gebhart/patrepeval huggingface dataset:
All-in-One Dual CRISPR-Cas12a (AIOD-CRISPR) Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV virus (2020)

A recent outbreak of novel coronavirus (SARS-CoV-2), the causative agent of COVID-19, has spread rapidly all over the world. Human immunodeficiency virus (HIV) is another deadly virus and causes acquired immunodeficiency syndrome (AIDS). Rapid and early detection of these viruses will facilitate early intervention and reduce disease transmission risk. Here, we present an <b>A</b>ll-<b>I</b>n-<b>O</b>ne <b>D</b>ual <b>CRISPR</b>-Cas12a (termed "AIOD-CRISPR") assay method for simple, rapid, ultrasensitive, one-pot, and visual detection of coronavirus SARS-CoV-2 and HIV virus. In our AIOD CRISPR assay, a pair of crRNAs was introduced to initiate dual CRISPR-Cas12a detection and improve detection sensitivity. The AIOD-CRISPR assay system was successfully utilized to detect nucleic acids (DNA and RNA) of SARS-CoV-2 and HIV with a sensitivity of few copies. Also, it was evaluated by detecting HIV-1 RNA extracted from human plasma samples, achieving a comparable sensitivity with real-time RT-PCR method. Thus, our method has a great potential for developing next-generation point-of-care molecular diagnostics.
A calorimetric study of the thermal denaturation of whey proteins in simulated milk ultrafiltrate (1977)

Summary Differential scanning calorimetry (DSC) was used to study thermal transitions of the following whey proteins and enzymes in milk ultrafiltrate solution: β-lactoglobulin, α-lactalbumin, serum albumin, γ-globulin, apo- and Fe-lactoferrin, lysozyme, ribonuclease, α-chymotrypsin and xanthine oxidase. Denaturation enthalpies (Δ H D ), denaturation temperatures ( T D ) and the half width of the denaturation peaks in DSC thermograms (Δ T ½ D ) were determined and the degree of renaturation was estimated by rescanning previously denatured samples. A fair correlation between the results obtained by DSC and other more classical methods was found in general. However, for some proteins (α-lactalbumin, lysozyme, ribonuclease and xanthine oxidase), which have so far been considered relatively thermostable, calorimetry reveals conformational changes starting at temperatures as low as about 45 °C. In these cases thermostability observed after heat treatment of milk should be interpreted in terms of renaturation and not of high temperatures of denaturation.
Simulation of SiO2 and Si feature etching for microelectronics and microelectromechanical systems fabrication: A combined simulator coupling modules of surface etching, local flux calculation, and profile evolution (2004)

A combined simulator linking gas flux data from a plasma reactor (experimental or simulated) to the feature profile evolution during etching/deposition processes is described. This combined simulator results from the coupling of surface etch, local flux calculation, and profile evolution modules. It is a modular tool, in the sense that different phenomena, surface models, and structures can be incorporated. In this work the combined simulator is applied in two processes: (a) in SiO2 feature etching to simulate reactive ion etching (RIE) lag and inverse RIE lag and (b) in etching of high aspect ratio Si trenches using the Bosch process. The profile evolution algorithm of the combined simulator, namely, the level set method, is applied to a process where etching and deposition occur, and tracking of two materials (Si and polymer formed during the Bosch deposition step) is needed.
Cumulative acknowledgement multicast repetition policy for wireless LANs or ad hoc network clusters (2003)

For a wireless LAN or a cluster of nodes in an ad hoc wireless network, multicast transmissions from a controlling station must be acknowledged by the nodes that are addressed. To ensure reliable reception at all the nodes, the multicast packet may be repeated on different transmissions, or on the same transmission as a form of diversity, or both. In this paper, policies for repeat transmissions of multicast packets are analyzed in terms of the average number of repeat transmissions required and the corresponding efficiency of the signaling on the multicast channel. The analytical results are parametric in packet/ACK error probability, the number of nodes, and the number of required ACKs. It is shown that a policy of accumulating ACKs and addressing only unacknowledged nodes on repeated non-diversity transmissions is more efficient than simply using a higher order of diversity on the multicast transmissions. Methods are shown for avoiding unnecessary repetitions in the case of a missing node.
The potential of methane‐oxidizing bacteria for applications in environmental biotechnology (2010)

