gebhart/patrepeval huggingface dataset:
ERMES-mediated ER-mitochondria contacts: molecular hubs for the regulation of mitochondrial biology (2010)

Organelles are separate yet interdependent units of eukaryotic cells. They provide an appropriate milieu for the catalysis of many biochemical reactions, and they must establish physical links to communicate and exchange metabolites throughout the cell. Interorganelle communication is an important, yet still poorly understood, aspect of cell biology. We recently identified a protein complex that we refer to as ERMES [endoplasmic reticulum (ER)-mitochondria encounter structure], the main function of which is to provide a tethering force between the ER and the mitochondria. This complex, composed of both ER and mitochondrial transmembrane proteins, is located at the interface of the two organelles and serves to zipper them together. Previous work had implicated several ERMES components in many different physiological processes. The identification of ERMES as an interorganelle tether allows us to re-examine the amply documented phenotypic consequences of the loss of this complex in the light of this new function, thus providing a unique opportunity to assess the physiological relevance of ER-mitochondria junctions. These phenotypes hint at a broad role for ER-mitochondria connections in regulating mitochondrial and cell physiology. In this Hypothesis, we speculate on the potential role of ER-mitochondria connections as hubs in regulating several aspects of mitochondrial biology, including the regulation of mitochondrial membrane biosynthesis, genome replication, Ca(2+) signaling and protein import. Finally, we discuss how cells might use ER-mitochondria communication to fine-tune these processes according to their metabolic needs.
A Designer Axially Chiral Amino Sulfonamide as an Efficient Organocatalyst for Direct Asymmetric <i>anti</i>‐Selective Mannich Reactions and <i>syn</i>‐Selective Cross‐Aldol Reactions (2009)

A direct asymmetric Mannich reaction using a novel axially chiral amino sulfonamide (S)-3 that is highly anti- and enantioselective has been developed. For instance, in the presence of a catalytic amount of (S)-3, the reactions between aldehydes and alpha-imino esters proceeded smoothly to give anti Mannich products with a significantly higher anti/syn ratio and enantioselectivity than previously possible. By utilizing N-Boc-protected aromatic imines instead of alpha-imino esters, the synthetically useful Boc protecting group and various aromatic or heteroaromatic substituents were installed into the anti Mannich products and consequently the substrate scope of the anti-selective Mannich reaction and the synthetic utility of the anti Mannich products have been expanded. The axially chiral amino sulfonamide (S)-3 has also been successfully applied to asymmetric direct cross-aldol reaction between two different aldehydes. The catalyst (S)-3 has the advantage of giving mainly syn products, whereas proline shows the opposite anti selectivity.
Event-Based Motion Segmentation by Motion Compensation (2019)

In contrast to traditional cameras, whose pixels have a common exposure time, event-based cameras are novel bio-inspired sensors whose pixels work independently and asynchronously output intensity changes (called "events"), with microsecond resolution. Since events are caused by the apparent motion of objects, event-based cameras sample visual information based on the scene dynamics and are, therefore, a more natural fit than traditional cameras to acquire motion, especially at high speeds, where traditional cameras suffer from motion blur. However, distinguishing between events caused by different moving objects and by the camera's ego-motion is a challenging task. We present the first per-event segmentation method for splitting a scene into independently moving objects. Our method jointly estimates the event-object associations (i.e., segmentation) and the motion parameters of the objects (or the background) by maximization of an objective function, which builds upon recent results on event-based motion-compensation. We provide a thorough evaluation of our method on a public dataset, outperforming the state-of-the-art by as much as 10%. We also show the first quantitative evaluation of a segmentation algorithm for event cameras, yielding around 90% accuracy at 4 pixels relative displacement.
Wavelength conversion from 1.3 to 1.55 mu m using split contact optical amplifiers (1991)

Wavelength conversion of data from an optical carrier at a wavelength of 1.31 mu m to an optical carrier within the 1.5- mu m telecommunications window was demonstrated using a split-contact semiconductor nonlinear Fabry-Perot optical amplifier. Conversion was achieved by modulating the amplifier gain seen by a 1.55- mu m continuous-wave signal by saturating an absorber section using a modulated 1.31- mu m signal. Data transfer was possible from 1.31 mu m up to wavelengths between 1.53 and 1.585 mu m for bit-rates of up to 400 Mb/s. The maximum output contrast ratio was 3:1 and the minimum power at 1.31 mu m required for switching was approximately 60 mu W. By optically pumping the amplifier to above the lasing threshold using the 1.31- mu m signal, conversion was obtained to a fixed multiwavelength output with a 10-dB contrast ratio.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Vacuum Assisted Venous Drainage Does Not Increase Trauma to Blood Cells (2001)

