gebhart/patrepeval huggingface dataset:
Significant association of the neurexin-1 gene (NRXN1) with nicotine dependence in European- and African-American smokers (2008)

The neurexin-1 gene (NRXN1) has been shown to play a fundamental role in synaptogenesis and synaptic maintenance, as well as Ca(2+) channel and NMDA receptor recruitment. A recent study reported that NRXN1 is associated with nicotine dependence (ND); this, together with the intriguing physiological functions of the gene, motivated us to investigate the involvement of NRXN1 with ND in independent samples. In this study, we analyzed 21 single nucleotide polymorphisms (SNPs) within NRXN1 for association with ND, which was assessed by smoking quantity (SQ), the heaviness of smoking index (HSI) and the Fagerström test for ND (FTND). Individual SNP and haplotype association tests were carried out in a sample consisting of 2037 individuals from 602 nuclear families of African-American (AA) or European-American (EA) origin. Individual SNP analysis revealed significant associations of rs2193225 with SQ, HSI and FTND (P = 0.00014-0.0010) in the EA sample and with SQ (P = 0.0019) in the pooled sample under the dominant model and rs6721498 with SQ, HSI and FTND in the AA (P = 0.000090-0.0000086) and pooled (P = 0.0010-0.00099) samples under the additive model, following correction for multiple testing. Haplotype analysis revealed six major haplotypes in the AA sample (minimum P-value = 0.000079), one major haplotype in the EA sample (P = 0.0062) and five major haplotypes in the pooled sample (minimum P-value = 0.00083), which showed significant association with all three ND measures; all of these contained one specific allele from one of the two aforementioned SNPs. Based on our findings that NRXN1 has significant association with ND in two independent samples, recent findings that NRXN1 plays an important role in synaptic development, and the previous report of association, we conclude that this gene represents a strong candidate for involvement in the etiology of ND.
Exploiting chromatic aberration to spectrally encode depth in reflectance confocal microscopy (2011)

We present chromatic confocal microscopy as a technique to axially scan the sample by spectrally encoding depth information to avoid mechanical scanning of the lens or sample. We have achieved an 800 &#956;m focal shift over a range of 680-1080 nm using a hyperchromat lens as the imaging lens. A more complex system that incorporates a water immersion objective to improve axial resolution was built and tested. We determined that increasing objective magnification decreases chromatic shift while improving axial resolution. Furthermore, collimating after the hyperchromat at longer wavelengths yields an increase in focal shift.
Fundamentals of Studying Orthognathic Surgery and Speech (2012)

Background Maxillary hypoplasia refers to a deficiency in the growth of the maxilla commonly seen in patients with a repaired cleft palate.Those who develop maxillary hypoplasia can be offered a repositioning of the maxilla to a functional and esthetic position.Velopharyngeal dysfunction is one of the important problems affecting speech after maxillary advancement surgery.The aim of this study was to investigate the impact of maxillary advancement on repaired cleft palate patients without preoperative deterioration in speech compared with non-cleft palate patients.Methods Eighteen patients underwent Le Fort I osteotomy between 2005 and 2011.One patient was excluded due to preoperative deterioration in speech.Eight repaired cleft palate patients belonged to group A, and 9 non-cleft palate patients belonged to group B. Speech assessments were performed preoperatively and postoperatively by using a speech screening protocol that consisted of a list of single words designed by Ok-Ran Jung.Wilcoxon signed rank test was used to determine if there were significant differences between the preoperative and postoperative outcomes in each group A and B. And Mann-Whitney U test was used to determine if there were significant differences in the change of score between groups A and B. Results No patients had any noticeable change in speech production on perceptual assessment after maxillary advancement in our study.Furthermore, there were no significant differences between groups A and B. Conclusions Repaired cleft palate patients without preoperative velopharyngeal dysfunction would not have greater risk of deterioration of velopharyngeal function after maxillary advancement compared to non-cleft palate patients.
A comprehensive mathematical model of microscopic dose deposition in photodynamic therapy (2006)

