gebhart/patrepeval huggingface dataset:
Identification of autoantigens recognized by the 2F5 and 4E10 broadly neutralizing HIV-1 antibodies (2013)

Many human monoclonal antibodies that neutralize multiple clades of HIV-1 are polyreactive and bind avidly to mammalian autoantigens. Indeed, the generation of neutralizing antibodies to the 2F5 and 4E10 epitopes of HIV-1 gp41 in man may be proscribed by immune tolerance because mice expressing the V(H) and V(L) regions of 2F5 have a block in B cell development that is characteristic of central tolerance. This developmental blockade implies the presence of tolerizing autoantigens that are mimicked by the membrane-proximal external region of HIV-1 gp41. We identify human kynureninase (KYNU) and splicing factor 3b subunit 3 (SF3B3) as the primary conserved, vertebrate self-antigens recognized by the 2F5 and 4E10 antibodies, respectively. 2F5 binds the H4 domain of KYNU which contains the complete 2F5 linear epitope (ELDKWA). 4E10 recognizes an epitope of SF3B3 that is strongly dependent on hydrophobic interactions. Opossums carry a rare KYNU H4 domain that abolishes 2F5 binding, but they retain the SF3B3 4E10 epitope. Immunization of opossums with HIV-1 gp140 induced extraordinary titers of serum antibody to the 2F5 ELDKWA epitope but little or nothing to the 4E10 determinant. Identification of structural motifs shared by vertebrates and HIV-1 provides direct evidence that immunological tolerance can impair humoral responses to HIV-1.
Step-by-Step Route for the Synthesis of Metal−Organic Frameworks (2007)

Using a novel layer-by-layer approach we have deposited metal−organic open frameworks (MOFs) based on benzenetricarboxylic acid ligands and Cu(II)-ions on a COOH-terminated organic surface. The deposited layers were characterized using a number of surface analysis techniques. XRD measurements show that the MOFs deposited using this method have the same bulk structure of HKUST-1.
Incorporating Endmember Variability into Spectral Mixture Analysis Through Endmember Bundles (1998)

Variation in canopy structure and biochemistry induces a concomitant variation in the top-of-canopy spectral reflectance of a vegetation type. Hence, the use of a single endmember spectrum to track the fractional abundance of a given vegetation cover in a hyperspectral image may result in fractions with considerable error. One solution to the problem of endmember variability is to increase the number of endmembers used in a spectral mixture analysis of the image. For example, there could be several tree endmembers in the analysis because of differences in leaf area index (LAI) and multiple scatterings between leaves and stems. However, it is often difficult in terms of computer or human interaction time to select more than six or seven endmembers and any non-removable noise, as well as the number of uncorrelated bands in the image, limits the number of endmembers that can be discriminated. Moreover, as endmembers proliferate, their interpretation becomes increasingly difficult and often applications simply need the aerial fractions of a few land cover components which comprise most of the scene. In order to incorporate endmember variability into spectral mixture analysis, we propose representing a landscape component type not with one endmember spectrum but with a set or bundle of spectra, each of which is feasible as the spectrum of an instance of the component (e.g., in the case of a tree component, each spectrum could reasonably be the spectral reflectance of a tree canopy). These endmember bundles can be used with nonlinear optimization algorithms to find upper and lower bounds on endmember fractions. This approach to endmember variability naturally evolved from previous work in deriving endmembers from the data itself by fitting a triangle, tetrahedron or, more generally, a simplex to the data cloud reduced in dimension by a principal component analysis. Conceptually, endmember variability could make it difficult to find a simplex that both surrounds the data cloud and has vertices that are realistic endmember spectra with reflectances between 0 and 1. In this paper, we create endmember bundles and bounding fraction images for an AVIRIS subscene simulated with a plant canopy radiative transfer model. The simulated subscene is spatially patterned after a subscene from the AVIRIS image acquired August, 1993 over La Copita, Texas. In addition, for comparison, we performed a traditional unmixing with image endmembers.
Effects of Polishing Pressure on Electrochemical Characteristics of Silicon Wafers during CMP (2008)

