gebhart/patrepeval huggingface dataset:
Acute sensorineural deafness in Lassa fever (1990)

A prospective audiometric evaluation of 69 hospitalized febrile patients in Sierra Leone, West Africa, revealed a sensorineural hearing deficit (SNHD) in 14 (29%) of 49 confirmed cases of Lassa fever and in 0 of 20 febrile controls. An SNHD was present in nine (17.6%) of 51 people who had evidence of previous Lassa virus infection. Twenty-six of 32 local residents who had previously sustained a sudden deafness had antibody titers to Lassa virus of 16 or greater, compared with six of 32 matched controls. Lassa fever is associated with an incidence of SNHD, which considerably exceeds that previously reported with any other postnatally acquired infection, and accounts for a prevalence of virus-related hearing impairment in the eastern province of Sierra Leone that is greater than that reported from anywhere else in the world. (<i>JAMA</i>. 1990;264:2093-2096)
Stixels estimation without depth map computation (2011)

Mobile robots require object detection and classification for safe and smooth navigation. Stereo vision improves such detection by doubling the views of the scene and by giving indirect access to depth information. This depth information can also be used to reduce the set of candidate detection windows. Up to now, most algorithms compute a depth map to discard unpromising detection windows. We propose a novel approach where a stixel world model is computed directly from the stereo images, without computing an intermediate depth map. We experimentally demonstrate that such approach can considerably reduce the set of candidate detection windows at a fraction of the computation cost of previous approaches.
Discursive construction of the ‘key’ moment in the Umbrella Movement (2016)

Abstract A mass civil disobedience movement brought Hong Kong’s key business and commercial districts to a standstill in September 2014 when low-key class boycotts coalesced into a wide-scale social movement propelled by thousands of people who flocked to the support of student protestors after an ‘unwarranted’ 87 rounds of tear gas were fired by the police. This paper will explore the discursive construction of this key precipitant ( Kimmel 1990 ), that is a ‘key’ moment, which recontextualised an on-going universal suffrage campaign into an historical event that allowed, “deeply seated structural forces to emerge as politically potent and begin to mobilize potential discontents” ( Kimmel 1990 , 9-10). Drawing on the multi-perspective framework of the Discourse of Illusion ( Bhatia 2015a ) the paper will analyse this key ‘moment’ in Hong Kong’s local memory, which represented one unitary moment of change that transformed the intended course of events. The Discourse of Illusion in this respect will draw on three interrelated components: historicity (one’s habitus as key to the creation of discursive illusions, dealing as it does with the growth and change of perceptions over time); linguistic and semiotic action (subjective conceptualisations of the world give rise to one’s linguistic and semiotic actions, often through dominant metaphorical rhetoric); and the degree of social impact (as language and actions of individuals and groups engender many categories and stereotypes).
The DNA sequence of the sulfate activation locus from Escherichia coli K-12. (1992)

The DNA sequence of the sulfate activation locus from Escherichia coli K-12 has been determined. The sequence includes the structural genes encoding the enzymes ATP sulfurylase (cysD and cysN) and APS kinase (cysC) which catalyze the synthesis of activated sulfate. These are the only genes known to reside in the sulfate activation operon. Consensus elements of the operon promoter were identified, and the start codons and open reading frames of the Cys polypeptides were determined. During this work, another gene, iap, was partially sequenced and mapped. The activity of ATP sulfurylase is stimulated by an intrinsic GTPase. Comparison of the primary sequences of CysN and Ef-Tu revealed that CysN has conserved many of the residues integral to the three-dimensional structure important for guanine nucleotide binding in Ef-Tu and RAS. nodP and nodQ, from Rhizobium meliloti, are essential for nodulation in leguminous plants. The Cys and Nod proteins are remarkably similar. NodP appears to be the smaller subunit of ATP sulfurylase. NodQ encodes homologues of both CysN and CysC; thus, these enzymes may be covalently associated in R. meliloti. The consensus GTP-binding sequences of NodQ and CysN are identical suggesting that NodQ encodes a regulatory GTPase.
Activation of Vα14+Natural Killer T Cells by α-Galactosylceramide Results in Development of Th1 Response and Local Host Resistance in Mice Infected withCryptococcus neoformans (2001)

