gebhart/patrepeval huggingface dataset:
2PT164 Norcamphor binding to cytochrome P450cam with a mutation to block pathway for the active site waters excluded by substrate(The 50th Annual Meeting of the Biophysical Society of Japan) (2012)

Tl]chnotogy
Zirconium Complexes Involving 2-Phosphorus-Substituted Indenyl Fragments (2005)

A series of 2-R2P-substituted indenes, where R2P = Ph2P, Cy2P, iPr2P, and tBu(H)P, were obtained via Pd-catalyzed reactions of 2-bromo-1H-indene (or 1H-inden-2-yl trifluoromethane sulfonate) with R2PH/Et3N. Analogous indenes bearing Me2P, tBu(Cl)P, and tBu2P substituents at position 2 were obtained through the reaction of 1H-inden-2-ylphosphonous dichloride with MeLi, tBuMgCl, and tBuMgCl/tBuLi−CuCN, respectively. Diethyl 1H-inden-2-ylphosphonate, prepared via the Ni-catalyzed Arbuzov reaction of 2-bromo-1H-indene with P(OEt)3, was found to be a convenient starting material for the synthesis of 2-H2P-substituted indene. 1H-Inden-2-yl(phenyl)phosphine, prepared via the Pd-catalyzed arylation of 2-H2P-substituted indene by PhI, turned out to react with 2-bromo-1H-indene in the presence of Pd(PPh3)4 and Et3N to form di(1H-inden-2-yl)(phenyl)phosphine in almost quantitative yield. Analogously, di(1H-inden-2-yl)(tert-butyl)phosphine was prepared via catalytic reaction of tBuPH2 with 2 equiv of 2-bromo-1H-indene. Triethylamine-promoted condensation of indenes bearing P(H)tBu and P(Cl)tBu fragments gave a mixture of cis- and trans-bis-indenyldiphosphines. Zirconium complexes (2-R2P-indenyl)2ZrCl2 (R2P = Ph2P, Me2P, Cy2P, iPr2P, tBu2P), as well as ansa-zirconocenes RP(2-indenyl)2ZrCl2 (R = Ph, tBu), were obtained in good yields from ZrCl4(THF)2 and lithium salts of the respective 2-P-substituted indenes. Ansa-zirconocene (tBuP)2(2-indenyl)2ZrCl2 including a P2R2 bridge was synthesized in a similar manner and isolated as the pure rac-isomer.
Experimental designs to model along-strike fault interaction (2002)

Revised: 8 August 2002Abstract We review the different designs and results of various previous models simulating the along-strikeinteraction between laterally offset faults, focusing on the formation of pull-apart basins in between strike-slipfaults or relay zones located between laterally offset normal faults.The design of most models traditionally includes the use of a basal sheet, whose edge acts as a velocitydiscontinuity onto which faults nucleate (Faugere and Brun, 1984; McClay and Ellis, 1987; Vendeville, 1991).One drawback of such design is that the location and orientation of faults in the relay zone are conditioned bythe shape of the edge of the basal sheet. An improved version of this design by Sims et al. (1999) using a strongviscous basal layer also forces faults to follow the basal velocity discontinuity. Using a third design by LeCalvez and Vendeville (1996), faults can freely propagate above a thin, weak viscous layer but fault blockscannot subside or rotate in response to deformation. We introduce a new design in which although fault locationis controlled by small instabilities at the brittle-ductile interface, faults can freely propagate along strike afterthey have nucleated. This design also allows fault blocks to subside, rise, or rotate in response to deformation.The main advantage of such design is that it forces the faults to form at a predetermined location. The ridgesare high enough (about one 20th of the brittle-layer thickness) to act as instabilities that trigger the nucleationof the main two faults, which thereby form with an initial lateral offset. But the ridges are low enough so that,once faults have formed in the brittle layer the fault planes act as dominant instabilities and freely propagatealong strike. Because this design provides much more freedom for fault interaction within the relay zone andfor fault-block rotation, results significantly differ from those of previous models.
Exposure Assessment Tools for Hypersensitivity Pneumonitis. An Official American Thoracic Society Workshop Report (2020)

