gebhart/patrepeval huggingface dataset:
Building a Virtual Library (2003)

Virtual libraries are organic and understanding the challenges as virtual libraries are developed and evolve are ongoing. These challenges range from content to interfaces, from digital video to geospatial infrastructures, from staffing to marketing. This book explores the dynamics of building a virtual library at the University of South Florida within the context of national developments and standards. This illustration will assist the reader in understanding and developing similar resources and services for his or her library. The chapter contributors have done an excellent job presenting both conceptual approaches and case illustrations in building a virtual library within an academic environment. Librarians will have a greater understanding of how technology and change impacts their environments. Staff in the traditional functional areas of libraries will see examples of how emerging technologies can be most efficiently and effectively utilized within their respective organizations. In addition, librarians in administrative positions will greatly benefit from the discussion of organizational change, the emergence of work teams, and staffing and personnel. In addition, the chapters on marketing, and statistics provide an clear picture of the importance of both of these activities to both libraries and their larger institutions. Finally, library and information science faculty will be interested in how the development of virtual libraries will re-engineer library education. This book is essential reading for those individuals currently planning or implementing virtual library services and resources within their academic environment.
Natural Antisense mRNAs to Hyaluronan Synthase 2 Inhibit Hyaluronan Biosynthesis and Cell Proliferation (2005)

We report the identification of a natural antisense mRNA of hyaluronan synthase 2 that we have chosen to designate as HASNT (for HA synthase 2 antisense) in human and mouse. HASNT is transcribed from the opposite strand of the HAS2 gene locus and is represented by several independent expressed sequence tags in human. Portions of the mouse Hasnt gene were identified through an exon-trapping approach. Sequence conservation is extremely low between human and mouse HASNT, and it is not clear whether these mRNAs contain functional open reading frames. HASNT has an alternate splice site in both human and mouse. This splice site is located at an identical position within the gene in both species and results in mRNAs of two different lengths. In each species, the antisense portion of the HASNT gene is complementary to the first exon of HAS2, which represents the 5'-untranslated region. To study the biological activity of HASNT, two human expressed sequence tag clones, representing long and short HASNT splice variants, were cloned into a tetracycline-inducible vector and were stably transfected into human osteosarcoma U2-OS Tet-on cells. The long and short HASNT-expressing cells had a reduction in HAS2 mRNA levels up to 94 and 86%, respectively, whereas hyaluronan biosynthesis was inhibited by 40 and 37%, respectively. Cell proliferation was reduced throughout the time frame of the experiment. Exogenous high molecular mass hyaluronan failed to rescue the suppressed cell proliferation, whereas adenoviral-mediated overexpression of hyaluronan synthase 3, which stimulated endogenous hyaluronan biosynthesis, was able to rescue. Collectively, our data suggest that natural antisense mRNAs of HAS2 are able to regulate HAS2 mRNA levels and hyaluronan biosynthesis in a cell culture model system and may have an important and novel regulatory role in the control of HAS2, HA biosynthesis, and HA-dependent cell functions in vivo.
IL-7 and IL-21 are superior to IL-2 and IL-15 in promoting human T cell–mediated rejection of systemic lymphoma in immunodeficient mice (2010)

The gamma(c)-cytokines are critical regulators of immunity and possess both overlapping and distinctive functions. However, comparative studies of their pleiotropic effects on human T cell-mediated tumor rejection are lacking. In a xenogeneic adoptive transfer model, we have compared the therapeutic potency of CD19-specific human primary T cells that constitutively express interleukin-2 (IL-2), IL-7, IL-15, or IL-21. We demonstrate that each cytokine enhanced the eradication of systemic CD19(+) B-cell malignancies in nonobese diabetic/severe combined immunodeficient (NOD/SCID)/gamma(c)(null) mice with markedly different efficacies and through singularly distinct mechanisms. IL-7- and IL-21-transduced T cells were most efficacious in vivo, although their effector functions were not as enhanced as IL-2- and IL-15-transduced T cells. IL-7 best sustained in vitro T-cell accumulation in response to repeated antigenic stimulation, but did not promote long-term T-cell persistence in vivo. Both IL-15 and IL-21 overexpression supported long-term T-cell persistence in treated mice, however, the memory T cells found 100 days after adoptive transfer were phenotypically dissimilar, resembling central memory and effector memory T cells, respectively. These results support the use of gamma(c)-cytokines in cancer immunotherapy, and establish that there exists more than 1 human T-cell memory phenotype associated with long-term tumor immunity.
DolphinAttack: Inaudible Voice Commands (2017)

