gebhart/patrepeval huggingface dataset:
Site-Selective [2+2+n] Cycloadditions for Rapid, Scalable Access to Alkynylated Polycyclic Aromatic Hydrocarbons (2019)

Polycyclic aromatic hydrocarbons (PAHs) are attractive synthetic building blocks for more complex conjugated nanocarbons, but their use for this purpose requires appreciable quantities of a PAH with reactive functional groups. Despite tremendous recent advances, most synthetic methods cannot satisfy these demands. Here we present a general and scalable [2+2+n] (n = 1 or 2) cycloaddition strategy to access PAHs that are decorated with synthetically versatile alkynyl groups and its application to seven structurally diverse PAH ring systems (thirteen new alkynylated PAHs in total). The critical discovery is the site-selectivity of an Ir-catalyzed [2+2+2] cycloaddition, which preferentially cyclizes tethered diyne units with preservation of other (peripheral) alkynyl groups. The potential for generalization of the site-selectivity to other [2+2+n] reactions is demonstrated by identification of a Cp&lt;sub&gt;2&lt;/sub&gt;Zr-mediated [2+2+1] / metallacycle transfer sequence for synthesis of an alkynylated, selenophene-annulated PAH. The new PAHs are excellent synthons for macrocyclic conjugated nanocarbons. As a proof of concept, four were subjected to Mo catalysis to afford large, PAH-containing arylene ethylene macrocycles, which possess a range of cavity sizes reaching well into the nanometer regime. More generally, this work is a demonstration of how site-selective reactions can be harnessed to rapidly build up structural complexity in a practical, scalable fashion.
Ion assisted selective thin film deposition (1986)

Ion bombardment of a growing film is one known way of changing film properties. Also in reactive etching, ions may assist surface reactions. We will present a study where different substrates are bombarded by energetic argon ions during deposition of titanium. If titanium is deposited onto three different substrates without influencing the substrate by any ion irradiation, a thin titanium film, equally thick, will be formed on all three substrates. If, however, the substrates are bombarded by energetic argon ions (500–800 eV) during deposition of titanium, we have found that quite different film thicknesses may be obtained on different substrates. In fact, a balance may be found where actually one substrate is sputter etched while another substrate under identical deposition conditions (same run) is deposited by titanium. Results from rf-bias sputtering in argon shows selectivity, e.g., between Si and Pt at 10 mTorr pressure, 1600 V target voltage and 800 V substrate bais. Ti is deposited onto silicon but the net surface effect on Pt is substrate etching. This demonstrates that selective deposition is possible to achieve by ion assisted thin film growth.
Heme-Spin Label Studies of Hemoglobin (1974)

Abstract Heme spin-labeled oxyferrohemoglobin was prepared by the recombination of mono-spin-labeled protoheme with human apohemoglobin and subsequent reduction with a ferredoxin reductase system. The spin-labeled oxyhemoglobin exhibited optical and oxygen-binding properties indistinguishable from those of native hemoglobin. The electron paramagnetic resonance spectrum of the spin label attached to the heme-moiety showed that the labels were moderately immobilized in the protein. Upon deoxygenation, the resonance amplitude was decreased to less than 50% of the original amplitude and there were small changes in the EPR line shape. Comparison between the optical and EPR measurements during the deoxygenation process clearly showed that the EPR changes are not proportional to the optical changes. This result is contrary to the model of oxygen binding to hemoglobin provided by the induced fit theory. Since the EPR change has no isosbestic point, it was concluded that the microscopic conformation in the vicinity of the heme can take more than two states during the oxygenation process. It was also shown that the EPR line shape of the heme spin-labeled oxyhemoglobin is different from that of the met form. This result suggests a conformational difference between these two hemoglobins in the dissolved state.
Using abstration to isolate hardware in an object-oriented simulation (1998)

A common problem faced in the design of an objectoriented simulation is how a complex simulation model should interface with the simulator hardware. This paper describes a design that isolates the hardware interface from the complex models of a simulation environment. A detailed description of the design is provided and the advantages and disadvantages of the design are discussed. A working example of the
Association Between Cognitive Impairment and Chronic Kidney Disease in Mexican Americans (2015)

