gebhart/patrepeval huggingface dataset:
Evolthon: A community endeavor to evolve lab evolution (2019)

In experimental evolution, scientists evolve organisms in the lab, typically by challenging them to new environmental conditions. How best to evolve a desired trait? Should the challenge be applied abruptly, gradually, periodically, sporadically? Should one apply chemical mutagenesis, and do strains with high innate mutation rate evolve faster? What are ideal population sizes of evolving populations? There are endless strategies, beyond those that can be exposed by individual labs. We therefore arranged a community challenge, Evolthon, in which students and scientists from different labs were asked to evolve Escherichia coli or Saccharomyces cerevisiae for an abiotic stress-low temperature. About 30 participants from around the world explored diverse environmental and genetic regimes of evolution. After a period of evolution in each lab, all strains of each species were competed with one another. In yeast, the most successful strategies were those that used mating, underscoring the importance of sex in evolution. In bacteria, the fittest strain used a strategy based on exploration of different mutation rates. Different strategies displayed variable levels of performance and stability across additional challenges and conditions. This study therefore uncovers principles of effective experimental evolutionary regimens and might prove useful also for biotechnological developments of new strains and for understanding natural strategies in evolutionary arms races between species. Evolthon constitutes a model for community-based scientific exploration that encourages creativity and cooperation.
Patient Eligibility for Standardized Treatment of the Edentulous Mandible: A Retrospective CBCT-Based Assessment of Mandibular Morphology (2019)

The aim of the study was to evaluate the proportion of patients recommended for full-arch mandibular restoration that would be eligible for treatment with a recently developed premanufactured full-arch prosthesis (Trefoil™, Nobel Biocare) based on the morphology of their lower jaw. Anonymized cone beam computed tomography (CBCT) data from 100 partially and fully edentulous patients referred for full-arch mandibular restoration were retrospectively collected from an imaging center database. Using custom-built software, CBCTs of mandibles were registered to a reference CBCT of a patient treated previously with a premanufactured full-arch prosthesis to determine if patients had adequate horizontal width and vertical height for implant placement. Bone height and thickness around simulated implants and distances to the incisive canal were evaluated. Mandibular arch width and semi-automated volume calculations were also performed. Using the system-specific 5.0 mm diameter implants with lengths of 13 and 11.5 mm, 85% and 86% of patients, respectively, were eligible for treatment with the standardized prosthesis. Eligibility was higher for men than women (odds ratio = 3.9, <i>p</i> = 0.045) due to increased bone volume. Based on mandibular morphology, our results suggest that the standardized treatment concept could serve a large percentage of patients with edentulous mandibles or failing dentition in the mandible.
Copy-number variation in control population cohorts (2007)

Copy-number variation (CNV) is the most prevalent type of structural variation in the human genome, and contributes significantly to genetic heterogeneity. It has already been recognized that some CNVs can contribute to human phenotype, including rare genomic disorders and Mendelian diseases. Other CNVs are now amenable to genome-wide association studies so that their influence on human phenotypic diversity and disease susceptibility may soon be more readily determined. Population studies and reference databases for control and disease-associated samples are required to provide an information resource about CNV frequencies and their relative contribution to phenotypic outcomes. The relatively high cost of screening individual samples has tended to limit the number of controls assayed, and use of the data has often been hampered by the variety of technology platforms and analysis techniques. As a result, there is still a paucity of data on population frequency and distribution of CNVs, particularly for those that are rare. Here, we provide an example of how to discover new CNVs from existing genotype data from large-scale genetic epidemiological studies. We also discuss the need to expand surveys of CNV in different population-based cohorts and to apply the information to studies of human variation and disease.
High Frequency Injection Based Rotor Position Self-Sensing for Synchronous Electrostatic Machines (2019)

The low loss during high torque, low speed operation demonstrated by synchronous electrostatic machines make them an attractive choice for low speed servo applications. The high pole count (p >50) of these machines necessitates the use of high resolution position sensors. This work proposes methods of rotor position self-sensing for separately excited synchronous electrostatic machines to reduce cost and complexity associated with using an external encoder. A high-frequency injection based self-sensing method, which takes advantage of the separate excitation of the machine is proposed for estimating rotor position at zero and low speeds. The performance of the proposed estimation method is experimentally verified using a current source inverter driving the electrostatic machine. Closed loop speed control without encoder feedback is demonstrated. A compensation technique to mitigate the effect of filter delays is implemented to improve estimation accuracy at higher fundamental frequencies.
ChemInform Abstract: Convergent Synthesis of (R,R)‐6,12‐Dimethylpentadecan‐2‐one (VII), the Female Sex Pheromone of the Banded Cucumber Beetle by Iron‐Mediated Chirality Transfer. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Blue Light Emitting Defective Nanocrystals Composed of Earth‐Abundant Elements (2019)

