gebhart/patrepeval huggingface dataset:
Pathogenic Escherichia coli O157:H7 and their detection. (1991)

Enterohaemorrhagic Escherichia coli O157:H7 is of major concern to the food industry due to high pathogenicity of this foodborne organism. For the detection of these bacteria a special agar medium with a fluorogenic substrate has been developed. The medium uses the characteristics of this E. coli serotype not to ferment sorbitol and not to produce beta-glucuronidase. In contrast, approximately 96% of all other strains of E. coli are sorbitol-positive and nearly all of them are beta-glucuronidase-positive. For discrimination between Proteus and E. coli O157:H7 which are both sorbitol- and beta-glucuronidase-negative, sodium thiosulphate and ferrio ammonium citrate were added. This leads to a brownish colour of the Proteus colonies due to their production of hydrogen sulphide. Growth of the gram-positive flora was inhibited by the addition of sodium deoxycholate.
Droplet and Vapor Drift from Butyl Ester and Dimethylamine Salt of 2,4-D (1972)

The relative drift of droplet and vapor of butyl ester and dimethylamine formulations of (2,4-dichlorophenoxy)acetic acid (2,4-D) was determined under conventional crop spraying procedures in the field. Labelled herbicides were mixed with spray solution or emulsion, and the ground deposit and the air-borne droplet and vapor clouds drifting from the target area were collected. The mass of the dimethylamine formulation drifting as droplets was 3 to 4% of the material sprayed. No significant amounts of this material were collected as vapor or particulate drift. For the butyl ester, in addition to the droplet drift, 25 to 30% of the material was collected as vapor drift in the half hour after spraying. Thus the drift potential from the butyl ester was about 8 to 10 times greater than that from the dimethylamine formulation under the conditions of these tests.
Template-based prediction of protein structure with deep learning (2020)

Abstract Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. Template-based modeling, including protein threading and homology modeling, is a popular method for protein tertiary structure prediction. However, accurate template-query alignment and template selection are still very challenging, especially for the proteins with only distant homologs available. We propose a new template-based modelling method called ThreaderAI to improve protein tertiary structure prediction. ThreaderAI formulates the task of aligning query sequence with template as the classical pixel classification problem in computer vision and naturally applies deep residual neural network in prediction. ThreaderAI first employs deep learning to predict residue-residue aligning probability matrix by integrating sequence profile, predicted sequential structural features, and predicted residueresidue contacts, and then builds template-query alignment by applying a dynamic programming algorithm on the probability matrix. We evaluated our methods both in generating accurate template-query alignment and protein threading. Experimental results show that ThreaderAI outperforms currently popular template-based modelling methods HHpred, CNFpred, and the latest contact-assisted method CEthreader, especially on the proteins that do not have close homologs with known structures. In particular, in terms of alignment accuracy measured with TM-score, ThreaderAI outperforms HHpred, CNFpred, and CEthreader by 56%, 13%, and 11%, respectively, on template-query pairs at the similarity of fold level from SCOPe data. And on CASP13’s TBM-hard data, ThreaderAI outperforms HHpred, CNFpred, and CEthreader by 16%, 9% and 8% in terms of TM-score, respectively. These results demonstrate that with the help of deep learning, ThreaderAI can significantly improve the accuracy of template-based structure prediction, especially for distant-homology proteins. Availability https://github.com/ShenLab/ThreaderAI
Immunoaffinity purification of factor IX from commercial concentrates and infusion studies in animals (1988)

Thrombosis and transmission of viral diseases are the principal adverse effects of current replacement therapy for factor IX deficiency when using heat-treated concentrates of vitamin K-dependent coagulation factors. More highly purified factor IX preparations could decrease the risk of disease transmission, reduce patient exposure to allogeneic proteins, and reduce the risk of thrombosis. In this study, two immunoaffinity-purified factor IX preparations from commercial vitamin K-dependent coagulation factor concentrates had specific activities of 134 and 155 U/mg. Crude concentrates and purified factor IX preparations were tested for thrombogenicity in rabbits. One of two crude concentrates tested in the stasis-thrombosis assay caused large thrombi at doses of 50 U/kg. Purified factor IX from this concentrate was not thrombogenic at 106 to 234 U/kg. A heparin-treated concentrate that was not active in the stasis model at 100 U/kg caused significant (P less than .05) delayed consumption of rabbit fibrinogen, platelets, antithrombin III antigen, and factor VIII activity at the same dose. Factor IX prepared from this concentrate caused no consumption of coagulation factors at 214 to 243 U/kg despite the presence of trace amounts of activated factor IX. These results indicate that more highly purified preparations could reduce the risk of thrombosis in replacement therapy for hemophilia B. Also, at least for the preparations tested, factor IX and factor IXa were not the thrombogenic components of the crude concentrates.
Comparison of Neurodegenerative Pathology in Transgenic Mice Overexpressing V717F β-Amyloid Precursor Protein and Alzheimer’s Disease (1996)

