gebhart/patrepeval huggingface dataset:
Control of gene expression and genetic manipulation in the Trypanosomatidae. (2003)

Mechanisms controlling gene expression in trypanosomatids depend on several layers of regulation, with most regulatory pathways acting at a post-transcriptional level. Consequently, these parasites can follow the rapid changes associated with transitions between the insect vector and the mammalian host, with instant reprogramming of genetic expression. Using primarily Trypanosoma brucei as a model, the basic controlling mechanisms have been elucidated and now researchers are beginning to define the cellular factors involved in the transcription, processing and translation of the mRNAs in these parasites. We describe some of the studies made on a subset of genes that are differentially expressed during the life cycles of T. brucei and T. cruzi. It is becoming evident that the regulatory strategies chosen by different species of trypanosomatids are not the same, and therefore, the lessons learned from one species do not necessarily apply to the others. Some of the tools available for genetic manipulation that have been developed along with these studies are also described. Two of them are of particular interest in this postgenomic period: inducible systems to express foreign genes and specific inhibition of gene expression by RNA interference.
Application of modern computer-aided technologies in the production of individual bone graft: A case report (2015)

Application of 3D CBCT images, computer-aided systems and software in manufacturing custom bone grafts represents the most recent method of guided bone regeneration. This method substantially reduces time of recovery and carries minimum risk of postoperative complications, yet the results fully satisfy the requirements of both the patient and the therapist.
High-level semantic optimization of numerical codes (1999)

Article Free Access Share on High-level semantic optimization of numerical codes Authors: Vijay Menon Department of Computer Science, Cornell University, Ithaca, NY Department of Computer Science, Cornell University, Ithaca, NYView Profile , Keshav Pingali Department of Computer Science, Cornell University, Ithaca, NY Department of Computer Science, Cornell University, Ithaca, NYView Profile Authors Info & Claims ICS '99: Proceedings of the 13th international conference on SupercomputingJune 1999 Pages 434–443https://doi.org/10.1145/305138.305230Published:01 May 1999Publication History 42citation389DownloadsMetricsTotal Citations42Total Downloads389Last 12 Months16Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Novel promising way to synthesize non-isocyanate polyurethanes (NIPUs) for innovative coating applications against corrosion protection of metal surfaces (2016)

Polyurethanes (PUs) are one of the most widely used polymeric materials with applications in automotive, as sealants, adhesives, decorative, aircraft topcoats, for coatings or as foams for thermal and/or acoustic insulation. Industrially, PUs are produced by copolymerization between polyols and polyisocyanates. Because of the toxicity issues related to the use of isocyanates, there is a need to develop greener and safer route to produce such polymers. This study reports on the synthesis of new sustainable isocyanates-free PU (NIPU) coatings for aluminium anticorrosion. In a first step, bio- and CO2-sourced cyclic carbonates monomers were synthesized by coupling of epoxydized vegetable oils with CO2 using a new efficient bicomponent organocatalyst. In second step formulations including cyclic carbonates/amines/additives were optimized to produce highly adhesive cross-linked NIPU coatings that show good resistance against solvents and long-term barriers preventing the corrosion of the aluminiumsubstrate
Surface and Interface Studies of ZnO using Reactive Dynamics Simulation (2010)

About 90% of all chemicals are produced with the help of catalysts, substances with the ability to accelerate reactions without being consumed. Metal oxides play a prominent role in catalysis, since they are able to act reversibly in many chemical processes. Zink oxide (ZnO) is used to catalyse a number of industrially important reactions. For many of these reactions water is present as a reactant, product, or byproduct. The surface structure has a significant impact on the catalytic activity. However, currently, no experimental method simultaneously offers the spatial and temporal resolution to directly follow a catalytic process. This thesis explores surface structure dependent dynamical behavior for ZnO surfaces, nanoparticles, and water interfaces, using the computational chemistry method Molecular Dynamics, which enables detailed studies of structural and dynamical processes. Quantum mechanical (QM) calculations have been performed to obtain the energetics of the materials as a function of structure. This data has been used to parametrize reactive force-fields (ReaxFF), since the catalytic processes require both far larger and longer simulations than the capabilities of QM calculations on current computers. The simulations show that when steps are present on the surface, during crystal growth of ZnO, the creation of energetically favorable structures is accelerated. At the ZnO - water interface, structures that favor hydrogen bonding is promoted. At low, monolayer, coverage water adsorbs both molecularly and dissociatively, whereas at high coverage dissociated adsorption is favored. During evaporation from the monolayers, the ratio of dissociated and molecular water is preserved. Surface steps stabilizes the dissociated state as well as increases the rate of dissociation. The dynamical properties of ZnO nanoparticles were explored using Raman measurements and simulation. In both simulation and experiment certain vibrations were suppressed in the nanoparticles, compared to bulk. The simulations show that a narrow surface region lack the bulk-specific vibrations.
Nonsteroidal antiinflammatory drugs and a selective cyclooxygenase 2 inhibitor uncouple mitochondria in intact cells (2003)