We examined the effect of alpha-galactosylceramide (alpha-GalCer) on the synthesis of gamma interferon (IFN-gamma) and local resistance in mice infected intravenously with Cryptococcus neoformans. The level of IFN-gamma in serum increased on day 3, reached a peak level on day 7, and decreased to the basal level on day 14 postinfection in mice treated with alpha-GalCer, while in vehicle-treated mice, no increase was detected at any time points except for a small increase on day 7. Such effects were not observed in NKT-KO mice. In CD4KO mice, minor synthesis of IFN-gamma was detected on day 3 in sera but was completely abolished by day 7. The alpha-GalCer-induced IFN-gamma production on day 3 was partially reduced in mice depleted of NK cells by treatment with anti-asialo-GM(1) antibody (Ab). Spleen cells obtained from infected and alpha-GalCer-treated mice on day 7 produced a large amount of IFN-gamma upon restimulation with live organisms, while only a marginal level of production was detected in splenocytes from infected and vehicle-treated mice. Such effects were abolished in CD4KO and NKT-KO mice. Finally, the fungal loads in the lungs and spleen on days 7 and 14 were significantly reduced in alpha-GalCer-treated mice compared to those in control mice. In NKT-KO mice, local resistance elicited by alpha-GalCer was completely abolished, although no obvious exacerbation of infection was detected. Furthermore, treatment with anti-IFN-gamma monoclonal Ab mostly abrogated the protective effect of this agent. Thus, our results indicated that activation of Valpha14(+) NKT cells resulted in an increased Th1 response and local resistance to C. neoformans through production of IFN-gamma.
Discovery, Engineering, and Synthetic Application of Transaminase Biocatalysts (2017)

Transaminases have attracted considerable interest in their use as biocatalysts for the synthesis of compounds containing chiral amine units, which are widespread within the pharmaceutical, agrochemical, and fine chemical industry. Recent developments in enzyme- and process-engineering have expedited their use in asymmetric synthesis; however, industrial applications are still hindered by a number of factors, including equilibrium thermodynamics, product inhibition, and poor substrate tolerance. Detailed and comprehensive approaches to each of these challenges have been reported during the last two decades; the most representative enzyme discovery and screening strategies, protein and equilibrium engineering, and immobilization techniques are reviewed herein. Furthermore, we present a detailed look into the applications of transaminases for the synthesis of a variety of amine-containing compounds and the integration of transaminases into multienzymatic systems that allow access to a variety of highly complex products for the end user.
Cis-acting RNA elements at the 5′ end of Sindbis virus genome RNA regulate minus- and plus-strand RNA synthesis (2001)

Alphavirus genome replication is a multistep asymmetric process. Several lines of evidence suggest that the template preference of the RNA replicase is regulated by proteolytic cleavage of the viral nonstructural polyprotein. Cis-acting RNA elements in the viral genome also play crucial roles in regulating genome replication and subgenomic RNA transcription. In this report, a series of RNA templates were analyzed in vitro and in vivo to define functional elements in the 5' end of the genome. The 5' UTR was shown to contain distinct core promoter elements for both minus- and plus-strand synthesis. In addition, two conserved stem-loop structures within the nsP1 coding sequence enhanced RNA replication but were not required. Studies with chimeric templates and trans-competition experiments suggest that the 5' determinant for minus-strand initiation can differ among alphaviruses and binds to one or more limiting replicase components. The results provide compelling evidence that the 5' and 3' ends of alphavirus genome RNAs must interact to initiate replication and we propose one model for how this interaction might occur. In addition to providing new insight into the initiation of alphavirus genome replication, these results have implications for the development of improved alphavirus vector systems with reduced recombination potential.
High INDO (indoleamine 2,3-dioxygenase) mRNA level in blasts of acute myeloid leukemic patients predicts poor clinical outcome (2008)

