gebhart/patrepeval huggingface dataset:
Conformationally Constrained Peptidomimetic Inhibitors of Signal Transducer and Activator of Transcription 3: Evaluation and Molecular Modeling (2009)

Signal transducer and activator of transcription 3 (Stat3) is involved in aberrant growth and survival signals in malignant tumor cells and is a validated target for anticancer drug design. We are targeting its SH2 domain to prevent docking to cytokine and growth factor receptors and subsequent signaling. The amino acids of our lead phosphopeptide, Ac-pTyr-Leu-Pro-Gln-Thr-Val-NH(2), were replaced with conformationally constrained mimics. Structure-affinity studies led to the peptidomimetic, pCinn-Haic-Gln-NHBn (21), which had an IC(50) of 162 nM (fluorescence polarization), compared to 290 nM for the lead phosphopeptide (pCinn = 4-phosphoryloxycinnamate, Haic = (2S,5S)-5-amino-1,2,4,5,6,7-hexahydro-4-oxo-azepino[3,2,1-hi]indole-2-carboxylic acid). pCinn-Haic-Gln-OH was docked to the SH2 domain (AUTODOCK), and the two highest populated clusters were subjected to molecular dynamics simulations. Both converged to a common peptide conformation. The complex exhibits unique hydrogen bonding between Haic and Gln and Stat3 as well as hydrophobic interactions between the protein and pCinn and Haic.
Sperm penetration through cumulus mass and zona pellucida (2008)

Mammalian fertilization requires sperm to penetrate the cumulus mass and egg zona pellucida prior to fusion with the egg. Although sperm penetration through these physical barriers is essential, the molecular mechanism has not yet been completely elucidated. In addition to sperm motility, hyaluronan-hydrolyzing and proteolytic enzymes of sperm have been suggested to participate in the penetration events. Here we focus on the functional roles of hyaluronidase and protease in sperm passage through the cumulus mass and zona pellucida.
Dynamics of femtosecond laser-induced breakdown in water from femtoseconds to microseconds (2002)

Using time-resolved imaging and scattering techniques, we directly and indirectly monitor the breakdown dynamics induced in water by femtosecond laser pulses over eight orders of magnitude in time. We resolve, for the first time, the picosecond plasma dynamics and observe a 20 ps delay before the laser-produced plasma expands. We attribute this delay to the electron-ion energy transfer time.
Human Factors and Behavioral Science: On Abbreviating Command Names (1983)

Test subjects' abbreviations of command names and randomly selected English words were examined for production regularities. Abbreviation rules based primarily on a word's number of syllables were devised to capture regularities observed in people's productions. This rule set was compared to two simpler abbreviation rules — vowel deletion and truncation. In subsequent learning experiments, separate groups of subjects learned the rule-derived abbreviations for words, while other groups learned the most frequently given abbreviation for each word. Subjects who studied rule-derived abbreviations remembered substantially more of them when prompted with full words than did subjects who studied the most frequently given abbreviations. Moreover, the rule-based abbreviations were superior even for those for which the rule-produced and the most frequently produced abbreviations were identical. When the task was reversed (recall the source term given an abbreviation), performance was best for vowel deletion abbreviations and worst for the rule set abbreviations. We suggest that both memorability of abbreviations and the probability that people will spontaneously produce a “correct” abbreviation are increased by: (1) selecting abbreviations using a vowel deletion rule for one-syllable words and an acronym rule for multiple-word terms, as well as (2) allowing variable length truncations of words.
A tunable dispersion compensating MEMS all-pass filter (2000)

A tunable dispersion compensating filter based on a multistage optical all-pass filter with a microelectromechanical (MEM) actuated variable reflector and a thermally tuned cavity is described. A two-stage device was demonstrated with a tuning range of /spl plusmn/100 ps/nm, 50-GHz passband and a group delay ripple less than /spl plusmn/3 ps. The device has negligible polarization dependence and is suitable for single or multiple channel compensation. An off-axis, two-fiber package with an excess loss <2 dB/stage avoids the need for a circulator. By cascading four stages, a passband to channel spacing ratio of 0.8 is obtained that allows both 40 Gb/s nonreturn-to-zero (NRZ) and return-to-zero (RZ) signals to be compensated.
Degradation of type I and II collagen by human C1&#x0304;s (1990)

