gebhart/patrepeval huggingface dataset:
The JatrophaFT ortholog is a systemic signal regulating growth and flowering time (2014)

Jatropha curcas is being promoted as a new bioenergy crop in tropical and subtropical regions due to its high amount of seed oil and its potential capacity to grow on marginal land for biofuel production. However, the productivity of the plant is constrained by the unfavorable flowering time and inflorescence architecture, which render harvesting of seeds time-consuming and labor-intensive. These flowering-related traits have limited further widespread cultivation of Jatropha. We identified a Jatropha curcas homolog of Flowering locus T (JcFT) and demonstrated its function by genetic complementation of the Arabidopsis ft mutant. The JcFT expression level was found to be remarkably correlated with leaf age. Overexpression of JcFT in Jatropha reduced flowering time and altered plant architecture by producing more branches. Grafting experiments suggested that the earlyflowering and alteration of plant architecture traits were graft-transmissible. We also showed that the FT-overexpressing transgenic Jatropha can be used as a root stock for grafting of scions derived from other Jatropha. We generated early flowering transgenic Jatropha plants that accumulate higher levels of the florigen FT. Not only early flowering but also plant growth was affected in JcFT overexpression lines. More seeds can be produced in a shorter time frame by shortening the flowering time in Jatropha, suggesting the possibility to increase seed yield by manipulating the flowering time.
Guanine-Rich Telomeric Sequences Stimulate DNA Polymerase Activity in Vitro (1999)

Guanine-rich oligonucleotides and short telomeric DNA sequences can self-associate into G-quartet stabilized complexes. We discovered that this self-association can occur in sequencing reactions and that higher-order structures stimulate DNA polymerase to synthesize extended DNA strands. Base analogues were used to identify Hoogsteen base pairings as stabilizing forces in these stimulatory DNA structures. Scanning force microscopy confirmed that quartet-DNA was formed from these oligomers and that these extended, four-stranded structures could be bound by DNA polymerase. Since guanine quartet-stabilized structures are proposed to exist in vivo, such structures may stimulate DNA polymerization in vivo.
Switching device based on the quantum Hall effect (1982)

Novel quantum device - a voltage amplifier - is proposed, based on controlled phase transition of percolation type in semiconductor inversion layers in strong transverse magnetic field.
Thyristor with integrated forward recovery protection function (2002)

A completely self-protected light-triggered high-power thyristor has been developed and fabricated. The integrated protection functions comprise overvoltage protection, dV/dt protection and forward recovery protection. Turn-on characteristics of 8 kV, 4000 A prototype samples under diverse conditions are presented, demonstrating the reliable operation of all the protection functions.
Equalization of modal dispersion in multimode fiber using spatial light modulators (2005)

Intersymbol interference (ISI) due to modal dispersion is the dominant limitation to the bit rate-distance product in multimode fiber-optic communication systems. If the light launched into the fiber excites only the desired principal modes, modal dispersion can be eliminated. We can achieve this by using spatial light modulators (SLMs) to perform adaptive spatial filtering on the electric fields of the light. In this paper, we develop an optimization framework for setting the SLMs to obtain an upper bound on the achievable performance and develop heuristics that nearly reach this upper bound Using this framework, we show that both a sophisticated semidefinite programming-based algorithm and a simple adaptive algorithm achieve performance close to the upper bound. Performance and system complexity tradeoff curves are constructed, showing that a 20/spl times/20 array of SLM pixels with binary phase control performs within 15% of more complex implementations. Finally, we extend the framework and present preliminary results showing the promise of further increases in the capabilities of multimode fiber by using the fiber as a multiple-input multiple-output (MIMO) transmission medium.
Real-time laser differential confocal microscopy without sample reflectivity effects (2014)

