gebhart/patrepeval huggingface dataset:
Virulence factors of influenza A viruses: WSN virus neuraminidase required for plaque production in MDBK cells (1977)

The genetic basis for the distinctive capacity of influenza A/WSN/33 (H0N1) virus (WSN virus) to produce plaques on bovine kidney (MDBK) cells was found to be related to virus neuraminidase. Recombinant viruses that derived only the neuraminidase of WSN virus were capable of producing plaques, whereas recombinant viruses identical to WSN except for neuraminidase did not produce plaques. With viruses that do not contain WSN neuraminidase, infectivity of virus yields from MDBK cells was increased approximately 1,000-fold after in vitro treatment with trypsin. In contrast, no significant increase in infectivity was observed after trypsin treatment of viruses containing WSN neuraminidase. In addition, polyacrylamide gel analysis of proteins of WSN virus obtained after infection of MDBK cells demonstrated that hemagglutinin was present in the cleaved form (HA1 + HA2), whereas only uncleaved hemagglutinin was obtained with a recombinant virus that derived all of its genes from WSN virus except its neuraminidase. These data are in accord with the hypothesis that neuraminidase may facilitate production of infectious particles by removing sialic acid residues and exposing appropriate cleavage sites on hemagglutinin.
On a Relationship Between the Arrhenius Parameters from Thermal Damage Studies (2003)

Technical Briefs On a Relationship Between the Arrhenius Parameters from Thermal Damage Studies Neil T. Wright Neil T. Wright Department of Mechanical Engineering, University of Maryland, Baltimore, MD 21250 Search for other works by this author on: This Site PubMed Google Scholar Author and Article Information Neil T. Wright Department of Mechanical Engineering, University of Maryland, Baltimore, MD 21250 Contributed by the Bioengineering Division for publication in the JOURNAL OF BIOMECHANICAL ENGINEERING. Manuscript received Oct. 2001; revised manuscript received Nov. 2002. Associate Editor: M. Toner. J Biomech Eng. Apr 2003, 125(2): 300-304 (5 pages) https://doi.org/10.1115/1.1553974 Published Online: April 9, 2003 Article history Received: October 1, 2001 Revised: November 1, 2002 Online: April 9, 2003
Two-dimensional permittivity and conductivity imaging by full waveform inversion of multioffset GPR data: a frequency-domain quasi-Newton approach (2014)

Full waveform inversion of ground-penetrating radar data is an emerging technique for the quantitative, high-resolution imaging of the near subsurface. Here, we present a 2-D frequency-domain full waveform inversion for the simultaneous reconstruction of the dielectric permittivity and of the electrical conductivity. The inverse problem is solved with a quasi-Newton optimization scheme, where the influence of the Hessian is approximated by the L-BFGS-B algorithm. This formulation can be considered to be fully multiparameter since it enables to update permittivity and conductivity values within the same descent step, provided we define scales of measurement through a reference permittivity, a reference conductivity, and an additional scaling factor. Numerical experiments on a benchmark from the literature demonstrate that the inversion is very sensitive to the parameter scaling, despite the consideration of the approximated Hessian that should correct for parameter dimensionalities. A proper scaling should respect the natural sensitivity of the misfit function and give priority to the parameter that has the most impact on the data (the permittivity, in our case). We also investigate the behaviour of the inversion with respect to frequency sampling, considering the selected frequencies either simultaneously or sequentially. As the relative imprint of permittivity and conductivity in the data varies with frequency, the simultaneous reconstruction of both parameters takes a significant benefit from broad frequency bandwidth data, so that simultaneous or cumulative strategies should be favoured. We illustrate our scaling approach with a realistic synthetic example for the imaging of a complex subsurface from on-ground multioffset data. Considering data acquired only from the ground surface increases the ill-posedness of the inverse problem and leads to a strong indetermination of the less-constrained conductivity parameters. A Tikhonov regularization can prevent the creation of high-wavenumber artifacts in the conductivity model that compensate for erroneous low-wavenumber structures, thus enabling to select model solutions. We propose a workflow for multiparameter imaging involving both parameter scaling and regularization. Optimal combinations of scaling factors and regularization weights can be identified by seeking regularization levels that exhibit a clear minimum of final data misfit with respect to parameter scaling. We confirm this workflow by inverting noise-contaminated synthetic data. In a surface-to-surface acquisition configuration, we have been able to reconstruct an accurate permittivity structure and a smooth version of the conductivity distribution, based entirely on the analysis of the data misfit with respect to parameter scaling, for different regularization levels.
Treatment of Asymptomatic Clostridium difficile Carriers (Fecal Excretors) with Vancomycin or Metronidazole (1992)

