gebhart/patrepeval huggingface dataset:
Fidelity of the eukaryotic codon-anticodon interaction: interference by aminoglycoside antibiotics (1984)

A homologous in vitro method was developed from Tetrahymena for ribosomal A-site binding of aminoacyl-tRNA to poly(uridylic acid)-programmed ribosomes with very low error frequency. The reaction mixture pH was the crucial factor in the stable A-site association of aminoacyl-tRNA with high fidelity. At a pH greater than 7.1, endogenous activity translocated A-site-bound aminoacyl-tRNA to the P site. If translocation was allowed to occur, a near-cognate amino-acyl-tRNA, Leu-tRNA, could stably bind to the ribosome by translocation to the ribosomal P site. Near-cognate aminoacyl-tRNA did not stably bind to either site when translocation was blocked. Misreading antibiotics stimulated the stable association of near-cognate aminoacyl-tRNA to the ribosomal A site, thereby increasing the error frequency by several orders of magnitude. Ribosome binding of total aminoacyl-tRNA near equilibrium was not inhibited by misreading antibiotics; however, initial rate kinetics of the binding reaction were dramatically altered such that a 6-fold rate increase was observed with paromomycin or hygromycin B. The rate increase was evident with both cognate and near-cognate aminoacyl-tRNAs. Several antibiotics were tested for misreading potency by the ribosome binding method. We found gentamicin G418 greater than paromomycin greater than neomycin greater than hygromycin B greater than streptomycin in the potentiation of misreading. Tetracycline group antibiotics effectively inhibited A-site aminoacyl-tRNA binding without promoting misreading.
Thermodynamics of intersubunit interactions in cholera toxin upon binding to the oligosaccharide portion of its cell surface receptor, ganglioside GM1 (1989)

The binding and the energetics of the interaction of cholera toxin with the oligosaccharide portion of ganglioside GM1 (oligo-GM1), the toxin cell surface receptor, have been studied by high-sensitivity isothermal titration calorimetry and differential scanning calorimetry. Previously, we have shown that the association of cholera toxin to ganglioside GM1 enhances the cooperative interactions between subunits in the B-subunit pentamer [Goins, B., & Freire, E. (1988) Biochemistry 27, 2046-2052]. New experiments presented in this paper reveal that the oligosaccharide portion of the receptor is by itself able to enhance the intersubunit cooperative interactions within the B pentamer. This effect is seen in the protein unfolding transition as a shift from independent unfolding of the B promoters toward a cooperative unfolding. To identify the origin of this effect, the binding of cholera toxin to oligo-GM1 has been measured calorimetrically under isothermal conditions. The binding curve at 37 degrees C is sigmoidal, indicating cooperative binding. The binding data can be described in terms of a nearest-neighbor cooperative interaction binding model. In terms of this model, the association of a oligo-GM1 molecule to a B protomer affects the association to adjacent B promoters within the pentameric ring. The measured intrinsic binding enthalpy per protomer is -22 kcal/mol and the cooperative interaction enthalpy -11 kcal/mol. The intrinsic binding constant determined calorimetrically is 1.05 x 10(6) M-1 at 37 degrees C and the cooperative Gibbs free energy equal to -850 cal/mol.(ABSTRACT TRUNCATED AT 250 WORDS)
Supramolecular Liquid Crystal Displays Construction and Applications (2004)

This thesis describes chemical methodologies, which can be ued to construct alignment layers for liquid crystal display purposes in a non-clean room environment, by making use of supramolecular chemistry. These techniques are subsequently used to attain control over LCD-properties, both pre- and post-LCD construction. In addition, the thesis describes the application of LCD technology in biosensors.
Bit Error Probability and Computational Complexity of Bi-directonal Fano Multiple Symbol Differential Detectors (2006)

We present in the paper a suboptimal multiple-symbol differential detector (MSDD) for differential PSK (DPSK) in Rayleigh flat fading channel that uses the Fano Algorithm as its decoding engine. In contrast to a conventional Fano decoder that only searches forward in time for the most promising transmitted pattern, our Fano decoder searches also in the reverse direction, thus providing a mechanism for error detection and correction. The resultant detector, termed a Bi-Fano MSDD, is capable of delivering excellent error performance at moderate implementation complexity over a wide range of signal-to-noise ration (SNR) and fading rates. As an example, for DQPSK modulation and a Doppler frequency of 3 percent the symbol rate, our Bi-Fano MSDD attains almost the same bit-error probability (BEP) performance as the sphere decoder (an efficient implementation of the optimal MSDD) and there is no noticeable irreducible error floor. The most interesting thing is that the computational complexity of the Bi-Fano MSDD is a very stable function of the SNR. In contrast, the sphere decoder has a complexity that grows exponentially as the SNR decreases. In conclusion, the Bi-Fano MSDD incorporates the desirable attributes of the sphere decoder and the DF-DD into one single embodiment. This is consistent with the observation that the Fano decoder is essentially an intelligent DF-DD that uses the accumulated path metric and a running threshold to guide its movement along the decoding tree
HIV infection of monocytes inhibits the T-lymphocyte proliferative response to recall antigens, via production of eicosanoids. (1992)

