gebhart/patrepeval huggingface dataset:
Size-Dependent Spectroscopy of InP Quantum Dots (1997)

The spectroscopic behavior of colloidal InP quantum dots (QDs) has been investigated as a function of the mean QD diameter (which ranged from 26 to 60 Å). Absorption spectra show up to three peaks or shoulders which reflect excited state transitions in the QDs. Global photoluminescence (PL) spectra (excitation well to the blue of the absorption onset and which consequently excites most of the QDs in the size distribution) show broad PL emission. The emission and absorption features shift to higher energy with decreasing QD size. Resonant PL spectra (size-selective excitation into the tail of the absorption onset) show increasing fluorescence line narrowing with increasing excitation wavelength; PL and photoluminescence excitation spectroscopy were used to derive the PL red shift as a function of QD size. The resonant red shifts for QDs of a single size were extracted from PL data that reflect the emission from an ensemble of QD diameters. An analysis of the single-dot resonant red shift (difference between PL peak and the first absorption peak) as a function of the single QD diameter indicate that the results are consistent with a model in which the emission occurs from an intrinsic, spin-forbidden state, split from its singlet counterpart, due to screened electron-hole exchange.
Compact all-optical bypass–exchange switch (1996)

An electronically or optically addressed compact optical bypass-exchange switch is investigated and experimentally demonstrated.The switch is polarization based and consists of a controllable λ/2 platesandwiched between two polarizing beam displacers. The input and the output signals propagate normal to the switching array, which makes the switch extremely attractive for cascading switching arrays, as found in multistage interconnect networks. A complete, all-optical interconnection network is suggested.
Emergence and significance of carbohydrate-specific antibodies (2020)

Carbohydrate-specific antibodies are widespread among all classes of immunoglobulins. Despite their broad occurrence, little is known about their formation and biological significance. Carbohydrate-specific antibodies are often classified as natural antibodies under the assumption that they arise without prior exposure to exogenous antigens. On the other hand, various carbohydrate-specific antibodies, including antibodies to ABO blood group antigens, emerge after the contact of immune cells with the intestinal microbiota, which expresses a vast diversity of carbohydrate antigens. Here we explore the development of carbohydrate-specific antibodies in humans, addressing the definition of natural antibodies and the production of carbohydrate-specific antibodies upon antigen stimulation. We focus on the significance of the intestinal microbiota in shaping carbohydrate-specific antibodies not just in the gut, but also in the blood circulation. The structural similarity between bacterial carbohydrate antigens and surface glycoconjugates of protists, fungi and animals leads to the production of carbohydrate-specific antibodies protective against a broad range of pathogens. Mimicry between bacterial and human glycoconjugates, however, can also lead to the generation of carbohydrate-specific antibodies that cross-react with human antigens, thereby contributing to the development of autoimmune disorders.
High-Temperature Cycling Performance of LiNi1/3Co1/3Mn1/3O2Cathode with DLC Protective Film (2014)

Diamond-like carbon film (DLC) is selected as a cathode-protective film because it has chemical inertness, mechanical hardness, and high electrical resistivity. For this study, a DLC protective film was deposited onto a cathode electrode rather than individual cathode particles. A hybrid process of plasma-based ion implantation and deposition was applied to a uniform deposition of the DLC protective film, even at low processing temperature on the cathode electrode having complex surface geometry and low melting point binder. The electrochemical performance of the DLC-coated LiNi1/3Co1/3Mn1/3O2 cathode was studied using galvano-static charge–discharge cycling at high operating temperature, compared to those of the pristine LiNi1/3Co1/3Mn1/3O2 cathode. The electrochemical stability of the DLC-coated electrode was discussed. The DLC film provides good protection against cathode/electrolyte interface degradation.
Development of marker-free strains of Bacillus subtilis capable of secreting high levels of industrial enzymes (2000)

