gebhart/patrepeval huggingface dataset:
The Role of Interleukin-7 in Early T-Cell Development (1998)

Interleukin-7 (IL-7) is a non redundant cytokine in thymic T-cell development. It binds to a dimeric receptor consisting of a specific IL-7Ralpha and a gamma-common subunit that it shares with the receptors for IL-2, 4, 9, 13 and 15. IL-7 is critical for early T-cell development but it also acts on immature B-cells and mature T-cells, and leads to secondary cytokine release. Its mechanisms of action in early T-cell development may be multiple. There is direct evidence to support a mechanistic involvement in TCR-gamma rearrangement that drives further TCR-gammadelta thymocyte commitment and maturation. There is indirect evidence for a role of IL-7 in TCR-beta rearrangement. It may however also act as a survival factor for TCR-beta rearranging thymocytes while the critical commitment selections are effected by other factors. The effects of IL-7 in fetal thymus organ culture are dose dependent, with a biphasic response: low doses of IL-7 are necessary for normal TCR-alphabeta thymocyte development but high doses block TCR-alphabeta maturation in favor of TCR-gammadelta development. A good understanding of the dose response of IL-7 in thymocyte development, mature T-cell stimulation, and of the release of secondary cytokines will be important for planning successful clinical trials with IL-7.
Formation of Spatially Patterned Colloidal Photonic Crystals through the Control of Capillary Forces and Template Recognition (2005)

We report the formation of microscopic patterns of substrate-supported, 3D planar colloidal crystals using physical confinement in conjunction with surfaces displaying predetermined binary patterns of hydropholicity. The formation process involves a primary self-assembly wherein nano- and microscale colloids order into a photonic fcc lattice via capillary interactions followed by a secondary template-induced crystal cleavage step. Following this method, arbitrary arrays of pattern elements, which preserve structural and orientational properties of the parent crystal, can be easily obtained.
The Biosynthesis of 3‐(trans‐2‐Nitrocyclopropyl)alanine, a Constituent of the Signal Metabolite Hormaomycin (2004)

Abstract Feeding experiments with Streptomyces griseoflavus using deuterium‐labeled racemic 3,3‐[D 2 ]‐ ( 6b ), 4,4‐[D 2 ]‐ ( 6c ), 5,5‐[D 2 ]‐ ( 6d ), and 6,6‐[D 2 ]‐lysine ( 6e ), and 3‐amino‐5‐(2‐amino‐1,1‐dideuterioethyl)‐4,5‐dihydrofuran‐2‐one dihydrochloride ( 34· 2HCl) were carried out in order to obtain detailed information about the hitherto unknown biosynthetic pathway from lysine to the unusual amino acid 3‐( trans ‐2′‐nitrocyclopropyl)alanine [(3‐Ncp)Ala] ( 2 ), which is a building block of hormaomycin 1a . The corresponding lysine dihydrochlorides were prepared in 33, 24, 19, and 30% overall yield, respectively, along a new efficient general synthetic route applying an alkylation of the lithium enolate of O′Donnel’s glycine equivalent 7 as a key step. In the attempted preparation of 5,5‐[D 2 ]‐4‐hydroxylysine ( 29 ), the respective γ‐lactone ( 34· 2 HCl) was obtained in five steps with 10% overall yield. The distribution of isotope labels in hormaomycins 1b − d led to the formulation of a reasonable cyclization mechanism of 2‐amino‐4‐hydroxy‐6‐(hydroxyimino)hexanoic acid, an ψ‐oxime analogue of 4‐hydroxylysine. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Role of the LKB1/AMPK pathway in tumor invasion and metastasis of cancer cells (Review) (2015)

Liver kinase B1 (LKB1), also known as serine/threo-nine kinase 11 (STK11), is a tumor suppressor that is inactivated in Peutz-Jeghers familial cancer syndrome. LKB1 phosphorylates and activates AMP-activated protein kinase (AMPK), which negatively regulates cancer cell proliferation and metabolism. However, recent evidence demonstrates that the LKB1/AMPK pathway is involved in the process of tumor invasion and migration, which is an important hallmark of carcinoma progression to higher pathological grades of malignancy. This review focuses on the function of the LKB1/AMPK pathway in the invasion and migration of cancer cells and provides an overview of therapeutic strategies aimed at this pathway in malignant tumors.
A Serum Proteomics Approach to the Diagnosis of Ectopic Pregnancy (2004)

