gebhart/patrepeval huggingface dataset:
Long‐term enhancement of CA1 synaptic transmission is due to increased quantal size, not quantal content (1991)

Quantal components of Schaffer collateral synaptic transmission recorded intracellularly from CA1 pyramidal cells were examined using 2 methods: simultaneous recordings of CA3-CA1 cell-pairs, and minimal electrical stimulation in stratum radiatum. Quantal parameters estimated by the method of failures and by a computer algorithm that optimized parameter estimates using deconvolution of background noise were highly correlated. EPSP-amplitude histograms of CA3-CA1 cell pairs (N = 10) and minimal electrical stimulation (N = 33) could be adequately described either by Poisson or binomial statistics, or by both, and exhibited similar estimates of unit quantal size (q) and mean quantal content (m). Paired-pulse stimulation with 50 msec between stimuli resulted in an expected facilitation in the EPSP amplitude and increase in m during the second response, as estimated by noise deconvolution, by the decrease in apparent failures, and by a decrease in the coefficient of variation of the EPSP. Tetanization of the Schaffer collaterals that induced long-term enhancement (LTE/LTP) of the population response was associated with an average increase in q for minimal-stimulation responses, with no significant change in any estimate of m. Taken together, these data indicate that, under the present experimental conditions, LTE is expressed as an increase in quantal size, rather than an increase in the number of quanta released per presynaptic impulse. Although this is not definitive evidence for a postsynaptic mechanism, these findings do further restrict the classes of possible presynaptic mechanisms that may be proposed to account for LTE expression.
Cell Resensitization during Protracted Dosing of Heterogeneous Cell Populations (1998)

When a tumor or other heterogeneous cell population is acutely exposed to ionizing radiation (or, for that matter, to chemotherapeutic agents or hyperthermia), cells that happen to be more sensitive will be preferentially removed, leaving behind a population more resistant as a whole. However, under broadly applicable assumptions, we here demonstrate mathematically that there is a natural tendency of the postirradiation population to recover from the irradiation in such a manner as to restore its original sensitivity composition, i.e. to undergo "resensitization". An important consequence in radiotherapy is that, if a fixed total radiation dose is delivered in a more protracted manner, e.g. as several fractions or as a continuous dose at low dose rate, resensitization occurring over the course of dose delivery will result in greater cell killing than would otherwise have occurred. That is, for a cell population with any form of diversity in radiosensitivity, the influence of redistribution is to make any prolonged dose more damaging than an acute dose of the same magnitude. This tendency toward an "inverse dose-rate effect" may be masked in practice by countervailing effects, such as repair of sublethal damage, but the tendency is demonstrated to hold under very general circumstances, being a consequence of cell-cell diversity and the dynamic response of the cell population to treatment.
Resolution of protein disulphide-isomerase and glutathione-insulin transhydrogenase activities by covalent chromatography (1980)

1. Protein disulphide-isomerase (EC 5.3.4.1) and glutathione-insulin transhydrogenase (EC 1.8.4.2) were resolved by covalent chromatography. Both activities, in a partially purified preparation from bovine liver, bind covalently as mixed disulphides to activated thiopropyl-Sepharose 6B, in a new stepwise elution procedure protein disulphide-isomerase is displaced in mildly reducing conditions whereas glutathione-insulin transhydrogenase is only displaced by more extreme reducing conditions. 2. This together with evidence for partial resolution of the two activities by ion-exchange chromatography, conclusively establishes that the two activities are not alternative activities of a single bovine liver enzyme. 3. Protein disulphide-isomerase, partially purified by a published procedure, has now been further purified by covalent chromatography and ion-exchange chromatography. The final material is 560-fold purified relative to a bovine liver homogenate; it has barely detectable glutathione-insulin transhydrogenase activity. 4. The purified protein disulphide-isomerase shows a single major band on sodium dodecyl sulphate/polyacrylamide-gel electrophoresis corresponding to a mol.wt. of 57000. 5. The purified protein disulphide-isomerase has Km values for 'scrambled' ribonuclease and dithiothreitol of 23 microgram/ml and 5.4 microM respectively and has a sharp pH optimum at 7.5. The enzyme has a broad thiol-specificity, and several monothiols, at 1mM, can replace dithiothreitol. 6. The purified protein disulphide-isomerase is completely inactivated after incubation with a 2-3 fold molar excess of iodoacetate. The enzyme is also significantly inhibited by low concentrations of Cd2+ ions. These findings strongly suggest the existence of a vicinal dithiol group essential for enzyme activity. 7. When a range of thiols were used as co-substrates for protein disulphide-isomerase activity, the activities were found to co-purify quantitatively, implying the presence of a single protein disulphide-isomerase of broad thiol-specificity. Glutathione-disulphide transhydrogenase activities, assayed with a range of disulphide compounds, did not co-purify quantitatively.
Genome-wide landscape of RNA-binding protein dysregulation reveals a major impact on psychiatric disorder risk (2020)

