gebhart/patrepeval huggingface dataset:
Dual control of subtilin biosynthesis and immunity in <i>Bacillus subtilis</i> (2002)

The production of the peptide antibiotic (lantibiotic) subtilin in Bacillus subtilis ATCC 6633 is highly regulated. Transcriptional organization and regulation of the subtilin gene cluster encompassing 11 genes was characterized. Two polycistronic mRNAs encoding transcript spaBTC (6.8 kb) and encoding transcript spaIFEG (3.5 kb) as well as the monocistronic spaS (0.3 kb) mRNA were shown by Northern hybridization. Primer extension experiments and beta-galactosidase fusions confirmed three independent promoter sites preceding genes spaB, spaS and spaI. beta-Galactosidase expression of spaB, spaS and spaI promoter lacZ fusions initiated in mid-exponential growth. Maximal activities were reached at the transition to stationary growth and were collinear with subtilin production. The lacZ activity was dependent on co-expression with the two-component regulatory system spaRK. The presence of subtilin was needed for efficient expression of all three promoter lacZ fusions. This suggests a transcriptional autoregulation according to a quorum-sensing mechanism with subtilin as autoinducer and signal transduction via SpaRK. Additionally, spaR expression was found to be under positive control of the alternative sigma factor H. Deletion of sigma H strongly decreased subtilin production. Full subtilin production could be restored after in-trans complementation of spaR. Deletion of the major B. subtilis transition state regulator AbrB strongly increased subtilin production. These results show that the spaRK two-component regulatory system, and hence subtilin biosynthesis and immunity, is under dual control of two independent regulatory systems: autoinduction via subtilin and transcriptional regulation via sigma factor H.
Simulasi Penjalaran Gelombang Tsunami Menggunakan Metode Optimal Time Stepping (2021)

Berada di kawasan Ring of Fire atau Cincin Api Pasifik menjadikan Indonesia wilayah yang rawan letusan gunung berapi, gempa dan tsunami. Tsunami adalah ombak yang terjadi setelah suatu gempa, gunung meletus atau hantaman meteor di laut. Banyak sekali kerugian yang didapat manusia ketika terjadinya tsunami sehingga banyak peneliti yang memodelkan penjalaran gelombang tsunami. Penjalaran gelombang tsunami dapat dikaji dengan berbagai teori, salah satunya menggunakan teori perairan air dangkal. Akan tetapi, model tersebut tidak bisa diselesaikan secara analitik. Untuk itu diperlukan pendekatan secara numerik sehingga didapat penyelesaian yang mendekati solusi sejatinya. Metode Optimal Time Stepping merupakan salah satu metode untuk mendapatkan solusi numerik dari persamaan diferensial parsial. Metode ini juga membutuhkan waktu yang lebih sedikit dan lebih akurat jika dibandingkan dengan metode lain. Penelitian ini akan mensimulasikan penjalaran gelombang tsunami dengan menggunakan metode Optimal Time Stepping.
<i>In‐vivo</i> non‐invasive study of the thermoregulatory function of the blood vessels in the rat tail using magnetic resonance angiography (2002)

In rats, a significant portion of total body heat loss occurs through sympathetically mediated changes in tail blood flow, making the rat tail a convenient model to study vasomotor activity during thermoregulation. Our aim was to perform a non-invasive study of the mechanisms of blood vessel control in the rat tail upon increasing body temperature. In anaesthetized rats, blood vessel temperature was monitored using non-invasive thermistors positioned on the skin surface, covering the ventral artery (Ta) and lateral vein (Tv), and changes in blood vessel size were measured using in-vivo magnetic resonance angiography (MRA). Two important regions of the tail (base and middle) were studied during a gradual rise of rectal temperature (Tr) from 37 to 40 degrees C. MRA data show that increasing Tr causes increased diameter of both arteries and veins of the tail, that venous diameter changes are greater than arterial diameter changes, and that diameter changes of both types of vessel are greater at the base of the tail than in the middle. Temperature data allowed calculation of (Ta - Tv), which we used as an index of flow through arteriovenous anastomoses (AVAs). The data suggest that AVAs near the base of the tail are important in heat exchange, and that they remain open only for Tr values between 38 and 39 degrees C.
Mouse Model for ROS1-Rearranged Lung Cancer (2013)

