gebhart/patrepeval huggingface dataset:
DNA sequence determination of the TOL plasmid (pWW0) <i>xylGFJ</i> genes of <i>Pseudomonas putida</i>: implications for the evolution of aromatic catabolism (1991)

The meta operon of the Pseudomonas putida TOL plasmid (pWWO) encodes all enzymes of a meta-cleavage pathway for the metabolism of benzoic acids to Krebs-cycle intermediates. We have determined and analysed the nucleic acid sequence of a 3442 bp region of the meta operon containing the xyl-GFJ genes whose products are involved in the post meta-ring fission transformation of catechols. Homology analysis of the xylGFJ gene products revealed evidence of biochemical relatedness, suggested enzymatic mechanisms, and permitted us to propose evolutionary events which may have generated the current variety of aromatic degradative pathways. The xylG gene, which specifies 2-hydroxymuconic semialdehyde dehydrogenase (HMSD), was found to encode a protein of 51.7 kDa. The predicted protein sequence exhibits significant homology to eukaryotic aldehyde dehydrogenases (ADHs) and to the products of two other Pseudomonas catabolic genes, i.e. xylC and alkH. Expansion of the ADH superfamily to include these prokaryotic enzymes permitted a broader analysis of functionally critical ADH residues and phylogenetic relationships among superfamily members. The importance of three regions of these enzymes previously thought to be critical to ADH activity was reinforced by this analysis. However glutamine-487, also thought to be critical, is less well conserved. The revised ADH phylogeny proposed here suggests early catabolic ADH divergence with subsequent interkingdom gene exchange. The xylF gene, which specifies 2-hydroxymuconic semialdehyde hydrolase (HMSH), was delineated by N-terminal sequence analysis of the purified gene product and is shown to encode a protein of 30.6 kDa. Homology analysis revealed sequence similarity to a chromosomally encoded serine hydrolase, especially in the region of the previously identified active-site serine residue, suggesting that HMSH may also possess a serine hydrolytic enzymatic mechanism. Likewise, the xylJ gene, which specifies 2-hydroxy-pent-2,4-dienoate hydratase (HPH), was delineated by N-terminal sequence analysis of purified HPH, and was found to encode a 23.9 kDa protein. Sequence comparisons revealed that both HMSH and HPH have analogues in the tod gene cluster, which specifies a toluene/benzene degradative pathway. Although the newly identified todF and todJ genes had been at least partially sequenced (Zylstra and Gibson, 1989), the open reading frames had not been positively identified. The presence of todJ provides strong evidence that the reactions following ring fission in the tod pathway are identical to those of the TOL pathway.(ABSTRACT TRUNCATED AT 400 WORDS)
Charge-coupled device (CCD) imaging at low light levels (1972)

We present the analysis, design, fabrication and evaluation of low light level, anti-blooming, charge-coupled device (CCD) image sensors in line and area arrays. The transfer of low light level charge is determined by the non-linear electric field beneath the gate electrode. The CCD image sensor array is analyzed with a figure-of-merit which is the product of signal-to-noise (S/N) and modulation transfer function (MFT). The noise equivalent signal (NES), S/N = 1, is formulated at the system output and referenced to the readout diode. The CCD arrays use a 2-phase, stepped-oxide, clock system with interline transfer. Front surface imaging is achieved with thin silicon-gate electrodes (1000-2000 Å) which also serve as a "field shield" and the bottom layer of the lower phase line. The lowerphase line is constructed with an aluminum-silicon sandwich to provide low charging time constants (< 5 nsec) and reduce the incidence of phase line-to-line substrate shorts over large areas. The upper phase line is aluminum and a 3rd level aluminum forms a light shield over the interline shift-registers and CMOS readout circuit. The latter in combination with an analog signal processor provides a low-noise, composite video output signal. A unique cell design is used to combine active CCD sensor, interline shift-register, transfer gate and "stopper" diffusions into compact 2 mil centers in the area array. 1 × 128 element line arrays and 75 × 100 element area arrays are discussed in terms of individual elements NES, responsivity and spectral response.
The fluid trampoline: droplets bouncing on a soap film (2009)