Lower eGFR was associated with significantly poorer neuropsychological functioning in Mexican Americans. A blood-based profile was generated that was highly accurate in detecting CKD-related MCI. A blood profile capable of predicting CKD-related cognitive impairment would be of benefit for the design of clinical interventions.
Colorimetric Determination of Poly(N-Vinyl-2-Pyrrolidone) in Contact Lens Solutions (1979)

A rapid colorimetric method is presented for the quantitative determination of poly(N-vinyl-2-pyrrolidone) in contact lens solutions. The method is simple, requires no sample pretreatment, and uses only a small volume of sample. The procedure is based on the measurement of the net absorbance of a poly(N-vinyl-2-pyrrolidone)- Congo red complex at 545 nm. An accuracy of greater than +/- 4% was obtained for the concetnration ranges usually found in contact lens solutions with a minimum detection level of 10 ppm. The method is useful as a screening procedure for solutions of unknown composition and as a quality assurance procedure for routine determinations.
Memorial Service for Werner Seligmann: Distiguished Professor of Architecture (1998)

Memorial Service for Werner Seligmann (1930-1998) was held in Hendricks Chapel, Syracuse University on December 6th, 1998 at 1:30pm.
Toward Energy-Efficient Trust System Through Watchdog Optimization for WSNs (2015)

Watchdog technique is a fundamental building block to many trust systems that are designed for securing wireless sensor networks (WSNs). Unfortunately, this kind of technique consumes much energy and hence largely limits the lifespan of WSN. Although the state-of-the-art studies have realized the importance of trust systems' efficiency in WSNs and proposed several preliminary solutions, they have overlooked to optimize the watchdog technique, which is perhaps among the top energy-consuming units. In this paper, we reveal the inefficient use of watchdog technique in existing trust systems, and thereby propose a suite of optimization methods to minimize the energy cost of watchdog usage, while keeping the system's security in a sufficient level. Our contributions consist of theoretical analyses and practical algorithms, which can efficiently and effectively schedule the watchdog tasks depending on the sensor nodes' locations and the target nodes' trustworthiness. We have evaluated our algorithms through experiments on top of a WSNET simulation platform and an in-door WSN testbed in our collaborative lab. The results have successfully confirmed that our watchdog optimization techniques can save at least 39.44% energy without sacrificing much security (<;0.06 in terms of trust accuracy and robustness), even in some cases enhance the protection against certain attacks.
4D Electron Microscopy: Imaging in Space and Time (2009)

It is instead an in-depth expose of the paradigm concepts and the developed techniques that can now be executed to gain new knowledge in the entire domain of biological and physical science, and in the four dimensions of space and time
Report: A Voice Password System for Access Security (1986)

A voice password system for access security using speaker verification technology has been designed for use over dial-up telephone lines. The voice password system (VPS) can provide secure access to telephone networks, computers, rooms, and buildings. It also has application in office automation systems, electronic funds transfer, and “smart cards” (interactive computers embedded in credit-card-sized packages). As increasing attention is focused on access security in the public, private, and government sectors, the voice password system (Figure 1) can provide a timely solution to the security dilemma.
Cellular localization and substrate specificity of isoelectric forms of human liver neuraminidase activity (1987)

The four major isoelectric forms of human liver neuraminidase (with pI values between 3.4 and 4.8) have been isolated by preparative isoelectric focusing and characterized with regard to their substrate specificity using glycoprotein, glycopeptide, oligosaccharide and ganglioside natural substrates. All forms exhibited a rather broad linkage specificity and were capable of hydrolyzing sialic acid glycosidically linked alpha 2-3, alpha 2-6 and alpha 2-8, although differential rates of hydrolysis of the substrates were found for each form. The most acidic form 1 (pI 3.4) was most active on sialyl-lactose, whereas form 2 (pI 3.9) and 3 (pI 4.4) were most active on the more hydrophobic ganglioside substrates. Form 4 (pI 4.8) was most active on the low-Mr hydrophilic substrates (fetuin glycopeptide, sialyl-lactose). Each form was less active on the glycoprotein fetuin than on a glycopeptide derived from fetuin. Organelle-enriched fractions were prepared from fresh human liver tissue and neuraminidase activity on 2'-(4-methylumbelliferyl)-alpha-D-N-acetylneuraminic acid was recovered in plasma membrane, microsomal, lysosomal and cytosolic preparations. Isoelectric focusing of the neuraminidase activity recovered in each of these preparations resulted in significantly different isoelectric profiles (number, relative amounts and pI values of forms) for each preparation. The differential substrate specificity of the isoelectric forms and the different isoelectric focusing profiles of neuraminidase activity recovered in subcellular-enriched fractions suggest that specific isoelectric forms with broad but defined substrate specificity are enriched at separate sites within the cell.
Research, Collaboration, and Open Science Using Web 2.0 (2010)

