gebhart/patrepeval huggingface dataset:
Identification of essential domains for Escherichia coli tRNAleu aminoacylation and amino acid editing using minimalist RNA molecules (2002)

Escherichia coli leucyl-tRNA synthetase (LeuRS) aminoacylates up to six different class II tRNA(leu) molecules. Each has a distinct anticodon and varied nucleotides in other regions of the tRNA. Attempts to construct a minihelix RNA that can be aminoacylated with leucine have been unsuccessful. Herein, we describe the smallest tRNA(leu) analog that has been aminoacylated to a significant extent to date. A series of tRNA(leu) analogs with various domains and combinations of domains deleted was constructed. The minimal RNA that was efficiently aminoacylated with LeuRS was one in which the anticodon stem-loop and variable arm stem-loop, but neither the D-arm nor T-arm, were deleted. Aminoacylation of this minimal RNA was abolished when the discriminator base A73 was replaced with C73 or when putative tertiary interactions between the D-loop and T-loop were disrupted, suggesting that these identity elements are still functioning in the minimized RNA. The various constructs that were significantly aminoacylated were also tested for amino acid editing by the synthetase. The anticodon and variable stem-loop domains were also dispensable for hydrolysis of the charged tRNA(leu) mimics. These results suggest that LeuRS may rely on identity elements in overlapping domains of the tRNA for both its aminoacylation and editing activities.
Effects of tetrahydrocannabinol content on marijuana smoking behavior, subjective reports, and performance (1989)

This study investigated the smoking topography of marijuana and its effect on heart rate, subjective reports, and cognitive/psychomotor task performance. Male subjects (N = 12) with histories of moderate marijuana use smoked ad lib one cigarette containing 0, 1.3, or 2.7% delta 9-THC on separate days. Smoking topography measures revealed smaller puff and inhalation volumes and shorter puff duration for the high marijuana dose compared to the low dose. No other smoking behavior differed between the active doses. Heart rate was increased dose dependently over placebo levels. Active marijuana also increased subjective reports of drug effect over placebo, but not dose dependently. Significant memory impairment was observed on a forward and reverse digit span task, and performance was impaired on the digit symbol substitution task by the high, but not low, dose of marijuana. Performance on a divided attention task was not affected by marijuana. Thus, although subjects adjusted their smoking of cigarettes varying in THC content, dose-related effects of marijuana were obtained on several measures. The observed differences and individual variation in smoking topography measures suggest that precise control of smoking behavior would improve the accuracy of marijuana dose delivery.
Decomposition of the Wiener topological index. Application to drug–receptor interactions (1988)

The Wiener index W is the sum of topological distances between carbon atoms in a hydrocarbon molecule. It was shown that W is made up of terms related to different substructures of the molecule and terms related to the interactions between these substructures. The contributions of substituents and the interaction terms are the substituent indices. Linear regression equations were derived relating the pharmacological potencies of compounds and the sum of the substituent indices, and linear regression equations were derived between these potencies and the various substituent indices. These regression equations were compared. The comparison allowed a decision on whether variations in the experimental pharmacological potencies were due to global effects linked with the bulk of the molecules or due to substituent effects attributable to various sites of the interacting molecules.
Distinct Sets of Genetic Alterations in Melanoma (2005)

The genetic alterations identified in melanomas at different sites and with different levels of sun exposure indicate that there are distinct genetic pathways in the development of melanoma and implicate CDK4 and CCND1 as independent oncogenes in melanomas without mutations in BRAF or N-RAS.
Obtaining breathing patterns from any sequential thoracic x-ray image set (2009)

