gebhart/patrepeval huggingface dataset:
Deletion and Allelic Exchange of the <i>Aspergillus fumigatus veA</i> Locus via a Novel Recyclable Marker Module (2005)

Detailed evaluation of gene functions in an asexual fungus requires advanced methods of molecular biology. For the generation of targeted gene deletions in the opportunistic pathogen Aspergillus fumigatus we designed a novel blaster module allowing dominant selection of transformants due to resistance to phleomycin as well as dominant (counter)selection of a Cre recombinase-mediated marker excision event. For validation purposes we have deleted the A. fumigatus pabaA gene in a wild-type isolate by making use of this cassette. The resulting pabaA::loxP strain served as the recipient for subsequent targeting of the velvet locus. Homologous reconstitution of the deleted gene was performed by an allele whose expression is driven in a nitrogen source-dependent manner, as validated by Northern analyses. Overexpression of the veA locus in A. fumigatus does not result in any obvious phenotype, whereas the sporulation capacities of the veA null mutant are reduced on nitrate-containing medium, a phenotype that is completely restored in the reconstituted strain.
Steep Slope Field-Effect Transistors With Ag/TiO<sub>2</sub>-Based Threshold Switching Device (2016)

In this letter, we demonstrate a steep slope field-effect transistor (FET) using a threshold switching (TS) device. The Ag/TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -based TS device reported in our previous work was implemented in series with the drain region of a transistor. Since the TS device has an abrupt transition between the OFF- and ON-states and vice versa, the transistor has a 5-mV/decade subthreshold slope and a high ON/OFF-current ratio (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ON</sub> /I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OFF</sub> ) of >10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sup> with a low drain voltage (0.3 V). Furthermore, the threshold voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th,FET</sub> ) of the transistor can be tuned by controlling the thickness of the TS device.
Individualized estimation of human core body temperature using noninvasive measurements (2018)

A rising core body temperature (T<sub>c</sub>) during strenuous physical activity is a leading indicator of heat-injury risk. Hence, a system that can estimate T<sub>c</sub> in real time and provide early warning of an impending temperature rise may enable proactive interventions to reduce the risk of heat injuries. However, real-time field assessment of T<sub>c</sub> requires impractical invasive technologies. To address this problem, we developed a mathematical model that describes the relationships between T<sub>c</sub> and noninvasive measurements of an individual's physical activity, heart rate, and skin temperature, and two environmental variables (ambient temperature and relative humidity). A Kalman filter adapts the model parameters to each individual and provides real-time personalized T<sub>c</sub> estimates. Using data from three distinct studies, comprising 166 subjects who performed treadmill and cycle ergometer tasks under different experimental conditions, we assessed model performance via the root mean squared error (RMSE). The individualized model yielded an overall average RMSE of 0.33 (SD = 0.18)°C, allowing us to reach the same conclusions in each study as those obtained using the T<sub>c</sub> measurements. Furthermore, for 22 unique subjects whose T<sub>c</sub> exceeded 38.5°C, a potential lower T<sub>c</sub> limit of clinical relevance, the average RMSE decreased to 0.25 (SD = 0.20)°C. Importantly, these results remained robust in the presence of simulated real-world operational conditions, yielding no more than 16% worse RMSEs when measurements were missing (40%) or laden with added noise. Hence, the individualized model provides a practical means to develop an early warning system for reducing heat-injury risk. NEW & NOTEWORTHY A model that uses an individual's noninvasive measurements and environmental variables can continually "learn" the individual's heat-stress response by automatically adapting the model parameters on the fly to provide real-time individualized core body temperature estimates. This individualized model can replace impractical invasive sensors, serving as a practical and effective surrogate for core temperature monitoring.
Templated Synthesis of Mesoporous Superparamagnetic Polymers (2007)