We present the results of a combined experimental and theoretical investigation of droplets falling onto a horizontal soap film. Both static and vertically vibrated soap films are considered. In the static case, a variety of behaviours were observed, including bouncing, crossing and partial coalescence. A quasi-static description of the soap film shape yields a force–displacement relation that provides excellent agreement with experiment, and allows us to model the film as a nonlinear spring. This approach yields an accurate criterion for the transition between droplet bouncing and crossing. Moreover, it allows us to rationalize the observed constancy of the contact time and scaling for the coefficient of restitution in the bouncing states. On the vibrating film, a variety of bouncing behaviours were observed, including simple and complex periodic states, multi-periodicity and chaos. A simple theoretical model is developed that captures the essential physics of the bouncing process, reproducing all observed bouncing states. The model enables us to rationalize the observed coexistence of multiple periodic bouncing states by considering the dependence of the energy transferred to the droplet on the phase of impact. Quantitative agreement between model and experiment is deduced for simple periodic modes, and qualitative agreement for more complex periodic and chaotic bouncing states. Analytical solutions are deduced in the limit of weak forcing and dissipation, yielding insight into the contact time and periodicity of the bouncing states.
Auf dem Weg zu makrocyclischen <i>para</i>‐Phenylenen (1993)

On the Way to Macrocyclic para‐ Phenylenes Strategies are presented to synthesize the hitherto unknown [O n ]Paracyclophanes 1 . Open chain belt‐type molecules based on 1,4‐connected carbocyclic six‐membered rings were prepared. Functionalization of the outer rings in 4‐position is the prerequisite for cyclization or lengthening of the molecular belts. In order to obtain the macrocyclic target molecules 1 , well preorganized cis ‐isomers of 1,4‐disubstituted cyclohexanes were prepared. X‐ray structural analyses reveal the static stereochemistry of the intermediates 8, 9, 17, 18 , and 24 . The macrocyclic hydrocarbon 29 containing five cyclohexylidene units was detected.
Effects of free and liposome-encapsulated taxol on two brain tumors xenografted into nude mice. (1992)

Free taxol and liposome-encapsulated taxol were compared for their antitumoral activities on two human brain tumors serially grafted into female athymic mice in the scapular region. In the first experiment, a human glioblastoma (15th and 16th passages) was studied. In the second experiment, a fast growing human gliosarcoma (19th passage) was used. Free taxol and liposomal taxol were administered intraperitoneally, at the same dose; 12.5 mg/kg (i.e. 1/15 of the evaluated LD 50 value). In the first experiment, the treatment was performed for four consecutive days, with four courses separated by three rest periods of three days in between. Both free taxol and encapsulated taxol produced a statistically significant delay in tumor growth, and at the end of the experiment some total tumor regressions were obtained. However, liposomes were observed to be more effective in their action on the two consecutive passages of the glioblastoma, giving a marked increase of the number of total tumor regressions. In the second experiment another schedule of treatment was chosen because of the fast growth pattern of the xenografted human gliosarcoma: free taxol and liposome-encapsulated taxol were administered for five consecutive days and three courses of treatment were performed with two rest periods of two days. The two forms of taxol had a significant inhibitory effect on gliosarcoma tumor growth; as before encapsulation in liposomes was found to increase the anti-tumoral activity of taxol, although, in this case no tumor regression was observed.
Cytotoxicity of Oxidized Low-Density Lipoprotein in Cultured RPE Cells Is Dependent on the Formation of 7-Ketocholesterol (2004)

Prolonged oxidation of LDL increases the levels of 7kCh due to further oxidation of 7 alpha HCh and 7 beta HCh. The formation of 7KCh seems to be responsible for most of the cytotoxicity associated with oxLDL internalization in ARPE19 cells.
A 1.5-v 12-bit power-efficient continuous-time third-order ΣΔ modulator (2003)