Abstract Methanotrophic bacteria possess a unique set of enzymes enabling them to oxidize, degrade and transform organic molecules and synthesize new compounds. Therefore, they have great potential in environmental biotechnology. The application of these unique properties was demonstrated in three case studies: (i) Methane escaping from leaky gas pipes may lead to massive mortality of trees in urban areas. Lack of oxygen within the soil surrounding tree roots caused by methanotrophic activity was identified as one of the reasons for this phenomenon. The similarity between metabolic reactions performed by the key enzymes of methanotrophs (methane monooxygenase) and ammonium oxidizers (ammonium monooxygenase) might offer a solution to this problem by applying commercially available nitrification and urease inhibitors. (ii) Methanotrophs are able to co‐metabolically degrade contaminants such as low‐molecular‐weight‐chlorinated hydrocarbons in soil and water in the presence of methane. Batch and continuous trichloroethylene degradation experiments in laboratory‐scale reactors using Methylocystis sp. GB 14 were performed, partly with cells entrapped in a polymer matrix. (iii) Using a short, two‐stage pilot‐scale process, the intracellular polymer accumulation of poly‐β‐hydroxybutyrate (PHB) in methanotrophs reached a maximum of 52%. Interestingly, an ultra‐high‐molecular‐weight PHB of 3.1 MDa was accumulated under potassium deficiency. Under strictly controlled conditions (temperature, pH and methane supply) this process can be nonsterile because of the establishment of a stable microbial community (dominant species Methylocystis sp. GB 25 ≥86% by biomass). The possibility to substitute methane with biogas from renewable sources facilitates the development of a methane‐based PHB production process that yields a high‐quality biopolymer at competitive costs.
Homoisoflavanone prevents mast cell activation and allergic responses by inhibition of <scp>S</scp>yk signaling pathway (2014)

Homoisoflavanone inhibited mast cell activation through the suppression of Syk pathway together with the inhibition of cPLA2 . Thus, it might be a good candidate molecule for allergic diseases.
Genome-wide RNAi screens in African trypanosomes identify the nifurtimox activator NTR and the eflornithine transporter AAT6 (2010)

To be effective, therapeutic compounds must typically enter target cells and, in some cases, must be concentrated or modified. Thus, uptake and activation mechanisms often form the basis of selectivity against infectious agents. Loss-of-function screens can be used to identify proteins involved in drug uptake and metabolism and may also identify clinically relevant potential resistance mechanisms. We used a genome-scale RNA interference (RNAi) library to identify loss-of-function resistance mechanisms in bloodstream-form Trypanosoma brucei. Nifurtimox-Eflornithine Combination Therapy (NECT) was recently introduced for Human African Trypanosomiasis and we focus on these drugs here. Screens for resistance to nifurtimox and a related drug, benznidazole, identified loss of nitroreductase (NTR) pro-drug activator function. A screen for resistance to the amino-acid analogue, eflornithine, identified loss of amino-acid transporter (AAT6) function. Our results confirm recent findings and suggest that NTR or AAT6 loss-of-function represent major potential mechanisms of resistance to these drugs. Thus, bloodstream-form T. brucei RNAi libraries present a versatile tool for selective genetic screening and for the rapid identification of drug-activation, uptake and potential resistance mechanisms.
Convergence in downward continuation for some simple geometries (1967)

