gebhart/patrepeval huggingface dataset:
A Robust True Direct-Print Technology for Tissue Engineering (2007)

Numerous solid freeform fabrication (SFF) or rapid prototyping (RP) techniques have been employed in the field of tissue engineering to fabricate specially organized three-dimensional (3-D) structures such as scaffolds. Some such technologies include, but are not limited to, laminated object manufacturing (LOM), three-dimensional printing (3-DP) or ink-jet printing, selective laser sintering (SLS), and fused deposition modeling (FDM). These techniques are capable of rapidly producing highly complex 3-D scaffolds or other biomedical structures with the aid of a computer-aided design (CAD) system. However, they suffer from lack of consistency and repeatability, since most of these processes are not fully controlled and cannot reproduce the previous work with accuracy. Also, these techniques (excluding FDM) are not truly direct-print processes. Certain material removing steps are involved, which in turn increases the complexity and the cost of fabrication. The FDM process has good repeatability; however, the materials that can be used are limited due to the high temperature needed to melt the feedstock. Some researchers also reported that the scaffolds fabricated by FDM lack consistency in the z-direction. In this paper, we will present a true direct-print technology for repeatedly producing scaffolds and other biomedical structures for tissue engineering with the aid of our Computer Aided Biological (CAB) tool. Unlike other SFF techniques mentioned above, our direct-print process fabricates scaffolds or other complex 3-D structures by extruding (dispensing) a liquid material onto the substrate with a prescribed pattern generated by a CAD program. This can be a layer-by-layer 2.5 dimension build or a true 3-D build. The dispensed liquid material then polymerizes or solidifies, to form a solid structure. The flexibility in the types of materials that can be extruded ranges from polymers to living cells, encapsulated in the proper material. True 3-D structures are now possible on a wide range of substrates, including even in vivo. Some of the advantages of the process are a) researchers have full control over the patterns to be created; b) it is a true direct-print process with no material removing steps involved; c) it is highly consistent and repeatable; and d) it is highly efficient and cost-effective. This paper will first give a detailed description of the CAB tool. Then, it will present a detailed process for printing polycaprolactone (PCL) into a defined 3-D architecture, where the primary focus for these constructs is for use in tissue engineering applications. Finally, mechanical characterization results of the printed scaffolds will be included in the paper.
Cholesteric liquid crystals as weathering indicators for marble surfaces (2000)

Cholesteric liquid crystals have been used to study the weathered surfaces of marble from the Sanctuary of Demeter in Eleusis, near Athens. Previous investigations have shown that when a cholesteric phase is spread across the surface of the stone, the pitch of the mesophase is sensitive to the topography of the surface. The wavelength of the maximum in the reflected spectrum varies therefore with the microtexture of the surface. Small samples of surface stone from the temple which had been weathered in distinctive ways, were investigated in the laboratory. There appears to be a significant correlation between the optical reflectance spectra and the surface microtopography investigated by SEM, as indicated by computer aided analysis (Digital Image Processing). The results point to the development of an effective in situ method of monitoring the weathering of marble surfaces using cholesteric liquid crystals.
ChemInform Abstract: A Method for Studying the Grown‐In Defect Density Spectra in Czochralski Silicon Wafers. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Experimental Investigation of Cyclic Variability on Combustion and Emissions of a High-Speed SI Engine (2015)