Different strategies have been employed to achieve high-level expression of single-copy genes encoding secreted enzymes in Bacillus subtilis. A model system was developed which utilizes the aprL gene from Bacillus clausii as a reporter gene for monitoring expression levels during stationary phase. An exceptionally strong promoter was constructed by altering the nuceotide sequence in the −10 and −35 regions of the promoter for the amyQ gene of Bacillus amyloliquefaciens. In addition, two or three tandem copies of this promoter were shown to increase expression levels substantially in comparison to the monomer promoter alone. Finally, the promoter and mRNA stabilization sequences derived from the cry3A gene of Bacillus thuringiensis were used in combination with the mutant amyQ promoter to achieve the highest levels of aprL expression. These promoters were shown to be fully functional in a high-expressing Bacillus strain grown under industrial fermentation conditions. The ability to obtain maximum expression levels from a single copy gene now makes it feasible to construct environmentally friendly, marker-free industrial strains of B. subtilis. Journal of Industrial Microbiology & Biotechnology (2000) 25, 204–212.
BCL-6 mutations in normal germinal center B cells: Evidence of somatic hypermutation acting outside Ig loci (1998)

The molecular mechanism involved in the process of antigen-driven somatic hypermutation of Ig genes is unknown, but it is commonly believed that this mechanism is restricted to the Ig loci. B cell lymphomas commonly display multiple somatic mutations clustering in the 5'-regulatory region of BCL-6, a proto-oncogene encoding for a POZ/Zinc finger transcriptional repressor expressed in germinal center (GC) B cells and required for GC formation. To determine whether BCL-6 mutations represent a tumor-associated phenomenon or reflect a physiologic mechanism, we screened single human tonsillar GC B cells for mutations occurring in the BCL-6 5'-noncoding region and in the Ig variable heavy chain sequences. Thirty percent of GC B cells, but not naive B cells, displayed mutations in the 742 bp region analyzed within the first intron of BCL-6 (overall frequency: 5 x 10(-4)/bp). Accordingly, an expanded survey in lymphoid malignancies showed that BCL-6 mutations are restricted to B cell tumors displaying GC or post-GC phenotype and carrying mutated Ig variable heavy chain sequences. These results indicate that the somatic hypermutation mechanism active in GC B cells physiologically targets non-Ig sequences.
PMA-responsive 5' flanking sequences of the human TNF gene. (1989)

In order to define functional domains involved in the control of TNF-gene transcription, 5'-flanking sequences of the TNF-gene were analysed by TNF-promoter deletion mutants linked to the CAT-gene and by gel retardation assays. To this, three TNF-promoter fragments of different length were fused to the CAT reporter gene and transiently transfected into several human cell lines. We found that a 315 bp long fragment encompassing positions -285 bp to +30 bp with respect to the TNF mRNA cap site is sufficient to function as a PMA inducible promoter/enhancer in all cell lines tested. By further deletion analysis of this clone we could narrow the PMA-inducible element within a 185 bp long sequence (-285 to -110 bp). In addition, we investigated specific interactions between nuclear proteins and TNF promoter sequences using gel-retardation assays. Besides several constitutive binding activities, we could demonstrate in several cell lines a nuclear protein that is induced by PMA and binds to the fragment of the TNF promoter containing the PMA-inducible element.
Timing of ovulation after gonadotrophin induction and its importance to successful intrauterine insemination in the tiger ( Panthera tigris ) (1996)