Indoleamine 2,3-dioxygenase degrades the amino acid tryptophan which is essential for T cells. Tryptophan depletion causes T-cell cycle arrest and solid tumors that express high levels of indoleamine 2,3-dioxygenase can create immune suppression. Recently, blasts of patients with acute myeloid leukemia were shown to express indoleamine 2,3-dioxygenase. We determined INDO (encoding gene for indoleamine 2,3-dioxygenase) mRNA expression in leukemic blasts of 286 patients with acute myeloid leukemia by gene-expression profiling. Results were validated by quantitative polymerase chain reaction analysis in blasts of an independent cohort of 71 patients. High INDO expression was correlated to significantly shortened overall and relapse-free survival. Correlation of INDO expression to relevant known prognostic factors and survival identified high INDO expression as a strong negative independent predicting variable for overall and relapse-free survival. Inhibition of indoleamine 2,3-dioxygenase expressed by myeloid leukemic blasts may result in breaking immune tolerance and offers new therapeutic options for patients with acute myeloid leukemia.
Wide Field of View Head Mounted Display for Tele-presence with An Omnidirectional Image Sensor (2003)

Recently, the omnidirectional image sensors have been applied to tele-presence systems, because the sensor can capture images with large field of views at video rate. On the other hand, head mount display (HMD) has been generally used as a personal display for virtual reality applications such as a tele-presence. However, almost all HMDs have a problem that the field of view (FOV), about 60 degree horizontally, of its presented image was terribly narrower than that of human. The problem makes reality and immersion lower in these applications. In this paper, we propose high-immersive visualization system that can display 180 degrees horizontal view by using a new catadioptrical HMD and an omnidirectional image sensor. The HMD consists of ellipsoidal and hyperboloidal curved mirrors, and can display 180 degrees horizontal view.
In Vivo Thrombus Formation in Murine Models (2007)

Platelets play a central role in hemostasis, but also in atherothrombosis, as they rapidly adhere to tissue and to one another as a response to any vascular injury. This process involves a large number of surface receptors, signaling pathways, and enzymatic cascades as well as their complex interplay. Although in vitro experiments proved successful in both identifying new receptors and pathways and developing potent and selective antithrombotic drugs, in vitro research cannot mimic the myriad hemodynamic and spatiotemporal cellular and molecular interactions that occur during the generation and propagation of thrombi in vivo. Animal models, and, with the availability of genetically modified mouse strains and of modern intravital imaging techniques, mouse models in particular, have opened new ways to identify both individual roles and the interplay of platelet proteins in complex in vivo settings. In vivo models revealed the important role of, eg, Gas6 or blood coagulation factor XII in thrombus formation, and results obtained in in vivo models raised the interesting possibility that (physiologic) hemostasis and (pathologic) thrombosis might represent 2 mechanistically different processes. This review summarizes in vivo findings that contributed significantly to our understanding of hemostatic and thrombotic processes and which may help to guide future research.
Direct determination of the amplitude and the phase of femtosecond light pulses (1991)

A direct measurement of the amplitude and the phase of a femtosecond light pulse is performed for the first time to our knowledge. The measurement is made in the frequency domain, and the time dependence of the field can be easily obtained by a Fourier transform. The technique relies on a pulse synthesis scheme to unravel the frequency dependence of the phase. A mask filters the spectrum, which gives rise to a pulse with a measurable temporal profile related to the frequency dependence of the phase. In particular, with a rectangular slit the time delay of the synthesized pulse is the first derivative of the phase with respect to the frequency of the original pulse at the central frequency of the filter. The amplitude of the spectrum is obtained from the power spectrum.
DFTT: Design for Trojan Test (2010)

Due to the globalization of the Integrated Circuit (IC) manufacturing industry, hardware Trojans constitute an increasingly probable threat to both commercial and military applications. As traditional testing methods fall short in finding hardware Trojans, several specialized detection methods have surfaced. To facilitate research in this area and embed internal barriers to prevent Trojan attacks both at the design level and at the manufacturing level, we propose a Design-for-Trojan-Test (DFTT) methodology. DFTT is based on one key principle: increase the complexity for hardware Trojan attackers, thereby making successful hardware Trojan-based attacks extremely difficult to accomplish. A DFTT tool is also developed to automate the hardening process. The effectiveness of our Trojan prevention method is demonstrated on the Trivium encryption core.
Two monoclonal anti-human T lymphocyte antibodies have similar biologic effects and recognize the same cell surface antigen. (1982)

