gebhart/patrepeval huggingface dataset:
Structural changes in the gut microbiome of constipated patients (2014)

Previous studies using culture-based methods suggested an association between constipation and altered abundance of certain taxa of the colonic microbiome. We aim to examine the global changes in gut microbial composition of constipated patients. A cross-sectional pilot study using 16S rRNA gene pyrosequencing was performed to compare stool microbial composition of eight constipated patients and 14 nonconstipated controls. Only obese children were enrolled so that the microbiome features associated with constipation would not be obscured by those associated with obesity. The sequencing reads were processed by QIIME for quantitative analysis of the microbial composition at genus and above levels. Dietary intake for all the individuals was assessed by dietary recalls and a food frequency questionnaire. The ecological diversities of fecal microbiome of the constipated patients differed from those of the controls. Significantly decreased abundance in Prevotella and increased representation in several genera of Firmicutes were observed in constipated patients compared with controls. The conventional probiotic genera Lactobacillus and Bifidobacteria were not decreased in the microbiomes of the constipated patients. These alterations in the fecal microbiome of constipated patients suggested that a novel probiotic treatment including certain Prevotella strains may be more effective than conventional probiotic products incorporating Lactobacillus or Bifidobacterium species. While it is possible that the observed changes in the microbiome in constipated subjects are a consequence of a low-fiber diet, these changes also predict a different pattern of bacterial fermentation end-products, such as increased butyrate production, which may contribute to pathogenesis of constipation.
Molecular Aspects of Seed Dormancy (2008)

Seed dormancy provides a mechanism for plants to delay germination until conditions are optimal for survival of the next generation. Dormancy release is regulated by a combination of environmental and endogenous signals with both synergistic and competing effects. Molecular studies of dormancy have correlated changes in transcriptomes, proteomes, and hormone levels with dormancy states ranging from deep primary or secondary dormancy to varying degrees of release. The balance of abscisic acid (ABA):gibberellin (GA) levels and sensitivity is a major, but not the sole, regulator of dormancy status. ABA promotes dormancy induction and maintenance, whereas GA promotes progression from release through germination; environmental signals regulate this balance by modifying the expression of biosynthetic and catabolic enzymes. Mediators of environmental and hormonal response include both positive and negative regulators, many of which are feedback-regulated to enhance or attenuate the response. The net result is a slightly heterogeneous response, thereby providing more temporal options for successful germination.
Functionalized Dibenzoborepins as Components of Small Molecule and Polymeric π-Conjugated Electronic Materials (2011)

We present the synthesis and characterization of dibenzo[b,f]borepins (DBBs) functionalized at the para and meta position with respect to the boron center in order to understand how regiochemical issues influence photophysical and electrochemical properties. An expanded synthetic repertoire is presented, using palladium catalysis (to perform Stille, Suzuki, Buchwald-Hartwig, and Sonogashira cross-coupling reactions) and lithium-halogen exchange to synthesize a series of extended π-conjugated DBBs. These chemistries are enabled by the use of a sterically bulky Mes* (2,4,6-tri-tert-butylphenyl) group on boron and the inclusion of reactive bromide handles on the DBB core. Photophysical, electrochemical, and computational analyses of these compounds indicate that relative to the protio-DBB the installation of groups at the meta positions decreases the optical band gap while para substitution raises the electron affinity of the system. Thus, both the HOMO-LUMO gap and specific frontier molecular orbital levels can be tuned by the installation of different conjugated substituents.
Stochastic Selection of Activation Layers for Convolutional Neural Networks (2020)

