gebhart/patrepeval huggingface dataset:
Photo-patterning of DNA oligonucleotides on silicon surfaces with micron-scale dimensions (2004)

A method is presented for the covalent attachment of oligonucleotides to silicon (100) surfaces patterned with micron-scale features. UV light exposure of hydrogen-terminated silicon (100) coated with alkenes functionalized with N-hydroxysuccinimide ester groups results in Si-C bonded monolayers. The N-hydroxysuccinimide ester surfaces act as a template for the subsequent covalent attachment of DNA oligonucleotides. In order to create patterns of surface attached DNA oligonucleotides with high density, the surface attachment chemistry has been investigated and optimised. Micron-scale patterning of surfaces was achieved by exposure with UV laser light via a mask. DNA oligonucleotide patterns, with feature sizes of several microns, were reliably produced over large areas. The patterned surfaces were characterised with scanning electron microscopy, epifluorescence microscopy and ellipsometry. Hybridisation with fluorescent label- and gold nanoparticle-conjugates of the complementary oligonucleotide is achieved. The methods offer reliable approaches for the creation of micron-scale motifs of DNA on surfaces.
Prenatal diagnosis of genomic disorders and chromosome abnormalities using array-based comparative genomic hybridization. (2007)

Cytogenetic analysis is a crucial tool of prenatal diagnosis. The ability to rapidly detect aneuploidy and identify small structural abnormalities of foetal chromosomes has been greatly improved by the use of molecular cytogenetic technologies. Microarray-based Comparative Genomic Hybridization (aCGH) has been recently employed in postnatal diagnosis of cryptic chromosomal aberrations, but use in prenatal diagnosis is still limited.We set-up a diagnostic protocol which uses aCGH technology on genomic DNA isolated from uncultured chorionic villus sampled at 11-12 week's gestation. We used a commercially targeted microarray (MDTelArray, Technogenetics Srl - Bouty Group, Sesto S. Giovanni, Milan, Italy) constituted by 167 genomic clones corresponding to 34 critical regions frequently involved in microdeletions and microduplications and 126 subtelomeric clones. Array validation has been carried-out via retrospective analysis of DNA isolated from a series of cytogenetically normal chorionic villus samples (CVS) and of DNA isolated from cytogenetically abnormal cultured amniocytes, CVS or peripheral blood. A pilot prospective study was undertaken analyzing 25 CVS obtained from foetuses at risk for chromosomal aberrations. aCGH results both for retrospective and prospective studies were in agreement with data obtained using "classical" cytogenetic analysis, and/or FISH analysis or DNA testing. Although these preliminary data support the usefulness of aCGH in prenatal diagnosis, further prospective studies are required to verify the feasibility of introducing this technique as part of the diagnostic armamentarium for identify affected foetuses.
Enhanced Bioavailability of Acetohexamide by &beta;-Cyclodextrin Complexation (1980)

An inclusion complex of acetohexamide (AHA) with β-cyclodextrin (β-CyD) in the molar ratio of 1 : 2 was prepared, and its permeation behavior through a cellophane membrane, in situ absorption behavior in rabbit small intestinal tract, and in vivo extent of bioavailability in rabbit were examined in comparison with those of AHA alone. The membrane permeation constant and in situ absorption rate of AHA in solution were found to decrease by the addition of β-CyD. However, the lesser permeability and absorptivity of the complex were significantly overcome by an improved solubility of AHA. The inclusion complexation of AHA with β-CyD was also effective in releasing drug from a hydrophobic suppository base such as Witepsol W35. The complex increased highly the levels of plasma concentration and cumulative urinary excretion of AHA and hydroxyhexamide, one of the metabolites of AHA, after oral or rectal administration to rabbits. The increase of bioavailability of AHA by means of the inclusion complexation suggested the possibility of smaller doses and fewer side effects in sulfonylurea therapy.
Immune Globulin for Intravenous Use: Enhancement of in Vitro Opsonophagocytic Activity of Neonatal Serum (1985)