Abstract We present a novel synthetic strategy for fabricating superparamagnetic nanoparticles randomly dispersed in a mesoporous polymeric matrix. This method is based on the use of mesoporous silica materials as templates. The procedure used to obtain these mesoporous magnetic polymers consisted in: a) generating iron oxide ferrite magnetic nanoparticles (FMNP) of size ∼ 7–8 nm within the pores of the silica, b) loading the porosity of the silica/FMNP composite with a polymer (Polydivinylbenzene), c) selectively removing the silica framework from the resulting silica/FMNP/polymer composite. Such magnetic porous polymeric materials exhibit large surface areas (up to 630 m 2 g –1 ), high pore volumes (up to 0.73 cm 3 g –1 ) and a porosity made up of mesopores. In this way, it is possible to obtain superparamagnetic mesoporous hybrid nanocomposites that are easily manipulated by an external magnetic field and display different magnetic behaviours depending on the textural properties of the template employed.
Successful treatment of angiofibromata of tuberous sclerosis complex with rapamycin (2010)

Tuberous sclerosis complex (TSC) is an autosomal dominant neurocutaneous syndrome manifesting as hamartomatous growths in multiple organs. We present two cases of patients with TSC and associated facial angiofibromata treated with topical and oral rapamycin and discuss the role for rapamycin in the treatment of these disfiguring lesions. Our patients demonstrated decreased numbers of angiofibromata and less redness with this treatment. This is the first published report on the use of topical rapamycin for the treatment of angiofibromata.
Towards high energy density lithium battery anodes: silicon and lithium (2019)

Silicon and lithium metal are considered as promising alternatives to state-of-the-art graphite anodes for higher energy density lithium batteries because of their high theoretical capacity. However, significant challenges such as short cycle life and low coulombic efficiency have seriously hindered their practical applications. In the past decades, various strategies have been proposed to address the major problems of Si and Li anodes. In this review, we summarize the understanding on Si and Li anodes, highlight the recent progress in the development and introduce advanced characterization techniques. We also indicate the remaining challenges of Si and Li anodes requiring more efforts for future widespread applications. We expect that this review provides an overall picture of the recent progress and inspires more efforts in the fundamental understanding and practical applications of Si and Li anodes.
Shape averaging under Time Warping (2009)

Dynamic time warping (DTW) distance measure has increasingly been used as a similarity measurement for various data mining tasks in place of traditional Euclidean distance metric due to its superiority in sequence-alignment flexibility. However, in some tasks where shape averaging is required, e.g., in template matching and k-means clustering problems, current averaging methods are inaccurate in that they produce undesired templates and cluster representatives. In this work, we emphasize the importance of the correctness of this averaging subroutine and propose a novel shape averaging method, called prioritized shape averaging (PSA), using hierarchical clustering approach. In experimental evaluation, our proposed method, PSA, achieves a lower discrepancy distance between an averaged sequence and every original sequence than existing method on various domains.
Dianin's compound as a zeolitic sorbent (1976)

Dianin's compound, suitably agitated, has been shown to sorb freely Ar, Kr, Xe, CO2, CH4, C2H6, C3H8, n-C4H10, iso-C4H10, and neo-C5H12, and behaves in some respects like an organic zeolite; the numbers of molecules filling each cavity in the host lattice varied from 6 for Ar (–196 °C) and CH4(–183°C) to 2 for iso-C4H10 and neo-C5H12(0 °C), and saturation numbers depended upon the size and shape of the guest molecules, in the same way as for zeolites.
62.3: 10.1 inch SVGA Ultra Thin and Flexible Active Matrix Electrophoretic Display (2006)

Abstract A 10.1 inch SVGA reflective type flexible active matrix electrophoretic displays were successfully fabricated on a thin metal foil substrate. It was developed a new multi‐barrier structure in order to use a rough metal foil as display substrate and designed a new TFT array structure for obtaining good performance. The backplane comprises a‐Si thin film transistor array fabricated using a conventional TFT manufacturing technologies. The 800×600 pixel display can be driven during extremely bending and measures only 0.3 mm in total thickness and weighs 32.8 grams. This prototype displays have a true paper‐like look and feel, with wide‐viewing angle and high contrast ratio.
A New Process for Antineoplastic Agent Clofarabine (2004)

