gebhart/patrepeval huggingface dataset:
Enhanced Raman scattering by molecules adsorbed at the surface of colloidal spheroids (1981)

Equations are derived and calculations are presented for the electrodynamic mechanism of enhanced Raman scattering by molecules at the surface of prolate and oblate spheroids in the small-particle limit. The molecules may be arbitrarily distributed; the particles may be arbitrarily oriented. Calculations are presented for a monolayer distributed over randomly oriented spheroids. The effects of particle shape are considered for Ag, Au, and Cu hydrosols. The peak enhancement moves to longer wavelengths, and in the case of Au and Cu the magnitude of the enhancement increases strikingly as the eccentricity increases. The relation between the dependence of the Raman enhancement upon excitation wavelength and the extinction spectra is discussed, including the precariousness of extrapolating such relations beyond the small-particle limit.
Neutralization of Virus Infectivity by Antibodies: Old Problems in New Perspectives (2014)

Neutralizing antibodies (NAbs) can be both sufficient and necessary for protection against viral infections, although they sometimes act in concert with cellular immunity. Successful vaccines against viruses induce NAbs but vaccine candidates against some major viral pathogens, including HIV-1, have failed to induce potent and effective such responses. Theories of how antibodies neutralize virus infectivity have been formulated and experimentally tested since the 1930s; and controversies about the mechanistic and quantitative bases for neutralization have continually arisen. Soluble versions of native oligomeric viral proteins that mimic the functional targets of neutralizing antibodies now allow the measurement of the relevant affinities of NAbs. Thereby the neutralizing occupancies on virions can be estimated and related to the potency of the NAbs. Furthermore, the kinetics and stoichiometry of NAb binding can be compared with neutralizing efficacy. Recently, the fundamental discovery that the intracellular factor TRIM21 determines the degree of neutralization of adenovirus has provided new mechanistic and quantitative insights. Since TRIM21 resides in the cytoplasm, it would not affect the neutralization of enveloped viruses, but its range of activity against naked viruses will be important to uncover. These developments bring together the old problems of virus neutralization-mechanism, stoichiometry, kinetics, and efficacy-from surprising new angles.
Discrimination of extended-spectrum beta-lactamases by a novel nitrocefin competition assay (1990)

We describe a nitrocefin competition assay for determining inhibition profiles as a useful adjunct to existing biochemical methods for the discrimination of beta-lactamases. The hydrolysis rate of nitrocefin was measured with a plate photometer as the change in A480 over 45 min in the presence of 17 inhibitors. Fourteen well-established beta-lactamases and 13 extended-spectrum beta-lactamases were tested. Correlations with data from isoelectric focusing and amino acid sequencing suggested that the inhibition profile reflects alterations in the active-site configuration of beta-lactamases. The method was especially useful in measuring the relative affinities of beta-lactamases against poorly hydrolyzed substrates and in screening large numbers of isolates for the detection of new beta-lactamase types.
Collagen metabolism in premature rupture of amniotic membranes. (1990)

Collagen content, acid-soluble collagen, degradation activity, and collagen biosynthesis were measured in 22 normal and 20 prematurely ruptured membranes from pregnancies near term (37 weeks or more). Although no significant differences were found in the collagen content, a clear correlation was found between this value and the interval from premature rupture to delivery. Collagenolytic activity and collagen solubility were higher and collagen synthesis was lower in amniotic membranes that ruptured prematurely. These studies suggest that premature rupture of membranes is associated with extensive changes in collagen metabolism.
High-speed wavelength-multiplexed fiber-optic sensors for biomedicine (2003)

In this paper, we introduce three novel fiber-optic sensor system designs to attain real time sample data such as blood flow rates via Doppler and reflectance measurements over a spatial domain of interest. In addition, we discuss the design and functionality of novel no-moving parts sensor heads. These front-end sensors include our miniaturized head (e.g., 1.8 mm cross-sectional diameter) for intra-cavity probing and a hand-held optical scanning head for external cavity sensing via Doppler and reflectance measurements. The non-coherent miniaturized fiber-optic scanning probe can also function as real time precision optical knife to remove fat in blood vessels or to make intra-cavity incisions with pinpoint accuracy. On the other hand, our nonscanning coherent fiber-optic probe system (using a broadband source) has the unique capability of producing multiple reconfigurable simultaneous beams and operating in slow and fast acquisition mode at the same time. System issues such as front-end probe beam angular scan, scan distance, and system insertion loss are addressed.
Transcription from TATA-less promoters: dihydrofolate reductase as a model. (1993)