Although gravity drainage has been the standard technique for cardiopulmonary bypass (CPB), the development of min imally invasive techniques for cardiac surgery has renewed interest in using vacuum assisted venous drainage (VAVD) Dideco (Mirandola, Italy) has modified the D903 Avant oxygenator to apply a vacuum to its venous reservoir. The impact of VAVD on blood damage with this device is analyzed. Six calves (mean body weight, 71.3 +/- 4.1 kg) were con nected to CPB by jugular venous and carotid arterial cannu lation, with a flow rate of 4-4.51 L/min for 6 h. They were assigned to gravity drainage (standard D903 Avant oxygen ator, n = 3) or VAVD (modified D903 Avant oxygenator, n = 3). The animals were allowed to survive for 7 days. A standard battery of blood samples was taken before bypass, throughout bypass, and 24 h, 48 h, and 7 days after bypass. Analysis of variance was used for repeated measurements. Thrombocyte and white blood cell counts, corrected by hematocrit and normalized by prebypass values, were not significantly different between groups throughout all study periods. The same holds true for hemolytic parameters (lactate dehydrogenase [LDH] and plasma hemoglobin). Both peaked at 24 hr in the standard and VAVD groups: LDH, 2,845 +/- 974 IU/L vs. 2,537 +/- 476 IU/L (p = 0.65), respectively; and plasma hemoglobin, 115 +/- 31 mg/L vs. 89 +/- 455 mg/L (p = 0.45), respectively. In this experimental setup with prolonged perfusion time, VAVD does not increase trauma to blood cells in comparison with standard gravity drainage.
Preservation of Biospecimens at Ambient Temperature: Special Focus on Nucleic Acids and Opportunities for the Biobanking Community (2016)

Several approaches to the preservation of biological materials at ambient temperature and the relative impact on sample stability and degradation are reviewed, with a focus on nucleic acids. This appraisal is undertaken within the framework of biobank risk, quality management systems, and accreditation, with a view to assessing how best to apply ambient temperature sample storage to ensure stability, reduce costs, improve handling logistics, and increase the efficiency of biobank procedures.
mTOR signaling controls iNKT cell differentiation and effector function (HEM3P.278) (2014)

Abstract Invariant natural killer T (iNKT) cells represent a unique T cell lineage that bears NK cell markers and a semi-invariant TCR recognizing glycolipids in the context of CD1d presentation. iNKT cells rapidly produce a variety of cytokines such as IFNg, IL-4, IL-2, IL-10 upon stimulation. Thus, iNKT cells play critical roles in bridging innate and adaptive immunity and have been implicated in multiple physiological and pathological settings. iNKT cells exhibit high proliferative capacity compared with conventional T cells during early stage development in the thymus. The mammalian target of rapamycin (mTOR) is a highly conserved serine/threonine kinase that integrates various environmental cues to regulate cell growth, proliferation and metabolism. Given the significance of mTOR signaling in controlling cell proliferation and metabolism, we have explored the role of mTORC1 and mTORC2 in iNKT cell development and function by using mice with T cell-restricted deletion of Raptor or Rictor. Here, we show, on the one hand, that mTORC1 is selectively required for iNKT cell but not for conventional T cells or Treg thymic development. On the other hand, mTORC2 is required to a lesser extent for thymic development as well as effector function of iNKT cells. In this regard, proper iNKT cell development and acquisition of effector functions is under the control of a dedicated mTOR signaling.
Seed‐specific overexpression of a potato sucrose transporter increases sucrose uptake and growth rates of developing pea cotyledons (2002)