A new real-time laser differential confocal microscopy (RLDCM) without sample reflectivity difference effects is proposed for imaging height topography of sample surface, which divides the confocal microscopy imaging light path into two confocal microscopy imaging paths before and after focus with the equal axial detector offset oriented in opposite direction. By dividing the difference of the two signals simultaneously detected from these two confocal imaging paths by the higher signal between these two signals, RLDCM separates the signal that comes from reflectivity heterogeneity from the topographic signal in real time for the first time. RLDCM significantly reduces the height topography imaging time by single-layer scanning for the sample surface with reflectivity heterogeneity, and it achieves high axial resolution and lateral resolution similar to CM by optimizing the axial detector offset. Theoretical analysis and experimental results demonstrate that RLDCM realizes the real-time surface imaging for line structures featuring Silicon Dioxide steps on a Silicon base and achieves 2-nm axial depth resolution without reducing lateral resolution.
Asymmetric-partition replication for highly scalable distributed transaction processing in practice (2020)

Database replication is widely known and used for high availability or load balancing in many practical database systems. In this paper, we show how a replication engine can be used for three important practical cases that have not previously been studied very well. The three practical use cases include: 1) scaling out OLTP/OLAP-mixed workloads with partitioned replicas, 2) efficiently maintaining a distributed secondary index for a partitioned table, and 3) efficiently implementing an online re-partitioning operation. All three use cases are crucial for enabling a high-performance shared-nothing distributed database system. To support the three use cases more efficiently, we propose the concept of asymmetric-partition replication , so that replicas of a table can be independently partitioned regardless of whether or how its primary copy is partitioned. In addition, we propose the optimistic synchronous commit protocol which avoids the expensive two-phase commit without sacrificing transactional consistency. The proposed asymmetric-partition replication and its optimized commit protocol are incorporated in the production versions of the SAP HANA in-memory database system. Through extensive experiments, we demonstrate the significant benefits that the proposed replication engine brings to the three use cases.
Monoterpene Synthases from Common Sage (Salvia officinalis ) (1998)

Common sage (Salvia officinalis) produces an extremely broad range of cyclic monoterpenes bearing diverse carbon skeletons, including members of the p-menthane (1,8-cineole), pinane (alpha- and beta-pinene), thujane (isothujone), camphane (camphene), and bornane (camphor) families. An homology-based polymerase chain reaction cloning strategy was developed and used to isolate the cDNAs encoding three multiproduct monoterpene synthases from this species that were functionally expressed in Escherichia coli. The heterologously expressed synthases produce (+)-bornyl diphosphate, 1, 8-cineole, and (+)-sabinene, respectively, as their major products from geranyl diphosphate. The bornyl diphosphate synthase also produces significant amounts of (+)-alpha-pinene, (+)-camphene, and (+/-)-limonene. The 1,8-cineole synthase produces significant amounts of (+)- and (-)-alpha-pinene, (+)- and (-)-beta-pinene, myrcene and (+)-sabinene, and the (+)-sabinene synthase produces significant quantities of gamma-terpinene and terpinolene. All three enzymes appear to be translated as preproteins bearing an amino-terminal plastid targeting sequence, consistent with the plastidial origin of monoterpenes in plants. Deduced sequence analysis and size exclusion chromatography indicate that the recombinant bornyl diphosphate synthase is a homodimer, whereas the other two recombinant enzymes are monomeric, consistent with the size and subunit architecture of their native enzyme counterparts. The distribution and stereochemistry of the products generated by the recombinant (+)-bornyl diphosphate synthase suggest that this enzyme might represent both (+)-bornyl diphosphate synthase and (+)-pinene synthase which were previously assumed to be distinct enzymes.
Enhancing Smart Grid cyber security using power fingerprinting: Integrity assessment and intrusion detection (2012)

Power Fingerprinting (PFP) provides an innovative, powerful integrity assessment tool that is particularly well suited for critical embedded systems, including resource-constrained and legacy platforms such as those still being used by energy providers. One of the main applications of PFP is cyber security monitoring of critical systems and the detection of malicious intrusions, tampering, and attacks. Among the advantages of PFP over other intrusion detection tools, is the ability to detect zero-day and targeted attacks while introducing almost negligible overhead on the system being monitored. In addition, it can be applied independent of the system hardware, operating system, and software application. For these reasons, PFP has the potential to play a key role in Smart Grid cyber security by protecting platforms and systems that are not covered by traditional security approaches, such as antivirus systems.
Toward the Rational Design of a Malaria Vaccine Construct Using the MSP3 Family as an Example: Contribution of Antigenicity Studies in Humans (2009)

