gebhart/patrepeval huggingface dataset:
Supplementary Table 4 from LY2606368 Causes Replication Catastrophe and Antitumor Effects through CHK1-Dependent Mechanisms (2023)

&lt;p&gt;Supplementary Table S4. LY2606368-dependent chromosome fragmentation is not caused by caspase-dependent apoptosis&lt;/p&gt;
Finding anomalies in time-series using visual correlation for interactive root cause analysis (2013)

Monitoring computer networks often includes gathering vast amounts of time-series data from thousands of computer systems and network devices. Threshold alerting is easy to accomplish with state-of-the-art technologies. However, to find correlations and similar behaviors between the different devices is challenging. We developed a visual analytics application to tackle this challenge by integrating similarity models and analytics combined with well-known, but task-adapted, time-series visualizations. We show in a case study, how this system can be used to visually identify correlations and anomalies in large data sets and identify and investigate security-related events.
515. Targeting Hypoglycosylation with a Chimeric Antigen Receptor (2015)

Genetically-engineering human T cells to target endogenously-expressed cell markers associated with both normal and malignant cells, whether upregulated or not, has shown tremendous efficacy in targeting CD 19-expressing leukemia and lymphoma cells and will undoubtedly demonstrate promise in other hematological malignancies. However, many of the tumor-associated antigens in epithelial malignancies are upregulated in malignant tissue but also expressed at lower-levels in normal tissue. As observed by the targeting of Her2 with CAR-T cells, targeting these antigens can present on-target, off-site toxicity and emphasizes the need for cancer cell-specific epitopes in CAR T cell therapy. Here, we have taken advantage of the disrupted glycosylation program that occurs during cancer transformation, which exposes cancer-specific glycoantigens that can be attractive targets for CAR development. Mucin-1 (Muc1) is a tumor-associated oncogene that is highly upregulated in many cancers and has been the target of many vaccine studies; less frequently targeted are the glycosylation changes of Muc1 that occurs during cancer transformation. Muc1 is heavily O- and N-glycosylated and transformed cells often fail to construct the complex oligosaccharide chains, exposing hypoglycosylated epitopes such as an O-linked GalNac (Tn antigen). We developed a CAR using the scFv sequence derived from the 5E5 mAb, which was developed against the Tn antigen of Mucin-1 (Muc1), and also using the endodomains of CD3zeta and 4- 1BB that promote T cell activation and co-stimulation, respectively. The resultant Muc1 Tn-antigen specific CAR (5E5CAR) was expressed in a lentiviral vector and we transduced normal human T cells. We showed that the 5E5 mAb and the 5E5CAR are specific to the hypoglycosylated epitope of Muc1, but not normal Muc1. In addition, we developed a safety profile of the 5E5 mAb against normal pediatric and adult human tissue. We demonstrate that human T cells expressing the 5E5CAR rapidly clear established Jurkat and Hs766T tumors in vitro and in NSG mouse xenograft models, as assessed by serial bioluminescence imaging and prolonged survival compared to mice expressing control CD19-specific CAR T cells (P<0.005). Restoring expression of wildtype Cosmc in Jurkat T cells abolishes the expression of the hypoglycosylated form of Muc1 and also abrogrates the cytotoxicity exhibited by 5E5CAR T cells, further highlighting the specificity of the 5E5CAR for the O-linked GalNac. In addition to the T cell leukemia and pancreatic cancer xenograft models, we also demonstrate that the 5E5CAR T cells are responsive to ovarian, breast, and lung cancers, among others. These results demonstrate that the 5E5CAR is specific for the Muc1 Tn antigen and provides a potent and safe cancer-specific immunotherapy for the targeting of malignancies.
Quantitative Ultramorphological Evaluation of Swim-Up Spermatozoa Used in Human in Vitro Fertilization and Transcervical Intrauterine Insemination (1986)

