gebhart/patrepeval huggingface dataset:
Target RNA Secondary Structure Is a Major Determinant of miR159 Efficacy (2017)

In plants, microRNA (miRNA)-target complementarity has long been considered the predominant factor determining the silencing outcome of the miRNA-target interaction, although the efficacy of such interactions have rarely been appraised in plants. Here, we perform in planta silencing efficacy assays on seven Arabidopsis <i>MYB</i> genes, all of which contain conserved miR159-binding sites of analogous complementarity. These genes were found to be differentially silenced by miR159; <i>MYB81</i>, <i>MYB97</i>, <i>MYB101</i>, <i>MYB104</i>, and <i>DUO1</i> were all poorly silenced, whereas <i>MYB33</i> and <i>MYB65</i> were strongly silenced. Curiously, this is consistent with previous genetic analysis defining <i>MYB33</i> and <i>MYB65</i> as the major functional targets of miR159. Neither the free energy of miR159-target complementarity, nor miRNA binding site accessibility, as determined by flanking region AU content, could fully explain the discrepancy of miR159 silencing efficacy. Instead, we found that <i>MYB33</i> and <i>MYB65</i> were both predicted to contain a distinctive RNA secondary structure abutting the miR159 binding site. The structure is composed of two stem-loops (SLs) that are predicted to form in <i>MYB33</i>/65 homologs of species as evolutionary distant as gymnosperms. Functional analysis found that the RNA structure in <i>MYB33</i> correlated with strong silencing efficacy; introducing mutations to disrupt either SL attenuated miR159 efficacy, while introducing complementary mutations to restore the SLs, but not the sequence, restored strong miR159-mediated silencing. Therefore, it appears that this RNA secondary structure demarcates <i>MYB33</i>/<i>65</i> as sensitive targets of miR159, which underpins the narrow functional specificity of Arabidopsis miR159.
Low friction and rotational dynamics of crystalline flakes in solid lubrication (2011)

Solids at incommensurate contact display low-friction, 'superlubric', sliding. For graphene flakes on a graphite surface, superlubric sliding is only temporary due to rotation of the flakes from incommensurate to commensurate contact with the substrate. We examine this rotational channel of friction in a prototype geometry of meso- and macroscopic solid lubrication. By molecular dynamics simulations and theoretical arguments we find that two surfaces lubricated by mobile, rotating graphene flakes exhibit stable superlubric sliding as for ideally incommensurate contacts also when they are covered by randomly oriented pinned graphene patches. For commensurate surfaces, we find a low friction state at low temperature where incommensurate states are not destroyed by thermal fluctuations.
SMT manufacturing parameters and their impact on system reliability (2002)

Producible electronic assembly using Surface Mount Technology (SMT) includes several issues which, when addressed concurrently, result in a product which can be expected to perform throughout an extended life. This paper focuses on SMT manufacturing parameters and their impact on system reliability. The data illustrate how the use of fatigue life projections can provide insight into the correct materials and processes selection and what the resultant impact on system reliability will be. Galaxy Microsystems have undertaken several programs, both commercial and military, to implement SMT as a new technology. These programs required that the designs be compatible with several printed wiring board (PWB) technologies, utilize a complex mixture of packaging approaches and be assembled using different manufacturing flows. For example, three designs resulted in 14 layer PWBs populated with standard SMT parts, fine pitch quad flat packs (QFPs) and pin grid arrays (PGAs). The paper describes the relationships between the critical parameters and the life cycle of the hardware delivered to the customer. A depot repair process that can accommodate this overall parametric mix while simultaneously reducing the impact on solder joint fatigue is also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Critical parameters in targeted drug development: the pharmacological audit trail (2016)

