gebhart/patrepeval huggingface dataset:
FullMonte: fast Monte-Carlo light simulator (2019)

Determining the light propagation in heterogeneous media is a challenging task which can only be approximated by solving the Boltzmann transport equation via diffusion theory. However, diffusion theory becomes very inaccurate at interfaces, boundaries, sources, and sinks, which are present in heterogeneous media. Monte Carlo methods are able to converge to the correct solution by simulating a sufficiently high number of photons, at the cost of increased runtime. Therefore, it is important to optimize the Monte Carlo simulator, thereby allowing more photons to be simulated and a more accurate solution within a given runtime. FullMonte is a full-featured simulator that uses processor-optimized operations to achieve the highest performance of any 3D tetrahedral Monte Carlo light propagation software to date. This paper presents two medical use cases which benefit from FullMonte, highlights new features and explains the optimizations that lead to its high performance.
Cotyledon-Generated Auxin Is Required for Shade-Induced Hypocotyl Growth in Brassica rapa (2014)

Plant architecture is optimized for the local light environment. In response to foliar shade or neighbor proximity (low red to far-red light), some plant species exhibit shade-avoiding phenotypes, including increased stem and hypocotyl growth, which increases the likelihood of outgrowing competitor plants. If shade persists, early flowering and the reallocation of growth resources to stem elongation ultimately affect the yield of harvestable tissues in crop species. Previous studies have shown that hypocotyl growth in low red to far-red shade is largely dependent on the photoreceptor phytochrome B and the phytohormone auxin. However, where shade is perceived in the plant and how auxin regulates growth spatially are less well understood. Using the oilseed and vegetable crop species Brassica rapa, we show that the perception of low red to far-red shade by the cotyledons triggers hypocotyl cell elongation and auxin target gene expression. Furthermore, we find that following shade perception, elevated auxin levels occur in a basipetal gradient away from the cotyledons and that this is coincident with a gradient of auxin target gene induction. These results show that cotyledon-generated auxin regulates hypocotyl elongation. In addition, we find in mature B. rapa plants that simulated shade does not affect seed oil composition but may affect seed yield. This suggests that in field settings where mutual shading between plants may occur, a balance between plant density and seed yield per plant needs to be achieved for maximum oil yield, while oil composition might remain constant.
Inference and segmentation in cortical processing (2006)

We present a modelling framework for cortical processing aimed at understanding how, maintaining biological plausibility, neural network models can: (a) approximate general inference algorithms like belief propagation, combining bottom-up and top-down information, (b) solve Rosenblatt's classical superposition problem, which we link to the binding problem, and (c) do so based on an unsupervised learning approach. The framework leads to two related models: the first model shows that the use of top-down feedback significantly improves the network's ability to perform inference of corrupted inputs; the second model, including oscillatory behavior in the processing units, shows that the superposition problem can be efficiently solved based on the unit's phases.
Reduced-complexity graphics (1989)

RISC (reduced-instruction-set-computer) CPU design concepts are used as the basis for a more general design philosophy applicable to graphics. The 3D graphics subsystem for the Apollo DN10000 is based on applying a RISC philosophy to the rendering problem. All structure-walking and floating-point computations are handled in the general-purpose CPU(s), and a simple, fast-cycle-time drawing engine synthesizes pixels and writes them into the bitmap. In the control and pixel-addressing logic, RISC ideas are applied directly and effectively; in color synthesis, however, they did not prove as useful. Several RISC concepts were ultimately fundamental to achieving design simplifications and allowed a better utilization of VLSI CMOS technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Privacy-Preserving Entropy-Driven Framework for Tracing DoS Attacks in VoIP (2013)

Network audit trails, especially those composed of application layer data, can be a valuable source of information regarding the investigation of attack incidents. Nevertheless, the analysis of log files of large volume is usually both complex (slow) and privacy-neglecting. Especially, when it comes to VoIP, the literature on how audit trails can be exploited to identify attacks remains scarce. This paper provides an entropy-driven, privacy preserving, and practical framework for detecting resource consumption attacks in VoIP ecosystems. We extensively evaluate our framework under various attack scenarios involving single and multiple assailants. The results obtained show that the proposed scheme is capable of identifying malicious traffic with a false positive alarm rate up to 3.5%.
Chiral Discrimination among Aminotransferases: Inactivation by 4-Amino-4,5-dihydrothiophenecarboxylic Acid (2010)

