gebhart/patrepeval huggingface dataset:
Systematic Determination of the Packaging Limit of Lentiviral Vectors (2001)

Because of their ability to transduce nondividing cells, human immunodeficiency virus type 1 (HIV)-based vectors have great potential for the therapeutic delivery of genes to cells. We describe here a systematic study of the packaging limit of HIV-based vectors. Restriction endonuclease-generated bacterial chromosomal DNA fragments of different lengths were cloned at three different positions within a lentiviral vector. Vesicular stomatitis virus G protein (VSV G) pseudotyped lentiviral particles were prepared and the different clones were titered on mammalian cells. We observed that the restriction endonuclease site positions at the 5' and 3' ends of the genome were superior with regard to insertional capacity of foreign DNA. In all cases, viral titers decreased semi-logarithmically with increasing vector length. There appears to be no absolute packaging limit because measurable titers were obtained even when the proviral length was in excess of 18 kb. The reduction in titer appears to occur at the level of viral encapsidation, although we cannot exclude limitations in nuclear export of proviral RNA. These results suggest that HIV-based vectors may have a secondary advantage over oncoretroviral vectors because of their greater packaging limit, although the very low titers of the larger vectors will be of limited utility.
Enhancement of drug susceptibility of Mycobacterium avium by inhibitors of cell envelope synthesis (1990)

Treatment of infections caused by Mycobacterium avium complex bacteria still remains a challenge since these organisms are resistant to a majority of antituberculous drugs. M. avium is very often linked with acquired immune deficiency syndrome-associated opportunistic infections. We earlier suggested that one of the strategies for circumventing multiple-drug resistance might be the enhancement of M. avium drug susceptibility by inhibiting the synthesis of the outermost layer of its envelope, which appears to act as an exclusionary barrier for drugs. In this investigation, we have examined this strategy by simultaneously using drugs and the following inhibitors of the M. avium cell envelope: m-fluoro-phenylalanine (an inhibitor of mycoside-C biosynthesis), DL-norleucine (an inhibitor of transmethylation reactions), ethambutol (an inhibitor of arabinogalactan synthesis), EDTA (a divalent-ion chelator), and colistin (an inducer of membrane flux of divalent cations). All the drugs were used in concentrations which were low enough for a possible medical application to be foreseen. This approach, tested on seven strains of the M. avium complex, showed that both m-fluoro-phenylalanine and ethambutol were interesting candidates because they caused significant enhancement of M. avium drug susceptibility.
THE RELATIVE IMPACT AND FUTURE BURDEN OF PROSTATE CANCER IN THE UNITED STATES (2004)

Efforts to evaluate and discover diagnostic and therapeutic markers for prostate cancer continue. One of these, prostate-specific membrane antigen (PSMA), a transmembrane protein expressed in all types of prostatic tissue, remains a useful diagnostic and possibly therapeutic target. The radio-immunoconjugate form of the anti-PSMA monoclonal antibody 7E11 is used in the commercially available and US Food and Drug Administration-approved diagnostic tool, the ProstaScint(R) (Cytogen Corporation, Princeton, NJ) scan. Recent studies have demonstrated other possible useful roles for PSMA as a target, not only in prostate cancer, but in other malignancies.
Temporally coherent luminance-to-luma mapping for high dynamic range video coding with H.264/AVC (2011)

This paper presents a technique for the efficient compression of high dynamic range video (HDR) sequences. Such video sequences usually represent several orders of magnitude of real-world luminance intensity levels. Therefore, they are mostly stored in a floating-point represention. In order to obtain a coded representation that is bit stream compatible with the H.264/AVC video coding standard, the float-valued HDR values have to be mapped to a suitable integer representation first. The mapping proposed in this paper is adapted to the dynamic range of each video frame. Furthermore, to compensate for the associated dynamic contrast variation across frames, a weighted prediction method and quantization adaptation are introduced. The experiments show that the proposed method offers highly efficient HDR video compression. Only a fraction of the bit rate of a non-adaptive reference method is required to represent an HDR video sequence at the same quality.
Phosphatidylserine colocalizes with epichromatin in interphase nuclei and mitotic chromosomes (2012)

