gebhart/patrepeval huggingface dataset:
Eukaryotic control on bacterial cell cycle and differentiation in the Rhizobium –legume symbiosis (2006)

Symbiosis between legumes and Rhizobium bacteria leads to the formation of root nodules where bacteria in the infected plant cells are converted into nitrogen-fixing bacteroids. Nodules with a persistent meristem are indeterminate, whereas nodules without meristem are determinate. The symbiotic plant cells in both nodule types are polyploid because of several cycles of endoreduplication (genome replication without mitosis and cytokinesis) and grow consequently to extreme sizes. Here we demonstrate that differentiation of bacteroids in indeterminate nodules of Medicago and related legumes from the galegoid clade shows remarkable similarity to host cell differentiation. During bacteroid maturation, repeated DNA replication without cytokinesis results in extensive amplification of the entire bacterial genome and elongation of bacteria. This finding reveals a positive correlation in prokaryotes between DNA content and cell size, similar to that in eukaryotes. These polyploid bacteroids are metabolically functional but display increased membrane permeability and are nonviable, because they lose their ability to resume growth. In contrast, bacteroids in determinate nodules of the nongalegoid legumes lotus and bean are comparable to free-living bacteria in their genomic DNA content, cell size, and viability. Using recombinant Rhizobium strains nodulating both legume types, we show that bacteroid differentiation is controlled by the host plant. Plant factors present in nodules of galegoid legumes but absent from nodules of nongalegoid legumes block bacterial cell division and trigger endoreduplication cycles, thereby forcing the endosymbionts toward a terminally differentiated state. Hence, Medicago and related legumes have evolved a mechanism to dominate the symbiosis.
Prevention of Kidney Ischemia/Reperfusion-induced Functional Injury and JNK, p38, and MAPK Kinase Activation by Remote Ischemic Pretreatment (2001)

MAPK activities, including JNK, p38, and ERK, are markedly enhanced after ischemia in vivo and chemical anoxia in vitro. The relative extent of JNK, p38, or ERK activation has been proposed to determine cell fate after injury. A mouse model was established in which prior exposure to ischemia protected against a second ischemic insult imposed 8 or 15 days later. In contrast to what was observed after 30 min of bilateral ischemia, when a second period of ischemia of 30- or 35-min duration was imposed 8 days later, there was no subsequent increase in plasma creatinine, decrease in glomerular filtration rate, or increase in fractional excretion of sodium. A shorter period of prior ischemia (15 min) was partially protective against subsequent ischemic injury 8 days later. Unilateral ischemia was also protective against a subsequent ischemic insult to the same kidney, revealing that systemic uremia is not necessary for protection. The ischemia-related activation of JNK and p38 and outer medullary vascular congestion were markedly mitigated by prior exposure to ischemia, whereas preconditioning had no effect on post-ischemic activation of ERK1/2. The phosphorylation of MKK7, MKK4, and MKK3/6, upstream activators of JNK and p38, was markedly reduced by ischemic preconditioning, whereas the post-ischemic phosphorylation of MEK1/2, the upstream activator of ERK1/2, was unaffected by preconditioning. Pre- and post-ischemic HSP-25 levels were much higher in the preconditioned kidney. In summary, post-ischemic JNK and p38 (but not ERK1/2) activation was markedly reduced in a model of kidney ischemic preconditioning that was established in the mouse. The reduction in JNK and p38 activation can be accounted for by reduced activation of upstream MAPK kinases. The post-ischemic activation patterns of MAPKs may explain the remarkable protection against ischemic injury observed in this model.
Turbulence modelling and numerical issues: from RANS to DNS and LES (2009)