Ultramorphological changes that occur on the sperm head during in vitro incubation of human spermatozoa was investigated using transmission electron microscopy (TEM). Motile spermatozoa that swim-up were processed for TEM. Washed but unincubated sperm heads had all of the fine structural characteristics of normal spermatozoa: intact plasma membrane, acrosome, equatorial segment, postacrosomal sheath, subacrosomal space filled with fine granular material, dense nucleus containing conspicuous nuclear vacuoles of differing sizes and numbers, and faintly discernible nuclear membrane. The procedure of washing and centrifugation did not alter the structural integrity of spermatozoa. Any evidence of ultramorphological changes in the incubated spermatozoa appeared to be confined to the surface of the anterior two-thirds of the sperm head. These changes were characterized by detachment of plasma membrane, fusion of plasma and acrosomal membranes, vesiculation of membranes, and exposure of acrosomal contents. There was a significant (p less than 0.001) time-dependent increase in the proportion of spermatozoa with such changes. The anterior border of these denuded sperm heads were bound only by the acrosome that appeared as electron-dense granular material on the outer margin and attached on its inner border to the inner acrosomal membrane. Furthermore, in vitro incubation of washed spermatozoa did not lead to any time-dependent degenerative changes.
Deep Brain Stimulation of the Pallidofugal Pathways to Rescue Severe Life-Threatening Dyskinesias after STN-DBS Lead Implantation (2021)

We present a patient with severe life-threatening dyskinesias due to a persistent microlesion effect after STN-DBS electrode implantation. The pallidofugal pathways were identified using patient-specific tractography, and steering the current toward this white matter structure resulted in complete resolution of the severe dyskinesias.
Retention of Coiled-Coil Dimer Formation in the Absence of Ion Pairing at Positions Flanking the Hydrophobic Core (2019)

Hydrophobic interactions govern how proteins fold and interact with other molecules, but the impact of nearby polar functionality on the effective hydrophobicity of nonpolar surfaces remains unclear. Here we use a common protein quaternary structure motif, the parallel coiled-coil dimer, to ask whether the identity of basic residues (arginine vs lysine; guanidinium vs ammonium) arrayed along one side of the constituent α-helices influences the favorability of dimerization driven by burial of hydrophobic surface on the other side of each helix. Significant sequence redesign was necessary to achieve the desired juxtaposition of nonpolar and cationic functionality, because we needed to eliminate charged side chains from positions flanking the nonpolar helix surface. Natural and designed sequences that form coiled coils are almost universally rich in acidic and basic residues at these flanking positions. Our arginine coiled-coil dimer was moderately more stable than the lysine analogue, which contrasts with behavior previously observed with helical β-amino acid oligomers bearing guanidinium versus ammonium groups. We attribute this backbone-dependent difference to variations in the extent to which the helical propensities of α- and β-residues can be modulated by design. These findings highlight the challenge of identifying noncovalent forces that direct structure formed by a flexible backbone.
Spatial Distribution of Spray Deposition from an Air-Carrier Sprayer (1989)

ABSTRACT An air-carrier, orchard sprayer was modified by segmenting the nozzle manifolds on each side into three sub-manifolds. Each sub-manifold represented the top, middle or bottom portion of the sprayer outlet. Spray deposition from each sub-manifold was quantified using water sensitive cards placed on vertical poles. Tests were conducted in both the presence and absence of tree foliage. The presence of tree foliage was found to substantially alter the deposition patterns from those found in the non-foliage tests. Overall, greatest spray deposition was achieved by the bottom manifold. At locations greater than 1.5 m outward from the sprayer and below 2 m in height, spray deposition from the top manifold was extremely poor.
Alcohol Testing (2007)

Ethanol, commonly also referred to as alcohol, is widely used as well as abused, and measurement of alcohol is a common test in clinical toxicology and forensic laboratories. Although blood alcohol measurement is most commonly used, alcohol can also be measured in breath, urine, saliva and vitreous humor. Whole blood alcohol levels are lower than serum alcohol levels, and the value depends on the hematocrit. Although enzymatic assays based on capability of alcohol dehydrogenase to convert alcohol to acetaldehyde is widely used for rapid determination of serum or plasma alcohol concentrations, values may be elevated in postmortem serum as well as in patients with highly elevated lactate and lactate dehydrogenase level in blood. Gas chromatographic methods widely used for determination of forensic alcohol are considered as the reference method, and there are also few reports of using gas chromatography combined with mass spectrometry for determination of alcohol concentrations in biological matrix.
Photonic bandgap disk laser (1999)