There is little doubt that the Internet has transformed the world in which we live. Information that was once archived in bricks and mortar libraries is now only a click away, and people across the globe have become connected in a manner inconceivable only 20 years ago. Although many scientists and educators have embraced the Internet as an invaluable tool for research, education and data sharing, some have been somewhat slower to take full advantage of emerging Web 2.0 technologies. Here we discuss the benefits and challenges of integrating Web 2.0 applications into undergraduate research and education programs, based on our experience utilizing these technologies in a summer undergraduate research program in synthetic biology at Harvard University. We discuss the use of applications including wiki-based documentation, digital brainstorming, and open data sharing via the Web, to facilitate the educational aspects and collaborative progress of undergraduate research projects. We hope to inspire others to integrate these technologies into their own coursework or research projects.
Fluid acceleration effects on suspended sediment transport in the swash zone (2003)

Suspended sediment concentrations and fluid velocities measured in the swash zone of a high‐energy steep beach were used to investigate the importance of fluid accelerations to suspended sediment transport. Swash flow acceleration was nearly constant at about one‐half downslope gravitational acceleration with two important exceptions. We observed strong, short‐lived periods of accelerating uprush at the beginning of the swash cycle and decelerating backwash at the end of the swash cycle (magnitudes of both approximately twice that of the expected downslope gravitational acceleration). Interestingly, spikes in suspended load followed the anomalies in acceleration in a way that was not apparent from the nearly symmetric (in magnitude) ensemble averaged velocity time series. Suspended load values were largest during accelerating uprush associated with the shoreward propagating turbulent bore or swash front. During backwash, suspended loads were generally not as large. Correspondingly, suspended sediment transport rates obtained from the sediment concentration and velocity measurements showed best comparisons with a modified sediment transport model that includes a physical mechanism for enhancing transport rates due to flow acceleration. The modified sediment transport model reduced the overall root‐mean square prediction error by up to 35% and shifted the predicted peak in uprush sediment transport rate earlier in the swash cycle, resulting in a better fit to the observations. These findings suggest that the inclusion of the acceleration term may account for physical mechanisms that include bore turbulence and horizontal pressure gradients typically associated with the accelerating portion of uprush.
Towards standardized mechanical characterization of microbial biofilms: analysis and critical review (2018)

Developing reliable anti-biofilm strategies or efficient biofilm-based bioprocesses strongly depends on having a clear understanding of the mechanisms underlying biofilm development, and knowledge of the relevant mechanical parameters describing microbial biofilm behavior. Many varied mechanical testing methods are available to assess these parameters. The mechanical properties thus identified can then be used to compare protocols such as antibiotic screening. However, the lack of standardization in both mechanical testing and the associated identification methods for a given microbiological goal remains a blind spot in the biofilm community. The pursuit of standardization is problematic, as biofilms are living structures, i.e., both complex and dynamic. Here, we review the main available methods for characterizing the mechanical properties of biofilms through the lens of the relationship linking experimental testing to the identification of mechanical parameters. We propose guidelines for characterizing biofilms according to microbiological objectives that will help the reader choose an appropriate test and a relevant identification method for measuring any given mechanical parameter. The use of a common methodology for the mechanical characterization of biofilms will enable reliable analysis and comparison of microbiological protocols needed for improvement of engineering process and screening.
Polysiloxane Thin Films Optimisation for Potassium Detection using EIS Characterisation with Microelectrode Structures (2007)