The objective of this work is to show possibilities and limitations of different turbulence models from RANS to DNS and LES. Firstly, standard approaches based on time averaging the governing equations (the so called Reynolds Averaged Navier-Stokes equations or RANS models) are presented. Attention is focused on explicit algebraic and eddy-viscosity linear and non-linear two-equation models. Aspects related to forced and natural convection, low-Reynolds number approaches, numerical issues, etc. are shown.
A different simulation level is then presented: the Direct Numerical Simulation or DNS approach. This kind of analysis describes the whole range of the turbulent motion scales, from the largest ones (similar to the domain size) to the smallest ones (also called dissipative or Kolmogorov scales), where the fluctuations are damped and turbulent energy is irreversibly converted into internal energy. Aspects related to the discretization of the governing equations and the necessity of preserving some properties of the Navier-Stokes equations are pointed out. Examples are shown with emphasis on the possibilities and limitations of this important approach where no empirical inputs are needed at all.
The paper ends with promising turbulence models based on the full simulation of the largest scales of the turbulent flow, while the smaller ones are modelled. This is called Large Eddy Simulation or LES approach. Discussion starts with classical techniques based on modelling the non-linear interactions of the convective operator as a diffusion term. Afterwards, the use of regularization techniques as a large eddy simulation model is discussed. The formulation is based on symmetry-preserving discretization methodology on non-structured and collocated meshes. In this approach, the length of the filter is the only empirical parameter used by the model. Examples of both natural and forced convection in well-known benchmark cases, and also in industrial applications, are presented.
Studies on the Interaction of Lectins with Saccharides on Lymphocyte Cell Surfaces (1979)

Research carried out mainly during the last decade has attested to the importance of the carbohydrate moieties of glycoproteins and glycolipids in biological recognition between cells or between molecules and cells (1-4). Concomitantly, there has been increased activity in the study of carbohydrate-binding proteins such as glycosidases (5), lectins (6-9), anti-carbohydrate antibodies (10), toxins (such as the cholera and botulinum toxins), and glycoprotein hormones (e.g., thyrotropin and human chorionic gonadotropin) (11,12). Investigations of these carbohydrate binding proteins and their interaction with cells are providing essential clues to the structure of cell-surface sugars and their possible roles in growth, differentiation and development, and in malignant transformation. I. Properties of Lectins Lectins are cell agglutinating proteins of nonimmune origin that are widely distributed in nature, being found in plants, microorganisms and animals. They bind mono- or oligo-saccharides with remarkable specificity, in the same way as enzymes bind substrates and antibodies bind antigens.
Economic Feasibility of Transporting Natural Gas Hydrates in Slurry Pipelines (2014)

Natural Gas Hydrates are cage-like structures that are composed of natural gas (methane, ethane, etc.) molecules contained or entrapped within a water lattice. The hydrate structure contains tightly packed gas in ratios of over 160 to 1. Thus, there is a huge conceived upside to transporting the gas in this mode efficiency-wise if one could transport hydrates to a central processing facility where the hydrate would be processed to meet natural gas pipeline grid specifications. The question is: can they be transported in slurry form with water or oil as a carrier fluid, and what are the pros and cons of such mode of transportation. This paper attempts to answer these questions, and presents a feasibility analysis of three pipeline transportation scenarios to transport equivalent of 116 MMSCFD of natural gas over 500 km distance. It was found that for transportation of natural gas in the form of hydrates to be economically feasible, it has to be combined with transportation of crude oil as a carrying fluid rather than water, so that the cost of transportation per unit energy of the combined hydrates/oil slurry mixture is shared between the two energy commodities. This will result in even a lower cost below that of conventional transportation of natural gas in gaseous (vapour) form.
Transcription initiated by RNA polymerase II and transcription factors from liver. Structure and action of transcription factors epsilon and tau. (1991)

We have fractionated rat liver and identified a set of transcription factors that are essential for accurate initiation by RNA polymerase II. These factors were resolved into five distinct enzyme fractions designated alpha, beta gamma, delta, epsilon, and tau. Four of these fractions can now be replaced with purified proteins. alpha and beta gamma were previously purified to apparent homogeneity (Conaway, J. W., and Conaway, R. C. (1989) J. Biol. Chem. 264, 2357-2362). Here, we report purification to near homogeneity of transcription factor epsilon. Epsilon has a native molecular mass of approximately 90 kDa and is composed of 34- and 58-kDa polypeptides. Both the 34- and 58-kDa polypeptides are required for runoff transcription. In addition, we show that transcription factor tau is a rat liver homologue of the TATA factor (TFIID or BTF1) that can be efficiently replaced in transcription in vitro by recombinant yeast TFIID. Comparison of the two factors reveals, however, that they differ significantly in their abilities to direct the transcription system to discriminate between promoters of different sequences.
Multihormonal carcinoid tumor of the pancreas. Secreting growth hormone-releasing factor as a cause of acromegaly (1984)