The Pharmacological Audit Trail (PhAT) comprises a set of critical questions that need to be asked during discovery and development of an anticancer drug. Key aspects include: (1) defining a patient population; (2) establishing pharmacokinetic characteristics; (3) providing evidence of target engagement, pathway modulation, and biological effect with proof of concept pharmacodynamic biomarkers; (4) determining intermediate biomarkers of response; (5) assessing tumor response; and (6) determining how to overcome resistance by combination or sequential therapy and new target/drug discovery. The questions asked in the PhAT should be viewed as a continuum and not used in isolation. Different drug development programmes derive different types of benefit from these questions. The PhAT is critical in making go-no-go decisions in the development of currently studied drugs and will continue to be relevant to discovery and development of future generations of anticancer agents.
Diastereoselective Friedel–Crafts Alkylation of Hydronaphthalenes (2011)

An efficient and versatile synthesis of chiral tetralins has been developed using both inter- and intramolecular Friedel-Crafts alkylation as a key step. The readily available hydronaphthalene substrates were prepared via a highly enantioselective metal-catalyzed ring opening of meso-oxabicyclic alkenes followed by hydrogenation. A wide variety of complex tetracyclic compounds have been isolated with high levels of regio-, diastereo-, and enantioselectivity.
Surface mesh quality evaluation (1999)

This paper proposes a method to evaluate the size quality as well as the shape quality of constrained surface meshes, the constraint being either a given metric or the geometric metric associated with the surface geometry. In the context of numerical simulations, the metric specifications are those related to the finite element method. The proposed measures allow to validate the surface meshes within a general mesh adaption scheme, the metric map being usually provided via an a posteriori error estimate. Several examples of surface meshes are proposed to illustrate the relevance of the approach. Copyright © 1999 John Wiley & Sons, Ltd.
Digoxin inhibits neuroblastoma tumor growth in mice. (2005)

Our data suggest that digoxin may be a specific neuroblastoma growth inhibitor and an unspecific inhibitor of angiogenesis.
Changes in Microbial Ecology Aft er Fecal Microbiota Transplantation for Recurrent C. Difficile Infection Depends on Underlying Inflammatory Bowel Disease (2016)

Author(s): Khanna, Sahil; Vzquez-Baeza, Yoshiki; Gonzalez, Antonio; Weiss, Sophie; Schmidt, Bradley; Muniz-Pedrogo, David; III, Rainey John F; Kammer, Patricia; Nelson, Heidi; Sadowsky, Michael; Khoruts, Alexander; Farrugia, Stefan L; Knight, Rob; Pardi, Darrell; Kashyap, Purna
Mechanisms and Treatment of Graft Failure (2015)

This chapter reviews the clinical aspects associated with, and treatment of, graft failure (GF). The restoration of adequate blood cell production after hematopoietic cell transplantation (HCT) requires a series of balanced interactions between the infused hematopoietic stem cell (HSC) and its complex supporting marrow microenvironment. It is well established that reduced-intensity conditioning (RIC) for allogeneic HCT is associated with incomplete eradication of host hematopoietic elements. A clearer understanding of the role of various donor T-cell populations, including Treg cells, veto cell populations, and costimulation signaling pathways, has the potential to reduce host-versus-graft (HVG) reactions that underlie immune-mediated allograft rejection. ABO incompatibility between donor and recipients occurs in approximately 25% of human leukocyte antigen (HLA)-matched allogeneic transplants. Preclinical models of BM transplantation demonstrated that following RIC, suboptimal immune suppression medication immediately post-transplantation increased the risk of early GF, whereas adequate dosing supported engraftment by inhibiting HVG reactions.
A Q&A approach to drug-induced liver injury (2007)

Hepatotoxicity accounts for approximately half of all cases of acute liver failure seen in the United States. Here is a handy summary of what you need to know to protect your patients, whenever possible, from the ravages of drug-induced liver injury.
Night Visibility Video for Accident Reconstruction (1996)

In this paper a new low light video recording system is described. This system can be used to document visibility conditions at nighttime accident scenes. The system includes a means for calibrating the recording and playback equipment for the prevailing illumination conditions while on location at an accident scene. Use of a hand-held grey scale chart facilitates calibration of the equipment, and provides a visual check during playback. The characteristics, use and adaptability of the system for a variety of accident reconstruction activities are described. (A) For the covering abstract of the conference see IRRD 898597.
Electromagnetically induced absorption and transparency due to long-lived Zeeman coherence (2009)