Mechanism-based inhibitors such as cycloserine and gabaculine can inactivate aminotransferases via reactions of the compounds with the pyridoxal phosphate cofactor forming an irreversible adduct. The reaction is chirally specific in that any one enzyme usually only recognizes one enantiomer of the inactivator. For instance, l-aspartate aminotransferase (l-AspAT) is inactivated by 4-amino-4,5-dihydro-2-thiophenecarboxylic acid (ADTA), however, only by the S-isomer. We have now shown that d-amino acid aminotransferase (d-a-AT) is irreversibly inactivated by the R-isomer of the same compound. The X-ray crystal structure (PDB code: 3LQS ) of the inactivated enzyme shows that in the product the enzyme no longer makes a Schiff base linkage to the pyridoxal 5'-phosphate (PLP) cofactor, and instead the compound has formed a derivative of the cofactor. The adduct is similar to that formed between d-cycloserine and d-a-AT or alanine racemase (Ala-Rac) in that the thiophene ring of R-ADTA is intact and seems to be aromatic. The plane of the ring is rotated by nearly 90 degrees with respect to the plane of the pyridine ring of the cofactor, in comparison with the enzyme inactivated by cycloserine. Based on the structure of the product, the mechanism of inactivation most probably involves a transamination followed by aromatization to form an aromatic thiophene ring.
Methods and Protocols for Reliable Electrochemical Testing in Post-Li Batteries (Na, K, Mg, and Ca) (2019)

While less mature than the Li-ion battery, technologies based on Na, K, Mg, and Ca are attracting more and more attention from the battery community. New material (cathode, anode, or electrolyte) testing for these post-Li systems commonly involves the use of an electrochemical setup called a half-cell in which metal counter and reference electrodes are used. Here we first describe the different issues that become critical when moving away from Li with respect to the cell hardware (cell design, current collector, separator, insulator) and the nature of the counter and reference electrodes. Workarounds are given, and a versatile setup is proposed to run reliable electrochemical tests for post-Li battery materials in general, in a broad range of electrolyte compositions.
Computed tomography of the gastrointestinal tract (2022)

Advancements in computed tomography (CT) technology allow scanning of the entire abdomen in a very short period of time, enabling images to be obtained in multiple phases of IV contrast enhancement which optimizes the detection and diagnosis of pathology. PO contrast agents, including neutral agents, such as water, or commercially available volume enhancing agents may be used to visualize the bowel wall, while positive agents such as iodine or barium suspensions may be used to help differentiate small bowel loops from adjacent structures. The images shown in this chapter relate to the gastrointestinal tract; the liver; the pancreas; the biliary tract; the peritoneum; and hernias.
Supplementary Table 1 from A Phase I Dose–Escalation Study of Regorafenib (BAY 73–4506), an Inhibitor of Oncogenic, Angiogenic, and Stromal Kinases, in Patients with Advanced Solid Tumors (2023)

&lt;p&gt;PDF file, 52KB, Adverse events that led to permanent treatment discontinuation.&lt;/p&gt;
Parallel communications for ATM network control and management (1997)

This paper describes an end-to-end parallel communications scheme based on a vector routing algorithm (VRA) for ATM network control and management. An information string is partitioned into m parts, which are then coded into k > m parts and sent out on k separate subchannels to the receiver. When m of the k parts are received correctly, the original information can be reconstructed. Two desirable effects are achieved in the context of ATM traffic control: (1) the burstiness of the source traffic can be smoothed out by the partition process; (2) the quality of service in terms of error, loss and delay can be controlled using the number of redundant routes k — m as a control parameter. Our results show that VRA is especially suitable for services with highly bursty traffic. We argue that several network management issues, including reliability, evolution and integration, security, and administration and billing can be addressed in a simple manner using the VRA framework.
Langzeiteffekt der selektiven Laser Trabekuloplastik (SLT) auf die Augeninnendrucksenkung bei okulärer Hypertension und Glaukom (2008)

