gebhart/patrepeval huggingface dataset:
Endocrine actions of interferon-tau in ruminants (2012)

The ovine conceptus releases interferon-tau (IFNT), which prevents upregulation of the endometrial estrogen receptor (ESR1) and, consequently, oxytocin receptor (OXTR), thereby disrupting pulsatile release of prostaglandin F2alpha (PGF) in response to oxytocin. IFNT, through paracrine action on the endometrium, protects the corpus luteum (CL) during maternal recognition of pregnancy. Pregnancy also induces IFN stimulated genes (ISGs) in peripheral blood mononuclear cells (PBMCs), which is interpreted to reflect a "prompted" antiviral and immune cell response peripherally in ruminants. IFNT was recently demonstrated to be released from the uterus in amounts of 200 microg (2 x 10(7) U)/24 h via the uterine vein and to induce ISGs in the CL during maternal recognition of pregnancy. Delivery of recombinant ovine (ro) IFNT into the uterine vein in a location that is upstream of the utero-ovarian plexus from Day 10 to 17 maintained serum progesterone concentrations and extended normal 16-17 d estrous cycles to beyond 32 d. It is concluded from these studies that IFNT is released into the uterine vein and initiates a peripheral antiviral response to protect pregnancy from maternal viral infection. It also may have endocrine action through inducing luteal resistance to PGF and longer-term survival of the CL and maintenance of pregnancy.
The Mechanism of Vagal Nerve Stimulation of Glucagon and Insulin Secretion in the Dog* (1986)

The mechanism of vagal nerve stimulation of glucagon (IRG) and insulin (IRI) secretion was investigated in halothane-anesthetized dogs. Both ventral and dorsal branches of the thoracic vagi were stimulated electrically (10 Hz, 5 msec, 13.5 mA, 10 min) below the heart. Arterial and superior pancreaticoduodenal venous plasma were sampled, superior pancreaticoduodenal venous plasma flow was measured, and net pancreatic output of IRG and IRI were calculated. During vagal nerve stimulation (n = 15) net pancreatic output of IRG doubled (delta = +0.83 +/- 0.28 ng/min, P less than 0.01; baseline = 0.81 +/- 0.15 ng/ min) and IRI quadrupled (delta = +3.5 +/- 1.5 mU/min, P less than 0.025; baseline = 1.1 +/- 0.3 mU/min). Arterial glucose levels increased by 7 +/- 2 mg/dl from 108 +/- 3 mg/dl (P less than 0.005). After atropine pretreatment (n = 7), the pancreatic IRI response to vagal nerve stimulation was +0.71 +/- 0.28 mU/min (P less than 0.025), a reduction of 80%. In contrast, atropine pretreatment changed neither the IRG response (delta = +0.87 +/- 0.36 ng/min; P less than 0.05) nor the arterial glucose response (delta = +9 +/- 3 mg/dl; P less than 0.025) to vagal nerve stimulation. Hexamethonium pretreatment (n = 9) abolished the pancreatic IRG response (delta = +0.13 +/- 0.11 ng/min; NS), the arterial glucose response (delta = +0.5 +/- 1.9 mg/dl; NS) and the pancreatic IRI response (delta = +0.16 +/- 0.31 mU/min; NS) to vagal nerve stimulation. It is concluded that vagal nerve stimulation in the dog produces a moderate increase of IRG secretion, mediated by a nonmuscarinic (peptidergic?) mechanism, and a marked increase of IRI secretion, mediated by a muscarinic mechanism. Both responses are dependent on nicotinic transmission.
New clues for platinum antitumor chemistry: Kinetically controlled metal binding to DNA (2003)

From the metal ions and metal compounds that are known to bind to DNA, many anticancer Pt(II) and Ru(II)Ru(III) compounds are known to have ligand-exchange kinetics in the same order of magnitude as the division of tumor cells. The present article discusses this process in detail with special attention to cisplatin and related compounds and the cellular binding sites and processes of such compounds. Detailed platinated DNA structures are presented and discussed in light of the mechanistic studies of metal antitumor compounds. It is now known that platinum antitumor drugs eventually end up on the DNA. However, it remains a challenge to understand how (fast) they reach the DNA and how they are removed. The kinetics of ligand exchange around platinum appear to play a crucial role, and the possible role of other ligands as intermediates, especially those with S-donor sites, is of great interest. New types of Pt compounds with additional functionalities influencing DNA binding and kinetics are discussed in the context of steric and H-bonding properties. A comparison is made with more sterically crowded Ru complexes. The effects on activity and correlations with structural and kinetic properties are clues in understanding the biological activities of these classes of compounds.
The EndoC-βH1 cell line is a valid model of human beta cells and applicable for screenings to identify novel drug target candidates (2017)

