gebhart/patrepeval huggingface dataset:
Chemical Approaches to Controlling Intracellular Protein Degradation (2004)

Inactive. Recent advances have yielded many ways to study proteins by means of inactivation. Traditional methods of genetic knockout are complimented by newer techniques, including RNAi and small molecules that induce proteolysis (see scheme). Although seemingly in competition, these techniques each offer solutions to specific problems in proteomic analysis.
Comparison of different pulsed and Q-switched solid state laser systems for endoscopic laser-induced shockwave lithotripsy: performance and laser/stone interactions (1990)

At present the laser induced shock wave lithotripsy (LISL) of urinary and biliary stones via fiber optic beam delivery is governed by two competing' laser systems: The flashlamp-pumped pulsed dye laser and the Q-switched Nd:YAG laser. The pulsed radiation of the dye system with pulse durations in the 1-2 .tsec region can be easily transmitted through extremely flexible fused silica fibers with core diameters of only 200 im whilst the Q-switched Nd:YAG laser with pulselengths of 5-25 nsec needs fibers with more than 400 tm core diameter. The dye laser releases acoustic shock waves for fragmentation simply by stone contact, the Q-switched Nd:YAG produces these waves in the surrounding aqueous medium by laser induced optical breakdown (LIB) when refocused by optical means or through additional metal absorbers, i.e. opto - mechanical couplers. We report on the system performances and laser/stone interactions of two alternative solid-state laser systems with variable pulselengths in the range of 1.7 - 30 sec and 30 - 1000 nsec, respectively: The pulsed psec-Nd:YAG laser and the Q-switched alexandrite laser. Regarding the endoscopic laser lithotripsy of urinary and biliary stones in the ureter or common bile duct, respectively, the laser energy delivery system, i.e. the optical fiber; is the most stressed part. Therefore we used long-pulse solid-state laser systems like the pulsed Nd:YAG laser with a pulse-slicing unit and a pulselength-tunable Q-switched alexandrite laser and studied fragmentation of synthetic plaster samples as well as urinary and biliary stones. The radiation of both laser systems can be effectively transmitted via standard 200 im core diameter optical quartz fibers what is absolutely necessary when used in conjunction with small caliber rigid or flexible endoscopes. As a compact and reliable solid-state system the alexandrite laser lithotripter is much less expensive than an extracorporeal shock wave lithotripter with the same fragmentation results and may become the laser of choice for LISL.
Optimization and Characterization of Dextran Membranes Prepared by Electrospinning (2004)

Dextran is soluble in both water and organic solvents, so it could be a versatile biomacromolecule for preparing nanofibrous electrospun membranes by blending with either water-soluble bioactive agents or hydrophobic biodegradable polymers for biomedical applications. We have formulated electrospun dextran membranes, and the effects of various processing parameters on the membrane properties were investigated. It was found that uniform nanofibrous dextran membranes could be formed by using water, DMSO/water, and DMSO/DMF mixtures as solvents through adjusting the processing conditions (solution concentration, voltage, and the distance between the electrode and the collecting plate). When water was used as a solvent, up to 10% (w/w) of bovine serum albumin (BSA) or lysozyme could be directly incorporated into the dextran electrospun membrane without compromising its morphology. No significant effect of the electrospinning process on lysozyme activity was observed. The composite electrospun membranes consisting of poly(D,L-lactide-co-glycolide) (PLGA) and dextran were obtained using DMSO/DMF (50/50, volume ratio) mixture as solvents. For cross-linking the electrospun membrane, dextran was modified by substitution of methacrylate groups at the hydroxyl sites. It was found that the electrospun membranes prepared from methacrylated dextran can be cured by UV irradiation in the presence of 1% of 2,2-dimethoxy-2-phenylacetophenone (DMPA) as a photoinitiator.
Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer (2013)

This proof-of-concept analysis showed that circulating tumor DNA is an informative, inherently specific, and highly sensitive biomarker of metastatic breast cancer. (Funded by Cancer Research UK and others.).
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) (1994)