ABSTRACT Plasmodium falciparum merozoite surface protein (MSP3) is a main target of protective immunity against malaria that is currently undergoing vaccine development. It was shown recently to belong, together with MSP6, to a new multigene family whose C-terminal regions have a similar organization, contain both homologous and divergent regions, and are highly conserved across isolates. In an attempt to rationally design novel vaccine constructs, we extended the analysis of antigenicity and function of region-specific antibodies, previously performed with MSP3 and MSP6, to the remaining four proteins of the MSP3 family using four recombinant proteins and 24 synthetic peptides. Antibodies to each MSP3 family antigen were found to be highly prevalent among malaria-exposed individuals from the village of Dielmo (Senegal). Each of the 24 peptides was antigenic, defining at least one epitope mimicking that of the native proteins, with a distinct IgG isotype pattern for each, although with an overall predominance of the IgG3 subclass. Human antibodies affinity purified upon each of the 24 peptides exerted an antiparasite antibody-dependent cellular inhibition effect, which in most cases was as strong as that of IgG from protected African adults. The two regions with high homology were found to generate a broad network of cross-reactive antibodies with various avidities. A first multigenic construct was designed using these findings and those from related immunogenicity studies in mice and demonstrated valuable immunological properties. These results indicate that numerous regions from the MSP3 family play a role in protection and provide a rationale for the tailoring of new MSP3-derived malaria vaccines.
Binocular visual characteristics-based stereoscopic image quality assessment metric for 3D video system (2016)

Compared with two-dimensional image quality assessment (2D-IQA), stereoscopic IQA (SIQA) has to take the binocular perception into consideration. In this paper, a new SIQA metric is proposed for three-dimensional video systems, which is based on binocular visual characteristics and contains two parts: binocular perceptual distortion evaluation (BPDE) and stereoscopic evaluation (SE). To get the results of the BPDE and SE, a simple-complex cell along with different human visual system characteristics are used to compute the quality of binocular fusion maps and disparity maps between original and distorted stereoscopic image pairs. The final quality score is obtained by a nonlinear combination of BPDE value and SE value. Experimental results show that proposed SIQA metric in which the Pearson linear correlation coefficient (PLCC) and Spearman rank order correlation coefficient (SROCC) exceed 0.94 and 0.93 outperform current 2D-IQA and SIQA metrics.
Mechanisms of a Mycobacterium tuberculosis Active Peptide (2023)

Multidrug-resistant tuberculosis (MDR) continues to pose a threat to public health. Previously, we identified a cationic host defense peptide with activity against <i>Mycobacterium tuberculosis</i> in vivo and with a bactericidal effect against MDR <i>M. tuberculosis</i> at therapeutic concentrations. To understand the mechanisms of this peptide, we investigated its interactions with live <i>M. tuberculosis</i> and liposomes as a model. Peptide interactions with <i>M. tuberculosis</i> inner membranes induced tube-shaped membranous structures and massive vesicle formation, thus leading to bubbling cell death and ghost cell formation. Liposomal studies revealed that peptide insertion into inner membranes induced changes in the peptides' secondary structure and that the membranes were pulled such that they aggregated without permeabilization, suggesting that the peptide has a strong inner membrane affinity. Finally, the peptide targeted essential proteins in <i>M. tuberculosis</i>, such as 60 kDa chaperonins and elongation factor Tu, that are involved in mycolic acid synthesis and protein folding, which had an impact on bacterial proliferation. The observed multifaceted targeting provides additional support for the therapeutic potential of this peptide.
Implication of the GABAb receptor in gamma vinyl-GABA's inhibition of cocaine-induced increases in nucleus accumbens dopamine (1999)