Overexpression of mutated human amyloid precursor protein (hAPP717V→F) under control of platelet-derived growth factor promoter (PDAPP minigene) in transgenic (tg) mice results in neurodegenerative changes similar to Alzheimer’s disease (AD). To clarify the pathology of these mice, we studied images derived from laser scanning confocal and electron microscopy and performed comparisons between PDAPP tg mice and AD. Similar to AD, neuritic plaques in PDAPP tg mouse contained a dense amyloid core surrounded by anti-hAPP- and anti-neurofilament-immunoreactive dystrophic neurites and astroglial cells. Neurons were found in close proximity to plaques in PDAPP tg mice and, to a lesser extent, in AD. In PDAPP tg mice, and occasionally in AD, neuronal processes contained fine intracellular amyloid fibrils in close proximity to the rough endoplasmic reticulum, coated vesicles, and electron-dense material. Extracellular amyloid fibrils (9–11 nm in diameter) were abundant in PDAPP tg and were strikingly similar to those observed in AD. Dystrophic neurites in plaques of PDAPP tg mouse and AD formed synapses and contained many dense multilaminar bodies and neurofilaments (10 nm). Apoptotic-like figures were present in the tg mice. No paired helical filaments have yet been observed in the heterozygote PDAPP tg mice. In summary, this study shows that PDAPP tg mice develop massive neuritic plaque formation and neuronal degeneration similar to AD. These findings show that overproduction of hAPP717V→F in tg mice is sufficient to cause not only amyloid deposition, but also many of the complex subcellular degenerative changes associated with AD.
A network-based knowledge representation and its natural deduction system (1977)

We describe a knowledge representation scheme called KNET and a problem solving system called SNIFFER designed to answer queries using a K-NET knowledge base. K-NET uses a partitioned semantic net to combine the expressive capabilities of the first-order predicate calculus with linkage to procedural knowledge and with full indexing of objects to the relationships in which they participate. Facilities are also included for representing taxonomies of sets and for maintaining hierarchies of contexts. SNIFFER is a manager and coordinator of deductive and problem-solving processes. The basic system includes a logically complete set of natural deduction facilities that do not require statements to be converted into clause or prenex normal form. Using SNIFFER's coroutine-based control structure, alternative proofs may be constructed in pseudo-parallel and results shared among them. In addition, SNIFFER can also manage the application of specialist procedures that have specific knowledge about a particular domain or about the topology of the K-NET structures, for example, specialist procedures are used to manipulate taxonomic information and to link the system to information in external data bases.
Depth image based compositing for stereo 3D (2012)

Compositing is an essential tool in modern film making. Established workflows exist for single-view video compositing, however new problems that demand new solutions arise when considering stereoscopic compositing. We investigate new methods for compositing live action stereo 3D, given two stereo camera systems and a corresponding depth map. We break the process up into three main steps; First, we show how to use trifocal tensors to robustly project 3D content from one video into another. Second, we analyze different image-based rendering methods for drawing objects to be composited into the new video. Finally, we describe a novel super-pixel based depth-test that increases robustness to errors in depth map accuracy. A user study was conducted to validate different steps of this process.
QUANTITATIVE EVALUATION OF RETINAL TUMOR VOLUME IN MOUSE MODEL OF RETINOBLASTOMA BY USING ULTRA HIGH-RESOLUTION OPTICAL COHERENCE TOMOGRAPHY (2008)

