gebhart/patrepeval huggingface dataset:
Optimization of Particle Bombardment Conditions by Monitoring of Transient sGFP(S65T) Expression in Transformed Soybean (2005)

In an attempt to increase the efficiency of soybean transformation by particle bombardment, we examined the effects of bombardment parameters such as gold particle size, target distance, acceleration pressure, amount of DNA per bombardment, and number of bombardments. Transgene delivery to embryogenic tissue grown in suspension culture was evaluated by monitoring the transient expression of a gene for a modified form of jellyfish green fluorescent protein [sGFP(S65T)]. Optimal transient expression of sGFP(S65T) was obtained when the tissue was bombarded twice at an acceleration pressure of 7.6 MPa (1,100 psi) and a distance of 6 cm with gold particles that were 0.6 μm in diameter and coated with 0.8 μg of DNA. Application of these optimized conditions proved effective for the generation of stable transgenic soybean plants. Stable transgene integration in the transformants was confirmed by Southern blot analysis. The average transformation efficiency achieved with the optimized protocol was siginificantly higher than that with the conventional protocol.
Purification of an 11 S regulator of the multicatalytic protease. (1992)

We have identified and purified a protein complex from human red blood cells that activates the multicatalytic protease (MCP). The complex, which we call the regulator, sediments at 11 S and is composed of 30-kDa subunits. The regulator does not hydrolyze fluorogenic peptides, but when multicatalytic protease and regulator are combined, MCP cleaves succinyl-Leu-Leu-Val-Tyr-7-amido-4-methylcoumarin and Leu-Leu-Glu-p-nitroanilide as much as 60-fold faster. Hydrolysis of several other fluorogenic peptides is stimulated to a lesser extent, and activated MCP does not degrade ubiquitin-lysozyme conjugates, bovine serum albumin, or lysozyme. Latent and activated forms of MCP display similar sensitivity to protease inhibitors, suggesting that activation does not generate new kinds of catalytic sites. In addition, ATP suppresses peptide hydrolysis by activated and latent MCPs to the same extent. Activation involves binding of regulator to MCP, and activated MCP migrates slower on native acrylamide gels. Dissociation of the MCP regulator complex during prolonged sedimentation on glycerol gradients releases active regulator and MCP molecules capable of being reactivated. Moreover, two-dimensional electrophoresis does not reveal changes in MCP or regulator subunits following activation. Thus, activation appears to result from reversible association of regulator subunits with MCP.
Single amino acid substitution in LC-CDR1 induces Russell body phenotype that attenuates cellular protein synthesis through eIF2α phosphorylation and thereby downregulates IgG secretion despite operational secretory pathway traffic (2017)

Amino acid sequence differences in the variable region of immunoglobulin (Ig) cause wide variations in secretion outputs. To address how a primary sequence difference comes to modulate Ig secretion, we investigated the biosynthetic process of 2 human IgG2κ monoclonal antibodies (mAbs) that differ only by one amino acid in the light chain complementarity-determining region 1 while showing ∼20-fold variance in secretion titer. Although poorly secreted, the lower-secreting mAb of the 2 was by no means defective in terms of its folding stability, antigen binding, and in vitro biologic activity. However, upon overexpression in HEK293 cells, the low-secreting mAb revealed a high propensity to aggregate into enlarged globular structures called Russell bodies (RBs) in the endoplasmic reticulum. While Golgi morphology was affected by the formation of RBs, secretory pathway membrane traffic remained operational in those cells. Importantly, cellular protein synthesis was severely suppressed in RB-positive cells through the phosphorylation of eIF2α. PERK-dependent signaling was implicated in this event, given the upregulation and nuclear accumulation of downstream effectors such as ATF4 and CHOP. These findings illustrated that the underlining process of poor Ig secretion in RB-positive cells was due to downregulation of Ig synthesis instead of a disruption or blockade of secretory pathway trafficking. Therefore, RB formation signifies an end of active Ig production at the protein translation level. Consequently, depending on how soon and how severely an antibody-expressing cell develops the RB phenotype, the productive window of Ig secretion can vary widely among the cells expressing different mAbs.
Scanning surface harmonic microscopy: Scanning probe microscopy based on microwave field-induced harmonic generation (1992)

