gebhart/patrepeval huggingface dataset:
Expression of argU, the Escherichia coli gene coding for a rare arginine tRNA (1992)

The Escherichia coli argU gene encodes the rare arginine tRNA, tRNA(UCUArg), which decodes the similarly rare AGA codons. The argU promoter is, with two exceptions, a typical, strongly expressed stable RNA gene promoter which is stimulated by an upstream activator sequence. Unlike other tRNA operons, however, argU expression is severely inhibited by sequences downstream of the transcription start point. In vivo, nucleotides +2 to +45 inhibited expression by 25- to 100-fold when measured by fusion of argU promoter regions to the chloramphenicol acetyltransferase reporter gene or by quantitative primer extension analysis. In vitro, linearized argU promoter fragments on which the argU region ended at +1 supported 5- to 10-fold-more transcription than when the argU region ended at +45. This difference in degree of inhibition between in vivo and in vitro conditions suggests that several factors, some of which could be absent in vitro, might limit expression in vivo. Alternatively, one mechanism might limit expression both in vivo and in vitro but function more efficiently in vivo. A second difference from strongly expressed stable RNA promoters is the fact the argU gene is relatively insensitive to growth rate regulation, at least when assayed on a multicopy plasmid.
Migraine in pregnancy and lactation: a clinical review (2007)

Migraine affects mostly women during their reproductive years and is far more prevalent than many people realise. Within 1 year, over 15% of women and 6% of men have attacks of migraine with or without aura. Although migraine without aura accounts for the majority of migraine, particularly in women, the overall 1-year prevalence of migraine with aura is around 5% for women and 2% for men. 1 Migraine prevalence varies with age, rising through early adult life, peaking at age 30-40 years and then declining in the late 40s and after 50 years in both males and females. 1 Drug treatment is usually necessary for effective control of migraine hence many women who are pregnant or planning a pregnancy will want to know what effects pregnancy will have on migraine and vice versa, and what treatments they can take safely during pregnancy and lactation.
Strong association between capsular type and virulence for mice among human isolates of Streptococcus pneumoniae (1992)

The relationship between capsular type and virulence for mice was examined with 69 fresh human isolates of Streptococcus pneumoniae. These isolates represented eight capsular types or groups. Serologic and molecular weight differences in PspA (pneumococcal surface protein A) indicated that the strains were clonally distinct. Mice were infected intravenously with washed bacteria of all 69 isolates in sterile salt solutions. Twenty-eight of the isolates were also injected intraperitoneally to permit comparisons between the intravenous and intraperitoneal routes. With a few exceptions, there was concordance between the ability of strains to cause fatal infections by the two routes. About 30% of the 69 isolates were virulent for mice. The abilities of the isolates to kill mice and the length of time between inoculation and death were strongly associated with capsular type. All type 4 isolates, 40% of type 3 isolates, and 60% of group 6 isolates were virulent for mice; type 1 isolates were marginally virulent; and all type or group 14, 19, and 23 isolates were avirulent. Times to death were generally longer for mice infected with group 6 or type 1 than for those infected with type 3 or 4 pneumococci. There was no relationship between clinical diagnosis or tissue source of the isolates and virulence for mice.
Predictors of Staphylococcus aureus Rectovaginal Colonization in Pregnant Women and Risk for Maternal and Neonatal Infections (2012)

S. aureus rectovaginal colonization was associated with an increased risk of infections in women but not in their infants. The frequency of MRSA infections was low. These data suggest that routine MRSA screening of pregnant women may not be indicated.
FALL DETECTION USING MODULAR NEURAL NETWORKS WITH BACK-PROJECTED OPTICAL FLOW (2007)