An ultra high resolution spectral-domain optical coherence tomography (SD-OCT) together with an advanced animal restraint and positioning system was built for noninvasive non-contact in vivo three-dimensional imaging of rodent models of ocular diseases. The animal positioning system allowed the operator to rapidly locate and switch the areas of interest on the retina. This function together with the capability of precise spatial registration provided by the generated OCT fundus image allows the system to locate and compare the same lesion (retinal tumor in the current study) at different time point throughout the entire course of the disease progression. An algorithm for fully automatic segmentation of the tumor boundaries and calculation of tumor volume was developed. The system and algorithm were successfully applied to monitoring retinal tumor growth quantitatively over time in the LH BETA T AG mouse model of retinoblastoma.
Cholera toxin subunit B inhibits IL-12 and IFN-γ production and signaling in experimental colitis and Crohn’s disease (2005)

These studies indicate that CT-B inhibits mucosal Th1 cell signaling and suggest that rCT-B may be a promising candidate for CD therapy.
Rapid Room-Temperature Synthesis and Characterization of Nanocrystals of a Prototypical Zeolitic Imidazolate Framework (2009)

Simply reacting Zn(NO3)2·6H2O with an excess of 2-methylimidazole in methanol at room temperature yields well-shaped nanocrystals of ZIF-8 with a narrow size distribution. The rapid growth has been monitored by time-resolved static light scattering. Nanoscale ZIF-8 powder is microporous and thermally stable up to ca. 200 °C.
Mediators of Inflammation in Blister Fluids From Patients With Pemphigus Vulgaris and Bullous Pemphigoid (1989)

Blister fluids from 39 previously untreated patients with pemphigus vulgaris (PV) and 28 patients with bullous pemphigoid (BP) were tested for the presence of inflammatory mediators. Blister fluids from patients with PV and BP showed interleukin 1 (IL-1)- and interleukin 2 (IL-2)-like activity and contained prostaglandin (PG) E2, F1 alpha, and F2 alpha, thromboxane B2 (TB2), leukotriene (LT) B4 and C4, serine esterases, and proteolysis inhibitors. Pemphigus blister fluid was distinguished by high IL-1-like activity, proteolytic activity, and high concentrations of TB2 and LTB4, while pemphigoid blister fluid was characterized by higher IL-2-like activity, antiprotease activity, and high PGE2 concentration. We also determined that the content of mediators of inflammation varied depending on the duration of blister development. In both PV and BP, the initially high IL-1-like activity, amount of serine proteases, and concentrations of PGF2 alpha, TB2, LTB4, and LTC4 decreased by the fifth day of blister existence, whereas antiprotease activity as well as PGE2 and PGF1 alpha concentrations gradually increased as blisters developed. These findings suggest certain differences in the character of the bullous inflammatory process in pemphigus and pemphigoid.
Does the Brown-marmorated Stink Bug, Halyomorpha halys (Stal) (Heteroptera: Pentatomidae) Reproduce by Feeding on the Cones of Japanese Cedar, Cryptomeria japonica D. Don? (2005)

The sexual maturation of adults and development of the larvae of Halyomorpha halys reared on Japanese cedar cones were investigated in Akita Prefecture, in the northern part of Japan in 2002 and 2003. Adult females reared on cones in the laboratory and in the field laid no eggs, and died shortly thereafter. Second-instar larvae reared on the cones never developed into the 3rd-instar both in the field and in the laboratory, except for only a few individuals in the field. All 3rd-instar and most 4th-instar larvae reared on the cones died without further development, although some 4th-instar larvae reared on cones collected after late July developed into the 5th-instar. In contrast, many 2nd-instar larvae fed the seeds that were taken out of cones collected after late July developed into the 3rd-instar. These results suggest that the mature seeds of cones are suitable for the development of H. halys larvae, but that indehiscent cones are not. Because most cones do not dehisce until October in Akita Prefecture, it is considered that most H. halys in this area cannot lay eggs and develop into adults by feeding on Japanese cedar cones.
Functional organization of the Aspergillus nidulans trpC promoter. (1987)