The promoters of many of the genes encoding the so-called "housekeeping" enzymes, oncogenes, growth factors and their receptors, and transcription factors, do not contain a canonical TATA box, which is known to direct transcription initiation. The mechanisms through which TATA-less promoters are regulated, and their transcription start sites selected, have begun to yield to investigation. Using the dihydrofolate reductase (DHFR) gene as a model, recent work on this group of genes has been reviewed. Control of transcription initiation and the role of "initiator" sequences, as well as their binding factors, in particular YY1 and E2F, are addressed. In the DHFR gene, neither the E2F site at the major initiation region nor the upstream Sp1 sites can alone produce wild-type initiation, despite the fact that each of these sites has certain properties of initiators. Many TATA-less genes are growth regulated, that is, transcription is increased in response to stimulation of cell proliferation. Although both Sp1 and E2F have been implicated in growth regulation, our recent studies suggest that Sp1 sites alone can confer a growth-dependent increase in transcription in the late G1 and early S phases of the cell cycle. The regulatory role of E2F, which binds to many TATA-less promoters and mediates viral stimulation of transcription, is also reviewed.
Social Network Effects in Contraceptive Behavior Among Adolescents (2011)

The findings of this study support the findings in the literature that peer effects are important determinants of contraception use even after controlling for potential biases in the data. Effective policy aimed at increasing contraception use among adolescents should consider these peer effects.
A Viral RNA That Binds ATP and Contains a Motif Similar to an ATP-binding Aptamer from SELEX (2003)

The intriguing process of free energy conversion, ubiquitous in all living organisms, is manifested in ATP binding and hydrolysis. ATPase activity has long been recognized to be a capability limited to proteins. However, the presence of an astonishing variety of unknown RNA species in cells and the finding that RNA has catalytic activity have bred the notion that RNA might not be excluded from the group of ATPases. All DNA-packaging motors of double-stranded DNA phages involve two nonstructural components with certain characteristics typical of ATPases. In bacterial virus phi29, one of these two components is an RNA (pRNA). Here we report that this pRNA is able to bind ATP. A comparison between the chemically selected ATP-binding RNA aptamer and the central region of pRNA reveals similarity in sequence and structure. The replacement of the central region of pRNA with the sequence from ATP-binding RNA aptamer produced chimeric aptRNA that is able to both bind ATP and assemble infectious viruses in the presence of ATP. RNA mutation studies revealed that changing only one base essential for ATP binding caused both ATP binding and viral assembly to cease, suggesting that the ATP binding motif is the vital part of the pRNA that forms a hexamer to drive the phi29 DNA-packaging motor. This is the first demonstration of a natural RNA molecule that binds ATP and the first case to report the presence of a SELEX-derived RNA aptamer in living organisms.
Ag conductive bridge RAMs for physical unclonable functions (2017)

Summary form only given. We are presenting a method to design reliable physical unclonable functions (PUFs), with silver based conductive-bridge random access memory (CB-RAM) arrays, to protect the internet of things (loT). The arrays that we fabricated in our pilot line, and characterized, operate at extremely low power which is highly desirable for security applications, and to protect cryptographic primitives. The experimental data presented in this work supports the selection of the programming voltage, the Vset, as the parameter, to generate PUF challenge-response pairs (CRP). The median Vset voltage at 0.12V is orders of magnitude lower than other non-volatile memory technologies, which can reduce the threat of side channel analysis. The level of stability, cell to cell, of the Vset that we characterized is acceptable when combined with methods based on ternary states, and resulted in low CRP error rates. Built-in-self-test capability (BIST) is used to differentiate unstable cells of the array, that carry the state “X”, from the solid cells carrying the states “0” and “1”, which are capable of generating reliable PUF CRPs. The use of machine learning algorithms can also compensate for the temperature drifts, noise, aging, and measurement instabilities normal variations. This research work is currently used to finalize and design a prototype with a custom state machine, and FPGA. We will fabricate various CB-RAM samples to optimize the quality of the PUFs.
Development of a 2001 National Land-Cover Database for the United States (2004)

Multi-Resolution Land Characterization 2001 (MRLC 2001) is a second-generation Federal consortium designed to create an updated pool of nation-wide Landsat 5 and 7 imagery and derive a second-generation National Land Cover Database (NLCD 2001). The objectives of this multi-layer, multi-source database are twofold: first, to provide consistent land cover for all 50 States, and second, to provide a data framework which allows flexibility in developing and applying each independent data component to a wide variety of other applications. Components in the database include the following: (1) normalized imagery for three time periods per path/row, (2) ancillary data, including a 30 m Digital Elevation Model (DEM) derived into slope, aspect and slope position, (3) per pixel estimates of percent imperviousness and percent tree canopy, (4) 29 classes of land cover data derived from the imagery, ancillary data, and derivatives, (5) classification rules, confidence estimates, and metadata from the land cover classification. This database is now being developed using a Mapping Zone approach, with 66 Zones in the continental United States and 23 Zones in Alaska. Results from three initial mapping Zones show single-pixel land cover accuracies ranging from 73 to 77 percent, imperviousness accuracies ranging from 83 to 91 percent, tree canopy accuracies ranging from 78 to 93 percent, and an estimated 50 percent increase in mapping efficiency over previous methods. The database has now entered the production phase and is being created using extensive partnering in the Federal government with planned completion by 2006.
<title>Noninvasive detection and staging of oral cancer in vivo with confocal optoacoustic tomography</title> (2000)