Neonates born with less-than-protective levels of transplacentally derived specific antibody are at risk for the development of disease due to type III, group B Streptococcus (III-GBS). The effect of immune serum globulin modified for intravenous use (MISG) on in vitro opsonophagocytosis of III-GBS was evaluated. Cord blood was obtained from 13 healthy, full-term neonates, and bactericidal activity for III-GBS was measured. Before the addition of MISG, one of three serum specimens with moderate levels of antibody to III-GBS, and eight of 10 specimens with low antibody levels demonstrated no bactericidal activity. The mean bactericidal index increased from 27.1% before the addition of MISG to 96.5% with MISG added in a volume equal to that of serum. The effect of MISG on opsonophagocytosis decreased with its dilution in buffer, and no effect was shown at dilutions greater than or equal to 1:4. Thus, MISG can substantially increase in vitro opsonophagocytosis of III-GBS in sera from newborns.
An Integrated Tool to Study MHC Region: Accurate SNV Detection and HLA Genes Typing in Human MHC Region Using Targeted High-Throughput Sequencing (2013)

The major histocompatibility complex (MHC) is one of the most variable and gene-dense regions of the human genome. Most studies of the MHC, and associated regions, focus on minor variants and HLA typing, many of which have been demonstrated to be associated with human disease susceptibility and metabolic pathways. However, the detection of variants in the MHC region, and diagnostic HLA typing, still lacks a coherent, standardized, cost effective and high coverage protocol of clinical quality and reliability. In this paper, we presented such a method for the accurate detection of minor variants and HLA types in the human MHC region, using high-throughput, high-coverage sequencing of target regions. A probe set was designed to template upon the 8 annotated human MHC haplotypes, and to encompass the 5 megabases (Mb) of the extended MHC region. We deployed our probes upon three, genetically diverse human samples for probe set evaluation, and sequencing data show that ∼97% of the MHC region, and over 99% of the genes in MHC region, are covered with sufficient depth and good evenness. 98% of genotypes called by this capture sequencing prove consistent with established HapMap genotypes. We have concurrently developed a one-step pipeline for calling any HLA type referenced in the IMGT/HLA database from this target capture sequencing data, which shows over 96% typing accuracy when deployed at 4 digital resolution. This cost-effective and highly accurate approach for variant detection and HLA typing in the MHC region may lend further insight into immune-mediated diseases studies, and may find clinical utility in transplantation medicine research. This one-step pipeline is released for general evaluation and use by the scientific community.
The Abundance of <i>atp</i> Gene Transcript and of the Membrane F <sub>1</sub> F <sub>0</sub> -ATPase as a Function of the Growth pH of Alkaliphilic <i>Bacillus firmus</i> OF4 (1994)

Molecular biological and biochemical studies of the F(1)F(0)-ATP synthase of alkaliphilic Bacillus firmus OF4 show that the enzyme used at pH 7.5 and pH 10.5 is a unique product of the atp operon, expressed at the same levels and yielding an enzyme with the same subunit properties and c-subunit/holoenzyme stoichiometry.
El autonomismo en el sistema de partidos en Puerto Rico: Inercia institucional e ideología hegemónica (2008)

La subordinación política en Puerto Rico parece constatar cierta "dependencia del rumbo", una suerte de inercia que evidencia la importancia de las instituciones en la orientación de las políticas a lo largo del tiempo. Pero ¿Cómo surgen estas instituciones? y ¿Por qué su continuidad? Una mirada al período formativo del sistema de partidos en Puerto Rico permite advertir que éste quedó envuelto en la maraña de la dinámica metropolitana (española primero y estadounidense después) convirtiéndose en un mero instrumento legitimador de la dependencia. El autonomismo, como ideología hegemónica, es resultado de la interacción de fuerzas e individuos mediatizados por las instituciones que han limitado el establecimiento de nuevos patrones políticos y cuya continuidad ha desembocado en el actual equilibrio estático. DOI: http://dx.doi.org/10.22518/16578953.752
Predicting Performance of Direct Acquisition for the M-Code Signal (2000)

This paper describes a matched filter acquisition algorithm referred to as the sideband correlation receiver. This algorithm provides an efficient approach for initial acquisition of the time of arrival (TOA) of the new military M code signal for GPS. A flowchart of the algorithm is given and analytical expressions are obtained for the probability of successful acquisition and mean time to acquire the signal. The results are illustrated for a number of cases of interest and verified by simulation.
Two-photon deep tissue ex vivo imaging of mouse dermal and subcutaneous structures (1998)