Previously, we demonstrated that gamma vinyl-GABA (GVG, Vigabatrin) dose-dependently inhibits cocaine-induced increases in dopamine (DA) concentrations in both the rodent and primate brain. Furthermore, it abolishes cocaine self-administration and conditioned place preference, while having no effect on locomotor activity or drug delivery to the brain. In an effort to better understand the mechanisms underlying this inhibition, we examined the effect of the selective GABA(B) receptor antagonist SCH 50911 on the GVG-induced decrease in cocaine's elevation of extracellular DA concentrations in the nucleus accumbens (NACC). Cocaine administration alone (20 mg/kg i.p.) produced a 480% increase in extracellular NACC DA levels. GVG (300 mg/kg i.p.) significantly reduced this increase by 25% (P<0.01). In sharp contrast, extracellular DA levels increased to 550% after the sequential administration of SCH 50911 (3 mg/kg i.p.), GVG, and cocaine. This increase is significantly different than GVG and cocaine (P<0.05) but similar to cocaine alone. These results demonstrate that the GABA(B) antagonist SCH 50911 was able to completely abolish GVG's inhibition of cocaine-induced increases in DA in the NACC and implicates the GABA(B) receptor in the mechanism underlying this inhibition.
Comparison of Interleukin-1β Expression by In Situ Hybridization in Monoclonal Gammopathy of Undetermined Significance and Multiple Myeloma (1999)

We investigated whether interleukin-1beta (IL-1beta) is differentially expressed in plasma cells from monoclonal gammopathy of undetermined significance (MGUS) and multiple myeloma (MM) patients because IL-1beta appears to play a major role in the development of lytic bone lesions, the major clinical feature distinguishing MGUS from myeloma. In situ hybridization (ISH) for IL-1beta was performed using bone marrow aspirates from 51 MM, 7 smoldering MM, 21 MGUS, and 5 normal control samples. Using the ISH technique IL-1beta mRNA was detectable in the plasma cells from 49 of 51 patients with active myeloma and 7 of 7 patients with smoldering myeloma. In contrast, 5 of 21 patients with MGUS and 0 of 5 normal controls had detectable IL-1beta message. Bone lesions were present in 40 of the 51 MM patients analyzed, and all 40 patients had IL-1beta mRNA by ISH. These results show that greater than 95% of MM patients but less than 25% of MGUS patients are positive for IL-1beta production. In the future, continued follow-up of IL-1beta positive and negative MGUS patients should determine whether aberrant expression of plasma cell IL-1beta is predictive of those MGUS patients that will eventually progress to active myeloma.
Computerized Diagnostics In Digital Mammography (2002)

Mammography is a major diagnostic procedure in early detection of breast cancer; however, the interpretation of mammograms for diagnosis of breast cancer can be problematic. A computerized diagnostic system has been developed to serve as a "second opinion" for radiologists. This system enhances the structures which appear in the mammogram and calculates parameters which characterize lesions. The authors have deevloped special versions for statistical classification and discrimination of mammographic lesions. Algorithms of recognition of lesions were constructed and examined on mammographic lesions with proven pathology.
Targeted deletion of <i>Smad4</i> shows it is required for transforming growth factor β and activin signaling in colorectal cancer cells (1998)

Smad4 (DPC4) is a candidate tumor suppressor gene that has been hypothesized to be critical for transmitting signals from transforming growth factor (TGF) beta and related ligands. To directly test this hypothesis, the Smad4 gene was deleted through homologous recombination in human colorectal cancer cells. This deletion abrogated signaling from TGF-beta, as well as from the TGF-beta family member activin. These results provide unequivocal evidence that mutational inactivation of Smad4 causes TGF-beta unresponsiveness and provide a basis for understanding the physiologic role of this gene in tumorigenesis.
Inhibition of Fibroblast Proliferation In Vitro Using Red Light-Emitting Diodes (2013)

At certain fluences, red LLLT can effectively inhibit fibroblast proliferation in vitro without altering viability and holds promise for the treatment of scars and other proliferative skin diseases.
Impact of Surface Recombination on the Performance of Phosphor-Free InGaN/GaN Nanowire White Light Emitting Diodes (2014)