Cycling eukaryotic cells rapidly re-establish the nuclear envelope and internal architecture following mitosis. Studies with a specific anti-nucleosome antibody recently demonstrated that the surface ("epichromatin") of interphase and mitotic chromatin possesses a unique and conserved conformation, suggesting a role in postmitotic nuclear reformation. Here we present evidence showing that the anionic glycerophospholipid phosphatidylserine is specifically located in epichromatin throughout the cell cycle and is associated with nucleosome core histones. This suggests that chromatin bound phosphatidylserine may function as a nucleation site for the binding of ER and re-establishment of the nuclear envelope.
Controlling Self-Assembly of Engineered Peptides on Graphite by Rational Mutation (2012)

Self-assembly of proteins on surfaces is utilized in many fields to integrate intricate biological structures and diverse functions with engineered materials. Controlling proteins at bio-solid interfaces relies on establishing key correlations between their primary sequences and resulting spatial organizations on substrates. Protein self-assembly, however, remains an engineering challenge. As a novel approach, we demonstrate here that short dodecapeptides selected by phage display are capable of self-assembly on graphite and form long-range-ordered biomolecular nanostructures. Using atomic force microscopy and contact angle studies, we identify three amino acid domains along the primary sequence that steer peptide ordering and lead to nanostructures with uniformly displayed residues. The peptides are further engineered via simple mutations to control fundamental interfacial processes, including initial binding, surface aggregation and growth kinetics, and intermolecular interactions. Tailoring short peptides via their primary sequence offers versatile control over molecular self-assembly, resulting in well-defined surface properties essential in building engineered, chemically rich, bio-solid interfaces.
Real-time traffic measurement on MAGNET II (1990)

Real-time traffic measurements on MAGNET II, an integrated network testbed based on asynchronous time sharing, are reported. The quality of service is evaluated by monitoring the buffer-occupancy distribution, the packet time-delay distribution, the packet loss, and the gap distribution of the consecutively lost packets. The experiments show that both time-delay and buffer-occupancy distributions of multiplexed video sources display a marked bimodal behavior, which does not seem to depend on the buffer size. The reliance of the network designer on traffic sources that do not exhibit substantial correlations can lead to implementations with serious congestion problems. For asynchronous-time-sharing-based networks with different traffic classes, the impact of a traffic class on the performance of the other classes tends to be diminished when compared to single-class-based asynchronous transfer mode (ATM) networks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rapid identification of Enterobacteriaceae with microbial enzyme activity profiles (1981)

A total of 539 clinical isolates belonging to 10 species of the Enterobacteriaceae family were identified by enzyme activity profiles within 30 min of test inoculation. Each isolate was grown at 37 degrees C for 18 h on Mueller-Hinton agar and suspended to an optical density of 200 Klett units on 0.85% saline. Enzyme activity profiles were obtained by inoculating 18 fluorogenic substrates with the standardized bacterial suspension and monitoring initial rates of hydrolysis over the first 30 min of analysis. Individual enzyme activity profiles were entered into a coded data bank, and identifications were based on the Bayesian theory of probabilities. At a confidence level of 95%, five species were identified with a greater than 90% efficiency, three species were identified between 83 and 88% efficiency, and two species demonstrated a 72 and 75% efficiency of identification. The enzyme activity profile method of bacterial identification is rapid, easily automated, and reproducible.
Immunosurgery of mouse blastocyst. (1975)