In recent years, the field of deep learning has achieved considerable success in pattern recognition, image segmentation, and many other classification fields. There are many studies and practical applications of deep learning on images, video, or text classification. Activation functions play a crucial role in discriminative capabilities of the deep neural networks and the design of new "static" or "dynamic" activation functions is an active area of research. The main difference between "static" and "dynamic" functions is that the first class of activations considers all the neurons and layers as identical, while the second class learns parameters of the activation function independently for each layer or even each neuron. Although the "dynamic" activation functions perform better in some applications, the increased number of trainable parameters requires more computational time and can lead to overfitting. In this work, we propose a mixture of "static" and "dynamic" activation functions, which are stochastically selected at each layer. Our idea for model design is based on a method for changing some layers along the lines of different functional blocks of the best performing CNN models, with the aim of designing new models to be used as stand-alone networks or as a component of an ensemble. We propose to replace each activation layer of a CNN (usually a ReLU layer) by a different activation function stochastically drawn from a set of activation functions: in this way, the resulting CNN has a different set of activation function layers.
Disrupted-in-Schizophrenia-1 expression is regulated by β-site amyloid precursor protein cleaving enzyme-1–neuregulin cascade (2010)

Neuregulin-1 (NRG1) and Disrupted-in-Schizophrenia-1 (DISC1) are promising susceptibility factors for schizophrenia. Both are multifunctional proteins with roles in a variety of neurodevelopmental processes, including progenitor cell proliferation, migration, and differentiation. Here, we provide evidence linking these factors together in a single pathway, which is mediated by ErbB receptors and PI3K/Akt. We show that signaling by NRG1 and NRG2, but not NRG3, increase expression of an isoform of DISC1 in vitro. Receptors ErbB2 and ErbB3, but not ErbB4, are responsible for transducing this effect, and PI3K/Akt signaling is also required. In NRG1 knockout mice, this DISC1 isoform is selectively reduced during neurodevelopment. Furthermore, a similar decrease in DISC1 expression is seen in beta-site amyloid precursor protein cleaving enzyme-1 (BACE1) knockout mice, in which NRG1/Akt signaling is reportedly impaired. In contrast to neuronal DISC1 that was reported and characterized, expression of DISC1 in other types of cells in the brain has not been addressed. Here we demonstrate that DISC1, like NRG and ErbB proteins, is expressed in neurons, astrocytes, oligodendrocytes, microglia, and radial progenitors. These findings may connect NRG1, ErbBs, Akt, and DISC1 in a common pathway, which may regulate neurodevelopment and contribute to susceptibility to schizophrenia.
The Advance of CRISPR-Cas9-Based and NIR/CRISPR-Cas9-Based Imaging System (2021)

The study of different genes, chromosomes and the spatiotemporal relationship between them is of great significance in the field of biomedicine. CRISPR-Cas9 has become the most widely used gene editing tool due to its excellent targeting ability. In recent years, a series of advanced imaging technologies based on Cas9 have been reported, providing fast and convenient tools for studying the sites location of genome, RNA, and chromatin. At the same time, a variety of CRISPR-Cas9-based imaging systems have been developed, which are widely used in real-time multi-site imaging <i>in vivo</i>. In this review, we summarized the component and mechanism of CRISPR-Cas9 system, overviewed the NIR imaging and the application of NIR fluorophores in the delivery of CRISPR-Cas9, and highlighted advances of the CRISPR-Cas9-based imaging system. In addition, we also discussed the challenges and potential solutions of CRISPR-Cas9-based imaging methods, and looked forward to the development trend of the field.
Expression of the 100‐kDa glucose‐regulated protein (grp100/endoplasmin) is associated with tumorigenicity in a model of rat colon adenocarcinoma (1994)

Resistance to glucose starvation and expression of glucose-regulated proteins (grp) were studied in a model of rat colon carcinoma. In this model, various clones originating from the same parental tumor showed distinct tumorigenic potential in syngeneic hosts. Some clones were tumorigenic while others were rejected by an immune-based mechanism. It appeared that the more tumorigenic clones were more resistant to glucose starvation and able to synthesize larger amounts of grp100 than non-tumorigenic clones in response to either glucose starvation or tunicamycin treatment. In contrast, there was no difference in the induced levels of synthesis of grp78 between tumorigenic and non-tumorigenic clones. These results suggest that the ability of cells to synthesize large amounts of the stress protein grp100 might allow them to resist marginal conditions imposed by fully immunocompetent hosts, thus conferring greater tumorigenicity.
Dynamic Magneto-Optic Correlator: Real-Time Operation (1987)

