gebhart/patrepeval huggingface dataset:
Structure−Activity Relationships of 2‘-Fluoro-2‘,3‘-unsaturated d-Nucleosides as Anti-HIV-1 Agents (2002)

We studied the structure-activity relationships of a series of 2'-fluoro-2',3'-unsaturated D-nucleosides against HIV-1 in human peripheral blood mononuclear (PBM) cells. The target compounds 10-21 and 28-33 were prepared by N-glycosylation of the acetate 4, which was readily prepared from 2,3-O-isopropylidene-D-glyceraldehyde in five steps. Among the newly synthesized nucleosides, 2-amino-6-chloropurine (11), adenine (14), inosine (16), guanine (18), 2,6-diaminopurine (20), and 5-fluorocytosine (30) derivatives were found to exhibit interesting anti-HIV activities with EC(50) values of 4.3, 0.44, 1.0, 2.6, 3.0, and 0.82 microM, respectively. The implications for drug resistance of the titled nucleosides with respect to lamivudine-resistant variants (M184V) were also examined, and no significant cross-resistance with the variants was observed with the D-series.
Polymerization of diallyldimethylammonium chloride in inverse emulsion, II. Molecular weight and electrical conductivity of the polymer (1989)

Abstract The dependence of molecular weight of poly(diallyldimethylammonium chloride) on conversion was studied and a model is proposed for the calculation of the conversion dependence of molecular weight under consideration of gel effect and chain transfer reactions to monomer and polymer. The influence of tetramethylammonium chloride concentration on the ionic conductivity of the solid polymer was studied. A maximum specific ionic conductivity of 2.2 · 10 −4 S cm −1 was measured.
TLR4 activation mediates kidney ischemia/reperfusion injury (2007)

Ischemia/reperfusion injury (IRI) may activate innate immunity through the engagement of TLRs by endogenous ligands. TLR4 expressed within the kidney is a potential mediator of innate activation and inflammation. Using a mouse model of kidney IRI, we demonstrated a significant increase in TLR4 expression by tubular epithelial cells (TECs) and infiltrating leukocytes within the kidney following ischemia. TLR4 signaling through the MyD88-dependent pathway was required for the full development of kidney IRI, as both TLR4(-/-) and MyD88(-/-) mice were protected against kidney dysfunction, tubular damage, neutrophil and macrophage accumulation, and expression of proinflammatory cytokines and chemokines. In vitro, WT kidney TECs produced proinflammatory cytokines and chemokines and underwent apoptosis after ischemia. These effects were attenuated in TLR4(-/-) and MyD88(-/-) TECs. In addition, we demonstrated upregulation of the endogenous ligands high-mobility group box 1 (HMGB1), hyaluronan, and biglycan, providing circumstantial evidence that one or more of these ligands may be the source of TLR4 activation. To determine the relative contribution of TLR4 expression by parenchymal cells or leukocytes to kidney damage during IRI, we generated chimeric mice. TLR4(-/-) mice engrafted with WT hematopoietic cells had significantly lower serum creatinine and less tubular damage than WT mice reconstituted with TLR4(-/-) BM, suggesting that TLR4 signaling in intrinsic kidney cells plays the dominant role in mediating kidney damage.
Continuous levodopa for advanced Parkinson's disease. (2007)

Parkinson's disease is characterized by the progression of the disease from the early stages where it still has little functional consequence for afflicted patients, to an advanced stage disease with large consequences in terms of function, quality of life and individual and societal costs. Motor fluctuations and symptoms of levodopa overdosage may occur in parallel with increasing Parkinsonian symptoms. This leads to a narrower therapeutic window which causes problems with traditional oral medication. Various ways of optimizing oral treatment should be tried but often have limited effects. In addition to the previous alternatives of neurosurgery (especially deep brain stimulation of the subthalamic nuclei) and continuous apomorphine treatment there is now also the alternative of continuous enteral levodopa administration via a trans-abdominal tube. The effect of the treatment may be tested individually via naso-duodenal administration before a decision is made whether to continue with permanent treatment. In the present article, the challenges to treatment of Parkinson's disease in these phases are described as well as the various treatment alternatives available. Focus is mainly on the clinical studies of continuous levodopa infusion therapies, especially enteral administration of levodopa/carbidopa gel. The place of enteral levodopa/carbidopa gel treatment among the other treatment methods is also discussed.
Implementing a multiple-valued decision diagram package (2002)