Mouse blastocysts with and without zonae pellucidae are susceptible to complement-dependent antibody cytotoxicity. Exposure of blastocysts to rabbit anti-mouse serum together with complement results in the death of all cells; however, when blastocysts are exposed to antiserum alone and then transferred to guinea pig complement, only the trophoblastic cells are killed. These results suggest that the mouse blastocyst is not permeable for certain antibodies. The inner cell masses can easily be separated from the remnants of trophoblastic cells and are then able to grow and differentiate in vitro. This method of immunosurgery can be used to obtain large quantities of pure inner cell masses in a relatively short period of time.
Two Different Lantibiotic-Like Peptides Originate from the Ericin Gene Cluster of Bacillus subtilis A1/3 (2002)

A lantibiotic gene cluster was identified in Bacillus subtilis A1/3 showing a high degree of homology to the subtilin gene cluster and occupying the same genetic locus as the spa genes in B. subtilis ATCC 6633. The gene cluster exhibits diversity with respect to duplication of two subtilin-like genes which are separated by a sequence similar to a portion of a lanC gene. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analyses of B. subtilis A1/3 culture extracts confirmed the presence of two lantibiotic-like peptides, ericin S (3,442 Da) and ericin A (2,986 Da). Disruption of the lanB-homologous gene eriB resulted in loss of production of both peptides, demonstrating that they are processed in an eriB-dependent manner. Although precursors of ericins S and A show only 75% of identity, the matured lantibiotic-like peptides reveal highly similar physical properties; separation was only achieved after multistep, reversed-phase high-performance liquid chromatography. Based on Edman and peptidase degradation in combination with MALDI-TOF MS, for ericin S a subtilin-like, lanthionine-bridging pattern is supposed. For ericin A two C-terminal rings are different from the lanthionine pattern of subtilin. Due to only four amino acid exchanges, ericin S and subtilin revealed similar antibiotic activities as well as similar properties in response to heat and protease treatment. For ericin A only minor antibiotic activity was found.
Synthesis of a cobalt complex of a pyrano[2,3-b]quinoxaline-3,4-dithiolate related to molybdopterin (1998)

B. Bradshaw and A. Dinsmore, Chem. Commun., 1998, 417 DOI: 10.1039/A708366A
Micromolding of Polymers in Capillaries:  Applications in Microfabrication (1996)

This paper describes the use of micromolding in capillaries (MIMIC) to produce complex polymeric microstructures supported on different substrates and the applications of these microstructures in microfabrication. Patterned microstructures of several organic polymerspolyurethane, polyacrylate, and epoxywere formed by molding in enclosed, continuous channels formed by conformal contact between a solid support and an elastomeric mold whose surface had been patterned with a relief structure having micrometer-scale dimensions. A liquid prepolymer filled these channels by capillary action and was allowed to cure photochemically or thermally. The mold was then removed. Polymeric microstructures formed on films of Saran Wrap could be folded into different shapes, while these microstructures retained their forms; they could also be stretched uniaxially to generate microstructures having distorted forms. The patterned polymeric microstructures formed on SiO2, glass, and metals (Au, Ag, and Cr) could be used directly as resists in the selective etching of underlying substrates. Free-standing polymeric microstructures fabricated by lift-off were used as disposable masks to generate patterned microfeatures of metals on the surfaces of both planar and nonplanar substrates in two different procedures: (a) evaporation of gold through the polymeric mask supported on a substrate; (b) formation of patterned self-assembled monolayers (SAMs) by exposure of a silver film covered by a polymeric mask to hexadecanethiol (HDT) in vapor, followed by selective etching of the regions that were not exposed to HDT (that is, the parts of the surface protected by the mask) in an aqueous solution containing K2S2O3 and K3Fe(CN)6/K4Fe(CN)6.
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis (2008)

The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.
Construction and characterization of a cDNA clone containing a portion of the bovine prolactin sequence (1980)