Human monocytes infected in vitro with human immunodeficiency virus (HIV) soon after adherence to plastic substrate demonstrated a significantly decreased ability to restimulate autologous immune T-lymphocyte proliferation after exposure to soluble (tetanus toxoid) and particulate [herpes simplex virus (HSV)] antigen. Incubation with the cyclo-oxygenase inhibitor, indomethacin (2-5 microM), prevented inhibition of antigen-stimulated lymphocyte proliferation. The inhibitory activity was identified in ultrafiltrates containing the low molecular weight fraction (less than 3000 MW) of supernatants from HIV-infected monocyte cultures. This activity was significantly and markedly reduced in similar ultrafiltrates prepared from indomethacin-treated cultures. Increased concentrations of prostaglandin E2 (PGE2) were detected in ultrafiltrates from HIV-infected monocyte cultures compared with uninfected cultures and cultures preincubated with indomethacin. Ultrafiltrates were inhibitory when added during the presentation of antigen to T lymphocytes but not when removed from monocyte cultures prior to the addition of lymphocytes. In addition, ultrafiltrates inhibited antigen-stimulated lymphocyte proliferation and PHA-induced lymphocyte proliferation to the same extent. These data indicate that cyclo-oxygenase products of arachidonic acid, including PGE2, are produced in excess by HIV-infected monocytes and that PGE2 and perhaps other cyclo-oxygenase products are implicated in the inhibition of antigen-stimulated lymphocyte proliferation via a direct effect on T lymphocytes.
“Humanized” Stem Cell Culture Techniques: The Animal Serum Controversy (2011)

Cellular therapy is reaching a pinnacle with an understanding of the potential of human mesenchymal stem cells (hMSCs) to regenerate damaged tissue in the body. The limited numbers of these hMSCs in currently identified sources, like bone marrow, adipose tissue, and so forth, bring forth the need for their in vitro culture/expansion. However, the extensive usage of supplements containing xenogeneic components in the expansion-media might pose a risk to the post-transplantation safety of patients. This warrants the necessity to identify and develop chemically defined or "humanized" supplements which would make in vitro cultured/processed cells relatively safer for transplantation in regenerative medicine. In this paper, we outline the various caveats associated with conventionally used supplements of xenogenic origin and also portray the possible alternatives/additives which could one day herald the dawn of a new era in the translation of in vitro cultured cells to therapeutic interventions.
Osteoclast formation from mononuclear phagocytes: role of bone-forming cells. (1984)

In a previous study, using co-cultures of embryonic bone rudiments stripped of periosteum, and mononuclear phagocytes of various sources, we found that multinucleated mineral-resorbing osteoclasts developed in vitro from radiosensitive mouse bone marrow mononuclear phagocytes (BMMP). (Burger, E. H., J. W. M. van der Meer, J. S. van de Gevel, C. W. Thesingh, and R. van Furth, 1982, J. Exp. Med. 156:1604-1614). In the present study, this co-culture technique was used to analyze the influence of bone-forming cells on osteoclast formation and bone resorption by BMMP or peritoneal exudate cells (PEC). BMMP or PEC were co-cultured with liver or dead bone, i.e., in the presence or absence of liver bone-forming cells. Mineral resorption and osteoclast formation were monitored via 45Ca release from prelabeled live or dead bone followed by histology. Osteoclasts developed from precultured BMMP as indicated by [3H]thymidine labeling, but only in live and not in dead bone. They formed readily from BMMP but only erratically, and after a longer culture period, from PEC. Macrophages from BMMP and PEC invaded live and dead bone rudiments but did not resorb the intact mineralized matrix. In contrast, ground bone powder was resorbed avidly by both cell populations, without formation of osteoclasts. We conclude that live bone-forming cells are required for osteoclast formation from progenitors. Live bone is only resorbed by osteoclasts, and not by macrophages. Osteoclast progenitors are abundant in cultures of BMMP but scarce in PEC, which makes a direct descendance of osteoclasts from mature macrophages unlikely.
Molecular Forms of Acetylcholinesterase and Butyrylcholinesterase in Human Plasma and Cerebrospinal Fluid (1987)