Abstract Laplacian fields can be continued either by the use of Taylor series, or by spectral analysis and synthesis. While the first method is applicable to non-Laplacian fields as well, the second, as it is presently developed, is not. The convergence properties of downward continuation by these methods have been investigated for some source geometries that frequently occur in nature. The cases treated include gravity, magnetic, electrical, and electromagnetic fields. When the spectral method is used, the boundary between regions of convergence and divergence is always a plane that is parallel to the plane of observation. With the Taylor series method, on the other hand, the boundary is a hyperboloid or a combination of hyperboloids. The position of these boundaries--plane or hyperboloid--depends upon the shape of the anomaly-causing body. For bodies with corners and edges, the plane passes through the shallowest corner or edge, or there is a hyperboloid apexed at each corner or edge so that the outermost envelope constitutes the boundary of convergence. For smooth bodies, like spheres and cylinders, these boundaries are positioned at some internal point, which, in the case of artificial-field methods, may correspond to an image. For instance, for the gravity effect of a sphere or a two-dimensional horizontal circular cylinder, or their magnetic and electrical effects under the influence of a uniform primary field, the plane or the hyperboloid passes through or is apexed at the center or the axis, as the case may be.The results of this paper provide the theoretical justification for using the method of continuation in interpretation of mining geophysical data, as reported empirically earlier.
Robust crowd counting using detection flow (2011)

Crowd counting which aims at obtaining the number of people within a scene is an important computer vision task. While most previous methods try to count people within one frame, this paper addresses this problem using the detection flow which is defined as a set of object detection responses along the temporal video sequence. We argue that counting based on detection flow provides a better way to estimate the crowd size with following merits: 1) it can greatly alleviate the common weakness of an object detector including miss detection and false alarms; 2) it is robust to temporal object occlusions and noises; 3) it is more competent to give specific descriptions of the crowd, e.g. crowd moving directions and target locations. Experiment results on PETS 2009 dataset demonstrate the potential of this method.
Kinetics of a US Contrast Agent in Benign and Malignant Adnexal Tumors (2003)

After microbubble contrast agent injection, malignant and benign adnexal lesions behave differently in degree, onset, and duration of Doppler US enhancement.
Rebate Rules in Threshold Public Good Provision (2008)

This paper considers how six alternative rebate rules affect voluntary contributions in a threshold publicgood experiment. The rules differ by (1) whether an individual can receive a proportional rebate of excess contributions, a winner-takes-all of any excess contributions, or a full rebate of one's contribution in the event the public good is provided and excess contributions exist, and (2) whether the probability of receiving a rebate is proportional to an individual's contribution relative to total contributions or is a simple uniform probability distribution set by the number of contributors. The paper adds to the existing experimental economics literature on threshold public goods by investigating both aggregate and individual demand revelation under the winner-take-all and random full-rebate rules. Half of the rules (proportional rebate, winner-take-all with uniform probability among all group members, and random full-rebate with uniform probability) provide total contributions that nearly equal total benefits, while the rest (winner-take-all with proportional probability, winner-take-all with uniform probability among contributors only, and random full-rebate with proportional probability) exceed benefits by over 30 percent. Only the proportional rebate rule is found to achieve both aggregate and individual demand revelation. Our experimental results have implications for both fundraisers and valuation practitioners.
Super-Resolution Effect of Semiconductor-Doped Glass (1999)

Semiconductor-doped glass is proposed as a super-resolution layer for future ultra-high-density optical disc systems. It was confirmed that this material system showed very fast response and large transmittance change by laser-beam irradiation when CdSSe-doped glass was used. The rise time of the transmittance change was less than 10 ns and the transmittance change reached 30%. These optical responses were obtained at a power density of the pumped laser beam of 1 MW/cm 2 . This power density corresponds to the readout power in digital versatile disk-read only memory (DVD-ROM) and digital versatile disk-random access memory (DVD-RAM) discs. This material system is regarded as a potential candidate for a super-resolution readout layer that is applicable to both ROM and RAM discs.
Detection and Sequence Analysis of Hepatitis B Virus Integration in Peripheral Blood Mononuclear Cells (1999)

A PCR-based technique was used to detect hepatitis B virus (HBV) integration in peripheral blood mononuclear cells from patients with chronic hepatitis B. Integrated HBV DNA sequences, with virus-cell junctions located in the cohesive region between direct repeat 1 (DR1) and DR2, were found in 2 of 10 studied patients.
Factors (TAFs) required for activated transcription interact with TATA box-binding protein conserved core domain. (1993)

