gebhart/patrepeval huggingface dataset:
Strings (1998)

Strings are one-dimensional arrays containing characters. In most cases the number of characters a string has will vary, depending on the input. Thus they must be declared with the maximum number of characters that is likely to occur. Typically they are used to store names. They can also be used when numeric values are entered into a program. With this the program reads the value as a string of characters and then converts it into the required numeric format. This allows the program to determine if the user has entered the value in an invalid numeric format, such as with letters.
Phylogenetics of Flowering Plants Based on Combined Analysis of Plastid atpB and rbcL Gene Sequences (2000)

Following (1) the large-scale molecular phylogeny of seed plants based on plastid rbcL gene sequences (published in 1993 by Chase et al., Ann. Missouri Bot. Gard. 80:528-580) and (2) the 18S nuclear phylogeny of flowering plants (published in 1997 by Soltis et al., Ann. Missouri Bot. Gard. 84:1-49), we present a phylogenetic analysis of flowering plants based on a second plastid gene, atpB, analyzed separately and in combination with rbcL sequences for 357 taxa. Despite some discrepancies, the atpB-based phylogenetic trees were highly congruent with those derived from the analysis of rbcL and 18S rDNA, and the combination of atpB and rbcL DNA sequences (comprising approximately 3000 base pairs) produced increased bootstrap support for many major sets of taxa. The angiosperms are divided into two major groups: noneudicots with inaperturate or uniaperturate pollen (monocots plus Laurales, Magnoliales, Piperales, Ceratophyllales, and Amborellaceae-Nymphaeaceae-Illiciaceae) and the eudicots with triaperturate pollen (particularly asterids and rosids). Based on rbcL alone and atpB/rbcL combined, the noneudicots (excluding Ceratophyllum) are monophyletic, whereas in the atpB trees they form a grade. Ceratophyllum is sister to the rest of angiosperms with rbcL alone and in the combined atpB/rbcL analysis, whereas with atpB alone, Amborellaceae, Nymphaeaceae, and Illiciaceae/Schisandraceae form a grade at the base of the angiosperms. The phylogenetic information at each codon position and the different types of substitutions (observed transitions and transversions in the trees vs. pairwise comparisons) were examined; taking into account their respective consistency and retention indices, we demonstrate that third-codon positions and transitions are the most useful characters in these phylogenetic reconstructions. This study further demonstrates that phylogenetic analysis of large matrices is feasible.
Pentoxifylline stimulates human sperm motility both in vitro and after oral therapy. (1991)

Pentoxifylline is a haemorrheologic agent often used in the treatment of peripheral vascular disorders. In this study, we measured sperm motility with a trans-membrane migration method and investigated the effect of this drug in the treatment of male infertility. We found that pentoxifylline increased motility of ejaculated spermatozoa in vitro from both normal and asthenozoospermic samples. After giving pentoxifylline to patients with asthenozoospermia for 3 months, sperm motility significantly increased, but sperm concentration did not increase. From the above results, it can be concluded that pentoxifylline is a useful drug in the treatment of normogonadotropic asthenozoospermia.
The Reflectance Spectrum of Human Skin (1999)

The automated detection of human skin has become an important task for machine vision systems. Prior vision and graphics research on this topic has primarily focused on images acquired with conventional color cameras. Formal spectrographic analyses have largely been undertaken in the medical domain and focus on the detection of pathology. We have constructed a facility capable of producing accurate, dense and repeatable reflectance measurements. The light reflected from the skin is measured using a high resolution, high accuracy spectrograph under precisely calibrated lighting conditions. This paper presents observations from the first body of data gathered at this facility. From the measurements collected thus far, we have observed population-independent factors of skin reflectance. We show how these factors can be exploited in skin recognition. Finally, we provide a biological explanation for the existence of a distinguishing pattern in human skin reflectance. 1 Introductio...
Proteasome Inhibitors: A Novel Tool to Suppress Human Cytomegalovirus Replication and Virus-Induced Immune Modulation (2003)