Genetic rearrangement of the ROS1 receptor tyrosine kinase was recently identified as a distinct molecular signature for human non-small cell lung cancer (NSCLC). However, direct evidence of lung carcinogenesis induced by ROS1 fusion genes remains to be verified. The present study shows that EZR-ROS1 plays an essential role in the oncogenesis of NSCLC harboring the fusion gene. EZR-ROS1 was identified in four female patients of lung adenocarcinoma. Three of them were never smokers. Interstitial deletion of 6q22-q25 resulted in gene fusion. Expression of the fusion kinase in NIH3T3 cells induced anchorage-independent growth in vitro, and subcutaneous tumors in nude mice. This transforming ability was attributable to its kinase activity. The ALK/MET/ROS1 kinase inhibitor, crizotinib, suppressed fusion-induced anchorage-independent growth of NIH3T3 cells. Most importantly, established transgenic mouse lines specifically expressing EZR-ROS1 in lung alveolar epithelial cells developed multiple adenocarcinoma nodules in both lungs at an early age. These data suggest that the EZR-ROS1 is a pivotal oncogene in human NSCLC, and that this animal model could be valuable for exploring therapeutic agents against ROS1-rearranged lung cancer.
Experimental Realization of a Quantum Dot Energy Harvester (2019)

We demonstrate experimentally an autonomous nanoscale energy harvester that utilizes the physics of resonant tunneling quantum dots. Gate-defined quantum dots on GaAs/AlGaAs high-electron-mobility transistors are placed on either side of a hot-electron reservoir. The discrete energy levels of the quantum dots are tuned to be aligned with low energy electrons on one side and high energy electrons on the other side of the hot reservoir. The quantum dots thus act as energy filters and allow for the conversion of heat from the cavity into electrical power. Our energy harvester, measured at an estimated base temperature of 75 mK in a He^{3}/He^{4} dilution refrigerator, can generate a thermal power of 0.13 fW for a temperature difference across each dot of about 67 mK.
The rubella virus E2 and E1 spike glycoproteins are targeted to the Golgi complex. (1993)

Rubella virus (RV) has been reported to bud from intracellular membranes in certain cell types. In this study the intracellular site of targeting of RV envelope E2 and E1 glycoproteins has been investigated in three different cell types (CHO, BHK-21 and Vero cells) transfected with a cDNA encoding the two glycoproteins. By indirect immunofluorescence, E2 and E1 were localized to the Golgi region of all three cell types, and their distribution was disrupted by treatment with BFA or nocodazole. Immunogold labeling demonstrated that E2 and E1 were localized to Golgi cisternae and indicated that the glycoproteins were distributed across the Golgi stack. Analysis of immunoprecipitates obtained from stably transfected CHO cells revealed that E2 and E1 become endo H resistant and undergo sialylation without being transported to the cell surface. Transport of RV glycoproteins to the Golgi complex was relatively slow (t1/2 = 60-90 min). Coprecipitation experiments indicated that E2 and E1 form a heterodimer in the RER. E1 was found to fold much more slowly than E2, suggesting that the delay in transport of the heterodimer to the Golgi may be due to the slow maturation of E1 in the ER. These results indicate that RV glycoproteins behave as integral membrane proteins of the Golgi complex and thus provide a useful model to study targeting and turnover of type I membrane proteins in this organelle.
Glowing Graphene Quantum Dots and Carbon Dots: Properties, Syntheses, and Biological Applications (2014)

The emerging graphene quantum dots (GQDs) and carbon dots (C‐dots) have gained tremendous attention for their enormous potentials for biomedical applications, owing to their unique and tunable photoluminescence properties, exceptional physicochemical properties, high photostability, biocompatibility, and small size. This article aims to update the latest results in this rapidly evolving field and to provide critical insights to inspire more exciting developments. We comparatively review the properties and synthesis methods of these carbon nanodots and place emphasis on their biological (both fundamental and theranostic) applications.
Temperature-controlled laser photocoagulation of soft tissue: In vivo evaluation using a tissue welding model (1996)