This paper presents a video-based algorithm for fall detection used the modular neural networks with the motion vectors computed by block-based optical flow back-projection (BOFB). From a video sequence, the moving object is extracted first and the pixels with high intensity variance in the extracted object are determined as feature points. The motion vector in this application is required to represent the actual motion displacement, rather than visually significant similarity. Therefore, we proposed BOFB which back-projects optical flows in a block to restore the motion vector from gradient-based optical flows that is employed to estimate the genuine motion of these feature points. The sequences of feature vectors are fed into the proposed Time-Delay Hierarchical modular Neural Network (TDHNN) for fall detection. The TDHNN consists of two major modular networks: several Time-Delay Neural Networks (TDNNs) trained by various feature characteristics and a Support Vector Machine (SVM) for final decision. This paper also purposed Slide Window Accumulate (SWA) mechanism for the increase of the robustness of the system in fall detection. The experimental results show that the proposed algorithm is efficacious and reliable in fall detection.
The impact of LH-containing gonadotropins on diploidy rates in preimplantation embryos: long protocol stimulation (2008)

Long protocol LH-containing ovarian stimulation improves embryonic ploidy in comparison to pure FSH stimulation. This observation may explain higher IVF pregnancy rates, reported for hMG stimulation in some studies.
SELECTED DESIGN PARAMETERS FOR RECLINING SEATS BASED ON ENGINEERING ANTHROPOMETRY (1977)

This report discusses selected engineering anthropometric design criteria for reclining cockpit seats. The reclining back-rest positions selected were 13, 27, 51 and 65 deg from the vertical line through the seat reference point (SRP). Two seat pan angles of 10 and 20 deg were utilized. Three seating components were considered in this report, these are: the head rest, arm rest, and foot rest. The specific engineering anthropometric design parameters addressed were: the head rest hinge point location, arm rest location and orientation in space as the seat reclines, location of foot rests and the synchronization of arm rest movement with back rest inclination.
Nutritional phases in Prader–Willi syndrome (2011)

Prader-Willi syndrome (PWS) is a complex neurobehavioral condition which has been classically described as having two nutritional stages: poor feeding, frequently with failure to thrive (FTT) in infancy (Stage 1), followed by hyperphagia leading to obesity in later childhood (Stage 2). We have longitudinally followed the feeding behaviors of individuals with PWS and found a much more gradual and complex progression of the nutritional phases than the traditional two stages described in the literature. Therefore, this study characterizes the growth, metabolic, and laboratory changes associated with the various nutritional phases of PWS in a large cohort of subjects. We have identified a total of seven different nutritional phases, with five main phases and sub-phases in phases 1 and 2. Phase 0 occurs in utero, with decreased fetal movements and growth restriction compared to unaffected siblings. In phase 1 the infant is hypotonic and not obese, with sub-phase 1a characterized by difficulty feeding with or without FTT (ages birth-15 months; median age at completion: 9 months). This phase is followed by sub-phase 1b when the infant grows steadily along a growth curve and weight is increasing at a normal rate (median age of onset: 9 months; age quartiles 5-15 months). Phase 2 is associated with weight gain-in sub-phase 2a the weight increases without a significant change in appetite or caloric intake (median age of onset 2.08 years; age quartiles 20-31 months;), while in sub-phase 2b the weight gain is associated with a concomitant increased interest in food (median age of onset: 4.5 years; quartiles 3-5.25 years). Phase 3 is characterized by hyperphagia, typically accompanied by food-seeking and lack of satiety (median age of onset: 8 years; quartiles 5-13 years). Some adults progress to phase 4 which is when an individual who was previously in phase 3 no longer has an insatiable appetite and is able to feel full. Therefore, the progression of the nutritional phases in PWS is much more complex than previously recognized. Awareness of the various phases will aid researchers in unraveling the pathophysiology of each phase and provide a foundation for developing rational therapies. Counseling parents of newly diagnosed infants with PWS as to what to expect with regard to these nutritional phases may help prevent or slow the early-onset of obesity in this syndrome.
Antibody Humanization Methods for Development of Therapeutic Applications (2014)

Recombinant antibody technologies are rapidly becoming available and showing considerable clinical success. However, the immunogenicity of murine-derived monoclonal antibodies is restrictive in cancer immunotherapy. Humanized antibodies can overcome these problems and are considered to be a promising alternative therapeutic agent. There are several approaches for antibody humanization. In this article we review various methods used in the antibody humanization process.
Enhanced Killing of Primary Ovarian Cancer by Retargeting Autologous Cytokine-Induced Killer Cells with Bispecific Antibodies: A Preclinical Study (2006)