NSAIDs and selective COX-2 inhibitors have significant and equally directed effects on cellular energy metabolism. They both uncouple mitochondrial respiration and inhibit substrate oxidation and ATP turnover. However, the topical effect and selective COX-2 inhibition may not be sufficient to cause NSAID-like damage to the GI tract.
Pros and Cons of the Bethe–Salpeter Formalism for Ground-State Energies (2020)

The combination of the many-body Green's function <i>GW</i> approximation and the Bethe-Salpeter equation (BSE) formalism has shown to be a promising alternative to time-dependent density functional theory (TD-DFT) for computing vertical transition energies and oscillator strengths in molecular systems. The BSE formalism can also be employed to compute ground-state correlation energies thanks to the adiabatic-connection fluctuation-dissipation theorem (ACFDT). Here, we study the topology of the ground-state potential energy surfaces (PESs) of several diatomic molecules near their equilibrium bond length. Using comparisons with state-of-art computational approaches (CC3), we show that ACFDT@BSE is surprisingly accurate and can even compete with lower-order coupled cluster methods (CC2 and CCSD) in terms of total energies and equilibrium bond distances for the considered systems. However, we sometimes observe unphysical irregularities on the ground-state PES in relation with difficulties in the identification of a few <i>GW</i> quasiparticle energies.
Damage Detection of Building Structures using AEKF(Adaptive Extended Kalman Filter) (2019)

본 논문에서는 EKF기법의 초기 파라미터 설정에 따른 상태벡터의 발산 문제를 해결하고자 AEKF기법을 제시한다. EKF 기법의 초기 파라미터는 상태벡터 수렴 및 안정성에 중요한 역할을 함으로 초기 파라미터의 적절한 설정은 EKF를 사용함 에 있어 매우 중요하다. AEKF방법은 초기 파라미터인 P행렬을 k스텝마다 업데이트하여 초기 상태벡터의 변화에 민감하게 반응할 수 있으며, 또한 초기 상태벡터와 실제 시스템 모델과의 차이가 크게 발생하여도 적응적으로 P행렬의 값을 조절하여 상태벡터의 수렴을 가능하게 한다. 또한 Q행렬 및 R행렬을 k스텝 업데이트하여 상태벡터의 수렴 안정성을 더욱 확보하였 다. 3DOF시스템을 통해서 AEKF기법의 결과와 EKF, UKF기법을 비교·검증하였다.
Contribution au Contrôle des Humains Virtuels Interactifs (2006)

Les humains virtuels contribuent à l'évolution des techniques d'ingénierie concourante. Ils doivent permettre de tester les réactions de l'humain face à une maquette virtuelle du produit en cours de développement. Nous développons une architecture d'animation qui permet l'interaction des humains virtuels avec la maquette numérique. Après un état de l'art des techniques d'animation des humains virtuels, nous soulevons des problèmes de perte de passivité qui peuvent se poser lors de l'interaction si l'on n'y prend pas garde, et proposons des éléments de réponse. Dans un second temps nous nous attachons à résoudre les contraintes liées à l'évolution de l'humain virtuel dans son environnement. Nous retenons la non pénétration de l'environnement, les limites articulaires, et surtout l'équilibre. Nous commençons par développer un contrôleur d'équilibre simple, qui ne prend en compte que les cas où les contacts avec l'environnement sont coplanaires (c'est le cas des mouvements de marche par exemple), puis nous étendons ce premier contrôleur à un cas plus général autorisant tout type de contacts. Nous avons mis en œuvre plusieurs types de modes de commande (libre, contraint, automatique ). Dans une dernière partie nous traitons de la problématique de leur ordonnancement, et de la continuité entre modes de commande. Nous exposons alors les résultats obtenus grâce à notre plateforme.
An improved nucleic acid sequence-based amplification method mediated by T4 gene 32 protein (2022)

