gebhart/patrepeval huggingface dataset:
Remington : the science and practice of pharmacy (2013)

Part I: Pharmaceutical Science Section 1: Pharmaceutical Chemistry Section 2: Pharmaceutical Analysis and Quality Control Section 3: Pharmaceutics Section 4: Pharmaceutical Dosage Forms: Manufacturing and Compounding Section 5: Pharmacokinetics and Pharmacodynamics Section 6: Pharmaceutical and Medicinal Agents (Drug Monographs). Part II: Pharmacy Practice Section 7: Fundamentals of Pharmacy Practice Section 8: The Scope of Pharmacy Practice Section 9: Social, Behavioral, Economic, and Administrative Sciences Section 10: Patient Care
Efficient Processing of Primary microRNA Hairpins by Drosha Requires Flanking Nonstructured RNA Sequences (2005)

Drosha is a member of the ribonuclease (RNase) III family that selectively processes RNAs with prominent double-stranded features. Drosha plays a key role in the generation of precursor microRNAs from primary microRNA (pri-miRNA) transcripts in animal cells, yet how Drosha recognizes its RNA substrates remains incompletely understood. Previous studies have indicated that, within the context of a larger pri-miRNA, an approximately 80-nucleotide-long RNA hairpin structure is necessary for processing by Drosha. Here, by performing in vitro Drosha processing reactions with RNA substrates of various sizes and structures, we show that Drosha function also requires single-stranded RNA extensions located outside the pri-miRNA hairpin. The sequence of these RNA extensions was largely unimportant, but a strong secondary structure within the extension or a blunt-ended pri-miRNA hairpin blocked Drosha cleavage. The requirement for single-stranded extensions on the pri-miRNA hairpin substrate for Drosha processing is currently unique among the RNase III enzymes.
Ultrasonic attenuation and grain-size evaluation using electromagnetic acoustic resonance (1995)

Electromagnetic acoustic resonance is applied for determining the frequency dependence of the ultrasonic attenuation and the average grain size of low-carbon steels. Use of a noncontacting electromagnetic acoustic transducer (EMAT) makes it possible to isolate the attenuation within the plate specimens. The method relies on the Lorentz force mechanism to couple the EMAT to the specimen surfaces and then eliminates the other losses, which may otherwise occur with the contacting piezoelectric transducers. The measurement is independent of the EMAT used, the specimen thickness, the surface condition, the lift-off, etc., and is stable because of the noncontacting nature. First, the resonant frequencies are measured, to the accuracy of 10 Hz, by sweeping the operating frequency and obtaining the amplitude spectrum over a band in the 0.5- 20-MHz range. The ringing signals are excited and received by a shear wave EMAT and then processed with a superheterodyne receiver. Second, the attenuation coefficient as a function of the resonant frequency is determined. At each resonant frequency, the output signal rings down exponentially with time and the attenuation coefficient is obtained from the time constant by fitting an exponential decay to them. After correcting for the diffraction effect, the average grain size is obtained from the fourth-power term in the frequency dependence. The final results are favorably compared with the average of the three-dimensional grain-size distribution of steels.
Regulated basal, inducible, and tissue-specific human erythropoietin gene expression in transgenic mice requires multiple cis DNA sequences. (1995)

Erythropoietin (Epo) gene expression in kidney and liver is inducible by anemia. To localize the sequences necessary for regulated expression of the Epo gene, we constructed transgenic mice containing five human Epo gene constructs and examined Epo expression under basal conditions and with anemia. Mice containing the Epo gene with 0.3 kb of 5' flanking sequence, 0.7 kb of 3' flanking sequence, and either all introns or only intron I alone were polycythemic, had Epo expression in various tissues (including non-Epo-producing tissues), and induction only in liver. In contrast, mice containing the Epo gene with 8.5 kb of 3' flanking sequence and either 9.5 or 22 kb of 5' flanking sequence had basal expression at low levels in appropriate tissues and were less likely to be markedly polycythemic. Mice with the smaller of these two constructs had induction only in the liver, whereas those with the larger construct had induction in the kidney and liver. These studies indicate that sequences sufficient for induction in the liver are located in close proximity to the Epo gene, including the immediate 5' and 3' flanking sequence and the first intron. They also indicate that sequences required for induction in the kidney are located more than 9.5 kb 5' to the gene. Furthermore, comparison of these and prior transgenic studies suggest that sequences that limit the basal expression of the Epo gene are located downstream of the gene. We conclude that multiple cis DNA sequences are required for regulated Epo gene expression.
Resource efficiency and sustainability in logistics and supply chain management (2017)