A scanning probe microscope has been integrated into a microwave resonator tunable from 2.2 to 3.4 GHz with a quality factor Q larger than 1000. Nonlinear phenomena caused generation of higher harmonics when rf fields in the range of 109 V/m were applied between tip and sample. Higher harmonic signals were detected at a bandwidth of 10 kHz on conductor surfaces as well as on thin insulating films and were used as feedback to the control loop for imaging graphite surface features and oxidized silicon surfaces with subnanometer resolution.
Role of lymphangiogenesis in lung cancer. (2010)

Lung cancer represents one of the most frequent causes of death due to neoplastic disease in Poland and around the world. The high mortality which accompany neoplastic diseases used to be ascribed mainly to dissemination of cancerous cells. Studies on animal models suggest that tumour lymphangiogenesis represents the principal factor in the process of metastases formation. Lymphangiogenesis involves a process of formation of new lymphatic vessels from already existing lymphatic capillaries. Lymphangiogenesis is stimulated by vascular endothelial growth factors (VEGF) and other, recently reported factors, such as, e.g., cyclooxygenase 2, fibroblast growth factor 2, angiopoetin-1 and the insulin-resembling growth factor. In lymphangiogenesis a key role is played by neutropilin 2 or podoplanin and this promoted development of studies on lymphangiogenesis. Activation of VEGF-C/VEGF-D/VEGFR-3 axis increases motility and invasiveness of neoplastic cells, promotes development of metastases in several types of tumours such as, e.g., lung cancer, mammary carcinoma, cancers of the neck, prostate and large intestine. In recent years lymphangiogenesis provided topic of many studies. A positive correlation was detected between expressions of VEGF-C/D and VEGFR-3 in non-small cell lung cancer. In patients with lung cancer with high expression of VEGF-C a markedly abbreviated survival was noted. Positive correlation was detected between expression of VEGF-C and VEGF-D on one hand and expression of LYVE-1 on the other in sentinel lymph nodes with metastases of neoplastic cells in patients with non-small cell lung cancer. Also, high density of lymphatic vessels and high density of intraneoplastic microvessels proved to be independent poor prognostic indices in patients with non-small cell lung cancer. Extensive hope is linked to studies on inhibitors of lymphangiogenesis, which may improve results of treatment also in tumour patients.
Hydrogenolysis, IV. Gas phase decarboxylation of carboxylic acids (1982)

Hydrogenolyse, IV. Decarboxylierung von Carbonsäuren in der Gasphase Ein neues einfaches Verfahren zur Decarboxylierung nicht aktivierter Carbonsäuren ist die heterogene Gasphasen‐Katalyse unter Normaldruck mit Wasserstoff als Reaktionsmedium. Nickel‐Katalysatoren decarboxylieren tertiäre aliphatische, aromatische und araliphatische Carbonsäuren bei 180°C, während Palladium‐Katalysatoren bei 330°C zur Decarboxylierung von primären und sekundären aliphatischen sowie aromatischen Carbonsäuren geeigneter sind. Selbst Phthalsäureanhydrid wird mit Palladium‐Katalysatoren vollständig defunktionalisiert.
Progressive parkinsonism in mice with respiratory-chain-deficient dopamine neurons (2007)

Mitochondrial dysfunction is implicated in the pathophysiology of Parkinson's disease (PD), a common age-associated neurodegenerative disease characterized by intraneuronal inclusions (Lewy bodies) and progressive degeneration of the nigrostriatal dopamine (DA) system. It has recently been demonstrated that midbrain DA neurons of PD patients and elderly humans contain high levels of somatic mtDNA mutations, which may impair respiratory chain function. However, clinical studies have not established whether the respiratory chain deficiency is a primary abnormality leading to inclusion formation and DA neuron death, or whether generalized metabolic abnormalities within the degenerating DA neurons cause secondary damage to mitochondria. We have used a reverse genetic approach to investigate this question and created conditional knockout mice (termed MitoPark mice), with disruption of the gene for mitochondrial transcription factor A (Tfam) in DA neurons. The knockout mice have reduced mtDNA expression and respiratory chain deficiency in midbrain DA neurons, which, in turn, leads to a parkinsonism phenotype with adult onset of slowly progressive impairment of motor function accompanied by formation of intraneuronal inclusions and dopamine nerve cell death. Confocal and electron microscopy show that the inclusions contain both mitochondrial protein and membrane components. These experiments demonstrate that respiratory chain dysfunction in DA neurons may be of pathophysiological importance in PD.
SIRPα-antibody fusion proteins stimulate phagocytosis and promote elimination of acute myeloid leukemia cells (2017)

