gebhart/patrepeval huggingface dataset:
The BH3‐only protein Puma is both necessary and sufficient for neuronal apoptosis induced by DNA damage in sympathetic neurons (2006)

DNA damage activates apoptosis in several neuronal populations and is an important component of neuropathological conditions. While it is well established that neuronal apoptosis, induced by DNA damage, is dependent on the key cell death regulators p53 and Bax, it is unknown which proteins link the p53 signal to Bax. Using rat sympathetic neurons as an in vitro model of neuronal apoptosis, we show that cytosine arabinoside is a DNA damaging drug that induces the expression of the BH3-only pro-apoptotic genes Noxa, Puma and Bim. Increased expression occurred after p53 activation, measured by its phosphorylation at serine 15, but prior to the conformational change of Bax at the mitochondria, cytochrome c (cyt c) release and apoptosis. Hence Noxa, Puma and Bim could potentially link p53 to Bax. We directly tested this hypothesis by the use of nullizygous mice. We show that Puma, but not Bim or Noxa, is a crucial mediator of DNA damage-induced neuronal apoptosis. Despite the powerful pro-apoptotic effects of overexpressed Puma in Bax-expressing neurons, Bax nullizygous neurons were resistant to Puma-induced death. Therefore, Puma provides the critical link between p53 and Bax, and is both necessary and sufficient to mediate DNA damage-induced apoptosis of sympathetic neurons.
Respiratory Waveform Estimation From Multiple Accelerometers: An Optimal Sensor Number and Placement Analysis (2018)

Respiratory patterns are commonly measured to monitor and diagnose cardiovascular, metabolic, and sleep disorders. Electronic devices such as masks used to record respiratory waveforms usually require medical staff support and obstruct the patients' breathing, causing discomfort. New techniques are being investigated to overcome such limitations. An emerging approach involves accelerometers to estimate the respiratory waveform based on chest motion. However, most of the existing techniques employ a single accelerometer placed on an arbitrary thorax position. The present work investigates the use and optimal placement of multiple accelerometers located on the thorax and the abdomen. The study population is composed of 30 healthy volunteers in three different postures. By means of a custom-made microcontrolled system, data are acquired from an array of ten accelerometers located on predefined positions and a pneumotachograph used as reference. The best sensor locations are identified by optimal linear reconstruction of the reference waveform from the accelerometer data in the minimum mean square error sense. The analysis shows that right-hand side locations contribute more often to optimal respiratory waveform estimates, a sound finding given that the right lung has a larger volume than the left lung. In addition, we show that the respiratory waveform can be blindly extracted from the recorded accelerometer data by means of independent component analysis. In conclusion, linear processing of multiple accelerometers in optimal positions can successfully recover respiratory information in clinical settings, where the use of masks may be contraindicated.
Identification of <i>Mycobacterium avium</i> Genes That Affect Invasion of the Intestinal Epithelium (2005)

Invasion of intestinal mucosa of the host by Mycobacterium avium is a critical step in pathogenesis and likely involves several different bacterial proteins, lipids, glycoproteins, and/or glycolipids. Through the screening of an M. avium genomic library in Mycobacterium smegmatis, we have identified a number of M. avium genes that are associated with increased invasion of mucosal epithelial cells. In order to further investigate these genes, we cloned six of them into a plasmid downstream of a strong mycobacterial promoter (L5 mycobacterial phage promoter), resulting in constitutive expression. Bacteria were then evaluated for increased expression and examined for invasion of HT-29 intestinal epithelial cells. The genes identified encode proteins that are similar to (i) M. tuberculosis coenzyme A carboxylase, (ii) M. tuberculosis membrane proteins of unknown function, (iii) M. tuberculosis FadE20, (iv) a Mycobacterium paratuberculosis surface protein, and (v) M. tuberculosis cyclopropane fatty acyl-phopholipid synthase. The constitutive expression of these genes confers to M. avium the ability to invade HT-29 intestinal epithelial cells with a severalfold increase in efficiency compared to both the wild-type M. avium and M. avium containing the vector alone. Using the murine intestinal ligated loop model, it was observed that the constitutive expression of M. avium proteins has a modest impact on the ability to enter the intestinal mucosa when compared with the wild-type control, suggesting that under in vivo conditions these genes are expressed at higher levels. Evaluation of the expression of these invasion-related genes indicated that under conditions similar to the intestinal lumen environment, the genes identified are upregulated. These data suggest that invasion of the intestinal mucosa is an event that requires the participation of several bacterial factors and the expression of the genes that encode them is less observed under standard laboratory growth conditions.
Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing (2012)

Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.
NONLINEAR RESPONSE OF A RECTANGULAR PLATE SUBJECTED TO INPLANE DYNAMIC MOMENT (1986)

In the present paper, the vibration of the web plate under sinusoidally time-varying inplane moment is examined from the point of view of dynamic instability. The web plate is idealized by one rectangular plate surrounded by the upper and lower flange plates and vertical stiffeners. Inplane static and sinusoidally time-varying moments act on the edges of the plate. The dynamic instability regions are analyzed by the small deflection theory of thin plate. The amplitudes of unstable motions are determined by large deflection theory considering geometric nonlinearity.Numerical results are presented for various boundary conditions, loading conditions and dampings of the plate.
ChemInform Abstract: Reactions of Some [C, N, O]‐Containing Molecules with Si Surfaces: Experimental and Theoretical Studies (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Chirality-Responsive Helical Polymers (2007)

Unique macromolecules that fold into a preferred-handed helical conformation induced by external chiral stimuli are mainly described in this review. In contrast to small molecular systems, the chiral information of nonracemic guest molecules transfers with a significant amplification in a dynamic helical polymer, such as stereoregular poly(phenylacetylene)s bearing functional pendant groups as an excess of a single-handed helix through noncovalent bonding interaction, which provides an efficient chirality-sensing system. The chirality sensing of other oligomers (foldamers) is also briefly described.
Fast directional chamfer matching (2010)

We study the object localization problem in images given a single hand-drawn example or a gallery of shapes as the object model. Although many shape matching algorithms have been proposed for the problem over the decades, chamfer matching remains to be the preferred method when speed and robustness are considered. In this paper, we significantly improve the accuracy of chamfer matching while reducing the computational time from linear to sublinear (shown empirically). Specifically, we incorporate edge orientation information in the matching algorithm such that the resulting cost function is piecewise smooth and the cost variation is tightly bounded. Moreover, we present a sublinear time algorithm for exact computation of the directional chamfer matching score using techniques from 3D distance transforms and directional integral images. In addition, the smooth cost function allows to bound the cost distribution of large neighborhoods and skip the bad hypotheses within. Experiments show that the proposed approach improves the speed of the original chamfer matching upto an order of 45×, and it is much faster than many state of art techniques while the accuracy is comparable.
Simulation software tools for designing switched reluctance motor in electric bicycles (2012)

Generally, brushless dc (BLDC) motor is widely used in electric bicycles. There are several advantages of this motor such as high efficiency, high dynamic response and low noise operation. However, an obvious disadvantage of BLDC motor is permanent magnets needed for the motor. At present, the cost of permanent magnets is sharply increasing due to their high demand. This circumstance might distract many people from the motor with permanent magnets to focus mainly on the motor without permanent magnets. Switched reluctance motor (SRM) is an interesting option to eliminate such problem. It does not require any permanent magnet and it has also a simple and robust construction. This paper presents a design process of SRM for an electric bicycle application using simulation software tools. The optimizing process of SRM model is simulated in PC-SRD program. The flux-linkage and torque as a function of rotor position and current can be obtained from the finite element method (FE method). Moreover, the dynamic simulation model of SRM model is generated in MATLAB/Simulink program. In this work, the outer rotor SRM for an electric bicycle is considered. Torque-speed and current density-speed characteristics of the designed SRM for electric bicycles are illustrated.
Precipitation Variability and Extreme Events in Eastern China during the Past 1500 Years (2006)

A proxy precipitation index dataset for the period 501 - 2000 over eastern China (east of 105°E; 25 - 40°N approximately) was statistically derived from three existing datasets, which were reconstructed based on Chinese historical documents and instrument measurements. The index was then used to analyze decadal-to-centennial precipitation variability with a focus on three subregions, North China Plain (34 - 40°N approximately), Jiang-Huai area (31 - 34°N approximately) and Jiang-Nan area (25 - 31°N approximately). In addition, major drought/flood events considering severity, persistency, and spatial coverage were also identified. On the centennial time scales, precipitation variation in eastern China exhibited four dry epochs (500s - 870s, 1000s - 1230s, 1430s - 1530s and 1920s - 1990s) and three wet epochs (880s -990s, 1240s - 1420s and 1540s - 1910s), with multi-decadal dry/wet fluctuations within each epoch. However, variation showed strong regional differences, for example, opposite trends were found in the Jiang-Nan area and Jiang-Huai area during the 11 - 13th centuries and in the North China Plain and Jiang-Nan area since the 16th century. The data also showed 16 drought and 18 flood events in eastern China, with the most severe drought event occurring in 1634 - 1644. Droughts dominated in the 12 - 14th centuries, but since the middle of the17th century eastern China has been more subject to flooding. The severity of floods during the 20th century was comparable in intensity to historical times, but the droughts were usually less severe.
The Creaming of Hevea Latex by Colloids (1938)