Abstract Despite the strong genetic basis of psychiatric disorders, the molecular origins of these diseases are still largely unmapped. RNA-binding proteins (RBPs) are responsible for most post-transcriptional regulation, from splicing to translational to localization. RBPs thus act as key gatekeepers of cellular homeostasis, especially in the brain. Here, we leverage a deep learning approach to interrogate variant effects genome-wide, and discover that the dysregulation of RBP target sites is a principal contributor to psychiatric disorder risk. We show that specific modes of RBP regulation are genetically linked to the heritability of psychiatric disorders, and demonstrate that diverse RBP regulatory functions are reflected in distinct genome-wide negative selection signatures. Notably, RBP dysregulation has a stronger impact on psychiatric disorders than common coding region variants and explains heritability not currently captured by large-scale molecular QTL studies (expression QTLs and splicing QTLs). We share genome-wide profiles of RBP target site dysregulation, which we used to identify DDHD2 as a candidate schizophrenia risk gene, in a public web server. This resource provides a novel analytical framework to connect the full range of RNA regulation to complex disease.
Susceptibility of Midge and Mosquito Vectors to SARS-CoV-2 (2021)

SARS-CoV-2 is a recently emerged, highly contagious virus and the cause of the current COVID-19 pandemic. It is a zoonotic virus, although its animal origin is not clear yet. Person-to-person transmission occurs by inhalation of infected droplets and aerosols, or by direct contact with contaminated fomites. Arthropods transmit numerous viral, parasitic, and bacterial diseases; however, the potential role of arthropods in SARS-CoV-2 transmission is not fully understood. Thus far, a few studies have demonstrated that SARS-CoV-2 replication is not supported in cells from certain insect species nor in certain species of mosquitoes after intrathoracic inoculation. In this study, we expanded the work of SARS-CoV-2 susceptibility to biting insects after ingesting a SARS-CoV-2-infected bloodmeal. Species tested included Culicoides sonorensis (Wirth & Jones) (Diptera: Ceratopogonidae) biting midges, as well as Culex tarsalis (Coquillett) and Culex quinquefasciatus (Say) mosquitoes (Diptera: Culicidae), all known biological vectors for numerous RNA viruses. Arthropods were allowed to feed on SARS-CoV-2-spiked blood and at a time point postinfection analyzed for the presence of viral RNA and infectious virus. Additionally, cell lines derived from C. sonorensis (W8a), Aedes aegypti (Linnaeus) (Diptera: Culicidae) (C6/36), Cx. quinquefasciatus (HSU), and Cx. tarsalis (CxTrR2) were tested for SARS-CoV-2 susceptibility. Our results indicate that none of the biting insects, nor the insect cell lines evaluated support SARS-CoV-2 replication, suggesting that these species are unable to be biological vectors of SARS-CoV-2.
Production of maximally aligned O(1D) atoms from two-step photodissociation of molecular oxygen (1998)

