gebhart/patrepeval huggingface dataset:
Structure of replicating DNA molecules of Bacillus subtilis bacteriophage phi 29 (1980)

We isolated phi 29 DNA replicative intermediates from extracts of phage-infected Bacillus subtilis, pulsed-labeled with [3H]thymidine, by velocity sedimentation in neutral sucrose followed by CsCl equilibrium density gradient centrifugation. During a chase, the DNA with a higher sedimentation coefficient in neutral sucrose and a lower sedimentation rate in alkaline sucrose than that of viral phi 29 DNA was converted into mature DNA. The material with a density higher than that of mature phi 29 DNA consisted of replicative intermediates, as analyzed with an electron microscope. We found two major types of molecules. One consisted of unit-length duplex DNA with one single-stranded branch at a random position. The length of the single-stranded branches was similar to that of one of the double-stranded regions. The other type of molecules was unit-length DNA with one double-stranded region and one single-stranded region extending a variable distance from one end. Partial denaturation of the latter molecules showed that replication was initiated with a similar frequency from either DNA end. These findings suggest that phi 29 DNA replication occurs by a mechanism of strand displacement and that replication starts non-simultaneously from either DNA end, as in the case of adenovirus.
Characteristics and performance of miniature NBS passive hydrogen masers (1987)

Recent data on the miniature (30 kg) passive hydrogen masers developed at the National Bureau of Standards (NBS) in cooperation with the Naval Research Laboratory (NRL) indicate a frequency stability of σ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</inf> (τ) ≤ (1.5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−12</sup> τ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−1/2</sup> ) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> + (5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−15</sup> ) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> 1 s < τ < 5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> s. These masers also have extremely low sensitivity to changes in the external magnetic field or temperature. The sensitivity to barometric pressure and or humidity, although very small, does dominate the residuals in one of the miniature masers for times beyond about a week. Frequency drift is so small as to be hidden in the present measurement precision. The fractional reproducibility under all changes, excluding the storage bulb, appears to be better than 5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−13</sup> . The concepts behind the physics and the electronics that made these advances possible as well as present limitations are explained in some detail.
Human fibroblasts in idiopathic retroperitoneal fibrosis express HLA-DR antigens (1991)

Idiopathic retroperitoneal fibrosis (IRF) is a rare human disease characterized by non-neoplastic fibroblastic proliferation associated with chronic inflammatory cells; its pathogenesis is obscure. We undertook an immunohistochemical study for the expression of HLA-DR antigens and other immune-related markers by retroperitoneal proliferating fibroblasts and inflammatory cells from 2 IRF patients. Patterns of immunoreactivity were compared with those expressed by human nodular fasciitis (NF) and granulation tissue. In IRF, most fibroblasts immunostained strongly for HLA-DR antigens, whereas fibroblasts in NF and granulation tissue did, not immunostain at all. The fibroblasts did not immunostain for interleukin 2 receptor, C3b receptor, CD-4, CD-8, or Leu-M1 in any of the tissue studied. Most macrophages and lymphocytes in IRF and NF immunostained Strangly for HLA-DR antigens. In IRF, the CD-4 and CD-8 immunostained T-lymphocytes appeared equally distributed. The expression of HLA-DR antigens by fibroblasts in IRF indicates that this rare disease may indeed be an immune-associated hypersensitivity disorder.
Preferential Loss of an Abundant Storage Protein from Soybean Pods during Seed Development (1989)

A temporary vegetative storage protein, composed of similar 25 kilodalton and 27 kilodalton subunits, was found to be abundant in soybean (Glycine max (L.) Herr. var Hobbit) leaves, stems, pods, flower petals, germinated cotyledons, and less abundant in roots, nodules and seeds. Total pod protein was highest at 3 weeks after flowering and declined by 37% within 3 weeks during seed development. During this time the vegetative storage protein declined from 18% to 1.5% of the total pod protein and accounted for 45% of the protein lost from pods. This indicates that the vegetative storage protein makes a significant contribution to the pool of nutrients mobilized from pods for transport to developing seeds.
Method for fractional solid-waste sampling and chemical analysis (2007)

