gebhart/patrepeval huggingface dataset:
Conflicting HLA assignment by three different typing methods due to the apparent loss of heterozygosity in the MHC region (2016)

Loss of heterozygosity (LOH) has been reported to cause false human leukocyte antigen (HLA) homozygous typing results in pre-transplant patients suffering from haematological malignancies, who in fact are HLA heterozygous. This poses a challenge for histocompatibility testing, as a stem cell graft from a genuinely HLA homozygous donor to a mistyped patient may lead to acute life-threatening graft-vs-host disease. LOH in the HLA region on chromosome 6 is known to be quite common in solid tumours, helping malignant cells to escape T-cell surveillance, but the incidence in haematological malignancies is less well known and the estimates vary. Here we report LOH in the HLA region of five patients with haematological malignancy. We found considerable differences in sensitivity between the three different HLA typing methods used in our laboratory: SSP was clearly the most sensitive method for detecting the lost haplotype, followed by rSSO, while SBT was the least sensitive technique. A subsequent, retrospective genotyping of 65 HLA homozygous haematological patients by SSP method showed no mistyped LOH cases in our laboratory in the past 10 years. The frequency of HLA homozygosity was found to be similar between haematological patients and control groups. It is important for an HLA laboratory to be aware of the differences in various HLA typing techniques' sensitivity for detecting an under-represented haplotype between HLA typing techniques when genotyping patients with haematological diseases. It is advisable for HLA laboratories to have at least two different methods with different sensitivities in their repertoire to be able to retype samples when a false homozygous result is suspected.
ChemInform Abstract: Polymeric Systems for Controlled Drug Release (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Chip package interaction (CPI): Thermo mechanical challenges in 3D technologies (2012)

The residual stresses generated during different processing steps and during thermal cycling of 3D stack packages, mimicking its service life, are quantified by Finite Element Modeling (FEM) together with measurements of dedicated FET arrays used as CPI sensors. Thermo-mechanical deformation of the package can be directly transferred to the Cu/low-k interconnect, inducing large local stresses to drive interfacial crack formation and propagation. The test vehicle used in this work is an imec's proprietary logic CMOS IC on top of which a commercial DRAM is stacked. Different test structures contained in the chip, allow monitoring thermo-mechanical stresses and electrical characteristics of TSV's and micro-bumps. It is shown that FET current shifts can be used to measure the stress in the surface of the chip. The use of standard FEM approach is insufficient to simulate the CPI due to the large dimensional difference between the packaging and interconnects structures. Due to size and speed limitations of commercial computers, a 3D thermo mechanical model of a 3D package cannot contain all the details from the package and at the same time simulate the small structures such as metal and dielectric layers in the BEOL. For this reason, multi-scale simulations are the best choice for identifying the critical regions of the package where high stresses and/or delamination failures are expected to occur. We have shown the methodology to follow to study the CPI.
Impact of Wind Forcing, Bottom Topography, and Inertia on Midlatitude Jet Separation in a Quasigeostrophic Model (1997)

The persistence of unrealistic Gulf Stream separation in numerical models of the ocean has prompted many theories about possible mechanisms that influence the separation of a western boundary current from the coast. In this paper, the joint effects of (a) coastline orientation, (b) bottom topography, and (c) inertia on the midlatitude jet separation are explored in a wind-driven two-layer quasigeostrophic model. It is shown that topographic effects are of importance in high eddy activity regions and that eddy-topography interactions strongly influence the separation process.
Characterization of memory effects in concurrent dual-band PAs (2011)

In this paper the nonlinearity of concurrent dual-band power amplifier (PA) is investigated by using modulated signals and digital multi-tone signals. The difference between ordinary inter-modulation distortion in single band power amplifier and the distortion from cross-modulation between dual bands in a concurrent dual-band PA has been verified and studied. According to AM-AM and AM-PM performances in different modes, the concurrent dual-band mode has more scattered behavior. To evaluate and quantify the memory due to the cross-modulation, and identification method is used to extract the amplitudes and phases of different inter-modulation products, which is useful for power amplifier behavior modeling and linearization.
The failure of perfectly matched layers, and towards their redemption by adiabatic absorbers (2008)

Although perfectly matched layers (PMLs) have been widely used to truncate numerical simulations of electromagnetism and other wave equations, we point out important cases in which a PML fails to be reflectionless even in the limit of infinite resolution. In particular, the underlying coordinate-stretching idea behind PML breaks down in photonic crystals and in other structures where the material is not an analytic function in the direction perpendicular to the boundary, leading to substantial reflections. The alternative is an adiabatic absorber, in which reflections are made negligible by gradually increasing the material absorption at the boundaries, similar to a common strategy to combat discretization reflections in PMLs. We demonstrate the fundamental connection between such reflections and the smoothness of the absorption profile via coupled-mode theory, and show how to obtain higher-order and even exponential vanishing of the reflection with absorber thickness (although further work remains in optimizing the constant factor).
Comparison between nasopharyngeal swabs and saliva as reliable specimens for the diagnosis of SARS-CoV-2 (2021)