Overall, the EndoC-βH1 cells strongly resemble human islet beta cells in terms of glucose and incretin stimulated insulin secretion capabilities. The cell line has an active cytokine induced caspase 3/7 apoptotic pathway and is responsive to ER stress initiation factors. The cells' ability to proliferate can be further increased by already known compounds as well as by novel peptides and proteins. Based on its robust performance during the functionality assessment assays, the EndoC-βH1 cell line was successfully used as a screening platform for identification of novel anti-diabetic drug candidates.
Characterization of New MiniSTR Loci to Aid Analysis of Degraded DNA (2004)

A number of studies have demonstrated that successful analysis of degraded DNA specimens from mass disasters or forensic evidence improves with smaller sized polymerase chain reaction (PCR) products. We have scanned the literature for new STR loci, unlinked from the CODIS markers, which can generate amplicons less than 125 bp in size and would therefore be helpful in testing degraded DNA samples. New PCR primers were designed and tested for the STR loci D1S1677, D2S441, D4S2364, D10S1248, D14S1434, and D22S1045, arranged into two miniSTR triplexes. All loci show a moderate degree of polymorphism among 474 U.S. population samples tested and were reliable and sensitive to at least 100 pg of DNA template under controlled laboratory conditions and pristine DNA samples. The utility of these new loci were confirmed in comparing the success of the miniSTR assays for typing degraded bone samples while partial profiles were observed with the majority of the samples using a commercial STR kit.
Droplet Actuation by Electrowetting-on-Dielectric (EWOD): A Review (2012)

Abstract This paper reviews publications that have fortified our understanding of the electrowetting-on-dielectric (EWOD) actuation mechanism. Over the last decade, growing interest in EWOD has led to a wide range of scientific and technological investigations motivated by its applicability in microfluidics, especially for droplet-based optical and lab-on-a-chip systems. At this point in time, we believe that it is helpful to summarize the observations, insights, and modeling techniques that have led to the current picture showing how forces act on liquid droplets and how droplets respond in EWOD microfluidic devices. We discuss the basic physics of EWOD and explain the mechanical response of a droplet using free-body diagrams. It is our hope that this review will inspire new research approaches and help design useful devices.
Direct Determination of the Complete Set of Iron Normal Modes in a Porphyrin-Imidazole Model for Carbonmonoxy-heme Proteins:  [Fe(TPP)(CO)(1-MeIm)] (2003)

Detailed Fe vibrational spectra have been obtained for the heme model complex [Fe(TPP)(CO)(1-MeIm)] using a new, highly selective and quantitative technique, Nuclear Resonance Vibrational Spectroscopy (NRVS). This spectroscopy measures the complete vibrational density of states for iron atoms, from which normal modes can be calculated via refinement of the force constants. These data and mode assignments can reveal previously undetected vibrations and are useful for validating predictions based on optical spectroscopies and density functional theory, for example. Vibrational modes of the iron porphyrin-imidazole compound [Fe(TPP)(CO)(1-MeIm)] have been determined by refining normal mode calculations to NRVS data obtained at an X-ray synchrotron source. Iron dynamics of this compound, which serves as a useful model for the active site in the six-coordinate heme protein, carbonmonoxy-myoglobin, are discussed in relation to recently determined dynamics of a five-coordinate deoxy-myoglobin model, [Fe(TPP)(2-MeHIm)]. For the first time in a six-coordinate heme system, the iron-imidazole stretch mode has been observed, at 226 cm(-)(1). The heme in-plane modes with large contributions from the nu(42), nu(49), nu(50), and nu(53) modes of the core porphyrin are identified. In general, the iron modes can be attributed to coupling with the porphyrin core, the CO ligand, the imidazole ring, and/or the phenyl rings. Other significant findings are the observation that the porphyrin ring peripheral substituents are strongly coupled to the iron doming mode and that the Fe-C-O tilting and bending modes are related by a negative interaction force constant.
Collagens and collagen-related diseases (2001)

