gebhart/patrepeval huggingface dataset:
COUP-TFs regulate eye development by controlling factors essential for optic vesicle morphogenesis (2010)

Transcriptional networks, which are initiated by secreted proteins, cooperate with each other to orchestrate eye development. The establishment of dorsal/ventral polarity, especially dorsal specification in the optic vesicle, is poorly understood at a molecular and cellular level. Here, we show that COUP-TFI (Nr2f1) and COUP-TFII (Nr2f2) are highly expressed in the progenitor cells in the developing murine eye. Phenotype analysis of COUP-TFI and COUP-TFII single-gene conditional knockout mouse models suggests that COUP-TFs compensate for each other to maintain morphogenesis of the eye. However, in eye-specific COUP-TFI/TFII double-knockout mice, progenitor cells at the dorso-distal optic vesicle fail to differentiate appropriately, causing the retinal pigmented epithelium cells to adopt a neural retina fate and abnormal differentiation of the dorsal optic stalk; the development of proximo-ventral identities, neural retina and ventral optic stalk is also compromised. These cellular defects in turn lead to congenital ocular colobomata and microphthalmia. Immunohistochemical and in situ hybridization assays reveal that the expression of several regulatory genes essential for early optic vesicle development, including Pax6, Otx2, Mitf, Pax2 and Vax1/2, is altered in the corresponding compartments of the mutant eye. Using ChIP assay, siRNA treatment and transient transfection in ARPE-19 cells in vitro, we demonstrate that Pax6 and Otx2 are directly regulated by COUP-TFs. Taken together, our findings reveal novel and distinct cell-intrinsic mechanisms mediated by COUP-TF genes to direct the specification and differentiation of progenitor cells, and that COUP-TFs are crucial for dorsalization of the eye.
The Rule of Five Revisited:  Applying Log <i>D</i> in Place of Log <i>P</i> in Drug-Likeness Filters (2007)

The much publicized "Rule of 5" has been widely adopted among the pharmaceutical industry. It is used as a first step filter to perform virtual screening of compound libraries, in an effort to quickly eliminate lead candidates that have poor physicochemical properties for oral bioavailabilty. One of the key parameters used therein is log P, which is a useful descriptor, but one that fails to take into account variation in the lipophilicity of a drug with respect to the ionic states present at key biological pH values. Given that the majority of commercial pharmaceuticals contain an ionizable moiety, we propose that log D is a better descriptor for lipophilicity in the context of the Rule of 5. It gives more physiologically relevant results, thereby reducing the number of potential false-negatives incorrectly eliminated in screening. Using a series of commercial compound libraries, this study showed that the adapted Rule of 5 using log D instead of log P provides notable improvement in pass rate for compounds that have the desired lipophilicity at a relevant physiological pH.
Hybrid generative-discriminative classification using posterior divergence (2011)

Integrating generative models and discriminative models in a hybrid scheme has shown some success in recognition tasks. In such scheme, generative models are used to derive feature maps for outputting a set of fixed length features that are used by discriminative models to perform classification. In this paper, we present a method, called posterior divergence, to derive feature maps from the log likelihood function implied in the incremental expectation-maximization algorithm. These feature maps evaluate a sample in three complementary measures: (1) how much the sample affects the model; (2) how well the sample fits the model; (3) how uncertain the fit is. We prove that the linear classification error rate using the outputs of the derived feature maps is at least as low as that of plug-in estimation. We present efficient algorithms for computing these feature maps for semi-supervised learning and supervised learning. We evaluate the proposed method on three typical applications, i.e. scene recognition, face and non-face classification and protein sequence analysis, and demonstrate improvements over related methods.
A fast Green's function method for calculating bulk wave frequency responses from SAW frequency responses (2002)

A method for the fast simulation of bulk wave second-order effects in SAW (surface acoustic wave) devices is described. It is shown that the bulk wave contribution to the total frequency response of a device can be computed from the real part of its surface wave frequency response. Similarly, the bulk wave input admittances can be found from the surface wave input conductances of the interdigital transducers. Being based on the electroacoustic Green's function for a piezoelectric halfspace with unmetallized surface, the analysis takes the full spectrum of nonreflected bulk waves into account.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Intrasystem transmission losses (1943)

