gebhart/patrepeval huggingface dataset:
Intra- and Extracellular β-Galactosidases from <i>Bifidobacterium bifidum</i> and <i>B. infantis</i> : Molecular Cloning, Heterologous Expression, and Comparative Characterization (2001)

Three beta-galactosidase genes from Bifidobacterium bifidum DSM20215 and one beta-galactosidase gene from Bifidobacterium infantis DSM20088 were isolated and characterized. The three B. bifidum beta-galactosidases exhibited a low degree of amino acid sequence similarity to each other and to previously published beta-galactosidases classified as family 2 glycosyl hydrolases. Likewise, the B. infantis beta-galactosidase was distantly related to enzymes classified as family 42 glycosyl hydrolases. One of the enzymes from B. bifidum, termed BIF3, is most probably an extracellular enzyme, since it contained a signal sequence which was cleaved off during heterologous expression of the enzyme in Escherichia coli. Other exceptional features of the BIF3 beta-galactosidase were (i) the monomeric structure of the active enzyme, comprising 1,752 amino acid residues (188 kDa) and (ii) the molecular organization into an N-terminal beta-galactosidase domain and a C-terminal galactose binding domain. The other two B. bifidum beta-galactosidases and the enzyme from B. infantis were multimeric, intracellular enzymes with molecular masses similar to typical family 2 and family 42 glycosyl hydrolases, respectively. Despite the differences in size, molecular composition, and amino acid sequence, all four beta-galactosidases were highly specific for hydrolysis of beta-D-galactosidic linkages, and all four enzymes were able to transgalactosylate with lactose as a substrate.
The Noncoding RNA <i>MALAT1</i> Is a Critical Regulator of the Metastasis Phenotype of Lung Cancer Cells (2012)

The long noncoding RNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), also known as MALAT-1 or NEAT2 (nuclear-enriched abundant transcript 2), is a highly conserved nuclear noncoding RNA (ncRNA) and a predictive marker for metastasis development in lung cancer. To uncover its functional importance, we developed a MALAT1 knockout model in human lung tumor cells by genomically integrating RNA destabilizing elements using zinc finger nucleases. The achieved 1,000-fold MALAT1 silencing provides a unique loss-of-function model. Proposed mechanisms of action include regulation of splicing or gene expression. In lung cancer, MALAT1 does not alter alternative splicing but actively regulates gene expression including a set of metastasis-associated genes. Consequently, MALAT1-deficient cells are impaired in migration and form fewer tumor nodules in a mouse xenograft. Antisense oligonucleotides (ASO) blocking MALAT1 prevent metastasis formation after tumor implantation. Thus, targeting MALAT1 with ASOs provides a potential therapeutic approach to prevent lung cancer metastasis with this ncRNA serving as both predictive marker and therapeutic target. Finally, regulating gene expression, but not alternative splicing, is the critical function of MALAT1 in lung cancer metastasis. In summary, 10 years after the discovery of the lncRNA MALAT1 as a biomarker for lung cancer metastasis, our loss-of-function model unravels the active function of MALAT1 as a regulator of gene expression governing hallmarks of lung cancer metastasis.
Enhanced and sustained activation of human B cells by anti-immunoglobulin conjugated to the EBV glycoprotein gp350 (2000)

We coupled a monoclonal anti-human IgD to the gp350 gylcoprotein of Epstein-Barr virus, which has been shown to bind to the complement receptor 2 (CR2), and compared its B cell stimulatory ability to that of anti-Ig and to a multivalent anti-Ig-dextran conjugate. The anti-Ig-gp350 conjugate stimulated higher levels of human B cell proliferation in vitro than did anti-Ig or anti-Ig conjugated to control viral protein, comparable to the proliferation stimulated by the multivalent anti-Ig-dextran. This enhanced proliferation was dependent on binding of the conjugate to CR2, inasmuch as an anti-CD2 antibody blocked the enhanced proliferative response. This enhanced proliferative response was associated with prolonged elevations of intracellular ionized calcium, which was comparable to the response stimulated by anti-Ig-dextran. These findings suggest the use of gp350 as a carrier molecule for weakly immunogenic peptides or antigens which, when bound to gp350, would enhance B cell clonal expansion and activation of antigen-specific B cells.
CD22 Regulates Time Course of Both B Cell Division and Antibody Response (2008)