Recently, we like others, demonstrated that systemic inflammation is the most important mechanism involved in (re)activation of human cytomegalovirus (HCMV) in both immunocompetent patients. By in vitro studies the eukaryotic transcription factor NF-kappaB could be identified as the key mediator of TNF-alpha- and IE1-dependent stimulation of the HCMV IE1/2 enhancer/promoter activity, which is crucial for initiation of viral gene expression during reactivation from latency as well as productive infection. The enzymatic proteasome complex plays a central role in regulating intracellular processes, including the activation of NF-kappaB. As present antiviral strategies target mainly late events in HCMV replication (DNA replication, virus assembly) that do not completely prevent virus mediated immunopathogenesis, we wondered whether proteasome inhibitors might be a novel tool for targeting the interaction between inflammation and HCMV (re)activation. Here, proteasome inhibitors like MG132, PSI, II and III (MG262) have been shown to block both TNF-alpha-associated up-regulation of the HCMV IE1/2 enhancer/promoter in monocytic cells in an in vitro transient transfection system and HCMV replication in permissive embryonal fibroblasts. Importantly, ganciclovir-resistant HCMV strains are sensitive to proteasome inhibitors. The effect of proteasome inhibitors on HCMV replication was found to be specific as replication of other herpes viruses, like HSV-1 and HSV-2, under identical experimental conditions was not influenced. Inhibition of HCMV replication correlated with a delayed and significantly reduced expression of IE proteins, particularly of the IE2 protein, suggesting that MG132 blocks HCMV replication at an immediate early stage of infection. Early and late protein synthesis as shown exemplary for the pp52 (DNA-binding protein) and p68 (structural protein) protein production and viral DNA synthesis were also inhibited. Suppression of HCMV replication could be correlated with an increased cytosolic accumulation of IkappaB as well as a reduced NF-kappaB binding activity in nuclear extracts of MG132-treated cells, which mainly regards NF-kappaB p50. MG132 also reduced the immune modulatory activity of the virus by abrogating virus-induced up-regulation of cellular ICAM-1. These data suggest that short-term therapy with proteasome inhibitors might be an alternative strategy to prevent (re)activation, replication and immune modulatory activity of HCMV in patients with systemic inflammation.
Challenges and Opportunities for UAV-Based Digital Elevation Model Generation for Flood-Risk Management: A Case of Princeville, North Carolina (2018)

Among the different types of natural disasters, floods are the most devastating, widespread, and frequent. Floods account for approximately 30% of the total loss caused by natural disasters. Accurate flood-risk mapping is critical in reducing such damages by correctly predicting the extent of a flood when coupled with rain and stage gage data, supporting emergency-response planning, developing land use plans and regulations with regard to the construction of structures and infrastructures, and providing damage assessment in both spatial and temporal measurements. The reliability and accuracy of such flood assessment maps is dependent on the quality of the digital elevation model (DEM) in flood conditions. This study investigates the quality of an Unmanned Aerial Vehicle (UAV)-based DEM for spatial flood assessment mapping and evaluating the extent of a flood event in Princeville, North Carolina during Hurricane Matthew. The challenges and problems of on-demand DEM production during a flooding event were discussed. An accuracy analysis was performed by comparing the water surface extracted from the UAV-derived DEM with the water surface/stage obtained using the nearby US Geologic Survey (USGS) stream gauge station and LiDAR data.
B-Type Natriuretic Peptide Concentrations Predict the Progression of Nondiabetic Chronic Kidney Disease: The Mild-to-Moderate Kidney Disease Study (2007)

Increased BNP and NT-proBNP concentrations indicate an increased risk for accelerated progression of CKD to ESRD and may prove to be valuable biomarkers for the assessment of prognosis in patients with CKD.
Synthesis and thermal properties of poly(arylene ether ketone)s containing phthalazinone moieties (1999)