An ectopic pregnancy (EP) occurs when implantation of the embryo occurs outside of the uterus. If left untreated, the developing fetus will continue to grow, leading to life-threatening consequences for the mother. A major difficulty with the diagnosis of ectopic pregnancy is that methods of detection are limited, and some, such as ultrasound, are not very reliable in the earliest days of gestation. Currently, no effective serum test exists to distinguish an ectopic pregnancy from a normal intrauterine pregnancy. The incidence of ectopic pregnancy is increasing and has doubled in the last 20 years. It is now the second most common cause of maternal death in the first trimester of pregnancy. To address this issue, we initiated a project to identify serum markers of ectopic pregnancy. The subjects for these studies presented at the Hospital of the University of Pennsylvania. We obtained over 140 serum samples from women with suspected ectopic pregnancy: women presenting with pain and/or bleeding in the first trimester of pregnancy. The approximate racial breakdown of the subjects is as follows: African American, 36%; Caucasian, 3%; Asian, 2%; Hispanic, 1%; unknown, 58%. Serum samples from 139 women (62 with ectopic pregnancy and 77 with a normal intrauterine pregnancy) were applied to WCX2 (weak ion exchange) protein chip surfaces and analyzed for serum markers using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS). Several proteins in the 7500-18,000 Da mass range were identified that may discriminate an ectopic pregnancy from an intrauterine pregnancy. The most promising markers were analyzed using classification and regression tree analysis (CART) with and without clinical variables (serum hCG value, length of amenorrhea). Two different algorithms were developed that classify the patients on the basis of sensitivity (number of EPs who screen positive/# of EPs) or specificity (# of healthy patients who screen negative/# of healthy). Our current approach is to refine these two "rule sets" to segregate patients into three groups: those who need immediate intervention for a probable ectopic pregnancy, those who appear to have a normal pregnancy, and those who need further monitoring for diagnosis.
An enhanced 16K E/sup 2/PROM (1982)

An enhanced 16K E/SUP 2/PROM is described. It makes the E/SUP 2/PROM to microprocessor interface simple to implement. It frees up the system bus during e/SUP 2/PROM programming by latching addresses, data, and all control signals on chip. It provides minimum ERASE/WRITE, time via a novel feedback subsystem that monitors the amount of charge on the floating gate of the cell and signals to the system by the READY/BUSY output pin when enough charge has been added to or removed from the gate. With an external V/SUB pp/ voltage fixed supply, the E/SUP 2/PROM generates its own RC ramp during ERASE/WRITE, increasing the endurance of the storage cell. On-chip control circuitry provides ERASE before WRITE, making writing appear as a single step to the user.
EFFECT OF WARM ISCHEMIA TIME AND ORGAN PERFUSION TECHNIQUE ON LIVER MICROVASCULAR PRESERVATION IN A NON-HEART-BEATING RAT MODEL 1 (2000)

These data underline the need and benefit of dual perfusion as well as the limitation of warm ischemic tolerance to 30 min for safe liver procurement of non-heart-beating donors.
The effect of TNP-470 on cell proliferation and urokinase-type plasminogen activator and its inhibitor in human lung cancer cell lines. (1996)

The plasminogen activator system has been found to modulate neoplastic spread and angiogenesis in tumors. An angiogenesis inhibitor, TNP-470, has been shown to possess potent antitumor activities in various types of cancer cells. We therefore investigated the inhibitory effect of TNP-470 on cancer cell proliferation, and the suppressive effect of TNP-470 on urokinase-type plasminogen activator (u-PA) and its inhibitor (PAI-1), in human lung cancer cell lines in vitro. TNP-470 inhibited cell proliferation in a dose-dependent manner in both cell lines. u-PA and PAI-1 in culture supernatants were suppressed with the concentrations of TNP-470, in association with a decrease in viable cancer cells. Unchanged serum levels of u-PA and PAI-1 would be of great advantage to the diseased patients, since the plasminogen activator system has a crucial function in the process of distant metastasis.
Vapor-liquid equilibria of triglycerides-methanol mixtures and their influence on the biodiesel synthesis under supercritical conditions of methanol (2007)