The collagen superfamily of proteins plays a dominant role in maintaining the integrity of various tissues and also has a number of other important functions. The superfamily now includes more than 20 collagen types with altogether at least 38 distinct polypeptide chains, and more than 15 additional proteins that have collagen-like domains. Most collagens form polymeric assemblies, such as fibrils, networks and filaments, and the superfamily can be divided into several families based on these assemblies and other features. All collagens also contain noncollagenous domains, and many of these have important functions that are distinct from those of the collagen domains. Major interest has been focused on endostatin, a fragment released from type XVIII collagen, which potently inhibits angiogenesis and tumour growth. Collagen synthesis requires eight specific post-translational enzymes, some of which are attractive targets for the development of drugs to inhibit collagen accumulation in fibrotic diseases. The critical roles of collagens have been clearly illustrated by the wide spectrum of diseases caused by the more than 1,000 mutations that have thus far been identified in 22 genes for 12 out of the more than 20 collagen types. These diseases include osteogenesis imperfecta, many chondrodysplasias, several subtypes of the Ehlers-Danlos syndrome, Alport syndrome, Bethlem myopathy, certain subtypes of epidermolysis bullosa, Knobloch syndrome and also some cases of osteoporosis, arterial aneurysms, osteoarthrosis, and intervertebral disc disease. The characterization of mutations in additional collagen genes will probably add further diseases to this list. Mice with genetically engineered collagen mutations have proved valuable for defining the functions of various collagens and for studying many aspects of the related diseases.
Most rhesus macaques infected with the CCR5-tropic SHIV AD8 generate cross-reactive antibodies that neutralize multiple HIV-1 strains (2012)

The induction of broadly reacting neutralizing antibodies has been a major goal of HIV vaccine research. Characterization of a pathogenic CCR5 (R5)-tropic SIV/HIV chimeric virus (SHIV) molecular clone (SHIV(AD8-EO)) revealed that eight of eight infected animals developed cross-reactive neutralizing antibodies (NAbs) directed against an envelope glycoprotein derived from the heterologous HIV-1(DH12) strain. A panel of plasmas, collected from monkeys inoculated with either molecularly cloned or uncloned SHIV(AD8) stocks, exhibited cross-neutralization against multiple tier 1 and tier 2 HIV-1 clade B isolates. One SHIV(AD8)-infected animal also developed NAbs against clades A and C HIV-1 strains. In this particular infected macaque, the cross-reacting anti-HIV-1 NAbs produced between weeks 7 and 13 were directed against a neutralization-sensitive virus strain, whereas neutralizing activities emerging at weeks 41-51 targeted more neutralization-resistant HIV-1 isolates. These results indicate that the SHIV(AD8) macaque model represents a potentially valuable experimental system for investigating B-cell maturation and the induction of cross-reactive NAbs directed against multiple HIV-1 strains.
Dimension reduction and coefficient estimation in multivariate linear regression Series B Statistical methodology (2007)

We introduce a general formulation for dimension reduction and coefficient estimation in the multivariate linear model. We argue that many of the existing methods that are commonly used in practice can be formulated in this framework and have various restrictions. We continue to propose a new method that is more flexible and more generally applicable. The method proposed can be formulated as a novel penalized least squares estimate. The penalty that we employ is the coefficient matrix's Ky Fan norm. Such a penalty encourages the sparsity among singular values and at the same time gives shrinkage coefficient estimates and thus conducts dimension reduction and coefficient estimation simultaneously in the multivariate linear model. We also propose a generalized cross-validation type of criterion for the selection of the tuning parameter in the penalized least squares. Simulations and an application in financial econometrics demonstrate competitive performance of the new method. An extension to the non-parametric factor model is also discussed.
Efficient accommodation of mobile fronthaul and secondary services in a TDM-PON system with wireless TDD frame monitor (2016)