▪Objective: To compare the efficacy of vancomycin and metronidazole for eradication of asymptomatic Clostridium difficile fecal excretion as a means of controlling nosocomial outbreaks of C. difficile diarrhea. ▪Design: Randomized, placebo-controlled, nonblinded trial. ▪Setting: Six hundred-bed regional referral Veterans Affairs Medical Center. ▪Patients: Thirty patients excreting C. difficilewithout diarrhea or abdominal symptoms. ▪Interventions: All patients were randomized to receive 10 days of oral vancomycin, 125 mg four times daily; metronidazole, 500 mg twice daily; or placebo, three times daily. ▪Measurements: Stool cultures were obtained during treatment and for 2 months after treatment. All C. difficile isolates were typed by restriction endonuclease analysis (REA). ▪Results: Clostridium difficile organisms were not detected during and immediately after treatment in 9 of 10 patients treated with vancomycin compared with 3 of 10 patients treated with metronidazole (P = 0.02) and 2 of 10 patients in the placebo group (P = 0.005). The fecal vancomycin concentration was 1406 ± 1164 µg/g feces, but metronidazole was not detectable in 9 of 10 patients. Eight of the nine evaluable patients who had negative stool cultures after treatment with vancomycin began to excrete C. difficile again 20 ± 8 days after completing treatment. Three of these patients received additional antibiotics before C. difficile excretion recurred, and five acquired new C. difficile REA strains. Four of six patients who received only vancomycin before C. difficile excretion recurred were culture-positiveat the end of the study compared with one of nine patients who received only placebo (P = 0.047). ▪Conclusions: Asymptomatic fecal excretion of C. difficile is transient in most patients, and treatment with metronidazole is not effective. Although treatment with vancomycin is temporarily effective, it is associated with a significantly higher rate of C. difficile carriage 2 months after treatment and is not recommended.
MR angiography of the pelvis with variable velocity encoding and a phased-array coil. (1994)

Use of a phased-array coil and variable velocity encoding improves depiction of segmental vascular anatomic structures of the pelvis.
Photoisomerism of Azobenzenes (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Fucosylation and gastrointestinal cancer (2010)

Fucose (6-deoxy-L-galactose) is a monosaccharide that is found on glycoproteins and glycolipids in verte-brates, invertebrates, plants, and bacteria. Fucosylation, which comprises the transfer of a fucose residue to oligosaccharides and proteins, is regulated by many kinds of molecules, including fucosyltransferases, GDP-fucose synthetic enzymes, and GDP-fucose transporter(s). Dramatic changes in the expression of fucosylated oligosaccharides have been observed in cancer and inflammation. Thus, monoclonal antibodies and lectins recognizing cancer-associated fucosylated oligosaccharides have been clinically used as tumor markers for the last few decades. Recent advanced glycomic approaches allow us to identify novel fucosylation-related tumor markers. Moreover, a growing body of evidence supports the functional significance of fucosylation at various pathophysiological steps of carcinogenesis and tumor progression. This review highlights the biological and medical significance of fucosylation in gastrointestinal cancer.
P‐glycoprotein‐overexpressing multidrug‐resistant cells are resistant to infection by enveloped viruses that enter via the plasma membrane 1 (2000)

