by granites eroded from the South Mountain Batholih. The oldest granite till is a compact till of restricted distribution, mianly observed In drumlin cores. Two younger granite tills dominate the surficial deposits of portions of the SMB and have textural properties ascribed to melt-out tills. The fourth till represents a farther-travelled till with a variable clast provenance typified by pebbles derived from both the SMB and regions to the north. Clast dispersal evidence suggests that all tills were transported in a general southward direction.&#x0D; &#x0D; Detailed clast examinations allow reliable conclusions concerning direction of Ice flow and lithologic relationship between till and bedrock of the SMB. The SMB is an area of multiple glaciatlon where till prospecting cannot be successful unless the direction of till transport and source areas are established.&#x0D; &#x0D; RÉSUMÉ&#x0D; Dn levé cartographique des dépôts quaternaires recouvrant le Batholite de South Mountain à permis de mettre en évidence quatre varlétés de tills en fonctlon de la lithologie des clastes, la texture, la position stratlgraphlque et la morphologic&#x0D; &#x0D; Dana trola tills, les clastes nontrent des lithologles caractérisées par des granites arrachés au Batholite de South Mountain (BSM). Le plus vleux till de granite est un till tasse. de faible étendue, observe surtout dans les noyaux de drumlins. Dans certaines portions du BSM, les dépôts de surface sont dominés par deux tills de granite plus recents qui possedent des caractéristlques texturales rapportées aux tills d'ablation. Le quatriéme till a parcouru une plus grande distance; la source de ses clastes est variable et comprend typiquement des galets provenant tant du BSM que des régions plus au nord. La dispersion des blocaux suggère un direction générale de transport des tills vers le sud.&#x0D; &#x0D; Un exanen approfondi des clastes permet de tirer de solides conclusions à propos de la direction de l’écouleroent glacialre et de la relation lithologique entre le till et le socle du BSM. Le BSM a subi de multiples glaciatlons et la prospection du till n'y est done guère profitable à molns de déterminer la direction de transport et la source du till.&#x0D; &#x0D; [Traduit par le journal]
Small-molecule probe targeting viral PPxY L-domain inhibits filovirus and arenavirus egress. (2016)

Abstract Viral matrix proteins containing a highly conserved PPxY Late (L) domain motif are critical for efficient viral budding of several emerging RNA viruses. The L domain motif functions by recruiting host cell proteins necessary for separation of virus particles from the cell surface during the budding process. The conserved nature of the PPxY motif and its importance for viral egress make it an attractive drug target with potential broad spectrum antiviral activity. Here we describe a PPxY inhibitor capable of reducing viral budding of four highly lethal, category A RNA viruses: Ebola, Marburg, Lassa, and Junín viruses.
Comparison Between Keyhole Weld Model and Laser Welding Experiments (2002)

A series of laser welds were performed using a high-power diode-pumped continuous-wave Nd:YAG laser welder. In a previous study, the experimental results of those welds were examined, and the effects that changes in incident power and various welding parameters had on weld geometry were investigated. In this report, the fusion zones of the laser welds are compared with those predicted from a laser keyhole weld simulation model for stainless steels (304L and 21-6-9), vanadium, and tantalum. The calculated keyhole depths for the vanadium and 304L stainless steel samples fit the experimental data to within acceptable error, demonstrating the predictive power of numerical simulation for welds in these two materials. Calculations for the tantalum and 21-6-9 stainless steel were a poorer match to the experimental values. Accuracy in materials properties proved extremely important in predicting weld behavior, as minor changes in certain properties had a significant effect on calculated keyhole depth. For each of the materials tested, the correlation between simulated and experimental keyhole depths deviated as the laser power was increased. Using the model as a simulation tool, we conclude that the optical absorptivity of the material is the most influential factor in determining the keyhole depth. Future work will be performed to further investigate these effects and to develop a better match between the model and the experimental results for 21-6-9 stainless steel and tantalum.
[A patient-specific co-ordinate system for the reproduction of irradiation parameters (author's transl)]. (1980)

The authors describe a position which can be taken by the patient during the irradiation as well as during the examiantion by computed tomography. This method allows to clearly associate the tomograms with the patient's position during the irradiation.
Gateway diversity for a future high throughput satellite system (2014)