We investigated the functional organization of the Aspergillus nidulans trpC promoter by the sequential removal of sequences upstream of the major trpC mRNA cap site (+1). DNA fragments containing promoter mutations were fused to the Escherichia coli lacZ gene, and a novel method was used to select for integration of the fusion gene at the Aspergillus argB locus. beta-Galactosidase assays and S1 nuclease protection experiments demonstrated that the promoter mutations affected gene expression in three ways: (i) 5' deletions up to -82 resulted in variable increases in beta-galactosidase activity, depending on the growth conditions; (ii) a deletion from -67 to -11 did not alter the level of beta-galactosidase activity, but did give rise to mRNAs with aberrant 5' ends; and (iii) a 5' deletion with an endpoint at -11 and an internal deletion from -142 to -11 abolished gene expression. These results indicate that sequences upstream of -82 reduce transcription of the trpC gene and that distinct DNA sequence elements are required for expression versus correct initiation of transcription of the trpC gene. The sequences essential for trpC expression do not include the common eucaryotic promoter elements CCAAT and TATAAA. To our knowledge, this is the first functional analysis of a promoter from a fungus other than Saccharomyces cerevisiae.
Infrared Temperature Control System for a Completely Noncontact Polymerase Chain Reaction in Microfluidic Chips (2007)

A completely noncontact temperature system is described for amplification of DNA via the polymerase chain reaction (PCR) in glass microfluidic chips. An infrared (IR)-sensitive pyrometer was calibrated against a thermocouple inserted into a 550-nL PCR chamber and used to monitor the temperature of the glass surface above the PCR chamber during heating and cooling induced by a tungsten lamp and convective air source, respectively. A time lag of less than 1 s was observed between maximum heating rates of the solution and surface, indicating that thermal equilibrium was attained rapidly. Moreover, the time lag was corroborated using a one-dimensional heat-transfer model, which provided insight into the characteristics of the device and environment that caused the time lag. This knowledge will, in turn, allow for future tailoring of the devices to specific applications. To alleviate the need for calibrating the pyrometer with a thermocouple, the on-chip calibration of pyrometer was accomplished by sensing the boiling of two solutions, water and an azeotrope, and comparing the pyrometer output voltage against the known boiling points of these solutions. The "boiling point calibration" was successful as indicated by the subsequent chip-based IR-PCR amplification of a 211-bp fragment of the B. anthracis genome in a chamber reduced beyond the dimensions of a thermocouple. To improve the heating rates, a parabolic gold mirror was positioned above the microfluidic chip, which expedited PCR amplification to 18.8 min for a 30-cycle, three-temperature protocol.
Nuclear β-catenin expression as a prognostic factor in advanced colorectal carcinoma (2008)

Nuclear beta-catenin expression provides additional information in predicting patient outcome in advanced CRC.
N-Myristoyltransferase isozymes exhibit differential specificity for human immunodeficiency virus type 1 Gag and Nef (2007)

Myristoylation of the human immunodeficiency virus type 1 (HIV-1) proteins Gag and Nef by N-myristoyltransferase (NMT) is a key process in retroviral replication and virulence, yet remains incompletely characterized. Therefore, the roles of the two isozymes, NMT1 and NMT2, in myristoylating Gag and Nef were examined using biochemical and molecular approaches. Fluorescently labelled peptides corresponding to the N terminus of HIV-1 Gag or Nef were myristoylated by recombinant human NMT1 and NMT2. Kinetic analyses indicated that NMT1 and NMT2 had 30- and 130-fold lower K(m )values for Nef than Gag, respectively. Values for K(cat) indicated that, once Gag or Nef binds to the enzyme, myristoylation by NMT1 and NMT2 proceeds at comparable rates. Furthermore, the catalytic efficiencies for the processing of Gag by NMT1 and NMT2 were equivalent. In contrast, NMT2 had approximately 5-fold higher catalytic efficiency for the myristoylation of Nef than NMT1. Competition experiments confirmed that the Nef peptide acts as a competitive inhibitor for the myristoylation of Gag. Experiments using full-length recombinant Nef protein also indicated a lower K(m) for Nef myristoylation by NMT2 than NMT1. Small interfering RNAs were used to selectively deplete NMT1 and/or NMT2 from HEK293T cells expressing a recombinant Nef-sgGFP fusion protein. Depletion of NMT1 had minimal effect on the intracellular distribution of Nef-sgGFP, whereas depletion of NMT2 altered distribution to a diffuse, widespread pattern, mimicking that of a myristoylation-deficient mutant of Nef-sgGFP. Together, these findings indicate that Nef is preferentially myristoylated by NMT2, suggesting that selective inhibition of NMT2 may provide a novel means of blocking HIV virulence.
A nitric oxide-like factor mediates nonadrenergic-noncholinergic neurogenic relaxation of penile corpus cavernosum smooth muscle. (1991)