The multidrug resistance gene product P-glycoprotein confers drug resistance to tumor cells by acting as a transporter that blocks the entry into the cell of a great variety of drugs and hydrophobic peptides. In this study we find that in drug-resistant cells, the insertion of the influenza virus fusion protein (hemagglutinin-2) into the plasma membrane is blocked and that the fusion of the viral envelope with the plasma membrane of these cells is impaired. Multidrug-resistant cells display significant resistance to infection by envelope viruses that invade cells by fusion with the plasma membrane, but not to infection by pH-dependent viruses that penetrate cells by fusion with endocytic vesicles. These observations suggest that multidrug resistance phenomena may protect cells from infection by a large group of disease-causing viruses that includes human immunodeficiency virus, herpes simplex virus, and some cancer-inducing retroviruses.
A Vector Space Modeling Approach to Spoken Language Identification (2006)

We propose a novel approach to automatic spoken language identification (LID) based on vector space modeling (VSM). It is assumed that the overall sound characteristics of all spoken languages can be covered by a universal collection of acoustic units, which can be characterized by the acoustic segment models (ASMs). A spoken utterance is then decoded into a sequence of ASM units. The ASM framework furthers the idea of language-independent phone models for LID by introducing an unsupervised learning procedure to circumvent the need for phonetic transcription. Analogous to representing a text document as a term vector, we convert a spoken utterance into a feature vector with its attributes representing the co-occurrence statistics of the acoustic units. As such, we can build a vector space classifier for LID. The proposed VSM approach leads to a discriminative classifier backend, which is demonstrated to give superior performance over likelihood-based n-gram language modeling (LM) backend for long utterances. We evaluated the proposed VSM framework on 1996 and 2003 NIST Language Recognition Evaluation (LRE) databases, achieving an equal error rate (EER) of 2.75% and 4.02% in the 1996 and 2003 LRE 30-s tasks, respectively, which represents one of the best results reported on these popular tasks
Small-sample precision of ROC-related estimates (2010)

edward@mail.ece.tamu.edu.
1-V operational amplifier with rail-to-rail input and output ranges (1989)

A bipolar operational amplifier (OA) with rail-to-rail input and output ranges which can operate at supply voltages down to 1 V is presented. At this supply voltage, the input offset voltage is typically 1.0 mV in an input common-mode voltage range that extends beyond both supply rails for about 300 mV, with a common-mode rejection ratio (CMRR) between 38 and 100 dB, depending on conditions. The output voltage can reach both supply rails within 100 mV, the output current is limited to +or-10 mA, the voltage gain is 100 dB, and the bandwidth is 450 kHz. The die is 2.5*5.5 mm/sup 2/. Qualities such as offset, input-bias current, and CMRR are improved when the supply voltage is increased and the dynamic level shift is autonomically turned off. The OA has been protected against unintentional reversal of the output signal when the inputs are substantially overdriven. The output stage of the circuit consists of two full complementary composite transistors, whose HF characteristics have been improved by internal Miller compensation and linearization of the transconductance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Recruiting Cytotoxic T Cells to Folate‐Receptor‐Positive Cancer Cells (2013)

A Fab-ulous killer: An anti-CD3 Fab-folate conjugate that targets cytotoxic T cells to folate-receptor-positive (FR+) tumors results in efficient killing of tumor cells by activated T cells. This chemical approach to the synthesis of bispecific antibodies using unnatural amino acids with orthogonal chemical reactivity affords homogenous conjugates with precise control over the relative geometry of the antibody binding sites in excellent yields.
Direct Visualization of Surfactant Hemimicelles by Force Microscopy of the Electrical Double Layer (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDirect Visualization of Surfactant Hemimicelles by Force Microscopy of the Electrical Double LayerS. Manne, J. P. Cleveland, H. E. Gaub, G. D. Stucky, and P. K. HansmaCite this: Langmuir 1994, 10, 12, 4409–4413Publication Date (Print):December 1, 1994Publication History Published online1 May 2002Published inissue 1 December 1994https://pubs.acs.org/doi/10.1021/la00024a003https://doi.org/10.1021/la00024a003research-articleACS PublicationsRequest reuse permissionsArticle Views2897Altmetric-Citations565LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Platelet lysates promote mesenchymal stem cell expansion: A safety substitute for animal serum in cell-based therapy applications (2005)