The uptake of Nucleic Acid Sequence-Based Amplification (NASBA) for point of care testing may be hindered by a complexity in the workflow due the requirement of a thermal denaturation step to initiate the cyclic isothermal amplification before the addition of the amplification enzymes. Despite reports of successful enhancement of other DNA and RNA amplification methods using DNA and RNA binding proteins, this has not been reported for NASBA. Here, three single-stranded binding proteins, RecA, Extreme Thermostable Single-stranded binding protein (ET SSB) and T4 gene gp32 protein (gp32), were incorporated in NASBA protocol and used for single pot, one-step NASBA at 41 °C. Indeed, all SSBs showed significantly improved amplifications compared with the 2-step process, but only gp32 showed no non-specific aberrant amplification, and slightly improved the time-to-positivity in comparison with the conventional NASBA. For synthetic HIV-1 RNA, gp32 was found to improve the time-to-positivity (ttp) by average of 13.6% of one-step NASBA and 6.7% of conventional NASBA for the detection of HIV-1 RNA, showing its potential for simplifying the workflow as desirable for point of care applications of NASBA.
Magnetic Resonance Appearance of the Inner Ear After Hearing-Preservation Surgery (2006)

We describe the T2-weighted magnetic resonance findings after hearing-preservation surgery for acoustic tumor removal. Loss of inner ear signal on T2-weighted images correlates with loss of hearing postoperatively, whereas preserved inner ear signal correlates with hearing preservation after middle fossa surgery for vestibular schwannoma removal.
Developmental validation of GlobalFiler™ PCR amplification kit: a 6-dye multiplex assay designed for amplification of casework samples (2018)

The GlobalFiler™ PCR Amplification Kit is a single multiplex assay that amplifies a set of 24 markers, which encompass the European Standard Set and CODIS (Combined DNA Index System) recommended composite set of loci. In addition to more loci and a 6-dye chemistry format, the Master Mix has been formulated to allow higher sample loading volume for trace DNA samples. The GlobalFiler™ Kit has been optimized to deliver high performance on casework samples, while also delivering fast thermal cycling, with an amplification time of approximately 80 min. Here, we report the results of the developmental validation study which followed the SWGDAM (Scientific Working Group on DNA Analysis Methods) guidelines and includes data for PCR-based studies, sensitivity, species specificity, stability, precision, reproducibility and repeatability, concordance, stutter, DNA mixtures, and performance on mock casework samples. The results validate the multiplex design as well as demonstrate the kit's robustness, reliability, and suitability as an assay for human identification with casework DNA samples.
Combining deep reinforcement learning with prior knowledge and reasoning (2018)

Recent improvements in deep reinforcement learning have allowed to solve problems in many 2D domains such as Atari games. However, in complex 3D environments, numerous learning episodes are required which may be too time consuming or even impossible especially in real-world scenarios. We present a new architecture to combine external knowledge and deep reinforcement learning using only visual input. A key concept of our system is augmenting image input by adding environment feature information and combining two sources of decision. We evaluate the performances of our method in 3D partially-observable environments from the Microsoft Malmo platform. Experimental evaluation exhibits higher performance and faster learning compared to a single reinforcement learning model.
Vertical-Cavity Surface-Emitting Lasers: Advanced Modulation Formats and Coherent Detection (2013)