The non-invasive determination of deep tissue three dimensional structure and biochemistry is the ultimate goal of optical biopsy. Two-photon microscopy has been shown to be a particularly promising approach. The use of infrared radiation in two-photon microscopy is critical for deep tissue imaging since tissue absorption and scattering coefficients for infrared light are much lower than for shorter wavelengths. Equally important, tissue photodamage is localized to the focal region where fluorescence excitation occurs. This report demonstrates that, by means of high resolution two-photon microscopy, skin and subcutaneous tissue structures can be imaged utilizing their endogenous fluorescence. From a freshly prepared tissue punch of a mouse ear, we were able to 3D resolve both the living and cornified keratinocytes in the epidermis, the collagen/elastin fibers in the dermal layer and the cartilage in the subcutaneous layer. The ability to non-invasively acquire 3D structures of these tissue components may find application in areas such as non-invasive diagnosis of skin cancer and the study of wound healing processes.
Materials for reflective multilayer coatings for EUV wavelengths (1998)

By operating at wavelength near 10-20 nm, EUV lithography can allow for imaging below 100 nm with limited diffractive losses. The reflective optics involved in such systems require multilayer coatings with stringent demands on throughput, uniformity, and stability. The performance of such multilayers is dependent on the optical properties leading to multilayer stacks requiring up to 40 layer pairs. An exhaustive study of potential material combinations has been performed. Detailed results from the investigation of candidate EUV reflective multilayers is presented. Beryllium and silicon are unique in the 10 to 20 nm wavelength range as materials with high index values and suitably low absorption. The best performing coatings within this range are therefore combinations of these two materials with low absorbing low index films, including many refractory metals. For each multilayer coating type investigated, the wavelength of maximum reflectivity has been optimized, and stress, thickness variation, scattering, and interfacial layer formation effects have been characterized.
Measurement of Differential Phasor Diagram of Multilevel DPSK Signals by Using an Adjustment-Free Delay Interferometer Composed of a 3$\,\times\,$3 Optical Coupler (2009)

We develop an adjustment-free differential-phase demodulator based on a delay-interferometer (DI) made of a 3 times 3 optical coupler, which is used as a 120-degree optical hybrid, and demonstrate the possibility of using it as a phasor monitor for the multilevel differential phase-shift keyed (DxPSK) signal. The key features of the proposed demodulator are twofold: (a) in-phase and quadrature (I-Q) components and the phasor diagram can be obtained only by using a single DI, and (b) the phase delay of the DI can be derived from the output power of the DI without the knowledge of the signal under test. These features enable us to demodulate the I-Q components of DxPSK signals without any adjustments. We formulate a theoretical model for deriving the differential phasor from the output signals of the 3 times 3 coupler regardless of unbalances in the phase retardations and the splitting ratios of the 3 times 3 coupler. Thus, the discrepancy from the ideal 120-degree optical hybrid is not a problem, and hence the requirements of the 3 times 3 couplers are greatly relaxed. For a demonstration, we implement the proposed demodulator by using a fiber Michelson interferometer with Faraday rotator mirrors and use it as a differential phasor monitor capable of the plug-and-play (wavelength- and polarization-independent) operation. We show that this phasor monitor can be used for diagnosis of differential phase-shift keyed (DPSK) and differential quadrature phase-shift keyed (DQPSK) transmitters by identifying the sources of impairments from the measured constellation diagram and phasor trajectories. The proposed phasor monitor can also be used for monitoring the optical signal-to-noise ratio (OSNR) of DPSK signal.
Phospholipid Oxygen Microbubbles for Image-Guided Therapy (2020)