Speech recognition (SR) systems such as Siri or Google Now have become an increasingly popular human-computer interaction method, and have turned various systems into voice controllable systems (VCS). Prior work on attacking VCS shows that the hidden voice commands that are incomprehensible to people can control the systems. Hidden voice commands, though hidden, are nonetheless audible. In this work, we design a totally inaudible attack, DolphinAttack, that modulates voice commands on ultrasonic carriers (e.g., f > 20 kHz) to achieve inaudibility. By leveraging the nonlinearity of the microphone circuits, the modulated low-frequency audio commands can be successfully demodulated, recovered, and more importantly interpreted by the speech recognition systems. We validated DolphinAttack on popular speech recognition systems, including Siri, Google Now, Samsung S Voice, Huawei HiVoice, Cortana and Alexa. By injecting a sequence of inaudible voice commands, we show a few proof-of-concept attacks, which include activating Siri to initiate a FaceTime call on iPhone, activating Google Now to switch the phone to the airplane mode, and even manipulating the navigation system in an Audi automobile. We propose hardware and software defense solutions, and suggest to re-design voice controllable systems to be resilient to inaudible voice command attacks.
Identification of the Site in the cGMP-inhibited Phosphodiesterase Phosphorylated in Adipocytes in Response to Insulin and Isoproterenol (1996)

Stimulation of rat adipocytes with insulin and isoproterenol results in serine phosphorylation and activation of the adipocyte cGMP-inhibited phosphodiesterase (cGI PDE), events believed to be important in the antilipolytic action of insulin (Degerman, E., Smith, C.J., Tornqvist, H., Vasta, V., Manganiello, V.C., and Belfrage, P. (1990) Proc. Natl. Acad. Sci. U.S.A. 87,533-537). Here we demonstrate, by two-dimensional phosphopeptide mapping, that the major phosphopeptide generated by trypsin, or trypsin followed by Asp-N protease digestion of [32P]cGI PDE phosphorylated in adipocytes in response to isoproterenol and/or insulin, in each case co-migrates with the phosphopeptide released by the same treatment of M297FRRPS(P)LPCISREQ310. This peptide was synthesized based on the deduced sequence of the cloned rat adipocyte cGI PDE and phosphorylated by cAMP-dependent protein kinase (protein kinase A). Radiosequencing of authentic and synthetic tryptic 32P-peptides showed that a single site in cGI PDE (Ser302) was phosphorylated in adipocytes incubated with isoproterenol and/or insulin. The more than additive phosphorylation and activation of cGI PDE in response to the two hormones found in this report and previously (Smith, C.J., Vasta, V., Degerman, E., Belfrage, P., and Manganiello, V.C. (1991) J. Biol. Chem. 266, 13385-13390) is proposed to reflect cross-talk between their respective signal transduction pathways at the level of the cGI PDE serine protein kinase or upstream regulatory component(s).
Severe respiratory disease in dairy cows caused by infection with bovine respiratory syncytial virus (1996)

Outbreaks of severe respiratory disease caused by bovine respiratory syncytial virus (BRSV) were recorded in dairy herds throughout Sweden in 1988 and subsequently. The virus was demonstrated in nasopharyngeal swab material from animals in the acute stage of the disease by culture, the polymerase chain reaction (PCR) and by immunofluorescence. Serological data from the herds investigated showed that the cows had seroconverted to BRSV rather than to bovine coronavirus, bovine viral diarrhoea virus or parainfluenza-3 virus. It was predominantly dairy herds in isolated areas that contracted a severe primary BRSV infection, often after the purchase of new animals. A nationwide survey for BRSV antibodies in bulk milk samples showed the highest prevalence, of 84 to 89 per cent, in the southernmost regions of Sweden and the lowest prevalence, of 41 to 51 per cent, in the north of the country. The prevalence of BRSV was highest in areas with the highest populations of cattle.
Structural requirements for and consequences of an antiviral porphyrin binding to the V3 loop of the human immunodeficiency virus (HIV‐1) envelope glycoprotein gp120 (1995)