This report describes the histologic, immunocytochemical, and ultrastructural study of a multihormonal carcinoid tumor of the pancreas, secreting a growth hormone releasing factor (GRF) which provoked acromegaly. The patient presented a nonfamilial multiple endocrine neoplasia, type 1. The absence of radiologic signs of a pituitary adenoma in conjunction with elevated plasma levels of pancreatic polypeptide, glucagon, somatostatin, as well as growth hormone (GH), led to the discovery of the tumor. Its surgical excision produced a rapid disappearance of most of the clinical and biologic disorders. No immunoreactive GH was found in the tumor using radioimmunoassay and immunocytochemistry. In contrast, three peptides with GH-releasing activity were extracted and characterized. Immunocytochemistry showed that the GRF-reactive cells, together with rare somatostatin-storing cells, made up areas which demonstrated a medullary pattern of growth with extracellular amyloid deposits. Under electron microscopic examination, actively secreting cells were observed which carried endocrine granules of 100 to 150 nm in diameter. The other regions of the tumor presented a different type of growth and were composed of pancreatic polypeptide-, glucagon-, or somatostatin-reacting cells. Cells immunostained with antisera raised against beta-endorphin were also noted. These data suggest that GRF may be a new biologic marker for pancreatic endocrine tumors.
<title>Novel scheme for a higher bandwidth sensor readout</title> (2002)

Circuit design for a novel scheme for converting a multiple- valued output voltage forma sensor into a binary-coded output for signal processing is described here. Floating gate MOSFETs and floating gate potential diagrams have been used to design a readout integrated circuit in a standard 1.5 micrometers digital CMOS VLSI technology. The physical design is simulated and tested with SPICE using MOSIS BSIM3 MOS model parameters. Initial results on fabricated devices for the conversion of quaternary input into binary output have shown agreement with the corresponding simulated values. The method is simple and compatible with current CMOS processes. The circuit can be integrated with output of a sensor fabricated in MEMS-CMOS technology.
Super Hi-Vision Video Parameters for Next-Generation Television (2012)

The crux of the move to ultrahigh-definition television is to simply deliver a wider field of view, which only requires an increase in pixel count to 3840 × 2160 or 7680 × 4320 pixels, which are well accepted standards. However, this overlooks important factors such as color/tone rendition and motion portrayal, which could be crucial to delivering an enhanced visual experience with next-generation television (next-gen TV) systems. To this end, system parameters are proposed including colorimetry and frame frequency for next-gen TV. The proposed colorimetry system is based on the real RGB color system and has a color gamut covering 99.9% of real surface colors while using physically realizable RGB primaries. Further, a frame frequency of 120 Hz is proposed on the basis of subjective assessments of motion picture quality.
Synthesis and Characterization of Chimeric 2‐5A‐DNA Oligonucleotides (2000)

This unit provides protocols for the synthesis and characterization of 2-5A-antisense nucleic acids. These chimeric oligonucleotides consist of 2',5'-phosphodiester-linked oligoadenylates ligated to 3',5'-deoxyribonucleotides and are readily prepared using phosphoramidite chemistry on CPG solid supports. The 3',5'-deoxyribonucleotide functions as the antisense domain to target a given mRNA sequence, while the 2',5'-phosphodiester-linked oligoadenylate serves to locally activate 2-5A-dependent RNase L, causing the targeted sequence to be cleaved.
Binary code suitable for line transmission (1969)

A practical method is described for encoding an unrestricted binary signal into a form suitable for transmission through a binary regenerated signal path while incurring only a small increase in modulation rate.
Sesquiterpene Coumarins and Related Derivatives from Ferula pallida (2000)