Two-step photodissociation of O2 with a total excitation energy of 7.7 eV yields O(1D) atoms with their angular momenta aligned perpendicular to the fragment recoil axis. Correlation rules linking the bound molecule with the separated atoms predict such strong alignment only for an adiabatic process.
Handbook of Food Science and Technology 3: Food Biochemistry and Technology (2016)

This third volume in the Handbook of Food Science and Technology Set explains the processing of raw materials into traditional food (bread, wine, cheese, etc.). The agri-food industry has evolved in order to meet new market expectations of its products; with the use of separation and assembly technologies, food technologists and engineers now increasingly understand and control the preparation of a large diversity of ingredients using additional properties to move from the raw materials into new food products.Taking into account the fundamental basis and technological specificities of the main food sectors, throughout the three parts of this book, the authors investigate the biological and biochemical conversions and physicochemical treatment of food from animal sources, plant sources and food ingredients.
Exploring RFCOAs and its application to products (2009)

A certificate of authenticity (COA) is an inexpensive physical object that has a random and unique multidimensional structure S which is hard to near-exactly replicate. An inexpensive device should be able to scan object's physical ¿fingerprint,¿ i.e., obtain a set of features in the form of a multidimensional signal x that pseudo-uniquely represents S. For a given ¿fingerprint¿ x and without access to S, it should be computationally difficult to construct an object of fixed dimensions with a ¿fingerprint¿ y which is at a bounded proximity from x according to a standardized distance metric. We introduce objects that behave as COAs in the electromagnetic field. The objective is to complement RFIDs so that they are physically, not only digitally, unique and hard to replicate. By enabling this feature, we introduce a tag whose information about the product can be read within a relative far-field, and also whose authenticity can be reliably verified within its near-field. In order to counterfeit a tag, the adversary faces two difficulties-a computational and a manufacturing one. In order to create an actual tag, the adversary must also manufacture a multidimensional object with a specific three-dimensional topology, dielectric properties, and conductivity. This technology can be applied to various systems such as credit cards and license tags/receipts.
Polycomb Group Gene OsFIE2 Regulates Rice (Oryza sativa) Seed Development and Grain Filling via a Mechanism Distinct from Arabidopsis (2013)

Cereal endosperm represents 60% of the calories consumed by human beings worldwide. In addition, cereals also serve as the primary feedstock for livestock. However, the regulatory mechanism of cereal endosperm and seed development is largely unknown. Polycomb complex has been shown to play a key role in the regulation of endosperm development in Arabidopsis, but its role in cereal endosperm development remains obscure. Additionally, the enzyme activities of the polycomb complexes have not been demonstrated in plants. Here we purified the rice OsFIE2-polycomb complex using tandem affinity purification and demonstrated its specific H3 methyltransferase activity. We found that the OsFIE2 gene product was responsible for H3K27me3 production specifically in vivo. Genetic studies showed that a reduction of OsFIE2 expression led to smaller seeds, partially filled seeds, and partial loss of seed dormancy. Gene expression and proteomics analyses found that the starch synthesis rate limiting step enzyme and multiple storage proteins are down-regulated in OsFIE2 reduction lines. Genome wide ChIP-Seq data analysis shows that H3K27me3 is associated with many genes in the young seeds. The H3K27me3 modification and gene expression in a key helix-loop-helix transcription factor is shown to be regulated by OsFIE2. Our results suggest that OsFIE2-polycomb complex positively regulates rice endosperm development and grain filling via a mechanism highly different from that in Arabidopsis.
Single-well Sonic Imaging: High-Definition Reservoir Cross-sections from Horizontal Wells (2000)

Abstract The limited resolution of conventional seismic surveys often results in challenges to successful reservoir development. Reservoir structure and thickness may not be determined from the seismic to the level of detail necessary, affecting the placement of the horizontal well. We describe a new sonic imaging technique that resolves these features. In addition the position of the well in relation to the reservoir perimeter can be determined with great accuracy Single-well sonic imaging places the acoustic transmitter and receivers in the same well, analogous to recording a micro-scale seismic reflection survey downhole. Using modified sonic logging technology, sound is broadcast into the formation and reflections are converted into a two- or three-dimensional spatial image of the zone around the borehole. Acoustic reflectors such as the top of the reservoir, calcite stringers, or fractures are mapped at distances of 10-15 meters from the well with resolution on the order of one-half meter. We show several examples of surveys conducted in horizontal wells to illustrate applications of the technique.
Maximizing Efficiency in Dynamic Matching Markets (2018)