This study was initiated to characterize nonadrenergic-noncholinergic (NANC) inhibitory neurotransmission in penile corpus cavernosum. Using organ baths, isometric tension measurements were made in strips of human and rabbit corpus cavernosum. In examining endothelium-mediated responses, cumulative additions of exogenous acetylcholine elicited dose-dependent relaxations which were significantly reduced or completely inhibited in tissues treated with NG-monomethyl L-arginine (L-NMMA; an inhibitor of nitric oxide synthesis), oxyhemoglobin (a nitric oxide scavenger), or methylene blue (a guanylate cyclase blocker). Tissues exposed to hypoxic conditions (PO2 = 5-10 mmHg) also did not respond to exogenous acetylcholine. Mechanical removal of the endothelium in human corporal strips or in situ treatment of rabbit corpora with detergent blocked the relaxation to acetylcholine. Transmural electrical stimulation of corporal tissue strips denuded of functional endothelium, in the presence of adrenergic blockade with bretylium and muscarinic receptor blockade with atropine, caused frequency-dependent relaxation. This neurogenic relaxation was reduced or prevented by L-NMMA, oxyhemoglobin, methylene blue, and hypoxia. The effects of L-NMMA were reversed by L-arginine and the effects of hypoxia were readily reversed by normoxic conditions. Authentic, exogenous nitric oxide relaxed corporal strips which were contracted with adrenergic agonists and this effect was significantly inhibited by oxyhemoglobin. It is concluded that (a) endothelium-mediated responses of corpus cavernosum smooth muscle are mediated by a diffusible nitric oxide-like substance; (b) NANC neurogenic inhibitory responses do not require functional endothelium, and (c) nitric oxide, or a closely related substance, may act as an inhibitory neurotransmitter in penile corpus cavernosum smooth muscle.
An Approach to Optimum Joint Beamforming Design in a MIMO-OFDM Multiuser System (2004)

This paper describes a multiuser scenario with several terminals acceding simultaneously to the same frequency channel. The objective is to design an optimal multiuser system that may be used as a comparative framework when evaluating other suboptimal solutions and to contribute to the already published works on this topic. The present work assumes that a centralized manager knows perfectly all the channel responses between all the terminals. According to this, the transmitters and receivers, using antenna arrays and leading to the so-called multiple-input-multiple-output (MIMO) channels, are designed in a joint beamforming approach, attempting to minimize the total transmit power subject to quality of service (QoS) constraints. Since this optimization problem is not convex, the use of the simulated annealing (SA) technique is proposed to find the optimum solution.
Rheumatoid arthritis after 9 years of human immunodeficiency virus infection: possible contribution of tritherapy. (2002)

Infection by human immunodeficiency virus (HIV) may affect joints in different ways. It usually increases the severity of reactive arthritis. Conversely, when rheumatoid arthritis (RA) is seen in association with HIV infection, remission of RA has been observed in some cases. We describe a patient who developed 3 successive forms of joint manifestations: early HIV related arthralgias followed by drug related arthritis, and more recently by typical RA. The first signs of joint manifestations started one year after HIV seroconversion and resolved when antiviral treatment with AZT was started. The second episode ended when lamivudine dosage was reduced. Finally, after 9 years of infection, the diagnosis of seropositive RA was made in this HLA-DR1 positive patient. The symptoms started when the immune status reached normal CD4 T cell levels, in response to antiviral tritherapy. This observation indicates the complex effect of HIV on joint inflammation.
An X-band SOS resistive gate&#8212;insulator&#8212;semiconductor (RIS) switch (1980)

The new X-Band Resistive Gate-Insulator-Semiconductor (RIS) switch has been fabricated on silicon-on-sapphire, and its equivalent circuit model characterized. An RIS SPST switch with 20-dB ON/OFF isolation, 1.2-dB insertion loss, and power-handling capacity in excess of 20-W peak has been achieved at X band. The device switching time is on the order of 600 ns, and it requires negligible control holding current in both ON and OFF states. The device is compatible with monolithic integrated-circuit technology and thus is suitable for integration into low-cost monolithic phase shifters or other microwave integrated circuits.