In recent work, oxygen microbubbles (OMB) have been shown to oxygenate hypoxic tumors, increase radio-sensitivity and improve tumor control by radiation therapy. Compared to intra-tumoral injection, intravenous delivery of adjuvant agents such as OMBs for radiotherapy offers an attractive means of achieving true theranostic function in a minimally invasive manner via contrast-enhanced ultrasound (CEUS), while reducing the risk of injury, infection or displacing tumor cells. However, short intravascular circulation times with conventional DSPC-lipid OMBs may lead to premature off-target dissolution of OMBs with an associated reduction in tumoral oxygen delivery. Prior work on microbubble stability and gas exchange suggests that increasing phospholipid acyl-chain length of the encapsulating shell and OMB size may increase circulation persistence, delivery and dissolved oxygen content. In the following studies, we investigate the effect of two phospholipid shell compositions, DSPC (C18:0) and DBPC (C22:0), as well as three size distributions (0.5-2 µm, 2-10 µm and polydisperse) on OMB circulation persistence utilizing CEUS in the kidneys of live C57B1/6 male and female mice, six weeks of age. DBPC OMB formulations demonstrated increased circulation half-lives versus DSPC formulations (2.4 ± 1.0 <i>vs.</i> 0.6 ± 0.5 s, p<0.01 for 2-10 µm), as well as an increased maximum intensity by over tenfold (p<0.01). Size-dependent effects remained consistent across both formulations with larger 2-10 µm microbubbles demonstrating significantly increased half-lives (2.4 ± 1.0 <i>vs</i>. 0.3 ± 0.2 s, p < 0.01) compared to smaller 0.5-2 µm formulations of DBPC. These studies indicate that DBPC 2-10 µm OMBs may be improved adjuvant agents for radiotherapy with significant potential for CEUS interrogation.
Management of Virtual Memory Systems under High Performance PCM-based Swap Devices (2015)

As high performance NVM storage such as PCM or STT-RAM emerges, legacy software layers optimized for HDDs should be revisited. This paper explores the performance of a system that uses PCM as the swap device of virtual memory and discusses how this system can be managed efficiently. Specifically, we explore the challenges and implications of using PCM swap devices with a broad range of experiments in comparison with traditional HDD swap devices. For PCM swap devices, we evaluate the performance by attaching PCM on DIMM slots, thereby eliminating the software stack overhead of block I/O and the context switch time. To assess the potential benefit of PCM swap devices, we change various configurations and perform experiments to quantify the effects of memory management mechanisms and parameters such as page size, read-ahead options, page replacement algorithms, and total memory capacity. The results show that reducing the page size and turning off the read-ahead option improve the performance of PCM-based swap systems where the page fault handling time is sufficiently small. We also show that the performance is not degraded even with a small DRAM memory under a PCM swap device, this leads to the reduction of DRAM's energy consumption significantly compared to HDD-based swap systems. We anticipate that our results will provide directions in system software development in presence of ever faster swap devices.
SCR-LDMOS. A novel LDMOS device with ESD robustness (2002)

A novel lateral power device structure with a very high degree of ESD (electrostatic discharge) robustness is presented. This device called the SCR-LDMOS is a modification of the lateral LDMOSFET with good on state and blocking characteristics.
Workload propagation - overload in bursty servers (2005)

Internet servers are developing into complex but central components in the information infrastructure and are accessed by an ever-increasing and diversified user population. As such, they are susceptible to unpredicted and transient overloads, making highly available, yet cost-effective service a critical challenge. System responsiveness during overload periods is at least as important as system behavior under average, steady state load. Using measurements from a 3-tier e-commerce server, we show how normal and overload conditions propagate through the system hierarchy, i. e., from the front-end server to the back-end database, focusing on CPU, memory, and I/O performance. We find that overload conditions at lower system levels occur not only when the number of users in the system increases, but also during rapid changes in the nature of the work requested by the current users. These observations advocate the development of system mechanisms at the lower levels that can detect overload and self-adapt their configuration parameters in order to ensure high service availability and graceful performance degradation. We illustrate the effectiveness of a scheduling mechanism at the disk and provide a proof of concept that such self-adaptive scheduling mechanisms at the lower levels are a step toward faster system recovery under conditions of transient overload, and can thus complement admission control at the front end.
Cardiovascular disease: potential impact of stem cell therapy (2003)