The non-catalytic synthesis of biodiesel (fatty acids methyl esters) from triglycerides and methanol proceeds at elevated pressures above 100 bar and temperatures above 523 K. Kinetic investigations of the system revealed an unusual behavior of the reaction rate constant with increasing temperature and pressure. In order to explain this phenomenon, the phase behavior of the triglycerides-methanol mixture was investigated. The phase equilibria of the binary system sunflower oil-methanol were measured at different temperatures between 473 and 503 K, and a range of pressures between 10 and 56 bar. The experimental data were correlated using the Peng-Robinson, Soave-Redlich-Kwong and Redlich-Kwong-Aspen equations of state and different mixing rules. The best results were obtained with the RK-ASPEN equation of state and the Van der Waals mixing rule (VdW), which were then used to calculate the distribution of the phases at pressures and temperatures usual for the non-catalytic synthesis of biodiesel under high pressures. The obtained data indicated a strong influence of the phase equilibria on the reaction kinetics. .
Show, Attend and Tell: Neural Image Caption Generation with Visual\n Attention (2015)

Inspired by recent work in machine translation and object detection, we\nintroduce an attention based model that automatically learns to describe the\ncontent of images. We describe how we can train this model in a deterministic\nmanner using standard backpropagation techniques and stochastically by\nmaximizing a variational lower bound. We also show through visualization how\nthe model is able to automatically learn to fix its gaze on salient objects\nwhile generating the corresponding words in the output sequence. We validate\nthe use of attention with state-of-the-art performance on three benchmark\ndatasets: Flickr8k, Flickr30k and MS COCO.\n
Synthesis of analogues of oligonucleotides; synthesis of unprotected C-linked di- and tri-nucleotides (1998)

The Wittig reaction between the N-benzyloxymethylthymidine-derived ylide 25 and the aldehyde 16 followed by hydrogenolysis gives access to the unprotected C-linked dinucleotide 20 on a multi-gram scale. Oxidation of the dinucleotide gives the aldehyde 27 which is condensed with the ylide 25 to give the unprotected bis-C-linked trinucleotide 29 after hydrogenolysis. The mono-C-linked trinucleotide 44 is prepared by oxidation of the dinucleotide ester 34 to the aldehyde 36 which is condensed with the ylide 25 followed by hydrogenolysis to give the mono-C-linked trinucleotide ester 38. This intermediate is also prepared from the C-linked dinucleotide 20 by conversion into the phosphoramidite 41 which is coupled with 3-acetylthymidine 15 to give the mono-C-linked trinucleotide phosphite 42. Oxidation and deprotection give the phosphate triester 38. Treatment of 38 with methanolic ammonia gives the fully unprotected mono-C-linked trinucleotide 44.
Study on the scattering characteristics of stable-stage wake vortices (2009)

The present paper decomposes the study of wake vortex's scattering characteristics into three key problems. Based on the study of these three problems in detail, we obtained the scattering characteristics of the wake vortex, which include the frequency characteristic of RCS, the radiation pattern, the relation between RCS and the detection range, and the time evolution characteristic of RCS. Research findings can provide supports for the development of radar detection technology on wake vortex.
RGB Phosphorescent Organic Light-Emitting Diodes by Using Host Materials with Heterocyclic Cores: Effect of Nitrogen Atom Orientations (2010)

A series of host materials 1−7 containing various heterocyclic cores, like pyridine, pyrimidine, and pyrazine, were developed for RGB phosphorescent organic light-emitting diodes (OLEDs). Their energy levels can be tuned by the change of heterocyclic cores and their nitrogen atom orientations, and decrease of singlet−triplet exchange energy (ΔEST) was achieved with introducing one or two nitrogen atoms into the central arylene; this is also consistent with density functional theory calculations. Their carrier mobilities can also be tuned by the choice of heterocyclic cores, giving improved bipolarity compared with that without any heterocyclic cores. Due to the high triplet energy level of the developed host materials, well confinement of triplet excitons of blue emitter iridium(III) bis(4,6-(difluorophenyl)pyridinato-N,C2′) picolinate (FIrpic) was achieved except for 7 due to its low ET. In contrast, triplet energy can be well confined on green emitter fac-tris(2-phenylpyridine) iridium (Ir(PPy)3) and red emitter tris(1-phenylisoquinolinolato-C2,N)iridium(III) (Ir(piq)3) for all the hosts, giving comparable lifetime (τ), photoluminescent quantum efficiency (ηPL), and radiative and nonradiative rate constants (kr and knr). Highly efficient blue and green phosphorescent OLEDs were achieved for 2, exhibiting one of the highest ever efficiencies to date, especially at much brighter luminance for lighting applications. In comparison, the highest efficiencies hitherto were achieved for the red phosphorescent OLED based on 6, which can be attributed to its lower-lying LUMO level and the smallest ΔEST, giving improved electron injection and carrier balance. Different from the blue and green phosphorescent OLEDs based on FIrpic and Ir(PPy)3, the host materials with lower-lying LUMO levels seem to be better hosts for a red emitter Ir(piq)3, achieving improved efficiency and reduced efficiency roll-off at high current density.
Modification of the Stöber Process by a Polyazamacrocycle Leading to Unusual Core−Shell Silica Nanoparticles (2008)