Because pathogens induce infectious symptoms in a time-dependent manner, a rapid immune response is beneficial for defending hosts from pathogens, especially those inducing acute infectious diseases. However, it is largely unknown how the time course of immune responses is regulated. In this study, we demonstrate that B cells deficient in the inhibitory coreceptor CD22 undergo accelerated cell division after Ag stimulation, resulting in rapid generation of plasma cells and Ab production. This finding indicates that CD22 regulates the time course of B cell responses and suggests that CD22 is a good target to shorten the time required for Ab production, thereby augmenting host defense against acute infectious diseases as "universal vaccination."
Automatic refractive-index profiling of optical fibers (1978)

A video-based system, which analyzes the output field of an interference microscope directly, has been developed to measure automatically the refractive-index distribution of optical fibers. Selected regions of the fringe field, detected with a silicon-vidicon, are digitized to 8-bit accuracy by an addressable video digitzer controlled with a programmable calculator. The calculator also makes fringe displacement measurements, corrects for certain misalignments, computes and plots the profile, and determines a best-fit power-law (alpha) curve. Profiles, with relative Deltan measured accurate to a few parts in 10(5), obtained at different wavelengths and for different fiber orientations are presented.
An iterative channel estimation method using superimposed training for IEEE 802.16E based OFDM systems (2008)

An iterative least squares (LS) based channel estimation method for superimposed training (ST) based OFDM systems is proposed. The performance of the method is analyzed in terms of the mean squared estimation error (MSEE) and its impact on the bit error rate (BER) of the OFDM system is studied. A training sequence selection criterion that jointly optimizes the MSEE and the BER of the OFDM system also proposed. The effectiveness of the mathematical analysis presented is demonstrated through a comparison with the simulation studies. Also, the proposed scheme is applied to the IEEE 802.16e OFDM standard and a case is made with the required design of the sequence.
An optimized Er gain band all-fiber chirped pulse amplification system (2004)

We demonstrate an all-fiber Er chirped pulse amplification (CPA) system based on compression in photonic band gap fiber (PBGF) that produces 570 fs pulses with 312 nJ pulse energy. The dispersion of the PBGF is measured precisely and used to design a dispersion-matched nonlinearly-chirped fiber Bragg grating stretcher. We analyze the trade-offs of such all-fiber CPA system design and compare different PBGFs in terms of the derived figure of merit. Such system architecture should be scalable to few micro-Joule level pulse energies close to the compressor nonlinearity limit when PBGFs with improved figure of merit become available.
High-Efficiency Photoelectrochemical Hydrogen Production Using Multijunction Amorphous Silicon Photoelectrodes (1998)

Photoelectrochemical solar-to-hydrogen conversion efficiencies as high as 7.8% (based on the lower heating value of hydrogen) have been demonstrated in outdoor testing using a photocathode fabricated from triple junction amorphous silicon-solar cells and a separate catalytic anode. The tests were conducted in a specially designed Teflon-sealed reactor in 1 N KOH with a photoactive area of 0.27 cm2 and anode and cathode areas of 1 cm2. The hydrogen production rates, inferred from direct measurement of the anodic/cathodic currents and confirmed by independent volumetric and gas chromatographic measurements of the evolved hydrogen, were in excellent agreement with the rates expected from the measured solid-state JV behavior of the solar cell and the overpotentials of the thin-film catalysts. The thin-film catalysts, CoMo hydrogen catalysts deposited by sputtering from a compound target and NiFeyOx oxygen catalysts deposited from nickel−iron Permalloy target by reactive sputtering, have, in separate tests, shown no degradation after over 7200 h of operation in 1 N KOH electrolyte. During outdoor testing, the solar-to-hydrogen conversion efficiency decreased in the late afternoon as the blue portion of the spectrum decreased, a result of the spectral sensitivity of the solar cell used to construct the photoelectrode. Detailed modeling of the multijunction amorphous silicon cells is being conducted to identify structures that are better load-matched to the catalyst performance and that could yield higher hydrogen production efficiencies. Future work to advance this technology includes development of improved thin-film catalysts and development of transparent protective coatings that will allow complete immersion of the active electrode into the electrolyte.
Efficient One‐Pot Synthesis of Water‐Compatible Molecularly Imprinted Polymer Microspheres by Facile RAFT Precipitation Polymerization (2011)