Six new compounds-two sesquiterpene coumarins, pallidones A and B (1, 2), and four related derivatives, pallidones C-F (3-6), as well as two known sesquiterpene coumarins, feselol (7) and conferol (8), have been isolated from the EtOAc extracts of the roots of Ferula pallida. All structures of these compounds were determined on the basis of spectral evidence, especially 2D NMR ((1)H-(1)H COSY, HSQC, HMBC, and NOESY) and HRMS. The possible biosynthetic pathway of pallidones C-F (3-6) is discussed.
Robust adaptive identification of dynamic systems by neural networks (2002)

This paper is concerned with the use of neural networks for robust and adaptive identification of dynamic systems. Two types of neural identifiers, that are robust to adaptation-unworthy environmental parameters and adaptive to adaptation-worthy ones, are discussed, one requiring online weight adjustment and the other not. Risk-sensitive criteria are proposed for both training neural identifiers off-line and adjusting their weights online. These criteria induce robust performance by emphasising large errors in an exponential manner. A robust adaptive neural identifier without online weight adjustment is a time lagged recurrent network (TLRN) synthesized from input/output data of the dynamic system at with respect to a risk-sensitive criterion. The neural identifier's ability to adapt to the adaptation-worthy environmental parameters is a manifestation of the ability of the TLRN to estimate these parameters internally. A robust adaptive neural identifier with online weight adjustment is a neural network with long- and short-term memories. The long-term memory, which consists of the nonlinear weights of the neural network, is determined in an a priori off-line training in such a way that it is independent of the adaptation-worthy variables. The short-term memory, which consists of the linear weights of the neural network, is adjusted online to adapt to the adaptation-worthy variables. The criteria used for both the off-line determination of the long-term memory and the online adjustment of the short-term memory are risk-sensitive to induce the neural identifier's robust performance.
Modulation of systemic hemostatic parameters by enoxaparin during gestation in women with thrombophilia and pregnancy loss (2005)

Recurrent pregnancy loss (PL) is associated with maternal thrombophilia and prophylaxis with low molecular weight heparin (LMWH) can improve pregnancy outcome in this setting. The aim of this study was to investigate the modulation of systemic hemostatic parameters by enoxaparin in women with recurrent PL and to evaluate plasmatic parameters that would potentially enable monitoring LMWH prophylaxis effect during pregnancy. Study group included 87 women with thrombophilia and PL treated with enoxaparin 40 mg daily vs. 40 mg twice daily. The control group comprised 40 women with normal pregnancies. Blood samples have been collected throughout the period starting at 5-10 weeks of gestation until 6-10 weeks postpartum. The determined plasmatic markers included: anti-Xa activity, total and free tissue factor pathway inhibitor (TFPI), D-dimer, prothrombin fragment 1+2 (PT1+2), activated protein C resistance (APC-SR) and free protein S. Successful pregnancy outcome was recorded in 70 (80.5%) women treated with enoxaparin, without correlation to enoxaparin dosage. Seventeen women (19.5%) had pregnancy loss at 16+/-7 (6-32) weeks of gestation. Anti-Xa levels at 10-15 weeks of gestation were higher (0.39+/-0.38 u/ml) in the successful pregnancy outcome group compared to the abortion group (0.22+/-0.2 u/ml). Prophylactic anti-Xa activity levels (0.28+/-0.13 u/ml) were documented from 15 weeks of gestation until delivery in the successful pregnancy outcome group. Significant increase in anti-Xa, total TFPI and free TFPI levels (P<0.001) was achieved after beginning of LMWH prophylaxis in successful pregnancy outcome group but not in the abortion group. D-dimer and PT1+2 levels appeared to be significantly increased while APC-SR and free protein S levels gradually decreased during pregnancy, with no difference between study groups. These results suggest that LMWH prophylaxis during pregnancy enables modulation of systemic hemostatic parameters via inhibition of factor Xa and increase in plasmatic total and free TFPI levels.
MEMBRANE DAMAGE INDUCED IN CULTURED HUMAN SKIN FIBROBLASTS BY UVA IRRADIATION (1993)