Das Ziel dieser prospektiven klinischen Studie war es, den Langzeiteffekt der selektiven Laser Trabekuloplastik (SLT) im Hinblick auf die Augeninnendrucksenkung (20%ige Drucksenkung bzw. 30%ige Drucksenkung) zu beleuchten. Methoden: 201 Augen von 141 Patienten wurden mittels einer SLT unter Verwendung eines Q-switched ND:YAG-Lasers (532nm) behandelt. 50 Herde wurden jeweils in die untere Hälfte und in 28 Fällen (13,9%) weitere 50 Herde in die obere Hälfte des Trabekelmaschenwerkes mit einer Energie von 0,5–1,2 mJ/spot appliziert. Die Patienten (mittleres Alter 62,7 Jahre; 41,7% weiblich; 58,3% männlich) hatten entweder eine okuläre Hypertension (65 Augen) oder ein manifestes Glaukom (146 Augen). Ergebnisse: Nach 6 Monaten wurde eine 20%ige Drucksenkung in 86 Augen erreicht (E) und in 63 Augen nicht erreicht (NE), von 52 Augen fehlten die Daten (FD). Eine 30%ige Drucksenkung wurde in 37 Augen erreicht (E) und 112 Augen nicht erreicht (NE). Der individuelle Zieldruck (ZD) (im Mittel: 15,3mmHg) wurde in 107 Augen erreicht (E) und in 42 Augen nicht erreicht (NE). Der Augeninnendruck sank signifikant von 19,5mmHg auf 15,1mmHg nach 1 Jahr. In 127 Augen wurde die drucksenkende Therapie reduziert. Schlussfolgerungen: Die SLT hat einen Langzeiteffekt auf die Augeninnendrucksenkung und trägt dazu bei, einen individuellen Zieldruck zu erreichen. Deshalb scheint die SLT eine sehr gute Option in der Glaukom-Langzeitbehandlung zu sein.
Cartilage and Muscle Cell Fate and Origins during Lizard Tail Regeneration (2017)

This study demonstrates that differentiated cartilage cells contribute to both regenerated muscle and cartilage tissues following tail loss, and in turn, differentiated muscle cells contribute to both tissue types as well. These findings suggest that dedifferentiation and/or transdifferentiation are at least partially responsible for the regenerative outcome in the mourning gecko.
Different Regions of the Immunophilin FKBP52 Determine Its Association with the Glucocorticoid Receptor, hsp90, and Cytoplasmic Dynein (1999)

FKBP52 is a high molecular mass immunophilin possessing peptidylprolyl isomerase (PPIase) activity that is inhibited by the immunosuppressant drug FK506. FKBP52 is a component of steroid receptor.hsp90 heterocomplexes, and it binds to hsp90 via a region containing three tetratricopeptide repeats (TPRs). Here we demonstrate by cross-linking of the purified proteins that there is one binding site for FKBP52/dimer of hsp90. This accounts for the common heterotetrameric structure of native receptor heterocomplexes being 1 molecule of receptor, 2 molecules of hsp90, and 1 molecule of a TPR domain protein. Immunoadsorption of FKBP52 from reticulocyte lysate also yields co-immunoadsorption of cytoplasmic dynein, and we show that co-immunoadsorption of dynein is competed by a fragment of FKBP52 containing its PPIase domain, but not by a TPR domain fragment that blocks FKBP52 binding to hsp90. Using purified proteins, we also show that FKBP52 binds directly to the hsp90-free glucocorticoid receptor. Because neither the PPIase fragment nor the TPR fragment affects the binding of FKBP52 to the glucocorticoid receptor under conditions in which they block FKBP52 binding to dynein or hsp90, respectively, different regions of FKBP52 must determine its association with these three proteins.
Molecular Screen Identifies Cardiac Myosin–Binding Protein-C as a Protein Kinase G-Iα Substrate (2015)

Taken together, these data support that PKGIα and cMyBP-C interact in the heart and that cMyBP-C is an anti remodeling PKGIα kinase substrate. This study provides the first identification of a myocardial-specific PKGIα LZ-dependent antiremodeling substrate and supports further exploration of PKGIα myocardial LZ substrates as potential therapeutic targets for heart failure.
Coded Sparse Matrix Computation Schemes That Leverage Partial Stragglers (2022)