Several porphyrin derivatives were reported to have anti-HIV-1 activity. Among them, meso-teta(4-carboxyphenyl)porphine (MTCPP) and other carboxyphenyl derivatives were the most potent inhibitors (EC50 <0.7 mu M). MTCPP bound to the HIV-1 envelope glycoprotein gp120 and to full-length V3 loop peptides corresponding to several HIV-1 isolates but not to other peptides from gp120 + gp41. However, it remained possible that MTCPP bound to regions on gp120 which cannot be mimicked by peptides. Further characterization of the binding domain for MTCPP is important for understanding the antiviral activity of porphyrins and for the design of anti-HIV-1 drugs interfering with functions of the virus envelope. Results presented here show that: (i) deletion of the V3 loop from the gp120 sequence resulted in drastically diminished MTCPP binding, suggesting that the V3 loop is the dominant if not the only target site on gp120; (ii) this site was only partially mimicked by full-length V3 loop peptides; (iii) MTCPP binding to the gp120 V3 loop elicited allosteric effects resulting in decreased accessibility of the CD4 receptor binding site; (iv) the binding site for MTCPP lies within the central portion of the V3 loop (KSIHIGPGRAFY for the HIV-1 subtype B consensus sequence) and does not involve directly the GPG apex of the loop. These results may help in designing antiviral compounds with improved activity.
Major outer membrane proteins and proteolytic processing of RgpA and Kgp of Porphyromonas gingivalis W50 (2002)

Porphyromonas gingivalis is an anaerobic, asaccharolytic Gram-negative rod associated with chronic periodontitis. We have undertaken a proteomic study of the outer membrane of P. gingivalis strain W50 using two-dimensional gel electrophoresis and peptide mass fingerprinting. Proteins were identified by reference to the pre-release genomic sequence of P. gingivalis available from The Institute for Genomic Research. Out of 39 proteins identified, five were TonB-linked outer membrane receptors, ten others were putative integral outer membrane proteins and four were putative lipoproteins. Pyroglutamate was found to be the N-terminal residue of seven of the proteins, and was predicted to be the N-terminal residue of 13 additional proteins. The RgpA, Kgp and HagA polyproteins were identified as fully processed domains in outer membranes prepared in the presence of proteinase inhibitors. Several domains were found to be C-terminally truncated 16–57 residues upstream from the N-terminus of the following domain, at a residue penultimate to a lysine. This pattern of C-terminal processing was not detected in a W50 strain isogenic mutant lacking the lysine-specific proteinase Kgp. Construction of another W50 isogenic mutant lacking the arginine-specific proteinases indicated that RgpB and/or RgpA were also involved in domain processing. The C-terminal adhesin of RgpA, designated RgpA27, together with RgpB and two newly identified proteins designated P27 and P59 were found to migrate on two-dimensional gels as vertical streaks at a molecular mass 13–42kDa higher than that calculated from their gene sequences. The electrophoretic behaviour of these proteins, together with their immunoreactivity with a monoclonal antibody that recognizes lipopolysaccharide, is consistent with a modification that could anchor the proteins to the outer membrane.
The Mechanism of the Condensation of Formaldehyde with Tetrahydrofolic Acid (1966)

Abstract The bell-shaped pH rate profile for the reaction of tetrahydrofolic acid with formaldehyde to form 5,10-methylene tetrahydrofolic acid has been shown to result from a change in rate-determining step with changing acidity. In alkaline solution, the rate-determining step is the acid-catalyzed dehydration of hydroxymethyl tetrahydrofolic acid and its conjugate base. This step is subject to general acid catalysis with a Bronsted slope, α, of approximately 0.75. In acid solution, attack of tetrahydrofolic acid on formaldehyde is rate-determining. This step is subject to catalysis by general acids, including the solvated proton, with a Bronsted slope of 0.20. At pH values above 4, the reaction is inhibited by thiols, which combine with formaldehyde in a base-catalyzed reaction to form hemithioacetals. Depending on the reaction conditions, this inhibition can result from a lowering of the equilibrium concentration of formaldehyde or from a trapping by thiol anion of unhydrated formaldehyde, as it is formed from formaldehyde hydrate. The equilibrium constant for hemithioacetal formation from formaldehyde and mercaptoethanol is approximately 620 m-1. Secondary amines such as morpholine and imidazole catalyze the reaction of tetrahydrofolic acid with formaldehyde by nucleophilic catalysis by a pathway which must involve the intermediate formation of cationic imines, [see PDF for structure]
MONOCYTOTOXIC ANTIBODIES AFTER BONE MARROW TRANSPLANTATION IN APLASTIC ANEMIA (1982)