A series of novel poly(arylene ether ketone)s were synthesized from the reaction of hydroquinone and 4-(4-hydroxyphenyl)-2,3-phthalazin-1-one with 4,4′-difluorobenzophenone in N-cyclohexylpyrrolidinone containing anhydrous potassium carbonate. The polymers exhibited high glass transition temperatures together with excellent thermooxidative stability. The chain structure of these polymers was studied by means of differential scanning calorimetry (DSC), wide-angle X-ray diffraction techniques (WAXD), and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS). The experimental results indicated that these “as-made” copoly(aryleneketone)s containing hydroquinone moieties exhibited a block chain structure with segments which mainly consisted of hydroquinone and 4,4′-difluorobenzophenone. These chain segments resulted in crystallites in the polymers although they are thermodynamically unstable. The polymers showed thermal properties comparable to commercial PEEK, but the conditions for synthesis are much milder. The glass transition temperatures and solubilities of the copoly(arylene ketone)s tended to increase with increasing phthalazinone moiety content, while the crystallite melting points and crystallinity appeared to decrease. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 1781–1788, 1999
Specific-heat spectroscopy of glycerol and propylene glycol near the glass transition (1986)

We have measured the frequency-dependent specific heat of glycerol and propylene glycol near the glass transition. The measurements, covering a frequency range of five decades, probe the linear response of these supercooled liquids to small perturbations from equilibrium. The specific heat of these two liquids contains a contribution which relaxes increasingly slowly as the temperature is lowered. The relaxation time measured by specific-heat spectroscopy has the same temperature dependence as that measured by other techniques. This suggests that a single mechanism is responsible for all of the observed phenomena associated with the glass transition in these materials.
Beam-quality improvement of a passively Q-switched Nd:YAG laser with a core-doped rod (1999)

We present experimental results that demonstrate the great efficiency of a core-doped Nd:YAG rod (a hexagonal Nd:YAG core surrounded by undoped YAG) in producing high output power and excellent beam quality. An additional improvement in beam quality is clearly observed when the core-doped rod is used in combination with a LiF:F(2)(-) crystal, which acts as a passive Q-switching element. This improvement is quantified by beam-propagation factors as low as M(2) approximately = at a maximum average output power of 9 W. We show that transversally pumped core-doped rods with the addition of LiF:F(2)(-) crystals fulfill the requirements for high-beam-quality, scalable, compact all-solid-state lasers in passively Q-switched operation.
Axial Strain Imaging Using a Local Estimation of the Scaling Factor from RF Ultrasound Signals (2000)

The main signal-processing techniques used in elastography compute strains as the displacement derivative. They perform well for very low deformations, but suffer rapidly from decorrelation noise. Aiming to increase the range of accurate strain measurements, we developed an adaptive method based on the estimation of strains as local scaling factors. Its adaptability makes this method appropriate for computing scaling factors resulting from larger strains or a wide spread of strain variations. First, segments corresponding to the same part of tissue are adaptively selected in the rest and stressed state echo signals. Then, local scaling factors are estimated by iteratively varying their values until reaching the zero of the phase of the complex cross-correlation function. Results from simulation and from experimental data are presented. They show how this adaptive method can track various local deformations and its accuracy for strain up to 7%.
Photo Material Readiness at the Eve of EUVL HVM (2017)

In the last years, the continuous efforts on the development of extreme ultraviolet (EUV) lithography has allowed to push the lithographic performance of the EUV photoresists on the ASML NXE:3300 full field exposure tool and today both chemically amplified (CAR) and metal-oxide (MOR) EUV photoresists have been introduced for patterning imec's 7nm node critical layers. However, the HVM requirement to have a cost-effective high sensitivity photoresist (< 20 mJ/cm2) still remains a big challenge and further efforts are needed to improve the photoresist sensitivity without affecting resolution and patterning quality. In this work, we present the results of the best performing photoresists (both CAR and MOR) at low exposure dose for dense line-space patterns at 32nm pitch, dense contact holes at 36nm pitch and dense pillars at 38nm pitch, reporting the most critical patterning challenges for the investigated structures. Furthermore, we discuss the role of the substrate underneath the EUV photoresist and its impact on the lithographic EUV process setup from both patterning and light-matter interaction standpoint. Finally, we introduce the tone reversal process (TRP) as alternative capability for pillar patterning.
Nonlinear phase correction with an extended statistical algorithm (2005)