Abstract Copper‐based ternary (I–III–VI) chalcogenide nanocrystals (NCs) are compositionally‐flexible semiconductors that do not contain lead (Pb) or cadmium (Cd). Cu‐In‐S NCs are the dominantly studied member of this important materials class and have been reported to contain optically‐active defect states. However, there are minimal reports of In‐free compositions that exhibit efficient photoluminescence (PL). Here, we report a novel solution‐phase synthesis of ≈4 nm defective nanocrystals (DNCs) composed of copper, aluminum, zinc, and sulfur with ≈20 % quantum yield and an attractive PL maximum of 450 nm. Extensive spectroscopic characterization suggests the presence of highly localized electronic states resulting in reasonably fast PL decays (≈1 ns), large vibrational energy spacing, small Stokes shift, and temperature‐independent PL linewidth and PL lifetime (between room temperature and ≈5 K). Furthermore, density functional theory (DFT) calculations suggest PL transitions arise from defects within a CuAl 5 S 8 crystal lattice, which supports the experimental observation of highly‐localized states. The results reported here provide a new material with unique optoelectronic characteristics that is an important analog to well‐explored Cu‐In‐S NCs.
Large time step discrete-time modeling of sharp wave activity in hippocampal area CA3 (2018)

Abstract Reduced models of neuronal spiking activity simulated with a fixed integration time step are frequently used in studies of spatio-temporal dynamics of neurobiological networks. The choice of fixed time step integration provides computational simplicity and efficiency, especially in cases dealing with large number of neurons and synapses operating at a different level of activity across the population at any given time. A network model tuned to generate a particular type of oscillations or wave patterns is sensitive to the intrinsic properties of neurons and synapses and, therefore, commonly susceptible to changes in the time step of integration. In this study, we analyzed a model of sharp-wave activity in the network of hippocampal area CA3, to examine how an increase of the integration time step affects network behavior and to propose adjustments of intrinsic properties of neurons and synapses that help minimize or remove the damage caused by the time step increase. Highlights Spiking models of neural network activity are sensitive to the integration step Larger integration time steps are preferable in simulating large networks Case study of CA3 sharp waves shows time step increase damages network dynamics Neuronal and synaptic parameters adjustments rescue the dynamics at large time step 1
Finding the worst voltage violation in multi-domain clock gated power network (2008)

This paper proposes an efficient method to find the worst case of voltage violation by multi-domain clock gating in an on-chip power network. We first present a voltage response in an arbitrary multi-domain clock gating pattern, using a superposition technique. Then, an integer linear programming (ILP) formulation is proposed to identify the worst-case gating pattern and the maximum variation area. The ILP based method is significantly faster than a conventional method based on enumeration. The experimental results are also compared with a case where peak voltage variation is induced, which shows the latter technique largely underestimated the overall variation effect.
Enhancing Rules For Cloud Resource Provisioning Via Learned Software Performance Models (2016)

In cloud computing, stakeholders deploy and run their software applications on a sophisticated infrastructure that is owned and managed by third-party providers. The ability of a given cloud infrastructure to effectively re-allocate resources to applications is referred to as elasticity. To enable elasticity, programmers study the behavior of applications and write scripts that guide the cloud to provision resources for these applications. This is an imprecise, laborious, manual and expensive approach that drastically increases the cost of application deployment and maintenance in the cloud. We propose an approach, coined as Provisioning Resources with Experimental SofTware mOdeling (PRESTO), to automatically learn behavioral models of software applications during performance testing in order to recommend programmers how to improve provisioning strategies that guide the cloud to (de)allocate resources to these applications. We applied PRESTO to two software applications and our experiments demonstrate that with PRESTO programmers can create rules for provisioning resources with a high degree of precision when the performance is about to worsen, so that the applications maintain their throughputs at the desired level.
Experimental measurements of the origin of self-phasing in passively coupled fiber lasers (2015)

We have directly measured the intensity distribution, gain, and induced phase shift between two fiber lasers that are coherently combined by a Dammann grating. The induced phase shift between the lasers has been shown to approximately cancel out any applied phase error introduced into the cavity, allowing the combined resonator to operate at an efficient low-loss state. We show that the origin of this self-phasing stems from a redistribution of power between the two lasers. The resulting difference in circulating intensity produces a differential change in saturated gain, which in turn produces a differential Kramers-Kronig phase shift that effectively cancels the applied phase error.
Spectroscopic Disease Diagnosis (2016)