A two-dimensional photonic crystal defined hexagonal disk laser which relies on Bragg reflection rather than the total internal reflection as in traditional microdisk lasers is described. The devices are fabricated using a selective etch to form free standing membranes suspended in air. Room temperature lasing at 1650 nm for a 150 nm thick, ~15 µm wide cavity fabricated in InP/InGaAsP is demonstrated with pulsed optical pumping.
Effects of Intranasal Administration of a Leptin-Secreting Lactococcus lactis Recombinant on Food Intake, Body Weight, and Immune Response of Mice (2007)

Leptin is an adipocyte-derived pleiotropic hormone that modulates a large number of physiological functions, including control of body weight and regulation of the immune system. In this work, we show that a recombinant strain of the food-grade lactic acid bacterium Lactococcus lactis (LL-lep) can produce and efficiently secrete human leptin. The secreted leptin is a fully biologically active hormone, as demonstrated by its capacity to stimulate a STAT3 reporter gene in HEK293 cells transfected with the Ob-Rb leptin receptor. The immunomodulatory activity of leptin-secreting L. lactis was evaluated in vivo by coexpression with the human papillomavirus type 16 E7 protein. In C57BL/6 mice immunized intranasally with a recombinant L. lactis strain coproducing leptin and E7 antigen, the adaptive immune response was significantly higher than in mice immunized with recombinant L. lactis producing only E7 antigen, demonstrating adjuvanticity of leptin. We then analyzed the effects of intranasally administered LL-lep in obese ob/ob mice. We observed that daily administration of LL-lep to these mice significantly reduced body weight gain and food intake. These results demonstrate that leptin can be produced and secreted in an active form by L. lactis and that leptin-producing L. lactis regulates in vivo antigen-specific immune responses, as well as body weight and food consumption.
Mid-Infrared Broadband Modulation Instability and 50 dB Raman Assisted Parametric Gain in Silicon Photonic Wires (2011)

We demonstrate broadband modulation instability, &gt; 40 dB parametric amplification with on-chip gain bandwidth &gt; 580 nm, and narrowband Raman-assisted peak on-chip gain exceeding 50 dB, using mid-infrared dispersion-engineered silicon nanophotonic wires.
Hippocampal CA1 gamma power predicts the precision of spatial memory judgments (2018)

The hippocampus plays a critical role in spatial memory. However, the exact neural mechanisms underlying high-fidelity spatial memory representations are unknown. We report findings from presurgical epilepsy patients with bilateral hippocampal depth electrodes performing an object-location memory task that provided a broad range of spatial memory precision. During encoding, patients were shown a series of objects along the circumference of an invisible circle. At test, the same objects were shown at the top of the circle (0°), and patients used a dial to move the object to its location shown during encoding. Angular error between the correct location and the indicated location was recorded as a continuous measure of performance. By registering pre- and postimplantation MRI scans, we were able to localize the electrodes to specific hippocampal subfields. We found a correlation between increased gamma power, thought to reflect local excitatory activity, and the precision of spatial memory retrieval in hippocampal CA1 electrodes. Additionally, we found a similar relationship between gamma power and memory precision in the dorsolateral prefrontal cortex and a directional relationship between activity in this region and in the CA1, suggesting that the dorsolateral prefrontal cortex is involved in postretrieval processing. These results indicate that local processing in hippocampal CA1 and dorsolateral prefrontal cortex supports high-fidelity spatial memory representations.
Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae (2004)

Taken together, this study examines the function and capacity of yeast's metabolic machinery and shows that the phenotypic phase plane can be used to accurately predict metabolic phenotypes and to interpret experimental data in the context of a genome-scale model.
Complete 360° circumferential SSOCT gonioscopy of the iridocorneal angle (2014)

The ocular iridocorneal angle is generally an optically inaccessible area when viewed directly through the cornea due to the high angle of incidence required and the large index of refraction difference between air and cornea (<i>n</i><sub><i>air</i></sub> = 1.000 and <i>n</i><sub><i>cornea</i></sub> = 1.376) resulting in total internal reflection. Gonioscopy allows for viewing of the angle by removing the aircornea interface through the use of a special contact lens on the eye. Gonioscopy is used clinically to visualize the angle directly but only en face. Optical coherence tomography (OCT) has been used to image the angle and deeper structures via an external approach. Typically, this imaging technique is performed by utilizing a conventional anterior segment OCT scanning system. However, instead of imaging the apex of the cornea, either the scanner or the subject is tilted such that the corneoscleral limbus is orthogonal to the optical axis of the scanner requiring multiple volumes to obtain complete circumferential coverage of the ocular angle. We developed a novel gonioscopic OCT (GOCT) system that images the entire ocular angle within a single volume via an “internal” approach through the use of a custom radially symmetric gonioscopic contact lens. We present, to our knowledge, the first complete 360&deg; circumferential volumes of the iridocorneal angle from a direct, internal approach.
Strength and Fracture of a Multifunctional Polystyrene Nanocomposite (2006)