We show that the performance of InGaN/GaN axial nanowire LEDs is largely limited by the poor carrier injection efficiency. We have further demonstrated high performance phosphor-free white LEDs using InGaN/GaN/AlGaN dot-in-a-wire core-shell heterostructures.
ChemInform Abstract: PYRAZOLODIAZEPINES. 2. 4‐ARYL‐1,3‐DIALKYL‐6,8‐DIHYDROPYRAZOLO(3,4‐E)(1,4)DIAZEPIN‐7(1H)‐ONES AS ANTIANXIETY AND ANTICONVULSANT AGENTS (1978)

Abstract Zur Untersuchung auf tranquillizierende und anticonvulsive Wirkung werden zahlreiche Pyrazolodiazepinone der angeführten Systeme hergestellt.
Discovery of a Potent, Selective Protein Tyrosine Phosphatase 1B Inhibitor Using a Linked-Fragment Strategy (2003)

Protein tyrosine phosphatase 1B (PTP1B) is an enzyme that downregulates the insulin receptor. Inhibition of PTP1B is expected to improve insulin action, and the design of small molecule PTP1B inhibitors to treat type II diabetes has received considerable attention. In this work, NMR-based screening identified a nonselective competitive inhibitor of PTP1B. A second site ligand was also identified by NMR-based screening and then linked to the catalytic site ligand by rational design. X-ray data confirmed that the inhibitor bound with the catalytic site in the native, "open" conformation. The final compound displayed excellent potency and good selectivity over many other phosphatases. The modular approach to drug design described in this work should be applicable for the design of potent and selective inhibitors of other therapeutically relevant protein tyrosine phosphatases.
Wafer-scale mitochondrial membrane potential assays (2012)

It has been reported that mitochondrial metabolic and biophysical parameters are associated with degenerative diseases and the aging process. To evaluate these biochemical parameters, current technology requires several hundred milligrams of isolated mitochondria for functional assays. Here, we demonstrate manufacturable wafer-scale mitochondrial functional assay lab-on-a-chip devices, which require mitochondrial protein quantities three orders of magnitude less than current assays, integrated onto 4'' standard silicon wafer with new fabrication processes and materials. Membrane potential changes of isolated mitochondria from various well-established cell lines such as human HeLa cell line (Heb7A), human osteosarcoma cell line (143b) and mouse skeletal muscle tissue were investigated and compared. This second generation integrated lab-on-a-chip system developed here shows enhanced structural durability and reproducibility while increasing the sensitivity to changes in mitochondrial membrane potential by an order of magnitude as compared to first generation technologies. We envision this system to be a great candidate to substitute current mitochondrial assay systems.
Superconducting single-photon detectors designed for operation at 1.55-µm telecommunication wavelength (2006)

We report on our progress in development of superconducting single-photon detectors (SSPDs), specifically designed for secure high-speed quantum communications. The SSPDs consist of NbN-based meander nanostructures and operate at liquid helium temperatures. In general, our devices are capable of GHz-rate photon counting in a spectral range from visible light to mid-infrared. The device jitter is 18 ps and dark counts can reach negligibly small levels. The quantum efficiency (QE) of our best SSPDs for visible-light photons approaches a saturation level of ∼30-40%, which is limited by the NbN film absorption. For the infrared range (1.55µm), QE is ∼6% at 4.2 K, but it can be significantly improved by reduction of the operation temperature to the 2-K level, when QE reaches ∼20% for 1.55-µm photons. In order to further enhance the SSPD efficiency at the wavelength of 1.55 µm, we have integrated our detectors with optical cavities, aiming to increase the effective interaction of the photon with the superconducting meander and, therefore, increase the QE. A successful effort was made to fabricate an advanced SSPD structure with an optical microcavity optimized for absorption of 1.55 µm photons. The design consisted of a quarter-wave dielectric layer, combined with a metallic mirror. Early tests performed on relatively low-QE devices integrated with microcavities, showed that the QE value at the resonator maximum (1.55-µm wavelength) was of the factor 3-to-4 higher than that for a nonresonant SSPD. Independently, we have successfully coupled our SSPDs to single-mode optical fibers. The completed receivers, inserted into a liquid-helium transport dewar, reached ∼1% system QE for 1.55 µm photons. The SSPD receivers that are fiber-coupled and, simultaneously, integrated with resonators are expected to be the ultimate photon counters for optical quantum communications.