A technique is presented to allow a breathing pattern to be obtained from any multi-slice CT, cone-beam or other series of sequential chest x-ray image sets. The technique requires no extra signals to be recorded and does not need specific external or internal oscillating structures to be visible in the field of view. The breathing pattern is instead acquired from analysing the variation in pixel values between projection images. For cone-beam image sets, slowly varying changes, due to an angular attenuation dependence, must be corrected before the breathing trace analysis can begin. All the results of the new technique were checked visually and were in good agreement. If the studied image set could be analysed using the existing 'Amsterdam shroud' technique, then the results it provided were also used for comparison. In cases that allowed comparison by both techniques, the results were in agreement. The new technique was also shown to provide a usable signal when applied to cardiac motion.
Can the Wound Healing Process Be Improved by Vitamin Supplementation? (1996)

The degree and rapidity of variations rather than the variations of the absolute values themselves of fibroblasts, hydroxyproline, Fe, Cu and Mg are significantly related to the enhancement of the mechanical properties of scars. From this study, it may be assumed that in order to obtain 'better', more solid and resistant scars, the decrease of Fe must be quick and acute in order to avoid the harmful effects of toxic radicals; the increase of Cu, Mg and Mn must be early and high in order to have more stable and solid collagen.
Molecular cloning and primary structure of the human blood group RhD polypeptide. (1992)

The RH (rhesus) blood group locus from RhD-positive donors is composed of two homologous structural genes, one of which encodes the Cc and Ee polypeptides, whereas the other, which is missing in the RhD-negative condition, encodes the D protein that carries the major antigen of the RH system. Recently, different splicing isoforms transcribed from the CcEe gene were isolated. We report now the characterization of two other Rh clones, RhII and RhXIII, generated by alternative choices for poly(A) addition sites that were identified as the RhD gene transcripts. That these cDNAs represented the RhD messenger and that the previously described Rh clones were derived from the CcEe gene was demonstrated by amplification of RhII/XIII sequences only from D-positive genomes and by cloning and sequencing of D- and CcEe-specific gene fragments. The predicted translation product of the RhD mRNA is a 417-amino acid protein (M(r) = 45,500) that exhibited a similar membrane organization with 13 bilayer-spanning domains compared with the polypeptide encoded by the CcEe gene. The D and Cc/Ee polypeptides differ by 36 amino acid substitutions (8.4% divergence), but the NH2- and COOH-terminal regions of the two proteins are well conserved. Similarly, five of the six cysteine residues of the Cc/Ee proteins were conserved in the D protein, including the unique exofacial cysteine, which is critical for antigenic reactivity. The sequence homology between the Cc/Ee and D proteins supports the concept that the genes encoding these polypeptides have evolved by duplication of a common ancestor gene.
Survival kinases in ischemic preconditioning and postconditioning (2006)

Despite nearly twenty years of research into the field of ischemic preconditioning, the actual mechanism of protection remains unclear. However, much progress has been made in elucidating the signal transduction pathways that convey the extracellular signal initiated by the preconditioning stimulus to the intracellular targets of cardioprotection, with many of these pathways involving the activation of a diverse array of survival protein kinase cascades. The powerful protective benefits of ischemic preconditioning have not yet been realised in the clinical arena, not least because of the prerequisite for any preconditioning intervention to be applied prior to the onset of index ischemia, which in the case of an acute myocardial infarction is difficult to institute. In this regard, the newly described phenomenon of ischemic postconditioning, which comprises a cardioprotective intervention that can be applied at the time of myocardial reperfusion, offers a far more attractive and amenable approach to myocardial protection. Interestingly, certain survival protein kinase cascades recruited at the time of myocardial reperfusion appear to be shared by both ischemic preconditioning and postconditioning, thereby offering a potentially common target of cardioprotection. The often disputed roles these different protein kinases play in mediating the cardioprotective effects of ischemic preconditioning and postconditioning are reviewed in this article, and include protein kinases C, G, and A, members of the MAPK family (Erk1/2, p38, JNK and BMK1), the PI3K-Akt cascade, and the JAK-STAT pathway.
Three CRISPR-Cas immune effector complexes coexist in Pyrococcus furiosus (2015)