Various non-nucleoside reverse transcriptase inhibitors (NNRTIs) have been reported to specifically inhibit human immunodeficiency virus type 1 (HIV-1): for example, tetrahydroimidazobenzodiazepinone (TIBO), hydroxyethoxymethylphenylthiothymine (HEPT), dipyridodiazepinone (i.e. nevirapine), pyridinone, bis(heteroaryl)piperazine (BHAP), tert-butyldimethylsilylspiroaminooxathioledioxide (TSAO), α-anilinophenylacetamide (α-APA) and quinoxaline derivatives. These compounds interact allosterically (i.e. non-competitively with respect to the natural substrate (dNTPs)) with a specific non-substrate binding site ‘pocket’ of the HIV-1 reverse transcriptase (RT). The most potent NNRTIs have been found to inhibit HIV-1 replication at nanomolar concentrations. These compounds therefore offer great potential for the treatment of HIV-1 infections. Yet, the virus may rapidly develop resistance to these drugs. The mutations conferring resistance have been mapped at the RT positions 100 (Leu × lle), 103 (Lys × Asn), 106 (Val × Ala), 108 (Val × lle), 138 (Glu × Lys), 179 (Val × Asp), 181 (Tyr × Cys), 188 (Tyr × Cys/His), 190 (Gly × Glu) and 236 (Pro × Leu). However, these mutations do not necessarily lead to cross-resistance among the various NNRTIs, and, in some cases, they have proved to be mutually suppressive. Several strategies could be envisaged to circumvent or prevent the resistance problem: switching from one NNRTI (to which the virus has developed resistance) to another (to which the virus has not developed resistance); combining different RT inhibitors that do not confer cross-resistance, or that may, in fact, even counteract development of resistance to one another; and, using sufficiently high (‘knocking-out’) concentrations of the NNRTIs from the start, so as to completely shut down virus replication and prevent resistance from emerging. NNRTIs differ in several aspects from the 2,3-dideoxynucleoside (ddN) type of RT inhibitors. An obvious strategy to be further pursued in clinical trials is based upon the combination of NNRTIs with ddNs, as such combinations may offer synergistic anti-HIV activity, while reducing the risk or rate of resistance development.
The yield of experimental yeast populations declines during selection (2012)

The trade-off between growth rate and yield can limit population productivity. Here we tested for this life-history trade-off in replicate haploid and diploid populations of Saccharomyces cerevisiae propagated in glucose-limited medium in batch cultures for 5000 generations. The yield of single clones isolated from the haploid lineages, measured as both optical and population density at the end of a growth cycle, declined during selection and was negatively correlated with growth rate. Initially, diploid populations did not pay this cost of adaptation but haploidized after about 1000-3000 generations of selection, and this ploidy transition was associated with a decline in yield caused by reduced cell size. These results demonstrate the experimental evolution of a trade-off between growth rate and yield, caused by antagonistic pleiotropy, during adaptation in haploids and after an adaptive transition from diploidy to haploidy.
Interactions among HIV gp120, CD4, and CXCR4: Dependence on CD4 Expression Level, gp120 Viral Origin, Conservation of the gp120 COOH- and NH2-Termini and V1/V2 and V3 Loops, and Sensitivity to Neutralizing Antibodies (1998)

The binding of HIV-derived recombinant soluble (s)gp120 to the CD4(+)/CXCR4(+) A3.01 T cell line inhibits the binding of the CXCR4-specific monoclonal antibodies 12G5, which interacts with the second extracellular loop, and 6H8, which binds the NH2 terminus. We have used this as an assay to analyse the interaction of recombinant sgp120 from diverse viral origins with CXCR4. The strength of the interaction between sgp120 and CXCR4 correlated with sgp120 affinity for the CD4-CXCR4 complex, and the interaction of sgp120MN and sgp120IIIB with CXCR4 was highly dependent on the level of CD4 expressed on a variety of different T cell lines. sgp120 from X4, R5X4, and R5 viruses interacted with CXCR4, although the R5 sgp120-CXCR4 interactions were weaker than those of the other gp120s. The interaction of sgp120IIIB or sgp120MN with CXCR4 was inhibited by neutralizing monoclonal antibodies that prevent the sgp120-CD4 interaction but also by antibodies specific for the gp120 V2 and V3 loops, the CD4-induced epitope and the 2G12 epitope, which interfere weakly or not at all with CD4-sgp120 binding. The binding to A3.01 cells of wild-type sgp120HxB2, but not of sgp120 deleted in the COOH and NH2 termini, interfered with 12G5 binding in a dose-dependent manner. Further deletion of the V1 and V2 loops restored CXCR4 binding activity, but additional removal of the V3 loop eliminated the gp120-CXCR4 interaction, without decreasing the affinity between mutated sgp120 and CD4. Taken together, these results demonstrate that the interactions between sgp120 and CXCR4 are globally similar to those previously observed between sgp120 and CCR5, with some apparent differences in the strength of the sgp120-CXCR4 interactions and their dependence on CD4.
Examining Intracellular Organelle Function Using Fluorescent Probes (2004)

