gebhart/patrepeval huggingface dataset:
Vehicle Routing Problem with Time Windows, Part II: Metaheuristics (2005)

This paper surveys the research on the metaheuristics for the Vehicle Routing Problem with Time Windows (VRPTW). The VRPTW can be described as the problem of designing least cost routes from one depot to a set of geographically scattered points. The routes must be designed in such a way that each point is visited only once by exactly one vehicle within a given time interval; all routes start and end at the depot, and the total demands of all points on one particular route must not exceed the capacity of the vehicle. Metaheuristics are general solution procedures that explore the solution space to identify good solutions and often embed some of the standard route construction and improvement heuristics described in the first part of this article. In addition to describing basic features of each method, experimental results for Solomon’s benchmark test problems are presented and analyzed.
Some Concepts about Substance, Chemical Compound and an Element (2014)

Chemistry is the science that deals with the composition and properties of matter. Properties of matter are generally grouped into two broad categories; these are physical and chemical properties. Physical property is the one that a sample of matter displays without changing its composition. The physical and chemical properties of a substance depend on its size and the arrangement of elements in the chemical compound. Considering physical and chemical properties of matter, it is demanded that the difference between atom and chemical element, chemical compound and substance concepts demand that we distinguish them. In this paper, these concepts are considered on microscopic and macroscopic levels.
Antifungal Activity of Amphotericin B Cochleates against <i>Candida albicans</i> Infection in a Mouse Model (2000)

Cochleates are lipid-based supramolecular assemblies composed of natural products, negatively charged phospholipid, and a divalent cation. Cochleates can encapsulate amphotericin B (AmB), an important antifungal drug. AmB cochleates (CAMB) have a unique shape and the ability to target AmB to fungi. The minimal inhibitory concentration and the minimum lethal concentration against Candida albicans are similar to that for desoxycholate AmB (DAMB; Fungizone). In vitro, CAMB induced no hemolysis of human red blood cells at concentrations of as high as 500 microg of AmB/ml, and DAMB was highly hemolytic at 10 microg of AmB/ml. CAMB protect ICR mice infected with C. albicans when the agent is administered intraperitoneally at doses of as low as 0.1 mg/kg/day. In a tissue burden study, CAMB, DAMB, and AmBisome (liposomal AmB; LAMB) were effective in the kidneys, but in the spleen CAMB was more potent than DAMB at 1 mg/kg/day and was equivalent to LAMB at 10 mg/kg/day. In summary, CAMB are highly effective in treating murine candidiasis and compare well with AmBisome and AmB.
A low cost lightweight subarray for multibeam phased arrays (2002)

Commercial off-the-shelf components and robotic manufacturing techniques have been employed to develop a lightweight low cost subarray. Dozens of these multilayer subarrays make up the phased array that operates in the telemetry band and electronically scans over a 120 deg cone of coverage. High-rel, multilayer fabrication techniques are described that guarantee that the subarray meets both its mechanical and RF requirements.
Protein localization to the nucleolus: a search for targeting domains in nucleolin (1993)

Nucleolin, a major nucleolar phosphoprotein, is presumed to function in rDNA transcription, rRNA packaging and ribosome assembly. Its primary sequence was highly conserved during evolution and suggests a multi-domain structure. To identify structural elements required for nuclear uptake and nucleolar accumulation of nucleolin, we used site-directed mutagenesis to introduce point- and deletion-mutations into a chicken nucleolin cDNA. Following transient expression in mammalian cells, the intracellular distribution of the corresponding wild-type and mutant proteins was determined by indirect immunofluorescence microscopy. We found that nucleolin contains a functional nuclear localization signal (KRKKEMANKSAPEAKKKK) that conforms exactly to the consensus proposed recently for a bipartite signal (Robbins, J., Dilworth, S.M., Laskey, R.A. and Dingwall, C. (1991) Cell 64, 615-623). Concerning nucleolar localization, we found that the N-terminal 250 amino acids of nucleolin are dispensible, but deletion of either the centrally located RNA-binding motifs (the RNP domain) or the glycine/arginine-rich C terminus (the GR domain) resulted in an exclusively nucleoplasmic distribution. Although both of these latter domains were required for correct subcellular localization of nucleolin, they were not sufficient to target non-nucleolar proteins to the nucleolus. From these results we conclude that nucleolin does not contain a single, linear nucleolar targeting signal. Instead, we propose that the protein uses a bipartite NLS to enter the nucleus and then accumulates within the nucleolus by virtue of binding to other nucleolar components (probably rRNA) via its RNP and GR domains.
Far-infrared and Raman vibrational transitions of a solid sphere: Selection rules (1992)