Editorial note:The Centre for Supply Chain Improvement at the University of Derby hosted the 20th Annual Logistics Research Network Conference (LRN 2015). The LRN Conference as part of the Chartered Institute of Logistics and Transport is a leading academic event that attracts academics and professionals from many sectors. As well as the depth and breadth of papers that provide the latest research insights in this area, it was a pleasure to introduce high-level speakers who are at the cutting-edge of logistics, transport and supply chain research and practice. The speakers were Simon Hobbs (Vice President – Supply Chain Development, CEVA Logistics), Catherine Weetman (Director, Re-think Solutions), Steve Pryce (Head of Marketing &amp; Wagon Management, DB Schenker Rail U.K.) and Professor Alan McKinnon (Kühne Logistics University).<br/><p class="Default"><b><i/></b>
Proteolytic fragments of troponin C. Interactions with the other troponin subunits and biological activity. (1981)

Fragments of rabbit skeletal muscle Ca2+-binding subunit of troponin (TnC), obtained by cleavage with trypsin, thrombin, and CNBr, were tested for their ability to form binary and ternary complexes with ATPase inhibitory subunit (TnI) and tropomyosin-binding subunit (TnT) and their ability to replace TnC in reversing TnI inhibition of actomyosin ATPase activity. Three regions of TnC were found to be involved in interaction with TnI. Regions near Ca2+-binding sites II and III require Ca2+ for the interaction, while a third region near Ca2+-binding site IV binds TnI whether or not Ca2+ is present. The TnT binding site has been localized in the NH2-terminal half of TnC. Several of the TnC fragments form soluble ternary complexes with TnI and TnT. Fragments that contain amino acid residues 89-100 and at least one pair of Ca2+-binding sites are able to reverse the TnI inhibition of actomyosin ATPase activity, which exhibits the same [Ca2+]1/2 regardless of which of the Ca2+-binding sites are present in the fragment.
Increased Formation of Distinct F2Isoprostanes in Hypercholesterolemia (1998)

Asymptomatic patients with moderate and severe hypercholesterolemia have evidence of oxidant stress in vivo.
Vaginal fluid hCG levels for detecting premature rupture of membranes (1997)

The hCG level in vaginal fluid is a useful marker of PROM during the second and third trimesters.
CD8+ T-cell clones deficient in the expression of the CD45 protein tyrosine phosphatase have impaired responses to T-cell receptor stimuli. (1991)

CD45 is a high-molecular-weight transmembrane protein tyrosine phosphatase expressed only by nucleated cells of hematopoietic origin. To examine function, mouse CD8+ cytolytic T-cell clones were derived that had a specific defect in the expression of CD45. Northern (RNA) blot analysis indicates that the CD45 deficiency is due to either a transcriptional defect or mRNA instability. The CD45-deficient cells were greatly diminished in their ability to respond to antigen. All functional parameters of T-cell receptor signalling analyzed (cytolysis of targets, proliferation, and cytokine production) were markedly diminished. A CD45+ revertant was isolated, and the ability to respond to antigen was restored. These results support a central and immediate role for this transmembrane protein tyrosine phosphatase in T-cell receptor signalling.
Absence of Chronic Human Immunodeficiency Virus Infection without Seroconversion in Intravenous Drug Users: A Prospective and Retrospective Study (1991)