Tissue temperatures can be controlled during laser photocoagulation of skin. The degree of acute and chronic tissue damage is highly dependent on the temperature during welding. By controlling the tissue temperature during laser procedures, the surgical outcome can be more reliably predicted and reproduced, as compared to the conventional open loop methods. In addition, the use of a TCPC system should significantly reduce the learning curve for photothermal surgical procedures.
Three-dimensional imaging of objects in accumulated snow using multifrequency holography (1988)

The three-dimensional (3-D) imaging of objects buried in snow using multifrequency holography is discussed. It is pointed out that the cross-sectional images obtained by radar used for target detection in soils, sand, and snow do not meet expectations in identifying the shapes of targets. A 3-D imaging reconstruction technique using multifrequency holography is proposed that is applied to recognize the shapes of the objects buried in snow. An experimental system using X-band microwaves was constructed and image reconstruction was accomplished mathematically by computer, with the image displayed on a CRT using a specially designed circuit. Field trials are reported in which it was possible to obtain 3-D images of metallic cylinders and a mannequin buried in snow.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Dynamic and Static Stability in Hexapedal Runners (1994)

Stability is fundamental to the performance of terrestrial locomotion. Running cockroaches met the criteria for static stability over a wide range of speeds, yet several locomotor variables changed in a way that revealed an increase in the importance of dynamic stability as speed increased. Duty factors (the fraction of time that a leg spends on the ground relative to the stride period) decreased to 0.5 and below with an increase in speed. The duration of double support (i.e. when both tripods, or all six legs, were on the ground) decreased significantly with an increase in speed. All legs had similar touch-down phases in the tripod, but the shortest leg, the front one, lifted off before the middle and the rear leg, so that only two legs of the tripod were in contact with the ground at the highest speeds. Per cent stability margin (the shortest distance from the center of gravity to the boundaries of support, normalized to the maximum possible stability margin) decreased with increasing speed from 60% at 10 cms-1 to values less than zero at speeds faster than 50 cms-1, indicating instances of static instability at fast speeds. The center of mass moved rearward or posteriorly with respect to the base of support as speed increased. Moments about the center of mass, as shown by the center of pressure (the equivalent of a single 'effective' leg), were variable, but were balanced by opposing moments over a stride. Thus, hexapods can exploit the advantages of both static and dynamic stability. Static or quasi-static assumptions alone were insufficient to explain straight-ahead, constant-speed locomotion and may hinder discovery of behaviors that are dynamic, where kinetic energy and momentum can act as a bridge from one step to the next.
Efficient commerce protocols based on one-time pads (2002)

Presents a new commerce protocol that allows customers and merchants to conduct face-to-face credit-card authorizations with a credit card company securely, with the option of anonymity for the customer, the merchant, or both. Our protocol guarantees that both parties agree to and know the outcome of each transaction. Our protocol has three advantages over others. First, we need only two message authentication code (MAC) operations per party per transaction, fewer than most popular protocols. Second, our own MAC function, OTPMAC (One-Time Pad MAC), does not rely on the existence of one-way functions or on any other unproven hypothesis. Third, our protocol generates a new one-time identifier per party per transaction, preventing the linkage of multiple transactions to a single party. Additionally, the protocol can operate in modes using alternatives to the one-time pad, including cryptographic pseudo-random number generators and conventional cryptographic MAC functions.
Performance of CTs and relays at low frequencies (2016)

When generators or motors are started via variable frequency drive (VFD), the initial frequency is very low, on the order of few hertz, and can be low for a considerable amount of time or even permanently. It is not well recognized in the industry about consequences of the low frequency for the currents transformers (CTs) performance and how this affects the protection performance as well. First of all, CTs are designed to operate at the nominal system frequency, at lower frequency CTs will saturate at much lower currents, this can happen even at CT nominal current. Secondly, there are limits of the system frequency measurements in the protective relays, which will impact the correct current magnitude estimation and therefore accuracy of the protection. And lastly, protective relays need full power cycle to measure current and power cycle will be considerably longer at lower frequency, therefore affecting fault clearance time. This paper will educate engineers on how to take into account CTs and protective relay's performance at lower frequencies to ensure adequate protection. It will also explore other solutions to address impact of the low frequency on the CTs and protection.
A Virus-Induced Disease of Mice Characterized by Erythrocytopoiesis and Lymphoid Leukemia (1962)