During the storage phase, cotyledons of developing pea seeds are nourished by nutrients released to the seed apoplasm by their maternal seed coats. Sucrose is transported into pea cotyledons by sucrose/H+ symport mediated by PsSUT1 and possibly other sucrose symporters. PsSUT1 is principally localised to plasma membranes of cotyledon epidermal and subepidermal transfer cells abutting the seed coat. We tested the hypothesis that endogenous sucrose/H+ symporter(s) regulate sucrose import into developing pea cotyledons. This was done by supplementing their transport activity with a potato sucrose symporter (StSUT1), selectively expressed in cotyledon storage parenchyma cells under control of a vicilin promoter. In segregating transgenic lines, enhanced [(14)C]sucrose influx into cotyledons above wild-type levels was found to be dependent on StSUT1 expression. The transgene significantly increased (approximately 2-fold) transport activity of cotyledon storage parenchyma tissues where it was selectively expressed. In contrast, sucrose influx into whole cotyledons through the endogenous epidermal transfer cell pathway was increased by only 23% in cotyledons expressing the transgene. A similar response was found for rates of biomass gain by intact cotyledons and by excised cotyledons cultured on a sucrose medium. These observations demonstrate that transport activities of sucrose symporters influence cotyledon growth rates. The attenuated effect of StSUT1 overexpression on sucrose and dry matter fluxes by whole cotyledons is consistent with a large proportion of sucrose being taken up at the cotyledonary surface. This indicates that the cellular location of sucrose transporter activity plays a key role in determining rates of sucrose import into cotyledons.
Dual‐functional, aromatic, epoxy‐methacrylate monomers from bio‐based feedstocks and their respective epoxy‐functional thermoplastics (2020)

ABSTRACT Dual‐functional monomers consist of two distinctly different functional groups that enable chemical versatility. The most readily available epoxy‐methacrylate dual‐functional monomer is glycidyl methacrylate (GMA). In an effort to produce bio‐based, aromatic complements to GMA, asymmetric phenolic diols (vanillyl alcohol, syringyl alcohol, gastrodigenin, and tyrosol) were identified and selectively epoxidized at the aromatic hydroxyl followed by subsequent esterification at the aliphatic hydroxyl to prepare dual functional monomers, vanillyl alcohol epoxy‐methacrylate (VAEM), syringyl alcohol epoxy‐methacrylate (SAEM), gastrodigenin epoxy‐methacrylate (GDEM), and tyrosol epoxy‐methacrylate (TEM). These monomers are viable platforms for a multitude of applications due to their unique chemical functionalities. VAEM, SAEM, GDEM, and TEM were homopolymerized individually to produce aromatic, bio‐based epoxy‐functional thermoplastics analogous to poly(GMA). The molecular weight distributions and thermal properties of each polymer were evaluated, as were the surface characteristics of flow‐coated thin films from these polymers. Most of the newly prepared epoxy‐functional thermoplastics exhibited increased thermal stability (initial decomposition temperatures >260 °C in air) relative to poly(GMA), while retaining similar glass transition temperatures (~ 65 °C) and surface energies (~ 53 mJ m −2 ); thus, these materials could be substituted for poly(GMA) and enable use in higher‐temperature applications. © 2020 Wiley Periodicals, Inc. J. Polym. Sci. 2020 , 58 , 673–682
Lessons Learned from Targeting IGF-I Receptor in Thyroid-Associated Ophthalmopathy (2021)

Complex immunological mechanisms underlie the pathogenesis of thyroid-associated ophthalmopathy (TAO). Historical models of Graves' disease and TAO have focused almost entirely on autoimmune reactivity directed against the thyrotropin receptor (TSHR). The insulin-like growth factor-I receptor (IGF-IR) has been proposed as a second participating antigen in TAO by virtue of its interactions with IGFs and anti-IGF-IR antibodies generated in Graves' disease. Furthermore, the IGF-IR forms with TSHR a physical and functional complex which is involved in signaling downstream from both receptors. Inhibition of IGF-IR activity results in attenuation of signaling initiated at either receptor. Based on the aggregate of findings implicating IGF-IR in TAO, the receptor has become an attractive therapeutic target. Recently, teprotumumab, a human monoclonal antibody IGF-IR inhibitor was evaluated in two clinical trials of patients with moderate to severe, active TAO. Those studies revealed that teprotumumab was safe and highly effective in reducing disease activity and severity. Targeting IGF-IR with specific biologic agents may result in a paradigm shift in the therapy of TAO.
Transient activation of RAF-1, MEK, and ERK2 coincides kinetically with ternary complex factor phosphorylation and immediate-early gene promoter activity in vivo. (1994)