The selection rules for far-infrared and Raman transitions of a solid sphere are derived from group theory. By far-infrared only the spheroidal dipolar modes are excited, by Raman scattering the spherical and spheroidal quadrupolar modes are observed.
Structure-activity relationship of 7 flavonoids on recombinant human protein kinase CK2 holoenzyme. (2009)

The inhibitory effect of flavonoid on protein kinase CK 2 in vitro may be determined by the position of their hydroxyl groups.
MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes (2012)

Mutational events as well as the selection of the optimal variant are essential steps in the evolution of living organisms. The same principle is used in laboratory to extend the natural biodiversity to obtain better catalysts for applications in biomanufacturing or for improved biopharmaceuticals. Furthermore, single mutation in genes of drug-metabolizing enzymes can also result in dramatic changes in pharmacokinetics. These changes are a major cause of patient-specific drug responses and are, therefore, the molecular basis for personalized medicine. MuteinDB systematically links laboratory-generated enzyme variants (muteins) and natural isoforms with their biochemical properties including kinetic data of catalyzed reactions. Detailed information about kinetic characteristics of muteins is available in a systematic way and searchable for known mutations and catalyzed reactions as well as their substrates and known products. MuteinDB is broadly applicable to any known protein and their variants and makes mutagenesis and biochemical data searchable and comparable in a simple and easy-to-use manner. For the import of new mutein data, a simple, standardized, spreadsheet-based data format has been defined. To demonstrate the broad applicability of the MuteinDB, first data sets have been incorporated for selected cytochrome P450 enzymes as well as for nitrilases and peroxidases. Database URL: http://www.MuteinDB.org.
The gene located at chromosome 18 band q21 is rearranged in uncultured diffuse lymphomas as well as follicular lymphomas (1987)

The karyotypic abnormality t(14;18)(q32;q21) is reported to occur in 75% of follicular lymphomas. This translocation results in the rearrangement of a putative oncogene bcl-2, which resides at chromosome 18 band q21 (the 18q21 gene). Using two human genomic DNA fragments cloned from the chromosome 18 band q21 as probes, we analyzed 65 uncultured human lymphoma samples by the Southern blot technique. The 18q21 gene was rearranged in 18 of 26 (69%) follicular lymphomas, 3 of 5 (60%) follicular lymphomas transformed to large cell lymphomas, 8 of 20 (40%) diffuse large cell lymphomas (DLCLs), and 2 of 7 (29%) small noncleaved cell lymphomas (SNCs). Our analysis detected rearrangement of the 18q21 gene in 10 of 13 (77%) cases in which the t(14;18)(q32;q21) translocation was found by cytogenetic techniques. Our analysis also proved helpful in difficult karyotyping situations: (a) identifying the donor chromosome fragment as chromosome 18 band q21 in 4 of 9 (44%) cases that cytogenetically displayed a 14q+ chromosome of unknown origin, and (b) identifying a rearrangement of chromosome 18 band q21 in 12 of 18 (67%) cases that cytogenetically yielded no cells in metaphase. We also demonstrated three cases of submicroscopic rearrangement of the 18q21 gene. In our studies, patients with DLCLs and rearrangement of the 18q21 gene had a significantly higher incidence of extranodal involvement when compared with patients with DLCLs and no 18q21 gene rearrangement (P = 0.03).
Gut bacteria in health and disease. (2013)

