gebhart/patrepeval huggingface dataset:
Hemolymph Proteins: Origin And Developmental Changes In The Last Larval Instar Of Calpodes Ethlius (lepidoptera: Hesperiidae) (1987)

Sheets of dorsal abdominal integument, ligated tubes of midgut, sheets of fat body and suspended hemocytes from mid fifth instar larvae of Calpodes ethlius (Lepidoptera: Hesperiidae) were incubated in artificial hemolymph in the presence of ({dollar}\\sp{lcub}35{rcub}{dollar}S) methionine to investigate protein synthesis and secretion. Epidermis secretes at least 13 polypeptides basally and 15 apically. Four basally secreted polypeptides were identified in the hemolymph labelled in vivo. Midgut secretes at least eight polypeptides basally and seven apically. Two basally secreted polypeptides were similar to those in the hemolymph. Fat body releases more than 14 polypeptides into the incubation medium and 12 of which are found in the hemolymph. Hemocytes secrete 11 polypeptides and seven of which could be identified in the hemolymph.;Antibodies made against hemolymph proteins recognized five epidermal, eight midgut, ten fat body and six hemocyte secretory polypeptides indicating that these four tissues contribute at least 29 polypeptides to the hemolymph protein pool. Arylphorin (Ar) is the major hemolymph protein secreted by all four tissues. Arylphorin synthesized and secreted in vitro by all four tissues has been identified through its precipitation with antibodies made against hemolymph Ar.;Fifth stage Calpodes larvae have three major hemolymph proteins SP1 (720 K), SP2 (580 K) and Ar (470 K). The 470 K protein is identified as Ar because it is rich in aromatic amino acids. Electron microscopy of negatively stained preparations show that each polymer has a different geometrical arrangement of subunits. SP1 is a cube made from eight subunits. SP2 is a hexamer in the form of a pentahedral prism. Ar is probably an octahedron made from six subunits.;Forty six hemolymph polypeptides are stage specific in addition to ten polypeptides that are present throughout the fourth, fifth stage larval and pupal hemolymph. Each growth phase is characterized by the presence of many minor polypeptides that are either absent at all other times or present during only one other phase. Some of the most abundant polypeptides also change with development. Ar is present from early in the stadium and continues into the pupa. SP1 is synthesized from 66 hr and SP2 appears two days later. Both storage proteins start to disappear at the beginning of pupation and are absent in the pupa.
Magnetically Induced Superresolution Magneto-Optical Disk Using an In-Plane Magnetization Mask Layer. (1997)

A high-density magneto-optical disk was realized through the use of center aperture detection (CAD), a magnetically induced superresolution (MSR) readout method, employing the magnetostatic coupling force. In this investigation, an in-plane magnetization mask layer having a low Curie temperature was formed over the readout layer of CAD. The in-plane magnetization mask of the readout layer was strengthened by the exchange coupling force between the readout layer and the in-plane magnetization mask layer. The use of the latter layer made it possible to obtain higher resolution.
Radical [1,3] Rearrangements of Breslow Intermediates (2015)

Abstract Breslow intermediates that bear radical‐stabilizing N substituents, such as benzyl, cinnamyl, and diarylmethyl, undergo facile homolytic CN bond scission under mild conditions to give products of formal [1,3] rearrangement rather than benzoin condensation. EPR experiments and computational analysis support a radical‐based mechanism. Implications for thiamine‐based enzymes are discussed.
Membranal and Blood‐Soluble HLA Class II Peptidome Analyses Using Data‐Dependent and Independent Acquisition (2018)

The interaction between HLA class II peptide complexes on antigen-presenting cells and CD4<sup>+</sup> T cells is of fundamental importance for anticancer and antipathogen immunity as well as for the maintenance of immunological tolerance. To study CD4<sup>+</sup> T cell reactivities, detailed knowledge of the presented peptides is necessary. In recent years, dramatic advances in the characterization of membranal and soluble HLA class I peptidomes could be observed. However, the same is not true for HLA class II peptidomes, where only few studies identify more than hundred peptides. Here we describe a MS-based workflow for the characterization of membranal and soluble HLA class II DR and DQ peptidomes. Using this workflow, we identify a total of 8595 and 3727 HLA class II peptides from Maver-1 and DOHH2 cells, respectively. Based on this data, a motif-based binding predictor is developed and compared to NetMHCIIpan 3.1. We then apply the workflow to human plasma, resulting in the identification of between 34 and 152 HLA-DR and between 100 and 180 HLA-DQ peptides, respectively. Finally, we implement a data-independent acquisition workflow to increase reproducibility and sensitivity of HLA class II peptidome characterizations.
Multilanguage interoperability in distributed systems. Experience report (2002)