CRISPR-Cas immune systems function to defend prokaryotes against potentially harmful mobile genetic elements including viruses and plasmids. The multiple CRISPR-Cas systems (Types I, II, and III) each target destruction of foreign nucleic acids via structurally and functionally diverse effector complexes (crRNPs). CRISPR-Cas effector complexes are comprised of CRISPR RNAs (crRNAs) that contain sequences homologous to the invading nucleic acids and Cas proteins specific to each immune system type. We have previously characterized a crRNP in Pyrococcus furiosus (Pfu) that contains Cmr (Type III-B) Cas proteins associated with one of two size classes of crRNAs and cleaves complementary target RNAs. Here, we have isolated and characterized two additional native Pfu crRNPs containing either Csa (Type I-A) or Cst (Type I-G) Cas proteins and distinct profiles of associated crRNAs. For each complex, the Cas proteins were identified by mass spectrometry and immunoblotting and the crRNAs by RNA sequencing and Northern blot analysis. The crRNAs associated with both the Csa and Cst complexes originate from all seven Pfu CRISPR loci and contain identical 5' ends (8-nt repeat-derived 5' tag sequences) but heterogeneous 3' ends (containing variable amounts of downstream repeat sequences). These crRNA forms are distinct from Cmr-associated crRNAs, indicating different 3' end processing pathways following primary cleavage of common pre-crRNAs. Like other previously characterized Type I CRISPR-Cas effector complexes, we predict that the newly identified Pfu Csa and Cst crRNPs each function to target invading DNA, adding an additional layer of protection beyond that afforded by the previously characterized RNA targeting Cmr complex.
ChemInform Abstract: Efficient Synthesis of Enantiomerically Pure C2‐Symmetric Diols via the Allylboration of Appropriate Dialdehydes. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Nanoscale thermal transport. II. 2003–2012 (2014)

A diverse spectrum of technology drivers such as improved thermal barriers, higher efficiency thermoelectric energy conversion, phase-change memory, heat-assisted magnetic recording, thermal management of nanoscale electronics, and nanoparticles for thermal medical therapies are motivating studies of the applied physics of thermal transport at the nanoscale. This review emphasizes developments in experiment, theory, and computation in the past ten years and summarizes the present status of the field. Interfaces become increasingly important on small length scales. Research during the past decade has extended studies of interfaces between simple metals and inorganic crystals to interfaces with molecular materials and liquids with systematic control of interface chemistry and physics. At separations on the order of ∼1 nm, the science of radiative transport through nanoscale gaps overlaps with thermal conduction by the coupling of electronic and vibrational excitations across weakly bonded or rough interfaces between materials. Major advances in the physics of phonons include first principles calculation of the phonon lifetimes of simple crystals and application of the predicted scattering rates in parameter-free calculations of the thermal conductivity. Progress in the control of thermal transport at the nanoscale is critical to continued advances in the density of information that can be stored in phase change memory devices and new generations of magnetic storage that will use highly localized heat sources to reduce the coercivity of magnetic media. Ultralow thermal conductivity—thermal conductivity below the conventionally predicted minimum thermal conductivity—has been observed in nanolaminates and disordered crystals with strong anisotropy. Advances in metrology by time-domain thermoreflectance have made measurements of the thermal conductivity of a thin layer with micron-scale spatial resolution relatively routine. Scanning thermal microscopy and thermal analysis using proximal probes has achieved spatial resolution of 10 nm, temperature precision of 50 mK, sensitivity to heat flows of 10 pW, and the capability for thermal analysis of sub-femtogram samples.
Cardiac mTORC1 Dysregulation Impacts Stress Adaptation and Survival in Huntington’s Disease (2018)