Most chemical or biochemical analysis use current-voltage I(V) characterization as detection principle. Thus, the development of microelectrodes using standard silicon technologies process is required: they show advantages of mass production, generic structure, small dimensions, low cost, and are well adapted for the detection of chemical, biochemical or biological species in aqueous environment using specific impedimetric measurement methods.
Nitride-based high electron mobility transistors with a GaN spacer (2006)

A GaN/ultrathin AlN∕GaN heterojunction has been used to introduce a GaN spacer between the GaN channel and the AlGaN barrier in AlGaN∕GaN high electron mobility transistors (HEMTs). In conventional AlGaN∕GaN devices, the alloy scattering of the electrons with the AlGaN barrier degrades the electron velocity at high electric fields. This effect is significantly reduced in GaN-spacer transistors, which therefore have much better high field transport properties. While the dc performance of these transistors is similar to conventional AlGaN∕GaN HEMTs, a 20% increase in the electron velocity has been measured by two different techniques.
Effect of Acidic Industrial Effluent Release on Microbial Diversity and Trace Metal Dynamics During Resuspension of Coastal Sediment (2018)

Both industrial effluent discharge and the resuspension of contaminated marine sediments are important sources of trace metals in seawater which potentially affect marine ecosystems. The aim of this study was to evaluate the impact of the industrial wastewaters having acidic pH (2-3) and containing trace metals on microbial diversity in the coastal ecosystem of the Gulf of Gabès (Tunisia, southern Mediterranean Sea) subjected to resuspension events of marine sediments. Four trace elements (As, Cd, U, and V) were monitored during 10-day sediment resuspension experiments. The highest enrichment in the seawater dissolved phase was observed for Cd followed by U, V, and As. Cd remobilization was improved by indigenous microbial community, while U release was mainly abiotic. Acidic effluent addition impacted both trace metal distribution and microbial diversity, particularly that of the abundant phylum <i>Bacteroidetes</i>. Members of the order <i>Saprospirales</i> were enriched from sediment in natural seawater (initial pH > 8), while the family <i>Flavobacteriaceae</i> was favored by acidified seawater (initial pH < 8). Some <i>Flavobacteriaceae</i> members were identified as dominant species in both initial sediment and experiments with acidic wastewater, in which their relative abundance increased with increasing dissolved Cd levels. It could be therefore possible to consider them as bioindicators of metal pollution and/or acidification in marine ecosystems.
SEROLOGIC METHODS FOR THE EARLY DIAGNOSIS OF PNEUMOCYSTIS CARINII INFECTION IN RENAL ALLOGRAFT RECIPIENTS (1986)

Because of the nephrotoxic action of trimethoprimsulfamethoxazole (TMP-SMX) in cyclosporine (CsA)-treated patients, combined with the (CsA)-treated patients, combined with the possibility of selecting resistant gram-negative or Nocardia asteroides organisms, a monitoring tool to detect early Pneumocystis carinii (PC) infection permitting a selective treatment approach is highly desirable. A review of 401 consecutive renal transplants revealed 26 cases (18 suspected and 8 histologically proved) of PC infection in 21 cadaver and 5 living-related renal recipients. The diagnosis was confirmed in 8/18 patients who were invasively studied by open-lung biopsy (1/2), bronchoscopy with transbronchial biopsy (4/9), bronchoscopy with brushing (1/2), bronchoscopy with bronchoalveolar lavage (2/5), and transpleural needle biopsy (0/1)-yielding a confirmed incidence of 2% (8/401). All positive invasive studies had been performed prior to or within 24 hr of the inception of TMP-SMX therapy. Nine of ten negative invasive studies were performed after more than 24 hr of treatment. The mean time from transplantation to the onset of clinical symptoms was 2.5 +/- 1.5 months. The infection rate would be 6.5%, assuming all 18 suspected cases would be PC-positive if studied pretreatment. In order to assess the efficacy of a variety of serologic methods of PC detection, qualitative counter-immunoelectrophoresis (CIE) for P carinii antigen (PC-Ag), IgG antibody reactive with PC (enzyme-linked immunosorbent assay [ELISA]), and a latex particle agglutination test (LPA) were performed on 279 sera; 85 sera from the 26 suspected or proved cases, 100 sera from normal age-matched controls, and 94 sera from 78 asymptomatic allograft recipients followed as outpatients. In the eight histologically proven cases, CIE was positive in only 3/8 and turned positive late in the clinical course. LPA was positive in all histologically proved cases; however, it was also positive in 60% of asymptomatic renal recipients. In cases that developed clinical disease, LPA increased in titer weeks to months prior to the onset of symptoms. Additionally, LPA titers decreased or stabilized during successful TMP-SMX therapy, providing an early therapeutic index. Measurement of anti-PC IgG was not useful per se, as it was elevated in both controls and documented PC infection. The combination of very low antibody titer (less than or equal to 1:16) with a positive or increasing LPA PC-Ag titer appeared to be disease-predictive.(ABSTRACT TRUNCATED AT 400 WORDS)
Design Rationale and Development Approach for Pegfilgrastim as a Long-Acting Granulocyte Colony-Stimulating Factor (2015)

