gebhart/patrepeval huggingface dataset:
High expression of the taurine transporter TauT in primary cilia of NIH3T3 fibroblasts (2005)

Taurine, present in high concentrations in various mammalian cells, is essential for regulation of cell volume, cellular oxidative status as well as the cellular Ca2+ homeostasis. Cellular taurine content is a balance between active uptake through the saturable, Na(+)-dependent taurine transporter TauT, and passive release via a volume-sensitive leak pathway. Here we demonstrate that: (i) TauT localizes to the primary cilium of growth-arrested NIH3T3 fibroblasts, (ii) long-term exposure to TNF(alpha) or hypertonic sucrose medium, i.e., growth medium supplemented with 100 mM sucrose, increases ciliary TauT expression and (iii) long-term exposure to hypertonic taurine medium, i.e., growth medium supplemented with 100 mM taurine, reduces ciliary TauT expression. These results point to an important role of taurine in the regulation of physiological processes located to the primary cilium.
Surface Structure and Interpretation (1996)

Combinatory Categorial Grammar (CCG) offers a new approach to the theory of natural language grammar. Coordination, relativization, and related prosodic phenomena have been analyzed in CCG in terms of a radically revised notion of surface structure. CCG surface structures do not exhibit traditional notions of syntactic dominance and command, and do not constitute an autonomous level of representation. Instead, they reflect the computations by which a sentence may be realized or analyzed, to synchronously define a predicate-argument structure, or logical form. Surface Structure and Interpretation shows that binding and control can be captured at this level, preserving the advantages of CCG as an account of coordination and unbounded dependency.The core of the book is a detailed treatment of extraction, a focus of syntactic research since the early work of Chomsky and Ross. The topics addressed include the sources of subject-object asymmetries and phenomena attributed to the Empty Category Principle (ECP), asymmetric islands, parasitic gaps, and the relation of coordination and extraction, including their interactions with binding theory. In his conclusion, the author relates CCG to other categorial and type-driven approaches and to proposals for minimalism in linguistic theory.Linguistic Inquiry Monograph No. 30
Low‐grade serous carcinomas of the ovary contain very few point mutations (2011)

It has been well established that ovarian low-grade and high-grade serous carcinomas are fundamentally different types of tumours. While the molecular genetic features of ovarian high-grade serous carcinomas are now well known, the pathogenesis of low-grade serous carcinomas, apart from the recognition of frequent somatic mutations involving KRAS and BRAF, is largely unknown. In order to comprehensively analyse somatic mutations in low-grade serous carcinomas, we applied exome sequencing to the DNA of eight samples of affinity-purified, low-grade, serous carcinomas. A remarkably small number of mutations were identified in seven of these tumours: a total of 70 somatic mutations in 64 genes. The eighth case displayed mixed serous and endometrioid features and a mutator phenotype with 783 somatic mutations, including a nonsense mutation in the mismatch repair gene, MSH2. We validated representative mutations in an additional nine low-grade serous carcinomas and 10 serous borderline tumours, the precursors of ovarian low-grade, serous carcinomas. Overall, the genes showing the most frequent mutations were BRAF and KRAS, occurring in 10 (38%) and 5 (19%) of 27 low-grade tumours, respectively. Except for a single case with a PIK3CA mutation, other mutations identified in the discovery set were not detected in the validation set of specimens. Our mutational analysis demonstrates that point mutations are much less common in low-grade serous tumours of the ovary than in other adult tumours, a finding with interesting scientific and clinical implications.
Preparation of13C and15N labelled RNAs for heteronuclear multi-dimensional NMR studies (1992)