Decision diagrams are the state-of-the-art representation for logic functions, both binary and multiple-valued. Here we consider issues regarding the efficient implementation of a package for the creation and manipulation of multiple-valued decision diagrams (MDDs). In particular we identify issues that differ from binary decision diagram packages. We describe a matrix method for level interchange in MDDs that is essential for implementing variable reordering strategies. In addition, it is the basis for a novel approach to performing logic operations on MDDs, which we also present. Experimental results demonstrate the efficiency of this approach.
Her-2/neu gene amplification in ductal carcinoma in situ of the breast. (2002)

This study evaluated the relative frequencies of HER-2/neu gene amplification in ductal carcinoma in situ (DCIS)-associated invasive breast cancer and DCIS alone. We examined archival tissue samples of 100 DCIS lesions with an invasive component (cases) and 100 without an invasive component (controls), with cases and controls matched by pathologic nuclear grade. HER-2/neu gene amplification was determined by fluorescence in situ hybridization. We compared HER-2/neu gene amplification in DCIS lesions only, irrespective of the presence or absence of an invasive component. HER-2/neu gene amplification occurred significantly less frequently in the cases (26%) than in the controls (40%), with an odds ratio of 0.35 (95% confidence interval, 0.17-0.72; P < 0.004) after adjustment for pathologic and quantitative-image-analyzed morphometric nuclear grade. The HER-2/neu gene also was amplified more frequently in higher- than in lower-grade DCIS alone (56% versus 19%, respectively; P < 0.0001) or in higher- than in lower-grade DCIS with invasive cancer (44% versus 2%, respectively; P < 0.00001). Future studies should examine the potential roles of HER-2/neu and other biomarkers (e.g., p21 and Rb) as markers of the risk of DCIS patients for invasive breast cancer and as molecular targets of chemoprevention in breast intraepithelial neoplasia.
MR receptor imaging: ultrasmall iron oxide particles targeted to asialoglycoprotein receptors. (1990)

Previously we have reported that ultrasmall superparamagnetic iron oxide (USPIO) particles migrate across capillary endothelium, a prerequisite for the design of particulate pharmaceuticals for MR receptor imaging. In the current study, USPIO particles are directed specifically to asialoglycoprotein (ASG) receptors by coupling galactose terminals in the form of arabinogalactan (AG) to these particles. Biodistribution data showed that ASG-directed, AG-coated USPIO (AG-USPIO) particles selectively accumulate in the liver but not in other organs. Electron microscopy of liver showed electron-dense iron oxide particles bound to hepatocyte cell-surface membranes and in large numbers within intracellular lysosomes. The specificity of AG-USPIO for asialoglycoprotein receptors was confirmed by incubation experiments with and without ASG-blocking agents such as D(+)galactose and asialofetuin. In vivo MR imaging in rats showed a significant decrease in liver signal intensity at low doses (2 mumol Fe/kg); no significant changes were observed in the spleen. This decrease in signal intensity is larger than that observed with conventional iron oxides at equal doses. These initial data suggest that, for the first time, superparamagnetic agents can be directed to specific sites for MR imaging by strategies such as receptor targeting.
Why MAC Address Randomization is not Enough (2016)

We present several novel techniques to track (unassociated) mobile devices by abusing features of the Wi-Fi standard. This shows that using random MAC addresses, on its own, does not guarantee privacy. First, we show that information elements in probe requests can be used to fingerprint devices. We then combine these fingerprints with incremental sequence numbers, to create a tracking algorithm that does not rely on unique identifiers such as MAC addresses. Based on real-world datasets, we demonstrate that our algorithm can correctly track as much as 50% of devices for at least 20 minutes. We also show that commodity Wi-Fi devices use predictable scrambler seeds. These can be used to improve the performance of our tracking algorithm. Finally, we present two attacks that reveal the real MAC address of a device, even if MAC address randomization is used. In the first one, we create fake hotspots to induce clients to connect using their real MAC address. The second technique relies on the new 802.11u standard, commonly referred to as Hotspot 2.0, where we show that Linux and Windows send Access Network Query Protocol (ANQP) requests using their real MAC address.
Universal Language Model Fine-tuning for Text Classification (2018)

