gebhart/patrepeval huggingface dataset:
Reply to Schmitt et al.: Data-filtering schemes for avoiding double-counting in circle sequencing (2014)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Associations of lipoprotein cholesterols, apolipoproteins A-I and B, and triglycerides with carotid atherosclerosis and coronary heart disease. The Atherosclerosis Risk in Communities (ARIC) Study. (1994)

Previous research shows generally greater proportional elevation in apolipoprotein B (apoB) levels than in low-density lipoprotein cholesterol (LDL-C) in coronary heart disease (CHD) case subjects compared with control subjects. The Atherosclerosis Risk in Communities study provided general populations of 7261 men and women free of cardiovascular symptoms for evaluating the associations between intima-media thickening in extracranial carotid arteries measured using ultrasound imaging and fasting plasma LDL-C, high-density lipoprotein cholesterol (HDL-C), apoB, apolipoprotein A-I (apoA-I), triglycerides, and HDL density subfractions. A CHD group was selected for comparison. Lipid factors show approximately linear associations with carotid thickness: positive for LDL-C and plasma apoB and negative for HDL-C and apoA-I levels. Apolipoproteins and HDL density subfractions did not contribute to the association after accounting for LDL-C and HDL-C. Compared with control subjects, persons whose carotid thickness exceeded 0.9 mm had greater proportional elevations in LDL-C than in apoB, whereas HDL-C reductions were small. CHD case subjects showed greater proportional elevations of apoB than LDL-C. Although the lipid profiles associated with asymptomatic carotid wall thickening and stenotic coronary disease are similar, the differences found suggest that LDL-C is the most important lipid factor in earlier stages of atherogenesis, whereas the metabolism of triglyceride-rich lipoproteins and its effects on LDL and HDL may be more relevant to later atherothrombotic processes.
High-speed gallop locomotion in the Thoroughbred racehorse. II. The effect of incline on centre of mass movement and mechanical energy fluctuation (2008)

During locomotion on an incline, mechanical work is performed to move an animal up the slope and increase the potential energy (PE) of the trunk and hence the centre of mass (CoM). Thus, at a given speed the total net mechanical work increases with the PE of the animal. In this study we investigate the mechanical energy (ME) fluctuations and the mechanical cost of transport (MCT) in six horses galloping up a range of gradients. We captured trunk movement with a six degrees-of-freedom inertial sensor mounted over the dorsal spinous process of the fourth to sixth thoracic vertebrae of the horse. Footfall timings were measured using a previously validated system of limb-mounted accelerometers. Speed was measured using a Global Positioning System (GPS) data logger. A track survey provided detailed incline information for the track. Linear (craniocaudal, mediolateral and dorsoventral) and rotational (roll, pitch and heading) kinematic parameters (displacement, velocity and acceleration) were calculated at speeds ranging from 9.0 to 12.0 m s(-1) during routine training over a range of inclines. Estimates of ME fluctuations and the MCT were made. Results showed the effect of incline on trunk motion during galloping was small. Increases in linear mechanical work and MCT were primarily explained by an increase in the work required to move the animal up the slope (and increase the PE of the CoM). Within the stride the majority of the work was performed during hindlimb stance. Our results have provided new insights into how horses power uphill locomotion.
Weekly nab-Paclitaxel in Combination With Carboplatin Versus Solvent-Based Paclitaxel Plus Carboplatin as First-Line Therapy in Patients With Advanced Non–Small-Cell Lung Cancer: Final Results of a Phase III Trial (2012)

The administration of nab-PC as first-line therapy in patients with advanced NSCLC was efficacious and resulted in a significantly improved ORR versus sb-PC, achieving the primary end point. nab-PC produced less neuropathy than sb-PC.
Embryonic development of four different subsets of cholinergic neurons in rat cervical spinal cord (1990)