Since its establishment at 1985, MIT Laser Biomedical Research Center has pioneered and advanced spectroscopic tissue diagnosis. By analyzing tissue intrinsic spectroscopic signals from diffuse reflectance, intrinsic fluorescence and Raman spectroscopy, disease states of tissue can be determined. Spectroscopic tissue diagnosis was successfully applied to various cancer diagnosis. At the same time, there has been effort to implement the noninvasive blood glucose monitoring based on NIR Raman spectroscopy. In this presentation, latest progresses on these topics will be discussed.
Cardiomyocyte differentiation in human embryonic stem cell progeny (2004)

This chapter describes the processes involved in the derivation and characterization of cardiomyocytes using the unique human embryonic stem (ES) cell differentiation system. It also describes the potential research and clinical applications of the new technology in cardiovascular medicine. ES cells can be propagated continuously in the undifferentiated state when grown on mouse embryonic fibroblast feeder layers. In the mouse model this can also be achieved in the feeder free setting by supplementing the medium with leukemia inhibitory factor. The most attractive application of human ES cells, and the one that receives the most attention, is in cell replacement therapy: to replace diseased, missing or degenerative tissue. The adult heart has only limited regenerative capacity and therefore any significant myocardial cell death resulting from ischemic heart disease, viral infection or immunopathological conditions may lead to permanent impairment of myocardial performance, and ultimately, heart failure.
[Case of retinal ischemia and retinal arteritis secondary to intravitreal nuclear drop]. (2011)

Incomplete branch retinal artery occlusion caused by phacoanaphylactic endophthalmitis secondary to lens fragments in the vitreous cavity seems to be a rare condition related to retinal whitening. The timing of pars plana vitrectomy should be considered before retinal arterial sheathing or retinal whitening can be noted.
Lactogenic hormones and Tenascin-C regulate C/EBP? and ? in mammary epithelial cells (2000)

Mammary epithelial cell differentiation depends on lactogenic hormones, growth factors, and cell-cell and cell-substrate interactions, all of which modulate transcription factors essential for milk protein gene expression. The CCAAT/enhancer binding protein (C/EBP) family and the signal transducer and activator of transcription 5 (Stat5) have been implicated in mammary epithelial cell growth and differentiation. We have investigated the effects of extracellular matrix components and lactogenic hormones on C/EBP and Stat5 activity. In the mammary gland, tenascin is expressed mainly during embryogenesis and carcinogenesis and in cell culture tenascin downregulates beta-casein gene expression. In HC11 mammary cells, we found that tenascin, but not laminin or fibronectin, specifically downregulated C/EBPalpha levels but had no effect on Stat5 amount or DNA binding activity. Furthermore, we found that the lactogenic hormones, glucocorticoids, prolactin, and insulin, had no effect on C/EBPalpha and C/EBPbeta protein levels but downregulated the DNA binding activity of the transcriptional repressor C/EBPbetaLIP. Thus, C/EBPalpha and beta are regulated by tenascin and lactogenic hormones in mammary epithelial cells.
A M2M-based Automotive Service Delivery Platform for Distributed Vehicular Applications. (2014)

Modern vehicles are connected with the Internet through a range of wireless cellular network technologies. This provides the basis for many novel applications and use-cases towards intelligent vehicles, offering enhanced vehicle safety, traffic management, and driver and passenger convenience capabilities. The connectivity further enables new distributed software architectures that can provide solutions to existing challenges in the field of automotive software engineering. This paper introduces the approach of an Automotive Service Delivery Platform, based on the Machine-to-Machine Communication Service Architecture. Experiences and findings are presented, gained by implementing core elements of the proposed architecture prototypically. This implementation makes apparent the range and capabilities of current Machine-to-Machine Service Architecture and describes remaining challenges to facilitate efficient distributed automotive services.
Biomechanical analysis of the role of wrist guards in "splint-top" forearm fractures [skating application] (2002)

The use of wrist guards has substantially reduced the incidence of wrist and forearm injuries. There is concern, however, that current wrist guard designs do not sufficiently protect the forearm. This study tests the hypothesis that, during a fall while wearing wrist guards, mid-shaft forearm stress can exceed the ultimate strength of cortical bone. Further, it investigates possible mechanisms by examining impacts at (1) the thenar eminence, vs. (2) the metacarpal heads, as well as examining stresses along the length of the forearm. A model of forearm, palm, and wrist guard biomechanics implemented parameter values from the literature and direct measurement to compute link forces and moments. Normal, shear and principal stresses were computed in cortical bone as a function of position along the forearm. The model supported the hypothesis: under a 2000N impact to the thenar eminence, the principal stress exceeds cortical bone ultimate strength, at 256 MPa. At the metacarpal heads, the maximum principal stress was 225 MPa, suggesting this unusual load pattern is not a mechanism for mid-shaft fracture. Forearm stresses did show a sharp increase at the proximal wrist guard edge, reflecting an abrupt end to load-sharing and suggesting large local stresses. In conclusion, the results suggest a new wrist guard design incorporating a gradual tapering of bending moment of inertia will diminish the load transfer rate at the wrist guard edge, possibly reducing the occurrence of "splint-top" fractures.
Abundance ofAeromonasspp. in various components of pond ecoysystems in Dhaka, Bangladesh (1992)