It has been reported that human immunodeficiency virus type 1 (HIV-1) infection may exist in persons without specific antibodies for years. To measure the frequency of a silent carrier state, a study was conducted in a cohort of 124 intravenous drug users (IVDUs) without anti-HIV-1 antibodies. All the participants had engaged in high-risk behavior for HIV-1 transmission for a number of years until 1987 or later. Samples were analyzed at 6-month intervals for the presence of HIV-1 provirus using DNA amplification and for the appearance of anti-HIV-1 antibodies. HIV-1 provirus and antibodies were undetectable in 122 participants, whereas seroconversion was observed in 2. In one of these, both amplified HIV-1 pol gene segment and anti-HIV-1 antibodies were detected simultaneously, and in the other, provirus was detected 1 month before seroconversion. This study suggests that long-term HIV-1 infection without anti-HIV-1 antibodies is rare and that repeated antibody testing is sufficient to determine the HIV-1 status of a person no longer at high risk for HIV-1 infection.
Targeting Adult and Pediatric Cancers via Cell-Based Vaccines and the Prospect of Activated B Lymphocytes as a Novel Modality (2003)

The delivery of cell-based vaccines that exploit natural mechanisms of antigen presentation represents a promising approach for immunotherapy of cancer. This strategy tests the hypothesis that ex vivo manipulation and reinjection of cellular products can induce immune responses and circumvent immune incompetence to achieve clinically significant results. Whole or modified tumor cell vaccines and antigen-loaded dendritic cells (DC) are under intense clinical and scientific evaluation, but other cell-based approaches including the use of activated B lymphocytes have shown promise in preclinical in vitro models. RNA-transfected CD40-activated B cells may fill a particular need in pediatric cancer patients and other patients in whom DC manufacturing is problematic. Thus far, evidence of immunological activity of cell-based vaccines has surpassed that of clinical efficacy, but recent advances and strong safety data from multiple approaches justifies randomized studies in healthier patients who are more likely to benefit.
Soluble Synthetic Multiporphyrin Arrays. 1. Modular Design and Synthesis (1996)

A set of porphyrin building blocks has been developed for the construction of light-harvesting model compounds and related molecular photonic devices. The porphyrins are facially encumbered to enhance solubility in organic solvents, are employed in a defined metalation state (free base (Fb) or zinc chelate), and bear peripheral functional groups such as iodo or ethyne for joining the porphyrins via covalent bonds. The coupling of an iodophenylporphyrin and an ethynylphenylporphyrin via mild Pd-mediated reactions (2−4 mM of each porphyrin in toluene/triethylamine (5:1) with Pd2(dba)3 and AsPh3 at 35 °C for 2 h) yields the corresponding diphenylethyne-linked multiporphyrin array in 70−80% yield. The arrays are easily purified by a sequence of flash silica chromatography, preparative size exclusion chromatography, and gravity elution silica chromatography. The diphenylethyne linkers give a center-to-center separation of the porphyrins of ∼20 Å. Model light-harvesting compounds are easily prepared using Zn and Fb porphyrin building blocks. In order to investigate the role of the linker in through-bond electronic communication, and the effect of through-bond electronic communication on the rates and yields of photoinduced energy transfer in the arrays, four ZnFb dimers have been prepared that have a systematic increase in steric hindrance in the diphenylethyne unit. The presence of steric hindrance inhibits rotation of the phenyl group toward coplanarity with the porphyrin, thereby modulating the electronic communication. A linear ZnFbZn trimer and a right-angle ZnFbZn trimer have been prepared to probe the effects of geometry on electronic communication pathways. A linear ZnZnFb trimer has been synthesized to investigate the photodynamics of energy migration among isoenergetic zinc porphyrins. These multiporphyrin arrays have sufficient solubility (∼5 mM) for routine handling in organic solvents such as toluene, CH2Cl2, or CHCl3, and can be examined spectroscopically (1−10 μM) in diverse solvents such as tetrahydrofuran, acetone, dimethyl sulfoxide, and castor oil. This building block approach should make diverse multiporphyrin arrays readily available.
Process considerations in restructurable VLSI for wafer-scale integration (1984)

Wafer-scale integration has recently been demonstrated using a technique called Restructurable VLSI. An array of logic cells embedded in programmable interconnect is fabricated on the wafer. All the parts are tested by wafer probing, and links are made or broken with a laser to wire the complete system. One such chip, a digital integrator 24 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in area with 25 MHz input data rate, has been successfully programmed. This paper will describe the RVLSI concept and discuss several aspects of wafer fabrication which are unusual in this technology.
Substratum-dependent stimulation of fibroblast migration by the gelatin-binding domain of fibronectin (1996)