A proof-of-principle, fully dynamic, hybrid digital optical correlator has been built and successfully tested in a real-world non-cooperative target recognition environment provided by the U.S. Army. Preliminary test results have demonstrated the feasibility of using the LIGHT-MODTm, a patented and trademarked product of Litton Data Systems, as the key component in a fieldable non-cooperative target recognition system.
Hypno-synthesis: IV. hypnotherapy of the sex offender (1954)

(1954). Hypno-synthesis: IV. hypnotherapy of the sex offender. Journal of Clinical and Experimental Hypnosis: Vol. 2, No. 1, pp. 13-26.
Chip-based platform for dynamic analysis of NK cell cytolysis mediated by a triplebody (2016)

Cancer therapy via redirected lysis mediated by antibodies and antibody-derived agents relies on the availability of substantial numbers of sufficiently active immune effector cells. To monitor antitumor responses before and during therapy, sensitive methods are needed, capable of quantitating specific lysis of target cells. Here we present a chip-based single-cell cytometric assay, which uses adherent human target cells arrayed in structured micro-fields. Using a fluorescent indicator of cell death and time-lapse microscopy in an automated high-throughput mode, we measured specific target cell lysis by activated human NK cells, mediated by the therapeutic single chain triplebody SPM-2 (33-16-123). This antibody-derived tri-specific fusion protein carries binding sites for the myeloid antigens CD33 and CD123 and recruits NK cells via a binding site for the Fc-receptor CD16. Specific lysis increased with increasing triplebody concentration, and the single-cell assay was validated by direct comparison with a standard calcein-release assay. The chip-based approach allowed measurement of lysis events over 16 hours (compared to 4 hours for the calcein assay) and required far smaller numbers of primary cells. In addition, dynamic properties inaccessible to conventional methods provide new details about the activation of cytolytic effector cells by antibody-derived agents. Thus, the killing rate exhibited a dose-dependent maximum during the reaction interval. In clinical applications ex vivo monitoring of NK activity of patient's endogenous cells will likely help to choose appropriate therapy, to detect impaired or recovered NK function, and possibly to identify rare subsets of cancer cells with particular sensitivity to effector-cell mediated lysis.
A PZT micro-actuated suspension for high TPI hard disk servo systems (2000)

A piezoelectrically actuated suspension for high TPI (tracks per inch) hard disk drives is presented. Two reinforced piezoelectric microactuators, placed in parallel between the base plate and the spring beam, are used for the secondary actuation. A stroke of 1.2 /spl mu/m at the head was observed when driven by 30 V. The first torsion and the sway mode frequencies are 6.28 kHz and 10.5 kHz, respectively. In addition, the actuated suspension also has some distinguishing features such as, a C-channel and meanderline springs for shock-resistance enhancement. A possible vertical motion of the suspension is helpful for contact-start-stop (CSS) friction reduction and gramload adjustment. It also makes the suspension free from twist due to two layers of piezoelectric plates on both sides of the beam. As a result, the developed actuated suspension can be used to support high TPI hard disk drive servo systems.
Sinus histiocytosis with massive lymphadenopathy: bilateral orbital involvement spanning 17 years. (1989)

We report a case of sinus histiocytosis with massive lymphadenopathy (SHML) with a right inferior orbital mass. The mass was excised and, on histopathologic examination, was believed to be a "lipogranuloma." Thirteen years later, the patient was seen at our institution for what appeared to be a recurrent orbital mass. Orbital tumors were removed from the right superior and inferior orbit and from the left superior orbit. Histopathologic examination of these tumors at this institution and at the Armed Forces Institute of Pathology showed them to be SHML. The original biopsy tissue obtained in 1969 was reexamined and found also to be SHML. The clinical and histopathologic features of this disease are discussed.
<title>Approaches to biometric watermarks for owner authentification</title> (2001)