We have developed a comprehensive theoretical model for rigorously describing the spatial and temporal dynamics of oxygen (3O2) consumption and transport and microscopic photodynamic dose deposition during photodynamic therapy (PDT) in vivo. Previously published models have been improved by considering perfused vessels as a time-dependent 3O2 source and linking the 3O2 concentration in the vessel to that within the tissue through the Hill equation. The time-dependent photochemical 3O2 consumption rate incorporates sensitizer photobleaching effects and an experimentally determined initially nonuniform photosensitizer distribution. The axial transport of 3O2 is provided for in the capillaries and in the surrounding tissue. A self-sensitized singlet oxygen (1O2)-mediated bleaching mechanism and the measured, initially nonuniform distribution of mesotetrahydroxyphenyl chlorin at 3 h after intravascular administration were used to demonstrate the capabilities of the model. Time-evolved distributions of 3O2 concentration were obtained by numerically solving two-dimensional diffusion-with-reaction equations both in the capillary and the adjacent tissue. Using experimentally established physiological and photophysical parameters, the mathematical model allows computation of the dynamic variation of hemoglobin-3O2 saturation (SO2) within the vessels, irreversible sensitizer degradation due to photobleaching, and the microscopic distributions of 3O2, sensitizer concentration, and 1O2 dose deposition under various irradiation conditions. The simulations reveal severe axial gradients in 3O2 and in photodynamic dose deposition in response to a wide range of clinically relevant treatment parameters. Thus, unlike former Krogh cylinder-based models, which assume a constant 3O2 concentration at the vessel, this new model identifies conditions in which 3O2 depletion and minimal deposition of reacting 1O2 exist near the end of axial segments of vessels and shows that treatment-limiting 3O2 depletion is induced at fluence rates as low as 10 mW cm(-2). These calculations also demonstrate that intercapillary heterogeneity of photosensitizer contributes significantly to the distribution of photodynamic dose. This more rigorous mathematical model enables comparison with experimentally observable, volume-averaged quantities such as SO2 and the loss of sensitizer fluorescence through bleaching that have not been included in previous analyses. Further, it establishes some of the intrinsic limitations of such measurements. Specifically, our simulations demonstrate that tissue measurements of SO2 and of photobleaching are necessarily insensitive to microscopic heterogeneity of photodynamic dose deposition and are sensitive to intercapillary spacing. Because prior knowledge of intercapillary distances in tumors is generally unavailable, these measurements must be interpreted with caution. We anticipate that this model will make useful dosimetry predictions that should inform optimal treatment conditions and improve current clinical protocols.
Mutagenic activity of the 4,5‐ and 9,10‐dihydrodiols of benzo[J]fluoranthene and their syn‐ and anti‐dihydrodiol epoxides in salmonella typhimurium (1993)

The objective of this study was to determine the relative mutagenic activities of the major dihydrodiol metabolites of benzo[j]fluoranthene (B[j]F) and their corresponding syn- and anti-dihydrodiol epoxides. Salmonella typhimurium tester strains TA97a, TA98, and TA100 were used to evaluate the mutagenic potencies of the parent hydrocarbon and these suspect proximate and ultimate mutagenic metabolites. B[j]F and the trans-dihydrodiol metabolites were active only in the presence of an external metabolic activation system (S9) with the exception of the B[j]F-4,5-diol, which was weakly active in TA98 and TA100 in the absence of S9. The B[j]F-4,5-diol was more mutagenic than the B[j]F-9,10-diol in tester strains TA98 and TA100, whereas the opposite effect was observed in TA97a. In the absence of S9, the anti-B[j]F-4,5-diol epoxide was more mutagenic than the syn-B[j]F-4,5-diol epoxide and the syn- and anti-B[j]F-9,10-diol epoxides in tester strains TA97a and TA100. The exceptional mutagenic potency of the anti-B[j]F-4,5-diol epoxide in TA100 resembles that observed by epoxides located within a fjord, or by the anti-diol epoxides of bay region methylated polycyclic aromatic hydrocarbons. In contrast, the mutagenicity of the pseudo bay region dihydrodiol epoxides arising from the B[j]F-9,10-diol more closely resembles that observed with the classical bay region dihydrodiol epoxides of chrysene. In summary, both dihydrodiol metabolites of B[j]F are mutagenic in S. typhimurium, and the relative potency varies among the tester strains. The highest mutagenic response was achieved in tester strain TA100, which detects base-pair substitutions. The most potent direct-acting dihydrodiol epoxide in this tester strain was the anti-B[j]F-4,5-diol epoxide, which agrees with the results of mouse skin painting studies that indicate that the B[j]F-4,5-diol is more tumorigenic that the parent hydrocarbon or the B[j]F-9,10-diol. A covalent DNA adduct formed between the anti-B[j]F-4,5-diol epoxide and deoxyguanosine was the major species of DNA adduct formed in S. typhimurium. This adduct corresponds to the major DNA adduct formed in mouse skin following application B[j]F.
Physics-based graphical keyboard design (2000)