Semiconductor silicon plays a significant role in the microelectronics industry. In this paper, the effects of polishing pressure on electrochemical characteristics of silicon wafers during chemical mechanical polishing (CMP) were investigated by dc polarization and ac impedance techniques. The results revealed that polishing pressure had a strong influence on the electrochemical behavior of silicon wafers. Mechanical abrasion improved the removal of the passivating layer and enhanced the wafer oxidation rate. The corrosion current density and the polishing rate increased sublinearly with applied pressure. Also, the CMP process of silicon wafers can be considered a sequential formation causing film removal, which was confirmed by testing the change with electrochemical impedance spectroscopy.
Validity of Neural Network in Sleep Apnea (1999)

Clinical assessment of obstructive sleep apnea (OSA) is poor. Overnight polysomnography (OPG) is the standard reference test, but it is expensive and time-consuming. We developed an artificial neural network (ANN) using anthropomorphic measurements and clinical information to predict the apnea-hypopnea index (AHI). All patients completed a questionnaire about sleep symptoms, sleep behavior, and demographic information prior to undergoing OPG. Neck circumference, height, and weight were obtained on presentation to the sleep center. Twelve variables were used as inputs. The output was an estimate of the AHI. The network was trained with a back-propagation algorithm on 189 patients and validated prospectively on 80 additional patients. Data from the derivation group was used to calculate the 95% confidence interval of the estimated AHI. Predictive accuracy at different AHI thresholds was assessed by the c-index, which is equivalent to the area under the receiver operator characteristic curve. The c-index for predicting OSA in the validation set was 0.96 +/- 0.0191 SE, 0.951 +/- 0.0203 SE, and 0.935 +/- 0.0274 SE, using thresholds of > 10, > 15, and > 20/hour respectively. The actual AHI of the 80 patients in the validation data set fell within the 95% confidence limits of the values predicted by the ANN. This study suggests that ANN may be useful as a predictive tool for OSA.
High speed, zero—bias modulation of low threshold MQW laser diodes (1989)

Abstract In realizing high‐speed and very dense opto‐electronic integrated circuits with optical connecting inside and between the LSI chips, investigations are made on how to avoid the need for output power stabilizing and biasing circuitry of present semiconductor lasers. If it becomes possible to reduce sufficiently the threshold current of semiconductor lasers, in comparison to the driving current, its output stability against temperature variations improves and the delay time to switch it on can be reduced even at zero bias pulse driving. Using a GaAs/GaAlAs multiquantum well laser with threshold current of 4 mA, high—speed, zero‐bias and output control—free modulation experiments were performed. The requirement in optical communication systems for the output power variations to be less than ±0.5 dB was satisfied because for the temperature range of 0 – 50°C and at 20 mA driving current, the variations were limited to +0.45 –0.45 dB. At zero biasing the switch on delay of 150 ps was realized at pulse current of 34 mA with sufficiently good response to a 1 Gbps NRZ signal. The spectrum showed stable longitudinal multimode oscillation, and from its poor coherency, it was expected that stability against the returning light would be good. It is believed that obstacles in development of opto‐electronic circuits can be removed using semiconductor lasers with threshold current of a few milliamps.
Printability and actinic AIMS review of programmed mask blank defects (2017)