A procedure is described for the efficient preparation of isotopically enriched RNAs of defined sequence. Uniformly labelled nucleotide 5'triphosphates (NTPs) were prepared from E.coli grown on 13C and/or 15N isotopically enriched media. These procedures routinely yield 180 mumoles of labelled NTPs per gram of 13C enriched glucose. The labelled NTPs were then used to synthesize RNA oligomers by in vitro transcription. Several 13C and/or 15N labelled RNAs have been synthesized for the sequence r(GGCGCUUGCGUC). Under conditions of high salt or low salt, this RNA forms either a symmetrical duplex with two U.U base pairs or a hairpin containing a CUUG loop respectively. These procedures were used to synthesize uniformly labelled RNAs and a RNA labelled only on the G and C residues. The ability to generate milligram quantities of isotopically labelled RNAs allows application of multi-dimensional heteronuclear magnetic resonance experiments that enormously simplify the resonance assignment and solution structure determination of RNAs. Examples of several such heteronuclear NMR experiments are shown.
Neuronal Chemorepellent Slit2 Inhibits Vascular Smooth Muscle Cell Migration by Suppressing Small GTPase Rac1 Activation (2006)

The Slits are secreted proteins with roles in axonal guidance and leukocyte migration. On binding to Robo receptors, Slit2 repels developing axons and inhibits leukocyte chemotaxis. Slit2 is cleaved into Slit2-N, a protein tightly binding to cell membranes, and Slit2-C, a diffusible fragment. In the present study, we characterized the functional role of Slit2-N in vascular smooth muscle cells (VSMCs) and the cell association properties of 2 truncated versions of Slit2-N. Here, we document for the first time that Slit2-N is a chemorepellent of VSMCs. Intact blood vessels expressed Slit2 and Robo receptors as demonstrated by immunohistochemistry and quantitative real time PCR. Recombinant Slit2-N prevented the platelet-derived growth factor (PDGF)-stimulated migration of VSMCs. Slit2-N also abrogated PDGF-mediated activation of small guanosine triphosphatase (GTPase) Rac1, a member of the Rho GTPase superfamily of proteins involved in regulating the actin cytoskeleton. Furthermore, Slit2-N inhibited the PDGF-induced formation of lamellipodia, a crucial cytoskeletal reorganization event for cell motility. Slit2-N had no effect on the PDGF-mediated increase in DNA synthesis determined by [3H]thymidine uptake, suggesting that VSMC growth is unaffected by Slit2. Analysis of 2 engineered Slit2-N fragments (Slit2-N/1118 and Slit2-N/1121) indicated that 3 amino acids upstream of the putative cleavage site (Arg1121, Thr1122) are involved in the association of Slit2-N to the cell membrane. Our data assign a novel functional role to Slit2 in vascular function and show that cell guidance mechanisms that operate in the developing central nervous system are conserved in VSMCs.
Detection and compensation of basis deviation in satellite-to-ground quantum communications (2014)

Basis deviation is the reference-frame deviation between a sender and receiver caused by satellite motion in satellite-to-ground quantum communications. It increases the quantum-bit error ratio of the system and must be compensated for to guarantee reliable quantum communications. We present a new scheme for compensating for basis deviation that employs a BB84 decoding module to detect basis deviation and half-wave plate to provide compensation. Based on this detection scheme, we design a basis-deviation compensation approach and test its feasibility in a voyage experiment. Unlike other polarization-correction schemes, this compensation scheme is simple, convenient, and can be easily implemented in satellite-to-ground quantum communications without increased burden to the satellite.
Effects of Food Restriction on Aging: Separation of Food Intake and Adiposity (2001)

Restricted feeding of rodents increases longevity, but its mechanism of action is not understood. We studied the effects of lifelong food restriction in genetically obese and normal mice of the same inbred strain in order to determine whether the reduction in food intake or the reduction in adiposity (the percentage of fatty tissue) was the critical component in retarding the aging process. This was possible because food-restricted obese ( ob/ob ) mice maintained a high degree of adiposity. In addition to determining longevities, changes with age were measured in collagen, immune responses, and renal function. Genetically obese female mice highly congenic with the C57BL/6J inbred strain had substantially reduced longevities and increased rates of aging in tail tendon collagen and thymus-dependent immune responses but not in urine-concentrating abilities. When their weight was held in a normal range by feeding restricted amounts, longevities were extended almost 50%, although these food-restricted ob/ob mice still had high levels of adiposity, with fat composing about half of their body weights. Their maximum longevities exceeded those of normal C57BL/6J mice and were similar to the longevities of equally food-restricted normal mice that were much leaner. Food-restricted ob/ob mice had greatly retarded rates of collagen aging, but the rapid losses with age in splenic immune responses were not mitigated. Thus, the extension of life-span by food restriction was inversely related to food consumption and corresponded to the aging rate of collagen. These results suggest that aging is a combination of independent processes; they show that reduced food consumption, not reduced adiposity, is the important component in extending the longevity of genetically obese mice. Reproduced by permission. David E. Harrison, Jonathan Archer, Clinton M. Astle, Effects of Food Restriction on Aging: Separation of Food Intake and Adiposity. Proc. Natl. Acad. Sci. U.S.A. 81 , 1835-1838 (1984).
The Anticonvulsant Action of Propofol on Epileptiform Activity in Rat Hippocampal Slices (2004)