Chemical characterization of solid waste is a demanding task due to the heterogeneity of the waste. This article describes how 45 material fractions hand-sorted from Danish household waste were subsampled and prepared for chemical analysis of 61 substances. All material fractions were subject to repeated particle-size reduction, mixing, and mass reduction until a sufficiently small but representative sample was obtained for digestion prior to chemical analysis. The waste-fraction samples were digested according to their properties for maximum recognition of all the studied substances. By combining four subsampling methods and five digestion methods, paying attention to the heterogeneity and the material characteristics of the waste fractions, it was possible to determine 61 substances with low detection limits, reasonable variance, and high accuracy. For most of the substances of environmental concern, the waste-sample concentrations were above the detection limit (e.g. Cd > 0.001 mg kg−1, Cr > 0.01 mg kg−1, Hg > 0.002 mg kg−1, Pb > 0.005 mg kg−1). The variance was in the range of 5–100%, depending on material fraction and substance as documented by repeated sampling of two highly different material fractions (‘Vegetable food’ and ‘Shoes, leather, etc.’). Statistical analysis showed for the ‘Vegetable food’ that the variance could not be attributed to a single step in the procedure, whereas in the case of ‘Shoes, leather, etc.’, the first coarse shredding was the main source of variance (20–85% of the overall variation). Only by increasing the sample size significantly can this variance be reduced. The accuracy and short-term reproducibility of the chemical characterization were good, as determined by the analysis of several relevant certified reference materials. Typically, six to eight different certified reference materials representing a range of concentrations levels and matrix characteristics were included. Based on the documentation provided, the methods introduced were considered satisfactory for characterization of the chemical composition of waste-material fractions.
CNN Features are also Great at Unsupervised Classification (2018)

This paper aims at providing insight on the transferability of deep CNN features to unsupervised problems. We study the impact of different pretrained CNN feature extractors on the problem of image set clustering for object classification as well as fine-grained classification. We propose a rather straightforward pipeline combining deep-feature extraction using a CNN pretrained on ImageNet and a classic clustering algorithm to classify sets of images. This approach is compared to state-of-the-art algorithms in image-clustering and provides better results. These results strengthen the belief that supervised training of deep CNN on large datasets, with a large variability of classes, extracts better features than most carefully designed engineering approaches, even for unsupervised tasks. We also validate our approach on a robotic application, consisting in sorting and storing objects smartly based on clustering.
Robot‐assisted Percutaneous Transfacet Screw Fixation Supplementing Oblique Lateral Interbody Fusion Procedure: Accuracy and Safety Evaluation of This Novel Minimally Invasive Technique (2019)

Our preliminary study of robot-assisted pTSF supplementing the OLIF procedure showed a high level of accuracy for screw insertion and this minimally invasive combination technique was found to be a feasible and safe procedure.
Characterization of a Cell Surface Protein of <i>Clostridium difficile</i> with Adhesive Properties (2001)

Our laboratory has previously shown that Clostridium difficile adherence to cultured cells is enhanced after heat shock at 60 degrees C and that it is mediated by a proteinaceous surface component. The present study was undertaken to identify the surface molecules of this bacterium that could play a role in its adherence to the intestine. The cwp66 gene, encoding a cell surface-associated protein of C. difficile 79-685, was isolated by immunoscreening of a C. difficile gene library with polyclonal antibodies against C. difficile heated at 60 degrees C. The Cwp66 protein (66 kDa) contains two domains, each carrying three imperfect repeats and one presenting homologies to the autolysin CwlB of Bacillus subtilis. A survey of 36 strains of C. difficile representing 11 serogroups showed that the 3' portion of the cwp66 gene is variable; this was confirmed by sequencing of cwp66 from another strain, C-253. Two recombinant protein fragments corresponding to the two domains of Cwp66 were expressed in fusion with glutathione S-transferase in Escherichia coli and purified by affinity chromatography using gluthatione-Sepharose 4B. Antibodies raised against the two domains recognized Cwp66 in bacterial surface extracts. By immunoelectron microscopy, the C-terminal domain was found to be cell surface exposed. When used as inhibitors in cell binding studies, the antibodies and protein fragments partially inhibited adherence of C. difficile to cultured cells, confirming that Cwp66 is an adhesin, the first to be identified in clostridia.
Scalable Influence Maximization in Social Networks under the Linear Threshold Model (2010)

Influence maximization is the problem of finding a small set of most influential nodes in a social network so that their aggregated influence in the network is maximized. In this paper, we study influence maximization in the linear threshold model, one of the important models formalizing the behavior of influence propagation in social networks. We first show that computing exact influence in general networks in the linear threshold model is #P-hard, which closes an open problem left in the seminal work on influence maximization by Kempe, Kleinberg, and Tardos, 2003. As a contrast, we show that computing influence in directed a cyclic graphs (DAGs) can be done in time linear to the size of the graphs. Based on the fast computation in DAGs, we propose the first scalable influence maximization algorithm tailored for the linear threshold model. We conduct extensive simulations to show that our algorithm is scalable to networks with millions of nodes and edges, is orders of magnitude faster than the greedy approximation algorithm proposed by Kempe et al. and its optimized versions, and performs consistently among the best algorithms while other heuristic algorithms not design specifically for the linear threshold model have unstable performances on different real-world networks.
Tying up the loose ends: circular permutation decreases the proteolytic susceptibility of recombinant proteins (2009)