Poly(A)-containing RNA from the bovine anterior pituitary has been used as a template for the enzymatic synthesis of double-stranded cDNA. The resulting double-stranded cDNA was inserted into the Pst I site of pBR322 with the oligo(dG)-oligo(dC) tailing technique and subsequently cloned in E. coli chi 1776. Clones containing sequences complementary to prolactin mRNA were identified by colony hybridization with partially purified prolactin cDNA. A 250 base pair sequence from one prolactin positive clone was extensively characterized and shown to contain the coding information for amino acids 119-192 of authentic bovine prolactin. The recombinant DNA from this clone was covalently attached to diazotized aminocellulose and used to purify prolactin mRNA from a mixture of mRNAs.
Possible Role of Non-Muscle Alpha-Actinins in Muscle Cell Mechanosensitivity (2014)

In 6 hours, alpha-actinin 1 and alpha-actinin 4 levels decreased in the membranous fraction of proteins of cardiomyocytes and soleus muscle fibers, respectively, but increased in the cytoplasmic fraction of the abovementioned cells. After 6-12 hours of suspension, the expression rates of beta-, gamma-actin, alpha-actinin 1 and alpha-actinin 4 were elevated in the soleus muscle fibers, but the alpha-actinin 1 expression rate returned to the reference level in 72 hours. After 18-24 hours, the expression rates of beta-actin and alpha-actinin 4 increased in cardiomyocytes, while the alpha-actinin 1 expression rate decreased in soleus muscle fibers. After 12 hours, the beta- and gamma-actin content dropped in the membranous fraction and increased in the cytoplasmic protein fractions from both cardiomyocytes and soleus muscle fibers. The stiffness of both cell types decreased after the same period of time. Further, during the unloading period the concentration of nonmuscle actin and different isoforms of alpha-actinins increased in the membranous fraction from cardiomyocytes. At the same time, the concentration of the abovementioned proteins decreased in the soleus muscle fibers.
Reverse staining of sodium dodecyl sulfate polyacrylamide gels by imidazole-zinc salts: sensitive detection of unmodified proteins. (1992)

We report here a modification to copper and zinc chloride staining methods. The introduction of a preincubation of the gels, prior to metal staining, with 0.2 M imidazole allows the formation of a homogeneous background for the subsequent precipitation of the metal chelate. The reported imidazole-zinc staining takes minutes, resulting in reproducible staining patterns with only slightly lower sensitivity than silver staining. The method allows efficient recovery of proteins from previously stained gels and is compatible with immunoidentification on Western blots and also with amino acid analysis and NH2-terminal sequence analysis of transferred proteins. A mechanism is proposed to explain the observed improvement in reproducibility and sensitivity of imidazole preincubation to zinc staining.
Oxaliplatin‐based chemotherapy (dexamethasone, high‐dose cytarabine, and oxaliplatin) ± rituximab is an effective salvage regimen in patients with relapsed or refractory lymphoma (2010)

This study confirms that dexamethasone, high-dose cytarabine, and oxaliplatin ± rituximab is an effective and feasible outpatient regimen for salvage therapy in patients affected by relapsed or refractory lymphoma. Moreover, the feasibility and efficacy of this scheme as an in vivo chemosensitive test in patients in autotransplantation programs was confirmed.
Reduced toxicity and enhanced antitumor efficacy of betacyclodextrin plumbagin inclusion complex in mice bearing Ehrlich ascites carcinoma. (1997)

Inclusion complex of plumbagin was prepared with betacyclodextrin employing neutralization method. The toxicity of the drug was reduced and the antitumor efficacy was enhanced on complexation with betacyclodextrin.
Radiology and the breast. (1993)

Mammography should be able to: Detect a high proportion of breast cancers well in advance of any other alternative currently available, and with good positive and negative predictive values. Provide access to impalpable lesions. Offer valuable information in many cases about the tumour, and useful correlation with clinical and pathological findings. Mammography can not: Find all breast cancers. Up to three per cent of even advanced cancers may be missed, especially those of the invasive lobular type. Offer close pathological correlation where the mammographic appearances are indeterminate or non specific. The role of mammography in benign breast disease or the role of radiological modalities other than mammography in the staging and follow up of diagnosed breast cancer has not been discussed. There is nevertheless a mounting excitement within the radiology community that in the absence of useful preventive measures to control the devastating effects of breast cancer, early and accurate diagnosis is the best we can do. The films must be of excellent quality and must be interpreted by experienced people with common sense, an openness to continuing education and a committed desire to do the best for every woman.
Randomized Phase II Study of Two Doses of Gefitinib in Hormone-Refractory Prostate Cancer: A Trial of the National Cancer Institute of Canada-Clinical Trials Group (2005)