This report is based on proceedings from the Exposure Assessment Tools for Hypersensitivity Pneumonitis (HP) Workshop, sponsored by the American Thoracic Society, that took place on May 18, 2019, in Dallas, Texas. The workshop was initiated by members from the Environmental, Occupational, and Population Health and Clinical Problems Assemblies of the American Thoracic Society. Participants included international experts from pulmonary medicine, occupational medicine, radiology, pathology, and exposure science. The meeting objectives were to <i>1</i>) define currently available tools for exposure assessment in evaluation of HP, <i>2</i>) describe the evidence base supporting the role for these exposure assessment tools in HP evaluation, <i>3</i>) identify limitations and barriers to each tool's implementation in clinical practice, <i>4</i>) determine which exposure assessment tools demonstrate the best performance characteristics and applicability, and <i>5</i>) identify research needs for improving exposure assessment tools for HP. Specific discussion topics included history-taking and exposure questionnaires, antigen avoidance, environmental assessment, specific inhalational challenge, serum-specific IgG testing, skin testing, lymphocyte proliferation testing, and a multidisciplinary team approach. Priorities for research in this area were identified.
The cut-off frequency of disturbance propagation in discrete inertia model of power networks (2013)

With the development of power grid interconnection, the disturbance propagation phenomena are more and more apparent which take the form of mechanical waves. Once a disturbance occurs, its propagation might cause cascading events and even large blackouts. However, with the help of advanced communications network in smart grid, new control strategies can be devised by the reveal of disturbance propagation mechanisms. In this paper, disturbance propagation in chained power network is studied from the point of view of network structure and parameters. The discrete inertia model of power systems is built. The increment motion equation of generator is formulated. Then, the wave transfer function is derived which can be used to describe the amplitude and phase variation of disturbance waves. The cut-off frequency of discrete inertia model is proposed to determine the upper limit of disturbance frequency. Furthermore, the computer simulations are carried out and the results demonstrate the validity of the proposed theory.
Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial (2020)

Gene expression data obtained in large studies hold great promises for discovering disease signatures or subtypes through data analysis. It is also prone to technical variation, whose removal is essential to avoid spurious discoveries. Because this variation is not always known and can be confounded with biological signals, its removal is a challenging task. Here we provide a step-wise procedure and comprehensive analysis of the MINDACT microarray dataset. The MINDACT trial enrolled 6693 breast cancer patients and prospectively validated the gene expression signature MammaPrint for outcome prediction. The study also yielded a full-transcriptome microarray for each tumor. We show for the first time in such a large dataset how technical variation can be removed while retaining expected biological signals. Because of its unprecedented size, we hope the resulting adjusted dataset will be an invaluable tool to discover or test gene expression signatures and to advance our understanding of breast cancer.
Mechanical Properties of Single-Walled Carbon Nanotube Solids Prepared by Spark Plasma Sintering (2007)

In this paper, a spark plasma sintering (SPS) method was employed to solidify single-walled carbon nanotubes (SWCNTs) only, and the effect of sintering conditions on the mechenical properties of the SWCNT solids were examined using a small punch (SP) testing method. The sintering temperature used in the range of 600-1 400°C, and the sintering pressure used 40 MPa and 120 MPa. It was demonstrated that the SPS method allowed SWCNTs to be solidified, without any additives. The experimental results showed that the purification of raw soot was critically importance. The SWCNT solid prepared from purified raw soot showed significant non-linear deformation response, producing quasi-ductile fracture behavior. In contrast, unpurified raw soot produced brittle SWCNT solids. The Young's modulus, fracture strength and work of fracture increased with increasing sintering temperature and pressure. The Raman scattering and SEM observations showed that the amount of the graphite-like materials were observed to increase with the increasing temperature and pressure, which indicate that the structure of the SWCNTs was changed partially into the graphite-like materials. The formation of graphite-like materials increased tendency of brittle fracture in the SWCNT solids. TEM observations revealed that the fracture surfaces of SWCNT solids were characterized by pull out of SWCNT bundles. This observation suggests that it may be possible to improve the mechanical properties of SWCNT solids by increasing the cohesion between SWCNTs.
Development of Fluconazole Resistance inCandida albicansCausing Disseminated Infection in a Patient Undergoing Marrow Transplantation (1997)