<div class="section abstract"><div class="htmlview paragraph">Cyclic combustion variability (CCV) is an undesirable characteristic of spark ignition (SI) engines, and originates from variations in gas motion and turbulence, as well as from differences in mixture composition and homogeneity in each cycle. In this work, the cycle to cycle variability on combustion and emissions is experimentally investigated on a high-speed, port fuel injected, spark ignition engine. Fast response analyzers were placed at the exhaust manifold, directly downstream of the exhaust valve of one cylinder, for the determination of the cycle-resolved carbon monoxide (CO) and nitric oxide (NO) emissions. A piezoelectric transducer, integrated in the spark-plug, was also used for cylinder pressure measurement. The impact of engine operating parameters, namely engine speed, load, equivalence ratio and ignition timing on combustion and emissions variability, was evaluated. The variations in mixture stoichiometry were found to have a strong effect on engine combustion variability. Rich cyclic mixture compositions exhibit lower coefficient of variation (COV) for the indicated mean effective pressure (IMEP) and NO emissions (COV<sub>NO</sub>) compared with lean mixtures. The mean value of CO emission was found to be mainly affected by stoichiometry while COV<sub>CO</sub> is affected by lambda fluctuations. At higher engine loads, maximum cylinder pressure and IMEP are increased, while COV<sub>IMEP</sub> decreased. Furthermore, ignition timing was found to strongly affect combustion and NO emissions, as it is related with early flame kernel development and thereby with flame propagation. Maximum braking torque (MBT) operation exhibits maximum IMEP and minimum COV<sub>IMEP</sub>. Compared to MBT operating conditions, advanced ignition timing leads to higher maximum cylinder pressure, higher NO and COV<sub>NO</sub>, while retarded ignition timings lead to lower maximum cylinder pressure, lower NO concentration and higher NO variability (COV<sub>NO</sub>).</div></div>
A digital-intensive receiver front-end using VCO-based ADC with an embedded 2nd-Order anti-aliasing Sinc filter in 90nm CMOS (2011)

One of the recent trends in multimode multiband (MMMB) receivers is to remove the analog filter or variable-gain amplifier (VGA) in the receiver chain and employ a wide-dynamic-range ADC directly after the mixer or include the mixer in the ADC. While such architecture provides ease of programmability once the signals are digitized, it puts a large burden on the ADC and anti-alias filter. Hence, ADCs typically use high-performance analog circuits for wide dynamic range, even though it is difficult to implement these circuits using low-voltage nanoscale CMOS processes. A promising ADC architecture for an MMMB receiver is the VCO-based ADC, since it offers 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> -order noise-shaping from its open-loop digital-intensive nature, thus allowing high sampling rate and high SNR. Furthermore, the VCO-based ADC provides an inherent anti-aliasing 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> -order Sinc filter due to the innate integrating ability of the VCO. Unfortunately, for multiband receivers that do not have an RF pre-filter, a Sinc filter alone does not provide enough out-of-band rejection and hence higher-order anti-aliasing filters are required. In order to solve this problem, we propose a 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> -order anti-aliasing Sinc filter (Sinc <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> filter) that provides double the rejection ratio of a Sinc filter. Furthermore, the proposed technique is highly digital and can be embedded in a VCO, resulting in little overhead.
NMR studies on self‐complementary oligonucleotides conjugated with methylene blue (2005)

A carboxyl-functionalized methylene blue (MB) derivative was synthesized and covalently coupled to three CG-rich self-complementary 2'-deoxyoligonucleotides at their 5'-end. Thermodynamic and structural details about the interactions between the dye and oligonucleotide duplexes were investigated employing ultraviolet (UV) melting and (1)H nuclear magnetic resonance (NMR) experiments. In contrast to previous findings on MB binding, no specific intercalation or binding in the minor or major groove of the double helix was found in a 100 mM NaCl buffer. Rather, proton chemical shift changes in the conjugates provide ample evidence for weak dye-DNA interactions largely through external MB stacking on the terminal base pairs.
Concentration dependent electrochemical properties and structural analysis of a simple magnesium electrolyte: magnesium bis(trifluoromethane sulfonyl)imide in diglyme (2016)

Development of Mg electrolytes that can plate/strip Mg is not trivial and remains one of the major roadblocks to advance Mg battery research.
Urinary screening tests for fetal Down syndrome: II. Hyperglycosylated hCG (1999)