A polystyrene polymer has been reinforced with single wall carbon nanotubes (SWNTs) to effect multifunctional capabilities. The SWNTs are produced by the HipCo process and are subsequently dispersed in the polystyrene resin matrix. The dispersion of the SWNTs in the polystyrene is enhanced by the use of a surfactant and composite samples at 0.0%, 0.1%, 0.2% 0.3% and 1.0% SWNT by weight are made. A multifunctional material is defined as a material with at least one additional property other than mechanical properties, and the desire is that the mechanical properties are not deteriorated due to the added nano-constituents. In this study SWNT reinforced polystyrene nano-composites are evaluated for their electrical conductivity as a function of SWNT weight percentage. The reinforced polystyrene nanocomposites are then evaluated for static strength, ductility and fracture properties to determine the effect of the nano-constituents on these mechanical properties.
Ferroelectric switching in the tilted smectic phases OF R-(-)-4-n-Hexyloxybenzylidene 4'-AMINO-(2-Chloropropyl)cinnamate (HOBACPC) (1984)

The ferroelectric switching behavior of the chiral smectic C*, smectic I* and the non-chiral smectic J* phases has been investigated in the material R-(-)-4-n-hexyloxybenzylidene 4'-amino-(2-chloropropyl)cin-namate (HOBACPC). The C* and I* phases were shown to exhibit bistability in cells of less than 5 μm thickness, but at greater thicknesses the two switched states relax in a finite time. However, in the smectic J* phase which unlike the C* and I* phases does not possess a helical structure, true bistable switching was obtained in cells of up to 33 μm thickness. Furthermore, in cells where the glass plate separation was greater than 12 μm four stable states were obtained. These may correspond to the different tilted orientations of the molecules in the hexagonally close-packed structure of the phase.
Supplementary Table S1 from Paternally Expressed Gene 10 (PEG10) Promotes Growth, Invasion, and Survival of Bladder Cancer (2023)

&lt;p&gt;Primary antibodies used in this study&lt;/p&gt;
Geräte- und transducerunabhängige 3D-Sonographie im Mund-Kiefer-Gesichtsbereich* (2008)

The method of 3D reconstruction of standard two-dimensional electronic scans, as presented here, is the first method of its kind enabling applicability in daily clinical routine thanks to rapid imaging. The images can be produced with any ultrasound unit or transducer. First clinical results in maxillofacial surgery clearly show improved diagnostic possibilities although there still room for an improvement of the image quality. The possibility of semi-automatic exact volumetry appears meaningful especially in the investigation of lymph nodes. Integration of colour duplex sonography will further enhance the diagnostic value of this method.
Hybrid MoS2+x Nanosheet/Nanocarbon Heterostructures for Lithium-Ion Batteries (2022)

Modulation of electron/ion transport in electrodes through the appropriate mesoscale electrode structural design is essential to achieving effective utilization of nanoscale electroactive materials. Herein, nanosheet MoS2+x/carbon [one-dimensional (1D) carbon nanotube (CNT) or two-dimensional (2D) graphene nanoplatelet (GNP)] heterostructures are prepared via a simple, one-step hydrothermal method, resulting in high-loading (16.2–21.0 mg/cm2) binder-free three-dimensional (3D) porous electrodes. In lithium-based batteries, an anionic S22––S2– redox system is demonstrated based on combined structural characterization using X-ray photoelectron spectroscopy, Raman spectroscopy, and in situ synchrotron-based X-ray absorption spectroscopy to elucidate the electrochemical behavior of the Mo and S centers. MoS2+x-GNP electrodes delivered 177 mAh/g (2.9 mAh/cm2) in the first cycle and 78 mAh/g (1.3 mAh/cm2) after 100 cycles at a current of 3.2 mA/cm2, representing high capacities despite such a high material loading for a sulfur-equivalent system, with 44% capacity retention and good rate capability. Conversely, the MoS2+x-CNT heterostructure displayed lower capacity and more capacity fade at all rates, attributed to aggregation of the active and carbonaceous materials in these electrodes and poor access to MoS2+x edge sites, as visualized via 3D Raman mapping and electron microscopy. The significantly improved capacity retention of the MoS2+x-GNP system is attributed to the (i) morphology because the arrangement of the 2D MoS2+x nanosheets on the GNP substrate allows for edge sites with excess sulfur to be exposed, (ii) increased stability of the structure during cycling, and (iii) homogeneous dispersion of the active and carbonaceous materials, resulting in good electrical contact.
Ideal Space Focusing in a Time-of-Flight Mass Spectrometer: An Optimization Using an Analytical Approach (2000)