A newly isolated, highly potent murine leukemogenic virus induced a dual type of disease in 90 to 100 percent of mice of different strains. The disease was characterized by rapid and extreme proliferation of predominantly erythrocytic and leukocytic elements as early as 7 days postparenteral inoculation. Within 15 days after inoculation of newborn or adult mice, 50 to 100 percent developed palpable spleens. Fifty percent of the animals, with spleens weighing 30 to 50 times those of normal mice, died within 25 to 35 days. In mice that survived, the erythrocytopoiesis was followed by the development of lymphocytic leukemia beginning 30 to 45 days after inoculation. Leukemic tissues transplanted with ease and killed 100 percent of the recipients. An intense viremia occurred in infected mice at least as early as 16 days after inoculation. The virus extracted from plasma or from leukemic tissues was of such potency that a 10−7 dilution of the test material induced the disease in 50 percent of the recipients within 95 days. Virus particles measuring 100 mμ were seen in thin sections of plasma pellets and in malignant lymphoblasts from spleen. Osborne-Mendel rats, 8 different inbred strains of mice, and random-bred Swiss mice, were all highly susceptible. The virus was stable to lyophilization, −70° C, formalin, and was not neutralized by antiserum prepared against the murine leukemia viruses of Friend, Moloney, or Schoolman-Schwartz. The ratio of mice responding with erythrocytopoiesis only to those developing erythrocytopoiesis plus lymphoid leukemia was influenced by the infecting dose of virus and by the strain and age of the recipients.
Deep Steering: Learning End-to-End Driving Model from Spatial and Temporal Visual Cues (2017)

In recent years, autonomous driving algorithms using low-cost vehicle-mounted cameras have attracted increasing endeavors from both academia and industry. There are multiple fronts to these endeavors, including object detection on roads, 3-D reconstruction etc., but in this work we focus on a vision-based model that directly maps raw input images to steering angles using deep networks. This represents a nascent research topic in computer vision. The technical contributions of this work are three-fold. First, the model is learned and evaluated on real human driving videos that are time-synchronized with other vehicle sensors. This differs from many prior models trained from synthetic data in racing games. Second, state-of-the-art models, such as PilotNet, mostly predict the wheel angles independently on each video frame, which contradicts common understanding of driving as a stateful process. Instead, our proposed model strikes a combination of spatial and temporal cues, jointly investigating instantaneous monocular camera observations and vehicle's historical states. This is in practice accomplished by inserting carefully-designed recurrent units (e.g., LSTM and Conv-LSTM) at proper network layers. Third, to facilitate the interpretability of the learned model, we utilize a visual back-propagation scheme for discovering and visualizing image regions crucially influencing the final steering prediction. Our experimental study is based on about 6 hours of human driving data provided by Udacity. Comprehensive quantitative evaluations demonstrate the effectiveness and robustness of our model, even under scenarios like drastic lighting changes and abrupt turning. The comparison with other state-of-the-art models clearly reveals its superior performance in predicting the due wheel angle for a self-driving car.
Pattern Recognition in Pulmonary Tuberculosis Defined by High Content Peptide Microarray Chip Analysis Representing 61 Proteins from M. tuberculosis (2008)

A uniform target MTB IgG-epitope recognition pattern exists in pulmonary tuberculosis. Unbiased, high-content peptide microarray chip-based testing of clinically well-defined populations allows to visualize biologically relevant targets useful for development of novel TB diagnostics and vaccines.
A permanent-magnet rotor for a high-temperature superconducting bearing (1996)