The Q system provides interoperability support for multilingual, heterogeneous component-based software systems. Initial development of Q began in 1988, and was driven by the very pragmatic need for a communication mechanism between a client program written in Ada and a server written in C. The initial design was driven by language features present in C, but not in Ada, or vice-versa. In time our needs and aspirations grew and Q evolved to support other languages, such as C++, Lisp, Prolog, Java, and Tcl. As a result of pervasive usage by the Arcadia SDE research project, usage levels and modes of the Q system grew and so more emphasis was placed upon portability, reliability, and performance. In that context we identified specific ways in which programming language support systems can directly impede effective interoperability. This necessitated extensive changes to both our conceptual model and our implementation of the Q system. We also discovered the need to support modes of interoperability far more complex than the usual client-server. The continued evolution of Q has allowed the architecture of Arcadia software to become highly distributed and component-based, exploiting components written in a variety of languages. In addition to becoming an Arcadia project mainstay, and has also been made available to over 100 other sites, and it is currently in use in a variety of other projects. This paper summarizes key points that have been learned from this considerable base of experience.
SpecLock: Speculative Lock Forwarding (2019)

As core counts increase, lock acquisition and release become even more critical because they lie on the critical path of shared memory applications. In this paper, we show that many applications exhibit regular and repeating lock sharing patterns. Based on this observation, we introduce SpecLock, an efficient hardware mechanism which speculates on the lock acquisition pattern between cores. Upon the release of a lock, the cache line containing the lock is speculatively forwarded to the next consumer of the lock. This forwarding action is performed via a specialized prefetch request and does not require coherence protocol modification. Further, the lock is not speculatively acquired, only the cache line containing the lock variable is placed in the private cache of the predicted consumer. Speculative forwarding serves to hide the remote core's lock acquisition latency. SpecLock is distributed and all predictions are made locally at each core. We show that SpecLock captures 87% of predictable lock patterns correctly and improves performance by an average of 10% with 64 cores. SpecLock incurs a negligible overhead, with a 75% area reduction compared to past work. Compared to two state of the art methods, SpecLock provides a speedup of 8% and 4% respectively.
Novel quantitative trait loci controlling collagen-induced arthritis in mice (2008)

Udgivelsesdato: 2008/8
Wideband supercontinuum generation in tapered tellurite microstructured fibers (2011)

Enhanced soliton trapping of dispersive waves in a tapered tellurite microstructured fiber pumped by a 1556 nm femtosecond fiber laser is demonstrated. The short wavelength edge of supercontinuum light is extended from 960 to 600 nm after tapering the tellurite microstructured fiber, which is caused by the enhanced soliton trapping of dispersive waves owing to the changing group velocities in tapered fibers. Wide-band supercontinuum light source spanning from 600 to >2400 nm is generated in tapered tellurite micro-structured fibers. Our experimental and simulated results show that short length (several centimeters) zero-dispersion-wave length decreasing highly nonlinear fiber has a potential for generating wideband supercontinuum light source expanding from visible to mid-infrared region.
Immune profiles to distinguish hospitalized versus ambulatory COVID-19 cases in older patients (2022)

A fraction of patients with COVID-19 develops severe disease requiring hospitalization, while the majority, including high-risk individuals, experience mild symptoms. Severe disease has been associated with higher levels of antibodies and inflammatory cytokines but often among patients with diverse demographics and comorbidity status. This study evaluated hospitalized vs. ambulatory patients with COVID-19 with demographic risk factors for severe COVID-19: median age of 63, >80% male, and >85% black and/or Hispanic. Sera were collected four to 243 days after symptom onset and evaluated for binding and functional antibodies as well as 48 cytokines and chemokines. SARS-CoV-2-specific antibody levels and functions were similar in ambulatory and hospitalized patients. However, a strong correlation between anti-S2 antibody levels and the other antibody parameters, along with higher IL-27 levels, was observed in hospitalized but not ambulatory cases. These data indicate that antibodies against the relatively conserved S2 spike subunit and immunoregulatory cytokines such as IL-27 are potential immune determinants of COVID-19.
Time reversal of optical waves (2019)

Using a spatially and polarization resolved spectral pulse shaper we demonstrate the ability to generate arbitrary spatiotemporal vector fields in optics at the distal end of a multimode optical fiber.
A Temporal Millimeter Wave Propagation Model for Tunnels Using Ray Frustum Techniques and FFT (2014)