The developmental stage at which a neuron becomes committed to a neurotransmitter phenotype is an important time in its ontogenetic history. The present study examines when choline acetyltransferase (ChAT) is first detected within each of four different subsets of cholinergic neurons previously identified in the cervical enlargement of the spinal cord: namely, motor neurons, partition cells, central canal cluster cells, and dorsal horn neurons. By examining the temporal sequence of embryonic development of these cholinergic neurons, we can infer the relationships between ChAT expression and other important developmental events. ChAT was first detected reliably on embryonic day 13 (E13) by both biochemical and immunocytochemical methods, and it was localized predominantly within motor neurons. A second group of primitive-appearing ChAT-positive cells was detected adjacent to the ventricular zone on E14. These neurons seemed to disperse laterally into the intermediate zone by E15, and, on the basis of their location, were tentatively identified as partition cells. A third group of primitive ChAT-immunoreactive cells was detected on E16, both within and around the ventral half of the ventricular zone. By E17, some members of this "U"-shaped group appeared to have dispersed dorsally and laterally, probably giving rise to dorsal horn neurons as well as dorsal central canal cluster cells. Other members of this group remained near the ventral ventricular zone, most likely differentiating into ventral central canal cluster cells. Combined findings from the present study and a previous investigation of neurogenesis (Phelps et al.: J. Comp. Neurol. 273:459-472, '88), suggest that premitotic precursor cells have not yet acquired the cholinergic phenotype because ChAT is not detectable until after the onset of neuronal generation for each of the respective subsets of cholinergic neurons. However, ChAT is expressed in primitive bipolar neurons located within or adjacent to the germinal epithelium. Transitional stages of embryonic development suggest that these primitive ChAT-positive cells migrate to different locations within the intermediate zone to differentiate into the various subsets of mature cholinergic neurons. Therefore, it seems likely that spinal cholinergic neurons are committed to the cholinergic phenotype at pre- or early migratory stages of their development. Our results also hint that the subsets of cholinergic cells may follow different migration routes. For example, presumptive partition cells may use radial glial processes for guidance, whereas dorsal horn neurons may migrate along nerve fibers of the commissural pathway. Cell-cell interactions along such diverse migratory pathways could play a role in determining the different morphological, and presumably functional, phenotypes expressed by spinal cholinergic neurons.
MWCNT for Enhancing Mechanical Properties of Oil Well Cement for HPHT Applications (2016)

Abstract Growing demand to drill High Pressure High Temperature (HPHT) wells requires improved technology to overcome the HPHT challenges. Oil well cementing has a greater impact on the production potential of a well as compared to other operational actions. A successful cementing job is dependent on how quickly and efficiently cement achieves strength. Achieving desired mechanical properties of cement becomes harder and complex at HPHT conditions. A wide variety of admixtures are commonly mixed with the oil well cement slurries to deal with the extensive range of pressure and temperature to acquire enhanced mechanical properties depending on the combination of admixture used. Carbon Nanotubes (CNT), declared as "Miracle Material", have been one of the most recent admixtures being used to achieve the desired mechanical properties of cement slurries. This paper highlights the study carried out to examine the mechanical properties comprising compressive strength of oil well cement slurries integrating chemical additives and CNT under high pressure high temperature (HPHT) conditions. Three different percentages of functionalized multi-walled CNT's (MWCNT), at 0.1%, 0.25% and 0.5% bwoc, were mixed with Type-G oil well cement together with other additives used in HPHT applications. Compressive strength investigations (Destructive and UCA) were carried out on those slurries. SEM investigations were also conducted on selected MWCNT mixes. The study indicated that incorporation of MWCNT, at a very small percentage, in cement slurries resulted in a significant increase in the compressive strength values.
C-terminal peptide of thrombospondin-1 induces platelet aggregation through the Fc receptor γ-chain–associated signaling pathway and by agglutination (2001)