This paper presents the design strategy, implementation, and experimental results of a power-efficient third-order low-pass ΣΔ analog-to-digital converter (ADC) using a continuous-time (CT) loop filter. The loop filter has been implemented by using active RC integrators. Several power optimizations, design requirements, and performance limitations relating to circuit nonidealities in the CT modulator are presented. The influence of the low supply voltage on the various building blocks such as the amplifier as well as on the overall ΣΔ modulator is discussed. The ADC was implemented in a 3.3-V 0.5-μm CMOS technology with standard threshold voltages. Measurements of the low-power 1.5-V CT ΣΔ ADC show a dynamic range and peak signal-to-noise-plus-distortion ratio of 80 and 70 dB, respectively, in a bandwidth of 25 kHz. The measured power consumption is only 135 μW from a single 1.5-V power supply.
Reduction of Diagnostic Window by New Fourth-Generation Human Immunodeficiency Virus Screening Assays (1998)

In order to reduce the diagnostic window between the time of human immunodeficiency virus (HIV) infection and laboratory diagnosis, new screening enzyme-linked immunosorbent assays (ELISAs) which permit the simultaneous detection of HIV antigen and antibody have been developed. Two fourth-generation assays, HIV DUO (Biomérieux) and HIV Combi (Boehringer Mannheim), for the combined detection of HIV antigen and antibody, were compared with a third-generation assay (HIV-1/HIV-2 3rd Generation Plus enzyme immunoassay [EIA]; Abbott) and a p24 antigen test (HIV-1 Ag monoclonal; Abbott). A total of 17 seroconversion panels, 15 cell culture supernatants infected with different HIV type 1 (HIV-1) subtypes, and 255 potentially cross-reactive serum samples were tested. Ten seroconversions were detected an average of 8.1 days earlier with HIV DUO and 7.5 days earlier with HIV Combi than with the third-generation ELISA. Overall, in the 17 seroconversion panels tested, HIV DUO detected HIV-1 infection an average of 4.8 days and HIV Combi detected infection an average of 4.4 days earlier than HIV-1/HIV-2 3rd Generation Plus EIA. HIV antigen was detected with HIV DUO and HIV Combi in all of the 15 cell culture supernatants infected with different HIV-1 subtypes, including subtype O. With fourth-generation assays, considerably fewer false-positive results (n = 4 to 6) were obtained, in comparison with the third-generation EIA (n = 18). Fourth-generation assays permit an earlier diagnosis of HIV infection than third-generation antibody screening assays through the detection of p24 antigen, which may be present in serum samples from individuals with recent HIV infection prior to seroconversion.
Dielectric properties of 1,2-diol solutions with water or electrolytes (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDielectric properties of 1,2-diol solutions with water or electrolytesBo Gestblom and Johan SjoeblomCite this: J. Phys. Chem. 1986, 90, 17, 4175–4178Publication Date (Print):August 1, 1986Publication History Published online1 May 2002Published inissue 1 August 1986https://pubs.acs.org/doi/10.1021/j100408a067https://doi.org/10.1021/j100408a067research-articleACS PublicationsRequest reuse permissionsArticle Views71Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
More is simpler (2013)

Similarity assessment is one of the core tasks in hyperlink analysis. Recently, with the proliferation of applications, e.g. , web search and collaborative filtering, SimRank has been a well-studied measure of similarity between two nodes in a graph. It recursively follows the philosophy that "two nodes are similar if they are referenced (have incoming edges) from similar nodes", which can be viewed as an aggregation of similarities based on incoming paths. Despite its popularity, SimRank has an undesirable property, i.e. , "zero-similarity": It only accommodates paths with equal length from a common "center" node. Thus, a large portion of other paths are fully ignored. This paper attempts to remedy this issue. (1) We propose and rigorously justify SimRank*, a revised version of SimRank, which resolves such counter-intuitive "zero-similarity" issues while inheriting merits of the basic SimRank philosophy. (2) We show that the series form of SimRank* can be reduced to a fairly succinct and elegant closed form, which looks even simpler than SimRank, yet enriches semantics without suffering from increased computational cost. This leads to a fixed-point iterative paradigm of SimRank* in O ( Knm ) time on a graph of n nodes and m edges for K iterations, which is comparable to SimRank. (3) To further optimize SimRank* computation, we leverage a novel clustering strategy via edge concentration. Due to its NP-hardness, we devise an efficient and effective heuristic to speed up SimRank* computation to O ( Kn m) time, where m is generally much smaller than m. (4) Using real and synthetic data, we empirically verify the rich semantics of SimRank*, and demonstrate its high computation efficiency.
Oxalate: From the Environment to Kidney Stones (2013)