We used extracellular electrophysiological recordings from the CA1 region in rat hippocampal slices to investigate the effects of propofol on the field excitatory postsynaptic potential (fEPSP), population spike, and epileptiform activity induced by a Mg(2+)-free condition. Propofol depressed the population spike, fEPSP, and epileptiform activity. Both aminophylline, a nonselective adenosine receptor antagonist, and 8-cyclopentyl-1,3-dipropylxanthine, an A(1) receptor antagonist, significantly reduced the effect of propofol on fEPSP amplitude. However, 3,7-dimethyl-1-propagylxanthine, an A(2) receptor antagonist, did not alter the effect of propofol on fEPSP amplitude. Picrotoxin, a specific chloride channel blocker, partly reduced the effect of propofol on epileptiform activity, but bicuculline, a competitive gamma-aminobutyric acid(A) receptor antagonist, failed to antagonize it. Aminophylline significantly reduced the action of propofol on the epileptiform activity. The anticonvulsant action of propofol was partly reduced by 8-cyclopentyl-1,3-dipropylxanthine, whereas 3,7-dimethyl-1-propagylxanthine failed to affect it. Adenosine depressed the amplitude of fEPSPs in a dose-dependent manner, and propofol enhanced this inhibition. The results demonstrated that, in rat hippocampal slices, propofol inhibits epileptiform activity. In addition, adenosine neuromodulation through the A(1) receptor may contribute to the anticonvulsant action of propofol.
Polymer latexes for cell-resistant and cell-interactive surfaces (2000)

Novel polymer latexes were prepared that can be applied in several ways for the control and study of cell behavior on surfaces. Acrylic latexes with glass transitions ranging from −30 to 100°C were synthesized by dispersion polymerization in a water and alcohol solution using an amphiphilic comb copolymer as a stabilizing agent. The comb had a poly(methyl methacrylate) backbone and hydrophilic poly(ethylene glycol) (PEG) side chains, which served to stabilize the dispersion and create a robust hydrophilic coating on the final latex particles. The end groups of the comb stabilizer can be selectively functionalized to obtain latex particles with a controlled density of ligands tethered to their surfaces. Latexes were prepared with adhesion peptides (RGD) linked to the surface of the acrylic beads to induce attachment and spreading of cells. Coalesced films obtained from the RGD-bearing latex particles promoted attachment of WT NR6 fibroblasts, while films from unmodified latex particles were resistant to these cells. Additionally, RGD-linked beads were embedded in cell-resistant comb polymer films to create cell-interactive surfaces with discrete clustered-ligand domains. Cell attachment and morphology were seen to vary with the surface density of the RGD-bearing latex beads. © 2000 John Wiley & Sons, Inc. J Biomed Mater Res, 50, 331–339, 2000.
Elastic Plasma-Protein-Film Blended with Platelet-Releasate Accelerates Healing of Diabetic Mouse Skin Wounds. (2005)