Pre- and post transplant sera from 51 cases of bone marrow transplants performed for severe aplastic anemia were tested on monocytes (M) and corresponding B cells (B) from a panel of unrelated donors. One-third of the sera were cytotoxic for B and M either from different or from the same individuals, while 45% reacted only to M and appeared to recognize non-HLA M-associated antigens. No significant reaction to endothelial cells was obtained from these sera. The subsequent clinical course was not associated with any reaction pattern of pre-transplant sera. There was a significant relationship between rejection and the development of M antibodies after grafting, but since these were also found in many other patients without rejection, their occurrence has no predictive value for an individual patient.
Incretins and their analogues as new antidiabetic drugs (2003)

Glucagon-like peptide 1 (GLP-1) is a gut (incretin) hormone with multiple actions that could potentially contribute to an antidiabetic effect. This includes: (a) glucose-dependent insulinotropic actions; (b) glucagonostatic actions; (c) a reduction in appetite/promotion of satiety leading to reduced food intake and weight reduction; (d) the deceleration of gastric emptying; and (e) the stimulation of islet growth, differentiation and regeneration. Thus, multiple aspects of the type 2 diabetic phenotype can potentially be improved or even corrected by GLP-1. The native gut hormone, however, after intravenous injection or absorption from subcutaneous depots, is proteolytically degraded and eliminated from the circulation too quickly to be useful for the treatment of diabetes. GLP-1 derivatives (receptor agonists) with prolonged pharmacokinetics that promise a potential for clinical use in the near future are being developed.
Potent and Selective Inhibitors of 8-Oxoguanine DNA Glycosylase (2018)

The activity of DNA repair enzyme 8-oxoguanine DNA glycosylase (OGG1), which excises oxidized base 8-oxoguanine (8-OG) from DNA, is closely linked to mutagenesis, genotoxicity, cancer, and inflammation. To test the roles of OGG1-mediated repair in these pathways, we have undertaken the development of noncovalent small-molecule inhibitors of the enzyme. Screening of a PubChem-annotated library using a recently developed fluorogenic 8-OG excision assay resulted in multiple validated hit structures, including selected lead hit tetrahydroquinoline 1 (IC<sub>50</sub> = 1.7 μM). Optimization of the tetrahydroquinoline scaffold over five regions of the structure ultimately yielded amidobiphenyl compound 41 (SU0268; IC<sub>50</sub> = 0.059 μM). SU0268 was confirmed by surface plasmon resonance studies to bind the enzyme both in the absence and in the presence of DNA. The compound SU0268 was shown to be selective for inhibiting OGG1 over multiple repair enzymes, including other base excision repair enzymes, and displayed no toxicity in two human cell lines at 10 μM. Finally, experiments confirm the ability of SU0268 to inhibit OGG1 in HeLa cells, resulting in an increase in accumulation of 8-OG in DNA. The results suggest the compound SU0268 as a potentially useful tool in studies of the role of OGG1 in multiple disease-related pathways.
Influence of serum factors on the prevalence of “normal” and “foreign” differentiation pathways in cultures of chick embryo neuroretinal cells (1981)

Embryonic (9-day) chick neuroretinal cells transdifferentiate extensively into lens and pigment cells during prolonged culture (4-5 weeks) in media containing foetal calf serum. Medium conditions which promote the attachment and differentiation of neural cells in other culture systems (e.g. horse serum, high glucose levels) both delay the onset and greatly reduce the extent of transdifferentiation in retinal cultures. In the presence of high glucose, horse serum (but not foetal calf serum) also favours cholinergic neuronal differentiation during the early phases of culture, as shown by the levels of choline acetyltransferase activity and accumulation of labelled choline. Substrate conditions have some effect on cholinergic differentiation (promoted by polylysine-coated dishes) but do not affect later transdifferentiation. These effects may be due in part to selective survival or growth of particular retinal cell types under the various medium conditions tested. Cultures stripped of neuronal cells contain negligible choline acetyltransferase activity, but still transdifferentiate into both lens and pigment cells, although more slowly than control cultures. Cell size distributions reveal a significant depletion of the larger cells in high glucose media with foetal calf serum, but not in those with horse serum.
QRS Duration and Shortening to Predict Clinical Response to Cardiac Resynchronization Therapy in Patients with End‐Stage Heart Failure (2004)