A temporal millimeter wave propagation model for tunnels is presented using ray frustum techniques and fast Fourier transform (FFT). To directly estimate or simulate effects of millimeter wave channel properties on the performance of communication services, time domain impulse responses of demodulated signals should be obtained, which needs rather large computation time. To mitigate the computational burden, ray frustum techniques are used to obtain frequency domain transfer function of millimeter wave propagation environment and FFT of equivalent low pass signals are used to retrieve demodulated waveforms. This approach is numerically efficient and helps to directly estimate impact of tunnel structures and surfaces roughness on the performance of millimeter wave communication services.
Abstract B230: NMS-P948, a potent dual FLT3/KIT inhibitor, also active on secondary resistance mutations. (2011)

Abstract FMS-like tyrosine kinase 3 (FLT3) and KIT are both members of the class III receptor tyrosine kinase family characterized by an autoinhibitory juxtamembrane (JM) domain that docks with the kinase domain to stabilize a catalytically inactive conformation. Therefore, mutations or deletion in this or in adjacent regions cause constitutive activation of these kinases as observed in 30% of AML patients for FLT3 and in 70% of adult GIST and a subset of melanoma patients for KIT. NMS-P948 is an alkoxy-indazole derivative potent dual inhibitor of FLT3 and KIT (IC50 26 and 89 nM, respectively), active also against FLT3 and KIT mutations that confer secondary resistance, such as the gatekeeper mutation T670I of KIT. It is a very selective compound, resulting, when tested on a panel of more than 150 human tumor cell lines, strongly active only on cell lines whose proliferation is driven by one of these two kinases (for FLT3: Eol-1, IC50= 8 nM; MV-4–11, IC50= 8 nM; MOLM-13, IC50= 18 nM and for KIT: GIST-430 IC50= 7 nM and GIST-882 IC50= 99 nM). Mechanism of action is demonstrated on both kinases, with activating and resistance mutations, at low nanomolar concentrations. NMS-P948 has good oral bioavailability in rodents. Antitumor efficacy is observed at as low as 10 mg/kg in xenograft models and no toxicity in terms of body weight loss was observed up to 60 mg/kg. In disseminated human AML MOLM-13 model (FLT3-ITD) NMS-P948 produces a very prolonged survival of treated mice (T/C= 390 at 60 mg/kg OS daily × 10) and this antitumor efficacy results superior to that of quizartinib administered with the same schedule at the MTD (T/C= 207 at 40 mg/kg). In conclusion, NMS-P948 is a promising dual inhibitor of mutated FLT3 and KIT with good in vitro and in vivo pharmacological and pharmacokinetic characteristics and with the potential to act also on patients that developed resistance to first line therapies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr B230.
Electric-field-controllable light scattering in helicoidal ferroelectric liquid crystals (2010)

This paper discusses light scattering in an electrooptic cell with a ferroelectric liquid crystal (FLC) at the dynamic domain structure that arises when there is a nonlinear reorientation process of the director of helicoidal FLC in a variable electric field. Choosing the optimum electric-control regime makes it possible to switch the scattering on and off in 150–200μs at a field of 6V∕μm. When there is a definite relationship between the amplitude and the width of the alternating pulses of the control voltage, a bistable operating regime of the cell is implemented. A new principle and a simple technique is proposed for suppressing speckle noise by means of a single-pixel FLC cell to which a sequence of bipolar electric pulses of special shape is applied.
Conffusion: Confidence Intervals for Diffusion Models (2022)

Diffusion models have become the go-to method for many generative tasks, particularly for image-to-image generation tasks such as super-resolution and inpainting. Current diffusion-based methods do not provide statistical guarantees regarding the generated results, often preventing their use in high-stakes situations. To bridge this gap, we construct a confidence interval around each generated pixel such that the true value of the pixel is guaranteed to fall within the interval with a probability set by the user. Since diffusion models parametrize the data distribution, a straightforward way of constructing such intervals is by drawing multiple samples and calculating their bounds. However, this method has several drawbacks: i) slow sampling speeds ii) suboptimal bounds iii) requires training a diffusion model per task. To mitigate these shortcomings we propose Conffusion, wherein we fine-tune a pre-trained diffusion model to predict interval bounds in a single forward pass. We show that Conffusion outperforms the baseline method while being three orders of magnitude faster.
Should women with genital condyloma acuminata have routine diagnostic colposcopy in addition to cervical smear screening? (1999)