The ovarian response to equine chorionic gonadotrophin (eCG) and human chorionic gonadotrophin (hCG), the effect of timing of ovulation relative to hCG injection and the use of laparoscopic intrauterine artificial insemination (AI) were examined in two subspecies of tiger (Panthera tigris). Adult female tigers were subjected to the same eCG/hCG treatment followed by laparoscopy under xylazine/diazapam/ketamine HCl anaesthesia at 39-42 h (Group I, n = 9), 46-49 h (Group II, n = 5) or 51-55 h (Group III, n = 5) after hCG. Six of these females, observed to be postovulatory at the time of laparoscopy (Group II, n = 3; Group III, n = 3), were subjected to intrauterine AI. The number of preovulatory follicles observed on the ovaries of Group I females was twofold greater (P < 0.05) than the number observed on ovaries of females in Group II and III. Fewer (P < 0.05) corpora lutea were observed on ovaries of Group I females (1.3 +/- 0.6) compared with the number of corpora lutea in Group II and III (combined average, 7.8 +/- 0.8 corpora lutea per female). Only one of ten females in Groups II and III failed to ovulate by the time of laparoscopy. Four Group I females never ovulated, based on a laparoscopic re-evaluation 4 weeks later. One female inseminated 46 h after hCG (Group II) became pregnant and delivered a healthy cub after a normal gestation. There were no apparent differences between subspecies in response to the same ovulation induction protocol. Results demonstrate the importance of the relationship between exogenous gonadotrophin treatment and onset of anaesthesia for laparoscopic examination and AI in tigers. Data clearly indicate that anaesthesia/laparoscopy conducted too early (39-42 h after hCG) compromises the number of females and proportion of follicles ovulating. In contrast, ovulation success is high if anaesthesia/laparoscopy is performed after this time, and intrauterine insemination can result in healthy young.
A Unified-RAM (URAM) Cell for Multi-Functioning Capacitorless DRAM and NVM (2007)

A novel partially-depleted (PD) SONOS FinFET is demonstrated for unified function of a high speed capacitorless 1T-DRAM and non-volatile memory (NVM). A floating body and O/N/O layer are combined in a single FinFET to provide multi-functional unified-RAM (URAM) operation. The fabricated URAM shows a V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> window of 3V with a retention time exceeding 10 years for NVM operation and a sensing margin of 9μA with a program/erase time of 10nsec for 1T-DRAM operation in a single memory cell transistor.
Environmental Factors Affecting The Formation Of Mesityloxide, Dimethylallylic Alcohol And Other Volatile Compounds Excreted By Anabaena cylindrica (1983)

Anabaena cylindrica excretes a large number of volatile products. The major components are dimethylallylic alcohol and mesityloxide, while the minor components detected include various nor-carotenoids and lipid degradation products. The formation of mesityloxide is strictly light-dependent, and ceases in the dark. A direct association with photosynthesis can be ruled out since 3-(3, 4-dichlorophenyl)-1,1-dimethylurea (DCMU) does not affect the formation of mesityloxide during the first hour after application, but immediately inhibits the evolution of oxygen.
Tumor-Penetrating Peptides (2013)

Tumor-homing peptides can be used to deliver drugs into tumors. Phage library screening in live mice has recently identified homing peptides that specifically recognize the endothelium of tumor vessels, extravasate, and penetrate deep into the extravascular tumor tissue. The prototypic peptide of this class, iRGD (CRGDKGPDC), contains the integrin-binding RGD motif. RGD mediates tumor-homing through binding to αv integrins, which are selectively expressed on various cells in tumors, including tumor endothelial cells. The tumor-penetrating properties of iRGD are mediated by a second sequence motif, R/KXXR/K. This C-end Rule (or CendR) motif is active only when the second basic residue is exposed at the C-terminus of the peptide. Proteolytic processing of iRGD in tumors activates the cryptic CendR motif, which then binds to neuropilin-1 activating an endocytic bulk transport pathway through tumor tissue. Phage screening has also yielded tumor-penetrating peptides that function like iRGD in activating the CendR pathway, but bind to a different primary receptor. Moreover, novel tumor-homing peptides can be constructed from tumor-homing motifs, CendR elements and protease cleavage sites. Pathologies other than tumors can be targeted with tissue-penetrating peptides, and the primary receptor can also be a vascular "zip code" of a normal tissue. The CendR technology provides a solution to a major problem in tumor therapy, poor penetration of drugs into tumors. The tumor-penetrating peptides are capable of taking a payload deep into tumor tissue in mice, and they also penetrate into human tumors ex vivo. Targeting with these peptides specifically increases the accumulation in tumors of a variety of drugs and contrast agents, such as doxorubicin, antibodies, and nanoparticle-based compounds. Remarkably the drug to be targeted does not have to be coupled to the peptide; the bulk transport system activated by the peptide sweeps along any compound that is present in the blood.
G protein-coupled receptors: In silico drug discovery in 3D (2004)