Huntington's disease (HD) is a dominantly inherited neurological disorder caused by CAG-repeat expansion in exon 1 of Huntingtin (HTT). But in addition to the neurological disease, mutant HTT (mHTT), which is ubiquitously expressed, impairs other organ systems. Indeed, epidemiological and animal model studies suggest higher incidence of and mortality from heart disease in HD. Here, we show that the protein complex mTORC1 is dysregulated in two HD mouse models through a mechanism that requires intrinsic mHTT expression. Moreover, restoring cardiac mTORC1 activity with constitutively active Rheb prevents mortality and relieves the mHTT-induced block to hypertrophic adaptation to cardiac stress. Finally, we show that chronic mTORC1 dysregulation is due in part to mislocalization of endogenous Rheb. These data provide insight into the increased cardiac-related mortality of HD patients, with cardiac mHTT expression inhibiting mTORC1 activity, limiting heart growth, and decreasing the heart's ability to compensate to chronic stress.
Posaconazole and Amphotericin B Combination Therapy against Cryptococcus neoformans Infection (2004)

To investigate the effects of posaconazole (POS) and amphotericin B (AMB) combination therapy in cryptococcal infection, we established an experimental model of systemic cryptococcosis in CD1 mice by intravenous injection of three distinct clinical isolates of Cryptococcus neoformans. Therapy was started 24 h after the infection and continued for 10 consecutive days. POS was given at 3 and 10 mg/kg of body weight/day, while AMB was given at 0.3 mg/kg/day. Combination therapy consisted of POS given at a low (combo 3) or at a high (combo 10) dose plus AMB. Survival studies showed that combo 3 was significantly more effective than POS at 3 mg/kg for two isolates tested (P value, < or = 0.001), while combo 10 was significantly more effective than POS at 10 mg/kg for all three isolates (P values ranging from <0.001 to 0.005). However, neither combination regimen was more effective than AMB alone. For two isolates, combination therapy was significantly more effective than each single drug at reducing the fungal burden in the brain (P values ranging from 0.001 to 0.015) but not in the lungs. This study demonstrates that the major impact of POS and AMB combination therapy is on brain fungal burden rather than on survival.
Oligoclonality of Vdelta1 and Vdelta2 cells in human peripheral blood mononuclear cells: TCR selection is not altered by stimulation with gram-negative bacteria. (1998)

Despite the enormous potential repertoire of gammadelta T cells, there are several observations which suggest that the expressed gammadelta repertoire in the periphery of normal individuals is often quite restricted. To assess selective expansions among gammadelta T cells from both adult and newborn blood samples, PBMC from 12 normal adults and cord blood from 15 normal newborns were analyzed for TCRDV1 and TCRDV2 junctional diversity by CDR3 size spectratyping and single-strand conformational polymorphism. Although TCRBV usage showed extensive heterogeneity in adults and newborns, both populations often showed CDR3 region restriction for TCRDV1 and TCRDV2. Analysis of the CDR3 spectratype patterns of newborn twins suggested that clonal selection for TCRDV is independent of genetic background. The possible role of Gram-negative bacteria in driving selective responsiveness of gammadelta T cells in PBMCs from adults was examined by in vitro stimulation with Escherichia coli and Pseudomonas aeruginosa. Donors whose TCRDV repertoire was highly clonal in the unstimulated blood cells showed the same predominant clones among the bacteria-stimulated cultures. In individuals whose gammadelta T cells were less restricted, in vitro stimulation did not select for clonality; rather, the TCRDV repertoires were similar before and after bacterial stimulation. Together, these data indicate that gammadelta T cells are often clonally restricted in adults as well as in newborns and suggest that the prominent stimulatory activity of Gram-negative bacteria does not by itself account for the restriction or diversity of the gammadelta T cell repertoire.
Mechanism of Helix Induction by Trifluoroethanol:  A Framework for Extrapolating the Helix-Forming Properties of Peptides from Trifluoroethanol/Water Mixtures Back to Water (1997)