Cytokine-induced killer (CIK) cells are ex vivo activated and expanded CD8+ natural killer T cells that have been shown to have antitumor activity. This is the first study exploring cell killing of primary ovarian carcinoma cells with and without bispecific antibodies. Primary cancer cells and autologous CIK cells were collected from women with epithelial ovarian cancer. Bispecific antibodies against cancer antigen-125 (BSAbxCA125) and Her2 (BSAbxHer2) were developed using chemical heteroconjugation. On fluorescence-activated cell sorting analysis, the expansion of CIK cells resulted in a significant increase of CD3+CD8+ and CD3+CD56+ T cells. With enhancement by bispecific antibodies, the mean percent lysis in a 51Cr release assay of fresh ovarian cancer cells exposed to autologous CIK cells increased from 21.7 +/- 0.3% to 89.4 +/- 2.1% at an E:T ratio of 100:1 (P < 0.001). Anti-NKG2D antibodies attenuated the CIK activity by 56.8% on primary cells (P < 0.001). In a xenograft severe combined immunodeficient mouse model, real-time tumor regression and progression was visualized using a noninvasive in vivo bioluminescence imaging system. Four hours after CIK cell injection, we were able to visualize CD8+NKG2D+ CIK cells infiltrating Her2-expressing cancer cells on fluorescence microscopy. Mice that underwent adoptive transfer of CIK cells redirected with BSAbxCA125 and BSAbxHer2 had significant reduction in tumor burden (P < 0.001 and P < 0.001) and improvement in survival (P = 0.05 and P = 0.006) versus those treated with CIK cells alone. Bispecific antibodies significantly enhanced the cytotoxicity of CIK cells in primary ovarian cancer cells and in our in vivo mouse model. The mechanism of cytolysis seems to be mediated in part by the NKG2D receptor.
Chromogenic and Neurotoxic Effects of an Aliphatic γ-Diketone:  Computational Insights into the Molecular Structures and Mechanism (2004)

First-principles electronic structure calculations have been performed to predict chromogenic properties of various candidate structures, including pyrrole monomers and dimers and their derivatives, of the chromophores formed from the reactions of 2,5-hexanedione (2,5-HD), a prototype of neurotoxic aliphatic γ-diketones, with NH3, amino acids, and proteins. The calculated results indicate that the pyrrole monomer structures and a previously proposed dimer structure do not have an absorption in the visible region (λ > ∼400 nm and < ∼700 nm), whereas a novel type of pyrrole dimer structure has absorptions (λ = ∼400 to 420 nm) in the visible region if the methyl (CH3) groups on the pyrrole rings are oxidized to CHO groups. The calculated results for the oxidized pyrrole dimer models for cross-linked proteins are consistent with all of the available experimental data for the chromogenic and neurotoxic effects of 2,5-HD. Our results strongly support the conclusion that the chromogenic effects of aliphatic γ-diketones are closely related to their neurotoxic effects and further predict that both the chromogenic and neurotoxic effects are associated with the same chemical reaction process. Such a reaction process most likely starts from the formation of the pyrrole−protein adducts followed by dimerization and further oxidization.
Avoiding Collateral Damage in Alzheimer's Disease Treatment (2006)

Although-secretase has been considered a relatively harmless target for drugs against Alzheimer9s disease, such drugs may damage nearby nerves.
Structural and Functional Analysis of the RANTES-Glycosaminoglycans Interactions (2001)