We study the problem of matching agents who arrive at a marketplace over time and leave after d time periods. Agents can only be matched while they are present in the marketplace. Each pair of agents can yield a different match value, and the planner's goal is to maximize the total value over a finite time horizon. We study matching algorithms that perform well over any sequence of arrivals when there is no a priori information about the match values or arrival times. Our main contribution is a 1/4-competitive algorithm. The algorithm randomly selects a subset of agents who will wait until right before their departure to get matched, and maintains a maximum-weight matching with respect to the other agents. The primal-dual analysis of the algorithm hinges on a careful comparison between the initial dual value associated with an agent when it first arrives, and the final value after d time steps. It is also shown that no algorithm is 1/2-competitive. We extend the model to the case in which departure times are drawn i.i.d from a distribution with non-decreasing hazard rate, and establish a 1/8-competitive algorithm in this setting. Finally we show on real-world data that a modified version of our algorithm performs well in practice.
Intubating conditions and neuromuscular effects of mivacurium during propofol‐alfentanil anaesthesia (1995)

In three groups of 20 patients, anaesthetized with propofol and alfentanil, tracheal intubation conditions and the onset of neuromuscular blockade after administration of three different doses of mivacurium chloride (0.11, 0.15, and 0.19 mg/kg = 1.5 x ED95, 2 x ED95, and 2.5 x ED95) were assessed. Intubation conditions were found to be clinically acceptable (good or excellent) in 83% of patients. Eighty-two per cent of patients were successfully intubated on the first attempt after 60-90 s. No difference in intubation scores or number of intubation attempts among the three dosage groups were found. We conclude that mivacurium chloride allows smooth intubation in most patients within 60-90 s, even with the lowest dose (0.11 mg/kg), after a propofol-alfentanil induction of anaesthesia. However, because there were a few patients in whom intubating conditions were inadequate at 60-90 s, we are reluctant to advocate the preference of mivacurium chloride over suxamethonium for rapid sequence induction in emergency situations.
Single-scan volumetric imaging throughout thick tissue specimens by one-touch installable light-needle creating device (2022)

Biological tissues and their networks frequently change dynamically across large volumes. Understanding network operations requires monitoring their activities in three dimensions (3D) with single-cell resolution. Several researchers have proposed various volumetric imaging technologies. However, most technologies require large-scale and complicated optical setups, as well as deep expertise for microscopic technologies, resulting in a high threshold for biologists. In this study, we propose an easy-to-use light-needle creating device for conventional two-photon microscopy systems. By only installing the device in one position for a filter cube that conventional fluorescent microscopes have, single scanning of the excitation laser light beam excited fluorophores throughout over 200 μm thickness specimens simultaneously. Furthermore, the developed microscopy system successfully demonstrated single-scan visualization of the 3D structure of transparent YFP-expressing brain slices. Finally, in acute mouse cortical slices with a thickness of approximately 250 μm, we detected calcium activities with 7.5 Hz temporal resolution in the neuronal population.
Comparison of a New QMS?? Zonisamide Assay* on the Hitachi?? 911/912 Systems to the Hitachi 717?? System** (2005)

s: Ninth International Congress of Therapeutic Drug Monitoring and Clinical Toxicology: Louisville, Kentucky April 23-28, 2005
A device for measuring the lateral wall cuff pressure of endotracheal tubes (1992)