This paper presents a new magnetic resonance imaging (MRI) phase correction method. The linear phase correction method using autocorrelation proposed by Ahn and Cho (AC method) is extended to handle nonlinear terms, which are often important for polynomial expansion of phase variation in MRI. The polynomial coefficients are statistically determined from a cascade series of n-pixel-shift rotational differential fields (RDFs). The n-pixel-shift RDF represents local vector rotations of a complex field relative to itself after being shifted by n pixels. We have found that increasing the shift enhances the signal significantly and extends the AC method to handle higher order nonlinear phase error terms. The n-pixel-shift RDF can also be applied to improve other methods such as the weighted least squares phase unwrapping method proposed by Liang. The feasibility of the method has been demonstrated with two-dimensional (2-D) in vivo inversion-recovery MRI data.
Task-oriented grasping with semantic and geometric scene understanding (2017)

We present a task-oriented grasp model, that encodes grasps that are configurationally compatible with a given task. For instance, if the task is to pour liquid from a container, the model encodes grasps that leave the opening of the container unobstructed. The model consists of two independent agents: First, a geometric grasp model that computes, from a depth image, a distribution of 6D grasp poses for which the shape of the gripper matches the shape of the underlying surface. The model relies on a dictionary of geometric object parts annotated with workable gripper poses and preshape parameters. It is learned from experience via kinesthetic teaching. The second agent is a CNN-based semantic model that identifies grasp-suitable regions in a depth image: regions where a grasp will not impede the execution of the task. The semantic model allows us to encode relationships such as “grasp from the handle.” A key element of this work is to use a deep network to integrate contextual task cues, and defer the structured-output problem of gripper pose computation to an explicit (learned) geometric model. Jointly, these two models generate grasps that are mechanically fit, and that grip on the object in a way that enables the intended task.
Iterative RF pulse refinement for magnetic resonance imaging (2002)

Selective RF pulses are needed for many applications in magnetic resonance imaging (MRI). The waveform required to produce a desired excitation profile is, to first-order, its Fourier transform. This approximation is most valid for small tip angles and the quality and accuracy of such excitations decreases with increasing tip angle. Since large-tip-angle excitations are required in most types of imaging, a better synthesis technique is necessary. While a variety of analytical and numerical synthesis techniques based on solution of the Bloch equations are available, these techniques fail to consider the effect of the physical scanner hardware and are often accompanied by computational complexity. We present a technique for selective RF pulse refinement which uses real-time feedback techniques in lieu of a solution to the Bloch equations. Physical experiments are conducted to demonstrate the effectiveness of this algorithm and an extension to pulses of 90 degrees is investigated.
Ultra-low delay lossy audio coding using DPCM and block companded quantization (2013)

Real-time audio transmission requires good quality for a restricted channel capacity and minimum latency. An ultra-low delay audio coding scheme based on differential pulse code modulation (DPCM) and block companded quantization is presented. The prediction filter of the base backward DPCM codec is attained as a FIR filter in lattice structure. The proposed block based audio coding introduces an algorithmic latency below one millisecond and an overhead of less than a half bit per sample. The advantage of the block companded quantization with DPCM is the capability to follow rapid changes in the signal. Therefore, it significantly improves the perceptual audio quality compared to a plain DPCM coding scheme with an adaptive quantizer.
Telomere dysfunction and fusion during the progression of chronic lymphocytic leukemia: evidence for a telomere crisis (2010)