Chemokines mediate their biological activity through activation of G protein coupled receptors, but most chemokines, including RANTES, are also able to bind glycosaminoglycans (GAGs). Here, we have investigated, by site-directed mutagenesis and chemical acetylation, the role of RANTES basic residues in the interaction with GAGs using surface plasmon resonance kinetic analysis. Our results indicate that (i) RANTES exhibited selectivity in GAGs binding with highest affinity (K(d) = 32.1 nM) for heparin, (ii) RANTES uses the side chains of residues R44, K45, and R47 for heparin binding, and blocking these residues in combination abolished heparin binding. The biological relevance of RANTES-GAGs interaction was investigated in CHO-K1 cells expressing CCR5, CCR1, or CCR3 and the various GAGs that bind RANTES. Our results indicate that the heparin binding site, defined as the 40s loop, is only marginally involved in CCR5 binding and activation, but largely overlaps the CCR1 and CCR3 binding and activation domain in RANTES. In addition, enzymatic removal of cell surface GAGs by glycosidases did not affect CCR5 binding and Ca(2+) response. Furthermore, addition of soluble GAGs inhibited both CCR5 binding and functional response, with a rank of potency similar to that found in surface plasmon resonance experiments. Thus, cell surface GAGs is not a prerequisite for receptor binding or signaling, but soluble GAGs can inhibit the binding and the functional response of RANTES to CCR5 expressing cells. However, the marked selectivity of RANTES for different GAGs may serve, in vivo, to control the concentration of specific chemokines in inflammatory situations and locations.
Random Mutagenesis Methods for In Vitro Directed Enzyme Evolution (2010)

Random mutagenesis is a powerful tool for generating enzymes, proteins, entire metabolic pathways, or even entire genomes with desired or improved properties. This technology is used to evolve genes in vitro through an iterative process consisting of recombinant generation. Coupled with the development of powerful high-throughput screening or selection methods, this technique has been successfully used to solve problems in protein engineering. There are many methods to generate genetic diversity by random mutagenesis and to create combinatorial libraries. This can be achieved by treating DNA or whole bacteria with various chemical mutagens, by passing cloned genes through mutator strains, by "error-prone" PCR mutagenesis, by rolling circle error-prone PCR, or by saturation mutagenesis. The next sections of this review article focus on recent advances in techniques and methods used for in vitro directed evolution of enzymes using random mutagenesis. Selected examples, highlighting successful applications of these methods, are also presented and discussed.
Divergent evolution in M6P/IGF2R imprinting from the Jurassic to the Quaternary (2001)

M6P/IGF2R imprinting first appeared approximately 150 million years ago following the divergence of prototherian from therian mammals. Although M6P/IGF2R is clearly imprinted in opossums and rodents, its imprint status in humans remains ambiguous. It is also still unknown if M6P/IGF2R imprinting was an ancestral mammalian epigenotype or if it evolved convergently. We report herein that M6P/IGF2R is imprinted in Artiodactyla, as it is in Rodentia and Marsupialia, but that it is not imprinted in Scandentia, Dermoptera and Primates, including ringtail lemurs and humans. These results are most parsimonious with a single ancestral origin of M6P/IGF2R imprinting followed by a lineage-specific disappearance of M6P/IGF2R imprinting in Euarchonta. The absence of M6P/IGF2R imprinting in extant primates, due to its disappearance from the primate lineage over 75 million years ago, demonstrates that imprinting at this locus does not predispose to human disease. Moreover, the divergent evolution of M6P/IGF2R imprinting predicts that the success of in vitro embryo procedures such as cloning may be species dependent.
Rapid Progression from Mild Cognitive Impairment to Alzheimer’s Disease in Subjects with Elevated Levels of Tau in Cerebrospinal Fluid and the <i>APOE </i>ε<i>4</i>/ε<i>4</i> Genotype (2009)

CSF T-tau and P-tau as well as the APOE epsilon4/epsilon4 genotype are robust predictors of AD and are also associated with a more rapid progression from MCI to AD.
The Neo-Hittite Kingdom Masuwari and the Aramaeans of Bit-Adini (1989)

The recent publication of fragament of Hieroglyphic Luwian inscription from Tell Ahmar (“Louvre fragment”) revealed the hitherto unkown Hittite equivalent for the name of the city Til-barsip: Masuwari—an evidnce which requires to reconsider the long debated relations between Hittites and Aramaeans in the land of Bit-Adini. A Hittite regime in Maswari prospered during the 10th century B. C. There is reason to assume to identify the “king of the land of Aram”, who conquered Pitru and Mutkinu, Assyrian colonies on the banks of the Euphrates during the reign of Ashurrabi II, with Hapatila the first king of Masuwari. In the first half of the coming century the Hittites of Masuwari came under the dominion of the Aramaeans of Bit-Adini whose last king Ahuni took the capital Masuwari (Tell Ahmar) as his own to change the name to Til-barsip, unitl it was finally conquered and renamed as Kar-Shalmaneser by Shalmaneser III of Assyria in 856 B. C.
Occurrence of yeasts in municipal wastes and their behaviour in presence of cadmium, copper and zinc (2003)