This thesis expands the state-of-the-art in coherent detection for optical fiber access networks employing vertical-cavity surface-emitting lasers (VC-SELs) as light sources. Bit rates up to 10 Gb/s over 25 km single-mode fibre (SMF) transmission distance have been achieved supporting a pas-sive optical splitting ratio for 199 users. Extended transmission reach over 40 km SMF and a splitting ratio supporting up to 1024 users have been experimentally demonstrated for a bidirectional bit rate of 5 Gb/s. These novel proposed VCSEL-based transmission systems satisfy the requirements for next generation optical fiber access networks regarding long reach, high splitting ratio, no optical amplification, no external modulation, and use of a single fiber for upstream and downstream transmission. An important contribution of this thesis is the novel concept of chirp-assisted coherent detection for direct current modulated VCSELs. A coher-ent receiver approach that exploits adiabatic frequency chirping of direct
Development and structuring of combined positive-negative/negative-positive resists using laser ablation as positive dry etching technique (2000)

Novel photopolymers, based on cinnamylidenemalonyl groups, were designed for excimer laser ablation lithography. These polymers are highly sensitive to laser ablation at a specific irradiation wavelength, i. e., 308 nm, but can also be applied as classical, negative photoresist. The crosslinking of the polymer is accomplished by irradiation at >395 nm. The sensitivity of the photopolymers to laser ablation before and after crosslinking is nearly equal. The combination of these two processes, i. e., laser ablation and photocrosslinking, can be applied for the fabrication of arrays of microstructures. The laser ablation step is used to fabricate microstructures, while the classical wet processing is used for large area structuring. Combined processes of crosslinking-wet development and laser microstructuring, but also vice versa were carried out. The microstructures had the same high resolution, independent of the processing order.
Supplementary Figures 1-7 from Navitoclax (ABT-263) Accelerates Apoptosis during Drug-Induced Mitotic Arrest by Antagonizing Bcl-xL (2023)

Supplementary Figures 1-7 from Navitoclax (ABT-263) Accelerates Apoptosis during Drug-Induced Mitotic Arrest by Antagonizing Bcl-xL
Ultimate Limits of Pattern Stability Due to Thermal Vibrations (2017)

The analysis of the thermal vibrations of nanoscale features due to random thermal noise shows that given a high enough aspect ratio, features will vibrate far enough that their ends can touch. Depending on the balance of elastic forces and van der Waals forces one of three possible results can occur: the tips release after contact, the tips stay in contact, or the sides of the two features fall into each other causing total collapse. Analytical formulas for calculating the probability of failure for simple geometric structures are shown, and a methodology for determining the same for more complex structures is explained.
Epistatic Relationships between sarA and agr in Staphylococcus aureus Biofilm Formation (2010)

The results we report suggest that inhibitors of sarA-mediated regulation could be used to limit biofilm formation in S. aureus and that the efficacy of such inhibitors would not be limited by spontaneous mutation of agr in the human host.
Cooperation between somatic mutations and germline susceptibility variants in tumorigenesis – a dangerous liaison (2015)

High-throughput genotyping and sequencing generate comprehensive catalogs of inherited genetic variations and acquired somatic mutations. However, their possible interactions and roles in tumorigenesis remain largely unexplored. We recently reported cooperation between the EWSR1-FLI1 (Ewing sarcoma breakpoint region 1 - Friend leukemia virus integration 1) fusion oncogene and a germline variant that regulates the EGR2 (early growth response 2) Ewing sarcoma susceptibility gene via a GGAA-microsatellite.
Energy density, temperature, and pressure upon generation and collapse of spherical cavitation bubbles in water produced by femtosecond optical breakdown (2009)

Optical breakdown and spherical bubble collapse are two different nonlinear mechanisms producing a large energy density within a small spatial region. Extreme states of matter with pressures p up to 107 MPa (100 Megabar) for femtosecond optical breakdown, and temperatures T ranging from 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> up to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> K for the collapse of bubbles oscillating in a sound field have been reported. However, because of the small spatial and temporal scale on which the extremes occur, it is impossible to directly measure p and T but they have to be inferred from other experimental information and equation of state (EOS) data, which is a challenging task.
Improved detection systems for TT virus reveal high prevalence in humans, non-human primates and farm animals (1999)