Atherosclerotic vascular disease becomes a clinical problem when there is sufficient atherosclerotic plaque burden and/or endothelial dysfunction to cause a limitation of nutrient blood flow to tissues. However, once myocardial infarction has occurred, there is little, if any, way to stimulate the growth of new blood vessels or cardiac muscle to replace that which has been lost. The potential use of hematopoietic stem cells (HSCs) to treat cardiovascular disease has recently been suggested from preclinical and clinical studies. HSCs are precursors of all the blood cells, but they may also give rise to cells of the vascular system, endothelial cells in the form of endothelial progenitor cells (EPCs). Clinical trials have been conducted in patients with either acute myocardial infarction or limb ischemia to determine the initial effectiveness and safety of this treatment approach. These studies demonstrated the potential clinical effectiveness of this stem cell approach to the treatment of patients with acute myocardial ischemia and limb ischemia. Today, more preclinical studies are planned to elucidate the mechanism by which transplanted stem cells can home and differentiate into these endothelial cells and cardiac muscle cells. At the same time, new clinical trials are planned to evaluate both chronic, stable as well as acute myocardial ischemia and limb ischemia with CD34+ and CD133+ stem cells, as well as with further selected EPCs and mesenchymal stem cells.
Current-mode implementation of discrete-time cellular neural networks using the pulse width modulation technique (2002)

In this paper, a novel implementation of discrete-time cellular neural networks (DT-CNNs) using the recently introduced current-mode pulse width modulation (CM-PWM) technique is presented. The CM-PWM technique can efficiently realize the delayed weighted summation required for DT-CNNs. All the weight currents are modulated to PWM pulses. Because of the translational invariance of a DT-CNN, a small number of weights (digital-like pulses) can be shared in the bus lines among all the cells. By changing the weight currents, a programmable DT-CNN can easily be achieved. This implementation of the DT-CNN results in small size of the whole system. This paper gives two application examples (a connected component detector and a hole filler).
Top-down Protein Sequencing and MS3 on a Hybrid Linear Quadrupole Ion Trap-Orbitrap Mass Spectrometer (2006)

Top-down proteomics, the analysis of intact proteins (instead of first digesting them to peptides), has the potential to become a powerful tool for mass spectrometric protein characterization. Requirements for extremely high mass resolution, accuracy, and ability to efficiently fragment large ions have often limited top-down analyses to custom built FT-ICR mass analyzers. Here we explore the hybrid linear ion trap (LTQ)-Orbitrap, a novel, high performance, and compact mass spectrometric analyzer, for top-down proteomics. Protein standards from 10 to 25 kDa were electrosprayed into the instrument using a nanoelectrospray chip. Resolving power of 60,000 was ample for isotope resolution of all protein charge states. We achieved absolute mass accuracies for intact proteins between 0.92 and 2.8 ppm using the "lock mass" mode of operation. Fifty femtomole of cytochrome c applied to the chip resulted in spectra with excellent signal-to-noise ratio and only low attomole sample consumption. Different protein charge states were dissociated in the LTQ, and the sensitivity of the orbitrap allowed routine, high resolution, and high mass accuracy fragment detection. This resulted in unambiguous charge state determination of fragment ions and identification of unmodified and modified proteins by database searching. Protein fragments were further isolated and fragmented in the LTQ followed by analysis of MS(3) fragments in the orbitrap, localizing modifications to part of the sequence and helping to identify the protein with these small peptide-like fragments. Given the ready availability and ease of operation of the LTQ-Orbitrap, it may have significant impact on top-down proteomics.
Comparative analysis of crystal structures of E,E-configured para-substituted acetophenone azines with halogen, oxygen, nitrogen and carbon functional groups (1995)

A comparative analysis is presented of the solid state structures of fifteen E,E-configured para-substituted acetophenone azines with halogen [–F (1a), –Cl (1b), –Br (1c)], oxygen [–OMe (2, 5 and 6), –OH (3), –OCOEt (3)], nitrogen [–NMe2(7), –NH2(8), –NHCOMe (9), –NO2(10)] and carbon [–Me (11), –CO2Et (12), –CN (13)] functional groups. The X-ray crystal structures of 2, 7–10 and 12 were determined and are reported. The data allow us systematically to examine the structural effects of the nature of the para-substituent in a series of closely related azines and to assess and distinguish between intrinsic electronic and steric effects and consequences of crystal packing. Stereoelectronic effects of the para-substituents are discussed in terms of contributions of various resonance forms and structural parameters are identified that may serve as indicators of their importance. Analyses are presented of conformational properties and of crucial bond lengths of the azines 1–13. The molecules also are analysed as para-disubstituted benzenes X–C6H4-Az and compared with X–C6H4-Z systems qualitatively to rank the electron-withdrawing ability of the Az group.