Despite current selection criteria (NYHA Class III-IV, LVEF < 35%, QRS > 120 ms with LBBB), 30% of patients do not benefit from cardiac resynchronization therapy (CRT). The use of QRS duration as selection criteria for CRT has not been evaluated systematically yet. Accordingly, the value of QRS duration at baseline (and reduction in QRS duration after CRT) to predict responders was studied. Patients were evaluated at baseline and after 6 months of CRT for NYHA Class, quality of life score, and 6-minute walk test. QRS duration was evaluated before, directly after implantation, and after 6 months of CRT. Sixty-one patients were included; 45 (74%) patients were classified as responders (improvement of NYHA Class, 6-minute walking distance and quality of life score) and 16 (26%) as nonresponders. QRS duration at baseline was similar between the two groups: 179 +/- 30 ms versus 171 +/- 32 ms, NS. Directly after implantation, QRS duration was reduced from 179 +/- 30 ms to 150 +/- 26 ms (P < 0.01) in responders; nonresponders did not exhibit this reduction (171 +/- 32 ms vs 160 +/- 26 ms, NS). After 6 months of CRT, QRS shortening was only observed in responders (from 179 +/- 30 ms to 159 +/- 25 ms, P < 0.01). ROC curve analysis showed that a reduction in QRS duration > 10 ms had a high sensitivity (73%) with low specificity (44%); conversely, a > 50 ms reduction in QRS duration was highly specific (88%) but not sensitive (18%) to predict response to CRT. No optimal cutoff value could be defined. QRS duration at baseline is not predictive for response to CRT; responders exhibit a significant reduction in QRS duration after CRT, but individual response varies highly, not allowing adequate selection of responders.
A Discrete-Time Mixing Receiver Architecture with Wideband Harmonic Rejection (2008)

The proposed SDR downconverter is aimed for the DVB-H standard (470 to 862MHz) and for emerging cognitive radio applications in the 200-to-900MHz band, which suffer from 3rd and 5th harmonic mixing. An inverter-based RF-amplifier (RFA) drives a passive switched-capacitor (SC) core consisting of three stages. The first stage is effectively an oversampler, second stage consists of I/Q DT mixers for downconversion and the third stage is a low-pass IIR filter. The chip fabricated in a 65nm CMOS process occupies an active area of 0.36mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The noise and linearity performances are competitive with those of continuous-time mixers at reasonable power consumption, which shows the feasibility of the proposed architecture for a practical receiver front-end.
FPscope: a field-portable high-resolution microscope using a cellphone lens (2014)

The large consumer market has made cellphone lens modules available at low-cost and in high-quality. In a conventional cellphone camera, the lens module is used to demagnify the scene onto the image plane of the camera, where image sensor is located. In this work, we report a 3D-printed high-resolution Fourier ptychographic microscope, termed FPscope, which uses a cellphone lens in a reverse manner. In our platform, we replace the image sensor with sample specimens, and use the cellphone lens to project the magnified image to the detector. To supersede the diffraction limit of the lens module, we use an LED array to illuminate the sample from different incident angles and synthesize the acquired images using the Fourier ptychographic algorithm. As a demonstration, we use the reported platform to acquire high-resolution images of resolution target and biological specimens, with a maximum synthetic numerical aperture (NA) of 0.5. We also show that, the depth-of-focus of the reported platform is about 0.1 mm, orders of magnitude longer than that of a conventional microscope objective with a similar NA. The reported platform may enable healthcare accesses in low-resource settings. It can also be used to demonstrate the concept of computational optics for educational purposes.
Self-Aligned, Gated Arrays of Individual Nanotube and Nanowire Emitters (2004)

We demonstrate the production of integrated-gate nanocathodes which have a single carbon nanotube or silicon nanowire/whisker per gate aperture. The fabrication is based on a technologically scalable, self-alignment process in which a single lithographic step is used to define the gate, insulator, and emitter. The nanotube-based gated nanocathode array has a low turn-on voltage of 25 V and a peak current of 5 μA at 46 V, with a gate current of 10 nA (i.e., 99% transparency). These low operating voltage cathodes are potentially useful as electron sources for field emission displays or miniaturizing electron-based instrumentation.