Two independently produced monoclonal antibodies, UCHT1, an IgG1 antibody, and OKT3, an IgG2 antibody, which specifically identify all human peripheral T lymphocytes, were shown to possess similar functional properties. Both were highly mitogenic to peripheral blood T lymphocytes, and UCHT1 blocked specific T lymphocyte killing of autologous B lymphoblasts when present during either the induction or the cytotoxic phase of the reaction; this, too, is a property reported for OKT3 in an analogous situation. Both antibodies also inhibited the 6-day proliferative response to soluble antigens and mixed lymphocyte culture, although this may be attributable to their strong mitogenicity earlier in culture. These properties were not found with other monoclonal antibodies directed against human T lymphocytes, and suggested that UCHT1 and OKT3 recognize important functional structure(s) on the T cell surface. The identity of the antigen recognized by these two antibodies was demonstrated by 2-directional co-capping, by cold antibody inhibition of binding of radiolabeled antibody, and by immunoprecipitation and two-dimensional gel analysis of labeled T cell surface proteins. Both UCHT1 and OKT3 bound with similar affinities (Ka approximately 2 X 10(9) M-1) to the same number of binding sites (2.8 X 10(4) sites/activated T cell), and both precipitated the same glycoprotein complex with a m.w. of approximately 19,000 in the presence of reducing agent.
Twin-free and High-Quality DAST Crystals − Effected through Solutions of Lower Supersaturation Coupled with Isothermal Solvent Evaporation (2006)

Growth of twin-free and high-quality 4-N,N-dimethylamino-4‘-N‘-methyl stilbazolium tosylate (DAST) crystals, with a surface roughness in the range of 1.7−3.8 nm (<4 nm) for as-grown crystals, has been achieved using solutions of lower supersaturation coupled with isothermal solvent evaporation. In addition, these efficient organic−ionic nonlinear optical (NLO) crystals possessed well-developed 001 and 001̄ faces that facilitate direct utilization of these crystals for electrooptic (EO) and terahertz (THz) applications. Since this modified growth method necessitates a relatively lower amount (about 46%) of the expensive starting material as compared to that required for routine methods, it is also proven to be cost-effective.
Rev is necessary for translation but not cytoplasmic accumulation of HIV-1 vif, vpr, and env/vpu 2 RNAs. (1991)

The effect of Rev on cytoplasmic accumulation of the singly spliced human immunodeficiency virus type 1 (HIV-1) vif, vpr, and env/vpu RNAs was examined by using a quantitative RNA polymerase chain reaction (PCR) analysis following transfection of complete proviral molecular clones into lymphoid cells. Previously published studies using subgenomic env constructs in nonlymphoid cell types concluded that Rev was necessary for cytoplasmic accumulation of high levels of unspliced env RNA and that, by analogy, Rev must be necessary for the cytoplasmic accumulation of all HIV-1 RNAs that contain the Rev-responsive element (RRE). We confirm those results in COS cells. Unexpectedly, in lymphoid cells, we find that although Rev acts somewhat to increase the cytoplasmic level of full-length HIV-1 RNA, Rev has little or no effect on cytoplasmic accumulation of singly spliced HIV-1 RNAs. However, Env protein expression was greatly reduced in the absence of Rev. Analysis of the cytoplasmic RNA revealed that in the absence of Rev or the RRE, the cytoplasmic vif, vpr, and env/vpu 2 RNAs were not associated with polysomes but with a complex of 40S-80S in size. Consequently, efficient expression of the Vif, Vpr, Vpu, and Env proteins from these RNAs is dependent on Rev. These results exclude a mechanism whereby the sole function of Rev is simply to export RNAs from nucleus to cytoplasm. We discuss other models to take into account the dependence on Rev for efficient translation of cytoplasmic HIV-1 RNAs.
Protein Denaturation during Heat Shock and Related Stress (1989)