The activated first component of human complement, C1-s, was shown to cleave type I and II collagen and gelatin. The proteolytic activity was heat labile and was inhibited by a monoclonal antibody (M241) which recognized light chain of active human C1-s or by a serine protease inhibitor, DFP, but not by a chelating agent.
Clonal Analysis of Human Embryonic Stem Cell Differentiation into Teratomas (2007)

Differentiation of human embryonic stem cells (HESCs) can be studied in vivo through the induction of teratomas in immune-deficient mice. Cells within the teratomas differentiate into all three embryonic germ layers. However, the exact nature of the proliferation and differentiation of HESCs within the teratoma is not fully characterized, and it is not clear whether the differentiation is cell autonomous or affected by neighboring cells. Here, we establish a genetic approach to study the clonality of differentiation in teratomas using a mixture of HESC lines. We first demonstrate, by means of 5-bromo-2'-deoxyuridine incorporation, that cell proliferation occurs throughout the teratoma, and that there are no clusters of undifferentiated-proliferating cells. Using a combination of laser capture microdissection and DNA fingerprinting analysis, we show that different cell lines contribute mutually to the same distinctive tissue structures. Further support for the nonclonal differentiation within the teratoma was achieved by fluorescence in situ hybridization analysis of sex chromosomes. We therefore suggest that in vivo differentiation of HESCs is polyclonal and, thus, may not be cell autonomous, stressing the need for a three-dimensional growth in order to achieve complex differentiation of HESCs. Disclosure of potential conflicts of interest is found at the end of this article.
When the Solvent Locks the Cage: Theoretical Insight into the Transmetalation of MOF-5 Lattices and Its Kinetic Limitations (2015)

Transmetalation is an innovative postsynthetic strategy for tailoring the properties of metal–organic frameworks (MOFs), allowing stable unprecedented metal coordination environments. Although the experimental synthetic protocol is well-established, the underlying mechanism for transmetalation is still unknown. In this work, we propose two different solvent-mediated reaction paths for the Ni transmetalation in Zn-MOF-5 lattices through density functional theory simulations. In both mechanisms, the bond strength between the exchanged metal and the solvent is the key descriptor that controls the degree of transmetalation. We also show that the role of the solvent in this process is twofold: it initially promotes Zn exchange, but if the metal–solvent bond is too strong, it blocks the second transmetalation cycle by restricting the lattice flexibility. The competition between these two effects leads the degree of incorporation of metal into MOF-5 to display a volcano-type dependence with respect to the metal–solvent bond strength for different transition metal ions.
Halting of Caspase Activity Protects Tau from MC1-Conformational Change and Aggregation (2016)

Intracellular neurofibrillary tangles (NFTs) are the hallmark of Alzheimer's disease and other tauopathies in which tau, a microtubule-associated protein, loses its ability to stabilize microtubules. Several post-translational modifications including phosphorylation and truncation increase tau's propensity to aggregate thus forming NFTs; however, the mechanisms underlying tau conformational change and aggregation still remain to be defined. Caspase activation and subsequent proteolytic cleavage of tau is thought to be a potential trigger of this disease-related pathological conformation. The aim of this work was to investigate the link between caspase activation and a disease-related conformational change of tau in a neuroblastoma cell-based model of spontaneous tau aggregation. We demonstrated that caspase induction initiates proteolytic cleavage of tau and generation of conformationally altered and aggregated tau recognized by the MC1 conformational antibody. Most importantly, these events were shown to be attenuated with caspase inhibitors. This implies that therapeutics aimed at inhibiting caspase-mediated tau cleavage may prove beneficial in slowing cleavage and aggregation, thus potentially halting tau pathology and disease progression.
Monoclonal antibodies against core and cellulose‐binding domains of Trichoderma reesei cellobiohydrolases I and II and endoglucanase I (1991)