CD47, expressed on a variety of tumor cells, confers immune resistance by delivering an inhibitory "don't eat me" signal to phagocytic cells via its myeloid-specific receptor SIRPα. Recent studies have shown that blocking the CD47-SIRPα axis with CD47-directed antibodies or antibody-derivatives enhances phagocytosis and increases antitumor immune effects. However, CD47 expression on healthy cells creates an antigen sink and potential sites of toxicity, limiting the efficacy of CD47-directed therapies. In this study, we first characterized CD47 expression in Acute Myeloid Leukemia (AML) patients (n = 213) and found that CD47 is highly expressed on both AML bulk and stem cells irrespective of the disease state. Furthermore, to inhibit the CD47-SIRPα signaling pathway at the tumor site, we developed a so-called local inhibitory checkpoint monoclonal antibody (licMAB) by grafting the endogenous SIRPα domain to the N-terminus of the light chain of an antibody targeting CD33, a surface antigen expressed in AML. LicMABs selectively bind CD33-expressing cells even in the presence of a large CD33-negative CD47-positive antigen sink, stimulate phagocytosis of AML cells and eliminate AML cell lines and primary, patient-derived AML cells. Our findings qualify licMABs as a promising therapeutic approach to confine the benefit of disrupting the CD47-SIRPα axis to tumor antigen-expressing cells.
Essentiality of Ribosomal and Transcription Antitermination Proteins Analyzed by Systematic Gene Replacement in Escherichia coli (2007)

We describe here details of the method we used to identify and distinguish essential from nonessential genes on the bacterial Escherichia coli chromosome. Three key features characterize our method: high-efficiency recombination, precise replacement of just the open reading frame of a chromosomal gene, and the presence of naturally occurring duplications within the bacterial genome. We targeted genes encoding functions critical for processes of transcription and translation. Proteins from three complexes were evaluated to determine if they were essential to the cell by deleting their individual genes. The transcription elongation Nus proteins and termination factor Rho, which are involved in rRNA antitermination, the ribosomal proteins of the small 30S ribosome subunit, and minor ribosome-associated proteins were analyzed. It was concluded that four of the five bacterial transcription antitermination proteins are essential, while all four of the minor ribosome-associated proteins examined (RMF, SRA, YfiA, and YhbH), unlike most ribosomal proteins, are dispensable. Interestingly, although most 30S ribosomal proteins were essential, the knockouts of six ribosomal protein genes, rpsF (S6), rpsI (S9), rpsM (S13), rpsO (S15), rpsQ (S17), and rpsT (S20), were viable.
Anterior cruciate ligament injury in female athletes: epidemiology. (1999)

I believe that appropriate intervention programs can reduce these alarming rates of ACL injuries.
A review of nanomaterials for nanofluid enhanced oil recovery (2017)

Utilizing nanomaterials in flooding techniques has the potential to enhance oil recovery.
Interference with bacteriophage phi 6 genomic RNA packaging by hairpin structures (1995)

Bacteriophage phi 6 has a genome of three segments of double-stranded RNA enclosed in a procapsid composed of four different proteins. The preformed procapsid is capable of packaging plus-strand transcripts of the genomic segments in an in vitro reaction. Minus-strand synthesis within the procapsid then results in the production of the double-stranded RNA genome. When plus-strand transcripts contain strong hairpin structures near the 3' ends, they are subject to heterologous recombination to remove the hairpins. We now find that the sequences bounded by the hairpins as well as those 3' to them are excluded from particles in packaging reactions. This finding implies that packaging occurs from the 5' end and that the explanation for the facilitation of recombination by the hairpin structures is the lack of entry of the 3' ends rather than a difficulty of progressing through the hairpin by the phage polymerase. Packaging of segment M is dependent on the packaging of segment S. An S segment containing a strong hairpin is able to facilitate the packaging of segment M. This result implies that there is more than one entry pore into the procapsid.
Hydrophobic Liquid-Infused Porous Polymer Surfaces for Antibacterial Applications (2013)