Mesenchymal stem cells (MSCs) are considered as emergent "universal" cells and various tissue repair programs using MSCs are in development. In vitro expansion of MSCs is conventionally achieved in medium containing fetal calf serum (FCS) and is increased by addition of growth factors. However, for widespread clinical applications, contact of MSCs with FCS must be minimized since it is a putative source of prion or virus transmission. Therefore, because platelets are a natural source of growth factors, we sought to investigate in vitro MSC expansion in response to platelet lysates (PL) obtained from platelet-rich plasma. Human MSCs were expanded in FCS (+/-bFGF)- or PL-supplemented medium through a process of subculture. We demonstrated that PL-containing medium is enriched by growth factors (platelet-derived growth factors (PDGFs), basic fibroblast growth factor (bFGF), transforming growth factor (TGF-beta), insulin-like growth factor-1 (IGF-1) ...) and showed that PL is able to promote MSC expansion, to decrease the time required to reach confluence, and to increase CFU-F size, as compared to the FCS medium. Furthermore, we demonstrated that MSCs cultured in the presence of PL maintain their osteogenic, chondrogenic, and adipogenic differentiation properties and retain their immunosuppressive activity. Therefore, we propose that PL may be a powerful and safe substitute for FCS in development of tissue- and cellular-engineered products in clinical settings using MSCs.
A yeast system for expression of human cystathionine beta-synthase: structural and functional conservation of the human and yeast genes. (1994)

Human cystathionine beta-synthase (CBS; EC 4.2.1.22) deficiency results in a recessive genetic disorder whose clinical and biochemical manifestations vary greatly among affected individuals. In an effort to identify and analyze mutations in the human CBS gene, we have developed a yeast expression system for human CBS. We have cloned and sequenced a human cDNA that codes for CBS and have expressed the human CBS protein in yeast cells lacking endogenous CBS. The human enzyme produced in yeast is functional both in vitro and in vivo. We have also cloned and sequenced the yeast gene, CYS4, that codes for CBS. The predicted human and yeast CBS proteins are 38% identical and 72% similar to each other, as well as sharing significant similarity with bacterial cysteine synthase. These results demonstrate the evolutionary conservation of CBS and establish the utility of a yeast expression system for studying human CBS.
Cutaneous necrotizing venulitis: a sequential analysis of the morphological alterations occurring after mast cell degranulation in a patient with a unique syndrome. (1978)

An unusual patient, with dermal nodules, flexion contractures of the fingers and toes, cold-induced urticaria, dermographism and serum hypocomplementaemia, had necrotizing cutaneous venulitis underlying the spontaneous lesions. Since necrotizing cutaneous venulitis could be experimentally induced by the physical stimuli of cold or trauma, the time-course of histopathological events was documented in the skin of this patient. The histopathological alterations were studied in 1 micron thick, Epon-embedded skin biopsy specimens over an interval of 6 days. The early massive degranulation of the mast cells was followed by the sequential infiltration of neutrophilic, eosinophilic and basophilic polymorphonuclear leucocytes, by the development of venular endothelial cell necrosis and by the deposition of fibrin. The persistent serum hypocomplementaemia involved the classic activating and amplification pathways. It seems possible that the unusual combination of pathobiological processes involving the mast cells and the complement system in this patient has created a unique syndrome, in which venules are damaged and the sheaths of the extensor tendons of the hands and feet become affected in time.
Photoacoustic tomography with a single detector in a reverberant cavity (2009)