TFIID is a multisubunit protein containing the TATA box-binding polypeptide (TBP) and associated factors (TFIID-TAFs) required for activated transcription by RNA polymerase II. TBPs from different eukaryotes contain a highly conserved carboxy-terminal domain and very divergent amino-terminal domains. Earlier studies proposed that the amino-terminal domains of metazoan TBPs are required for activated transcription. However, we report that a human TFIID complex containing an amino-terminal truncated TBP contains all the major TFIID-TAFs and supports in vitro transcriptional stimulation by different classes of activation domains and from a TATA-less promoter. Protein blotting experiments revealed direct interactions between the conserved domain of TBP and the two largest TAFs. The results suggest a model for the interaction of TFIID-TAFs with TBP.
Localization of herpes simplex virus in the trigeminal and olfactory systems of the mouse central nervous system during acute and latent infections by in situ hybridization. (1984)

The precise anatomical location of latent herpes simplex virus (HSV) infection of the mouse central nervous system (CNS) has been identified by application of a 3H-labeled HSV-specific probe to deparaffinized sections of mouse brain tissue in situ. At times after corneal inoculation with HSV type 1 (HSV-1), strain F, representing the acute and latent phases of infection, BALB/c mice were perfused with a fixative containing sodium m-periodate, lysine, and paraformaldehyde and their CNS tissues and trigeminal ganglia embedded in paraffin, sectioned, and and subjected to hybridization. During the acute phase, HSV-1 was localized to neurons and some small supporting cells in the sensory portion of the 5th cranial nerve including the trigeminal ganglia and nerve root, principal sensory nucleus, mesencephalic nucleus, descending tract and nuclei, and cerebral cortex. During the latent phase, HSV-1 was found only in neurons located primarily in the descending nuclei and mesencephalic nucleus. Evidence was also obtained that implicated the olfactory tract as an additional route of entry into the CNS, in that positive hybridization was found in the olfactory bulb, the entorhinal cortex, and adjacent cerebral cortex. Additionally, HSV-1 established latent infections in neurons of the olfactory system. HSV-1-specific RNA was detected in ganglionic and CNS neurons throughout the acute and latent phases of infection, whereas HSV-1-specific DNA was detected only during the acute phase, indicating that the relationship between HSV and latently infected CNS and ganglionic neurons involves limited transcription of the viral genome.
Evaluation of photomask flatness compensation for extreme ultraviolet lithography (2016)

As the semiconductor industry continues to strive towards high volume manufacturing for EUV, flatness specifications for photomasks have decreased to below 10nm for 2018 production, however the current champion masks being produced report P-V flatness values of roughly ~50nm. Write compensation presents the promising opportunity to mitigate pattern placement errors through the use of geometrically adjusted target patterns which counteract the reticle’s flatness induced distortions and address the differences in chucking mechanisms between e-beam write and electrostatic clamping during scan. Compensation relies on high accuracy flatness data which provides the critical topographical components of the reticle to the write tool. Any errors included in the flatness data file are translated to the pattern during the write process, which has now driven flatness measurement tools to target a 6σ reproducibility <1nm. Using data collected from a 2011 Sematech study on the Alpha Demo Tool, the proposed methodology for write compensation is validated against printed wafer results. Topographic features which lack compensation capability must then be held to stringent specifications in order to limit their contributions to the final image placement error (IPE) at wafer. By understanding the capabilities and limitations of write compensation, it is then possible to shift flatness requirements towards the “non-correctable” portion of the reticle’s profile, potentially relieving polishers from having to adhere to the current single digit flatness specifications.
A 0.99-μm/sup 2/ loadless four-transistor SRAM cell in 0.13-μm generation CMOS technology (2002)