Hyperglycosylated hCG is a form of hCG with more complex oligosaccharide side chains. A specific immunoassay was developed to measure hyperglycosylated hCG. Levels were measured in urine samples from 1157 women between 11 to 22 weeks of gestation, undergoing genetic analysis because of advanced maternal age. Values were normalized to urine creatinine concentration and plotted against gestational age, median values were determined and multiples of the control median (MoM) calculated. The median MoM and log standard deviation (log SD) of the 1134 control samples was 1.0 and 0.47, and of the 23 Down syndrome cases was 7.8 and 0.48, respectively. This indicated a 7.8-fold increase in hyperglycosylated hCG levels in Down syndrome cases. In the accompanying article, a stability problem was found with β-core fragment measurements in frozen urine samples. In anticipation of similar problems, nine urine samples were tested for hyperglycosylated hCG fresh and after storage in the freezer. No clear difference was found in hyperglycosylated hCG values. In addition, no trend was found in hyperglycosylated hCG MoM values or in Down syndrome detection rates in urine samples stored for one, two or three years in the freezer. Samples were split into five equal groups according to creatinine concentration. A trend was observed, hyperglycosylated hCG MoM values decreasing with advancing creatinine concentration (1.77, 1.08, 1.01, 0.73 and 0.60 at 0.25, 0.50, 0.79, 1.11 and 1.73 mg l, respectively). An error was noted. This was corrected with a regression equation. After correction, the median MoM and log SD of the control samples was 1.0 and 0.44, and of Down syndrome samples was 7.3 and 0.42, respectively. Correction of this error, while reducing the elevation of Down syndrome cases, tightened the spread of samples. Samples were ranked and centiles determined. 18 of 23 Down syndrome cases (78 per cent) exceeded the 95th centile of the control population. ROC analysis indicated 79 per cent detection at 5 per cent false-positive rate. Urine samples were collected during two periods of gestation, an early period (11th to 14th completed week) and the period when chemical screening is normally performed (15th to 21st week). ROC analysis indicated 80 per cent and 78 per cent detection rates, respectively, at 5 per cent false-positive rate, in the two gestational periods. Hyperglycosylated hCG values were modelled with β-core fragment values, total oestriol values and maternal age. ROC analysis indicated 97 per cent detection rate at 5 per cent false-positive rate. This detection rate and this level of Down syndrome and control patient discrimination surpasses that of any other serum, urine or ultrasound screening protocol. Hyperglycosylated hCG should be considered as a new screening test for aneuploid pregnancies, with the potential of detecting almost all cases of Down syndrome. Evaluation is needed by other centres in order to bring hyperglycosylated hCG into clinical practice. Copyright © 1999 John Wiley & Sons, Ltd.
Active Learning with Model Selection in Linear Regression (2008)

Optimally designing the location of training input points (active learning) and choosing the best model (model selection) are two important components of supervised learning and have been studied extensively. However, these two issues seem to have been investigated separately as two independent problems. If training input points and models are simultaneously optimized, the generalization performance would be further improved. In this paper, we propose a new approach called ensemble active learning for solving the problems of active learning and model selection at the same time. We demonstrate by numerical experiments that the proposed method compares favorably with alternative approaches such as iteratively performing active learning and model selection in a sequential manner.
Synthesis and characterization of new polyimides containing calix[4]arenes in the polymer backbone (1999)

Two diaminocalix[4]arene monomers were synthesized from p-tert-butylcalix[4]arene through a 4-step reaction sequence. New copoly(amic acid)s containing calix[4]arene moieties on the polymer backbone were successfully synthesized in N-methyl-2-pyrrolidone by polycondensations of 4,4′-oxydiphthalic anhydride (ODPA) with the diaminocalix[4]arene monomers using 4,4′-oxydiphenylene diamine (ODA) as a comonomer. These copoly(amic acid)s were soluble in aprotic polar solvents, so that they can be processed in various ways. The copoly(amic acid) precursors were thermally converted to the corresponding copolyimides in films. The copolyimide films are amorphous, but insoluble in common solvents. They are thermally stable up to 366°C. The copolyimides exhibit relatively high TEC's, low Tg's, low refractive index, low dielectric constant, low optical anisotropy, low dielectric anisotropy, and low water uptake, compared to those of conventional ODPA-ODA polyimide. These property characteristics were interpreted in regard to bulky, cone-like calix[4]arene moieties and their effects on the chain conformation and morphological structure. The processability and property characteristics support that both of the copolyimides containing calix[4]arene moieties are potential candidate materials suitable for membranes, antioxidant additives, chemical sensor devices, and microelectronic devices. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 2013–2026, 1999
On the use of photobleaching to reduce fluorescence background in Raman spectroscopy to improve the reliability of pigment identification on painted textiles (2006)