We aimed to evaluate the difference in the pick up rate of high grade cervical abnormalities using both primary colposcopy and cervical smear compared with cervical cytology screen only on women with genital warts. We also wished to establish whether this group was at high risk of sexually transmittable infections (STIs) and whether there is a correlation between those with high grade CIN and other STIs. This was a retrospective analysis based in the Department of Genito-Urinary Medicine, Dundee Teaching Hospitals Trust, Dundee, UK. We studied all women (n =117) attending the Department with genital warts between January 1995 and March 1997 who were screened by both cervical cytology and colposcopy High grade cervical abnormalities (CIN II-CIN III) were diagnosed in 10 patients (8.5.%) using cervical screening only and in 41 patients (35%) (CIN II-III) when primary colposcopy and histopathology were undertaken. Of 117 women screened for sexual transmittable infection there were 53 with a positive diagnosis (48%). Of the 53 positive there were 17 women (30%) with high grade CIN. We conclude that women with genital warts are a high risk group, both in terms of having high grade cervical abnormalities and sexually transmittable infection. The result suggests that, when practicable primary colposcopy should be performed as a routine screening tool, on this group of patients over and above cervical cytology screening. All patients with genital warts should be referred to genitourinary medicine for STI screening.
Comparative optimization of combinatorial CRISPR screens (2022)

Combinatorial CRISPR technologies have emerged as a transformative approach to systematically probe genetic interactions and dependencies of redundant gene pairs. However, the performance of different functional genomic tools for multiplexing sgRNAs vary widely. Here, we generate and benchmark ten distinct pooled combinatorial CRISPR libraries targeting paralog pairs to optimize digenic knockout screens. Libraries composed of dual Streptococcus pyogenes Cas9 (spCas9), orthogonal spCas9 and Staphylococcus aureus (saCas9), and enhanced Cas12a from Acidaminococcus were evaluated. We demonstrate a combination of alternative tracrRNA sequences from spCas9 consistently show superior effect size and positional balance between the sgRNAs as a robust combinatorial approach to profile genetic interactions of multiple genes.
Optocoupler Radiation Survey Test (2015)

This report describes an active radiation test of 28 optocouplers (19 different devices) conducted at the Sandia National Laboratories (SNL) Annular Core Research Reactor (ACRR). The optocouplers consisted of commercially available components in one of three different package configurations: (1) commercially available as a single, sealed component, (2) commercially available as two sealed components that were aligned with external fixturing, and (3) commercially available as die that were packaged into a single, sealed component.
Scatter factors in proton therapy with a broad beam (2006)

In the absence of a predictor of beam output in proton therapy using a broad beam, the beam output is obtained for individual treatments by calibrating the beam monitors. The calibration is carried out under conditions similar to the treatment conditions but with a phantom instead of the patient. However, the dose in the phantom a priori differs from that in the patient. In order to deliver the accurate dose, a correction factor has been introduced to correct the difference. This correction factor is referred to as a scatter factor in an analogy with photon therapy, and is defined as the ratio of the dose at the prescription point in the patient to the dose at the calibration point in the phantom. Under the calibration conditions at Hyogo Ion Beam Medical Center (HIBMC), the range compensator and the collimator, which are usually required in proton therapy with a broad beam, are not used. Therefore the scatter factor includes the effects of the devices as well as the difference between the dose in the patient and that in the phantom. We have developed an estimator using a dose calculation based on the pencil beam algorithm and implemented it in a treatment planning system (TPS) for clinical use. This estimator estimates the scatter factor by calculating the ratio of the doses under the same conditions in the TPS. In order to evaluate the performance of the estimator, demonstrations were carried out for cases with measurable outcomes using a gantry nozzle at HIBMC. We observed 2-3% differences between the measurements and the estimations. These differences were considered to result from the limitations of the dose calculation algorithm in modelling the beam and the patient.
Diagnostic Accuracy of 3 Physical Examination Tests in the Assessment of Hip Microinstability (2017)

The AB-HEER test most accurately predicted hip instability, followed by the HEER test and the prone instability test. However, the high specificity of the prone instability test makes it a useful test to "rule in" abnormalities. A positive result from any test predicted hip instability in 86.3% to 90.9% of patients, but a negative test result did not conclusively rule out hip instability, and other measures should be considered in making the diagnosis. The use of these tests may aid the clinician in diagnosing hip instability, which has been considered a difficult diagnosis to make because of its dynamic nature.
A full-band Monte Carlo model for hole transport in silicon (1997)

Hole transport in bulk silicon is explored using an efficient and accurate Monte Carlo (MC) tool based on the local pseudopotential band structure. Acoustic and optical phonon scattering, ionized impurity scattering, and impact ionization are the dominant scattering mechanisms that have been included. In the interest of computational efficiency, momentum relaxation times have been used to describe ionized impurity scattering and self-scattering rates have been computed in a dynamic fashion. The temperature and doping dependence of low-field hole mobility is obtained and good agreement with experimental data has been observed. MC extracted impact ionization coefficients are also shown to agree well with published experimental data. Momentum and energy relaxation times are obtained as a function of the average hole energy for use in moment based hydrodynamic simulators. The MC model is suitable for studying both low-field and high-field hole transport in silicon.