Oral candidiasis due to azole-resistant Candida albicans is an increasing problem in patients with AIDS who received prolonged periods of fluconazole prophylaxis. Infection with C. albicans is also frequent in patients undergoing transplantation. However, azole resistance has not been appreciated as a major problem for these patients, presumably because they receive a relatively short duration of fluconazole prophylaxis. We describe a case of disseminated candidiasis due to fluconazole-resistant C. albicans in a patient following marrow transplantation. Restriction fragment length polymorphism analysis with use of the C. albicans strain-specific Ca3 probe was performed on sequential isolates. Identical banding patterns were obtained, thereby confirming that a fluconazole-susceptible endogenous C. albicans acquired azole resistance during a brief exposure to the drug and subsequently caused disseminated infection. This observation raises questions regarding the incidence, significance, and mechanism of azole resistance in fungi causing infection in this population.
ChemInform Abstract: Similarities and Differences Between the “Relativistic” Triad Gold, Platinum, and Mercury in Catalysis (2012)

Abstract Review: 110 refs.
A Genomic Approach to Human Autoimmune Diseases (2010)

The past decade has seen an explosion in the use of DNA-based microarrays. These techniques permit assessment of RNA abundance on a genome-wide scale. Medical applications emerged in the field of cancer, with studies of both solid tumors and hematological malignancies leading to the development of tests that are now used to personalize therapeutic options. Microarrays have also been used to analyze the blood transcriptome in a wide range of diseases. In human autoimmune diseases, these studies are showing potential for identifying therapeutic targets as well as biomarkers for diagnosis, assessment of disease activity, and response to treatment. More quantitative and sensitive high-throughput RNA profiling methods are starting to be available and will be necessary for transcriptome analyses to become routine tests in the clinical setting. We expect this to crystallize within the coming decade, as these methods become part of the personalized medicine armamentarium.
Clustering Time Series with Nonlinear Dynamics: A Bayesian Non-Parametric and Particle-Based Approach (2018)

We propose a general statistical framework for clustering multiple time series that exhibit nonlinear dynamics into an a-priori-unknown number of sub-groups. Our motivation comes from neuroscience, where an important problem is to identify, within a large assembly of neurons, subsets that respond similarly to a stimulus or contingency. Upon modeling the multiple time series as the output of a Dirichlet process mixture of nonlinear state-space models, we derive a Metropolis-within-Gibbs algorithm for full Bayesian inference that alternates between sampling cluster assignments and sampling parameter values that form the basis of the clustering. The Metropolis step employs recent innovations in particle-based methods. We apply the framework to clustering time series acquired from the prefrontal cortex of mice in an experiment designed to characterize the neural underpinnings of fear.
Dopamine D2 Receptor‐Deficient Mice Exhibit Decreased Dopamine Transporter Function but No Changes in Dopamine Release in Dorsal Striatum (1999)

Presynaptic D2 dopamine (DA) autoreceptors, which are well known to modulate DA release, have recently been shown to regulate DA transporter (DAT) activity. To examine the effects of D2 DA receptor deficiency on DA release and DAT activity in dorsal striatum, we used mice genetically engineered to have two (D2+/+), one (D2+/-), or no (D2-/-) functional copies of the gene coding for the D2 DA receptor. In vivo microdialysis studies demonstrated that basal and K+-evoked extracellular DA concentrations were similar in all three genotypes. However, using in vivo electrochemistry, the D2-/- mice were found to have decreased DAT function, i.e., clearance of locally applied DA was decreased by 50% relative to that in D2+/+ mice. In D2+/+ mice, but not D2-/- mice, local application of the D2-like receptor antagonist raclopride increased DA signal amplitude, indicating decreased DA clearance. Binding assays with the cocaine analogue [3H]WIN 35,428 showed no genotypic differences in either density or affinity of DAT binding sites in striatum or substantia nigra, indicating that the differences seen in DAT activity were not a result of decreased DAT expression. These results further strengthen the idea that the D2 DA receptor subtype modulates activity of the striatal DAT.
BILLNET: A Binarized Conv3D-LSTM Network with Logic-gated residual architecture for hardware-efficient video inference (2022)