Built upon the Fitts' law and digraph model developed by MacKenzie and colleague [2, 3], we introduce two physics-based methods to graphical keyboard design. One method uses physical simulation of digraph springs and the other uses the Metropolis method. Both methods produced keyboard layouts comparable to or better than existing best designs by manual trial and error methods. We also corrected an error in previous predictions and concluded that the upper bound performance of a graphical keyboard should be at 40 to 44 wpm. The effect of varying key size and the use of multiple space keys are discussed.
Asymptotic Behavior of Sequence Models (2019)

In this paper we study the limiting dynamics of a sequential process that generalizes Polya's urn. This process has been studied also in the context of language generation, discrete choice, repeat consumption, and models for the web graph. The process we study generates future items by copying from past items. It is parameterized by a sequence of weights describing how much to prefer copying from recent versus more distant locations. We show that, if the weight sequence follows a power law with exponent $\alpha \in [0,1)$, then the sequences generated by the model tend toward a limiting behavior in which the eventual frequency of each token in the alphabet attains a limit. Moreover, in the case $\alpha &gt; 2$, we show that the sequence converges to a token being chosen infinitely often, and each other token being chosen only constantly many times.
Multi-spectral scanning fiber endoscope with concurrent autofluorescence mitigation for enhanced target-to-background ratio imaging (2014)

We developed a multispectral fluorescence-reflectance scanning fiber endoscope (SFE) for wide-field molecular imaging of fluorescence-labeled molecular probes. Concurrent multi-channels imaging with the wide-field SFE also allows for real-time mitigation of background autofluorescence (AF) signal, especially when the FDA approved fluorescein is used as the target fluorophore. In the current study, we demonstrated a real-time AF mitigation algorithm on a tissue phantom which featured molecular probe targeted cells of high grade dysplasia on a substrate containing AF species. The targetto- background ratio was enhanced by over an order of magnitude when applying the real-time AF mitigation algorithm. By minimizing the background signal, multispectral fluorescence imaging can provide sufficient image contrast and quantitative target information for detecting small pre-cancerous lesions in vivo.
Styrene–Butadiene Copolymers (2001)

Abstract Styrene–butadiene (SB) copolymers are the largest volume, and hence industrially most significant, copolymers currently in use. They are typically divided into three classes. Styrene–butadiene rubbers (SBRs) are mostly used for tire applications. SBRs are manufactured both by emulsion process and by solution process, utilizing anionic polymerization. High impact polystyrene (HIPS), the largest by volume of the three, is a thermoplastic resin and is used in food packaging, consumer electronics, and appliances. HIPS is manufactured by grafting of the polybutadiene rubber in solution during the production of polystyrene. SB block copolymers are utilized in the manufacture of transparent, impact‐resistant polystyrene as well as impact modification in other areas. SB block copolymers are exclusively manufactured by anionic polymerization of styrene and butadiene.
Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins bycorrelationplus (2021)