Distributed matrix computations over large clusters can suffer from the problem of slow or failed worker nodes (called stragglers) which can dominate the overall job execution time. Coded computation utilizes concepts from erasure coding to mitigate the effect of stragglers by running “coded” copies of tasks comprising a job; stragglers are typically treated as erasures. While this is useful, there are issues with applying, e.g., MDS codes in a straightforward manner. Several practical matrix computation scenarios involve sparse matrices. MDS codes typically require dense linear combinations of submatrices of the original matrices which destroy their inherent sparsity. This is problematic as it results in significantly higher worker computation times. Moreover, treating slow nodes as erasures ignores the potentially useful partial computations performed by them. Furthermore, some MDS techniques also suffer from significant numerical stability issues. In this work we present schemes that allow us to leverage partial computation by stragglers while imposing constraints on the level of coding that is required in generating the encoded submatrices. This significantly reduces the worker computation time as compared to previous approaches and results in improved numerical stability in the decoding process. Exhaustive numerical experiments on Amazon Web Services (AWS) clusters support our findings.
Techniques for robot-aided intraocular surgery using monocular vision (2018)

This paper presents techniques for robot-aided intraocular surgery using monocular vision in order to overcome erroneous stereo reconstruction in an intact eye. We propose a new retinal surface estimation method based on a structured-light approach. A handheld robot known as the Micron enables automatic scanning of a laser probe, creating projected beam patterns on the retinal surface. Geometric analysis of the patterns then allows planar reconstruction of the surface. To realize automated surgery in an intact eye, monocular hybrid visual servoing is accomplished through a scheme that incorporates surface reconstruction and partitioned visual servoing. We investigate the sensitivity of the estimation method according to relevant parameters and also evaluate its performance in both dry and wet conditions. The approach is validated through experiments for automated laser photocoagulation in a realistic eye phantom in vitro. Finally, we present the first demonstration of automated intraocular laser surgery in porcine eyes ex vivo.
Programming events in the regulation of cell proliferation and death (1993)

Abstract In developing new and more successful therapies for preventing and treating cancer, it is critical to understand what normally regulates cell proliferation and cell death and what are the specific dysfunctions associated with these regulations in individual cancers. Here we review the programmed series of molecular, cellular, and biochemical events required for a cell's entrance and progression through the proliferative vs death processes as a starting point for such approaches to new therapies.
A Digital Neuromorphic Architecture Efficiently Facilitating Complex Synaptic Response Functions Applied to LSMs. (2018)

Abstract not provided.
The role of metagenomics in understanding the human microbiome in health and disease (2014)

The term microbiome refers to the genetic material of the catalog of microbial taxa associated with humans. As in all ecosystems, the microbiota reaches a dynamic equilibrium in the human body, which can be altered by environmental factors and external stimuli. Metagenomics is a relatively new field of study of microbial genomes within diverse environmental samples, which is of increasing importance in microbiology. The introduction of this ecological perception of microbiology is the key to achieving real knowledge about the influence of the microbiota in human health and disease. The aim of this review is to summarize the link between the human microbiota (focusing on the intestinal, vaginal, skin, and airway body sites) and health from this ecological point of view, highlighting the contribution of metagenomics in the advance of this field.
A Selectivity‐Driven Supramolecular Polymerization of an AB Monomer (2006)

Aus zwei wird eins: Ein AB-Monomer mit jeweils vier H-Brücken bildenden 2-Ureido-4[1H]-pyrimidinon- und 2,7-Diamido-1,8-naphthyridin-Einheiten entsteht durch selektive Olefin-Kreuzmetathese. Mit ihm lässt sich das stöchiometrische Ungleichgewicht bei der Selbstorganisation von supramolekularen AA+BB-Polymeren umgehen. Da der Linker zwischen den beiden Motiven flexibel ist, liegt das Monomer bei niedriger Konzentration als Cyclus vor. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2006/z504192_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Blind Fractional Interference Alignment (2013)