A peptide from the C-terminal domain of thrombospondin-1 (Arg-Phe-Tyr-Val-Val-Met-Trp-Lys; known as 4N1-1) has been reported to induce platelet aggregation and to bind to the integrin-associated protein (IAP), which is also known as CD47. In this study, it was discovered that 4N1-1 or its derivative peptide, 4N1K, induces rapid phosphorylation of the Fc receptor (FcR) gamma chain, Syk, SLP-76, and phospholipase C gamma2 in human platelets. A specific inhibitor of Src family kinases, 4-amino-4-(4-methylphenyl)-7-(t-butyl) pyrazola[3,4-d]pyrimidine, prevented phosphorylation of these proteins, abolished platelet secretion, and reduced aggregation by approximately 50%. A similar inhibition of aggregation to 4N1-1 was obtained in the presence of Arg-Gly-Asp-Ser in mouse platelets deficient in FcR gamma chain or SLP-76 and in patients with type I Glanzmann thrombasthenia. These results show that 4N1-1 signals through a pathway similar to that used by the collagen receptor glycoprotein (GP) VI. The alphaIIbbeta3-independent aggregation induced by 4N1-1 was also observed in fixed platelets and platelets from patients with Bernard-Soulier syndrome, which are deficient in GPIbalpha. Surprisingly, the ability of 4N1-1 to stimulate aggregation and tyrosine phosphorylation was not altered in platelets pretreated with anti-IAP antibodies and in IAP-deficient mice. These results show that the C-terminal peptide of thrombospondin induces platelet aggregation through the FcR gamma-chain signaling pathway and through agglutination. The latter pathway is independent of signaling events and does not use GPIbalpha or alphaIIbbeta3. Neither of these pathways is mediated by IAP.
The Complete Genome Sequence of <i> Bacillus licheniformis </i>DSM13, an Organism with Great Industrial Potential (2004)

The genome of Bacillus licheniformis DSM13 consists of a single chromosome that has a size of 4,222,748 base pairs. The average G+C ratio is 46.2%. 4,286 open reading frames, 72 tRNA genes, 7 rRNA operons and 20 transposase genes were identified. The genome shows a marked co-linearity with Bacillus subtilis but contains defined inserted regions that can be identified at the sequence as well as at the functional level. B. licheniformis DSM13 has a well-conserved secretory system, no polyketide biosynthesis, but is able to form the lipopeptide lichenysin. From the further analysis of the genome sequence, we identified conserved regulatory DNA motives, the occurrence of the glyoxylate bypass and the presence of anaerobic ribonucleotide reductase explaining that B. licheniformis is able to grow on acetate and 2,3-butanediol as well as anaerobically on glucose. Many new genes of potential interest for biotechnological applications were found in B. licheniformis; candidates include proteases, pectate lyases, lipases and various polysaccharide degrading enzymes.
Structure of a modified nucleoside in archaebacterial tRNA which replaces ribosylthymine. 1-Methylpseudouridine. (1982)

The structure of a modified nucleoside isolated from Halococcus morrhuae tRNA has been established as 1-methylpseudouridine, based on mass spectrometry and gas chromatography carried out on 0.2 A260 unit of material. Not previously found in nucleic acids, 1-methylpseudouridine appears to be unique to archaebacterial tRNA, where it replaces ribosylthymine in the T psi C loop of most of the tRNAs examined thus far.
Neural cells derived by in vitro differentiation of P19 and embryonic stem cells. (1998)

The past decade has seen great progress in understanding the key genes involved in GABAergic transmission. The genes for GAD, multiple subunits of the ionotropic GABA receptors, metabotropic GABA receptors, and GABA uptake proteins have been cloned. Analysis of the cloned genes has yielded a plethora of fundamental insights into the role of the corresponding proteins in mediating GABAergic signals (reviewed in Tobin et al. and Erlander and Tobin). Tools based on these new studies, ranging from monoclonal antibodies to gene probes, have also allowed detailed mapping of expression patterns in the central nervous system (CNS). These new studies reveal that some components of GABAergic transmission have a very wide distribution, being expressed by GABAergic neurons throughout the CNS. Others have a much more restricted pattern of expression. The highly specific expression of GABAergic genes poses a set of fundamental challenges to developmental neurobiology. What genetic mechanisms underlie these patterns of expression? How are complex structures such as receptors assembled? How do the components of a GABAergic synapse come to be localized in proximity to each other so as to make functional transmission possible? Cell lines that express GABAergic phenotypes play an important part in answering these and related questions. With appropriate cell lines it should be possible to manipulate genes related to the GABAergic phenotype in ways that shed light on these questions. Recently, work from several laboratories, including our own, has shown that two pluripotent cell lines from the mouse, the P19 embryonal carcinoma line and embryonic stem (ES) cells, are capable of differentiating into neuron-like cells with GABAergic phenotypes. Since these cell lines are highly suitable for genetic manipulation, they should be extremely useful for studying the relationship between GABA-related genes and the phenotypes they encode.
Molecular and Cellular Biology Associated with Endosperm Mobilization in Germinating Cereal Grains (1989)