TT virus is a newly described agent infecting humans. Initially isolated from a patient (initials T.T.) with unexplained hepatitis, the virus has since been found in both normal and diseased individuals. In the present study, we utilized genomic-length sequences from distinct genotypes of TT virus to design PCR-based assays using conserved oligonucleotide primers from three independent regions of the virus genome. Each of the three assays was found to be superior to the PCR-based assays previously published. The most sensitive of the new assays was utilized to demonstrate the prevalence of TT virus to be at least 34.1% in volunteer blood donors, 39.6% in commercial blood donors, 59.6% in non-A-GB hepatitis cases, 81.7% in injectable drug users and 95.9% in haemophiliacs. In an attempt to identify a possible source of human infection, we found TT virus sequences to be present in 19% of chickens, 20% of pigs, 25% of cows and 30% of sheep. Sequence determination and phylogenetic analyses demonstrated that isolates from farm animals were not genetically distinct from those found in humans. This study clearly demonstrates that previously reported PCR assays dramatically underestimate the true prevalence of TT virus within the human population. Due to the high rate of infection in both blood donors and those with non-A-GB hepatitis, these results question the causal role of TT virus in cases of unexplained hepatitis. Further, it is possible that domesticated farm animals serve as a source of human infection.
Prostatic arterial embolization for the treatment of lower urinary tract symptoms in men with benign prostatic hyperplasia (2022)

Compared to TURP, PAE may provide similar improvement in urologic symptom scores and quality of life. While we are very uncertain about major adverse events, PAE likely increases retreatment rates. While erectile function may be similar, PAE may reduce ejaculatory disorders. Certainty of evidence for the outcomes of this review was low or very low except for retreatment (moderate-certainty evidence), signaling that our confidence in the reported effect size is limited or very limited, and that this topic should be better informed by future research.
Epigenetics of diabetic complications (2010)

Type 1 and Type 2 diabetes are complex diseases associated with multiple complications, and both genetic and environmental factors have been implicated in these pathologies. While numerous studies have provided a wealth of knowledge regarding the genetics of diabetes, the mechanistic pathways leading to diabetes and its complications remain only partly understood. Studying the role of epigenetics in diabetic complications can provide valuable new insights to clarify the interplay between genes and the environment. DNA methylation and histone modifications in nuclear chromatin can generate epigenetic information as another layer of gene transcriptional regulation sensitive to environmental signals. Recent evidence shows that key biochemical pathways and epigenetic chromatin histone methylation patterns are altered in target cells under diabetic conditions and might also be involved in the metabolic memory phenomenon noted in clinical trials and animal studies. New therapeutic targets and treatment options could be uncovered from an in-depth study of the epigenetic mechanisms that might perpetuate diabetic complications despite glycemic control.
Spatial Association between L‐type Calcium Channels and Integrins (2007)

Current through the L‐type calcium channel (Cav1.2) is enhanced by α 5 β 1 integrin activation in vascular smooth muscle cells and neurons. We examined the spatial association between α 5 β 1 integrin and Cav1.2 using Cav1.2 mutants either with truncation of the Cav1.2 C‐terminal region just proximal to the PKA phosphorylation site at Ser 1901 (stop5) or missing the two C‐terminal proline rich domains between amino acids 1955–1973 (dp1/p2). The effects on Cav1.2 current and integrin interaction were determined using co‐immunoprecipitation (IP) and patch clamp recording of Cav1.2 current in HEK293 cells transfected with wild type (WT) or mutant neuronal Cav1.2 cDNA. After integrin activation with α 5 β 1 integrin antibody, current was potentiated by 107% in WT Cav1.2, by 10% in the stop5 mutant, and by 88% in the dp1/p2 mutant. Co‐association of Cav1.2 with β 1 integrin was detected by IP in cells plated on fibronectin (FN), but not on poly‐l‐lysine. On FN, notably less co‐association of Cav1.2 with β 1 integrin was seen in the dp1/p2 mutant (59% of WT, p&lt;0.05), but only slightly less co‐association with β 1 integrin was seen in the stop5 mutant (79% of WT). Lack of correlation between the patch clamp and IP data may result either from the differences in the timing of integrin activation in the two protocols and/or by a requirement for other regulatory regions in Cav1.2 that mediate acute signaling events upon integrin activation. Overall, our data suggest that regions in the C‐terminal of Cav1.2 are crucial for association with β 1 integrin, but their roles in modulating the effects of integrin activation on Cav1.2 need further investigation.