Long Short-Term Memory (LSTM) and 3D convolution (Conv3D) show impressive results for many video-based applications but require large memory and intensive computing. Motivated by recent works on hardware-algorithmic co-design towards efficient inference, we propose a compact binarized Conv3D-LSTM model architecture called BILLNET, compatible with a highly resource-constrained hardware. Firstly, BILLNET proposes to factorize the costly standard Conv3D by two pointwise convolutions with a grouped convolution in-between. Secondly, BILLNET enables binarized weights and activations via a MUX-OR-gated residual architecture. Finally, to efficiently train BILLNET, we propose a multi-stage training strategy enabling to fully quantize LSTM layers. Results on Jester dataset show that our method can obtain high accuracy with extremely low memory and computational budgets compared to existing Conv3D resource-efficient models.
Expression of adhesion molecule CD44 in metastatic brain tumors. (1998)

Expression of CD44 (m.w. 80-95 kD) in 48 metastatic brain tumors was examined using monoclonal antibody on paraffin sections. The CD44 expression was found in 48% of studied tumors. The most constant expression of CD44 was observed in metastases from thyroid, skin and breast cancer. The brain metastases were characterized by quite heterogenous distribution of CD44 glycoprotein--the most pronounced expression was seen in individual neoplastic cells embedded in abundant stroma and in the vicinity of preserved neural tissue. Such a topographical distribution of CD44 supports its role in interactions of cancer cells with extracellular matrix components of the tumor stroma as well as of neural tissue.
On the Feasibility of Optical Circuit Switching for High Performance Computing Systems (2005)

The interconnect plays a key role in both the cost and performance of large-scale HPC systems. The cost of future high-bandwidth electronic interconnects mushrooms due to expensive optical transceivers needed between electronic switches. We describe a potentially cheaper and more power-efficient approach to building high-performance interconnects. Through empirical analysis of HPC applications, we find that the bulk of inter-processor communication (barring collectives) is bounded in degree and changes very slowly or never. Thus we propose a two-network interconnect: An Optical Circuit Switching (OCS) network handling long-lived bulk data transfers, using optical switches; and a secondary lower-bandwidth Electronic Packet Switching (EPS) network. An OCS could be significantly cheaper, as it uses fewer optical transceivers than an electronic network. Collectives and transient communication packets traverse the electronic network. We present compiler techniques and dynamic run-time policies, using this two-network interconnect. Simulation results show that our approach provides high performance at low cost.
Special Issue on Broadband Access Networks (2010)

The 16 papers in this special issue focus on broadband access networks. The first six papers address various issues related to wireline access networks, the seventh paper covers PON-WiMax integration, and the rest of the papers discuss aspects of different wireless networks such as WiMax, WiFi, 4G access networks, and cognitive radio networks.
Trends in Radical Prostatectomy: Centralization, Robotics, and Access to Urologic Cancer Care (2020)

Robotic surgery has been widely adopted for radical prostatectomy. We hypothesize that this change is rapidly shifting procedures away from hospitals that do not offer robotics and consequently increasing patient travel.
On the Ziv-Lempel proof and related topics (1994)

Results concerning the celebrated Ziv-Lempel sequence compression algorithm are revisited taking a rather intuitive approach. Also presented are ideas, which were previously formalized and extensions of these results to compression of two-dimensional data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evidence of mTOR Activation by an AKT-Independent Mechanism Provides Support for the Combined Treatment of PTEN-Deficient Prostate Tumors with mTOR and AKT Inhibitors (2012)