Cellulases from Trichoderma reesei form an enzyme group with a common structural organization. Each cellulase enzyme is composed of two functional domains, the core region containing the active site and the cellulose-binding domain (CBD). To facilitate the specific detection of each domain, monoclonal antibodies (mAb) against cellobiohydrolase I (CBHI), cellobiohydrolase II (CBHII) and endoglucanase I (EGI) were produced. Five mAb were obtained against CBHI, ten against CBHII and eight against EGI. The location of the antigenic epitope for each antibody was mapped by allowing the antibodies to react with truncated cellulases, synthesized from deleted cDNA in Saccharomyces cerevisiae. Proteolytic fragments of Trichoderma cellulases, obtained by papain digestion, were used to confirm the results. Specific antibodies were detected against the core and the CBD epitopes for all three cellulases. Using the truncated enzymes, it was possible to locate the epitopes to a reasonably short region within the protein. To obtain a quantitative assay for each enzyme, a specific mAb against each antigen was chosen, based on the affinity to the corresponding antigen on Western-blot staining and on filter blots of the cellulolytic yeasts. The mAb were used to quantitative the corresponding enzymes in T. reesei culture medium. Specific quantitation of each cellulase enzyme has not been possible by biochemical assays or using polyclonal antibodies, due to their cross-reactions. Now, these mAb can be specifically used to recognize and quantitate different domains of these three important cellulolytic enzymes.
A Comparative Chemical and Serological Study of the Full and Empty Particles of Foot-and Mouth Disease Virus (1975)

The chemical and serological properties of the full, naturally occurring empty and artificially produced empty particles of foot-and-mouth disease virus, serotype A(subtype 10, strain 16) have been studies. The full 146S particles comprised the virus RNA, three polypeptides (VP1 to VP3) mol. wt. about 30 X 10-3, one polypeptide (VP4) mol. wt. about 13-5 X 10-3, and a small amount of a polypeptide (VPo) mol. wt. about 43 X 10-3. The naturally occurring 75S empty particles contained no RNA and much less VP1 and VP4 than were found in the fall particles. However they contained a much greater proportion of VPo than the full particles. Dialysis of purified full particles against tris-EDTA, pH 7-6, produced artificial 75S empty particles which contained only a small amount of RNA and no VP4; otherwise the polypeptide composition was similar to that of the full particles. Immunological and serological tests showed that the full particles were antigenically similar to the naturally occurring empty particles but distinct from the artificial empty particles. The latter particles, however, had serological properties similar to those of the 12S protein subunit of the virus. Both the full and naturally occurring empty particles attached efficiently to susceptible cells, whereas the artificial empty particles attached only to a limited extent. The results are related to the function of the individual polypeptides of the virus particle and compared with published work on other picornaviruses.
Multiple sclerosis disease activity correlates with gadolinium‐enhanced magnetic resonance imaging (1987)

Magnetic resonance imaging provides a method of visualizing multiple sclerosis plaques, but the age and activity of these plaques cannot be determined with routine magnetic resonance images. Gadolinium DTPA is a paramagnetic contrast agent that does not cross an intact blood-brain barrier. We studied 16 patients with multiple sclerosis, using magnetic resonance imaging, gadolinium-enhanced magnetic resonance imaging, and computed tomographic scans. Gadolinium enhancement of multiple sclerosis plaques correlated with the clinical activity of the disease and corresponded anatomically with the symptoms and signs. We conclude that gadolinium enhancement of magnetic resonance images is a promising tool in the investigation of multiple sclerosis lesions and that it may provide a method for objective follow-up in clinical trails.
Core 2 Branching β1,6-N-Acetylglucosaminyltransferase and High Endothelial Venule-restricted Sulfotransferase Collaboratively Control Lymphocyte Homing (2004)