A new method for measuring the lateral wall pressure on the trachea from cuffs of endotracheal tubes is presented. The method is based on measuring the force necessary to force a small, constant flow of air through a Teflon or silicone rubber envelope, placed between the cuff and the tracheal wall. The pressures recorded are 0.1 to 0.3 kPa higher than the theoretically correct values. The response time is 0.28 s for 90% of full deflection. Dynamic recordings of the lateral wall pressure of high and low residual volume cuffs can be obtained for analysis of the interaction between the cuff and the tracheal compliance. No method for accurate, dynamic recording of the lateral wall cuff pressure has previously been published.
Belonging Across Cultures: Immigration and Citizenship in A Free Life (2012)

Published in 2007, Ha Jin's A Free Life garnered attention from book critics as the first “American” novel written by the prolific Chinese-born author. This essay explores how A Free Life reimagines the relationship between culture and citizenship with which Asian American literary studies has long struggled, foregrounding how formal legal status is anything but secure for immigrant Asian Americans. The novel urges its reader to ask what is the cultural position and legal status of the immigrant subject who gives up identification with one nation for another, and, as a result, finds himself with no sense of identity or existential security from either.
Towards Real-time Stereo using Non-uniform Image Sampling and Sparse Dynamic Programming (2008)

Constructing the 3D mesh of a scene from stereo images is a major task in computer vision. It usually involves several steps including stereo matching and meshing. Unfortunately, the time required to generate the 3D mesh is time demanding due to the large amount of pixels to be processed. In this work, we propose a framework to accelerate the overall process. The key issue is to first reduce the number of pixels by approximating an image with a content adaptive mesh. The nodes of the mesh are sparse and they represent the non-uniform samples of the image. To benefit from the reduced set of pixels, we formulate a dynamic programming based stereo matching algorithm which computes the depth only at the sparse samples. We then show by setting up some tests using some real images that the non-uniform samples are sufficient to recover the original dense depth map of the scene by interpolating them using the mesh. The results obtained also show that the employment of the proposed strategy reduces the overall processing time of stereo matching to more than 50% of the original time. We are now able to construct scenes in real-time using less computational resources.
Biological control of Aspergillus flavus growth and subsequent aflatoxin B 1 production in sorghum grains (2010)

Sorghum grains suffer from severe infection and colonization by several toxigenic fungi and subsequent production of mycotoxins, posing a threat to human and animal health. Among all the mycotoxins, aflatoxins represent one of the most important toxicants considered as important constraint of grain quality and sorghum production. Various physical and chemical methods of reducing mycotoxins have been recommended, but only few have been accepted for practical use. Biodegradation of aflatoxins, deploying microbes is an attractive strategy for mycotoxin management. This study, therefore explored the potential use of certain biocontrol agents for the reduction of growth of toxigenic Aspergillus flavus and subsequent aflatoxin B1 (AFB1) production in sorghum. Among all the biocontrol agents tested, culture filtrate of Rhodococcus erythropolis completely inhibited the A. flavus growth and AFB1 production at 25 mlkg-1 concentration. The other biocontrol agents, Bacillus subtilis, Pseudomonas fluorescens and Trichoderma viride showed 72, 74 and 65% inhibition of A. flavus growth whereas 54, 62.6 and 39% reduction of AFB1 at 200 mlkg-1 of sorghum grains, respectively.
Detecting inversions with PCA in the presence of population structure (2020)

Chromosomal inversions can lead to reproductive isolation and adaptation in insects such as Drosophila melanogaster and the non-model malaria vector Anopheles gambiae. Inversions can be detected and characterized using principal component analysis (PCA) of single nucleotide polymorphisms (SNPs). To aid in developing such methods, we formed a new benchmark derived from three publicly-available insect data. We then used this benchmark to perform an extended validation of our software for inversion analysis (Asaph). Through that process, we identified and characterized several problematic test cases liable to misinterpretation that can help guide PCA-based inversion detection. Lastly, we re-analyzed the 2R chromosome arm of 150 An. gambiae and coluzzii samples and observed two inversions (2Rc and 2Rd) that were previously known but not annotated in these particular individuals. The resulting benchmark data set and methods will be useful for future inversion detection based solely on SNP data.