The measurement of cholinesterase activities in either plasma or cerebrospinal fluid (CSF) may ultimately prove to be relevant in the diagnosis of neurological and neuropsychiatric disorders. However, studies to date have examined only total enzyme activities. Therefore in the present study we have examined the distribution of the individual molecular forms of both acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) in plasma and CSF using sucrose density gradient centrifugation. Although the total activities of AChE were of the same order of magnitude in plasma and CSF, there was a considerable difference (120-500-fold) between total BChE activity in the CSF and the BChE-rich plasma. The analysis of the individual molecular forms revealed that the predominant molecular species of AChE and BChE in the CSF--both lumbar and ventricular--was the G4 form. The G4 form also constituted the majority of the plasma BChE activity and, on average, over half (56%) of the plasma AChE activity. The significance of the AChE and BChE molecular form compositions of both plasma and CSF and their possible relationship to pathological states are discussed.
Characterization, Outcome, and Prognosis in 273 Patients with Primary Sclerosing Cholangitis: A Single Center Study (2006)

A persistent bilirubin elevation for longer than 3 months from the time of diagnosis could be identified as a novel marker correlating with a poor outcome. A new prognostic model was developed to predict progression of PSC, which may be useful in timing of liver transplantation.
Counterion Effect in the Reaction Mechanism of NHC Gold(I)-Catalyzed Alkoxylation of Alkynes: Computational Insight into Experiment (2014)

Experimental data suggest that anions that provide a compromise between the hydrogen-bond acceptor and the coordinating powers rather than poor coordinating anions unexpectedly increase the efficiency of L–Au–X (L = ligand, X = anion) catalyzed alkyne alkoxylation reactions, where the nucleophilic attack is the rate-determining step. No systematic computational studies about the role of the anion in the different steps of the catalytic cycle are available yet. In this paper, the remarkable anion influence on the catalytic efficiency of [NHCAuX] (X = BF4–, OTf–, OTs–, TFA–, and OAc–) complexes in the intermolecular addition of methanol to 2-butyne process has been analyzed through a density functional theory (DFT) approach. The role of the anion has been considered in all the steps of the reaction mechanism: pre-equilibrium, nucleophilic addition, and protodeauration. In the nucleophilic attack step, the anion acts (i) as a template, holding the methanol in the right position for the outer-sphere attack; (ii) as a hydrogen-bond acceptor, enhancing the nucleophilicity of the attacking methanol; (iii) as catalyst deactivator, by either its strong coordinating and/or basicity power, preventing the alkyne coordination or forming free alkoxide, respectively. In the protodeauration step, the anion acts as a proton shuttle, lowering the activation barrier. DFT calculations support intermediate coordinating and basicity power anions as the most efficient catalysts.
Human macrophage metalloelastase expression in gastric cancer and its relationship with gastric cancer prognosis. (2007)

The mechanism of gastric cancer development and its etiology has not been completely elucidated so far. Macrophage Metalloelastase (HME) plays an important role in tumor growth, infiltration and metastasis. The aim of the present study was to investigate the expression of HME mRNA and protein in both gastric cancer cell lines and tumor specimens and evaluate its role in the development of gastric cancer, and its correlation with patient prognosis. Using Real-time PCR, Western Blot and Immunohistochemistry, we detected the HME mRNA and protein expression in gastric cancer cell lines and specimens, and further analyzed the association between HME expression and clinical data. The results showed that both HME mRNA and protein expression were found in all three gastric cancer cell lines. The expression of HME mRNA and protein in gastric cancer specimens was increased significantly compared with that in normal tissues (P<0.05). Meanwhile, the rate of lymph node metastasis of HME mRNA positive cases was lower than in HME negative ones (P<0.05); two-year survival rate in HME mRNA positive cases was higher than in HME negative ones (P<0.05). HME may be a novel gastric tumor biomarker and its expression in gastric cancers may be related with lower metastatization rates with conseguent better prognosis.
Thermal stability of undoped strained Si channel SiGe heterostructures (1996)

We have investigated the thermal stability of Si/SiGe n-channel heterostructures. To eliminate the complication of dopant diffusion, we have fabricated undoped Si/SiGe heterostructure Hall effect devices. With no modulation doping used in our structures, the electron concentration in the strained Si channel is controlled from a back gate. Our devices show high electron mobility of up to 19 500 cm2/V s at 77 K and are stable with negligible 77 K mobility reduction after anneals at 800 °C for 30 min and at 950 °C for 3 min. These results conform well with a simulation of the diffusion of Ge into the Si channel.
ImAble system for upper limb stroke rehabilitation (2011)

ImAble is an integrated upper limb (UL) exercise system comprising three devices (Able-B, Able-M and Able-X) targeting UL rehabilitation using computer games and virtual reality (VR). The system can be tailored to different levels of ability and strength, depending on the presentation of the stroke. Results from pilot testing and case studies indicate a therapeutic benefit for both movement outcome and patient motivation.
Borrelidin is an Angiogenesis Inhibitor; Disruption of Angiogenic Capillary Vessels in a Rat Aorta Matrix Culture Model. (1997)