Activation of the phosphoinositide 3-kinase pathway is commonly observed in human prostate cancer. Loss of function of phosphatase and tensin homolog (PTEN) is associated with the activation of AKT and mammalian target of rapamycin (mTOR) in many cancer cell lines as well as in other model systems. However, activation of mTOR is also dependent of kinases other than AKT. Here, we show that activation of mTOR is not dependent on AKT in a prostate-specific PTEN-deficient mouse model of prostate cancer. Pathway bifurcation of AKT and mTOR was noted in both mouse and human prostate tumors. We demonstrated for the first time that cotargeting mTOR and AKT with ridaforolimus/MK-8669 and M1K-2206, respectively, delivers additive antitumor effects in vivo when compared to single agents. Our preclinical data suggest that the combination of AKT and mTOR inhibitors might be more effective in treating prostate cancer patients than current treatment regimens or either treatment alone.
Puffing and inhalation behaviour in cigarette smoking: Implications for particle diameter and dose (2009)

Inhalation of tobacco smoke aerosol is a two-step process involving puffing followed by inhalation. Measured smoke deposition efficiencies in the lung (20-70%) are greater than expected for smoke particles of diameter 150 -- 250 nm CMD. Various mechanisms have been put forward to explain this enhanced deposition pattern, including coagulation, hygroscopic growth, condensation and evaporation, changes in composition, or changes in inhalation behaviour. This paper represents one of a series of studies seeking to better quantify smoke chemistry, inhalation behaviour and cumulative particle growth. The studies have been conducted to better understand smoke dosimetry and links to disease as part of a wider programme defining risk and potential harm reduction. In this study, it was noted that particle deposition increased with increasing inhalation depth, and that smoke inhalation volumes were generally greater than normal tidal breathing volumes. A weak association was observed between particle diameter and puff flow, but no strong association between particle diameter and retention efficiency.
Au-Ge Based Alloys for Novel High-T Lead Free Solder Materials – Fundamentals and Applications (2012)

Low melting Au based alloys offer a combination of high corrosion and creep resistance as well as good electrical and thermal conductivity, and they support the capability for fluxless soldering. Despite their high price, Au alloys are of special interest for high temperature solder applications where these characteristics are essential, e.g. special MEMS devices, sensors exposed to aggressive media, biomedical applications or in space technology. The alloying system Au-Ge is characterized by a deep eutectic point with a melting temperature of 360°C, but information on the use of eutectic Au-Ge as solder material is very limited.&lt;br /&gt;In this work, the results of a group project within the European COST Action MP0602 "High Temperature Lead Free Solders" on the feasibility of Au-Ge based alloys as high-temperature lead free solder will be summarized. Beside the thermodynamic assessment of a number of important alloying systems (Cu-Ge, Ge-Ni, Au-Ge-Sb, Au-Ge-Si, Au-Ge-Sn) wetting and soldering tests using eutectic Au-Ge alloy and Cu and Ni substrates were performed. Sound joints with a high strength could be produced.
Plasmodium Cysteine Repeat Modular Proteins 3 and 4 are essential for malaria parasite transmission from the mosquito to the host (2011)

PCRMP3 and 4 play multiple roles during the Plasmodium life cycle; they are essential for the establishment of sporozoite infection in the mosquito salivary gland, and subsequently for development in hepatocytes. However, although Δpcrmp3 and Δpcrmp4 parasites are completely growth-impaired in the liver, immunization with live sporozoites does not induce the protective immune responses that have been shown for other genetically-attenuated parasites.
Real-time assessment of renal cortical microvascular perfusion heterogeneities using near-infrared laser speckle imaging (2010)

Laser speckle imaging (LSI) is able to provide full-field perfusion maps of the renal cortex and allows quantification of the average LSI perfusion within an arbitrarily set region of interest and the recovery of LSI perfusion histograms within this region. The aim of the present study was to evaluate the use of LSI for mapping renal cortical microvascular perfusion and to demonstrate the capability of LSI to assess renal perfusion heterogeneities. The main findings were that: 1) full-field LSI measurements of renal microvascular perfusion were highly correlated to single-point LDV measurements; 2) LSI is able to detect differences in reperfusion dynamics following different durations of ischemia; and 3) renal microvascular perfusion heterogeneities can be quantitatively assessed by recovering LSI perfusion histograms.