In an attempt to question the toxic effect of heat shock and related stress, we have studied the activity of reporter enzymes during stress. Escherichia coli beta-galactosidase and Photinus pyralis luciferase were synthesized in mouse and Drosophila cells after transfection of the corresponding genes. Both enzymes are rapidly inactivated during hyperthermia. The corresponding polypeptides are not degraded but become insoluble even in the presence of non-ionic detergents. The heat inactivation is more dramatic in vivo within the living cell than in vitro, in a detergent-free crude cell lysate. The extent of enzyme inactivation at a given temperature depends on the cell type in which the enzyme is expressed. Luciferase is inactivated at lower temperatures within Drosophila cells than within mouse cells, whereas beta-galactosidase is inactivated at higher temperatures in E. coli than in mouse cells. A "priming" heat shock confers a transient increased resistance (thermotolerance) of cells against a second "challenging" heat shock. Enzyme inactivation during heat shock or exposure of the cells to ethanol is attenuated in heat shock-primed cells. A comparable thermoprotection is raised by a priming heat shock for both luciferase activity and protein synthesis. Thus, the study of reporter enzyme inactivation is a promising tool for understanding the molecular basis of the toxicity of heat shock and related stress as well as the mechanisms leading to thermotolerance.
Factoring repeated content within and among images (2008)

We reduce transmission bandwidth and memory space for images by factoring their repeated content. A transform map and a condensed epitome are created such that all image blocks can be reconstructed from transformed epitome patches. The transforms may include affine deformation and color scaling to account for perspective and tonal variations across the image. The factored representation allows efficient random-access through a simple indirection, and can therefore be used for real-time texture mapping without expansion in memory. Our scheme is orthogonal to traditional image compression, in the sense that the epitome is amenable to further compression such as DXT. Moreover it allows a new mode of progressivity, whereby generic features appear before unique detail. Factoring is also effective across a collection of images, particularly in the context of image-based rendering. Eliminating redundant content lets us include textures that are several times as large in the same memory space.
Cell Adhesion and the Molecular Processes of Morphogenesis (1985)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Induced Pluripotent Stem Cell Derivation and Ex Vivo Gene Correction Using a Mucopolysaccharidosis Type 1 Disease Mouse Model (2019)

Mucopolysaccharidosis type 1 (MPS-1), also known as Hurler's disease, is a congenital metabolic disorder caused by a mutation in the alpha-L-iduronidase (IDUA) gene, which results in the loss of lysosomal enzyme function for the degradation of glycosaminoglycans. Here, we demonstrate the proof of concept of ex vivo gene editing therapy using induced pluripotent stem cell (iPSC) and CRISPR/Cas9 technologies with MPS-1 model mouse cell. Disease-affected iPSCs were generated from <i>Idua</i> knockout mouse embryonic fibroblasts, which carry a disrupting neomycin-resistant gene cassette (Neo<sup>r</sup>) in exon VI of the Idua gene. Double guide RNAs were used to remove the Neo<sup>r</sup> sequence, and various lengths of donor templates were used to reconstruct the exon VI sequence. A quantitative PCR-based screening method was used to identify Neo<sup>r</sup> removal. The sequence restoration without any indel mutation was further confirmed by Sanger sequencing. After induced fibroblast differentiation, the gene-corrected iPSC-derived fibroblasts demonstrated Idua function equivalent to the wild-type iPSC-derived fibroblasts. The Idua-deficient cells were competent to be reprogrammed to iPSCs, and pluripotency was maintained through CRISPR/CAS9-mediated gene correction. These results support the concept of ex vivo gene editing therapy using iPSC and CRISPR/Cas9 technologies for MPS-1 patients.
Natural Sunlight Tests at Petal, of A Trial Mim String at Concentrations up to 1000X (2006)

Within the framework of the HiConPV project (European Commission, Framework 6), we present preliminary results of I-V curve measurements that are being performed on a trial dense-array CPV module under natural sunlight conditions at various concentrations up to 1000X. This module, approximately 10 cmtimes10 cm, will be tiled with 24 GaAs "MIM" chips with a total nominal power rating of 1.8 kWp at 1,000X. However, for the present tests a single string of 4 series-connected MIMs was employed. For illumination we used PETAL, the 400 m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> parabolic dish concentrator at Sede Boqer, covering its mirror panels according to the degree of concentration needed