Clofarabine is a promising DNA polymerase inhibitor currently in clinical trials for a variety of liquid and solid tumor indications. The efforts for development of a new manufacturing process for clofarabine are presented. This new process allows for the reliable and efficient production of drug substance in high anomeric excess and high overall purity, without using chromatography. The high anomeric selectivity is achieved by reacting 2-chloroadenine with 1-bromo-2-deoxy-2-fluoro-3,5-di-O-benzoyl-α-d-ribofuranose (4) and potassium tert-butoxide in a mixture of three solvents. Following crystallization, anomeric ratios exceeding 50 (β/α) are achieved. Deprotection and additional crystallization afford a clofarabine drug substance containing less than 0.1% of the α-anomer.
An RFID Reader Network Based on SOAP (2010)

This paper describes an RFID reader network system that is based on the open SOAP protocol. It mainly comprises one or more RFID reader devices, a control server and one or more applications. The components communicate with each other through so called SOAP messages which are transferred over the http(s) standard protocol. These messages are coded by using a specific XML format, and contain commands or other information (parameters, status, etc.). Many different kinds of reader devices (LF-, HF-, UHF-RFID) can be connected to the network, even others than RFID readers like active sensor devices. The control server is the central device in the network and can be implemented on standard PC hardware or embedded in a microcontroller system. It manages the communication within the network. All applications and readers link to the control server. The applications control and access the readers, e.g. they execute available reader functions, store collected data or provide an user interface.
Docosahexaenoic acid accumulates in cardiolipin and enhances HT-29 cell oxidant production (1998)

The objective of this study was to investigate membrane fatty acids for their effects on mitochondrial function in live cells. Mitochondrial potential and oxidant production were measured in human colonic adenocarcinoma (HT-29) cells with membranes enhanced in either oleic acid, linoleic acid, arachidonic acid, eicosapentaenoic acid, or docosahexaenoic acid. Docosahexaenoic acid-enriched cells had increased mitochondrial potential and produced 5-fold more cellular oxidants than did cells enriched with any other fatty acid. Oxidant production in fatty acid-enriched HT-29 cells did not correlate with the degree of unsaturation for total membrane fatty acids. However, there was a strong correlation between the degree of fatty acid unsaturation of cardiolipin, a critical inner-mitochondrial membrane phospholipid, and oxidant production. Cardiolipin acyl composition is known to influence the activity of electron transport complexes, an effect that can increase mitochondrial oxidant production. Docosahexaenoic acid was enriched to 48 mol% of the fatty acids present in HT-29 cell cardiolipin. These results demonstrate the importance of membrane acyl composition to mitochondrial potential and oxidant production in live cells. Additionally, results suggest that docosahexaenoic acid increases cell oxidant production by accumulating in cardiolipin, where its presence alters electron transport efficiency.
Differential expression of uterine calcium transporter 1 and plasma membrane Ca<sup>2+</sup>ATPase 1b during rat estrous cycle (2006)

Calcium-related proteins include the calcium transporters 1 and 2 (CaT1 and CaT2), plasma membrane Ca2+-ATPase 1b (PMCA1b), and calbindin-D9k and -D28k. The expression of CaT1 and PMCA1b and their potential roles in the uterine tissue remain to be clarified. Thus, in the present study, the expression patterns of CaT1 and PMCA1b were examined to predict their roles in rat uterus during the estrous cycle. Both CaT1 and PMCA1b mRNAs were detected in rat uterus. Uterine CaT1 mRNA was highly expressed at diestrus compared with proestrus, whereas PMCA1b expression was not altered during the estrus cycle. To evaluate the sex steroids involved in uterine CaT1 mRNA regulation, 17beta-estradiol (E2) and/or progesterone (P4) were injected into immature rats. Treatment with P4 or E2 plus P4 resulted in an increase in CaT1 mRNA, but a synergetic effect of E2 plus P4 was not detected. Uterine CaT1 mRNA was induced by P4 in a time- and dose-dependent manner, with maximal transcript detected 12 h after the final P4 injection. Treatment with RU486, a progesterone receptor (PR) antagonist, completely blocked P4-induced CaT1 mRNA, indicating that P4 regulates CaT1 mRNA expression via a PR-mediated pathway. In addition, CaT1 mRNA was expressed in uterine endometrium and glandular endometrium at diestrus in P4-treated rats. Together, these results suggest that CaT1 is regulated by P4 at diestrus via a PR-dependent pathway.
Purification and Characterization of 7β-Hydroxysteroid Dehydrogenase from Ruminococus sp. of Human Intestine (1987)