THIS paper describes a new method of calculating transmission losses within power systems. Reasonable accuracy is obtained with longhand calculation, although the same general scheme with the load-flow determinations carried out on a d-c calculating board would provide greater accuracy with less work. The use of an a-c calculating board with separate tabulations of kilowatt and kilovar flows would be even more advantageous. The method is based on the principle of superimposing the load distribution from each source, determining the current in each line as a sum of the individual load flows (with each in its proper direction), squaring this expression for current, and setting up an equation for losses in terms of megawatt generation at the various plants and of megawatt flows (in or out) at each interchange point. An outward flow of power at an interchange point is considered negative generation.
Molecular Weight of Human Angiotensin I (1972)

Human angiotensin I converting enzyme from lung tissues, when partially purified by ammonium sulfate precipitation followed by Sephadex G-200 gel filtration chromatography, has an estimated molecular weight of 480,000. With the techniques used it was possible to separate angiotensin I converting enzyme activity from angiotensinase activity. Evidence is provided for more than one angiotensin I converting enzyme.
Myelination of the developing lateral olfactory tract and anterior commissure (2018)

Both the lateral olfactory tract (LOT) and anterior limb of the anterior commissure (AC) carry olfactory information. The LOT forms the projection from the olfactory bulb to the ipsilateral olfactory cortices, while the AC carries odor information across the midline to the contralateral olfactory cortex and bulb. The LOT and AC differ on a number of dimensions, including early development and functional onset. The present work, examining their myelination in mice, reveals additional important differences. For example, the LOT initiates myelination 3-4 days earlier than the AC, evidenced by both an earlier increase in myelin basic protein staining seen with immunohistochemistry and an earlier appearance of myelinated fibers using electron microscopy. While both exhibit a period of rapid myelination, it occurs 4-5 days earlier in the LOT than the AC. The tracts also respond differently to early sensory restriction. Unilateral naris occlusion from the day after birth to postnatal day 30 had no consistent effects on the AC but resulted in significantly thinner myelin sheaths relative to axon caliber in the LOT. Finally, the two tracts differ structurally (the LOT contains larger, more densely packed axons with significantly thicker myelin sheaths resulting in a conduction velocity that is more than twice as fast as the AC). The findings indicate that these two large, accessible tracts provide an important means for studying brain maturation due to basic differences in both the timing of their maturation and general organization.
Data Stream Clustering for Online Anomaly Detection in Cloud Applications (2015)

This paper introduces a new approach for the online detection of performance anomalies in cloud virtual machines (VMs). It is designed for cloud infrastructure providers to detect during runtime unknown anomalies that may still be observed in complex modern systems hosted on VMs. The approach is drawn on data stream clustering of per-VM monitoring data and detects at a fine granularity where anomalies occur. Its operations are independent of the types of applications deployed over VMs. Moreover it deals with frequent changes in systems normal behaviors during runtime. The parallel analyses of each VM makes this approach scalable to a large number of VMs composing an application. The approach consists of two online steps: 1) the incremental update of sets of clusters by means of data stream clustering, and 2) the computation of two attributes characterizing the global clusters evolution. We validate our approach over a VMware vSphere testbed. It hosts a typical cloud application, MongoDB, that we study in normal behavior contexts and in presence of anomalies.
Recent Progress on Gold-Nanocluster-Based Fluorescent Probe for Environmental Analysis and Biological Sensing (2019)

Gold nanoclusters (AuNCs) are one of metal nanoclusters, which play a pivotal role in the recent advances in the research of fluorescent probes for their fluorescence effect. They are favored by most researchers due to their strong stability in fluorescence and adjustability in fluorescence wavelength when compared to traditional organic fluorescent dyes. In this review, we introduce various synthesis strategies of gold-nanocluster-based fluorescent probes and summarize their application for environmental analysis and biological sensing. The use of gold-nanocluster-based fluorescent probes for the analysis of heavy metals and inorganic and organic pollutants is covered in the environmental analysis while biological labeling, imaging, and detection are presented in biological sensing.
Visualizing legacy stratigraphic data from archaeological handbooks (2003)