We propose a novel technique for the accommodation of mobile base stations (BSs) and a secondary system with a time division duplex (TDD) frame monitor. By increasing the number of BSs accommodated in a passive optical network (PON), the cost of mobile fronthaul (MFH) can be reduced. To realize even further cost reduction, a secondary system is accommodated in the PON with the MFH while the mobile signal is transferred with low latency. We propose a technique for overlapping the signal of the secondary system on the signals of the TDD mobile BSs by using a function for distinguishing the unallocated interval of TDD uplink signals. We evaluate the improvement in the optical uplink bandwidth efficiency with a numerical calculation. By employing the proposed technique, in a numerical simulation we greatly increase the optical bandwidth of the secondary system compared with that without a TDD frame monitor. For the uplink of the mobile system, the MFH latency is kept at a low value regardless of TDD frame monitoring.
Future Biomarkers for Detection of Ischemia and Risk Stratification in Acute Coronary Syndrome (2005)

Specifications that have been addressed for cardiac troponins and natriuretic peptides will need to be addressed with the same scrutiny for the biomarkers discussed in this review. They include validating analytical imprecision and detection limits, calibrator characterization, assay specificity and standardization, pre-analytical issues, and appropriate reference interval studies. Crossing boundaries from research to clinical application will require replication in multiple settings and experimental evidence supporting a pathophysiologic role and, ideally, interventional trials demonstrating that monitoring single or multiple biomarkers improves outcomes.
Flotillin and Epidermal Surface Antigen Define a New Family of Caveolae-associated Integral Membrane Proteins (1997)

Caveolae are plasmalemmal microdomains that are involved in vesicular trafficking and signal transduction. We have sought to identify novel integral membrane proteins of caveolae. Here we describe the identification and molecular cloning of flotillin. By several independent methods, flotillin behaves as a resident integral membrane protein component of caveolae. Furthermore, we have identified epidermal surface antigen both as a flotillin homologue and as a resident caveolar protein. Significantly, flotillin is a marker for the Triton-insoluble, buoyant membrane fraction in brain, where to date mRNA species for known caveolin gene family members have not been detected.
Speaking the Same Language: Matching Machine to Human Captions by Adversarial Training (2017)

While strong progress has been made in image captioning recently, machine and human captions are still quite distinct. This is primarily due to the deficiencies in the generated word distribution, vocabulary size, and strong bias in the generators towards frequent captions. Furthermore, humans – rightfully so – generate multiple, diverse captions, due to the inherent ambiguity in the captioning task which is not explicitly considered in today's systems. To address these challenges, we change the training objective of the caption generator from reproducing ground-truth captions to generating a set of captions that is indistinguishable from human written captions. Instead of handcrafting such a learning target, we employ adversarial training in combination with an approximate Gumbel sampler to implicitly match the generated distribution to the human one. While our method achieves comparable performance to the state-of-the-art in terms of the correctness of the captions, we generate a set of diverse captions that are significantly less biased and better match the global uni-, bi- and tri-gram distributions of the human captions.
Production of ethanol from mannitol by Zymobacter palmae (2000)

Extracts from brown seaweeds could possibly be fermented to ethanol, particularly seaweeds harvested in the autumn, which contain high levels of easily extractable laminaran and mannitol. Few microorganisms are able to utilise mannitol as a substrate for ethanol production and Zymobacter palmae was tested for this purpose. Bacterial growth as well as ethanol yield depended on the amount of oxygen present. Strictly anaerobic growth on mannitol was not observed. At excessive aeration, a change in the fermentation pattern was observed with high production of acetate and propionate. Under oxygen-limiting conditions, the bacteria grew and produced ethanol in a synthetic mannitol medium with a yield of 0.38 g ethanol (g mannitol)−1. Z. palmae was also successfully applied for fermentation of mannitol from Laminaria hyperborea extracts. Journal of Industrial Microbiology & Biotechnology (2000) 24, 51–57.
Eremophilane and Serrulatane Terpenoids from Eremophila rotundifolia (1985)

The new terpenoids, 9-oxoeremophila-10,11(13)-dien-12-al (3) and 5,8- dihydroxyserrulat-14-en-18-al (2) have been isolated and their absolute stereochemistry established by chemical correlation with known compounds.
Unsupervised Lexical Simplification for Non-Native Speakers (2016)

Lexical Simplification is the task of replacing complex words with simpler alternatives. We propose a novel, unsupervised approach for the task. It relies on two resources: a corpus of subtitles and a new type of word embeddings model that accounts for the ambiguity of words. We compare the performance of our approach and many others over a new evaluation dataset, which accounts for the simplification needs of 400 non-native English speakers. The experiments show that our approach outperforms state-of-the-art work in Lexical Simplification.
Left atrial flow velocity distribution and flow coherence using four‐dimensional FLOW MRI: A pilot study investigating the impact of age and Pre‐ and Postintervention atrial fibrillation on atrial hemodynamics (2013)