One major application domain for digital watermarks is copyright protection. Besides the design of watermarking algorithms, technologies for copyright holder identification have to be investigated. To ensure authenticity of an individual person, a wide number of biometric procedures exist. We define and describe new biometric watermarks, which denote the application of biometric reference data of individuals within digital watermarks to identify and verify ownership. Amongst the two classes of physiological and senso-motoric biometric schemes, the later appears more appropriate for biometric watermarks, as only these provide implicit expressions of intention. As such, we choose on-line handwriting as an appropriate base technology for our three new scenarios in biometric watermarking. In the first approach, embedding keys are being generated from biometric reference data, which requires stable and robust features and leads to rather complex keys. To overcome the complexity boundaries, the second approach develops a biometric reference hash, allowing key look-ups in key certifying servers. Although this proceeding leads to less complex keys, it still requires stable features. The third approach describes the embedding of biometric reference data within a watermark, allowing owner verification by more variant features, but limitations apply due to capacity of watermarking systems and also protection of the reference data is required. While most handwriting-based verification systems are limited to signature contexts, we discuss two additional context types for user authentication: passphrases and sketches.
Homotopic non-local regularized reconstruction from sparse positron emission tomography measurements (2015)

A new reconstruction method was developed for the purpose of improving the quality of positron emission tomography reconstruction from sparse measurements. We illustrate that promising reconstruction performance can be achieved for the proposed approach even at low sampling fractions, which allows for the use of significantly fewer detectors and have the potential to reduce scanner costs.
Identification of the platelet-derived chemokine CXCL4/PF-4 as a broad-spectrum HIV-1 inhibitor (2012)

The natural history of HIV-1 infection is highly variable in different individuals, spanning from a rapidly progressive course to a long-term asymptomatic infection. A major determinant of the pace of disease progression is the in vivo level of HIV-1 replication, which is regulated by a complex network of cytokines and chemokines expressed by immune and inflammatory cells. The chemokine system is critically involved in the control of HIV-1 replication by virtue of the role played by specific chemokine receptors, most notably CCR5 and CXCR4, as cell-surface coreceptors for HIV-1 entry; hence, the chemokines that naturally bind such coreceptors act as endogenous inhibitors of HIV-1. Here, we show that the CXC chemokine CXCL4 (PF-4), the most abundant protein contained within the α-granules of platelets, is a broad-spectrum inhibitor of HIV-1 infection. Unlike other known HIV-suppressive chemokines, CXCL4 inhibits infection by the majority of primary HIV-1 isolates regardless of their coreceptor-usage phenotype or genetic subtype. Consistent with the lack of viral phenotype specificity, blockade of HIV-1 infection occurs at the level of virus attachment and entry via a unique mechanism that involves direct interaction of CXCL4 with the major viral envelope glycoprotein, gp120. The binding site for CXCL4 was mapped to a region of the gp120 outer domain proximal to the CD4-binding site. The identification of a platelet-derived chemokine as an endogenous antiviral factor may have relevance for the pathogenesis and treatment of HIV-1 infection.
Experimental Study on Measurement Method of Flow Electrification (2010)

When a relative motion occurring between liquid and solid, electric charges with opposite signs come out separately on each side by friction which phenomena is called flow electrification. As the amount of charge generated by flow electrification is small, and part of which neutralize each other at the same time, the test method of flow electrification becomes one of discussion topics for scientists of all countries. This paper introduces an experimental measurement method of flow electrification, which is a comparative method by inserting electrodes in pipelines, and acquisition amplifier circuit, with high resolution and strong anti-jamming ability. Experiments show that the measurement method could be applied to system testing for flow electrification.
Forestville North Dye Trace: September 5, 2008 to November 12, 2008 (2008)

Two Dye Traces with field notes, tables and figures. A collaborative effort between the Minnesota Department of Natural Resources and the University of Minnesota.
Turboelectric Aircraft Drive Key Performance Parameters and Functional Requirements (2015)