In this paper, a system for the visualization and entry of 3D stratigraphic layers into a new Geographic Information System (GIS) based on the varying and sometimes incomplete records of the field archaeologist is presented. This paper presents a computer-based system that allows for incomplete and ambiguous data, indicating problems associated with this entry and shows how inaccuracies are represented so that later misinterpretation is avoided.
Non-Traditional Targets of Endocrine Disrupting Chemicals: The Roots of Hormone Signaling (2005)

The topic of endocrine disruption and the broad range of physiological effects caused by endocrine disrupting chemicals (EDCs) can only be meaningfully framed within an ecological and evolutionary context. Environmental pollutants and EDCs operate by disrupting the "chemical communication" that coordinates signaling within an organism. Here we discuss how EDCs are also able to disrupt the chemical communication between plants and soil bacteria necessary for initiating nitrogen-fixing symbiosis. We also examine, through examples of pollutant-related impacts on a wide range of invertebrates, the need for identifying emerging targets of EDCs. We suggest broadening the defined field of endocrine disruption to encompass the effects of synthetic chemicals that interfere with signaling and communication, not only within an organism, but also between organisms and linking ecosystems. The ecological consequences of failing to recognize novel targets of chemical pollutants and EDCs may be a net loss of biological diversity and a further imbalance of the global nitrogen cycle.
Immune response in mice infected in the genital tract with mouse pneumonitis agent (Chlamydia trachomatis biovar) (1984)

Female Swiss-Webster mice were inoculated intravaginally with mouse pneumonitis agent (MoPn), a Chlamydia trachomatis biovar. Inoculation with 3.5 X 10(5) egg lethal doses per mouse resulted in shedding of the agent from the genital tract for as long as 21 days. Immunoglobulin M antibodies to MoPn were detected in plasma by day 7 post-inoculation, and immunoglobulin G antibodies were detected by day 14. Antibodies were detected in genital secretions by day 20, and titers in plasma and secretions were still considerable on day 56. Delayed-type hypersensitivity tests, determined by footpad swelling, were not positive in appreciable numbers of animals until after day 25. Delayed-type hypersensitivity reactions were maximal 24 h after testing and were preceded by an Arthus-like reaction, which appeared within 3 h and declined by 12 h. Convalescent animals were rechallenged by intravaginal inoculation and were found to be solidly immune.
<i>In Vivo</i>Virtual Biopsy of Human Skin by Using Noninvasive Higher Harmonic Generation Microscopy (2009)

Higher harmonic generation microscopy (HHGM), combining both second- and third-harmonic generation (SHG and THG) modalities, is a new paradigm for <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vivo</i> noninvasive virtual biopsy. With the ability to achieve noninvasiveness, high resolution, and high penetrability at the same time, HHGM is a promising tool for future noninvasive diagnosis of skin diseases. In this paper, we report our preliminary pilot clinical trial results on <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vivo</i> virtual biopsy of human skin by using HHGM. <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">In vivo</i> virtual biopsy imaging has been performed on 21 volunteers' inside and outside forearm skin along with the damage evaluation. Together with an embryo viability study, our results not only indicate a superior viability performance of the developed system, but also a much improved penetrability in different skin types. <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ex vivo</i> studies further confirm the capability of the developed virtual biopsy system to pathohistologically distinguish different skin diseases. Our <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vivo</i> HHGM biopsy study of human skin with different colors also reveals the central role of melanin in the epi-THG resonance enhancement and attenuation. With a unique capability to molecular image the melanin distribution, epi-THG microscopy is also highly valuable for diagnosing and screening early melanocytic lesions.
New chemistry on old CDs (2004)