Fluorescence microscopy imaging has become one of the most useful techniques to assess the activity of individual cells, subcellular trafficking of signals to and between organelles, and to appreciate how organelle function is regulated. The past 2 decades have seen a tremendous advance in the rational design and development in the nature and selectivity of probes to serve as reporters of the intracellular environment in live cells. These probes range from small organic fluorescent molecules to fluorescent biomolecules and photoproteins ingeniously engineered to follow signaling traffic, sense ionic and nonionic second messengers, and report various kinase activities. These probes, together with recent advances in imaging technology, have enabled significantly enhanced spatial and temporal resolution. This review summarizes some of these developments and their applications to assess intracellular organelle function.
Metalloenzymes, Structural Motifs, and Inorganic Models (1993)

Metalloenzymes effect a variety of important chemical transformations, often involving small molecule substrates or products such as molecular oxygen, hydrogen, nitrogen, and water. A diverse array of ions or metal clusters is observed at the active-site cores, but living systems use basic recurring structures that have been modified or tuned for specific purposes. Inorganic chemists are actively involved in the elucidation of the structure, spectroscopy, and mechanism of action of these biological catalysts, in part through a synthetic modeling approach involving biomimetic studies.
Heat extraction through the palm of one hand improves aerobic exercise endurance in a hot environment (2005)

In situations where the accumulation of internal heat limits physical performance, enhanced heat extraction from the body should improve performance capacity. The combined application of local subatmospheric pressure (35-45 mmHg) to an entire hand (to increase blood volume) and a heat sink (18-22 degrees C) to the palmar surface were used to draw heat out of the circulating blood. Subjects walked uphill (5.63 km/h) on a treadmill in a 40 degree C environment. Slopes of the treadmill were held constant during paired experimental trials (with and without the device). Heat extraction attenuated the rate of esophageal temperature rise during exercise (2.1 +/- 0.4 degrees and 2.9 +/- 0.5 degrees C/h, mean +/- SE, with and without the device, respectively; n = 8) and increased exercise duration (46.1 +/- 3.4 and 32.3 +/- 1.7 min with and without the device, respectively; n = 18). Hand cooling alone had little effect on exercise duration (34.1 +/- 3.0, 38.0 +/- 3.5, and 57.0 +/- 6.4 min, for control, cooling only, and cooling, and subatmospheric pressure, respectively; n = 6). In a longer term study, nine subjects participated in two or four trials per week for 8 wk. The individual workloads (treadmill slope) were varied weekly. Use of the device had a beneficial effect on exercise endurance at all workloads, but the benefit proportionally decreased at higher workloads. It is concluded that heat can be efficiently removed from the body by using the described technology and that such treatment can provide a substantial performance benefit in thermally stressful conditions.
Aqueous outflow - A continuum from trabecular meshwork to episcleral veins (2016)

In glaucoma, lowered intraocular pressure (IOP) confers neuroprotection. Elevated IOP characterizes glaucoma and arises from impaired aqueous humor (AH) outflow. Increased resistance in the trabecular meshwork (TM), a filter-like structure essential to regulate AH outflow, may result in the impaired outflow. Flow through the 360° circumference of TM structures may be non-uniform, divided into high and low flow regions, termed as segmental. After flowing through the TM, AH enters Schlemm's canal (SC), which expresses both blood and lymphatic markers; AH then passes into collector channel entrances (CCE) along the SC external well. From the CCE, AH enters a deep scleral plexus (DSP) of vessels that typically run parallel to SC. From the DSP, intrascleral collector vessels run radially to the scleral surface to connect with AH containing vessels called aqueous veins to discharge AH to blood-containing episcleral veins. However, the molecular mechanisms that maintain homeostatic properties of endothelial cells along the pathways are not well understood. How these molecular events change during aging and in glaucoma pathology remain unresolved. In this review, we propose mechanistic possibilities to explain the continuum of AH outflow control, which originates at the TM and extends through collector channels to the episcleral veins.
Transdermal Nicotine as Maintenance Therapy for Ulcerative Colitis (1995)