Recombinant proteins often suffer from poor expression because of proteolysis. Existing genetic engineering or fermentation strategies work for only a subset of cases where higher recombinant protein expression is needed. In this paper, we describe the use of circular permutation, wherein the original termini of a protein are concatenated and new termini are generated elsewhere with the sequence, as a general protein engineering strategy to produce full-length, active recombinant protein. We show that a circularly permuted variant of the thermosome (Group II chaperonin) from Methanocaldococcus jannaschii exhibited reduced proteolysis and increased expression in three different strains of Escherichia coli. Circular permutation of a different protein, TEM-1 beta-lactamase, by a similar method increased the expression lifetime of the protein in the periplasm of E. coli. Both circularly permuted proteins maintained activity near their wild-type counterparts and design criteria for selecting the sites for circular permutation are discussed. It is expected that this method will find broad utility for enhanced expression of recombinant proteins when proteolysis is a factor.
Application of Cloud Storage on BIM Life-Cycle Management (2014)

Because of its high information intensity, strong consistency and convenient visualization features, building information modelling (BIM) has received widespread attention in the fields of construction and project management. However, due to large amounts of information, high integration, the need for resource sharing between various departments, the long time-span of the BIM application, challenges relating to data interoperability, security and cost all slow down the adoption of BIM. This paper constructs a BIM cloud storage concept system using cloud storage, an advanced computer technology, to solve the problem of mass data processing, information security, and cost problems in the existing application of BIM to full life-cycle management. This system takes full advantage of the cloud storage technique. Achievements are reached in four areas of BIM information management, involving security and licensing management, file management, work process management and collaborative management. The system expands the time and space scales, improves the level of participation, and reduces the cost of BIM. The construction of the BIM cloud storage system is one of the most important directions of the development of BIM, which benefits the promotion and further development of BIM to better serve construction and engineering project management.
On Radiation Modes of Anisotropic Plain Weave Textile Antenna (2011)

In this paper we present a concept involving utilizing both conductive and nonconductive elements in an anisotropic plain weave to form a microstrip antenna (MSA). This configuration results in a novel antenna structure with unique radiation modes. A reference MSA, a grating MSA, and an anisotropic plain weave antenna (APWA) were fabricated and tested. A Full wave finite element method (FEM) simulation of the antenna's performance was performed and compared with experimental results. The results show that the anisotropic plain weave configuration eliminated the TM010 mode, while enabling higher order modes.
Monitoring the community structure of wastewater treatment plants: a comparison of old and new techniques (1998)

Wastewater treatment is a process of increasing importance in a world with an ever growing human population. Today, most wastewater treatment processes make use of the natural self-purification capacity of aquatic environments which is the result of the presence and action of microbial communities. Consequently, wastewater treatment facilities are designed to maintain high densities and activities of those microorganisms that satisfy the various purification demands. The performance, at least of large plants, has to be constantly monitored and is subject to strict regulation. Nevertheless, malfunctions resulting in decreased purification efficacy are frequent. This has, over the decades, prompted many microbiologists to compare the structure, dynamics and function of these `good' or `bad', but always complex, microbial communities. Part of these studies was targeted to a basic understanding of the various processes, another part, however, deals with the monitoring of community structure as a means to direct the plant operation towards higher elimination rates and overall stability. Even though the last decade has seen a molecular revolution in microbiology, the standard methods for monitoring wastewater treatment plants still rely on the tools available to the researcher at the beginning of this century, the microscope and agar plates. It is the goal of this MiniReview to compare the potential of the newly available molecular methods with the old monitoring techniques.
Exchange Control in Central Europe. By Howard S. Ellis. (Harvard Economic Studies, vol. LXIX. ) Cambridge, Mass.: Harvard University Press. 1941. Pp. xviii, 413. ($4.00) (1941)

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The CD8α+ Dendritic Cell Is Responsible for Inducing Peripheral Self-Tolerance to Tissue-associated Antigens (2002)

We previously described a mechanism for the maintenance of peripheral self-tolerance. This involves the cross-presentation of tissue-associated antigens by a bone marrow-derived cell type that stimulates the proliferation and ultimate deletion of self-reactive CD8 T cells. This process has been referred to as cross-tolerance. Here, we characterize the elusive cell type responsible for inducing cross-tolerance as a CD8alpha(+) dendritic cell (DC). To achieve this aim, transgenic mice were generated expressing yellow fluorescent protein (YFP) linked to CTL epitopes for ovalbumin and glycoprotein B (gB) of herpes simplex virus under the rat insulin promoter (RIP). Although tracking of YFP was inconclusive, the use of a highly sensitive gB-specific hybridoma that produced beta-galactosidase on encounter with antigen, enabled detection of antigen presentation by cells isolated from the pancreatic lymph node. This showed that a CD11c(+)CD8alpha(+) cell was responsible for cross-tolerance, the same DC subset as previously implicated in cross-priming. These data indicate that CD8alpha(+) DCs play a critical role in both tolerance and immunity to cell-associated antigens, providing a potential mechanism by which cytotoxic T lymphocyte can be immunized to viral antigens while maintaining tolerance to self.
T cell receptor‐induced Fas ligand expression in cytotoxic T lymphocyte clones is blocked by protein tyrosine kinase inhibitors and cyclosporin A (1994)