Confocal opto-acoustic transducer (COAT) was developed and applied for detection of early stages of squamous cell carcinoma in hamster model of oral cancer. COAT is a novel imaging modality with optical and acoustic lens utilized for detecting in-depth opto-acoustic front surface transducer is an improved lateral resolution of 60-micrometers . The bandwidth of the confocal opto-acoustic transducer is more than 100 MHz. Therefore, in-depth axial resolution defined by the laser pulse duration and detection system equals 15-micrometers . Imaging was performed at the wavelength of the Nd:YAG laser second harmonic, which provided sufficient depth of monitoring and significant tissue contrast. Correlation of the opto- acoustic images with H and E histology sections in control animals and in animals treated with carcinogenic agent, DMBA, confirmed previous findings that early cancer lesions invisible by the naked eye may be detected with the opto- acoustic tomography. Compact design of COAT allows, in principle, application of the opto-acoustic imaging in any organ of the human digestive system.
Highly nonlinear photoluminescence threshold in porous silicon (1999)

Porous silicon is excited using near-infrared femtosecond pulsed and continuous wave radiation at an average intensity of ∼106 W/cm2 (8×1010 W/cm2 peak intensity in pulsed mode). Our results demonstrate the presence of micron-size regions for which the intensity of the photoluminescence has a highly nonlinear threshold, rising by several orders of magnitude near this incident intensity for both the pulsed and continuous wave cases. These results are discussed in terms of stimulated emission from quantum confinement engineered intrinsic Si–Si radiative traps in ultrasmall nanocrystallites, populated following two-photon absorption.
Decellularized liver scaffolds effectively support the proliferation and differentiation of mouse fetal hepatic progenitors (2013)

Decellularized whole organs represent ideal scaffolds for engineering new organs and/or cell transplantation. Here, we investigate whether decellularized liver scaffolds provide cell-friendly biocompatible three-dimensional (3-D) environment to support the proliferation and differentiation of hepatic progenitor cells. Mouse liver tissues are efficiently decellularized through portal vein perfusion. Using the reversibly immortalized mouse fetal hepatic progenitor cells (iHPCs), we are able to effectively recellularize the decellularized liver scaffolds. The perfused iHPCs survive and proliferate in the 3-D scaffolds in vitro for 2 weeks. When the recellularized scaffolds are implanted into the kidney capsule of athymic nude mice, cell survival and proliferation of the implanted scaffolds are readily detected by whole body imaging for 10 days. Furthermore, epidermal growth factor (EGF) is shown to significantly promote the proliferation and differentiation of the implanted iHPCs. Histologic and immunochemical analyzes indicate that iHPCs are able to proliferate and differentiate to mature hepatocytes upon EGF stimulation in the scaffolds. The recellularization of the biomaterial scaffolds is accompanied with vascularization. Taken together, these results indicate that decullarized liver scaffolds effectively support the proliferation and differentiation of iHPCs, suggesting that decellularized liver matrix may be used as ideal biocompatible scaffolds for hepatocyte transplantation.
Human breast cancer: prognostic significance of the c-erbB-2 oncoprotein compared with epidermal growth factor receptor, DNA ploidy, and conventional pathologic features. (1992)

This study suggests that overexpression of the c-erbB-2 oncoprotein appears to be an important indicator of relapse in stage I-II breast cancer when singly evaluated. Multivariate analysis shows that the determination both of nodal status and DNA ploidy improves our ability to identify subsets of patients with different prognoses, and allows for a better selection of patients for systemic adjuvant treatments.
Adding Ibrutinib to Standard Therapy Reduces Disease Progression by 80% in Previously Treated Patients with CLL. (2015)

A subanalysis of the phase 3 clinical trial RESONATE showed that adherence to the recommended dose of ibrutinib in patients with chronic lymphocytic leukemia (CLL) who had received previous therapy improved extended progression-free survival (PFS) compared with patients who did not adhere to the treatment regimen, suggested Paul Barr, MD, Assistant Professor of Medicine and Director of the Clinical Trials Office, Wilmot Cancer Institute, Rochester, NY, who presented the results at ASCO 2015.