Aeromonas spp. are considered to be waterborne agents of human gastroenteritis. A study was carried out in five ponds in Dhaka city over a period of one year to investigate the distribution and seasonality of these organisms in various components of pond ecosystems. Samples were collected from plants, water, phytoplankton and sediment every 15 days over 12 months and cultured for Aeromonas spp. using enrichment techniques. A. sobria, A. hydrophila and A. caviae were isolated from 199 (41.46%), 29 (6.04%) and 21 (4.38%) of the 480 samples, respectively. Two distinct peaks of A. sobria were observed in all components; one during the warmer months of May‐July and the other at the beginning of winter in November. Aeromonas spp. were isolated from all components from all ponds during the study period. This study gives some insight into the epidemiology of diarrhoea due to Aeromonas spp. in Bangladesh.
The Activity of a Developmentally Regulated Cysteine Proteinase Is Required for Cyst Wall Formation in the Primitive EukaryoteGiardia lamblia (2002)

Giardia is an intestinal parasite that belongs to the earliest diverging branch of the eukaryotic lineage of descent. Giardia undergoes adaptation for survival outside the host's intestine by differentiating into infective cysts. Encystation involves the synthesis and transport of cyst wall constituents to the plasma membrane for release and extracellular organization. Nevertheless, little is known about the molecular events related to cyst wall biogenesis in Giardia. Among the components of the cyst wall there are two proteins that we have previously identified and characterized: CWP1 (26 kDa) and CWP2 (39 kDa). Expression of these proteins is coordinately induced, and both concentrated within encystation-specific secretory vesicles before their extracellular polymerization. Although highly similar to each other at the amino terminus, CWP2 includes a COOH-terminal 121-amino acid extension. Here, we show that this extension, rich in basic residues, is cleaved from CWP2 before cyst wall formation by an intracellular cysteine proteinase activity, which is induced during encystation like CWPs. Specific inhibitors prevent release of cyst wall materials, abolishing cyst wall formation. We also report the purification, cloning, and characterization of the encystation-specific cysteine proteinase responsible for the proteolytic processing of CWP2, which is homologue to lysosomal cathepsin C. Encystation-specific cysteine proteinase ESCP possesses unique characteristics compared with cathepsins from higher eukaryotes, such as a transmembrane domain and a short cytoplasmic tail. These features make this enzyme the most divergent cathepsin C identified to date and provide new insights regarding cyst wall formation in Giardia.
Full characterization of ultrathin 5-nm low-k dielectric bilayers: Influence of dopants and surfaces on the mechanical properties (2020)

Ultrathin films and multilayers, with controlled thickness down to single atomic layers, are critical for advanced technologies ranging from nanoelectronics to spintronics to quantum devices. However, for thicknesses less than 10 nm, surfaces and dopants contribute significantly to the film properties, which can differ dramatically from that of bulk materials. For amorphous films being developed as low dielectric constant interfaces for nanoelectronics, the presence of surfaces or dopants can soften films and degrade their mechanical performance. Here we use coherent short-wavelength light to fully and nondestructively characterize the mechanical properties of individual films as thin as 5 nm within a bilayer. In general, we find that the mechanical properties depend both on the amount of doping and the presence of surfaces. In very thin (5-nm) silicon carbide bilayers with low hydrogen doping, surface effects induce a substantial softening---by almost an order of magnitude---compared with the same doping in thicker (46-nm) bilayers. These findings are important for informed design of ultrathin films for a host of nano- and quantum technologies, and for improving the switching speed and efficiency of next-generation electronics.
Tocotrienols from palm oil: Electron spin resonance spectra of tocotrienoxyl radicals (1990)

Abstract The major vitamin E components present in palm oil, viz. α‐tocopherol, α − , ψ‐and δ‐tocotrienols, have been isolated and their structures verified by the NMR spectra of their acetate and succinate derivatives. Oxidation of γ‐and δ‐tocotrienols with alkaline K 3 Fe(CN) 6 gave isolable dimeric species, which were studied by 13 C NMR. Free radicals generated from the monomeric and dimeric tocotrienols were investigated using ESR spectroscopy. The distinction between antioxidant activity and antioxidant capacity of vitamin E isomers is discussed.