We have investigated the early in vivo signaling events triggered by serum that lead to activation of the c-fos proto-oncogene in HeLa cells. Both RAF-1 and MEK kinase activities are fully induced within 3 min of serum treatment and quickly decrease thereafter, slightly preceding the activation and inactivation of p42MAPK/ERK2. ERK2 activity correlates tightly with a transient phosphatase-sensitive modification of ternary complex factor (TCF), manifested by the slower electrophoretic mobility of TCF-containing protein-DNA complexes. These induced complexes in turn correlate with the activity of the c-fos, egr-1, and junB promoters. Phorbol ester treatment induces the same events but with slower and prolonged kinetics. Inhibition of serine/threonine phosphatase activities by okadaic acid treatment reverses the repression of the c-fos promoter either after induction or without induction. This corresponds to the presence of the induced complexes and of ERK2 activity, as well as to the activation of a number of other kinases. Inhibition of tyrosine phosphatase activities by sodium vanadate treatment delays but does not block ERK2 inactivation, TCF dephosphorylation, and c-fos repression. The tight linkage in vivo between the activity of MAP kinase, TCF phosphorylation, and immediate-early gene promoter activity is consistent with the notion that a stable ternary complex over the serum response element is a direct target for the MAP kinase signaling cascade. Furthermore, serine/threonine phosphatases are implicated in regulating the kinase cascade, as well as the state of TCF modification and c-fos promoter activity, in vivo.
Role of reciprocal exchange, one-ended invasion crossover and single-strand annealing on inverted and direct repeat recombination in yeast: different requirements for the RAD1, RAD10, and RAD52 genes. (1995)

We have constructed novel DNA substrates (one inverted and three direct repeats) based on the same 0.6-kb repeat sequence to study deletions and inversions in Saccharomyces cerevisiae. Spontaneous deletions occur six to eight times more frequently than inversions, irrespective of the distance between the repeats. This difference can be explained by the observation that deletion events can be mediated by a recombination mechanism that can initiate within the intervening sequence of the repeats. Spontaneous and double-strand break (DSB)-induced deletions occur as RAD52-dependent and RAD52-independent events. Those deletion events initiated through a DSB in the unique intervening sequence require the Rad1/Rad10 endonuclease only if the break is distantly located from the flanking DNA repeats. We propose that deletions can occur as three types of recombination events: the conservative RAD52-dependent reciprocal exchange and the nonconservative events, one-ended invasion crossover, and single-strand annealing (SSA). We suggest that one-ended invasion is RAD52 dependent, whereas SSA is RAD52 independent. Whereas deletions, like inversions, occur through reciprocal exchange, deletions can also occur through SSA or one-ended invasion. We propose that the contribution of reciprocal exchange and one-ended invasion crossover vs. SSA events to overall spontaneous deletions is a feature specific for each repeat system, determined by the initiation event and the availability of the Rad52 protein. We discuss the role of the Rad1/Rad10 endonuclease on the initial steps of one-ended invasion crossover and SSA as a function of the location of the initiation event relative to the repeats. We also show that the frequency of recombination between repeats is the same independent of their location (whether on circular plasmids, linear minichromosomes, or natural chromosomes) and have similar RAD52 dependence.
Purification and culture of adult rat dorsal root ganglia neurons (1989)

To study the trophic requirements of adult rat dorsal root ganglia neurons (DRG) in vitro, we developed a purification procedure that yields highly enriched neuronal cultures. Forty to fifty ganglia are dissected from the spinal column of an adult rat. After enzymatic and mechanical dissociation of the ganglia, myelin debris are eliminated by centrifugation on a Percoll gradient. The resulting cell suspension is layered onto a nylon mesh with a pore size of 10 microns. Most of the neurons, the diameter of which ranged from 17 microns to greater than 100 microns, are retained on the upper surface of the sieve; most of the non-neuronal cells with a caliber of less than 10 microns after trypsinization go through it. Recovery of neurons is achieved by reversing the mesh onto a Petri dish containing culture medium. Neurons to non-neurons ratio is 1 to 10 in the initial cell suspension and 1 to 1 after separation. When these purified neurons are seeded at a density of 3,000 neurons/cm2 in 6 mm polyornithine-laminin (PORN-LAM) coated wells, neuronal survival (assessed by the ability to extend neurites), measured after 48 hr of culture, is very low (from 0 to 16%). Addition of nerve growth factor (NGF) does not improve neuronal survival. However, when neurons are cultured in the presence of medium conditioned (CM) by astrocytes or Schwann cells, 60-80% of the seeded, dye-excluding neurons survive. So, purified adult DRG neurons require for their short-term survival and regeneration in culture, a trophic support that is present in conditioned medium from PNS or CNS glia.(ABSTRACT TRUNCATED AT 250 WORDS)
Mitochondrial Metabolism Modulates Differentiation and Teratoma Formation Capacity in Mouse Embryonic Stem Cells (2008)