We report on the printability, mitigation and actinic mask level review of programmed substrate blank pit and bump defects in a EUV lithography test mask. We show the wafer printing behavior of these defects exposed with an NXE:3300 EUV lithography scanner and the corresponding mask level actinic review using the AIMS<sup>TM</sup> tool. We will show which categories of these blank substrate defects print on wafer and how they can be mitigated by hiding these defects under absorber lines. Furthermore we show that actinic AIMS<sup>TM</sup> mask review images of these defects, in combination with a simple thresholded resist transfer model, can accurately predict their wafer printing profiles. We also compare mask level actinic AIMS<sup>TM</sup> to top down mask SEM review in their ability to detect these defects.
A New Planar Artificial Transmission Line and Its Applications to a Miniaturized Butler Matrix (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> A miniaturized quadrature hybrid coupler, a rat-race coupler, and a 4 <formula><tex>$\times$</tex></formula> 4 Butler matrix based on a newly proposed planar artificial transmission line are presented in this paper for application in ultra-high-frequency (UHF) radio-frequency identification (RFID) systems. This planar artificial transmission line is composed of microstrip quasi-lumped elements and their discontinuities and is capable of synthesizing microstrip lines with various characteristic impedances and electrical lengths. At the center frequency of the UHF RFID system, the occupied sizes of the proposed quadrature hybrid and rat-race couplers are merely 27% and 9% of those of the conventional designs. The miniaturized couplers demonstrate well-behaved wideband responses with no spurious harmonics up to two octaves. The measured results reveal excellent agreement with the simulations. Additionally, a 4<formula formulatype="inline"><tex>$\,\times\,$</tex></formula>4 Butler matrix, which may occupy a large amount of circuit area in conventional designs, has been successfully miniaturized with the help of the proposed artificial transmission line. The circuit size of the Butler matrix is merely 21% of that of a conventional design. The experimental results show that the proposed Butler matrix features good phase control, nearly equal power splitting, and compact size and is therefore applicable to the reader modules in various RFID systems. </para>
Abstract 3777: The role of IFITMs in maintaining glioma stem cells (2020)

Abstract Glioblastoma (GBM), one of the most lethal and heterogeneous primary brain tumors, contains cellular hierarchies with both quiescent and self-renewing highly tumorigenic glioblastoma stem cells (GSCs). Cancer stem cells within the context of the brain likely contribute to a lack of progress in patient survival time as they appear to have an innate resistance to both chemotherapeutic drugs and radiotherapy. The aim of this study is to elucidate how constitutive expression of interferons (IFNs) and their downstream signalling pathways maintain GSCs thereby supporting treatment resistance and tumor reoccurrence. To understand the mechanism of action of a subset of IFN regulated genes, originally characterized as a signature for radiation and chemotherapy resistance (IRDS), a panel of patient derived glioma stem cells was generated and manipulated using CRISPR/Cas9 mediated gene-editing. Phenotypic changes in growth, viability and drug resistance were characterised in the edited cells and linked to molecular level events using transcriptomic and proteomic techniques. Using this approach, in conjunction with patient tissue analysis, signalling under basal as well as IFN-activated conditions was studied in the context of GSC status. Immunohistopathology of a glioma tissue micro-array identified an increased expression of IFN induced transmembrane receptors (IFITMs), which co-localised with Nestin, around the blood vessels suggesting that IFITM positive cells were in the stem cell niche. Further analysis showed the presence of both IFITM1 and IFITM3 in GSCs and established that loss of IFITM function impacted on growth rate and cell cycle progression as well as treatment sensitivity. By using wild-type and gene-edited GSC to focus on the relationship between IFITM1 and IFITM3, we have compelling phenotypic and molecular evidence that IFN-induced changes in the localisation of IFITMs impact on the ability of stem cells to ‘escape' normal growth control mechanisms. Taking into consideration the constitutive expression of interferons in the tumor microenvironment, our study provides evidence that IFITMs regulate glioma stem cell self-renewal and are involved in maintaining a quiescent population which can escape chemotherapy. Citation Format: Erisa Nita, Bernard Evers, Marta Nekulova, Gillian Morrison, Kathryn Ball. The role of IFITMs in maintaining glioma stem cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3777.
Common circuit defect of excitatory-inhibitory balance in mouse models of autism (2009)

The online version of this article (doi:10.1007/s11689-009-9023-x) contains supplementary material, which is available to authorized users.
If Orchids Mycorrhizal Fungi Are So Specific, How Do Natural Hybrids Cope? (2005)