7 beta-Hydroxysteroid dehydrogenase (7 beta-HSD) was produced by Ruminococcus sp. PO1-3 obtained from among human intestinal bacteria. The enzyme was purified from a crude extract by ammonium sulfate fractionation, and Butyl-Toyopearl 650M, Sephadex G-150, Matrex Red A and Octyl-Sepharose chromatographies. The purified enzyme was obtained as a single band on polyacrylamide gel electrophoresis with enzyme activity staining and as one band corresponding to a molecular weight of 30,000 on SDS-polyacrylamide gel electrophoresis. On gel filtration, its apparent molecular weight was estimated to be 60,000. The enzyme had a sulfhydryl group(s) in its active site. Substrate specificity studies revealed that the enzyme showed absolute specificity for the beta-configuration of a hydroxyl group at the 7 position of bile acids, and required NADP+ and NADPH as cosubstrates. The Km values for ursodeoxycholic acid, 7-k etolithocholic acid, NADP+, and NADPH were 5.0, 8.5, 7.7, and 24 microM, respectively.
A multipath model for the powerline channel (2002)

The development of powerline communication (PLC) systems for Internet, voice, and data services requires measurement-based models of the transfer characteristics of the mains network suitable for performance analysis by simulation. This paper presents an analytic model describing complex transfer functions of typical powerline networks using only a small set of parameters. The model is based on physical signal propagation effects in mains networks including numerous branches and impedance mismatching. Besides multipath propagation accompanied by frequency-selective fading, signal attenuation of typical power cables increasing with length and frequency is considered. A verification of the model at a test network, as well as its use for definition of attenuation profiles and reference channels, demonstrate the practical value of the proposed model.
Increased expression and copy number amplification of LINE-1 and SINE B1 retrotransposable elements in murine mammary carcinoma progression (2013)

In higher eukaryotic genomes, Long Interspersed Nuclear Element 1 (LINE-1) retrotransposons and endogenous retroviruses represent large families of repeated elements encoding reverse transcriptase (RT) proteins. Short Interspersed Nuclear Element B1 (SINE B1) retrotrasposons do not encode RT, but use LINE-1-derived RT for their retrotransposition. We previously showed that many cancer types have an abundant endogenous RT activity. Inhibition of that activity, by either RNA interference-dependent silencing of active LINE-1 elements or by RT inhibitory drugs, reduced proliferation and promoted differentiation in cancer cells, indicating that LINE-1-encoded RT is required for tumor progression. Using MMTV-PyVT transgenic mice as a well-defined model of breast cancer progression, we now report that both LINE-1 and SINE B1 retrotransposons are up-regulated at a very early stage of tumorigenesis; LINE-1-encoded RT product and enzymatic activity were detected in tumor tissues as early as stage 1, preceding the widespread appearance of histological alterations and specific cancer markers, and further increased in later progression stages, while neither was present in non-pathological breast tissues. Importantly, both LINE-1 and SINE B1 retrotransposon families undergo copy number amplification during tumor progression. These findings therefore indicate that RT activity is distinctive of breast cancer cells and that, furthermore, LINE-1 and SINE B1 undergo copy number amplification during cancer progression.
A Novel Integrated Approach Using Dynamic Thresholding and Edge Detection (IDTED) for Automatic Detection of Exudates in Digital Fundus Retinal Images (2007)

The automatic screening of patients for early detection and prevention of diabetic retinopathy (DR) has been the prime focus in recent times due to the large ratio of patients to medical ophthalmologists. Exudate detection is one of the main steps of DR. A reliable method for detection of exudates is presented in this paper. Optic disc (OD) is localized by the principle component analysis (PCA). Active contour based approach is used for accurate segmentation of boundary of OD. In our IDTED method, pre-processing techniques such as histogram specification and local contrast enhancement are integrated with dynamic thresholding (DT) and edge detection for exudate detection. The IDTED algorithm, when tested on 25 digital fundus retinal images and compared with the performance of a human grader, has shown a mean sensitivity of 99% and a mean predictivity of 93%
Stable Multilineage Chimerism without Graft versus Host Disease Following Nonmyeloablative Haploidentical Hematopoietic Cell Transplantation (2006)