Narrowly dispersed water-compatible molecularly imprinted polymer (MIP) microspheres with surface-grafted hydrophilic polymer brushes were synthesized by RAFT precipitation polymerization (RAFTPP) mediated by hydrophilic macromolecular chain-transfer agents (Macro-CTA). The easy availability of hydrophilic Macro-CTAs and the versatility of the RAFTPP technique make it a general and promising strategy. CDB=cumyl dithiobenzoate. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
[Strategies and tools for metabolic engineering in Bacillus subtilis]. (2021)

As a typical food safety industrial model strain, Bacillus subtilis has been widely used in the field of metabolic engineering due to its non-pathogenicity, strong ability of extracellular protein secretion and no obvious codon preference. In recent years, with the rapid development of molecular biology and genetic engineering technology, a variety of research strategies and tools have been used to construct B. subtilis chassis cells for efficient synthesis of biological products. This review introduces the research progress of B. subtilis from the aspects of promoter engineering, gene editing, genetic circuit, cofactor engineering and pathway enzyme assembly. Then, we also summarized the application of B. subtilis in the production of biological products. Finally, the future research directions of B. subtilis are prospected.
Pearls and Pitfalls of Optical Coherence Tomography Angiography Imaging: A Review (2019)

Optical coherence tomography angiography (OCTA) has significantly expanded our knowledge of the ocular vasculature. Furthermore, this imaging modality has been widely adopted to investigate different ocular and systemic diseases. In this review, a discussion of the fundamental principles of OCTA is followed by the application of this imaging modality to study the retinal and choroidal vessels. A proper comprehension of this imaging modality is essential for the interpretation of OCTA imaging applications in retinal and choroidal disorders.
Selection of a Recombinant Marek's Disease Virus In Vivo Through Expression of the Marek's EcoRI-Q (Meq)–Encoded Oncoprotein: Characterization of an rMd5-Based Mutant Expressing the Meq of Strain RB-1B (2012)

Marek's disease (MD) is a highly contagious viral disease of chickens (Gallus gallus domesticus) caused by MD virus (MDV), characterized by paralysis, neurologic signs, and the rapid onset of T-cell lymphomas. MDV-induced T-cell transformation requires a basic leucine zipper protein called Marek's EcoRI-Q-encoded protein (Meq). We have identified mutations in the coding sequence of Meq that correlated with virus pathotype (virulent, very virulent, and very virulent plus). The aim of this study was to determine whether recombinant viruses could be isolated based on Meq expression through in vivo selection. Chicken embryo fibroblasts (CEFs) were cotransfected with an rMd5 strain-based Meq deletion virus (rMd5deltaMeq) and meq loci from strains representing different pathotypes of MDV. Transfected CEFs were inoculated into chickens in two independent studies. We were able to isolate a single recombinant virus, rMDV-1137, in a contact-exposed chicken. rMDV-1137 had recombined two copies of the meq gene of RB-1B and was found to have pathogenicity similar to both RB-1B and rMd5 parental strains. We found the RB-1B- and rMd5-induced lymphomas showed differences in composition and that rMDV-1137-induced lymphomas were intermediate in their composition. We were able to establish cell lines from both RB-1B- (MDCC-UD35, -UD37) and rMDV-1137 (MDCC-UD36, -UD38)-induced, but not rMd5-induced, lymphomas. To date, no rMd5- or parent Md5-transformed T-cell lines have been reported. Our results suggest that 1) a recombinant MDV can be selected on the basis of oncogenicity; 2) changes in Meq sequence seem to affect tumor composition and the ability to establish cell lines; and 3) in addition to meq, other genomic loci affect MDV pathogenicity and oncogenicity.
Optical local and superficial probing of tissues for in vivo diagnosis (2003)