The genus Caladenia (spider orchids) is one of the most diverse in southwest Western Aus- tralia, and Caladenia species have among the most specific mycorrhizal relationships known in the orchid family. Caladenia species, however, also hybridize frequently and prolifically in nature. This study consid- ered five natural hybrids within Caladenia and its closest relatives to elucidate the issue of mycorrhizal specificity in the hybrids and their parental species. Symbiotic cross-germination studies of parental and hybrid seed on fungi from the species and the naturally occurring hybrids were compared with data from genetic fingerprinting (amplified fragment length polymorphism, AFLP) studies of the fungi. The germi- nation study found that, while hybrid seeds can utilize the fungi from either parental species under labo- ratory conditions, it is likely that the natural hybrids in-situ share the fungus of one parent only. In contrast, the genetic analysis indicated that while the parental species always possessed genetically distinct fungal strains, the hybrids may share the mycorrhizal fungus of one parental species or possess a genetically distinct fungal strain, which is more closely related to the fungus of one parental species than the other. These findings confirm the specificity of mycorrhizal relationships in Caladenia and suggest the potential of hybridization and the utilization of novel fungi as a possible pathway to speciation.
Quantum cascade laser based tetrafluoromethane and nitrogen oxide measurements for emission monitoring applications (2014)

Mid-infrared measurements of tetrafluoromethane at ambient temperature and nitric oxide at elevated temperatures have been performed using continuous-wave room-temperature quantum cascade lasers and second harmonic detection.
Short-term therapy for acute myelogenous leukemia. (1988)

Since 1978, 187 patients (age range, 15 to 59, median 44 years) have received short-term chemotherapy as part of three sequential open studies (B-IX, X, Xb) or a randomized clinical trial (B-XI). An intended six cycles of Adriamycin (ADR) (doxorubicin; Adria Laboratories, Columbus, OH), cytarabine (ara-C), and thioguanine (TG) were administered with as short an intercycle time as possible. No further therapy was administered. Complete remission (CR) was achieved in 118 of 187 patients (63%). On univariate and multivariate analyses achievement of CR correlated adversely with a low serum albumin at presentation and an antecedent marrow disorder. Forty-five patients continue in first remission between 15 months and 8 1/2 years, no relapses being seen after 3 1/2 years (median follow-up, 3 1/2 years). The median duration of remission was 1 year. M3 morphology, a blast count less than 100 x 10(9)/L, and absence of hepatosplenomegaly correlated favorably with remission duration. There was no difference in duration of remission between patients receiving 3, 4, 5, or 6 cycles. The best results overall were achieved in patients under the age of 40, with 43% projected to remain free of disease at 5 years. Fifty patients remain alive between 17 months and 9 years, the predicted actuarial survival being 25% at 5 years.
Systems analysis reveals a transcriptional reversal of the mesenchymal phenotype induced by SNAIL-inhibitor GN-25 (2013)

Our systems and network investigations provide convincing pre-clinical evidence in support of the clinical application of GN-25 for the reversal of EMT and thereby reducing cancer cell aggressiveness.
Mutation Effects on Remote Epitopes of An Autoantigen Decoded with Simulated B-Factors (2019)

Proteinase 3 (PR3) is a neutrophil serine protease targeted by anti-neutrophil cytoplasmic antibodies (ANCAs) in the autoimmune disease granulomatosis with polyangiitis (GPA) 1–5 . PR3 mutants were developed to investigate how PR3 interacts with the ANCAs and whether the interactions can be intervened by therapeutics. One mutant with a Ser195Ala mutation (iPR3-Val 103 ) recognized as many ANCAs as wild-type PR3 (PR3-Val 103 ) 6–9 , indicating that PR3-Val 103 and iPR3-Val 103 have equivalent ANCA-binding capabilities. A triple mutant of the latter (iHm5-Val 103 ) bound a monoclonal antibody (moANCA518) from a patient with GPA on an epitope remote from the mutation sites. Unexpectedly, the corresponding epitope of iPR3-Val 103 was inaccessible to moANCA518 under the same experimental conditions 10,11 . These observations demonstrate that a latent epitope of PR3 can be activated surprisingly by remote mutations in PR3 11 . Here we report a comparative analysis of simulated B-factors (i.e., measurements of local mobility) of PR3-Val 103 , iPR3-Val 103 , and iHm5-Val 103 , demonstrating that the binding of moANCA518 to iHm5-Val 103 is enabled by an increase in main-chain flexibility in the latent epitope caused by the remote muta-tions in iHm5-Val 103 . This epitope activation—achieved in vitro by remote mutations as we demonstrated or in vivo conceivably by remote protein»protein interactions 12 or remote po-lymorphisms—may be a fundamental feature of antibody-mediated autoimmune diseases. Rigidifying B-cell epitopes on an autoantigen with therapeutics designed using the B-factor analysis disclosed here may lead to effective treatments for these autoimmune diseases by making the autoantigen inaccessible to existing autoantibodies. This analysis may also be used to predict and characterize epitopes and remote mutation effects.
Toward Bicelle Stability with Ether-Linked Phospholipids:  Temperature, Composition, and Hydration Diagrams by2H and31P Solid-State NMR (2005)