Seven immune factors, lysozyme, hepcidin, heat-shock protein (HSP) 70, HSP90, immunoglobulin M, C-type lectin, and Lily-type lectin, were measured by PCR in the livers, spleens, and head kidneys of turbot infected with Vibrio anguillarum. Additive main effects and multiplicative interaction (AMMI) and genotype main effects and genotype × environment interaction (GGE) biplot analysis were used to analyze genotype × tissue interactions for immunological factors. The AMMI analysis revealed that immune factor expression was significantly affected by genotype, tissue, and genotype × tissue interactions. Genotype (65.85%) was the major contributor to the total variation in immune factor expression in comparison to tissue effects (7.54%) and genotype × tissue interactions (12.52%). GGE biplot analysis revealed differences in the ranking of the seven immune factors in the three tissues; head kidney possessed the strongest ability to distinguish the seven immune factors. The test tissue locations were divided into liver-spleen and head kidneys regions; HSP70 was expressed the highest in the liver-spleen regions, and lysozyme had the highest expression in the head kidney region. Overall, HSP70 and HSP90 had the best expression and stability in the three tissues.
Atomic layer etching removal of damaged layers in a contact hole for low sheet resistance (2013)

A damaged layer remains on silicon substrates after high-aspect-ratio contact (HARC) etching when using a fluorocarbon gas. Atomic layer etching (ALET) is a technique that can be applied to remove the damaged layer of silicon, removing about 1.36 Å per etch cycle. The characteristics of contact damage removal by ALET are investigated and compared with the conventional damage removal technique of low-power CF4 plasma etching. The low-power CF4 plasma etching technique not only has inadequate etch depth control, but also introduces secondary damage by implanting impurities about 25 Å into the contact bottom of the silicon surface. However, ALET allows contact damage to be removed effectively without introducing secondary damage to the substrate, and with precision etch depth control at the angstrom scale. When ALET is applied subsequent to low-power CF4 plasma etching, the fluorine- and carbon-damaged silicon is effectively removed in about 10 cycles. The sheet resistance of HARC etched silicon decreases from 142 to 137 Ω/◻ after using low-power CF4 plasma etching, and subsequent ALET treatment further decreases the sheet resistance to 129 Ω/◻, which is close to the reference value of 124 Ω/◻.
SOX2 expression correlates with lymph-node metastases and distant spread in right-sided colon cancer (2011)

We demonstrated that increased expression of either SOX2 or nuclear β-catenin are associated with distant metastases in right-sided CC. Additionally, SOX2 is also associated with lymph-node metastases. These data underline the importance of stemness-associated markers for the identification of CC with high risk for distant spread.
Differences in susceptibility to German cockroach frass and its associated proteases in induced allergic inflammation in mice (2007)

While both strains of mice were able to induce experimental asthma following GC frass sensitization and challenge, the active serine proteases in GC frass only play a role in airway hyperresponsiveness in Balb/c mice that were susceptible to sensitization via inhalation. The differences in the method of sensitization suggest genetic differences between strains of mice.
Infarct Pattern, Perfusion Mismatch Thresholds, and Recurrent Cerebrovascular Events in Symptomatic Intracranial Stenosis (2019)

IBZ infarcts may be a surrogate marker of distal perfusion status and RCVE risk. Larger multicenter, prospective, core-lab blindly adjudicated studies are needed to confirm our findings.
Call for Emergency Action to Limit Global Temperature Increases, Restore Biodiversity, and Protect Health (2021)

> Wealthy nations must do much more, much faster.

The United Nations General Assembly in September 2021 will bring countries together at a critical time for marshalling collective action to tackle the global environmental crisis. They will meet again at the biodiversity summit in Kunming, China, and the climate conference (Conference of the Parties (COP)26) in Glasgow, UK. Ahead of these pivotal meetings, we—the editors of health journals worldwide—call for urgent action to keep average global temperature increases below 1.5°C, halt the destruction of nature and protect health.