Flow-sensitive MRI shows that patients with a history of AF had global hemodynamics in the LA similar to those of age-matched volunteers. Additional studies with larger cohorts of AF patients and correlation with outcome are needed to further investigate the potential of atrial 4D flow MRI to flow patterns indicative of stroke risk in AF.
T-Cell Vaccine Strategies for Human Immunodeficiency Virus, the Virus with a Thousand Faces (2009)

Although there is increasing evidence that individuals already infected with human immunodeficiency virus type 1 (HIV-1) can be infected with a heterologous strain of the virus, the extent of protection against superinfection conferred by the first infection and the biologic consequences of superinfection are not well understood. We explored these questions in the simian immunodeficiency virus (SIV)/rhesus monkey model of HIV-1/AIDS. We infected cohorts of rhesus monkeys with either SIVmac251 or SIVsmE660 and then exposed animals to the reciprocal virus through intrarectal inoculations. Employing a quantitative real-time PCR assay, we determined the replication kinetics of the two strains of virus for 20 weeks. We found that primary infection with a replication-competent virus did not protect against acquisition of infection by a heterologous virus but did confer relative control of the superinfecting virus. In animals that became superinfected, there was a reduction in peak replication and rapid control of the second virus. The relative susceptibility to superinfection was not correlated with CD4(+) T-cell count, CD4(+) memory T-cell subsets, cytokine production by virus-specific CD8(+) or CD4(+) cells, or neutralizing antibodies at the time of exposure to the second virus. Although there were transient increases in viral loads of the primary virus and a modest decline in CD4(+) T-cell counts after superinfection, there was no evidence of disease acceleration. These findings indicate that an immunodeficiency virus infection confers partial protection against a second immunodeficiency virus infection, but this protection may be mediated by mechanisms other than classical adaptive immune responses.
Retroviral-mediated transfer of the human acid sphingomyelinase cDNA: correction of the metabolic defect in cultured Niemann-Pick disease cells. (1992)

Types A and B Niemann-Pick disease (NPD) result from inherited deficiencies of the lysosomal hydrolase, acid sphingomyelinase (ASM; sphingomyelin cholinephosphohydrolase, EC 3.1.4.12). To evaluate the feasibility of somatic gene therapy for the treatment of these disorders, retroviral-mediated gene transfer was used to introduce the full-length ASM cDNA into cultured fibroblasts from two unrelated type A NPD patients. The ASM activities in these cells were less than 4% of mean normal levels, and, consequently, they accumulated approximately 3-fold elevated levels of sphingomyelin. After retroviral-mediated transfer of the ASM cDNA, ASM activities in the NPD cells increased to levels up to 16-fold those found in normal fibroblasts. In addition, the sphingomyelin content was reduced to normal levels, indicating that the vector-encoded enzyme was properly targeted to lysosomes, where it was enzymatically active and able to degrade the accumulated substrate. In situ cell-loading studies also were undertaken to evaluate the effects of retroviral-mediated gene transfer on the pathology of NPD fibroblasts. When a pyrene derivative of sphingomyelin was introduced into the lysosomes of cultured fibroblasts from a type A NPD patient by using apolipoprotein E-mediated endocytosis, only approximately 6% of the delivered substrate was degraded. In contrast, normal cells and NPD cells transduced (i.e., "corrected") by retroviral-mediated gene transfer could degrade approximately 80% of the delivered sphingomyelin. These results provided further evidence that retroviral-mediated gene transfer may be used to correct the pathology of NPD cells. Cell-loading studies were also used to develop a selection system for discriminating between NPD cells and those transduced by retroviral-mediated gene transfer. This selection scheme was based on the fluorescence emission of intact NPD cells, which, when loaded with pyrene-labeled sphingomyelin, was 3- to 5-fold that of normal or transduced cells. As a consequence, the NPD and transduced cells could be efficiently sorted by flow cytometry with a fluorescence-activated cell sorter. In addition, the NPD cells could be selectively killed by photosensitization after irradiation with a long-wavelength UV light. These results should permit direct selection of ASM-expressing cells after retroviral-mediated gene transfer without the need to preselect for a cotransferred marker gene.