The purpose of this paper is to propose specific power and efficiency as the key performance parameters for a turboelectric aircraft power system and investigate their impact on the overall aircraft. Key functional requirements are identified that impact the power system design. Breguet range equations for a base aircraft and a turboelectric aircraft are found. The benefits and costs that may result from the turboelectric system are enumerated. A break-even analysis is conducted to find the minimum allowable electric drive specific power and efficiency that can preserve the range, initial weight, operating empty weight, and payload weight of the base aircraft.
Cell drop threshold architecture for multi-class shared buffer with finite memory size (2011)

Shared buffer is commonly used to utilize the buffer in the switch. In order to minimize the cell lost of high class traffic in multi-class switch, the threshold is set to drop the low class cells in the shared buffer. This will give more space to accommodate the high class traffic cells. In this paper, we analyse the performance of shared buffer with different threshold settings. The multi-class shared buffer architecture is developed for 16×16 ports switch, which is targeted for Xilinx FPGA implementation. The performance of the multi-class shared buffer switch is analysed in term of the achievable throughput as well as the drop probability. Based on the simulation with different threshold settings, it is observed that the optimum selection of cell drop threshold depends on the size of the shared buffer that triggers the RAM threshold.
Simulated Microgravity, Erythroid Differentiation, and the Expression of Transcription Factor GATA-1 in CD34<SUP>+</SUP> Cells (2011)

In the RCCS group, GlyA+ (glycophorin A) expression was lower and CD33+ expression higher than in the 1-g liquid control group (22.21% +/- 3.02% and 60.05% +/- 3.08%, vs. 52.12% +/- 1.92% and 18.87% +/- 1.41%, respectively). The proportion of differentiated cells in the 1-g methylcellulos e group (Gly+% = 54.39% +/- 2.86%, CD33+% = 21.09% +/- 3.19%) was similar to that in the 1-g liquid control group. As shown by real-time quantitative PCR, the relative expression of GATA-1 mRNA in the RCCS group was only 20% of that in the -g control group. CONCLUSIONSs: The differentiation of CD3+ cells, and especially erythroid differentiation, was inhibited by simulated microgravity by a mechanism that appears to involve the suppression of GATA-1 mRNA expression. The results of this study may be useful in understanding the critical effect of simulated microgravity on the pathogenesis of space anemia.
Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4 (2006)

Histone arginine methylation is a posttranslational modification linked to the regulation of gene transcription. Unlike other posttranslational modifications, methylation has generally been regarded as stable, and enzymes that demethylate histone arginine residues have not been identified. However, it has recently been shown that human peptidylarginine deiminase 4 (PAD4), a Ca(2+)-dependent enzyme previously known to convert arginine residues to citrulline in histones, can also convert monomethylated arginine residues to citrulline both in vivo and in vitro. Citrullination of histone arginine residues by the enzyme antagonizes methylation by histone arginine methyltransferases and is thus a novel posttranslational modification that regulates the level of histone arginine methylation and gene activity. Here we present the crystal structures of a Ca(2+)-bound PAD4 mutant in complex with three histone N-terminal peptides, each consisting of 10 amino acid residues that include one target arginine residue for the enzyme (H3/Arg-8, H3/Arg-17, and H4/Arg-3). To each histone N-terminal peptide, the enzyme induces a beta-turn-like bent conformation composed of five successive residues at the molecular surface near the active site cleft. The remaining five residues are highly disordered. The enzyme recognizes each peptide through backbone atoms of the peptide with a possible consensus recognition motif. The sequence specificity of the peptide recognized by this enzyme is thought to be fairly broad. These observations provide structural insights into target protein recognition by histone modification enzymes and illustrate how PAD4 can target multiple arginine sites in the histone N-terminal tails.
Characterization of Antineurofilament Autoantibodies in Creutzfeldt-Jakob Disease (1984)

The antineurofilament antibodies found in the serum of a chimpanzee with experimental Creutzfeldt-Jakob disease reacted specifically with the 200,000-dalton polypeptide of the purified neurofilament triplet. They also reacted strongly with thoroughly characterized neurofilament swellings of proximal axons of spinal cord motoneurons from beta,beta' iminodipropionitrile (IDPN)-intoxicated rats.