Abstract Numerous plasma proteins and cytokines derived from platelets mediate wound healing process that is characterized by the migration and differentiation of several cell populations that give rise to angiogenesis, collagen synthesis, wound contraction and re-epithelialization. To evaluate the efficacy of the blood derived factors in wound healing, we have exploited a novel wound dressing consisting of human plasma proteins and platelet-releasate. Human blood unit was drawn into a bag containing ACD after obtaining informed consent from healthy donors. Platelet-rich plasma was separated and the plasma proteins were concentrated together with platelets using cold ethanol precipitation method. The thrombin activity from the same unit was added to the concentrate, thereby leading to emergence of elastic soft layer consisting of the concentrated plasma proteins with platelet-relaseate (CPPP). The CPPP has enough strength to dress cutaneous wounds and contains considerable amount of cytokines and fibronectin (Table). We applied the CPPP to excisional skin wound in db/db mouse: a well-known animal model of impaired wound healing. Full-thickness skin defects were created on the mice symmetrically on both sides. One side of the wound was covered with the CPPP and the fresh clot from the same blood donor was applied to the other side as a control. Both of the wounds were then covered with polyurethane film. These wounds were evaluated 10 days after wounding. Bioactive factors for wound healing in the Serum and CPPP Serum CPPP (Day 0) CPPP (Day 7) ND = non-detectable, NE = not evaluated bFGF (pg/mL) ND 106 (75-150) 43 (21-72) VEGF (pg/mL) 172 (20-405) 870 (500-1125) 706 (550-1100) PDGF-AB (ng/mL) 30 (20-40) 68 (25-1670) 116 (100-140) TGF β1 (ng/mL) 43 (34-48) 218 (110-415) &gt;250 Fibronectin (mg/mL) 0.6 (0.2-0.8) 13 (8-20) NE CPPP sustains these cytokines at substantial level on Day 7 (Table), suggesting that these growth factors are delivered continuously to the wound. Every wound edge was traced and the area was measured. Skin sections were stained with anti-CD31 antibody to visualize the blood vessels and determined its density (i.e., number of blood vessels/mm2 in the section). The area of CPPP treated wounds significantly decreased compared with that of the control (65% vs. 94% of the original size, respectively, p=.032). The immunostained section revealed the striking effect of CPPP on vasculalization. The mean vascular density of CPPP treated wounds was 13.2/mm2. In contrast, that of the control wounds was 2.7/mm2 (p=.013). Our results suggest that CPPP is a promising bioactive dressing for the treatment of full-thickness skin wound. Every biological component of CPPP is from a unit of collected blood; namely, CPPP can be an entirely autologous biological dressing, suggesting that CPPP is free from the risk of transmission of pathogens through blood products. Taken together, we may be able to design and conduct a clinical trial to evaluate the efficacy of CPPP for patients with non-healing wound.
The systemic amyloidoses: clearer understanding of the molecular mechanisms offers hope for more effective therapies (2004)

Knowledge about the systemic amyloidoses has increased considerably during the last few years. This group of diseases is characterized by great biochemical variability, including at least 11 different amyloid fibril proteins and a remarkable range of clinical manifestations. With the understanding that the pathogenesis is different in the various forms of amyloidosis, it is now being increasingly accepted that an early and accurate diagnosis, including that of the underlying biochemical nature, is crucial for a successful treatment. The elucidation of the molecular mechanisms involved in amyloidogenesis is at the basis of the recent blossoming of new, innovative and more effective therapeutic approaches.
The effect of growth conditions of Corynebacterium glutamicum on the transformation frequency obtained by electroporation (1990)

A rapid and efficient method of transforming Corynebacterium glutamicum by electroporation is described. A number of factors are important in determining the level of transformation obtained. Cells grown in the presence of glycine and isonicotinic acid hydrazide and harvested in early exponential growth phase were much easier to transform. The recovery medium on which transformants were isolated also had a significant effect on the number of transformants obtained because cells were osmotically or electrochemically sensitive following electroporation. Transformation efficiencies of up to 5 x 10 5 transformants per g plasmid DNA with homologously derived DNA and 2 x 10 3 transformants per g of DNA derived from Escherichia coli were obtained.
Acaricidal Activity of Melaleuca alternifolia (Tea Tree) Oil (2004)