In the view of designing functional nanoparticles, the encapsulation of 1,4,7,10-tetraazacyclododecane (cyclen) within silica nanoparticles using the Stöber process was studied. In the presence of cyclen and tetraethoxysilane (TEOS), silica particles exhibiting an unusual core-shell structure were obtained. On then basis of TEM, DLS, and NMR data, we suggest that the particle core is constituted of hybrid primary nanoparticles resulting from cyclen-silica interactions, whereas the shell formation results from further condensation of unreacted silica precursors. Control experiments performed with the zinc-cyclen complex and ammonia addition suggest that cyclen-TEOS interactions arise from the activation of the silicon alkoxide hydrolysis with the polyazamacrocycle amine groups. These data are discussed in the context of silica biomineralization mechanisms, where polyamine/silica interactions have been shown to play a major role. Moreover, the possibility to control the size and the structure of these nanoparticles makes them promising materials for pharmaceutical applications.
Oestrogens regulate pituitary alpha2,3-sialyltransferase messenger ribonucleic acid levels in the female rat (1999)

Follicle-stimulating hormone (FSH) is synthesized by the anterior pituitary gland in multiple molecular forms. Increased acidic/sialylated FSH charge isoforms are associated with conditions characterized by a low oestrogen output. In the present study, we analysed the dynamics of the changes in mRNA levels of the enzyme Galbeta1,3[4]GlcNAc alpha2,3-sialyltransferase (2,3-STase) (one of the enzymes that incorporate sialic acid residues into the FSH molecule) in intact and ovariectomized rats. The anterior pituitaries of 4-day regularly cyclic adult female Wistar rats were obtained at 1000 h on the days of pro-oestrus (P), oestrus (O), dioestrus 1 (D1) and dioestrus 2 (D2), at 0200 h, 1400 h, 1800 h and 2200 h on D1, at 1800 h on day of O and at 1000 h after 7, 14, 21, 28 and 45 days of oophorectomy performed on the morning of P. Total RNA was isolated from each gland and the 2,3-STase levels were measured by Northern blot hybridization analysis employing a 346-base pair cDNA probe encoding for a non-conserved amino acid sequence of the catalytic domain of the enzyme. Maximal levels of the enzyme mRNA were detected at 1000 h on D1; thereafter, they progressively decreased by 60% during the ensuing 24 h, reaching the lowest concentration values (26% of the maximally observed level on D1) at 1000 h on day of P and remaining unchanged during the morning of O. Administration of the potent oestradiol receptor antagonist ICI 182,780 at 1000 h on D1 completely reverted the time-dependent decrease in 2,3-STase mRNA levels observed during the afternoon of D1, whereas oestradiol benzoate administered at 1000 h on day of O significantly reduced the enzyme mRNA levels (to 21% of the levels detected in vehicle-treated controls). In ovariectomized rats, the alpha2,3-STase mRNA progressively increased from day 21 to day 45 post castration. Administration of oestradiol benzoate on day 28 after oophorectomy significantly reduced the 2,3-STase mRNA levels (to 36% of the levels detected in vehicle-injected controls); ICI 182,780 partially counteracted this oestradiol-mediated effect. The dynamics of these changes in 2,3-STase mRNA levels partially correlated with changes in the relative abundance of the FSH charge isoforms separated by preparative chromatofocusing of anterior pituitary extracts, particularly in glands obtained during the morning of P and O. These data demonstrate for the first time that pituitary 2,3-STase is a hormonally-regulated enzyme and that the changes in transcription and/or stability of its mRNA may be involved, in part, in the post-translational processing of the FSH molecule during certain physiological conditions.
Comparison of RNA interference silencing of PAX 2 expression in PC3 and Du145 prostate cancer cell lines. (2005)