An optical tissue diagnosis technique, often called "optical biopsy", has been developed, It is based on the simultaneous determination of the optical properties of tissues such as the reduced scattering coefficient μ<sub>s</sub>’ and the absorption coefficient μ<sub>a</sub>. These data are obtained by applying a small diameter probe (ψ 2mm) on tissues, through the working channel of usual endoscopes. The simultaneous determination of μ<sub>a</sub> and μ<sub>s</sub>’ with a local probe was made possible by the consideration of the first two moments of the phase function and a proven model of light propagation in tissues at propagation length comparable to the scattering mean free path. Non-invasive measurements of the optical coefficients of superficial tissues have been obtained in vivo (stomach) at different wavelength.
Actively stabilized Brillouin fiber laser with high output power and low noise (2006)

We demonstrate an actively stabilized Brillouin fiber ring laser with high power and low noise. Significant reduction (/spl sim/20 dB) of both relative intensity noise (RIN) and frequency noise was observed in the Brillouin Stokes radiation with linewidth of 200 Hz.
Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries (2015)

Synthetic oligonucleotides are the main cost factor for studies in DNA nanotechnology, genetics and synthetic biology, which all require thousands of these at high quality. Inexpensive chip-synthesized oligonucleotide libraries can contain hundreds of thousands of distinct sequences, however only at sub-femtomole quantities per strand. Here we present a selective oligonucleotide amplification method, based on three rounds of rolling-circle amplification, that produces nanomole amounts of single-stranded oligonucleotides per millilitre reaction. In a multistep one-pot procedure, subsets of hundreds or thousands of single-stranded DNAs with different lengths can selectively be amplified and purified together. These oligonucleotides are used to fold several DNA nanostructures and as primary fluorescence in situ hybridization probes. The amplification cost is lower than other reported methods (typically around US$ 20 per nanomole total oligonucleotides produced) and is dominated by the use of commercial enzymes.
PO-348 Two novel synthetic analogues of miR-1207–3 p, NB5 and NB1207, target AR-V7 and C-MYC and demonstrate in vivo therapeutic efficacy in metastatic castrate-resistant prostate cancer (mCRPC) (2018)

Introduction Chromosome 8q24 prostate cancer (PCa) susceptibility region encodes miR-1207–3 p which directly targets fibronectin type III domain containing 1 (FNDC1) to regulate fibronectin (FN1) and subsequently the androgen receptor (AR), and FNDC1/FN1/AR is overexpressed in metastatic PCa (Das et al, Exp Cell Res, 2016). Material and methods Expression of miR-1207–3 p and c-MYC in histologically confirmed normal prostate, benign prostatic hyperplasia (BPH) and PCa from prostatectomy or transrectal ultrasound-guided biopsies was analysed. Molecular mechanisms were elucidated using mCRPC cell lines. Effects of NB1207 and NB5, two novel synthetic analogues of miR-1207–3 p, on AR-V7 (implicated in PCa therapeutic resistance), mCRPC tumour growth in mice were studied. Results and discussions miR-1207–3 p is underexpressed in PCa (0.10±0.02, 95% CI [0.1, 0.2], p=0.000) in comparison to normal prostate (1.02±0.17, 95% CI [0.7, 1.4], p=0.000) and BPH (0.74±0.15, 95% CI [0.4, 1.1] p=0.004). c-MYC was overexpressed in PCa (34.76±8.11, 95% CI [18.1, 51.4], p=0.000; normal: 1.99±0.34, 95% CI [1.3, 2.7]; BPH: 1.01±0.21, 95% CI [0.6, 1.4], p=0.000). miR-1207–3 p was underexpressed by nearly 3-fold in PCa with Gleason score ≥8 versus those with Gleason score Conclusion This study shows potential diagnostic and prognostic value of miR-1207–3 p in mCRPC, and that NB5 and NB1207, novel analogues of miR-1207–3 p, may be candidate therapeutics for mCRPC.
Fully Connected Object Proposals for Video Segmentation (2015)