In conventional biomedical photoacoustic tomography (PAT), ultrasonic pulses generated through the absorption of nanosecond pulses of near-infrared light are recorded over an array of detectors and used to recover an image of the initial acoustic pressure distribution within soft tissue. This image is related to the tissue optical coefficients and therefore carries information about the tissue physiology. For high resolution imaging, a large-area detector array with a high density of small, sensitive elements is required. Such arrays can be expensive, so reverberant-field PAT has been suggested as a means of obtaining PAT images using arrays with a smaller number of detectors. By recording the reflections from an acoustically reverberant cavity surrounding the sample, in addition to the primary acoustic pulse, sufficient information may be captured to allow an image to be reconstructed without the need for a large-area array. An initial study using two-dimensional simulations was performed to assess the feasibility of using a single detector for PAT. It is shown that reverberant-field data recorded at a single detector are sufficient to reconstruct the initial pressure distribution accurately, so long as the shape of the reverberant cavity makes it ray-chaotic. The practicalities of such an approach to photoacoustic imaging are discussed.
Xanthine oxidase: a critical mediator of myocardial injury during ischemia and reperfusion? (1986)

Myocardial ischemia initiates a series of cellular reactions which unless checked will culminate in cell death and tissue necrosis. Although reperfusion provides a means of preventing cell death it is not without hazard. In cases of mild ischemia, where tissue injury is in its reversible phase, reperfusion may precipitate potentially lethal ventricular arrhythmias and in cases of severe injury it may actually accelerate the process of cell death leading to hemorrhage and other forms of severe injury. The identity of mediators of cellular injury, and particularly the critical transition from reversible to irreversible injury, remains controversial. Whereas for a number of years ATP depletion, calcium overload and catecholamines have been considered as key factors in tissue injury, attention has recently been directed towards oxygen-derived free radicals (e.g. superoxide and the hydroxyl radical). In this article we discuss sources of free radicals in the mammalian heart (xanthine oxidase, mitochondria, leucocytes, and catecholamines) and present arguments based on quantitative and temporal considerations that the xanthine oxidase-mediated degradation of hypoxanthine is the most important source of free radicals and as such is the most appropriate target for therapeutic intervention. To support our arguments we present data from two species, the dog and the rat, in which we have shown how allopurinol, the specific inhibitor of xanthine oxidase, can afford a reduction of infarct size in the dog and can dramatically reduce the incidence of potentially lethal reperfusion-induced arrhythmias in the rat. Arising from these and other studies is the proposition that anti-free radical interventions (particularly those directed towards xanthine oxidase inhibition) may provide an important new therapeutic principle in the management of ischemia and reperfusion.
Lysis of nonnucleated red blood cells by cytotoxic T lymphocytes (1987)

To establish the role of direct membrane damage in cytotoxic T lymphocytes (CTL)-mediated lysis we investigated whether CTL would be capable of lysing nonnucleated target cells. By antibody-mediated targeting we show that CTL are indeed capable of lysing sheep and human red blood cells.
Platinum(IV) Prodrugs – A Step Closer to Ehrlich's Vision? (2016)

The concept of the “magic bullet”, a medicine designed to hit a specific biological target, was pioneered by Paul Ehrlich, the father of chemotherapy, some 100 years ago. Building on Ehrlich's vision, we have endeavoured to showcase not only how targeted Pt IV prodrugs may be exploited to reduce systemic toxicities associated with modern‐day chemotherapeutics, including classical Pt II drugs, but also how these prodrugs may overcome resistance issues that have plagued many chemotherapeutic regimes. A summary of advances in this field over the past decade is provided, with an emphasis on Pt IV prodrugs that target not only DNA but also enzymes, proteins, peptides and hormones. Synthetic strategies for accessing Pt IV chemistry are also provided.