Inductive transfer learning has greatly impacted computer vision, but existing approaches in NLP still require task-specific modifications and training from scratch. We propose Universal Language Model Fine-tuning (ULMFiT), an effective transfer learning method that can be applied to any task in NLP, and introduce techniques that are key for fine-tuning a language model. Our method significantly outperforms the state-of-the-art on six text classification tasks, reducing the error by 18-24% on the majority of datasets. Furthermore, with only 100 labeled examples, it matches the performance of training from scratch on 100 more data. We opensource our pretrained models and code 1 .
Impact of Rapid Detection of Viral and Atypical Bacterial Pathogens by Real-Time Polymerase Chain Reaction for Patients with Lower Respiratory Tract Infection (2005)

Implementation of real-time PCR for the etiological diagnosis of LRTI increased the diagnostic yield considerably, but it did not reduce antibiotic use or costs.
Protection of the rat retina from ischemic injury by brain-derived neurotrophic factor, ciliary neurotrophic factor, and basic fibroblast growth factor. (1994)

BDNF, CNTF, and bFGF transiently protect the retina from pressure-induced ischemic injury when given 2 days before ischemia, and a second injection of BDNF given postischemically can prolong the protective effect. Moreover, protection afforded by BDNF can be seen even when applied only 1 or 3 days after the ischemic insult, although the protective effect is greater at 1 day than at 3 days postischemia.
Evidence for autocrine/paracrine growth stimulation by transforming growth factor‐α during the process of skin tumor promotion (1991)

A single topical application of 12-O-tetradecanoylphorbol-13-acetate (TPA) to mouse skin decreased 125I-labeled epidermal growth factor (EGF) binding in epidermal membrane preparations within 1 h while 1,8-dihydroxy-3-methyl-9-anthrone (chrysarobin) gradually reduced binding with maximum inhibition at 15 h. Subsequently, 125I-EGF binding increased to approximately 200% of control in epidermal membrane preparations from both TPA- and chrysarobin-treated mice. A single application of TPA but not chrysarobin resulted in a rapid translocation of protein kinase C (PKC) to the membrane; however, treatment with both promoters ultimately led to a time-dependent loss of PKC activity in both membrane and cytosol fractions. The initial inhibition of 125I-EGF binding was sustained for at least 24 h after single and multiple treatments with both promoting agents. Acid washing restored EGF binding to control levels in membrane preparations obtained 24 h after a single application, whereas acid washing of membrane preparations obtained 24 h after a second application of TPA or chrysarobin increased binding (2.5-fold and 1.5-fold that of the control, respectively). The presence of increased amounts of ligands for the EGF receptor in tumor promoter-treated epidermis was initially confirmed in 125I-EGF binding competition experiments using NRK-49F cells. A single topical application of TPA or chrysarobin induced elevated levels of transforming growth factor-alpha (TGF-alpha) mRNA at 6 h or 15-24 h, respectively. Elevated levels of a TGF-alpha precursor (21 kDa) were subsequently observed in cytosol and membrane preparations after single and multiple applications of TPA or chrysarobin. These results suggest that repeated topical application of tumor promoters may lead to sustained loss of a negative-feedback mechanism involving phosphorylation at Thr-654 of the EGF receptor by PKC. The concomitant elevation of ligands, such as TGF-alpha, may provide a mechanism for sustained cell proliferation essential for skin tumor promotion.
Inhibition of recombinant human immunodeficiency virus type 1 replication by a site-specific recombinase (1997)