A new era in medical science has dawned with the realization of the critical role of the "forgotten organ," the gut micro-biota, in health and disease. Central to this beneficial interaction between the microbiota and host is the manner in which bacteria and most likely other microorganisms contained within the gut communicate with the host's immune system and participate in a variety of metabolic processes of mutual benefit to the host and the microbe. The advent of high-throughput methodologies and the elaboration of sophisticated analytic systems have facilitated the detailed description of the composition of the microbial constituents of the human gut, as never before, and are now enabling comparisons to be made between health and various disease states. Although the latter approach is still in its infancy, some important insights have already been gained about how the microbiota might influence a number of disease processes both within and distant from the gut. These discoveries also lay the groundwork for the development of therapeutic strategies that might modify the microbiota (eg, through the use of probiot-ics). Although this area holds much promise, more high-quality trials of probiotics, prebiotics, and other microbiota-modifying approaches in digestive disorders are needed, as well as laboratory investigations of their mechanisms of action.
Analysis of a concatenated coding scheme for a discrete multitone modulation system (2002)

Discrete multitone (DMT) modulation partitions a band-limited transmission channel into a number of independent, parallel subchannels and maximizes performance by sending more bits over those subchannels with large signal-to-noise ratios. The combination of DMT modulation with powerful coding techniques results in a high-performance transceiver that may be used in a variety of high-speed applications. This study investigates the performance of a concatenated coding scheme consisting of an inner trellis code and outer Reed-Solomon code, when applied to a DMT system. Theoretical coding gain projections are derived for several band-limited channels that are representative of the asymmetric digital subscriber line (ADSL) application. Some laboratory test results obtained from a DMT prototype for ADSL are also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
RESONANCE RAMAN SPECTRA AND NORMAL MODE DESCRIPTIONS OF A BACTERIOCHLOROPHYLL <i>a</i> MODEL COMPLEX (1988)

Abstract— Resonance Raman (RR) spectra are reported for the bacteriochlorophyll a (BChl a) model complex, copper methylbacteriopheophorbide a (CuBPheo a). The spectra are acquired at a number of excitation wavelengths in the Q y+ Q x and B regions of the absorption spectrum. The RR data obtained for CuBPheo a are correlated to those previously reported for BChl a. The normal modes of the BChl structure are calculated by using the semiempirical quantum chemistry force field (QCFF/ PI) method of Warshel and Karplus [J. Am. Chem. Soc. 94 ,5612–5625 (1972)]. The vibrational data are used in conjunction with the calculations to obtain a cohesive assignment for the normal modes of BChl a with frequencies between 1100 and 1700 cm ‐1 . The forms of the normal modes of BChl a are predicted to be different both from those of chlorophyll a and from those of porphyrins.
Elevation of plasma thioredoxin levels in HIV-infected individuals (1996)

Thioredoxin (Trx), a ubiquitous protein intimately involved in redox and protein disulfide reductions, has been shown to be released from cells and to have cytokine-like activities. In addition, Trx has been implicated in the redox regulation of immunological responses and shown to be deficient in tissues from AIDS patients. In studies presented here, plasma Trx levels were measured by ELISA in plasma samples from HIV-infected individuals (n = 136) and HIV-negative controls (n = 47). To account for the release of Trx into plasma due to hemolysis, the Trx measurements were corrected according to the level of hemoglobin in the plasma sample. Data presented show that, in contrast to tissue Trx levels, corrected plasma Trx levels are significantly higher in HIV-infected individuals than in controls (P < 0.0001). Furthermore, approximately 25% of the HIV-infected individuals studied have plasma Trx levels greater than the highest levels found in controls (37 ng/ml). Detailed multiparameter FACS analysis of peripheral blood mononuclear cells (PBMC) from the infected individuals demonstrates that those with higher plasma Trx levels (37 ng/ml or greater) tend to have lower overall CD4 counts. In addition, increases in plasma Trx levels correlate with decreases in monochlorobimane staining (indicative of lower intracellular glutathione levels in PBMC) and with changes in surface antigen expression (CD62L, CD38 and CD20) that occur in the later stages of HIV infection. These correlations suggest that elevation of plasma Trx levels may be an important component of advanced HIV disease, perhaps related to the oxidative stress that often occurs at this stage.
Setting defensible performance standards on OSCEs and standardized patient examinations (2003)