Here we report that stable multilineage chimerism and engraftment can be established across haploidentical major histocompatibility complex barriers with minimal treatment-related toxicity and without significant risk of graft-versus-host disease.
The signal sequence receptor has a second subunit and is part of a translocation complex in the endoplasmic reticulum as probed by bifunctional reagents. (1990)

Bifunctional cross-linking reagents were used to probe the protein environment in the ER membrane of the signal sequence receptor (SSR), a 24-kD integral membrane glycoprotein (Wiedmann, M., T. V. Kurzchalia, E. Hartmann, and T. A. Rapoport. 1987. Nature [Lond.]. 328:830-833). The proximity of several polypeptides was demonstrated. A 22-kD glycoprotein was identified tightly bound to the 34-kD SSR even after membrane solubilization. The 34-kD polypeptide, now termed alpha SSR, and the 22-kD polypeptide, the beta SSR, represent a heterodimer. We report on the sequence of the beta SSR, its membrane topology, and on the mechanism of its integration into the membrane. Cross-linking also produced dimers of the alpha-subunit of the SSR indicating that oligomers of the SSR exist in the ER membrane. Various bifunctional cross-linking reagents were used to study the relation to ER membrane proteins of nascent chains of preprolactin and beta-lactamase at different stages of their translocation through the membrane. The predominant cross-linked products obtained in high yields contained the alpha SSR, indicating in conjunction with previous results that it is a major membrane protein in the neighborhood of translocating nascent chains of secretory proteins. The results support the existence of a translocon, a translocation complex involving the SSR, which constitutes the specific site of protein translocation across the ER membrane.
Conformational analysis of 2-aminoindans and 2-(aminomethyl)indans in relation to their central dopaminergic effects and a dynamic dopamine receptor concept (1987)

Conformational analyses on differently substituted 2-aminoindans of significant pharmacological interest were carried out by the molecular mechanics method (MM2). An X-ray structure of (R)-4-methoxy-2-aminoindan has shown the ammonium nitrogen [-)-D-tartaric acid salt) in an axial position. From comparison with other, highly potent, centrally acting dopamine (DA) receptor agonists, it can be predicted that the active enantiomer (R)-4-hydroxy-2-(di-n-propylamino)indan should have its nitrogen atom in an equatorial position. This places it close to the aromatic ring plane, which is one of several prerequisites for potent DA receptor agonism. MM2 correctly calculates (R)-4-methoxy-2-aminoindan and (R)-4-hydroxy-2-(dialkylamino)indan to be more stable in the N-axial and N-equatorial conformations, respectively. Conformational analysis of the dimethyl model compound of the moderately potent dopaminergic phenylpropylamine analogue 4-hydroxy-2-[(di-n-propylamino)methyl]indan was also carried out, in order to see if any conformations of this compound satisfy the requirements for dopaminergic agonism. Two such stable conformations were found.
Automated asphere centration testing with AspheroCheck UP (2017)

With aspheres being incorporated in optical designs across all industry fields, there is high demand for fast and flexible metrology solutions for aspheric lenses. While many systems support measuring the surface topography, the process is limited to a specific design or based on a time-consuming scanning process. Centration measurement with such systems requires additional probes or the inclusion of external reference surfaces in the measurement process. In this paper, we present AspheroCheck UP [1], a highly automated lens testing system based on the well-established AspheroCheck principle. The paraxial centering errors of both optical surfaces are measured in reflection using a focusing autocollimator. This centration measurement is combined with a fully motorized, non-contact distance sensor that measures the aspheric surface run-out. All three measurements can be performed in parallel during a single rotation of the sample, greatly reducing overall measurement time. The sensor can also be used for referencing to outer diameter, flange and/or interlock surfaces and even double-aspheric lenses. A five-axis motorized table enables the automatic alignment of the optical axis of the sample to the rotation axis. This significantly reduces setup time and allows for fully automatic testing without user interaction, ensuring both high measurement accuracy and high repeatability independent of the operator. A full cycle time of less than 1 minute including loading and unloading is possible, enabling applications in both R&D and production environments. In addition to supporting ISO and Q-type polynomial surfaces, the system supports most other rotationally symmetric surface types, including Fresnel and diffractive surfaces.