Current molecular genetic strategies to inhibit productive human immunodeficiency virus type 1 (HIV-1) replication have involved the generation of gene products which provide intracellular inhibition of essential virally encoded proteins or RNA structures. A molecular strategy to excise proviral DNA from HIV-1-infected cells and render these cells virus free would provide an attractive direct antiviral strategy, providing a mechanism to remove viral genes from infected cells. The potential of such a molecular genetic intervention was examined by using the Cre-loxP recombination system. A recombinant HIV-1 clone, designated HIV(lox), that contains loxP within a nonessential U3 region of the long terminal repeats was synthesized. The loxP motif was maintained during replication of HIV(lox) in CEM cells, as demonstrated by reverse transcriptase PCR analyses of genomic RNA isolated from virions. Two different types of HIV-1-permissive cells, CEM cells and 293 cells expressing the CD4 glycoprotein, were transformed with a Cre expression vector which was shown to encode Cre DNA binding and recombinase activities. HIV(lox) infection of CEM or CD4+ 293 cells expressing Cre resulted in a substantial reduction in virus replication compared to control cells, and evidence for the presence of the expected excision product was found. Site-specific excision of HIV-1 can therefore be achieved by using this model system with acute infection. These studies represent one step toward the development of a novel antiviral strategy for the treatment of AIDS.
Analysis of Chlamydia pneumoniae Growth in Cells by Reverse Transcription-PCR Targeted to Bacterial Gene Transcripts (2002)

Chlamydia pneumoniae is an obligate intracellular bacterium and has a unique development cycle consisting of an elementary body (EB) and reticular body (RB). EBs survive in extracellular environments as well as infect susceptible host cells. However, EBs display no measurable metabolic activity. In contrast, RBs are metabolically active and can replicate in a host cell but are noninfectious. Therefore, analysis of C. pneumoniae growth in infected cells by conventional bacterial culture may not permit sufficient information about growth of the bacteria in cells. In this study, therefore, we examined the usefulness of the reverse transcription (RT)-PCR method for analysis of bacterial transcripts to evaluate C. pneumoniae growth in HEp-2 cells because the levels of bacterial gene transcripts are known to show the metabolic activity of bacteria. The transcripts for the C. pneumoniae hsp60 gene and 16S rRNA in the cells were easily detected just after infection, followed by a marked increase. In contrast, pyk and omcB transcripts slowly increased after a latent period. The hydrocortisone treatment of C. pneumoniae-infected cells induced an increase of all bacterial transcripts tested compared with the control group. The treatment of the infected cells with the antibiotic minocycline showed a selective inhibition of bacterial gene transcripts, even though the complete inhibition of EB production determined by the bacterial culture assay was evident. These results indicate that the determination of bacterial gene transcripts by RT-PCR might be a powerful method to analyze in detail growth of C. pneumoniae in host cells, particularly altered bacterial growth caused by agents such as antimicrobials.
Deep Store: An Archival Storage System Architecture (2005)

We present the Deep Store archival storage architecture, a large-scale storage system that stores immutable data efficiently and reliably for long periods of time. Archived data is stored across a cluster of nodes and recorded to hard disk. The design differentiates itself from traditional file systems by eliminating redundancy within and across files, distributing content for scalability, associating rich metadata with content, and using variable levels of replication based on the importance or degree of dependency of each piece of stored data. We evaluate the foundations of our design, including PRESIDIO, a virtual content-addressable storage framework with multiple methods for interfile and intra-file compression that effectively addresses the data-dependent variability of data compression. We measure content and metadata storage efficiency, demonstrate the need for a variable-degree replication model, and provide preliminary results for storage performance.
Wound Healing Angiogenesis (1990)

Basic fibroblast growth factor (bFGF) was tested for its ability to stimulate angiogenesis in vivo using the rabbit corneal assay. Basic FGF (50–1,000 ng) was incorporated into 10% Hydron, and 50–500 ng of bFGF were incorporated into 10% Elvax. Human serum albumin (HSA)(10 ng) and 50 ng of transforming growth factor-beta (TGF-β) served as negative and positive controls. Pellets of the polymers containing test compunds were implanted in the rabbit cornea, examined daily, and after 7 days corneal angiogenesis was scored on a graded scale [(-) for no response and +4 for a maximum response]. Histologic analysis of the corneas was performed on days 2 and 7. Basic FGF (50–500 ng) in Hydron failed to stimulate significant angiogenesis, though it did induce angiogenesis accompanied by inflammation at the 1,000-ng dose. Basic FGF in Elvax elicited inflammation-associated +3 to +4 responses at all doses tested. New blood vessels did not form in response to HSA in Hydron or Elvax, while TGF-β induced +4 angiogenesis accompanied by vigorous inflammation. In vivo release kinetics for bFGF in Hydron and Elvax were compared, and the release of bioactive bFGF from Hydron nd Elvax was demonstrated in vitro. These results suggest that the bFGF and Elvax combination incites an inflammatory response which stimulates indirect angiogenesis, while the same concentrations of bFGF delivered in Hydron produced no inflammation or angiogenesis. Although bFGF alone is a potent mitogen for endothelial cells, it does not appear to directly stimulate in vivo angiogenesis.
Evaluation of a long-contextual-Span hidden trajectory model and phonetic recognizer using a* lattice search (2005)