Recently, standardized patient assessments and objective structured clinical examinations have been used for high-stakes certification and licensure decisions. In these testing situations, it is important that the assessments are standardized, the scores are accurate and reliable, and the resulting decisions regarding competence are equitable and defensible. For the decisions to be valid, justifiable standards, or cut-scores, must be set. Unfortunately, unlike the body of research specifically dedicated to multiple-choice examinations, relatively little research has been conducted on standard-setting methods appropriate for use with performance-based assessments. The purpose of this article is to provide the reader with some guidance on how to set defensible standards on performance assessments, especially those that utilize standardized patients in simulated medical encounters. Various methods are discussed and contrasted, highlighting the relevant strengths and weaknesses. In addition, based on the prevailing literature and research, ideas for future studies and potential augmentations to current performance-based standard setting protocols are advanced.
PROGRESS IN CONTINUAL EYE PRESSURE MONITORING (1983)

Observations of intraocular pressure (IOP) variations in response to CO2, adrenaline, speech and compression of the neck veins were documented by continual monitoring of IOP by radiotelemetry. Carbon dioxide increased IOP in the supine, but not in the erect, conscious subject. Adrenaline 2% caused a rapid short-lived painful increase in IOP, followed by a profound decrease. This was due to an increase in facility of outflow and was associated with paralysis of the sympathetic supply to the iris. Speech caused a small rise in IOP which was reversed by rest in silence. Compression of the neck veins caused a variable increase in IOP. These physiological variations in IOP may contribute to the errors of tonometry.
DNA-binding activity of retinoblastoma protein is intrinsic to its carboxyl-terminal region. (1990)

The retinoblastoma (RB) gene encodes a nuclear phosphoprotein with a molecular weight of 110,000 (pp110RB) associated with DNA-binding activity. This sequence-nonspecific DNA binding activity was further studied by Southwestern and DNA-cellulose chromatography using purified fusion proteins expressed in Escherichia coli. Three fusion proteins, containing amino acids 612-775, 776-928, and 612-928 of pp110RB, bound to DNA; the binding affinity of the latter was approximately 20-fold higher than those of either smaller region. Other regions of pp110RB had no detectable binding activity, indicating that the carboxyl-terminal region of the RB protein is the major domain responsible for interacting with DNA. Since several potential phosphorylation sites reside within this region, isoforms of RB protein from cellular lysates with various degrees of phosphorylation were compared with respect to their DNA-binding affinity. The hyperphosphorylated form was eluted from DNA-cellulose columns at 0.1-0.3 M NaCl, whereas the hypophosphorylated form appeared in the eluates only at salt concentrations of 0.4-0.7 M, implying that phosphorylation of RB protein may affect its DNA-binding activity. That pp110RB can bind DNA intrinsically, and that this activity can be modulated by phosphorylation, is consistent with the proposed regulatory role of the RB protein in cell growth and differentiation.
Allosteric Control of Acetylcholinesterase Catalysis by Fasciculin (1995)

The interaction of fasciculin 2 was examined with wild-type and several mutant forms of acetylcholinesterase (AChE) where Trp86, which lies at the base of the active center gorge, is replaced by Tyr, Phe, and Ala. The fasciculin family of peptides from snake venom bind to a peripheral site near the rim of the gorge, but at a position which still allows substrates and other inhibitors to enter the gorge. The interaction of a series of charged and uncharged carboxyl esters, alkyl phosphoryl esters, and substituted trifluoroacetophenones were analyzed with the wild-type and mutant AChEs in the presence and absence of fasciculin. We show that Trp86 is important for the alignment of carboxyl ester substrates in the AChE active center. The most marked influence of Trp86 substitution in inhibiting catalysis is seen for carboxyl esters that show rapid turnover. The extent of inhibition achieved with bound fasciculin is also greatest for efficiently catalyzed, charged substrates. When Ala is substituted for Trp86, fasciculin becomes an allosteric activator instead of an inhibitor for certain substrates. Analysis of the kinetics of acylation by organophosphates and conjugation by trifluoroacetophenones, along with deconstruction of the kinetic constants for carboxyl esters, suggests that AChE inhibition by fasciculin arises from reductions of both the commitment to catalysis and diffusional entry of substrate into the gorge. The former is reflected in the ratio of the rate constant for substrate acylation to that for dissociation of the initial complex. The action of fasciculin appears to be mediated allosterically from its binding site at the rim of the gorge to affect the orientation of the side chain of Trp86 which lies at the gorge base.
The relationship between infection and inflammation in the early stages of lung disease from cystic fibrosis (1995)