We performed single-molecule telomere length and telomere fusion analysis in patients at different stages of chronic lymphocytic leukemia (CLL). Our work identified the shortest telomeres ever recorded in primary human tissue, reinforcing the concept that there is significant cell division in CLL. Furthermore, we provide direct evidence that critical telomere shortening, dysfunction, and fusion contribute to disease progression. The frequency of short telomeres and fusion events increased with advanced disease, but importantly these were also found in a subset of early-stage patient samples, indicating that these events can precede disease progression. Sequence analysis of fusion events isolated from persons with the shortest telomeres revealed limited numbers of repeats at the breakpoint, subtelomeric deletion, and microhomology. Array-comparative genome hybridization analysis of persons displaying evidence of telomere dysfunction revealed large-scale genomic rearrangements that were concentrated in the telomeric regions; this was not observed in samples with longer telomeres. The telomere dynamics observed in CLL B cells were indistinguishable from that observed in cells undergoing crisis in culture after abrogation of the p53 pathway. Taken together, our data support the concept that telomere erosion and subsequent telomere fusion are critical in the progression of CLL and that this paradigm may extend to other malignancies.
Broadband Amplifier Gain Slope Equalization with a Single Passive Component (2006)

With the new and This article describes the increasing performance of a newly-demand of the developed component Internet and multimedia intended for amplifier gain on the commercial side, slope equalization over fre- and the broadband high quency and temperature data rate communications links on the aerospace and military side, RF and microwave amplifiers are being used in many broadband applications in the 2 to 20 GHz range. Gallium Arsenide (GaAs) monolithic microwave integrated circuit (MMIC) amplifiers lose gain with increasing temperature and increase in gain with decreasing temperature. The ratio of gain change/ºC tends to increase with frequency, making it difficult to compensate the amplifiers in a chain and causing unwanted equalization effects. There are three variables which must be considered when designing GaAs amplifier lineups: gain, gain slope versus frequency, and gain variation versus temperature.
JITSafe: a framework against Just‐in‐time spraying attacks (2013)

A new code‐reuse attack, named Just‐in‐time (JIT) spraying attack, leverages the predictable generated JIT compiled code to launch an attack. It can circumvent the defenses such as data execution prevention and address space layout randomisation built‐in in the modern operation system, which were thought the insurmountable barrier so that the attackers cannot construct the traditional code injection attacks. In this study, the authors describe JITSafe, a framework that can be applied to existing JIT‐based virtual machines (VMs), in the purpose of preventing the attacker from reusing the JIT compiled code to construct the attack. The authors framework narrows the time window of the JIT compiled code in the executable pages, eliminates the immediate value and obfuscates the JIT compiled code. They demonstrate the effectiveness of JITSafe that it can successfully prevent existing JIT spraying attacks with low performance overhead.
<i>GSTP1</i> Promoter Haplotypes Affect DNA Methylation Levels and Promoter Activity in Breast Carcinomas (2008)

The CpG island spanning the transcription start of the glutathione S-transferase P1 becomes methylated in a variety of human cancers including breast cancer. To study the effect of sequence variation on hypermethylation of the GSTP1 promoter, we analyzed the genetic and epigenetic variability in 90 tumors from patients with locally advanced breast cancer. High-resolution quantitative analysis revealed large variability in the DNA methylation levels. Lack of methylation was more often observed in the basal and normal-like estrogen receptor (ER)-negative tumors, and methylated GSTP1 was associated with better overall survival (P = 0.00063). Studies of the genetic variation identified 14 different haplotypes. The distribution of methylation levels of tumors homozygous for the most frequent haplotype was significantly different from other haplotype combinations (P = 0.011), the difference being more pronounced in ER-positive (P = 0.005) and progesterone receptor-positive (P = 0.008) tumors. Regression modeling identified the ER status and haplotype as the main determinants of DNA methylation variability. We identified a putative c-Myb response element (MRE) that was present in one of two minimal promoter haplotypes. In vitro analysis showed that c-Myb binds to the MRE, but binding was weakened by the two polymorphisms. Transient cotransfections in luminal-type and basal-like breast cancer cell lines confirmed cell-specific differential binding of c-Myb to the polymorphic sites, leading to a change in the expression from the GSTP1 promoter in vivo. GSTP1 expression was moderately but significantly (P = 0.01) reduced after siRNA-mediated knockdown of c-Myb. Our results indicate that haplotype structure of a promoter is important for the extent of DNA methylation.