Seven yeasts strains have been isolated from sewage sludge. Also six samples of compost with different sieving, composting times and origins, have been analysed. Apparently, composting processes negatively affect the viability of yeasts, as none could be isolated from the compost samples. The margins of tolerance of the yeasts to Cd, Cu and Zn have been determined. The physiological response to metals was similar in all the species studied, and in general, kinetic parameters (mu and lag) were affected. Metal uptake ability was also studied and inter- and intra-specific heterogeneity was detected, thus indicating that both the tolerance to metals and the capacity of the uptake were dependent on ionic metal and yeast species. The effect of the presence of multi-metal ions on the uptake capacity of each individual metal was assayed for two selected yeasts, Pichia guilliermondii and Torulaspora delbrueckii. The uptake of each individual metal varied with the combination assayed, and when both strains were compared different results were also found.
The neu Gene: an erb B-Homologous Gene Distinct from and Unlinked to the Gene Encoding the EGF Receptor (1985)

The neu oncogene, identified in ethylnitrosourea-induced rat neuroglioblastomas, had strong homology with the erbB gene that encodes the epidermal growth factor receptor. This homology was limited to the region of erbB encoding the tyrosine kinase domain. It was concluded that the neu gene is a distinct novel gene, as it is not coamplified with sequences encoding the EGF receptor in the genome of the A431 tumor line and it maps to human chromosome 17.
Helicobacter pylori Infection and the Development of Gastric Cancer (2001)

Gastric cancer develops in persons infected with H. pylori but not in uninfected persons. Those with histologic findings of severe gastric atrophy, corpus-predominant gastritis, or intestinal metaplasia are at increased risk. Persons with H. pylori infection and nonulcer dyspepsia, gastric ulcers, or gastric hyperplastic polyps are also at risk, but those with duodenal ulcers are not.
Lidocaine block of cardiac sodium channels. (1983)

Lidocaine block of cardiac sodium channels was studied in voltage-clamped rabbit purkinje fibers at drug concentrations ranging from 1 mM down to effective antiarrhythmic doses (5-20 muM). Dose-response curves indicated that lidocaine blocks the channel by binding one-to-one, with a voltage-dependent K(d). The half-blocking concentration varied from more than 300 muM, at a negative holding potential where inactivation was completely removed, to approximately 10 muM, at a depolarized holding potential where inactivation was nearly complete. Lidocaine block showed prominent use dependence with trains of depolarizing pulses from a negative holding potential. During the interval between pulses, repriming of I (Na) displayed two exponential components, a normally recovering component (tauless than 0.2 s), and a lidocaine-induced, slowly recovering fraction (tau approximately 1-2 s at pH 7.0). Raising the lidocaine concentration magnified the slowly recovering fraction without changing its time course; after a long depolarization, this fraction was one-half at approximately 10 muM lidocaine, just as expected if it corresponded to drug-bound, inactivated channels. At less than or equal to 20 muM lidocaine, the slowly recovering fraction grew exponentially to a steady level as the preceding depolarization was prolonged; the time course was the same for strong or weak depolarizations, that is, with or without significant activation of I(Na). This argues that use dependence at therapeutic levels reflects block of inactivated channels, rather than block of open channels. Overall, these results provide direct evidence for the "modulated-receptor hypothesis" of Hille (1977) and Hondeghem and Katzung (1977). Unlike tetrodotoxin, lidocaine shows similar interactions with Na channels of heart, nerve, and skeletal muscle.
Towards Oil Independence Through Renewable Methanol Chemistry (2012)

Recycling of CO(2) into methanol, dimethyl ether (DME), and derived fuels and materials is a feasible approach to address our carbon conundrum. It would free humankind from its dependence on fossil fuel while at the same time help mitigate the problems associated with excessive CO(2) emission. The energy needed for this carbon cycle can come from renewable sources (hydro, solar, wind) as well as atomic energy.