Health is already being harmed by global temperature increases and the destruction of the natural world, a state of affairs health professionals have been bringing attention to for decades.1 The science is unequivocal; a global increase of 1.5°C above the preindustrial average and the continued loss of biodiversity risk catastrophic harm to health that will be impossible to reverse.2 3 Despite the world’s necessary preoccupation with COVID-19, we cannot wait for the pandemic to pass to rapidly reduce emissions.

Reflecting the severity of the moment, this editorial appears in health journals across the world. We are united in recognising that only fundamental and equitable changes to societies will reverse our current trajectory.

The risks to health of increases above 1.5°C are now well established.2 Indeed, no temperature rise is ‘safe’. In the past 20 years, heat-related mortality among people aged over 65 has increased by more than 50%.4 Higher temperatures have brought increased dehydration and renal function loss, dermatological malignancies, tropical infections, adverse mental health outcomes, pregnancy complications, allergies, and cardiovascular and pulmonary morbidity and mortality.5 6 Harms disproportionately affect the most vulnerable, including children, older populations, ethnic minorities, poorer communities and those with underlying health problems.2 4 

Global heating is also contributing to the decline in …
Load balancing in dynamic structured P2P systems (2005)

Most P2P systems that provide a DHT abstraction distribute objects randomly among "peer nodes" in a way that results in some nodes having /spl theta/(log N) times as many objects as the average node. Further imbalance may result due to non-uniform distribution of objects in the identifier space and a high degree of heterogeneity in object loads and node capacities. Additionally, a node's load may vary greatly over time since the system can be expected to experience continuous insertions and deletions of objects, skewed object arrival patterns, and continuous arrival and departure of nodes. We propose an algorithm for load balancing in such heterogeneous, dynamic P2P systems. Our simulation results show that in the face of rapid arrivals and departures of objects of widely varying load, our algorithm achieves load balancing for system utilizations as high as 90% while moving only about 8% of the load that arrives into the system. Similarly, in a dynamic system where nodes arrive and depart, our algorithm moves less than 60% of the load the underlying DHT moves due to node arrivals and departures. Finally, we show that our distributed algorithm performs only negligibly worse than a similar centralized algorithm, and that node heterogeneity helps, not hurts, the scalability of our algorithm.
METASTABLE Co–Au ALLOYS: EXAMPLE OF AN AMORPHOUS FERROMAGNET (1965)

First Page
The flowering time regulator CONSTANS is recruited to the FLOWERING LOCUS T promoter via a unique cis ‐element (2010)

CONSTANS is an evolutionarily-conserved central component of the genetic pathway that controls the onset of flowering in response to daylength. However, the specific biochemical mechanism by which the CONSTANS protein regulates the expression of its target genes remains largely unknown. *By using a combination of cell-based expression analysis and in vitro DNA binding studies, we have demonstrated that CONSTANS possesses transcriptional activation potential and is capable of directly binding to DNA. *CONSTANS was found to bind DNA via a unique sequence element containing a consensus TGTG(N2-3)ATG motif. This element is present in tandem within the FLOWERING LOCUS T promoter and is sufficient for CO binding and activity. The conserved CCT (CONSTANS, CONSTANS-like and TOC1) domain of CONSTANS was shown to be required for its recruitment to the DNA motif and other CCT-containing proteins were also found to have the ability to regulate gene expression via this element. *The CCAAT box, which has been previously hypothesized as a recruitment site for complexes containing the CONSTANS protein, potentiated CONSTANS-mediated activation but was not essential for CONSTANS recruitment to a target promoter or for its activity as a transcriptional factor.
Regional Fractures II: Fracturing of Mesaverde Reservoirs in the Piceance Basin, Colorado (1) (1991)