Phosphorus and deuterium wide line NMR was used to determine diagrams of binary mixtures of 1,2-di-O-tetradecyl-sn-glycero-3-phosphocholine (DIOMPC) and 1,2-di-O-hexyl-sn-glycero-3-phosphocholine (DIOHPC) ether-phospholipids. By varying the hydration, h, the temperature, T, and the mole fraction, X, of long-chain ether-phospholipids, we delineated the conditions for which such systems are oriented by the magnetic field, in the presence of 100 mM KCl. The 3D domain is found for X = 62-90%, T = 27-50 degrees C, and h = 70-98%. At 80% hydration, the domain shape (X = 70-90% and T = 27-42 degrees C) is close to that already observed for ester-phospholipids mixtures (Raffard, G.; Steinbruckner, S.; Arnold, A.; Davis, J. H.; Dufourc, E. J. Langmuir 2000, 16, 7655-7662) where disc-shaped bicelles of 300-600 A have been found by electron microscopy (Arnold, A.; Labrot, T.; Oda, R.; Dufourc, E. J. Biophys. J. 2002, 83, 2667-2680). Systems made of ether-linked lipids are much more stable on time and acidic conditions than those made of ester lipids. Assuming that the disc-shaped species are also found with ether lipids, their diameter as determined from integration of phosphorus NMR lines ranges from 240 to 440 A +/- 10%; it is generally independent of hydration and temperature but decreases with decreasing long-chain lipid content, X. The structure and the dynamics of water in the DIOMPC-DIOHPC were characterized by (2)H NMR. Water exchanges between the membrane surface where it is bound and a bulk isotropic pool lead to an average ordered state for temperatures in the bicelle region and above, thus offering a larger thermal span for structural studies of dissolved molecules.
Running Biomechanics Before Injury and 1 Year After Anterior Cruciate Ligament Reconstruction in Division I Collegiate Athletes (2021)

After ACLR, surgical limb knee running biomechanics were not restored to the preinjury state by 12M, while nonsurgical limb mechanics remained unchanged as compared with preinjury. Collegiate athletes after ACLR demonstrate substantial deficits in running mechanics as compared with preinjury that persist beyond the typical return-to-sport time frame. The nonsurgical knee appears to be a valid reference for recovery of the surgical knee mechanics during running, owing to the lack of change within the nonsurgical limb.
Neuromechanics of Coordination during Swallowing inAplysia californica (2006)

Bernstein (1967) hypothesized that preparation of the periphery was crucial for correct responses to motor output. To test this hypothesis in a behaving animal, we examined the roles of two identified motor neurons, B7 and B8, which contribute to feeding behavior in the marine mollusk Aplysia californica. Neuron B7 innervates a hinge muscle and has no overt behavioral effect during smaller-amplitude (type A) swallows, because the hinge muscle is too short to exert force. Neuron B8 activates a muscle (I4) that acts solely to grasp material during type A swallows. During larger-amplitude (type B) swallows, the behavioral actions of both motor neurons change, because the larger-amplitude anterior movement of the grasper sets up the periphery to respond differently to motor outputs. The larger anterior movement stretches the hinge muscle, so that activating neuron B7 mediates the initial retraction phase of swallowing. The changed position of the I4 muscle allows neuron B8 not only to induce grasping but also to pull material into the buccal cavity, contributing to retraction. Thus, larger-amplitude swallows are associated with the expression of two new degrees of freedom (use of the hinge to retract and use of the grasper to retract) that are essential for mediating type B swallows. These results provide a direct demonstration of Bernstein's hypothesis that properly positioning the periphery can be crucial for its ability to correctly respond to motor output and also demonstrate that biomechanical context can alter the functions of identified motor neurons.