Documentation of resistance against antiectoparasitic compounds is increasing. Reported S scabiei treatment failures with lindane, crotamiton, and benzyl benzoate, as well as likely emerging resistance to 5% permethrin and oral ivermectin, are of concern and advocate for the identification and development of novel acaricidal drugs. Tea tree oil is a membrane-active biocide extracted from the tree M alternifolia. It is a principal antimicrobial in a wide range of pharmaceuticals sold in Australia, with the main active component being oxygenated terpenoids. The results suggest that TTO has a potential role as a new topical acaricide and confirm terpinen-4-ol as the primary active component.
A new pathway encompassing calpain 3 and its newly identified substrate cardiac ankyrin repeat protein is involved in the regulation of the nuclear factor‐κB pathway in skeletal muscle (2010)

A multiprotein complex encompassing a transcription regulator, cardiac ankyrin repeat protein (CARP), and the calpain 3 protease was identified in the N2A elastic region of the giant sarcomeric protein titin. The present study aimed to investigate the function(s) of this complex in the skeletal muscle. We demonstrate that CARP subcellular localization is controlled by the activity of calpain 3: the higher the calpain 3, the more important the sarcomeric retention of CARP. This regulation would occur through cleavage of the N-terminal end of CARP by the protease. We show that, upon CARP over-expression, the transcription factor nuclear factor NF-κB p65 DNA-binding activity decreases. Taken as a whole, CARP and its regulator calpain 3 appear to occupy a central position in the important cell fate-governing NF-κB pathway. Interestingly, the expression of the atrophying protein MURF1, one of NF-κB main targets, remains unchanged in presence of CARP, suggesting that the pathway encompassing calpain 3/CARP/NF-κB does not play a role in muscle atrophy. With NF-κB also having anti-apoptotic effects, the inability of calpain 3 to lower CARP-driven inhibition of NF-κB could reduce muscle cell survival, hence partly accounting for the dystrophic pattern observed in limb girdle muscular dystrophy 2A, a pathology resulting from the protease deficiency.
Structural basis for potency differences between GDF8 and GDF11 (2017)

These studies identify distinctive structural features of GDF11 that enhance its potency, relative to GDF8; however, the biological consequences of these differences remain to be determined.
Acidic fibroblast growth factor promotes vascular repair. (1991)

Intravascular injury to arteries can result in thickening of the intimal smooth muscle layer adjacent to the lumen by migration and proliferation of cells from the underlying medial smooth muscle layer accompanied by deposition of extracellular matrix. This pathological response, which decreases lumen diameter, might, in part, be the result of the access of smooth muscle cells to plasma and platelet-derived growth factors as a consequence of denudation of the overlying confluent monolayer of vascular endothelial cells. Injured rat carotid arteries were treated by i.v. administration of acidic fibroblast growth factor, a heparin-binding protein that is chemotactic and mitogenic for vascular endothelial cells. The growth factor treatment resulted in dose-dependent inhibition of intimal thickening with parallel promotion of endothelial regeneration over the injured area. Therefore, acidic fibroblast growth factor might be efficacious in the prevention of restenosis caused by intimal thickening following angioplasty in humans.
Real-Time Motion Planning for Agile Autonomous Vehicles (2002)

Planning the path of an autonomous, agile vehicle in a dynamic environment is a very complex problem, especially when the vehicle is required to use its full maneuvering capabilities. Recent efforts aimed at using randomized algorithms for planning the path of kinematic and dynamic vehicles have demonstrated considerable potential for implementation on future autonomous platforms. This paper builds upon these efforts by proposing a randomized path planning architecture for dynamical systems in the presence of fixed and moving obstacles. This architecture addresses the dynamic constraints on the vehicle's motion, and it provides at the same time a consistent decoupling between low-level control and motion planning. The path planning algorithm retains the convergence properties of its kinematic counterparts. System safety is also addressed in the face of finite computation times by analyzing the behavior of the algorithm when the available onboard computation resources are limited, and the planning must be performed in real time. The proposed algorithm can be applied to vehicles whose dynamics are described either by ordinary differential equations or by higher-level, hybrid representations. Simulation examples involving a ground robot and a small autonomous helicopter are presented and discussed.
Position Statement Executive Summary: Guidelines and Recommendations for Laboratory Analysis in the Diagnosis and Management of Diabetes Mellitus (2011)

The guidelines provide specific recommendations based on published data or derived from expert consensus. Several analytes are found to have minimal clinical value at the present time, and measurement of them is not recommended.