Irradiation of cultured human skin fibroblasts with ultraviolet light from 320 to 400 nm (UVA) leads to a decrease in the membrane fluidity exemplified by an enhanced fluorescence anisotropy of the lipophilic fluorescent probe 1-[4-trimethylamino)-phenyl]-6-phenylhexa-1,3,5-triene. This UVA-induced decrease in fluidity is associated with lactate dehydrogenase leakage in the supernatant. Vitamin E, an inhibitor of lipid peroxidation, exerts a protective effect on both phenomena. Therefore, this UVA-induced damage in membrane properties may be related to lipid peroxidation processes. Moreover, exponentially growing cells are more sensitive to these UVA-induced alterations than confluent cells.
Endocrinology of Pregnancy (2015)

A coordinated sequence of events must occur in order to establish and successfully maintain a healthy pregnancy. Synchrony between the development of the early embryo and establishment of a receptive endometrium is necessary to allow implantation and subsequent progression of pregnancy. The endocrinology of human pregnancy involves endocrine and metabolic changes that result from physiological alterations at the boundary between mother and fetus. Known as the feto-placental unit (FPU), this interface is a major site of protein and steroid hormone production and secretion. Many of the endocrine and metabolic changes that occur during pregnancy can be directly attributed to hormonal signals originating from the FPU. The initiation and maintenance of pregnancy depends primarily on the interactions of neuronal and hormonal factors. Proper timing of these neuro-endocrine events within and between the placental, fetal, and maternal compartments is critical in directing fetal growth and development and in coordinating the timing of parturition. Maternal adaptations to hormonal changes that occur during pregnancy directly affect the development of the fetus and placenta. Gestational adaptations that take place in pregnancy include establishment of a receptive endometrium; implantation and the maintenance of early pregnancy; modification of the maternal system in order to provide adequate nutritional support for the developing fetus; and preparation for parturition and subsequent lactation. For complete coverage of all related areas of Endocrinology, please visit our on-line FREE web-text, WWW.ENDOTEXT.ORG .
Finite element stress analysis of thin die detachment process (2003)

One of the major developments in high-density electronic packaging assembly processes is the capability of handling very thin semiconductor devices. In order to achieve high production yield in the assembly processes and high reliability for the final packages, careful study on the handling method of very thin dice is therefore needed. In this article, we focus on the die detachment process of very thin dice in the die bonding process. Both 2D and 3D finite element models are built to simulate the die detachment process of a thin die, which is adhered to a plastic adhesive film. We report the stress distribution of the die when it is subjected to a displacement load by multiple push-up pins.
A view toward the future of subsurface characterization: CAT scanning groundwater basins (2008)

In this opinion paper we contend that high‐resolution characterization, monitoring, and prediction are the key elements to advancing and reducing uncertainty in our understanding and prediction of subsurface processes at basin scales. First, we advocate that recently developed tomographic surveying is an effective and high‐resolution approach for characterizing the field‐scale subsurface. Fusion of different types of tomographic surveys further enhances the characterization. A basin is an appropriate scale for many water resources management purposes. We thereby propose the expansion of the tomographic surveying and data fusion concept to basin‐scale characterization. In order to facilitate basin‐scale tomographic surveys, different types of passive, basin‐scale, CAT scan technologies are suggested that exploit recurrent natural stimuli (e.g., lightning, earthquakes, storm events, barometric variations, river‐stage variations, etc.) as sources of excitations, along with implementation of sensor networks that provide long‐term and spatially distributed monitoring of excitation as well as response signals on the land surface and in the subsurface. This vision for basin‐scale subsurface characterization faces many significant technological challenges and requires interdisciplinary collaborations (e.g., surface and subsurface hydrology, geophysics, geology, geochemistry, information and sensor technology, applied mathematics, atmospheric science, etc.). We nevertheless contend that this should be a future direction for subsurface science research.