Abstract Hevea latex is generally considered to be a suspension of rubber particles of various dimensions up to about 3 µ. The rubber hydrocarbon contains no “ionogenic groups,” and it is believed that part of the serum components imparts a negative charge to the rubber particles. Almost all latex imported into Europe is preserved by means of 0.5 to 0.7 per cent of ammonia. This ammonia plays a three-fold part: (1) it prevents premature souring of the latex; (2) it increases somewhat the charge on the particles; and (3) it attacks all types of serum components so that within a short time the “preserved” latex is hardly comparable with natural latex. As with all suspensions in which the dispersed phase is lighter than the dispersing medium, rubber latex exhibits the phenomena of creaming. The density of the rubber particles is approximately 0.914, that of the medium, 1.020. By means of creaming, it is possible to obtain a latex (1) which has a higher rubber content, whereby transportation space and cost are saved, and (2) which contains no components having a tendency to deposit a sediment. The natural creaming of latex, which is of no importance technically, was observed by Faraday as early as 1825.
Multi-model fuzzy controller for vehicle lane tracking (2014)

A fuzzy-logic-based multi-model lateral controller for vehicle trajectory following is presented. It is designed to control the steering angle based on the lateral deviation and the yaw angle. Firstly, local controllers are designed for four speed regions respectively. Then, by using a weighted integration of the four local outputs through a fusion module, a global control output is obtained so as to ensure the global performance. The multi-model fuzzy controller, which inherits the advantages of both the multi-model control and fuzzy control, can be used for wide range operation of vehicle speed. To verify the robustness and effectiveness of the proposed controller, two simulation tests are carried out using AMESim and Matlab/Simulink. The results from the first simulation show the ability of the proposed controller in different speed operations, and the other test demonstrates that the proposed controller achieves satisfactory results for different curvature of trajectory.
Production of recombinant antibodies using bacteriophages (2014)

Recombinant antibody fragments such as Fab, scFv, diabodies, triabodies, single domain antibodies and minibodies have recently emerged as potential alternatives to monoclonal antibodies, which can be engineered using phage display technology. These antibodies match the strengths of conventionally produced monoclonal antibodies and offer advantages for the development of immunodiagnostic kits and assays. These fragments not only retain the specificity of the whole monoclonal antibodies but also easy to express and produce in prokaryotic expression system. Further, these antibody fragments are genetically stable, less expensive, easy to modify in response to viral mutations and safer than monoclonal antibodies for use in diagnostic and therapeutic applications. This review describes the potential of antibody fragments generated using phage display and their use as diagnostic reagents.
Development of Heat Shock Proteins with Controlled Distribution Properties and Their Application to Vaccine Delivery (2007)

Antigen delivery to antigen-presenting cells (APCs) is a key issue in developing effective cancer vaccines. Controlling the tissue distribution of antigens, which are administered in a peptide/protein or DNA form, can increase antigen-specific immune responses, including the induction of cytotoxic T lymphocytes. Heat-shock protein 70 (Hsp70), a member of a highly conserved family of molecular chaperones, forms complexes with a variety of tumor-related antigens via its polypeptide binding domain. Because Hsp70 is taken up by APCs through the recognition by Hsp receptors, such as CD91 and LOX-1, its application to antigen delivery systems has been examined both in experimental and clinical settings. A tissue distribution study revealed that Hsp70 is mainly taken up by the liver, especially by hepatocytes, after intravenous injection in mice. A significant amount of Hsp70 was also delivered to regional lymph nodes when it was injected subcutaneously, supporting the hypothesis that Hsp70 is a natural targeting system to APCs. Model antigens were complexed with or conjugated to Hsp70, by which greater antigen-specific immune responses were achieved. Cytoplasmic delivery of Hsp70-antigen further increased the efficacy of the Hsp70-based vaccines. These findings indicate that effective cancer therapy can be achieved by developing Hsp70-based anticancer vaccines when their tissue and intracellular distribution is properly controlled.
Comparative evaluation of new synergists containing a butynyl-type synergophore group and piperonyl butoxide derivatives (2001)