Nanomolar concentrations of native fibronectin and its RGDS-containing cell-binding domain have previously been reported to stimulate fibroblast migration in the transmembrane (or 'Boyden chamber') assay; in contrast, the gelatin-binding domain (GBD) of fibronectin has consistently been reported to be devoid of migration-stimulating activity in this assay. We have examined the effects of fibronectin and several of its purified functional domains on the migration of human skin fibroblasts in what is presumably a more physiologically relevant assay involving the movement of cells into a 3-D matrix of native type I collagen fibrils. We report that: (a) femtomolar concentrations of GBD stimulate fibroblast migration into such collagen matrices; and (b) fibronectin, as well as peptides containing all other of its functional domains, do not exhibit migration-stimulating activity when tested in the femtomolar to nanomolar concentration range (i.e. 0.1 pg/ml to 1 microgram/ml). The correct assignment of migration-stimulating activity to GBD, rather than to a contaminant, was confirmed by: (a) the use of several fibronectin and GBD purification protocols; (b) the neutralization of GBD migration-stimulating activity by monoclonal antibodies directed against epitopes present in this domain; (c) the time-dependent generation of migration-stimulating activity by the proteolytic degradation of native fibronectin; and (d) obtaining an identical dose-response curve with a genetically engineered GBD peptide. The cryptic migration-stimulating activity of GBD was not affected by the presence of serum or native fibronectin, but was inhibited by TGF-beta 1. Parallel experiments using the transmembrane assay confirmed that GBD was devoid of migration-stimulating activity in this assay when membranes coated with gelatin were used, but revealed that significant stimulation of migration was achieved with membranes coated with native type I collagen. Cells preincubated with GBD for 24 hours whilst growing on plastic tissue culture dishes and then plated onto native collagen matrices in the absence of further GBD also displayed an elevated migration compared to controls. Taken together, these observations suggest that: (a) the interaction of GBD with a putative cell surface receptor (and not the collagen substratum) initiates a persistent alteration in cell phenotype which is manifest by an increase in migratory activity when these cells are cultured on a native collagen substratum; and (b) GBD may play a hitherto unrecognised role in the control of cell migration in response to the local release of proteases during pathological processes, such as tumour invasion and wound repair.
Mass spectrometry imaging for the proteomic study of clinical tissue (2015)

Over the last decade, MALDI-MS imaging has been used by researchers to explore areas of proteomics, lipidomics and metabolomics in samples of clinical origin for both targeted and global biomarker analysis. Numerous technological advancements in MS and clinical tissue MS imaging have been accomplished; hence, in this article we aim to critically discuss whether MS imaging has now in fact become a true champion of the 'Omics Era'. In order to assess the potential for it to be routinely used in the clinical setting, it is pertinent to discuss some of its limitations, and to examine how these have been addressed by researchers. The key limitations of the technique we will discuss in this viewpoint article are as follows: sample throughput; relevance to patients, the availability of validated/standardised techniques; and integration with conventional pathology and other medical imaging techniques. Good progress has been made over the last 5 years in overcoming these limitations that had previously restricted the use of this technology in the clinical setting.
Applied Geophysics (1990)

This is the completely revised and updated version of the popular and highly regarded textbook, Applied Geophysics. It describes the physical methods involved in exploration for hydrocarbons and minerals, which include gravity, magnetic, seismic, electrical, electromagnetic, radioactivity, and well-logging methods. All aspects of these methods are described, including basic theory, field equipment, techniques of data acquisition, data processing and interpretation, with the objective of locating commercial deposits of minerals, oil, and gas and determining their extent. In the fourteen years or so since the first edition of Applied Geophysics, many changes have taken place in this field, mainly as the result of new techniques, better instrumentation, and increased use of computers in the field and in the interpretation of data. The authors describe these changes in considerable detail, including improved methods of solving the inverse problem, specialized seismic methods, magnetotellurics as a practical exploration method, time-domain electromagnetic methods, increased use of gamma-ray spectrometers, and improved well-logging methods and interpretation.
Differential Proteomic Analysis of Nuclear Matrix in Muscle‐Invasive Bladder Cancer: Potential to Improve Diagnosis and Prognosis (2008)