The randomized, multicenter, international, head-to-head RESONATE trial included 373 patients with CLL and 18 patients with small lymphocytic leukemia. Patients were randomized to once-daily, 420-mg orally administered ibrutinib, a first-in-class inhibitor of Bruton's tyrosine kinase inhibitor, or to intravenous ofatumumab, a CD20 antigen inhibitor. The most common nonhematologic adverse events observed in patients who received ibrutinib included diarrhea, fatigue, pyrexia, and nausea.

The goal of this subanalysis of RESONATE was to investigate the impact of adhering to the recommended dose of ibrutinib in patients with CLL. A total of 195 patients with previously treated CLL received 420 mg of ibrutinib for 8.3 months. At the end of the treatment period, the mean dose intensity—defined as the proportion of actually used doses versus planned doses of ibrutinib 420 mg—was 95%. Overall, the majority of dose interruptions reinstated the 420 dose after the dose reduction: 3.6% of the patients had 1 dose reduction and 0.5% had 2 dose reductions because of adverse events.

The PFS duration was longer among patients who used the recommended 420-mg dose of ibrutinib (median not yet reached at the time of the analysis) compared with 11 months for the patients who took lower doses. This had no relation to high-risk factors in this patient population (such as deletion 17p or p53 mutation).

Furthermore, patients who missed the recommended ibrutinib dose for ≥8 consecutive days had significantly more adverse events compared with patients who adhered to the recommended 420-mg dose (33% vs 13%, respectively).

“These data show that when patients take Imbruvica daily, at the recommended dose, it can improve their chance of achieving a sustained treatment response and delay disease progression,” Dr Barr said. “As clinicians, it is important that we ensure that patients take this once-daily, oral medication as recommended in order to achieve the best possible outcome in treating their cancer.”
Community‐Acquired Pneumonia in Adults: Guidelines for Management (1998)

This is part of the series of practice guidelines commissioned by the Infectious Diseases Society of America through its Practice Guidelines Committee. The purpose of this guideline is to provide assistance to clinicians in the diagnosis and treatment of community-acquired pneumonia. The targeted providers are internists and family practitioners. The targeted groups are immunocompetent adult patients. Criteria are specified for determining whether the inpatient or outpatient setting is appropriate for treatment. Differences from other guidelines written on this topic include use of laboratory criteria for diagnosis and approach to antimicrobial therapy. Panel members and consultants are experts in adult infectious diseases. The guidelines are evidence based where possible. A standard ranking system is used for the strength of the recommendations and the quality of the evidence cited in the literature reviewed. The document has been subjected to external review by peer reviewers as well as by the Practice Guidelines Committee and was approved by the IDSA Council. An executive summary and tables highlight the major recommendations. The guidelines will be listed on the IDSA home page at http://www.idsociety.org.
Functional consequences of interleukin 2 receptor expression on resting human lymphocytes. Identification of a novel natural killer cell subset with high affinity receptors. (1990)

In this study, we have used radiolabeled IL-2 binding assays, Northern blot analysis, immunofluorescent flow cytometry and cell sorting, as well as proliferation and cytotoxicity assays to perform an extensive phenotypic and functional characterization of the IL-2 receptor in normal resting human peripheral blood lymphocytes. Our results indicate that almost all T cells (greater than 98%) express neither the high affinity IL-2 receptor nor the functional intermediate affinity p75 chain of the IL-2 receptor without prior activation. In contrast, most NK cells constitutively express the isolated intermediate affinity p75 IL-2 receptor. In addition, a subpopulation of NK cells, distinguished by high density expression of the NKH1 antigen, constitutively express the high affinity IL-2 receptor, in addition to an excess of the isolated intermediate affinity p75 IL-2 receptor. These NKH1bright+ cells exhibit a brisk proliferative response to IL-2, similar to that seen with antigen-activated T cells, yet do so in the absence of any known antigenic stimuli. No other resting peripheral blood lymphocyte population, including CD4+, CD8+, and CD20 cells, exhibits this property. The intermediate affinity p75 IL-2 receptor, as it exists in its isolated form on resting NK cells, does not transduce a growth signal equivalent to that seen in NK cells expressing the high affinity IL-2 receptor, despite doses of IL-2 that are known to fully saturate the isolated p75 chain. This strongly suggests that additional structural or functional components are involved in generating the proliferative response following the binding of IL-2 to the high affinity heterodimeric form of the IL-2 receptor. The constitutive expression of this functional high affinity IL-2 receptor on a small population of resting NK cells provides further evidence in support of a role for these cells in the host's early defense against viral infection or malignant transformation, before the more delayed but specific T cell response.