Biofilms represent a fundamental problem in environmental biology, water technology, food hygiene as well as in medical and technical systems. Recently introduced slippery liquid-infused porous surface (SLIPS) showed great promise for preventing biofilm formation owing to the low surface energy of such surface in combination with its self-cleaning properties. In this study we demonstrated a novel hydrophobic liquid-infused porous poly(butyl methacrylate-co-ethylene dimethacrylate) surface (slippery BMA-EDMA) with bacteria-resistance in BM2 mineral medium and long-term stability in aqueous environments. We showed that the slippery BMA-EDMA surface prevents biofilm formation of different strains of opportunistic pathogen Pseudomonas aeruginosa for at least up to 7 days in low nutrient medium. Only ∼1.8% of the slippery surface was covered by the environmental P. aeruginosa PA49 strain under investigation. In uncoated glass controls the coverage of surfaces reached ∼55% under the same conditions. However, in high nutrient medium, more relevant to physiological conditions, the biofilm formation on the slippery surface turned out to be highly dependent on the bacterial strain. Although the slippery surface could prevent biofilm formation of most of the P. aeruginosa strains tested (∼1% surface coverage), the multiresistant P. aeruginosa strain isolated from wastewater was able to cover up to 12% of the surface during 7 days of incubation. RAPD-PCR analysis of the used P. aeruginosa strains demonstrated their high genome variability, which might be responsible for their difference in biofilm formation on the slippery BMA-EDMA surface. The results show that although the slippery BMA-EDMA surface has a great potential against biofilm formation, the generality of its bacteria resistant properties is still to be improved.
DIAGNOSTIC VALUE OF SERUM PROCALCITONIN AND C-REACTIVE PROTEIN IN EGYPTIAN CHILDREN WITH STREPTOCOCCAL TONSILLOPHARYNGITIS (2006)

We investigated serum procalcitonin (PCT) and C-reactive protein (CRP) in children with streptococcal tonsillopharyngitis or nonstreptococcal tonsillopharyngitis and in healthy children. The median (range) for PCT was 0.374 (0.11-6.5), 0.105 (0.01-0.53) and 0.02 (0.01-0.08) ng/mL in the streptococcal, nonbacterial tonsillopharyngitis and control groups, respectively. PCT had a greater specificity than CRP for detection of bacterial tonsillopharyngitis.
Megawatt peak-power pulsed fiber sources (2006)

We report on master-oscillator/power-amplifier (MOPA) systems featuring Yb-doped photonic crystal fiber (PCF) amplifiers and designed to generate high peak and average powers in beams of good spectral and spatial quality. In the first setup, a 1064nm-wavelength Q-switched Nd:YAG micro-chip laser emitting 500ps pulses at pulse repetition frequency (PRF) ~13.5-kHz is amplified in a 40&#956;m-core, Yb-doped PCF to obtain peak power ~1.1 MW in a diffraction-limited beam (M<sup>2</sup> = 1.05) of peak spectral brightness ~ 10 kW/(cm<sup>2</sup> sr Hz). In the second setup, a 1ns-pulse Nd:LSB microchip laser (1062nm wavelength, single frequency, PRF = 9.6 kHz) is used to seed a dual-stage amplifier featuring the same 40&#956;m-core Yb-doped PCF as the final stage. From this MOPA, we obtained diffraction-limited pulses of 1.1mJ energy, peak/average power ~1.1 MW/~10.2 W, and spectral linewidth ~9GHz. In the third setup, a single-polarization, single-transverse-mode Yb-doped PCF was used as the final amplifier, which permitted to obtain high-peak-power, spectrally narrow, 100:1 linearly-polarized pulses directly usable for wavelength conversion. The PCF output was frequency doubled, tripled, and quadrupled in nonlinear crystals to generate peak power in excess of 400 kW in the visible and ~200 kW in the UV. Finally, in the fourth setup, an Yb-doped, 70&#956;m-core, intrinsically single-mode photonic-crystal rod (PCR) was used to generate near-diffraction-limited (M<sup>2</sup> ~ 1.1) ~1ns pulses of 2.25mJ energy and peak-power >2.2 MW.
Synthesis and anticancer activity of epipolythiodiketopiperazine alkaloids (2013)