Extracting dynamical pairwise correlations and identifying key residues from large molecular dynamics trajectories or normal-mode analysis of coarse-grained models are important for explaining various processes like ligand binding, mutational effects, and long-distance interactions. Efficient and flexible tools to perform this task can provide new insights about residues involved in allosteric regulation and protein function. In addition, combining and comparing dynamical coupling information with sequence coevolution data can help to understand better protein function. To this aim, we developed a Python package called <i>correlationplus</i> to calculate, visualize, and analyze pairwise correlations. In this way, the package aids to identify key residues and interactions in proteins. The source code of <i>correlationplus</i> is available under LGPL version 3 at https://github.com/tekpinar/correlationplus. The current version of the package (0.2.0) can be installed with common installation methods like conda or pip in addition to source code installation. Moreover, docker images are also available for usage of the code without installation.
The black esophagus. (1995)

A dark-pigmented (black) esophagus is a rare observation during the course of upper endoscopy. The differential diagnosis of a black esophagus includes acute necrotizing esophagitis, exogenous dye ingestion, lye ingestion, malignant melanoma, melanosis, and pseudomelanosis esophagi. Many of these conditions are suggested by the history and associated endoscopic findings. In most patients, a biopsy is needed to establish a definitive diagnosis and explanation for the black-appearing esophagus. We describe a patient with a black esophagus encountered during routine endoscopy. The clinical, endoscopic, and histopathological features of this unusual finding are presented, along with a review of the literature.
An optimal quasisuperlattice design to further improve thermal stability of tantalum nitride diffusion barriers (2000)

X-ray diffraction and transmission electron microscopy, along with electrical and film stress measurements, were used to evaluate the effectiveness of 40-nm-thick amorphous Ta2N and microcrystalline TaN diffusion barriers, both single and multilayered, against Cu penetration. Failure of the single-layered Ta2N diffusion barrier upon annealing is initialized by crystallization/grain growth, mainly helped by frozen-in compressive stress (3–4 GPa) to transform itself into a columnar structure with a comparable grain size to the thickness of the barrier. However, when subjected to annealing, the Ta2N/TaN alternately layered diffusion barrier with an optimum bilayer thickness (10 nm) remains almost stress-free (0–0.7 GPa) and transforms itself into an equiaxed structure with grain sizes of only ⩽3 nm. Such quasisuperlattice films can present lengthening and complex grained structures to effectively block Cu diffusion, thus acting as much more effective barriers than Ta2N (and TaN) single-layered films.
Runtime On-Stack Parallelization of Dependence-Free For-Loops in Binary Programs (2019)

With the multicore trend, the need for automatic parallelization is more pronounced, especially for legacy and proprietary code where no source code is available and/or the code is already running and restarting is not an option. In this paper, we engineer a mechanism for transforming at runtime a frequent for-loop with no data dependencies in a binary program into a parallel loop, using on-stack replacement. With our mechanism, there is no need for source code, debugging information or restarting the program. Also, the mechanism needs no static instrumentation or information. The mechanism is implemented using the Padrone binary modification system and pthreads, where the remaining iterations of the loop are executed in parallel. The mechanism keeps the running program state by extracting the targeted loop into a separate function and copying the current stack frame into the corresponding frames of the created threads. Initial study is conducted on a set of kernels from the Polybench workload. Experimental results show from 2× to 3.5× speedup from sequential to parallelized code on four cores, which is similar to source code level parallelization.
Optical phase conjugation in phase-modulated transmission systems: experimental comparison of different nonlinearity-compensation methods (2010)

We experimentally compare the effectiveness of three different optical-phase-conjugation-based nonlinearity-compensation strategies on a transmission system employing phase-modulated signals, and hence affected by the Gordon-Mollenauer effect. We demonstrate that it is possible to obtain significant nonlinearity compensation, but that no improvement is obtained using configurations specifically aimed at the compensation of the nonlinear phase noise.
Assessment of Gaussian-2 and density functional theories for the computation of enthalpies of formation (1997)