An exact, analytical solution for an electric field in a nonlinear acceleration region of an ion source for the cases of linear and reflectron time-of-flight (TOF) mass spectrometers has been found to achieve universal temporal focusing of ions having an initial space distribution. The general solutions are valid for an arbitrary electric field distribution in the drift region (from the ion source to an ion detector) of a linear TOF mass spectrometer, and in the upstream (from the ion source to the reflectron) and downstream (from the reflectron to an ion detector) regions of a reflectron TOF instrument. This may include, for example, electrostatic lenses commonly used after an ion source for angular focusing of ions onto the detector to increase the instrument sensitivity and additional acceleration of ions before their detection. Using analytical expressions obtained for an arbitrary case, convenient working formulae are derived for the widely used single- and dual-stage ion extraction schemes in the cases of linear and reflectron TOF mass spectrometers. The formulae are used in optimizing the TOF mass spectrometer design by decreasing the curvature of the nonlinear acceleration potential in the ion source. The relationship has been shown between the conditions for an ideal space focusing using an optimized curved extraction field and a finite-order space-focusing using a linear extraction field in an ion source. The results obtained are especially useful for designing miniature TOF mass spectrometers or instruments with large volume ion sources.
Preoperative Warming Up Exercises Improve Laparoscopic Operative Times in an Experienced Laparoscopic Surgeon (2011)

Performing warm-up exercises before complex laparoscopic surgery may improve operative times and performance in the operating room, especially for complex laparoscopic surgeries.
Electric Characteristics of Diamond Film Synthesized by Combustion Flame (Effect of Synthesis Condition on Electrical Resistivity) (2008)

The purpose of this research was to clarify the electric characteristics of diamond film synthesized by combustion flame and to synthesize a suitable diamond film for use in electronic device applications. When the film contains amorphous carbon, the electrical resistivity (volume resistivity) decreases, i.e., the electric characteristics of the diamond film become worse. To decrease the content of amorphous carbon in the diamond film we utilized two methods, the detection of the optimal equivalence ratio and the optimal substrate temperature. These methods can decrease the amount of amorphous carbon effectively, thus systematically changing the factors influencing the optimal synthesis for improving the film's electric characteristics. We have successfully developed a method for producing high-quality diamond film with excellent electric characteristics, which has high electrical resistivity (1010-1013Ω·m) at room temperature.
Electrophilic bromination of bicyclo[3.2.0]hept-2-en-6-ones (1975)

Bromination of bicyclo[3.2.0]hept-2-en-6-one (3) and 7,7-dimethylbicyclo[3.2.0]hept-2-en-6-one (2) in a variety of solvents gave high yields of the corresponding 2-exo-bromo-3-endo-substituted bicycloheptanones. The configurations of the products were deduced from n.m.r. spectra. The observed stereospecificity of the reaction is due to the preferential formation of the intermediate bromonium ion on the exo-face of the cyclopentene ring. 7-Chlorobicyclo[3.2.0]hept-2-en-6-ones (1) and (4) gave mixtures of the corresponding 2,3-disubstituted bicycloheptenones and 3,8-disubstituted 2-oxatricyclo[3.2.1.03,6]octanones when brominated in solvents capable of addition across the activated carbonyl group. Spectral evidence suggests that the 3-endo- and 7-endo-substituents determine the preferred conformation of the bicycloheptanones.