Proc Amer Assoc Cancer Res, Volume 46, 2005

66 

Paired box genes are a family of transcriptional regulators that encode for transcription factors that help to guide expression of genes needed for normal development. Paired box genes have been implicated in acting as proto-oncogenes [1]. For example, Pax 2 is expressed in undifferentiated and highly mitotic tissues. The Pax 2 gene has been identified in renal cell carcinoma, Wilm’s tumor, and prostate cancer [2,3,4]. In this study, we are examining the role of Pax 2 in prostate cancer. Studies have shown that Pax 2 binds to the promoter region and may inhibit the expression of the tumor suppressor gene, P53. Previous studies have shown that Pax 2 may be required for cancer cell survival. Moreover, rapid induction of apoptosis is seen in bladder and ovarian cancer following RNA interference against Pax 2 expression [5]. Here we compare the effects of Pax 2 siRNA on cell viability in P53 null (PC3) versus P53 mutant (Du145) prostate cancer cells. The two cell lines were treated with a chemically synthesized siRNA of Pax2 for a 2, 4, and 6 day incubation time. Cellular proliferation and viability were measured in the siRNA treated cells using an in vitro MTT assay. Also, Pax 2 expression was assessed by Western Blot analysis. We established that the percent cell death of PC3 cells transfected with Pax 2 siRNA duplex was 3.7% at day 2 and increased to 37% by day 4 and further increased to approximately 63% by day 6. In contrast, Du145 cells transfected with Pax 2 siRNA duplex experienced approximately 18% cell death with no significant change at the four and six day incubation period. Western blot analysis confirmed lost of expression of Pax 2 as early as the fourth day. It appears that the P53 null PC3 cells treated with siRNA against Pax 2 experience more cell death than the mutated P53 Du145 cells treated with siRNA against Pax 2. This data suggest that Pax 2 may inhibit the function of P53 in PC3 cells which up on inhibition of Pax 2 expression, a P53- mediated pathway to cellular apoptosis may occur. Therefore, this study suggests that oncogenic activity of Pax 2 is mediated through the inhibition of P53- mediated apoptotic pathways.
LOSS OF CONSTITUTIONAL HETEROZYGOSITY IN HUMAN CANCER (1991)

Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More
Simultaneous NO and CO_2 measurement in human breath with a single IV–VI mid-infrared laser (2002)

A tunable diode laser absorption spectroscopy (TDLAS) system equipped with a IV-VI mid-IR laser operating near 5.2>mu;m was used to measure exhaled nitric oxide (eNO) and carbon dioxide (CO(2)) simultaneously in human breath over a single exhalation. Breath was sampled in real time, and eNO levels were measured from seven volunteers, two steroid-naive asthmatics and five nonasthmatics. Measured CO(2) levels were used as an internal standard to verify correct breath collection and calculate eNO values. Calculated eNO concentrations agreed well with reported values for asthmatic and nonasthmatic individuals.
Synovial Fluid Crystals (1979)

Synovial fluid was aspirated from the Joints of unselected groups of patients suffering from rheumatoid arthritis (30), osteoarthritis (34), pyrophosphate arthropathy (25) and gout (six). Specially selected patients with osteoarthritis (10) and other miscellaneous forms of arthropathy (six) were also Included. Total and differential cell counts were performed, and the fluids were examined by polarized light microscopy and analytical electron microscopy to determine crystal content. fluids from patients with rheumatoid arthritis and gout had a higher total cell count, and greater proportion of polymorphonuclear cells. There was no difference in the cell content in patients with osteoarthritis and chronic pyrophosphate arthropathy. Osteoarthritic fluids containing crystals did not have a significantly different cell count from those without. Polarized light microscopy was confirmed as a good technique for differentiating urate from pyrophosphate crystals. However, pyrophosphate crystals varied greatly in appearance, and were occasionally too small to be visualized. Crystals thought to be brushite, formed in some fluids after aspiration, causing confusion on polarized light examinations, and other unidentified birefringent material was often seen. Analytical and scanning electron microscopy revealed a wide variation in the morphology and elemental content of synovial fluid crystals. Hydroxyapatite crystals were identified in nine out of 34 unselected osteoarthrltlc fluids, in 10 selected cases, and six with synovitis of unknown cause. Hydroxyapatite was seen in combination with pyro phosphate in six cases, and was the only crystal identified in one case of ‘pyrophosphate’ nrthropathy. Small pyrophosphate crystals, not seen with the light microscope, were identified in two cases. Other crystalline particles containing calcium and phosphorus were seen in some cases, but could not be identified. No crystals were identified in rheumatoid arthritis fluids. Crystal phagocytosis was visualized using scanning electron microscopy. It is concluded that hydroxyapatite crystals are commonly present in synovial fluids in chronic arthritis, with or without pyrophosphate, and that a range of other calcium phosphate salts remain to be identified.