Oxalate urolithiasis (nephrolithiasis) is the most frequent type of kidney stone disease. Epidemiological research has shown that urolithiasis is approximately twice as common in men as in women, but the underlying mechanism of this sex-related prevalence is unclear. Oxalate in the organism partially originate from food (exogenous oxalate) and largely as a metabolic end-product from numerous precursors generated mainly in the liver (endogenous oxalate). Oxalate concentrations in plasma and urine can be modified by various foodstuffs, which can interact in positively or negatively by affecting oxalate absorption, excretion, and/or its metabolic pathways. Oxalate is mostly removed from blood by kidneys and partially via bile and intestinal excretion. In the kidneys, after reaching certain conditions, such as high tubular concentration and damaged integrity of the tubule epithelium, oxalate can precipitate and initiate the formation of stones. Recent studies have indicated the importance of the SoLute Carrier 26 (SLC26) family of membrane transporters for handling oxalate. Two members of this family [Sulfate Anion Transporter 1 (SAT-1; SLC26A1) and Chloride/Formate EXchanger (CFEX; SLC26A6)] may contribute to oxalate transport in the intestine, liver, and kidneys. Malfunction or absence of SAT-1 or CFEX has been associated with hyperoxaluria and urolithiasis. However, numerous questions regarding their roles in oxalate transport in the respective organs and male-prevalent urolithiasis, as well as the role of sex hormones in the expression of these transporters at the level of mRNA and protein, still remain to be answered.
p70 <sup>s6k</sup> Integrates Phosphatidylinositol 3-Kinase and Rapamycin-Regulated Signals for E2F Regulation in T Lymphocytes (1999)

In T lymphocytes, the hematopoietic cytokine interleukin-2 (IL-2) uses phosphatidylinositol 3-kinase (PI 3-kinase)-induced signaling pathways to regulate E2F transcriptional activity, a critical cell cycle checkpoint. PI 3-kinase also regulates the activity of p70s6k, the 40S ribosomal protein S6 kinase, a response that is abrogated by the macrolide rapamycin. This immunosuppressive drug is known to prevent T-cell proliferation, but the precise point at which rapamycin regulates T-cell cycle progression has yet to be elucidated. Moreover, the effects of rapamycin on, and the role of p70s6k in, IL-2 and PI 3-kinase activation of E2Fs have not been characterized. Our present results show that IL-2- and PI 3-kinase-induced pathways for the regulation of E2F transcriptional activity include both rapamycin-resistant and rapamycin-sensitive components. Expression of a rapamycin-resistant mutant of p70s6k in T cells could restore rapamycin-suppressed E2F responses. Thus, the rapamycin-controlled processes involved in E2F regulation appear to be mediated by p70s6k. However, the rapamycin-resistant p70s6k could not rescue rapamycin inhibition of T-cell cycle entry, consistent with the involvement of additional, rapamycin-sensitive pathways in the control of T-cell cycle progression. The present results thus show that p70s6k is able to regulate E2F transcriptional activity and provide direct evidence for the first time for a link between IL-2 receptors, PI 3-kinase, and p70s6k that regulates a crucial G1 checkpoint in T lymphocytes.
Disk cache-aware task scheduling for data-intensive and many-task workflow (2014)