Design, fabrication, and performance of a 0.39-m diam., 6.8-kg flywheel rotor with only one bearing is discussed. To achieve low-loss energy storage, the rotor's segmented-ring permanent magnet (PM) is optimized for levitation and circumferential homogeneity. A PM figure of merit is proposed that appears to correlate with loss data. Pre compression of the PM with fiber-composite banding is necessary for practical rotor speeds.
Supporting collaborative writing of hyperdocuments in SEPIA (1992)

Today, most cooperative systems support primarily either asynchronous or synchronous (real time) cooperative work. We feel that both synchronous and asynchronous cooperation are extremely important aspects of working in groups, and to ignore one or the other is to supply only half a solution to users. In this paper, we describe the extension of the hypertext authoring system SEPIA developed at GMD-IPSI to support cooperative work among hypertext authors. Cooperative SEPIA is unique not only in its ability to support cooperative work in both of these categories, but also in how smoothly and naturally it supports the transition between these two categories.
Event driven persistent sensing: Overcoming the energy and lifetime limitations in unattended wireless sensors (2016)

The DARPA Near Zero Power RF and Sensor Operations (N-ZERO) program seeks to overcome the power limitations of persistent sensing by developing wireless, event-driven sensing capabilities that allow physical, electromagnetic and other sensors to remain dormant - effectively asleep yet aware - until an event of interest awakens them. State-of-the-art sensors use active electronics to monitor the environment for such external triggers. The power consumed by these electronic circuits limits the sensor lifetime to durations of weeks to months. In contrast, N-ZERO seeks to exploit the energy in signal signatures to detect and recognize attention-worthy events, such as the presence of a particular machinery type or radio communications protocol, while rejecting noise and interference. This paper will discuss the new architectural approaches and component technologies being developed under the N-ZERO program, which are predicted to extend the lifetime of wireless sensors to several years under many operational scenarios.
Genome Sequence of Bacillus endophyticus and Analysis of Its Companion Mechanism in the Ketogulonigenium vulgare-Bacillus Strain Consortium (2015)

Bacillus strains have been widely used as the companion strain of Ketogulonigenium vulgare in the process of vitamin C fermentation. Different Bacillus strains generate different effects on the growth of K. vulgare and ultimately influence the productivity. First, we identified that Bacillus endophyticus Hbe603 was an appropriate strain to cooperate with K. vulgare and the product conversion rate exceeded 90% in industrial vitamin C fermentation. Here, we report the genome sequencing of the B. endophyticus Hbe603 industrial companion strain and speculate its possible advantage in the consortium. The circular chromosome of B. endophyticus Hbe603 has a size of 4.87 Mb with GC content of 36.64% and has the highest similarity with that of Bacillus megaterium among all the bacteria with complete genomes. By comparing the distribution of COGs with that of Bacillus thuringiensis, Bacillus cereus and B. megaterium, B. endophyticus has less genes related to cell envelope biogenesis and signal transduction mechanisms, and more genes related to carbohydrate transport and metabolism, energy production and conversion, as well as lipid transport and metabolism. Genome-based functional studies revealed the specific capability of B. endophyticus in sporulation, transcription regulation, environmental resistance, membrane transportation, extracellular proteins and nutrients synthesis, which would be beneficial for K. vulgare. In particular, B. endophyticus lacks the Rap-Phr signal cascade system and, in part, spore coat related proteins. In addition, it has specific pathways for vitamin B12 synthesis and sorbitol metabolism. The genome analysis of the industrial B. endophyticus will help us understand its cooperative mechanism in the K. vulgare-Bacillus strain consortium to improve the fermentation of vitamin C.
Identification of an Erythrocyte Component Carrying the Duffy Blood Group Fy <sup>a</sup> Antigen (1984)

The erythrocyte component carrying the Duffy blood group antigen Fya has been identified as a 35- to 43-kilodalton protein. The protein is degraded by proteases, chymotrypsin, and Pronase, which destroy its antigenicity on intact erythrocytes. Its unusual property of aggregating on being boiled in 5 percent sodium dodecyl sulfate with 5 percent 2-mercaptoethanol distinguishes it from other erythrocyte membrane proteins described to date.