Gefitinib did not result in any responses in PSA or objective measurable disease at either dose level. Gefitinib has minimal single-agent activity in HRPC.
Room-temperature Al single-electron transistor made by electron-beam lithography (2000)

We present a lithographically made Al single-electron transistor that shows gate modulation at room temperature. The temperature dependence of the modulation agrees with the orthodox theory, however, energy-level quantization in a tiny metallic island affects the device characteristics below 30 K. The charge-equivalent noise of the device at 300 K was measured to be ∼4×10−2 e/Hz1/2 at 1 Hz and is expected to be 1000 times lower in the white-noise regime at higher frequencies.
Molecular characterization of Marek's disease herpesvirus B antigen (1986)

The Marek's disease herpesvirus (MDHV) B antigen (MDHV-B) was identified and molecularly characterized as a set of three glycoproteins of 100,000, 60,000, and 49,000 apparent molecular weight (gp100, gp60, and gp49, respectively) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) after immunoprecipitation from [35S]methionine-labeled infected cells by specific rabbit antiserum directed against MDHV-B (R alpha B), as previously determined by immunodiffusion. Further identification was accomplished by blocking this immunoprecipitation with highly purified MDHV-B. The same set of three polypeptides was also immunoprecipitated from [35S]methionine- and 14C-labeled infected cells with two other sera shown to have anti-B activity, i.e., rabbit anti-MDHV-infected-cell plasma membrane (R alpha PM) and immune chicken serum from birds naturally infected with MDHV. The three herpesvirus of turkeys (HVT) B-antigen (HVT-B) glycoproteins immunoprecipitated with all three sera containing anti-B activity were also shown to be identical in size to those of MDHV-B by immunoprecipitation and SDS-PAGE. These data serve to clarify the molecular identification of the polypeptides found in common between MDHV and HVT by linking them to MDHV-B, previously identified only by immunodiffusion, and to a similarly sized set of immunologically related common glycoproteins called gp100, gp60, and gp49, detected with monoclonal antibody by other workers. Tunicamycin inhibition of N-linked glycosylation resulted in either nonglycosylated or O-linked glycosylated putative precursors of MDHV-B and HVT-B with apparent molecular weights of 88,000, called pr88, and 44,000, tentatively called pr44, both immunoprecipitable with all three sera. However, the relationships of these two polypeptides to each other and to the overall precursor-processing relationship of the MDHV-B complex remains to be elucidated. The three fully glycosylated B-antigen polypeptides were not connected by disulfide linkage. Collectively, the data presented here and by others support the conclusion that all three glycoproteins now identified as gp100, gp60, and gp49 have MDHV-B determinants. Finally, detection of the same three polypeptides with well-absorbed R alpha PM, which was directed against purified infected-cell plasma membranes, suggests that at least one component of the B-antigen complex has a plasma membrane location in the infected cell.(ABSTRACT TRUNCATED AT 400 WORDS)
Intravenous Fat Emulsions in Clinical Practice (1992)

The use of intravenous fat emulsions has become an integral part of the provision of parenteral nutrition. In the past, this was achieved by the administration of lipids separately from the dextrose-amino acid base solution. More recently, lipids have been admixed along with the dextrose-amino acid formula as a total nutrient admixture (TNA). This article discusses the advantages and disadvantages of TNAs, the factors that affect the stability of emulsions, the potential for microbial growth in TNAs, and guidelines for the compounding of TNAs.