A long-contextual-span Hidden Trajectory Model (HTM) developed recently captures underlying dynamic structure of speech coarticulation and reduction using a highly compact set of context-independent parameters. However, the longspan nature of the HTM makes it difficult to develop efficient search algorithms for its full evaluation. In this paper, we describe our initial effort in meeting this challenge. The basic search algorithm is time-asynchronous A*. Given the structural complexity of the long-span HTM, special considerations are needed to take into account the fact that the HTM score for each frame depends on the model parameters associated with a variable number of adjacent phones. Specifically, we present details on how the nodes and links in the lattices are expanded via look-ahead, how the A* heuristics are estimated, and what pruning strategies are applied to speed up the search. The experiments on TIMIT phonetic recognition show the capability of our newly developed lattice search algorithm in evaluating billions of hypotheses based on long-span HTM scores. The results significantly extend our earlier work from N-best rescoring to A* search over lattices.
Colorado River. Jan-Mar (1922)

Correspondence includes discussions of silt impoundment, equitable apportionment of water, prospective agreement with Mexico, proposed water distribution. Contains correspondence to/from Herbert Hoover
Sensing and three-dimensional OCT imaging of the cochlea and temporal bone: image-guided cochlear implantation (2013)

We describe a novel dual-functional optical coherence tomography (OCT) system with both a 3-D OCT real time scanner and a fiber probe using a sapphire ball lens for imaging and sensing the critical structures of the temporal bone. To prevent injury to facial nerve, 3-D visualization links anatomic landmarks to 3-D map of critical intracochlear structures. We used a graphics processing unit to boost the computing and 3-D rendering performance of swept source OCT. Both the intracochlear structures and facial nerve trunk of cadaveric human temporal bones are clearly identified with 3-D OCT volumetric rendering.
Vascular Remodeling in Transplant Vasculopathy (2007)

As therapeutic strategies to prevent acute rejection progressively improve, transplant vasculopathy (TV) constitutes the single most important limitation for long-term functioning of solid organ allografts. In TV, allograft arteries characteristically develop severe, diffuse intimal hyperplastic lesions that eventually compromise luminal flow and cause ischemic graft failure. Traditional immunosuppressive strategies that check acute allograft rejection do not prevent TV; indeed 50% of transplant recipients will have significant disease within five years of organ transplantation, and 90% will have significant TV a decade after their surgery. TV can involve the entire length of the transplanted arterial bed, including penetrating intraorgan arterioles. Indeed, the luminal narrowing of such penetrating vessels may be the most functionally significant because arterioles represent the major contributors to tissue vascular resistance. Because of the diffuseness of TV involvement in the allograft vascular bed, the only currently definitive therapy requires re-transplantation. Nevertheless, as we better understand the pathogenesis and critical mediators of these lesions, pharmacological advances can be anticipated. Other articles in this thematic review series focus on the specifics of the inciting injury, the cytokines and chemokines that drive TV development, and the nature of the recruited cells in TV lesions, as well as the pathogenic similarities between TV and other vascular lesions such as atherosclerosis. This review focuses on the mechanisms of vascular wall remodeling in TV, including the intimal accumulation of smooth muscle-like cells and associated extracellular matrix, medial smooth muscle cell degeneration, and adventitial fibrosis. A brief overview highlights the aneurysmal changes that can accrue when vessel wall inflammation has a cytokine profile distinct from the typical proinflammatory interferon-gamma-dominated milieu.