L-selectin mediates lymphocyte homing by facilitating lymphocyte adhesion to carbohydrate ligands expressed on high endothelial venules (HEV) of the secondary lymphoid organs. Previous studies demonstrated that L-selectin ligand sulfotransferase (LSST) forms 6-sulfo sialyl Lewis x (sLe(x)) on both core 2 branch and MECA-79-positive extended core 1 O-glycans, but the chemical nature and roles of HEV ligands elaborated by LSST and core 2 beta1,6-N-acetylglucosaminyltransferase-1 (Core2GlcNAcT) have been undefined. In the present study, we have generated mutant mice with deficient LSST and show that inactivation of LSST gene alone leads to only partial impairment of lymphocyte homing to peripheral lymph nodes and moderate reduction in lymphocyte counts in the peripheral lymph nodes, despite the fact that L-selectin ligands that contain 6-sulfo sLe(x) are reduced at HEV. By contrast, LSST/Core2GlcNAcT double null mice exhibited a markedly reduced lymphocyte homing and reduced lymphocyte counts as a result of significantly decreased 6-sulfo sLe(x) on HEV L-selectin counterreceptors, relative to LSST- or Core2GlcNAcT-single null mice. Moreover, induction of LSST and Core2GlcNAcT transcripts was observed in HEV-like structure formed in the salivary gland of the non-obese diabetic mouse, which displays chronic inflammation. These results indicate that LSST and Core2GlcNAcT cooperatively synthesize HEV-specific L-selectin ligands required for lymphocyte homing and suggest that LSST and Core2GlcNAcT play a critical role in lymphocyte trafficking during chronic inflammation.
Comparison of commercial DNA preparation kits for the detection of Brucellae in tissue using quantitative real-time PCR (2010)

We observed differences in DNA yield as high as two orders of magnitude for some samples between the best and the worst DNA extraction kits and inhibition was observed occasionally. This indicates that DNA purification may be more relevant than expected when the amount of DNA in tissue is very low.
Preferential expression and frequent IgG responses of a tumor antigen, SOX5, in glioma patients (2007)

We previously reported to identify SOX5 as a glioma antigen by serological screening using a testis cDNA library. The present study was designed to analyze SOX5 expression, its immunoreactivity, and the correlation between SOX5 IgG responses and clinical features in glioma patients to evaluate the possibility of its use as a diagnostic marker. Quantitative RT-PCR and Western blot analysis revealed that SOX5 was expressed in glioma tissues, but not in normal adult tissues, except in the testis. An immunohistochemical analysis showed that SOX5 was expressed in glioma cells, but only a few SOX5-positive cells were detected in non-neoplastic tissues from the cerebral cortex. IgG antibodies against SOX5 were detected in sera from 8 of the 27 glioma patients (27.6%), 0 of the 14 patients with other brain diseases (0%), 1 of the 54 other cancer patients (1.9%) and 1 of the 37 healthy individuals (2.7%). Patients with glioblastoma (GBM) who showed IgG responses against SOX5 exhibited significantly better survival periods than GBM patients without SOX5 antibodies. In summary, SOX5 is aberrantly expressed in glioma and can be recognized as a glioma antigen using IgGs from the sera of glioma patients. Furthermore, there is a statistically significant correlation between the presence of SOX5 IgGs and survival in GBM patients, suggesting that the glioma antigen SOX5 may be useful not only as a diagnostic marker, but also as a prognostic marker in glioma patients.
Narrow-beam five-layer (GaAl)As/GaAs heterostructure lasers with low threshold and high peak power (1976)

A variety of (GaAl)As/GaAs heterostructure injection lasers have been fabricated with two pairs of heterojunctions, the inner pair for carrier confinement and the outer pair for optical confinement. Asymmetrical versions of this design have given, at one extreme, threshold current density Jt at 300 K as low as 500 A/cm2 and at the other extreme far-field angular beam widths to the half-power point of 15° with Jt&amp;lt;1000 A/cm2, for 500-μm-long sawn cavity lasers with reflectors on one face. The incremental quantum efficiency from one end of 300-μm-long lasers with reflectors was over 40%. The peak optical power from lasers of 100 μm width was up to 3 W for 200-ns pulses. The temperature variation of threshold over the range 290–355 K was Jt355/Jt290∼1.5. Double-heterostructure lasers with narrow active layers and 20% AlAs confinement steps gave almost comparable performance in Jt and beam width (650 A/cm2 for 33° and 1200 A/cm2 for 15°), but the linearity of light versus current was poorer, the temperature sensitivity of threshold was Jt355/Jt290⩾2, and efficiency also dropped with temperature. The optical distribution has been calculated for various multilayer heterostructure waveguides and related both to the far-field beam width and to the threshold current. A universal gain/current density relation for the active layer has been deduced from the measurements and agrees reasonably with published theory.
Modeling interaction between individuals, social networks and public policy to support public health epidemiology (2009)