The epipolythiodiketopiperazine (ETP) alkaloids are a highly complex class of natural products with potent anticancer activity. Herein, we report the application of a flexible and scalable synthesis, allowing the construction of dozens of ETP derivatives. The evaluation of these compounds against cancer cell lines in culture allows for the first expansive structure-activity relationship (SAR) to be defined for monomeric and dimeric ETP-containing natural products and their synthetic cognates. Many ETP derivatives demonstrate potent anticancer activity across a broad range of cancer cell lines, and kill cancer cellsviainduction of apoptosis. Several traits thatbode well for the translational potential of the ETP class of natural products includeconcise and efficient synthetic access, potent induction of apoptotic cell death, activity against a wide range of cancer types, and a broad tolerance for modifications at multiple sitesthat should facilitate small-molecule drug development, mechanistic studies, and evaluation <i>in vivo</i>.
Cholesterol-lowering diets. A review of the evidence (1995)

To evaluate the efficacy of the high-risk approach and the population approach for cholesterol lowering, large trials of dietary intervention (n≥150) and smaller trials of angiographic assessment of the impact of diet on coronary disease were reviewed. Two trials of dietary therapy as intensive individualized counseling in individuals at usual risk for coronary disease achieved 75% to 80% of the cholesterol lowering predicted by metabolic ward studies and produced a 5% to 14% reduction in total cholesterol levels. Four studies in high-risk individuals exceeded predictions and achieved a 4% to 17% reduction in total cholesterol levels. Similar efficacy was observed in six of the seven trials of diet for secondary prevention. Four trials employing the population approach achieved smaller but often significant reductions in total cholesterol levels of 1% to 11%. No tachyphylaxis to dietary therapy occurred in trials in which dietary counseling was maintained during the trial. The effectiveness of diet is enhanced when individualized counseling is used, follow-up is maintained, and weight reduction is achieved. (Arch Intern Med. 1995;155:17-26)
RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy (2014)

Supplementary data are available at Bioinformatics online.
Local injection of OK432 can augment the TH1-type T-cell response in tumor-draining lymph node cells and increase their immunotherapeutical potential (1997)

The effect of local injections with streptococcal preparation OK432 on the therapeutical potential of tumor-draining lymph node (LN) cells was investigated in mice. Peritumoral injections with OK432 on days 2, 4, 6, 8 and 10 showed no effect on the in vivo growth of s.c. inoculated B16F10 melanoma. The B16F10-draining OK432-treated LN cells, however, showed a high level of anti-B16F10 cytolytic activity after an in vitro culture first with both anti-CD3 monoclonal antibody (MAb) and activated B cell blasts, and subsequently with interleukin (IL)-2 without in vitro restimulation. Such in vitro expanded LN cells showed a remarkable antitumor effect against pulmonary metastasis of B16F10 melanoma, even without the concurrent administration of IL-2. In addition, the therapeutical protocol was also found to be moderately effective against poorly immunogenic MCA fibrosarcoma, and the in vivo antitumor effect was specific to the tumor from which the LNs were harvested. Interestingly, 2 kinds of comparative analyses of the cytokines revealed that the B16F10-bearing state induced the draining LN cells to develop a Th2-type response. However, the OK432 treatment was able to effectively augment their Th1-type response. Collectively, our results suggest that peritumoral injections with OK432 significantly increased the therapeutical potential of the tumor-draining LN cells by augmenting their Th1-type response.
Effect of 12-hydroxyeicosatetraenoic acid on cytosolic calcium in human neutrophils. (1994)

12-Hydroxy-5,8,10,14-eicosatetraenoic acid (12-HETE) has been reported to be a chemoattractant for human neutrophils. To assess its cellular mechanism, we focused on the effect of 12-HETE on cytosolic Ca2+ ([Ca2+]i) and characterized the effect of 12-HETE on [Ca2+]i in human neutrophils. 12(S)- and 12(R)-HETE increased [Ca2+]i in the presence and absence of extracellular Ca2+ in a concentration-related fashion. The elevation of [Ca2+]i by 12(R)-HETE was completely abolished by pertussis toxin treatment. U-73122, a selective phospholipase C inhibitor, depressed the 12(S)- and 12(R)-HETE-induced rise in [Ca2+]i in the presence and absence of extracellular Ca2+. 12(R)-HETE resulted in the rapid production of inositol 1,4,5-trisphosphate (IP3). Furthermore, 12(R)-HETE elicited slight depolarization of neutrophils as assessed using the fluorescent dye bis-oxonol. These results provide evidence demonstrating the signal transduction pathway in human neutrophils after stimulation with 12-HETE and suggest that 12-HETE causes a rapid rise of [Ca2+]i by mobilizing Ca2+ from an IP3-sensitive intracellular Ca2+ pool in human neutrophils.