Transdermal nicotine alone was no better than placebo in the maintenance of remission of ulcerative colitis, and premature withdrawal due to side effects was more common in the nicotine group.
Direct binding of myelin basic protein and synthetic copolymer 1 to class II major histocompatibility complex molecules on living antigen-presenting cells--specificity and promiscuity. (1994)

Copolymer 1 (Cop 1) is a synthetic basic random copolymer of amino acids that has been shown to be effective in suppression of experimental allergic encephalomyelitis and is being tested as a candidate drug for multiple sclerosis. It has been previously demonstrated that Cop 1 is immunologically cross-reactive with the autoantigen myelin basic protein (BP) and competitively inhibits the response to BP of T-cell lines and clones of different major histocompatibility complex (MHC) restrictions, of both mouse and human origin. In the present study we demonstrated the direct binding of Cop 1, using its biotinylated derivative, to MHC molecules on living antigen-presenting cells. Binding of biotinylated BP and peptide p84-102 (an immunodominant epitope of BP) was also demonstrated. Cop 1 and BP bound in a promiscuous manner to different types of antigen-presenting cells of various H-2 and HLA haplotypes. The specificity of the binding was confirmed by its inhibition with either the relevant anti-MHC class II antibodies or unlabeled analogs. Cop 1 exhibited the most extensive and fast binding to antigen-presenting cells. In addition, Cop 1 inhibited the binding of biotinylated derivatives of BP and of p84-102 to the MHC class II molecules and even displaced these antigens when already bound. Thus, these results suggest that Cop 1 indeed competes with BP for MHC binding and, thereby, inhibits T-cell responses to BP. The binding of Cop 1 to different DR alleles, probably because of its multiple MHC binding motifs, may indicate its potential as a broad-spectrum drug for multiple sclerosis.
Rapid-freezing cytochemistry: preservation of tubular lysosomes and enzyme activity. (1991)

We show that tubular structures present in phorbol ester-stimulated macrophages are sensitive to commonly used chemical fixatives (i.e., they usually become fragmented during fixation). These structures are well preserved in macrophages that are physically fixed by rapid-freezing and subsequent freeze-substitution in osmium-acetone. We have developed methods that combine rapid-freezing, freeze-substitution, and enzyme cytochemistry for preservation of these tubular structures and for detection of endocytosed material (i.e., horseradish peroxidase). This method of rapid-freeze cytochemistry may be useful in other situations where chemical fixation does not adequately preserve cell structures, particularly of membrane compartments.
Acoustofluidics 1: Governing equations in microfluidics (2011)

In Part 1 of the thematic tutorial series "Acoustofluidics--exploiting ultrasonic standing waves forces and acoustic streaming in microfluidic systems for cell and particle manipulation", we establish the governing equations in microfluidics. Examples of basic flow solutions are presented, and equivalent circuit modeling for determining flow rates in microfluidic networks is introduced.
Use of Reprogrammed Cells to Identify Therapy for Respiratory Papillomatosis (2012)

A patient with a 20-year history of recurrent respiratory papillomatosis had progressive, bilateral tumor invasion of the lung parenchyma. We used conditional reprogramming to generate cell cultures from the patient's normal and tumorous lung tissue. Analysis revealed that the laryngeal tumor cells contained a wild-type 7.9-kb human papillomavirus virus type 11 (HPV-11) genome, whereas the pulmonary tumor cells contained a 10.4-kb genome. The increased size of the latter viral genome was due to duplication of the promoter and oncogene regions. Chemosensitivity testing identified vorinostat as a potential therapeutic agent. At 3 months after treatment initiation, tumor sizes had stabilized, with durable effects at 15 months.
Indium-cadmium-oxide films having exceptional electrical conductivity and optical transparency: Clues for optimizing transparent conductors (2001)