Cretaceous strata in the east-central Piceance basin of northwestern Colorado were subjected to several phases of stress due to horizontal tectonic compression, burial, and uplift. These rocks contain a regional set of west-northwest extension fractures, observed in abundant vertical and deviated core from the U.S. Department of Energy's Multiwell Experiment and Slant Hole Completion Test wells. Time-depth relationships, fracture orientation, and fluid inclusion analyses indicate that the fractures formed at about 36-40 Ma, during a phase of increased Laramide west-northwest compression, and in a pressure-temperature regime compatible with the geologically reconstructed maximum burial depths. This regional fracturing is an example of load-parallel extension fracturing and basinwide dilatancy at depth, under conditions of high pore pressure and anisotropic, tectonically created, horizontal stress.
In Situ Generation of PhI+CF3 and Transition‐Metal‐Free Oxidative sp2 CH Trifluoromethylation (2013)

These things are sent to tri us: The introduction of CF3 units into organic molecules is important and requires the development of convenient trifluoromethylating reagents. Here, PhI+CF3, an acyclic electrophilic “CF3+” species, is described, including its in situ generation from TMSCF3, PhI(OAc)2, and KF and its direct applications in sp2 CH trifluoromethylations under mild transition-metal-free conditions (see scheme). As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. 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.
Supplementary Data from The Pan-Tumor Landscape of Targetable Kinase Fusions in Circulating Tumor DNA (2023)

Supplementary Data from The Pan-Tumor Landscape of Targetable Kinase Fusions in Circulating Tumor DNA
Quantum-chemical study of organic reaction mechanisms: I. Addition of selenium dihalides to the double bond of vinyl ethers (2013)

The mechanism of addition of selenium dihalides to vinyl ethers was studied at the B3LYP/6-311+G(d,p) level of theory. The reaction goes in two steps through seleniranium intermediate. High selectivity of the addition is ensured by consistent effects of the charge and orbital factors.
Theory of spin torque due to spin-orbit coupling (2009)

The combined effect of spin-orbit coupling and exchange interaction in a single ferromagnetic layer is investigated. It is shown that, in nonequilibrium regime, the spin-orbit interaction (SOI) gives rise to a transverse spin density that exerts a torque on the local magnetization. The spin torque depends on the symmetry properties of the SOI. For the inversion-symmetry-preserved SOI such as the impurity SOI and the Luttinger spin-orbit band, the spin torque is a high-order effect too small to lead to a reasonable critical switching current density. For the inversion-symmetry-broken SOI, e.g., Rashba and Dresselhaus SOIs, the torque is on the first order of the SOI parameter and can be effectively used to control the magnetization direction using critical switching current densities as low as ${10}^{4}--{10}^{6}\text{ }\text{A}/{\text{cm}}^{2}$. We also address the relation between the spin torque and the anisotropic magnetoresistance. Finally, a number of systems are proposed for the experimental observation of the SOI-induced torque.
Boolean Gossip Networks (2017)

This paper proposes and investigates a Boolean gossip model as a simplified but non-trivial probabilistic Boolean network. With positive node interactions, in view of standard theories from Markov chains, we prove that the node states asymptotically converge to an agreement at a binary random variable, whose distribution is characterized for large-scale networks by mean-field approximation. Using combinatorial analysis, we also successfully count the number of communication classes of the positive Boolean network explicitly in terms of the topology of the underlying interaction graph, where remarkably minor variation in local structures can drastically change the number of network communication classes. With general Boolean interaction rules, emergence of absorbing network Boolean dynamics is shown to be determined by the network structure with necessary and sufficient conditions established regarding when the Boolean gossip process defines absorbing Markov chains. Particularly, it is shown that for the majority of the Boolean interaction rules, except for nine out of the total 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">16</sup> - 1 possible nonempty sets of binary Boolean functions, whether the induced chain is absorbing has nothing to do with the topology of the underlying interaction graph, as long as connectivity is assumed. These results illustrate the possibilities of relating dynamical properties of Boolean networks to graphical properties of the underlying interactions.