Old compact discs (CDs) have been found to be useful for modern chemical research. Their metal reflective film is suitable for the preparation of high-quality self-assembled monolayers (SAMs) and for electrochemical analysis; pre-grooved polycarbonate base is ideal for the "customized" fabrication of material micro/nanostructures; and the immobilization of biomolecules on CDs, in conjunction with a conventional CD drive, promises to be an inexpensive tool for point-of-care biomedical diagnosis and gene analysis.
REGIONAL ARTERIOVENOUS DIFFERENCES IN Pco2 AND pH CAN REFLECT CRITICAL ORGAN OXYGEN DELIVERY DURING ENDOTOXEMIA (1996)

The goal of this study was to assess whether serial measurements of regional veno-arterial PcoC2 (VAPco2) and arteriovenous pH (AVpH) differences reflect the onset of tissue hypoxia in various organs during endotoxemia. In 12 anesthetized, mechanically ventilated dogs, ultrasonic flow probes were placed around superior mesenteric, renal, and femoral arteries to measure regional blood flow. The corresponding veins were cannulated for blood sampling. Oxygen uptake (V02) was determined from exhaled gas analysis, and oxygen delivery (D02) was calculated as the product of thermodilution cardiac output and arterial oxygen content. Six dogs served as controls, and six received Escherichia coli endotoxin. Cardiac tamponade was induced to reduce D02. Systemic, mesenteric, and femoral critical D02 (DO2crit) were higher in the endotoxic than in the control group (systemic: 12.1 + or - 2.2 vs. 7.9 + or - 2.6 mL/kg min; mesenteric: 8.2 + or - 2.5 vs. 4.1 + or - .6 mL/100 g tissue-min; femoral: 8.3 + or - 2.3 vs. 4.6 + or - .9 mL/min; all p < .05). Systemic and regional critical oxygen extraction ratio (O2ERcrit) were lower in the endotoxic than in the control group (systemic: 45.1 + or - 9.7 vs. 74.1 + or - 9.1%; mesenteric: 37.1 + or - 15.4 vs. 71.1 + or - 7.4%; renal: 30.7 + or - 24.6 vs. 53.9 + or - 28.7%; femoral: 48.1 + or - 9.2 vs. 75.3 + or - 6.9%; all p < .05). With and without endotoxin, systemic and regional DO2crit calculated from V02, VAPco2, or AVpH were similar. In conclusion, systemic and regional VAPco2 and AVpH gradients can reflect hypoxic threshold in the presence, as in the absence, of endotoxemia.
Adaptation of the HMM distributions: Application to a VQ codebook and to a noisy environment (1992)

The authors report on the application of the adaptation of parameters of HMM distributions to a vector quantization (VQ) codebook and a noisy environment after a short training session. The adaptation to the codebook was applied to an isolated word recognition task with the 26 words of the English phonetic alphabet in speaker-independent experiments. The noise adaptation technique was applied to an isolated digit recognition task in a car. In both applications the adaptation technique significantly improved the recognition performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
PLASMONIC COLOR FILTERS (2014)

Plasmon-assisted color filtering devices have drawn increasing attention recently, thanks to their great potential for ultrahigh resolution display technology. In this paper, both transmission and reflection type color filters based on tuning surface plasmon resonance will be summarized. Transmission type color filters using nanohole arrays, nanoslits with grooves, metal–insulator–metal gratings and coaxial apertures will be reviewed first. Then reflective color filters using nanorods with ultrasmall separations will be discussed briefly. We believe more practical achievements of plasmon-based devices will be readily realized in the near future.
Dark Tourism Consumption - A call for research (2005)

There is an increasing plethora of sites associated with death, tragedy or the macabre that have become significant tourist ‘attractions’. As a result, the term ‘dark tourism’ has entered academic discourse. However, dark tourism literature is both eclectic and theoretically fragile. This is especially the case with regards to consumption and its implications for understanding the ‘dark tourist’. Thus it is suggested that the dimensions of dark tourism consumption have not been extracted or interrogated – only assumed. Consequently, with death and the nature of dying at the crux of the dark tourism concept, this article calls for the development of consumer behaviour models, which incorporate contemporary socio-cultural aspects of death and dying. It is suggested that this in turn will lead to a better understanding of consumer motives within the dark tourism domain.
Autonomous Car Parking System through a Cooperative Vehicular Positioning Network (2017)