We present a novel approach to video segmentation using multiple object proposals. The problem is formulated as a minimization of a novel energy function defined over a fully connected graph of object proposals. Our model combines appearance with long-range point tracks, which is key to ensure robustness with respect to fast motion and occlusions over longer video sequences. As opposed to previous approaches based on object proposals, we do not seek the best per-frame object hypotheses to perform the segmentation. Instead, we combine multiple, potentially imperfect proposals to improve overall segmentation accuracy and ensure robustness to outliers. Overall, the basic algorithm consists of three steps. First, we generate a very large number of object proposals for each video frame using existing techniques. Next, we perform an SVM-based pruning step to retain only high quality proposals with sufficiently discriminative power. Finally, we determine the fore-and background classification by solving for the maximum a posteriori of a fully connected conditional random field, defined using our novel energy function. Experimental results on a well established dataset demonstrate that our method compares favorably to several recent state-of-the-art approaches.
Promising ferromagnetic Ni–Co–Al shape memory alloy system (2001)

A system of ferromagnetic β phase Ni–Co–Al alloys with an ordered B2 structure that exhibits the shape memory effect has been developed. The alloys of this system within the composition range Ni (30–45 at. %) Co–(27–32 at. %) Al, undergo a paramagnetic/ferromagnetic transition as well as a thermoelastic martensitic transformation from the β to the β′(L10) phase. The Curie and the martensitic start temperatures in the β phase can be controlled independently to fall within the range of 120–420 K. The specimens from some of the alloys undergoing martensitic transformation from ferromagnetic β phase to ferromagnetic β′ phase are accompanied by the shape memory effect. These ferromagnetic shape memory alloys hold great promise as new smart materials.
Route Based QoS and the Biased Early Drop Algorithm (BED) (2005)

DiffServ offers an attractive solution to quality of service (QoS) for mobile ad-hoc networks (MANET)s since the overhead of alternative flow based QoS metrics and signaling is not required. However, within prioritized classes and in the presence of dynamically forming bottlenecks, DiffServ can lead to brittle failure modes in which all flows are highly penalized and subsequently fail rather than maintaining some flows at required QoS levels for latency or packet loss. This problem is particularly difficult for UDP traffic, which does not respond to random early detection (RED) like throttling mechanisms in the presence of congestion. This paper proposes an augmentation of DiffServ QoS over MANET that utilizes metrics available through routing protocols to prevent, and resolve congestion. This is done in a manner that promotes maintenance of some high priority UDP (for example voice over IP) flows in the presence of bottlenecks. The biased early drop (BED) algorithm is introduced to maintain high continuity of UDP flows in the presence of congestion within the same class of service.
Development of [sup 10]B-Based [sup 3]He Replacement Neutron Detectors (2011)

Radiation portal monitors (RPM) are currently deployed at United States border crossings to passively inspect vehicles and persons for any emission of neutrons and/or gamma rays, which may indicate the presence of unshielded nuclear materials. The RPM module contains an organic scintillator with 3He proportional counters to detect gamma rays and thermalized neutrons, respectively. The supply of 3He is rapidly dwindling, requiring alternative detectors to provide the same function and performance. Our alternative approach is one consisting of a thinly‐coated 10B flat‐panel ionization chamber neutron detector that can be deployed as a direct drop‐in replacement for current RPM 3He detectors. The uniqueness of our approach in providing a large‐area detector is in the simplicity of construction, scalability of the unit cell detector, ease of adaptability to a variety of applications and low cost. Currently, Rapiscan Laboratories and Helicon Thin Film Systems have designed and developed an operational 100 cm2 multi‐layer prototype 10BB‐based ionization chamber.
Gas Diffusion Electrodes for Efficient Manufacturing of Chlorine and Other Chemicals (2017)

Electrochemical chlorine production is one of the most energy-intensive processes in the chemical industry. Chlorine producers are interested in sustainable ways of optimizing these processes to reduce their energy consumption and carbon footprint. A significant improvement was made possible by Covestro and its technology partners by using the oxygen reduction reaction (ORR) and a gas diffusion electrode—the oxygen depolarized cathode (ODC)—in the electrolysis process. Energy savings of up to 30% can be achieved with this configuration. Gas diffusion electrodes are also used in fuel cells, and due to ongoing efforts in research and development, they are expected to enable the industrial implementation of new, sustainable electrochemical processes including electrosynthesis, water treatment, power generation, and energy storage.