Abstract Subjecting a specimen of red lead watercolour paint on silk to photobleaching was demonstrated to be a simple means by which to engineer a reduction in the magnitude of the fluorescent background that was approximately exponential with time, with a corresponding improvement in the signal to noise ratio of the Raman spectrum, thus rendering the characteristic peaks more easily visible and allowing more confident identification of the pigment. However, relative heights of the Raman peaks obtained from the sample were seen to alter progressively as a result of irradiation, indicating that some component of the sample was undergoing degradation that may result in longer‐term damage to a fragile historic artefact. It was also shown that crystals of the lead monoxide pigment massicot were present in the samples of red lead on a painted silk artefact dating from 1750. It is concluded that this was either due to deliberate mixing of pigments by the artist, contrary to historic records, or as a result of the roasting techniques used to create red lead pigments at the time and not due to thermal degradation of the pigment during Raman analysis. Copyright © 2006 John Wiley & Sons, Ltd.
Altering Expression of <i>Benzoic Acid/Salicylic Acid Carboxyl Methyltransferase 1</i> Compromises Systemic Acquired Resistance and PAMP-Triggered Immunity in <i>Arabidopsis</i> (2009)

Methyl salicylate (MeSA), which is synthesized in plants from salicylic acid (SA) by methyltransferases, has roles in defense against microbial and insect pests. Most of the MeSA that accumulates after pathogen attack is synthesized by benzoic acid/SA carboxyl methyltransferase 1 (AtBSMT1). To investigate the role of AtBSMT1 in plant defense, transgenic Arabidopsis with altered AtBSMT1 function or expression were assessed for their ability to resist pathogen infection. A knockout mutant (Atbsmt1) failed to accumulate MeSA following pathogen infection; these plants also failed to accumulate SA or its glucoside in the uninoculated leaves and did not develop systemic acquired resistance (SAR). However, the Atbsmt1 mutant exhibited normal levels of effector-triggered immunity and pathogen-associated molecular pattern (PAMP)-triggered immunity to Pseudomonas syringae and Hyaloperonospora arabidopsidis. Analyses of transgenic Arabidopsis plants overexpressing AtBSMT1 revealed that they accumulate elevated levels of MeSA in pathogen-infected leaves but fail to develop SAR. Since the levels of SA and its glucoside were reduced in uninoculated systemic leaves of these plants whereas MeSA levels were elevated, AtBSMT1-mediated conversion of SA to MeSA probably compromised SAR development by suppressing SA accumulation in uninoculated leaves. PAMP-triggered immunity also was compromised in the AtBSMT1 overexpressing plants, although effector-triggered immunity was not.
XEN Gel Implant: a new surgical approach in glaucoma (2017)

The XEN Gel Implant effectively lowers IOP and medication use, with a favorable safety profile. Long-term data on its success and cost-effectiveness are lacking. The studies have shown it to be without any serious adverse events and to have good safety profile encouraging future research on this novel implant. There is a need to correctly identify selection criteria for patients, who would benefit the most from the XEN Gel Implant.
The nuclear pore: at the crossroads (1992)