The increasing development of the automotive industry towards a fully autonomous car has motivated the design of new value-added services in Vehicular Sensor Networks (VSNs). Within the context of VSNs, the autonomous car, with an increasing number of on-board sensors, is a mobile node that exchanges sensed and state information within the VSN. Among all the value added services for VSNs, the design of new intelligent parking management architectures where the autonomous car will coexist with traditional cars is mandatory in order to profit from all the opportunities associated with the increasing intelligence of the new generation of cars. In this work, we design a new smart parking system on top of a VSN that takes into account the heterogeneity of cars and provides guidance to the best parking place for the autonomous car based on a collaborative approach that searches for the common good of all of them measured by the accessibility rate, which is the ratio of the free parking places accessible for an autonomous car. Then, we simulate a real parking lot and the results show that the performance of our system is close to the optimum considering different communication ranges and penetration rates for the autonomous car.
Molecular dimension explored in evolution to promote proteomic complexity (2004)

The architecture of present-day protein interaction networks depends on how protein associations evolved. Here, we explore how and why evolution-related mutations influence protein structure to promote protein associations, and thereby network development. We specifically address two questions: (i) How can protein folds remain conserved while proteins accommodate new binding partnerships as genes duplicate? (ii) What is the structural/molecular basis for hub proteins being the most likely to acquire new connections? The answers stem from the examination of the structure wrapping, or protection from water attack. Wrapping is shown to be a crucial consideration in the exploration and evolution of proteomic interactivity.
The relationship between the oxidative polymers of soybean oil and flavor reversion (1954)

Summary The polymers formed during the autoxidation of soybean oil at 60°C. were isolated by a solvent‐extraction method, using diethyl ether and pentanehexane as solvents. The more polar polymer fraction was further oxidized by air at 30°C., and the volatile material obtained was fractionated and characterized. It contained the same carbonyl compounds as the volatile material which has previously been obtained from reverted soybean oil, namely acetaldehyde, propionaldehyde, n‐hexanal, and 2‐pentenal. The more polar polymer fraction contained 21.04% of oxygen and degraded to volatile carbonyl compounds under vacuum as well as under oxygen‐free nitrogen. Depolymerization and ethanolysis of these polymers were carried out in ethyl alcohol which had been adjusted to a normality of 3.5 with anhydrous hydrogen chloride. The polymeric substance formed on the filter presses of a soybean oil refinery could be depolymerized in a similar manner. It is therefore evident that oxidative polymers could be unintentionally introduced into soybean oil in various ways and serve as precursors of reversion compounds.
The Influence of Amine Functionalities on Anion Binding in Polyamide-Containing Macrocycles (2009)

Mixed amide/amine macrocyclic anion hosts of varying sizes and with different amine substituents have been synthesized and characterized. Host 2, containing a 28-membered ring and secondary amines, has shown selective binding for HSO(4)(-) over other oxo anions and halides in DMSO-d(6) using NMR titrations. Crystal structures of SO(4)(2-), HPO(4)(2-), H(2)PO(4)(-), and H(2)P(2)O(7)(2-) with the 28-membered ring hosts indicate different macrocyclic conformations depending on the N-substituent. Anion affinities appear to be correlated with macrocycle conformation.
Plant Biotechnology: A Practical Approach (2003)

To understand biotechnology, it is essential that students learn elementary laboratory protocols on plant tissue culture and recombinant DNA technology. This practical lab manual is designed to familiarize students with such protocols. The book describes simple plant tissue culture protocols that can be performed on easily available plant material, and also those meant for specific materials. Worksheets are provided to record the results of the experiments. Exercises are linked, for a better understanding of the rationale for performing them.