Fractional Interference Alignment (FIA) is a transmission scheme which achieves any value between [0,1] for the Symbols transmitted per Antenna per Channel use (SpAC). FIA was designed in [1] specifically for Finite Alphabet (FA) signals, under the constraint that the Minimum Distance (MD) detector is used at all the receivers. Similar to classical interference alignment, the FIA precoder also needs perfect channel state information at all the transmitters (CSIT). In this work, a novel Blind Fractional Interference Alignment (B-FIA) scheme is introduced, where the basic assumption is that CSIT is not available. We consider two popular channel models, namely: Broadcast channel, and Interference channel. For these two channel models, the maximum achievable value of SpAC satisfying the constraints of the MD detector is obtained, but with no CSIT, and also a precoder design is provided to obtain any value of SpAC in the achievable range. Further, the precoder structure provided has one distinct advantage: interference channel state information at the receiver (I-CSIR) is not needed, when all the transmitters and receivers are equipped with one antenna each. When two or more antennas are used at both ends, I-CSIR must be available to obtain the maximum achievable value of SpAC. The receiver designs for both the Minimum Distance and the Maximum Likelihood (ML) decoders are discussed, where the interference statistics is estimated from the received signal samples. Simulation results of the B-FIA show that the ML decoder with estimated statistics achieves a significantly better error rate performance when compared to the MD decoder with known statistics, since the MD decoder assumes the interference plus noise term as colored Gaussian noise.
Comparison of an in-line asymmetric directional coupler modulator with distributed optical loss to other linearized electrooptic modulators (1999)

The transfer function of an external modulator is the critical factor that determines the spurious free dynamic range, signal power gain, and noise figure of a wide-band analog RF-photonic link. We present an in-line asymmetric directional coupler modulator with distributed optical loss capable of providing a transfer function linearized to the fourth order for multioctave bandwidths. This modulator compares favorably with multiple modulator suboctave linearization techniques consisting of series symmetric directional coupler and series Mach-Zehnder modulators and superoctave parallel Mach-Zehnder, and cascaded sections containing series Mach-Zehndersymmetric directional coupler modulators. The optimum bias point for the asymmetric directional coupler modulator is determined by device dimensions and material parameters with relative insensitivity to errors introduced during fabrication. Optical insertion loss imposes significant limitations on modulator performance. An implementation of an in-line asymmetric directional coupler modulator is discussed that eliminates excess loss due to fiber coupling in order to achieve a large RF power gain and competitive noise figure compared to the linearization configurations.
Applications of Convolution and Deconvolution to Transient Well Tests (1990)

Summary This paper presents the application of convolution and deconvolution interpretation methods. Two well-test field examples, interpreted with these methods, suggest that the downhole flow rate is crucial for system identification and parameter estimation and that the wellbore volume below the pressure gauge and flowmeter must be taken into account. A new generalized rate-convolution method is presented to obtain the reservoir pressure. This new method gives better results than both the Horner and modified Horner methods. A new formula also is presented to determine the vertical permeability for partially penetrated wells.
Engineering Multifunctional Stratified LiCoO2 Catalysts: Structural Disorder to Microstructural Exfoliation (2022)

The stratified nature of LiCoO2 (LCO) makes such materials suitable for rechargeable Li-ion batteries. The existing synthesis technology for LCO, however, results in a low surface area, low activity, and a limited density of active sites, which limit its applications in catalysis, in which the material’s functionality is determined by the reactions that occur on its surface. The present work reports a simplified and high-yield strategy for using bulk LCO in multifunctional two-dimensional (2D) catalysts. The recovery involves ordered and/or disordered leaching of Li+ as a result of H+ intercalation and formation of catalytically active oxygen vacancies at high concentrations (∼32 atom %). This is followed by exfoliation of the LCO into porous nanosheets through intercalation of tetramethylammonium hydroxide. The catalytic performance of the etched and exfoliated LCOs was investigated; the 1 M HCl-etched LCO exhibited the highest photocatalytic dye degradation (99.9%) under simulated solar light, while the etched and fully exfoliated LCO showed outstanding CO oxidation, with a T90% = 140 °C, which is significantly lower than that of the bulk LCO catalyst (T90% = 360 °C).