Fas/APO-1 is a member of the tumor necrosis factor receptor family of proteins that induces apoptosis when cross-linked with monoclonal antibody (mAb) or with its physiological ligand. Recently, both a perforin-based and a Fas-based mechanism have been proposed to account for T cell-mediated cytotoxicity. In the present study we used a murine CD8+ cytotoxic T lymphocyte (CTL) clone (KB5 C20) specific for H-2Kb and a T cell receptor (TcR)-negative variant of the same clone (2005-D4) to test (i) whether the same cell can exert both cytotoxic effector mechanisms and (ii) the role of TcR engagement in the induction of Fas-based cytotoxicity. We demonstrate that both the TcR+ and TcR- clones were able to express the Fas ligand after stimulation with phorbol 12-myristate 13-acetate (PMA)/ionomycin, and that TcR engagement of the KB5.C20 clone by means of antigen-bearing cells or of its anticlonotypic mAb (Désiré-1), which leads to Ca(2+)-dependent, presumably perforin-based, cytotoxicity, was also able to induce Fas-based cytotoxicity. In addition, using inhibitors we investigated the signal transduction pathway(s) involved in the induction of Fas-based cytotoxicity and expression of the Fas ligand mRNA in the CTL clones. The involvement of src-like protein tyrosine kinases (PTK) in Fas ligand induction through TcR engagement, was strongly suggested by inhibition with the src-like PTK inhibitor herbimycin A. Inhibition of Fas ligand induction by genistein, a more general TPK inhibitor, even upon stimulation by PMA plus ionomycin, suggested the possible involvement of PTK activities downstream of protein kinase C (PKC) in Fas ligand induction in CTL. Finally, the implication of the Ca2+/calmodulin-dependent protein phosphatase calcineurin in Fas ligand induction was demonstrated by the partial inhibition of Fas ligand induction with cyclosporin A. Thus, in CTL clones, Fas ligand expression is inducible by TcR engagement through a pathway similar to that involved in expression of some lymphokine genes.
An Aza-Wittig/π-Furan Cyclization Approach Toward the Homoerythrina Alkaloid (±)-Selaginoidine (2005)

[reaction: see text] A one-pot procedure was developed to efficiently prepare hexahydroindolinones containing a tethered furan ring. Reaction of a furanyl azide with Bu3P delivered the iminophosphorane, which was allowed to react with 1-methyl-(2-oxocyclohexyl)acetic acid to give the desired hexahydroindolinone ring system. Further treatment with trifluoroacetic acid afforded the tetracyclic lactam skeleton found in the alkaloid (+/-)-selaginoidine.
Ultrasound Identification and Lysis of Clots (2004)

Poor recovery after systemic tissue plasminogen activator (tPA) therapy could result from the initial severity of ischemic insult and slow and incomplete thrombolysis. Persisting arterial occlusions can be identified at bedside using portable diagnostic ultrasound by detecting residual flow signals around the thrombus (thrombolysis in brain ischemia [TIBI] flow grades). A narrow pulsed ultrasound beam can be steadily aimed at the thrombus/residual flow interface, exposing more thrombus surface and structures to tPA, and tPA activity can be enhanced with 2 MHz transcranial Doppler (TCD). A randomized, multicenter, clinical trial called CLOTBUST (Combined Lysis of Thrombus in Brain ischemia using transcranial Ultrasound and Systemic tPA) trial showed a 49% rate of complete recanalization or dramatic clinical recovery from stroke within 2 hours after tPA bolus when tPA infusion was continuously monitored with TCD, compared with 30% among patients who received tPA without ultrasound monitoring (P=0.03, number needed to treat, 5). Early complete recanalization was sustained at 2 hours by 38% of monitored patients compared with 12.7% controls. The CLOTBUST Trial showed a trend toward sustaining complete recovery at 3 months (41.5% versus 28%, modified Rankin Scale scores 0 to 1), subject for a pivotal phase III trial. Ultrasound is an inexpensive, noninvasive, real-time monitoring tool to identify nonresponders to systemic tPA and select patients with persisting occlusions for intraarterial interventions. Early brain perfusion augmentation, complete recanalization, and dramatic clinical recovery are feasible goals for ultrasound-enhanced thrombolysis.