Workflow scheduling to maximize I/O performance is one of the key issues in data-intensive, many-task computing. In our previous work, we proposed locality-aware workflow scheduling method using the Multi-Constraint Graph Partitioning. In this work, we focus on read performance of input files from the disk cache (buffer cache or page cache on main memory). In order to maximize the disk cache hit rate of input files, a LIFO-order scheduling is effective since created intermediate files may be read soon. However, LIFO policy has a disadvantage of so-called “trailing task problem.” We propose a hybrid scheduling strategy of LIFO and HRF (Highest Rank First). In our strategy, one of two policies is applied depending on the number of highest-rank tasks in the queue to avoid the problem. In addition, scheduling for the overlap of computation and I/O is proposed. We implement our scheduling strategy for the Pwrake workflow system and the Gfarm distributed file system and evaluate it by executing data-intensive workflows using a computer cluster. Our scheduling strategy improves the performance of copyfile workflow by 30% due to increase in disk cache hit rate, and the performance of Montage workflow by 12% due to increase in core utilization.
Surgical therapy for tremor in multiple sclerosis (2001)

1) QMA is a reliable, objective and valid measure of MS tremor that could be used in a clinical trial. 2) The box and blocks test can detect the improvement in prehensile function that follows surgery, but standard disability scales are poorly responsive to this change. 3) Preoperative QMA values may predict which patients are most amenable to functional improvement after surgery.
Periovulatory Patterns of Rat Serum Follicle Stimulating Hormone and Luteinizing Hormone During the Normal Estrous Cycle: Effects of Pentobarbital (1971)

Contrary to a previous report by others, significant FSH activity could not be detected in pooled sera obtained from rats on the late afternoon of proestrus, despite injection of 20 ml of serum/test rat in the HCG-augmentation assay. A comparison of the patterns of serum FSH and LH concentrations around the time of pvulation in regularly cycling adult female rat was accomplished, however, by use of recently developed, differential radioimmunoassay systems (NIAMD-Rat FSH and LH radioimmunoassay systems). A striking difference in these patterns was revealed. Serum LH concentration was elevated only on the late afternoon of proestrus (mean value of approximately 1000 ng NIAMD-Rat-RP-1/ml) and, to a lesser extent, on the evening of proestrus. Serum FSH concentration, largely undetectable during diestrus, also began to rise on the late afternoon of proestrus, but did not attain a maximum until 8–9 PM proestrus (at approximately 500 ng NIAMDRat FSH-RP-1/ml). This maximal elevation of serum FSH persisted until 4–5 AM of estrus. Thereafter, serum FSH levels declined, but only slowly, and were still detectable in many cases on the afternoon of metestrus. Administration of pentobarbital (3.5 mg/100 g) on the early afternoon of proestrus was highly effective in inhibiting the surge of serum LH which normally occurs on the late afternoon of proestrus. Following pentobarbital treatment, the surge of serum LH occurred, instead, on the late afternoon of the next day. However, pentobarbital treatment was only partially effective in inhibiting the “surge” of serum FSH occurring on the late afternoon of proestrus, and almost totally ineffective in preventing the occurrence of elevated serum FSH levels normally observed on the early morning of estrus. The protracted nature of the FSH “surge” which begins during proestrus suggests that its function is stimulation of the growth of the crop of follicles next scheduled to ovulate. However, participation of FSH in the induction of ovulation is another possible function. The differences in the patterns of serum FSH and LH during the estrous cycle and the differences in the response of FSH and LH to the inhibitory influence of pentobarbital suggest that these 2 gonadotropins may not share a common releasing or regulatory mechanism. (Endocrinology88: 653, 1971)
Synthesis of 1-<i>tert</i>-Butyl-4-chloropiperidine:  Generation of an <i>N</i>-<i>tert</i>-Butyl Group by the Reaction of a Dimethyliminium Salt with Methylmagnesium Chloride (2005)

Two efficient routes to 1-tert-butyl-4-chloropiperidine are described. In the first route, the key thionyl chloride mediated chlorination reaction features the use of tetrabutylammonium chloride as an additive that effectively suppresses the formation of an elimination-derived side product. In the second route, a novel alternative synthesis of 1-tert-butyl-4-chloropiperidine was developed in which the tertiary butyl group on the nitrogen is efficiently generated through the addition of methylmagnesium chloride to a dimethyliminium salt in 71% overall yield.