Relatively little is known regarding the role of mitochondrial metabolism in stem cell biology. Here we demonstrate that mouse embryonic stem cells sorted for low and high resting mitochondrial membrane potential (DeltaPsi(m)L and DeltaPsi(m)H) are indistinguishable morphologically and by the expression of pluripotency markers, whereas markedly differing in metabolic rates. Interestingly, DeltaPsi(m)L cells are highly efficient at in vitro mesodermal differentiation yet fail to efficiently form teratomas in vivo, whereas DeltaPsi(m)H cells behave in the opposite fashion. We further demonstrate that DeltaPsi(m) reflects the degree of overall mammalian target of rapamycin (mTOR) activation and that the mTOR inhibitor rapamycin reduces metabolic rate, augments differentiation, and inhibits tumor formation of the mouse embryonic stem cells with a high metabolic rate. Taken together, our results suggest a coupling between intrinsic metabolic parameters and stem cell fate that might form a basis for novel enrichment strategies and therapeutic options.
Therapeutic CD94/NKG2A blockade improves natural killer cell dysfunction in chronic lymphocytic leukemia (2016)

Natural killer (NK)-cell count is predictive of chronic lymphoid leukemia (CLL) disease progression and their dysfunction is well documented, but the etiology of this is currently lacking. CLL cells have been shown to over-express HLA-E, the natural ligand for NKG2A expressed on NK-cells that generates a distinct negative signal relative to direct NK-cell cytotoxicity in other disease models. Utilizing a novel anti-NKG2A monoclonal blocking antibody (mAb), monalizumab, we explored the <i>in vitro</i> preclinical activity of targeting the NKG2A receptor, and the NKG2A/HLA-E interaction as a mechanism of tumor evasion in CLL patients. Our work confirmed overexpression of HLA-E on CLL B-cells and demonstrated NKG2A expression on CD56+/16+ NK-cells from CLL patients. We also demonstrate that blocking NKG2A on CLL NK-cells was sufficient to restore direct cytotoxicity ability of NK-cells against HLA-E-expressing targets without impacting NK-cell mediated antibody-dependent cellular cytotoxicity. Additionally, we proved the specificity of monalizumab in blocking NKG2A through Fc-blocking mechanisms. This paper provides justification for the potential clinical utility of monalizumab in the treatment of patients with CLL.
O PROBLEMA DA REMOÇÃO DE ÍONS SULFATO NO REÚSO DE ÁGUAS TRATADAS DE DAM´s NO SUL DO BRASIL (2011)

Uma série de estudos de tratamento de efluentes ácidos da mineração de carvão (DAMs) no sul do Brasil tem sido publicada nos últimos anos e operações industriais (ETE´s) já existem desde 2006. Entretanto, o destino da água tratada continua a ser discutido e o reuso para fins mais nobres é dificultada pela remoção ineficiente dos íons sulfato. O principal problema é diminuir a concentração de 1800 mg.L-1, (solubilidade das espécies tipo CaSO4), para valores limites de potabilidade e de qualidade de águas doces, de 250 mg.L-1 de SO4-2. Frente a este desafio técnico, que é mundial, este trabalho tem como objetivo o desenvolvimento e discussão de uma nova alternativa técnica de precipitação de íons sulfato presentes em DAM de carvão, via interação desses ânions com espécies de alumínio em pH 4,5. A pesquisa incluiu estudos de caracterização dos precipitados coloidais em função do pH e da razão Al:SO4-2 (tamanho, MEV-EDS, DRX, FRX, potencial zeta) e estudos experimentais de remoção pelo processo PF-SL-precipitacão-floculação e sedimentação lamelar em nível de bancada e piloto. A distribuição do tamanho dos precipitados Al- SO4-2 em pH 4,5 variou entre partículas finas (
Probing based wireless channel bandwidth estimation and its application to video streaming over wireless networks (2008)

We propose an efficient bandwidth estimation method to wireless networks. In the proposed method, the available bandwidth (AB) is estimated based on a packet pair probing technique (PPPT) that is a well-known mechanism for measuring the capacity of an end-to-end path without any information of network routers. To adapt the PPPT to the wireless network, in this paper, the cross traffic and the capacity variation of wireless link are considered to estimate the AB. We also introduce a video streaming application using the estimated AB. Experimental results show that the proposed method does not only estimate the accurate bandwidth, but also improve the performance of video streaming application over wireless networks.