Cross-substituted derivatives of piperonyl butoxide (PBO) and MB-599 (proposed common name: verbutin) were synthesized and investigated as carbofuran and permethrin synergists against housefly, Musca domestica L. The majority of PBO and MB-599 derivatives were significantly more potent synergists for carbofuran than for permethrin. PBO, the most important representative of this series was not the most potent synergist for carbofuran or for permethrin. Cleavage of the methylenedioxy ring of methylenedioxyphenyl (MDP) polyether compounds resulted in complete loss of synergistic activity with both insecticides, but it could be restored or even improved by incorporating an alkynyl ether moiety into the molecule. The improved synergistic activity was found to be closely associated with the 2-butynyloxymethyl side-chain, suggesting that this can be regarded as a characteristic synergophore group. MB-599, one of the most promising compounds bearing this group showed considerably higher activity with carbofuran (synergist ratio, SR = 37.8) than with PBO (SR = 6.4). There was no significant difference between synergistic activities of MB-599 (SR = 4.6) and PBO (SR = 4) for permethrin.
Method of Measuring Diffuse RMS Granularity (1970)

The rms granularity values normally produced by an optical scanner are in terms of semispecular instrument density. It is shown that these semispecular values can be converted to a diffuse density basis by dividing by a quantity q that is defined as the ratio of the instrument density of the sample to the diffuse density. The q factor has been measured by two methods, one of which is convenient for use in the routine measurement of diffuse granularity with existing equipment. It has been found that, except at very low density levels, the q of a given material varies only slightly as the diffuse density changes. It does, however, increase significantly as the numerical aperture of the optical system decreases. When a range of samples is measured, maximum values of q occur at moderate values of sample granularity.
THE CURRENT STATUS OF BLADDER PRESERVATION IN THE TREATMENT OF MUSCLE INVASIVE BLADDER CANCER (2000)

Bladder preserving strategies for muscle invasive bladder cancer have evolved from single modality to multimodality treatment approaches with improved results.We review the rationale for a multimodality approach to treat invasive bladder cancer and the results of some recent multimodality bladder sparing treatments. In addition, we compare this approach to radical cystectomy.Multimodality bladder sparing treatment involves combined transurethral bladder resection, external beam radiation with concurrent radiosensitizers and cisplatin based chemotherapy. With this approach overall 5-year survival is 48% to 63% and overall 5-year survival with the bladder intact is 36% to 43%. Survival with this approach is comparable to that in series of patients treated with primary radical cystectomy. The primary impetus for a multimodality bladder sparing approach is the improved quality of life associated with retaining the native bladder. However, the multimodality bladder sparing approach involves a complex treatment schedule associated with significant morbidity and mortality. Cystectomy is eventually required after attempted bladder preservation in 34% to 45% of cases and the rate of superficial recurrence is approximately 28%.Multimodality bladder sparing treatment is a viable option at centers with a dedicated multidisciplinary team. However, primary radical surgery remains the standard of care for invasive bladder cancer.
A New Look at Changma (2011)

This study revisits the definition of Changma, which is the major rainy season in Korea and corresponds to a regional component of the East Asian summer monsoon system. In spite of several decades of researches on Changma, questions still remain on many aspects of Changma that include its proper definition, determination of its onset and retreat, and relevant large-scale dynamical and thermodynamical features. Therefore, this study clarifies the definition of Changma (which is a starting point for the study of interannual and interdecadal variability) using a basic concept of air mass and front by calculating equivalent potential temperature () that considers air temperature and humidity simultaneously. A negative peak in the meridional gradient of this quantity signifies the approximate location of Changma front. This front has previously been recognized as the boundary between the tropical North Pacific air mass and cold Okhotsk sea air mass. However, this study identifies three more important air masses affecting Changma: the tropical monsoon air mass related to the intertropical convergence zone over Southeast Asia and South China Sea, the tropical continental air mass over North China, and intermittently polar continental air mass. The variations of these five air masses lead to complicated evolution of Changma and modulate intensity, onset and withdrawal dates, and duration of Changma on the interannual time scale. Importantly, use of , 500-hPa geopotential height and 200 hPa zonal wind fields for determining Changma onset and withdrawal dates results in a significant increase (up to~57%) in the hindcast skill compared to a previous study.