The continuous increase of traffic demands for satellite networks motivates the evolution of the telecommunication
satellite technology towards wider channels and multiple beam operation with frequency re-use across the coverage.
This is made possible by the use of higher frequency bands. Recent research projects 1,2 have investigated multi-beam
coverages with more than 200 user beams operated in Ka band, to offer very large data throughputs over Europe. Since
2012, the European Commission project Broadband Access via integrated Terrestrial and Satellite systems (BATS) has
explored a similar concept based on a dual satellite solution offering around 302 user beams over EU27 and Turkey,
targeting 2020 timeframe, see Figure 1. In all these systems, so as to maximize the user link capacity, the whole civil
band allocated to Fixed Satellite Services (FSS) in Ka band (20/30 GHz) is dedicated to the user links. The feeder
links thus have to be operated in another band. An attractive option is to rely on Q/V bands (30/40 GHz) to provide
the gateway-to-satellite links. Despite the large available bandwidths in Q/V band (5 GHz in each direction), the very
large user aggregated bandwidths are required to implement several tens of gateways to provide the necessary capacity.
Myocardial boundary extraction using coupled active contours (2003)

Automatic extraction of object boundaries in medical images using active contours is a popular research item. A problem with active contours is that they may fail to give correct results in cases of low contrast, noise or the neighbourhood of other edges. If there exists a geometrical relation between several boundaries this may be exploited to improve the robustness of active contours. In this way a set of coupled active contours results. This paper describes the simultaneous extraction of epi- and endocardial boundaries using a set of coupled active contours in MR short axis cine recordings.
Efficiency and cost trade-offs for designing module integrated converter photovoltaic systems (2012)

Photovoltaic (PV) systems are moving away from the traditional series-string PV structure and towards a module-integrated-converter (MIC) configuration for improved energy capture. A MIC approach trades off increased power production with increased cost and overhead power consumption. This research compares efficiency and cost of series-string, micro-converter, and micro-inverter PV system configurations. Analytical models for power production, cost, and cost per watt are developed for each configuration. Design choices such as the current sensor type, microcontroller, and maximum power point tracking (MPPT) algorithm affect power production and cost. Various design cases are explored to identify the number of MICs that minimize system cost per watt.
[125I]Aminobenzyladenosine, a new radioligand with improved specific binding to adenosine receptors in heart. (1985)

The density of adenosine receptors in membranes derived from rat hearts in 25 times lower than the density of receptors in rat brain membranes. Consequently, adenosine radioligands which are useful in brain such as l-[3H]phenylisopropyladenosine, [3H]cyclohexyladenosine, [3H]-2-chloroadenosine and l-[125I]hydroxyphenylisopropyladenosine are of limited usefulness in heart, due to a high ratio of nonspecific to specific binding. We have synthesized a new radioligand, [125I]-N6-4-aminobenzyladenosine, which binds to rat heart membranes with one-sixth the nonspecific binding of the other radioligands. [125I]-N6-4-aminobenzyladenosine bound to rat ventricle membranes with a KD equivalent to that of l-[125I]hydroxyphenylisopropyladenosine and a Bmax of 15.2 fmol/mg protein. [125I]-N6-4-aminobenzyladenosine bound with a higher affinity to brain (KD = 1.93 nM) than to heart membranes (KD = 11.6 nM). At the radioligand KD, 60% of the total [125I]-N6-4-aminobenzyladenosine bound to heart membranes was specifically bound. Iodination of aminobenzyladenosine increased its affinity for the adenosine receptor by 22-fold, possibly due to a steric or hydrophobic effect of iodine. The new ligand was found to be a full adenosine agonist based on its ability to inhibit cyclic adenosinemonophosphate accumulation in isolated embryonic chick heart cells and rat adipocytes. [125I]-N6-4-Aminobenzyladenosine bound to a single affinity site and was displaced from cardiac and brain adenosine receptors by other adenosine analogues with a potency order of l-phenylisopropyladenosine greater than 5'-N-ethylcarboxamide adenosine. These characteristics suggest that the radioligand binds to an Ri adenosine receptor.