The nuclear pore complex is at the crossroads of macromolecular traffic across the nuclear envelope. Our knowledge of the mechanism whereby nuclear transport is mediated by the nuclear pore complex is also at a crossroads; a molecular understanding of this process has major implications for applied medical sciences. This becomes obvious with the realization that nuclear proteins are synthesized in the cytoplasm and yet function in the nucleus, and that RNA is transcribed in the nucleus but translated in the cytoplasm. Thus, control of macromolecular traffic across the nuclear membrane is an important means for altering the levels and activities of such molecules as steroid hormone receptors, transcription factors, and enzymes involved in DNA replication. Nuclear proteins have been found to contain nuclear localization sequences (NLS) rich in basic amino acids, which target them for transport through the nuclear pore to the nucleus. It is also clear that a group of novel glycoproteins having a unique carbohydrate modification are required for transport across the nuclear pore complex. However, the mechanism by which the NLS is recognized to mediate transport across the nuclear envelope is poorly understood. It is the aim of this brief review to attempt a synthesis of what is known of this mechanism and what may be newly inferred on the basis of current experimental data.
Enzyme-linked immunosorbent assay analyses of the hyaluronate-binding region and the link protein of proteoglycan aggregate. (1982)

An enzyme-linked immunosorbent assay, in combination with an independent inhibition step, was established to quantitate two components of the proteoglycan aggregate, namely link protein and hyaluronate-binding region, at concentrations below 100 ng/ml. The presence of other components of the aggregate in the samples to be tested influenced quantitation in a specific manner. The apparent antigenicity of link protein increased 2-5 times when either purified proteoglycan monomer, purified hyaluronate-binding region, or purified hyaluronate (macromolecular or oligomers) were present in the link protein samples. These findings are interpreted as showing different states of conformation or degree of association of the link protein with other components of aggregate in solution. In separate experiments, a 2-4-fold increase in the apparent antigenicity of purified hyaluronate-binding region was observed when hyaluronate molecules with at least 20 disaccharides were present in the samples. Co-incubation of the hyaluronate-binding region or proteoglycan monomer with either purified link protein or with smaller hyaluronate oligomers did not change its antigenicity in the assay. However, when hyaluronate oligomers with 8 disaccharides were included in a mixture of macromolecular hyaluronate with hyaluronate-binding region, the increase in apparent antigenicity was blocked. The results illustrate the inherent difficulties in using the enzyme-linked immunosorbent assay for the quantitation of link protein or proteoglycan monomers in samples where these macromolecules can associate with themselves or other components of proteoglycan aggregates.
An analysis of algorithms for the Dutch National Flag Problem (1978)

Solutions to the Dutch National Flag Problem have been given by Dijkstra [1] and Meyer [3]. Dijkstra starts with a simple program and arrives at an improved program by refinement. Both of the algorithms given by Dijkstra are shown to have an expected number of swaps which is 2/3 N + θ(1) and that these values differ at most by 1/3 of a swap and asymptotically by 1/4 of a swap. The algorithm of Meyer is shown to have expected swap complexity 5/9 N .
Applicability of tandem mass spectrometry to the automated comparative sequencing of long-chain oligonucleotides (2004)

An algorithm for the comparative sequencing (COMPAS) of oligonucleotides is shown to be suitable for the sequence verification of nucleic acids ranging in length from a few to 80 nucleotides. The algorithm is based on the matching of a fragment ion spectrum generated by collision-induced dissociation to m/z values predicted from a known reference sequence employing established fragmentation pathways. Prior to mass spectrometric investigation, the oligonucleotides were on-line purified by ion-pair reversed-phase high-performance liquid chromatography using monolithic separation columns. This study evaluated the potential and the limits of COMPAS regarding the length and the charge state of oligonucleotides, the selected collision energy, and the analyzed amount of sample using a quadrupole ion trap mass spectrometer. The results revealed that oligonucleotides could be very reliably re-sequenced up to 60-mers, although the algorithm was successfully used to even verify sequences up to 80-mers. The relative collision energy was typically in the range between 13 and 20%, which allowed in most cases a verification of the reference sequence in a window of at least three consecutive collision energies. To select a proper charge state for fragmentation, a compromise had to be found between high signal intensity and low charge state. Furthermore, by reducing the eluent flow rate during elution of the oligonucleotide, the sequence of a 50-mer was successfully verified from the analysis of 295 fmol of the raw product. COMPAS was proven to be reproducible and was applied to the genotyping of the polymorphic, Y-chromosomal locus M9 contained in a 62-base pair polymerase chain reaction product.