The application of structure-based in silico methods to drug discovery is still considered a major challenge, especially when the x-ray structure of the target protein is unknown. Such is the case with human G protein-coupled receptors (GPCRs), one of the most important families of drug targets, where in the absence of x-ray structures, one has to rely on in silico 3D models. We report repeated success in using ab initio in silico GPCR models, generated by the predict method, for blind in silico screening when applied to a set of five different GPCR drug targets. More than 100,000 compounds were typically screened in silico for each target, leading to a selection of <100 "virtual hit" compounds to be tested in the lab. In vitro binding assays of the selected compounds confirm high hit rates, of 12-21% (full dose-response curves, Ki < 5 microM). In most cases, the best hit was a novel compound (New Chemical Entity) in the 1- to 100-nM range, with very promising pharmacological properties, as measured by a variety of in vitro and in vivo assays. These assays validated the quality of the hits as lead compounds for drug discovery. The results demonstrate the usefulness and robustness of ab initio in silico 3D models and of in silico screening for GPCR drug discovery.
Expression of basement membrane antigens and matrix metalloproteinases 2 and 9 in cutaneous basal and squamous cell carcinomas. (2000)

Our findings further upheld the role of BM antigens and MMPs in the process of tumor aggressiveness. The reduced expression of collagen IV, combined with an increased expression of both MMP2 and MMP9 could account for the increased metastatic potential of SCC vs BCC through an increased invasion of the extracellular matrix and the vascular space.
Use of Tunable Liquid Crystal Filters to Link Radiometric and Photometric Standards (1991)

A Lyot filter has been developed which uses precision liquid crystal waveplates to achieve tuning of the filter pass band over hundreds of nanometres. Tuning is rapid and non-mechanical, and produces a neglible shift in the transmitted image. Transmission is high (50%), and can be characterized using the methods developed for fixed-wavelength interference filters. Such a filter, coupled with a silicon photodiode trap detector whose radiometric response is well known, offers a direct method for linking detector-based radiometry and photometry.
Fermentative production of short-chain fatty acids in Escherichia coli (2014)

Escherichia coli was engineered for the production of even- and odd-chain fatty acids (FAs) by fermentation. Co-production of thiolase, hydroxybutyryl-CoA dehydrogenase, crotonase and trans-enoyl-CoA reductase from a synthetic operon allowed the production of butyrate, hexanoate and octanoate. Elimination of native fermentation pathways by genetic deletion (ΔldhA, ΔadhE, ΔackA, Δpta, ΔfrdC) helped eliminate undesired by-products and increase product yields. Initial butyrate production rates were high (0.7 g l(-1) h(-1)) but quickly levelled off and further study suggested this was due to product toxicity and/or acidification of the growth medium. Results also showed that endogenous thioesterases significantly influenced product formation. In particular, deletion of the yciA thioesterase gene substantially increased hexanoate production while decreasing the production of butyrate. E. coli was also engineered to co-produce enzymes for even-chain FA production (described above) together with a coenzyme B12-dependent pathway for the production of propionyl-CoA, which allowed the production of odd-chain FAs (pentanoate and heptanoate). The B12-dependent pathway used here has the potential to allow the production of odd-chain FAs from a single growth substrate (glucose) in a more energy-efficient manner than the prior methods.
A novel parameter from PPG dicrotic notch for estimation of systolic blood pressure using pulse transit time (2008)

This paper proposes a new calibration parameter from the dicrotic notch of photoplethysmography (PPG) waveform for systolic blood pressure (SBP) estimation using pulse transit time (PTT). An experiment including exercise was conducted on twelve subjects. The results show that estimation with PTT and a new parameter, i.e. the Relative Amplitude of Secondary peak (RAS), can predict SBP within 1.7±6.8 mmHg of the reference for all the subjects before and after exercise (including within 5 minutes and 20–40 minutes after exercise). The underestimated bias after exercise if PTT was used alone can be largely reduced when RAS is introduced. The preliminary analysis indicates that RAS is a promising parameter for calibrating the PTT-based approach for cuffless BP estimation.
Transient intermediates of the methane monooxygenase catalytic cycle. (1993)