Regulation de l'expression genique durant la germination de caryopses de cereales; contribution non seulement de l'aleurone mais aussi du scutellum dans la mobilisation de l'albumen
Temporal Ensembling for Semi-Supervised Learning (2016)

In this paper, we present a simple and efficient method for training deep neural networks in a semi-supervised setting where only a small portion of training data is labeled. We introduce self-ensembling, where we form a consensus prediction of the unknown labels using the outputs of the network-in-training on different epochs, and most importantly, under different regularization and input augmentation conditions. This ensemble prediction can be expected to be a better predictor for the unknown labels than the output of the network at the most recent training epoch, and can thus be used as a target for training. Using our method, we set new records for two standard semi-supervised learning benchmarks, reducing the (non-augmented) classification error rate from 18.44% to 7.05% in SVHN with 500 labels and from 18.63% to 16.55% in CIFAR-10 with 4000 labels, and further to 5.12% and 12.16% by enabling the standard augmentations. We additionally obtain a clear improvement in CIFAR-100 classification accuracy by using random images from the Tiny Images dataset as unlabeled extra inputs during training. Finally, we demonstrate good tolerance to incorrect labels.
Levels of Automation for Human Influence of Robot Swarms (2013)

Autonomous swarm algorithms and human-robot interaction (HRI) have both attracted increasing attention from researchers in recent years. However, HRI has rarely extended beyond single robots or small multi-robot teams. While one of the benefits of robot swarms is their robust capabilities and the ability of their distributed algorithms to deal autonomously with the complex interactions amongst swarm members, there is undoubtedly a need for humans to influence such swarms in some circumstances—especially when these swarms are operating in unknown or hostile environments. In this paper, we approach the problem of human-swarm interaction (HSI) using previous research in levels of automation (LOAs) in HRI. We create a target searching task whereby the swarm can operate at two different levels of autonomy: an autonomous dispersion algorithm, or user-defined goto points. We investigate what environmental conditions are conducive to different amounts of human influence, and at what point further human intervention has a detrimental effect on the swarm’s performance. The results show that for complex environments containing numerous obstacles and small passageways, there is indeed a need for some human influence; however, after a certain point, further influence causes performance degradation.
The Notch Ligand Jagged-1 Represents a Novel Growth Factor of Human Hematopoietic Stem Cells (2000)

The Notch ligand, Jagged-1, plays an essential role in tissue formation during embryonic development of primitive organisms. However, little is known regarding the role of Jagged-1 in the regulation of tissue-specific stem cells or its function in humans. Here, we show that uncommitted human hematopoietic cells and cells that comprise the putative blood stem cell microenvironment express Jagged-1 and the Notch receptors. Addition of a soluble form of human Jagged-1 to cultures of purified primitive human blood cells had modest effects in augmenting cytokine-induced proliferation of progenitors. However, intravenous transplantation of cultured cells into immunodeficient mice revealed that human (h)Jagged-1 induces the survival and expansion of human stem cells capable of pluripotent repopulating capacity. Our findings demonstrate that hJagged-1 represents a novel growth factor of human stem cells, thereby providing an opportunity for the clinical utility of Notch ligands in the expansion of primitive cells capable of hematopoietic reconstitution.
A Selective Phenelzine Analogue Inhibitor of Histone Demethylase LSD1 (2014)

Lysine-specific demethylase 1 (LSD1) is an epigenetic enzyme that oxidatively cleaves methyl groups from monomethyl and dimethyl Lys4 of histone H3 (H3K4Me1, H3K4Me2) and can contribute to gene silencing. This study describes the design and synthesis of analogues of a monoamine oxidase antidepressant, phenelzine, and their LSD1 inhibitory properties. A novel phenelzine analogue (bizine) containing a phenyl-butyrylamide appendage was shown to be a potent LSD1 inhibitor in vitro and was selective versus monoamine oxidases A/B and the LSD1 homologue, LSD2. Bizine was found to be effective at modulating bulk histone methylation in cancer cells, and ChIP-seq experiments revealed a statistically significant overlap in the H3K4 methylation pattern of genes affected by bizine and those altered in LSD1-/- cells. Treatment of two cancer cell lines, LNCaP and H460, with bizine conferred a reduction in proliferation rate, and bizine showed additive to synergistic effects on cell growth when used in combination with two out of five HDAC inhibitors tested. Moreover, neurons exposed to oxidative stress were protected by the presence of bizine, suggesting potential applications in neurodegenerative disease.
Effect of tumor necrosis factor alpha on insulin-dependent diabetes mellitus in NOD mice. I. The early development of autoimmunity and the diabetogenic process. (1994)