We examined the relationship of pulmonary infection and inflammation in cystic fibrosis (CF) by performing 31 bronchoalveolar lavages (BAL) in 14 young children with minimal lung disease from CF. While 10 of the 14 patients had elevated polymorphonuclear leukocyte (PMN) counts initially, only 4 had bacteria generally regarded as pathogenic in the recovered BAL fluid. Three of these 4 and 6 of the others had follow-up bronchoscopies at 6 months intervals. PMN counts remained normal for only one patient. However, pathogenic bacteria were recovered during the repeat BALs only in those patients who were colonized initially. Proinflammatory cytokines and proteinases were generally elevated, and interleukin-8 (IL-8) concentration correlated inversely with oxygen saturation (SaO2). No complications of the procedure occurred. We conclude that BAL identifies inflammation and the presence of bacteria in the lower airway at an early stage of the disease. This information may be used to guide therapy in patients too young or otherwise unable to produce sputum. These data also suggest that inflammation is present early in the course of CF lung disease before colonization and infection of the lungs with potentially pathogenic bacteria occurs. Since inflammation appears to be the earliest detectable evidence of lung disease in CF, monitoring of inflammation with BAL may serve as a useful marker of clinical benefits from new treatments in patients with minimal lung disease.
In Vitro and In Vivo Activity of Azithromycin (CP 62,993) Against the Mycobacterium avium Complex (1989)

Journal Article In Vitro and In Vivo Activity of Azithromycin (CP 62,993) Against the Mycobacterium avium Complex Get access Clark B. Inderlied, Clark B. Inderlied Please address requests for reprints to Dr. Clark B. Inderlied, Department of Pathology and Laboratory Medicine, 4650 Sunset Boulevard, Los Angeles, CA 90027. Search for other works by this author on: Oxford Academic PubMed Google Scholar Peter T. Kownoski, Peter T. Kownoski Search for other works by this author on: Oxford Academic PubMed Google Scholar Martin Wu, Martin Wu Search for other works by this author on: Oxford Academic PubMed Google Scholar Lowell S. Young Lowell S. Young Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 159, Issue 5, May 1989, Pages 994–997, https://doi.org/10.1093/infdis/159.5.994 Published: 01 May 1989 Article history Received: 01 September 1988 Revision received: 23 November 1988 Published: 01 May 1989
Peptidyl-Gly cine<i>α</i>-Amidation Activity in Tissues and Serum of the Adult Rat* (1985)

Bioactive peptides frequently terminate in a carboxyl-terminal alpha-amide. The tissue distribution of enzymatic activity capable of converting [125I]D-Tyr-Val-Gly into [125I]D-Tyr-Val-NH2 has been determined. Assay conditions have been established so that enzyme activity can be measured in crude homogenates. In adult male rats, the highest concentrations of activity are found in the anterior and neurointermediate lobes of the pituitary. Lower concentrations of activity are found in the hypothalamus, submandibular glands, and the rest of the brain. Enzyme activity is also easily assayed in serum. Taking into account the mass of each tissue, the submandibular glands and the brain are the major tissue sources of enzymatic activity; serum contains more enzymatic activity than is found in the pituitary gland. In all tissues and in serum, enzyme activity is stimulated by the addition of copper sulfate and ascorbate and is dependent on molecular oxygen. This activity is, therefore, referred to as peptidyl glycine alpha-amidating monooxygenase (PAM) activity. The pH optima for PAM activity in the pituitary and submandibular glands are near neutrality, whereas the pH optima for PAM activity in serum and hypothalamus are broad, with substantial activity at alkaline pH.