Summary form only given. We present an ultra-high-density embedded loadless four-transistor SRAM cell for 0.13-/spl mu/m logic LSIs. The cell size is 0.99 /spl mu/m/sup 2/, which is the smallest of all reported SRAM cells. In addition, its fabrication process is fully compatible with CMOS logic technologies. The following three technologies reduce the cell area to less than 1 /spl mu/m/sup 2/, and provide highly stable operation at 1.2 V. The double-exposure technique using KrF excimer laser lithography with complementary phase-shift masks reduces the spacing between the drive-transistor gate and the word line. Using the borderless-contact etching process expands shared contact up to 0.21 /spl mu/m without contact leakage current to obtain sufficient misalignment tolerance. The thickness of the gate dielectrics in the cell is controlled to suppress the direct tunneling current to less than the off-state current in order to retain the cell data from -40 to 125/spl deg/C.
Novel 0.2 mu m i-lithography by phase-shifting on the substrate (POST) (2002)

The authors propose a novel i-line lithography by phase-shifting on the substrate (POST). with POST, 0.2 mu m resist patterns have been achieved by using an i-line stepper and conventional masks without phase shifters. It was confirmed that fine patterns were formed by the phase-shifting effect in the resist on the substrate. Simulation suggests that POST has a better resolution than a phase-shifting mask. It has been demonstrated that, with POST, it is possible to define patterns for ULSIs such as the 256 Mbit DRAM by i-line lithography.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Two-photon microscopy using fiber-based nanosecond excitation (2016)

Two-photon excitation fluorescence (TPEF) microscopy is a powerful technique for sensitive tissue imaging at depths of up to 1000 micrometers. However, due to the shallow penetration, for in vivo imaging of internal organs in patients beam delivery by an endoscope is crucial. Until today, this is hindered by linear and non-linear pulse broadening of the femtosecond pulses in the optical fibers of the endoscopes. Here we present an endoscope-ready, fiber-based TPEF microscope, using nanosecond pulses at low repetition rates instead of femtosecond pulses. These nanosecond pulses lack most of the problems connected with femtosecond pulses but are equally suited for TPEF imaging. We derive and demonstrate that at given cw-power the TPEF signal only depends on the duty cycle of the laser source. Due to the higher pulse energy at the same peak power we can also demonstrate single shot two-photon fluorescence lifetime measurements.
Analysis of physiological tremor mechanisms in surface electromyogram (2013)

Rhythmical grouping of action potential in the low frequency band have been observed during steady, constant force contractions. The origins of this rhythmical pattern have always been associated to tremor oscillations. However, literature concerning physiological tremor has shown that the origin of tremor remains inconclusive with various works providing valid arguments and counter-arguments for the various mechanisms proposed. Physiological tremor oscillation has consistently been associated with the following four mechanisms: a) synchronisation of motor units; b) mechanical feedback resonance; c) feedback resonance from neural delay and d) central oscillations. It is largely believed that the overall tremor oscillation is either the interaction effect of various oscillatory mechanisms acting in parallel with each other or one or other mechanisms acting predominantly in various situations. The objective of this research was to determine the role of neural feedback and muscle mechanics in the generation of physiological tremor oscillation. This research developed a neuromuscular model to simulate the individual and resulting oscillatory mechanisms of tremor. The oscillations found in EMG signal were also analysed empirically from EMG data from 54 subjects using Hilbert Transform and rectification to obtain the envelope of the signal. The time between rhythmical waveform patterns in the EMG signal, TC was found to be 78ms. This value corresponded to the supraspinal neural delay, 50-80ms reported in literature and the theoretical value of the supraspinal feedback simulated from the model. The theoretical model also reported a predominant mechanical resonance frequency in the resulting oscillation between muscle and spinal feedback and the resulting oscillation between muscle, spinal and supraspinal feedback. These observations coincide with the physiological tremor oscillations reported in literature: the mechanical-reflex and the 8-12Hz. The mechanical-reflex oscillation is defined to be the product of spinal feedback and muscle mechanics and is found to be highly influenced by the mechanical properties of muscle. The 8-12Hz component is reported to originate from the interaction of supraspinal and central mechanisms. TC has shown to coincide with the supraspinal neural delay time and the theoretical supraspinal value suggesting that TC correlates to the 8-12Hz component.<br>