Human behavior, social networks, and civil infrastructure are closely intertwined. Understanding their co-evolution is critical for designing public policies. Human behaviors and day-to-day activities of individuals create dense social interactions that provide a perfect fabric for fast disease propagation. Conversely, people's behavior in response to public policies and their perception of the crisis can dramatically alter normally stable social interactions. Effective planning and response strategies must take these complicated interactions into account. The basic problem can be modeled as a coupled co-evolving graph dynamical system and can also be viewed as partially observable Markov decision process. As a way to overcome the computational hurdles, we describe an High Performance Computing oriented computer simulation to study this class of problems. Our method provides a novel way to study the co-evolution of human behavior and disease dynamics in very large, realistic social networks with over 100 Million nodes and 6 Billion edges.
Fast three-step phase-shifting algorithm (2006)

We propose a new three-step phase-shifting algorithm, which is much faster than the traditional three-step algorithm. We achieve the speed advantage by using a simple intensity ratio function to replace the arctangent function in the traditional algorithm. The phase error caused by this new algorithm is compensated for by use of a lookup table. Our experimental results show that both the new algorithm and the traditional algorithm generate similar results, but the new algorithm is 3.4 times faster. By implementing this new algorithm in a high-resolution, real-time three-dimensional shape measurement system, we were able to achieve a measurement speed of 40 frames per second at a resolution of 532 x 500 pixels, all with an ordinary personal computer.
Optimally sparse representation in general (nonorthogonal) dictionaries via ℓ 1 minimization (2003)

Given a dictionary D = {d(k)} of vectors d(k), we seek to represent a signal S as a linear combination S = summation operator(k) gamma(k)d(k), with scalar coefficients gamma(k). In particular, we aim for the sparsest representation possible. In general, this requires a combinatorial optimization process. Previous work considered the special case where D is an overcomplete system consisting of exactly two orthobases and has shown that, under a condition of mutual incoherence of the two bases, and assuming that S has a sufficiently sparse representation, this representation is unique and can be found by solving a convex optimization problem: specifically, minimizing the l(1) norm of the coefficients gamma. In this article, we obtain parallel results in a more general setting, where the dictionary D can arise from two or several bases, frames, or even less structured systems. We sketch three applications: separating linear features from planar ones in 3D data, noncooperative multiuser encoding, and identification of over-complete independent component models.
Co-registration of an Antarctic digital elevation model with SSM/I brightness temperatures (1993)

The Special Sensor Microwave/Imager (SMM/I) instrument provides daily measures of microwave brightness temperatures T b over the polar regions. Data are available from 1987 to the present and have a demonstrated utility for sea-ice studies. In this paper we investigate applications to polar ice sheets with a view towards correlating patterns of T b with ice-sheet elevation. We go on to discuss the T b signature of processes linked to temperature anomalies and accumulation zone boundaries. Our approach consists of combining SSM/I T b values provided on CD-ROM by the National Snow and Ice Data Center (NSIDC) with a digital elevation model (DEM) of Antarctica derived originally from the Scott Polar Research Institute Antarctic Map Folio. We focused on 37 GHz data which is mapped onto a 316 × 332 polar stereographic grid at 25 km resolution. The DEM consists of a 281 × 281 array of elevation values with a 20 km resolution. The DEM was resampled to be compatible with the SSM/I data by transforming the elevation data from the original projection place to geodetic coordinates. The elevation data were than transformed onto the SSM/I projection plane. Elevation data were interpolated to yield ice-sheet surface heights at 25 km intervals coinciding with SSM/I point T b assignments. By co-registering the two data sets, it is possible to “drape” the brightness temperature data over the elevation data. The resulting image highlights the relationship (and variations) between ice-sheet topography and brightness temperature.
Liquid crystal polymer composite films for reconfigurable photomasking applications (2007)

We show proof of concept of a real-time reconfigurable photomask fabricated from holographically formed polymer-dispersed liquid crystal (H-PDLC) reflection gratings on etched indium tin oxide patterned electrodes. H-PDLC films were formed using a thiolene based polymer to have a reflection wavelength that modulates 440nm, the peak sensitivity wavelength of Shipley 1800 series positive photoresist. A working prototype of this adaptable photomask device is shown by comparing patterns formed using the H-PDLC mask and similar patterns formed using a static contact photomask showing that H-PDLC films have the ability to modulate 440nm light and control the exposure dose of photoresist.