Filgrastim, a recombinant methionyl human granulocyte colony-stimulating factor (G-CSF) (r-metHuG-CSF), is efficacious in stimulating neutrophil production and maturation to prevent febrile neutropenia (FN) in response to chemotherapy. Because of its relatively short circulating half-life, daily filgrastim injections are required to stimulate neutrophil recovery. In an effort to develop a long-acting form of filgrastim that was as safe and efficacious as filgrastim but had a longer in vivo residence time, a number of strategies were considered. Ultimately, fusion of filgrastim to polyethylene glycol (PEG) was selected. Following extensive analysis of conjugation chemistries as well as in vitro and in vivo characterization of a panel of PEGylated proteins, a construct containing a 20 kDa PEG moiety covalently conjugated to the N-terminus of filgrastim was chosen for advancement as pegfilgrastim. Pegfilgrastim is primarily cleared by neutrophils and neutrophil precursors (rather than the kidneys), meaning that clearance from the circulation is self-regulating and pegfilgrastim is eliminated only after neutrophils start to recover. Importantly, addition of PEG did not alter the mechanism of action and safety profile compared to filgrastim. Clinical evaluation revealed that a single 6 mg dose effectively reduces the duration of neutropenia and risk of FN in patients receiving chemotherapy. This work demonstrates the benefit of using PEGylation to generate pegfilgrastim, which allows for once-per-chemotherapy cycle administration while maintaining similar safety and efficacy profiles as those for multiple daily administration of filgrastim. Approaches that may provide advances for therapeutic agonists of G-CSF receptor are also discussed.
Modes of Benign Mechanical Transport of Breast Epithelial Cells to Axillary Lymph Nodes (2005)

The status of axillary lymph nodes is a key prognostic indicator available for the management of patients with breast cancer. Sentinel lymph node (SLN) evaluation as a predictor of lymph node status has led to increased use of ancillary methods, principally immunohistochemistry, to increase the sensitivity of the SLN biopsy. So-called "occult" micrometastases detected by such methods have led to speculation that some may have reached the SLNs by benign mechanical transport (BMT) rather than a metastatic process. We review evidence suggesting two potential modes of BMT: lymphatic transport of epithelial cells displaced by biopsy of the primary breast tumor and by breast massage-assisted SLN localization. The biopsy techniques under most scrutiny include fine needle aspiration and large-gauge core biopsy. The evidence implicating breast massage prior to SLN biopsy as a mode of BMT has been supported by statistical analysis; however, no method of distinguishing massage-associated cells in SLNs from true occult micrometastases is available. The significance of small epithelial clusters in SLNs is currently unknown. Thus, deviation from current biopsy and SLN-localizing practices is unwarranted.
Randomized controlled comparison of cross-sectional survey approaches to optimize follow-up completeness in clinical studies (2019)

Both contact strategies were equally successful in contacting almost all patients cross-sectionally. If systematically timed, direct phone calls were less complicated to organize and faster completed. Given the low time and effort per patient, outcome studies should invest in systematic follow-up surveys to minimize attrition bias.