A set of 148 molecules having well-established enthalpies of formation at 298 K is presented. This set, referred to as the G2 neutral test set, includes the 55 molecules whose atomization energies were used to test Gaussian-2 (G2) theory [J. Chem. Phys. 94, 7221 (1991)] and 93 new molecules. The G2 test set includes 29 radicals, 35 nonhydrogen systems, 22 hydrocarbons, 47 substituted hydrocarbons, and 15 inorganic hydrides. It is hoped that this new test set will provide a means for assessing and improving new theoretical models. From an assessment of G2 and density functional theories (DFT) on this test set it is found that G2 theory is the most reliable method both in terms of average absolute deviation (1.58 kcal/mol) and maximum deviation (8.2 kcal/mol). The largest deviations between experiment and G2 theory occur for molecules having multiple halogens. Inclusion of spin–orbit effects reduces the average absolute deviation to 1.47 kcal/mol and significantly improves the results for the chlorine substituted molecules, but little overall improvement is seen for the fluorine substituted molecules. Of the two modified versions of G2 theory examined in this study, G2(MP2,SVP) theory (average absolute deviation=1.93 kcal/mol) performs better than G2(MP2) theory (2.04 kcal/mol). The G2(MP2,SVP) theory is found to perform very well for hydrocarbons, radicals, and inorganic hydrides. Of the seven DFT methods investigated, the B3LYP method has the smallest average absolute deviation (3.11 kcal/mol). It also has a significantly larger distribution of error than the G2 methods with a maximum deviation of 20.1 kcal/mol.
Intermodular Communication in Polyketide Synthases:  Comparing the Role of Protein−Protein Interactions to Those in Other Multidomain Proteins (2001)

Although the role of protein-protein interactions in transducing signals within biological systems has been extensively explored, their relevance to the channeling of intermediates in metabolism is not widely appreciated. Polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) are two related families of modular megasynthases that channel covalently bound intermediates from one active site to the next. Recent biochemical studies have highlighted the importance of protein-protein interactions in these chain transfer processes. The information available on this subject is reviewed, and its possible mechanistic implications are placed in context by comparisons with selected well-studied multicomponent protein systems.
Substrate Mapping and Ablation for Ventricular Tachycardia in Patients with Structural Heart Disease: How to Identify Ventricular Tachycardia Substrate (2019)

Catheter ablation for ventricular tachycardia (VT) has been increasingly used over the past two decades in patients with structural heart disease (SHD). In these individuals, a substrate mapping strategy is being more commonly applied to identify targets for VT ablation, which has been shown to be more effective versus targeting mappable VTs alone. There are a number of substrate mapping methods in existence that aim to explore potential VT isthmuses, although their success rates vary. Most of the reported electrogram-based mapping studies have been performed with ablation catheters; meanwhile, the use of multipolar mapping catheters with smaller electrodes and closer interelectrode spacing has emerged, which allows for an assessment of detailed near-field abnormal electrograms at a higher resolution. Another recent advancement has occurred in the use of imaging techniques in VT ablation, particularly in refining the substrate. The goal of this paper is to review the key developments and limitations of current mapping strategies of substrate-based VT ablation and their outcomes. In addition, we briefly summarize the role of cardiac imaging in delineating VT substrate.
High level synthesis: Where are we? A case study on matrix multiplication (2013)

One of the pitfalls of FPGA design is the relatively long implementation time when compared to alternative architectures, such as CPU, GPU or DSP. This time can be greatly reduced however by using tools that can generate hardware systems in the form of a hardware description language (HDL) from high-level languages such as C, C++, or Python. Such implementations can be optimized by applying special directives that focus the high-level synthesis (HLS) effort on particular objectives, such as performance, area, throughput, or power consumption. In this paper we examine the benefits of this approach by comparing the performance and design times of HLS generated systems versus custom systems for matrix multiplication. We investigate matrix multiplication using a standard algorithm, Strassen algorithm, and a sparse algorithm to provide a comprehensive analysis of the capabilities and usability of the Xilinx Vivado HLS tool. In our experience, a hardware-oriented electrical engineering student can achieve up to 61% of the performance of custom designs with 1/3 the effort, thus enabling faster hardware acceleration of many compute-bound algorithms.