To establish a framework for extrapolating the helix-forming properties of peptides from TFE/H2O mixtures (TFE = 2,2, 2-trifluoroethanol) back to water, the thermal unfolding curves have been measured by circular dichroism for four repeating-sequence peptides, with chain lengths from 7 to 22 residues. The unfolding curves were measured between 0 and 50 volume percent TFE and were fitted to the modified Lifson-Roig theory. A single set of helix-coil parameters fits the results for the four peptides at each TFE concentration; only two of the basic helix-coil parameters, <w>, the mean helix propagation parameter of residues in the sequence repeat, and DeltaH, the enthalpy change per residue on unfolding the helix, are allowed to vary with TFE molarity. The success in fitting these curves over a wide range of experimental variables shows that helix formation is basically the same in TFE/H2O mixtures as in water. Moreover, a simple model based on a linear dependence of ln <w> and DeltaH on TFE molarity can be used to extrapolate the results from 25% TFE (approximately 4 M) back to water. The results also give curves of helix formation induced by TFE at constant temperature, and the properties of these helix induction curves explain some of the puzzling results shown by other peptides in the literature. The average helix propensity increases regularly from 0 to 25% TFE but levels off at higher TFE concentrations, which explains why the extent of helix formation levels off in this range. The change in the apparent cooperativity of thermal unfolding curves in concentrated TFE solutions results from the decrease of the enthalpy change for helix unfolding at higher TFE concentrations. The rapid decrease in the plateau values of apparent helix content with increasing temperature results mainly from the strong temperature dependence of the ellipticity of the complete helix. To determine whether the helix-stabilizing effect of TFE arises from strengthening the hydrogen bonds in the helix backbone, the strength of the hydrogen bond in a model compound, salicylic acid, has been measured in TFE/H2O mixtures from the pKa difference between salicylic acid and a similar compound which cannot form the hydrogen bond. The curve of hydrogen bond strength versus increasing TFE concentration matches both in shape and magnitude the increase in average helix propensity in TFE/H2O mixtures.
Critical Business Requirements Model and Metrics for Intranet Roi (2005)

This research provides the first theoretical model, the Intranet Efficiency and Effectiveness Model (IEEM), to measure intranet overall value contributions based on a corporation’s critical business requirements by applying a balanced baseline of metrics and conversion ratios linked to key business processes of knowledge workers, IT managers and business decision makers-- in effect, closing the gap of understanding between them and enabling better software to be designed for Intranet portals.
Cycloadditions of C-benzoyl-N-phenylnitrone with furocondensed derivatives (1981)

Single regioisomeric cycloadduct IIa was formed in a 35% yield upon cycloaddition of the title nitrone Ia with benzofuran. The 1,3-dipolar cycloaddition proceeded with derivatives of 4-R-furo[3,2- b ]pyrrole V or VI to the furan ring to form only one regioisomer VIIa or VIIIa in a high yield (93-95%). Dehydrogenation of the latter with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone led to the nitrone X or XII . Also C,N-diphenylnitrone reacted with furopyrroles to afford the cycloadduct VIIIb . Exclusively endo -cycloadducts originated; their transition state was stabilized by secondary orbital interactions.
Fuzzy reasoning for multisensor management (2002)

A multisensor management scheme is proposed in this contribution, intended to be applicable to a generalized suite of several multitask sensors, deployed for multitarget surveillance purposes. The objective of the multisensor management function is to optimize, in a coordinated fashion, the measurement process of each sensor using overall system performance information. The coordination manager will provide each sensor with a list of sensor-level tasks, ranked according to their priorities, which are in turn obtained from the inferred global system-level necessity of fulfilling the task. Each sensor-level task will be also accompanied with an indication of the sensing performance objective desired to achieve with it, expressed in different terms depending on the type of task. The management process will be performed by means of a symbolic reasoning process starting from the output information of the data fusion and situation assessment functions. Fuzzy reasoning strategies and possibility theory concepts, in conjunction with heuristic search techniques, are applied to the processes of system-level task necessity evaluation, sensor-level task priority computation, specification of the sensing performance objectives (desired to guarantee with each task) and sensor(s)-to-task(s) assignment.