Three new intermediates of the catalytic cycle of the soluble form of methane monooxygenase (MMO) isolated from Methylosinus trichosporium OB3b have been detected using transient kinetic techniques. MMO consists of hydroxylase (MMOH), reductase, and "B" (MMOB) components. MMOH contains an oxygen-bridged [Fe(III).Fe(III)] cluster that catalyzes O2 activation and insertion chemistry. At 4 degrees C, rapid mixing of O2 with diferrous MMOH ([Fe(II).Fe(II)]) in the presence of a 2-fold excess of MMOB resulted in loss of the g = 16 EPR signal characteristic of the diferrous cluster at an apparent first order rate of 22 +/- 5 s-1 (O2 approximately 700 microM). Subsequently, an EPR silent, chromophoric (lambda max = 330 and 430 nm, epsilon approximately 7500 M-1 cm-1 at each wavelength) intermediate (compound Q) formed with an average first order rate constant of 1 +/- 0.1 s-1 and then decayed at 0.05 +/- 0.01 s-1. Since compound Q formed much more slowly than diferrous MMOH disappeared, at least one other undetected intermediate (compound P) must have formed before compound Q. MMO substrates had little or no effect on the formation rate of compound Q, but they caused the decay rate to increase linearly with the concentration added. The substrates methane, furan, and nitrobenzene caused compound Q decay to occur with second order rate constants of 19,000 M-1 s-1, 9000 M-1 s-1, and 200 M-1 s-1 (+/- 5%), respectively. When nitrobenzene was used as a substrate, a second chromophoric intermediate (compound T, lambda max = 325 nm, with a shoulder at 395 nm, epsilon 395 approximately 6000 M-1 cm-1) formed at the same rate as compound Q decay. Chemical quench studies showed that compound T is an enzyme-product complex that decays with a rate constant of 0.02 +/- 0.005 s-1. This rate is approximately the same as kcat for nitrobenzene turnover at 4 degrees C catalyzed by the reconstituted MMO system, suggesting that product release is the rate-limiting step in catalysis. The characteristics of compound Q suggest that it may be the activated form of the enzyme that directly catalyzes substrate oxidation.
Antagonistic effect exerted by three strictly anaerobic strains against various strains of Clostridium perfringens in gnotobiotic rodent intestines (1987)

Our purpose was to study bacterial antagonism between a limited number of strictly anaerobic strains and Clostridium perfringens in the intestinal tract of gnotobiotic rodents. Gnotobiotic mice harboring a Bacteroides thetaiotaomicron, a Fusobacterium necrogenes, and a Clostridium sp. strain were protected against pathogenic B, C, and D C. perfringens serotypes. A drastic antagonistic effect of this three-strain association was also observed against a nonpathogenic C. perfringens serotype A (CpA). It was less efficient in gnotobiotic rats than in mice and less efficient in gnotobiotic mice fed an autoclaved diet than in mice fed the same diet sterilized by irradiation. No diffusible inhibitory substances against CpA were detected in feces of gnotobiotic mice harboring the three antagonistic strains, and no nutrient depletion was demonstrated in filtrates prepared from 10-fold diluted feces of these mice. In vitro mixed cultures of the three antagonistic strains failed to inhibit growth of CpA, whereas CpA did not multiply in a 10-fold diluted feces from gnotobiotic mice. A reverse correlation between the initial number of antagonistic strains and the division number of CpA was determined using serially diluted fecal suspensions. Thus, large numbers of viable cells of both antagonistic strains were required to inhibit the target strain in fecal suspensions as was also found in gnotobiotic mice intestines. However, no diffusible inhibitory substance was detectable nor could depletion of growth factors be identified as causing antagonism. Whatever factors that may be responsible for antagonism were found to be influenced by the host and its diet.
Human Colonic Bacteria: Role in Nutrition, Physiology, and Pathology (1995)

Microbial ecology of the human large intestine molecular genetics of intestinal anaerobes carbohydrate metabolism in the colon proteolysis and amino acid fermentation short chain fatty acids bacterial infections and diarrhea and the role of the intestinal bacteria in etiology and maintenance of inflammatory bowel disease. (Part contents).