Borrelidin, an antibiotic from Streptomyces rochei, was found to be an angiogenesis inhibitor in a rat aorta matrix culture model which forms capillary vessels in vitro. Borrelidin strongly inhibited capillary tube formation with a 50%-inhibitory concentration value of 0.8 nM, and decreased the number of capillary tubes within 24 hours when added after maturation of tube formation. Borrelidin remarkably disrupted capillary tubes in a dose-dependent manner, by inducing apoptosis of the tube-forming cells.
Broad Distribution of Energetically Important Contacts across an Extended Protein Interface (2011)

Infection of cells by HIV depends upon profound structural rearrangements within the trimeric viral protein gp41. Critical to this process is the formation of a six-helix bundle in which a set of three N-terminal heptad repeat (NHR) helices assemble to form a core displaying long grooves that provide docking sites for three C-terminal heptad repeat (CHR) helices. We report experiments designed to discriminate between two alternative hypotheses regarding the source of affinity between individual CHR helices and the complementary groove: (1) affinity is dominated by interactions of a small cluster of side chains at one end of the CHR helix; or (2) affinity depends upon interactions distributed across the long CHR helix. We have employed two complementary experimental designs, and results from both favor the latter hypothesis.
Transcriptional regulatory circuits controlling mitochondrial biogenesis and function (2004)

We are witnessing a period of renewed interest in the biology of the mitochondrion. The mitochondrion serves a critical function in the maintenance of cellular energy stores, thermogenesis, and apoptosis. Moreover, alterations in mitochondrial function contribute to several inherited and acquired human diseases and the aging process. This review summarizes our understanding of the transcriptional regulatory mechanisms involved in the biogenesis and energy metabolic function of mitochondria in higher organisms.
Context-aware filtering for collaborative web systems (2005)

We propose a context-based filtering process which aims at adapting the awareness information delivered to mobile users by collaborative web systems. This filtering process relies on a model of context which integrates both a physical and an organizational dimensions and allows to represent the user's current context as well as general profiles. These profiles are descriptions of user's potential contexts and express the awareness information filtering rules to apply when the user's current context matches one of them. These rules reflect the user's preferences given a context. We describe how the filtering process performs in two steps, one for identifying the general profiles that apply, and a second for selecting the awareness information. We also discuss the patterns matching algorithms used in the filtering process to compare the contexts descriptions.
A Randomized Crossover Trial of the Impact of Additional Spermicide on Condom Failure Rates (2008)

Additional water-based external lubricant significantly reduced condom failures despite low failure rates among this stable, experienced group of condom users. Our results suggest that this may be a useful supplement to condom use, particularly among couples who experienced condom failures previously.
<title>Factors affecting fluorescent backlight operation</title> (1995)

Fluorescent lamps have been used as a general source of illumination for many years. Today, as LCD technology is growing rapidly, more special fluorescent lamps have been manufactured for use in backlighting of displays, with emphasis on high luminance, corrected color, and long life. Because performance can be significantly affected by many factors during the lamp manufacturing and operation, it is essential to have a better understanding of these factors.
Alzheimerʼs β-amyloid peptide is conformationally modified by apolipoprotein E in vitro (1996)

Amyloid beta-peptide (A beta) is a major component of neuritic plaques, a feature of Alzheimer's disease (AD) brains. Recently, we showed that A beta adopts two major conformational states in solution, which differ in their abilities to form amyloid. These are highly amyloidogenic conformer (A beta ac) with a high content of beta-sheet and a slowly amyloidogenic conformer (A beta nac) with a random coil conformation. Apolipoprotein E (apoE), particularly the E4 isoform, which is genetically associated with AD, binds to A beta and modulates fibrillogenesis in vitro. In the present work, the influence of apoE on the conformation of A beta peptides was studied. The results suggest that, under the conditions used, apoE enhances amyloid formation by inducing the conformational transition from A beta nac into A beta ac. We propose that an important step in A beta fibrillogenesis is the transformation induced by apoE of the soluble non-amyloidogenic into the pathological amyloidogenic conformer of A beta.
Female sterile mutations on the second chromosome of Drosophila melanogaster. I. Maternal effect mutations. (1989)

In mutagenesis screens for recessive female sterile mutations on the second chromosome of Drosophila melanogaster 529 chromosomes were isolated which allow the homozygous females to survive, but cause them to be sterile. In 136 of these lines, mutant females produce morphologically normal eggs which cannot support normal embryonic development. These "maternal-effect" mutations fall into 67 complementation groups which define 23 multiply hit and 44 singly hit loci. In eggs from 14 complementation groups development is blocked before the formation of a syncytial blastoderm. In eggs from 12 complementation groups development is abnormal before cellularization, 17 complementation groups cause abnormal cellularization, 12 complementation groups cause changes in cellular morphology in early gastrulation stages, and 12 complementation groups seem to affect later embryonic development.