Materials with high electrical conductivity and optical transparency are needed for future flat panel display, solar energy, and other opto-electronic technologies. In(x)Cd(1-x)O films having a simple cubic microstructure have been grown on amorphous glass substrates by a straightforward chemical vapor deposition process. The x = 0.05 film conductivity of 17,000 S/cm, carrier mobility of 70 cm2/Vs, and visible region optical transparency window considerably exceed the corresponding parameters for commercial indium-tin oxide. Ab initio electronic structure calculations reveal small conduction electron effective masses, a dramatic shift of the CdO band gap with doping, and a conduction band hybridization gap caused by extensive Cd 5s + In 5s mixing.
Role of complement component C1q in phagocytosis of Listeria monocytogenes by murine macrophage-like cell lines (1993)

Listeria monocytogenes is a facultative intracellular pathogen of a great variety of cells. Among them, macrophages constitute the major effector cells of listerial immunity during the course of an infection. Although the molecular bases of L. monocytogenes attachment and entry to phagocytes are not completely understood, it has been demonstrated that C3b significantly increases L. monocytogenes uptake by macrophages via complement receptor type 3. The first component of complement, C1q, is present in organic fluids at a relatively high concentration, and C1q receptor sites in macrophages are also abundant. In the present report, results of studies on the role of C1q in the internalization and infectivity of L. monocytogenes by macrophages are presented. L. monocytogenes uptake is enhanced by prior treatment of bacteria with normal sera. Heated serum or C1q-deficient serum abrogates this enhancement. Purified C1q specifically restored uptake. This effect was blocked by the addition of F(ab')2 anti-C1q antibody but not by an irrelevant matched antibody. Direct binding of C1q to L. monocytogenes was specific, saturable, and dose dependent with both fluorescent and radiolabeled C1q. N-Acetyl-D-alanyl-L-isoglutamine, diaminopimelic acid, and L-rhamnose caused a significant dose-dependent inhibition of C1q binding to bacteria, suggesting that these molecules, at least, are involved in the attachment of C1q to L. monocytogenes cell wall. When C1q binding structures on macrophage-like cells were blocked with saturating concentrations of C1q, the uptake of C1q-opsonized bacteria was less than in untreated cells. These experiments demonstrate that, in addition to other reported mechanisms, L. monocytogenes binds C1q, which mediates enhanced uptake by macrophages through C1q binding structures.
Bright, efficient, and color-stable violet ZnSe-based quantum dot light-emitting diodes (2015)

In this paper, highly stable violet-blue emitting ZnSe/ZnS core/shell QDs have been synthesized by a novel "low temperature injection and high temperature growth" method. The resulting nearly monodisperse ZnSe/ZnS core/shell QDs exhibit excellent characteristics such as a high color saturation (typical spectral full width at half-maximum between 12 and 20 nm), good emission tunability in the violet-blue range of wavelengths from 400 to 455 nm, a high absolute PL quantum yield (up to 83%), and superior chemical and photochemical stability. By employing ZnSe/ZnS core/shell quantum dots (QDs) as emitters with a fully solution processable method, bright, efficient, and color-stable violet Cd-free quantum dot-based light-emitting diodes (QD-LEDs) with maximum luminance up to 2632 cd m(-2) and a peak EQE of 7.83% have been demonstrated successfully. Considering the factors of the photopic luminosity function, the brightness and efficiency results of such violet QD-LEDs not only represent a 12-fold increase in device efficiency and an extraordinary 100 times increase in luminance compared with previous Cd-free QD-LEDs but also can be much superior to the best performance (1.7%) of their Cd-based violet counterparts. These results demonstrate significant progress in short-wavelength QD-LEDs and shed light on the acceleration of commercial application of environmentally-friendly violet QD-based displays and lighting.
Expression and Function of CD44 in Epithelial Ovarian Carcinoma (2015)

CD44, a cell surface glycoprotein, has been increasingly implicated in the pathogenesis and progression of epithelial ovarian cancer, the deadliest gynecologic malignancy in women. Here, we review recent reports on the expression and function of CD44 in epithelial ovarian carcinoma. Further functional data for CD44 in peritoneal adhesion and metastatic progression and its association with stem cells is highlighted. Recent studies utilizing CD44 for therapeutic targeting are also discussed.