Tumor necrosis factor (TNF) alpha is a cytokine that has potent immune regulatory functions. To assess the potential role of this cytokine in the early development of autoimmunity, we investigated the effect of TNF on the development of insulin-dependent diabetes mellitus (IDDM) in nonobese diabetic (NOD) mice, a spontaneous murine model for autoimmune, insulin-dependent type I diabetes. Treatment of newborn female NOD mice with TNF every other day for 3 wk, led to an earlier onset of disease (10 versus 15 wk of age in control mice) and 100% incidence before 20 wk of age (compared to 45% at 20 wk of age in control phosphate-buffered saline treated female mice). In contrast, administration of an anti-TNF monoclonal antibody, TN3.19.12, resulted in complete prevention of IDDM. In vitro proliferation assays demonstrated that mice treated with TNF developed an increased T cell response to a panel of beta cell autoantigens, whereas anti-TNF treatment resulted in unresponsiveness to the autoantigens. In addition, autoantibody responses to the panel of beta cell antigens paralleled the T cell responses. The effects mediated by TNF appear to be highly age dependent. Treatment of animals either from birth or from 2 wk of age had a similar effect. However, if treatment was initiated at 4 wk of age, TNF delayed disease onset. These data suggest that TNF has a critical role in the early development of autoimmunity towards beta-islet cells.
Perspectives on socially shared cognition. (1991)

This volume contains reports on the way thought works, from investigators in psychology, social psychology, anthropology, sociology, linguistics and literature. It argues that our thinking is shaped by others in a process known as socially shared cognition.
Dry etched molybdenum silicide photomasks for submicron integrated circuit fabrication (1991)

The aim of this paper is to demonstrate a manufacturable molybdenum silicide mask process. Each step of the fabrication of a mask was addressed: lithography, dry etching, cleaning, inspection, and repair. SAL601 resist (Shipley) was chosen for the etch mask as dry etch resistance and almost vertical resist profiles are required [J. W. Thackeray, G. W. Orsula, E. Pavelcheck, D. Canistro, L. E. Bogan, A. K. Berry, and K. A. Graziano, Proc. SPIE 1086 (1989)]. Etching experiments of the molybdenum silicide were performed using different fluorinated gas mixtures. Two of them, CF4+O2, SF6+O2, were chosen and optimized for selectivity (ratio of molybdenum silicide etch rate versus resist etch rate) using a statistical experimental design approach. Results indicate a higher selectivity for the CF4+O2 mixture but lower loading effects for SF6+O2 leading to a better uniformity in the latter case. In both cases, the pressure was chosen low enough (below 200 mTorr to get anisotropic etching conditions even if the selectivity is reduced. Inspection has been performed using standard optical equipment from KLA Instrument Corporation. None of the defects found were related to lithography and dry etching processes. Repair feasibility has been demonstrated with both laser beam and focused ion beam (FIB). Thanks to its fine grain structure, very smooth edges have been obtained, after FIB repair, for molybdenum silicide as compared to chrome.
Polar Orientation of Dyes in Robust Multilayers by Zirconium Phosphate-Phosphonate Interlayers (1991)

Polar orientation of molecules in solids leads to materials with potentially useful properties such as nonlinear optical and electrooptical activity, electrochromism, and pyroelectricity. A simple self-assembly procedure for preparing such materials is introduced that yields multiple polar dye monolayers on solid surfaces joined by zirconium phosphate-phosphonate interlayers. Second harmonic generation (SHG) shows that the multilayers have polar order that does not decrease with increasing numbers (up to a large number) of monolayers in the film. The inorganic interlayers, as determined by SHG, impart excellent orientational stability to the dye molecules, with the onset of orientational randomization above 150 degrees C.