Important alterations in NM proteins occur in muscle-invasive bladder cancer. The differentially expressed proteins include biomarkers potentially useful for disease diagnosis, progression and prognosis. Our findings beyond improving the understanding of the biology of bladder cancer, could help to stratify patients into different prognostic subgroups and to select those who might be better candidate to multimodal therapeutic approaches.
Analysis of the Effects of a gerP Mutation on the Germination of Spores of Bacillus subtilis (2012)

As previously reported, gerP Bacillus subtilis spores were defective in nutrient germination triggered via various germinant receptors (GRs), and the defect was eliminated by severe spore coat defects. The gerP spores' GR-dependent germination had a longer lag time between addition of germinants and initiation of rapid release of spores' dipicolinic acid (DPA), but times for release of >90% of DPA from individual spores were identical for wild-type and gerP spores. The gerP spores were also defective in GR-independent germination by DPA with its associated Ca(2+) divalent cation (CaDPA) but germinated better than wild-type spores with the GR-independent germinant dodecylamine. The gerP spores exhibited no increased sensitivity to hypochlorite, suggesting that these spores have no significant coat defect. Overexpression of GRs in gerP spores did lead to faster germination via the overexpressed GR, but this was still slower than germination of comparable gerP(+) spores. Unlike wild-type spores, for which maximal nutrient germinant concentrations were between 500 μM and 2 mM for l-alanine and ≤10 mM for l-valine, rates of gerP spore germination increased up to between 200 mM and 1 M l-alanine and 100 mM l-valine, and at 1 M l-alanine, the rates of germination of wild-type and gerP spores with or without all alanine racemases were almost identical. A high pressure of 150 MPa that triggers spore germination by activating GRs also triggered germination of wild-type and gerP spores identically. All these results support the suggestion that GerP proteins facilitate access of nutrient germinants to their cognate GRs in spores' inner membrane.
rf ion source development for neutron generation and for material modification (2002)

rf driven multicusp ion sources have been successfully used in various different applications. Lately the Plasma and Ion Source Technology Group at Lawrence Berkeley National Laboratory has been developing a rf ion source for neutron production and a high current density cw-operated ion source for SIMOX (Separation by Implantation of Oxygen)-application. The group has developed a small ion source, which consists of a quartz plasma chamber, an external rf-antenna, an extraction electrode, and a target assembly, all in a tube that is approximately 25 cm in length and 5 cm in diameter. Another neutron generator currently under development is a multiaperture, high power generator. The neutron generator currently operates at 1% duty cycle, 80 kV, and 150 mA of deuterium beam. The neutron yield measured from the generator is 1.6×107 n/s. For oxygen implantation, the group has been developing a source which could provide a high percentage of O+ at high current density using cw operation. A dual-antenna has been developed for the source to ensure reliable long life operation. The development of these sources will be discussed in this article.
Improved image decompression for reduced transform coding artifacts (1995)

The perceived quality of images reconstructed from low bit rate compression is severely degraded by the appearance of transform coding artifacts. This paper proposes a method for producing higher quality reconstructed images based on a stochastic model for the image data. Quantization (scalar or vector) partitions the transform coefficient space and maps all points in a partition cell to a representative reconstruction point, usually taken as the centroid of the cell. The proposed image estimation technique selects the reconstruction point within the quantization partition cell which results in a reconstructed image that best fits a non-Gaussian Markov random field (MRF) image model. This approach results in a convex constrained optimization problem that can be solved iteratively. At each iteration, the gradient projection method is used to update the estimate based on the image model. In the transform domain, the resulting coefficient reconstruction points are projected to the particular quantization partition cells defined by the compressed image. Experimental results will be shown for images compressed using scalar quantization of block DCT and using vector quantization of subband wavelet transform. The proposed image decompression provides a reconstructed image with reduced visibility of transform coding artifacts and superior perceived quality.
Novel HLA‐B alleles associated with antigens in the 8C CREG (2001)

This paper describes 13 novel HLA-B locus alleles, B*0809, B*0812, B*0813, B*0814, B*14062, B*3804, B*3806, B*3914, B*3915, B*3918, B*3919, B*3920, and B*3922 which represent new patterns of known polymorphic residues.