Introduction: The SARS-CoV-2 virus is a positive-strand RNA virus. The virus can also be detected in many different specimens as throat swabs, nasal swabs, sputum, saliva, blood, etc.Objective: The aim of this paper is to compare the reliability of different types of specimen collection, saliva and swabs samples for the detection of SARS-CoV-2.Material and Methods: A sample of 22 COVID-19 positive patients was selected. Paired samples from saliva, nasopharyngeal, oropharyngeal and nasopharyngeal + oropharyngeal swabs were collected on the 7th day after diagnosis. The hyssops and medium employed was IMPROSWAB and IMPROVIRAL NAT Medium, Germany. The sample evaluation was conducted through RT-PCR. The results were compared using Fisher’s exact test and ROC curve. The gold standard proposed in this paper was the nasopharyngeal + oropharyngeal swabs specimen.Results: The gold standard method detected 10 true positive cases, of which oropharyngeal swabs, nasopharyngeal swabs and saliva only detected three positive cases. Significant differences (Fisher’s exact test p = 0.003) were detected in the comparison between saliva and the gold standart proposed. The ROC curve analysis showed that saliva had an area under the curve of 0.650, with a 30% of sensibility. However, the nasopharyngeal and nasopharyngeal + oropharyngeal samples had an area under curve of 0.950 and 1.000, respectively, with a sensibility of 90% and 100%, respectively.Conclusion: Saliva samples are not a reliable specimen for SARS-CoV-2 RNA detection. In turn, the most reliable specimens are nasopharyngeal and nasopharyngeal + oropharyngeal samples collected by swabbing.
55‐1: Invited Paper: Prediction of Overall HDR Quality by using Perceptually Transformed Display Measurements (2017)

The need for metrics to evaluate HDR display subjective performance is becoming widely recognized. Yet most existing performance metrics focus on physical measurements rather than subjective impact. We found that applying perceptual transforms to five key HDR performance characteristics better predicts display quality compared to existing physical metrics.
The FeTouch project: an application of haptic technologies to obstetrics and gynaecology (2004)

Ultrasound technologies have been widely used in gynecology and obstetrics. Modern ultrasound systems allow the reconstruction of a 3D model of the subject being scanned, but even though visual interfaces have reached very high standards, the problem of representing a 3D image on a 2D computer screen still exists. Moreover no physical interaction is possible with such a model. The FeTouch system, developed at Siena University in the last two years, partially solves such issues by using stereo visual feedback and haptic devices. While the system can be used with any 3D model obtained from ultrasound scans, its current prime use is to allow mothers to interact with a model of the fetus they are carrying. The system is freely available on the project web page.
Programming for dependability in a service-based grid (2003)

Service-based Grid infrastructures emphasize service composition rather than sharing of low level resources. The idea is to build Grid applications out of computational services provided by the different sites of the Grid. Recent developments in the area of Web services have strengthened this idea by standardizing procedures like service description, publication and invocation. What is still missing is the infrastructure necessary to support the complete life cycle of applications running on service based Grids, i.e., suitable programming paradigms, execution infrastructure, and the ability to monitor and control such computations. Moreover, once computations are made of composable services, dependability becomes a key issue that needs to be addressed by the infrastructure as it cannot be addressed separately by each individual service. To address these concerns, we have developed the BioOpera Grid computing platform. BioOpera is a process support system for dependable cluster computing that has been extended with additional functionality to provide adequate support for service-based Grids. In this paper we describe how BioOpera can be used to develop, execute, and administer highly dependable computations over service-based Grids.
Silica-Coated Magnetite Nanoparticles Supported Rhodium Catalyst (2006)

A recyclable rhodium-complexed dendron anchored on silica-coated magnetite nanoparticles 1 was developed. The hydroformylation reaction of styrene by using catalyst 1 (50 mg) and a 1:1 mixture of carbon monoxide and hydrogen pressurized to 1000 psi gave the formylated products at complete conversion (branch 2/linear 3 = 48:1). Catalyst 1 was reused five times without any loss of catalytic activity and selectivity (see scheme for details). Eleven examples of the hydroformylation reaction of various olefins were demonstrated (5-100% conversion, branch/linear = 42/1-100/0).
Imaging Algorithms for Evaluating Suspected Rotator Cuff Disease: Society of Radiologists in Ultrasound Consensus Conference Statement (2013)

The Society of Radiologists in Ultrasound convened a panel of specialists from a variety of medical disciplines to reach a consensus about the recommended imaging evaluation of painful shoulders with clinically suspected rotator cuff disease. The panel met in Chicago, Ill, on October 18 and 19, 2011, and created this consensus statement regarding the roles of radiography, ultrasonography (US), computed tomography (CT), CT arthrography, magnetic resonance (MR) imaging, and MR arthrography. The consensus panel consisted of two co-moderators, a facilitator, a statistician and health care economist, and 10 physicians who have specialty expertise in shoulder pain evaluation and/or treatment. Of the 13 physicians on the panel, nine were radiologists who were chosen to represent a broad range of skill sets in diagnostic imaging, different practice types (private and academic), and different geographical regions of the United States. Five of the radiologists routinely performed musculoskeletal US as part of their practice and four did not. There was also one representative from each of the following clinical specialties: rheumatology, physical medicine and rehabilitation, orthopedic surgery, and nonoperative sports medicine. The goal of this conference was to construct several algorithms with which to guide the imaging evaluation of suspected rotator cuff disease in patients with a native rotator cuff, patients with a repaired rotator cuff, and patients who have undergone shoulder replacement. The panel hopes that these recommendations will lead to greater uniformity in rotator cuff imaging and more cost-effective care for patients suspected of having rotator cuff abnormality.
Effects of Aeration on Water Quality from Septic System Leachfields (2004)

We conducted a pilot-scale study at a research facility in southeastern Connecticut to assess the effects of leachfield aeration on removal of nutrients and pathogens from septic system effluent. Treatments consisted of lysimeters periodically aerated to maintain a headspace O(2) concentration of 0.209 mol mol(-1) (AIR) or vented to an adjacent leachfield trench (LEACH) and were replicated three times. All lysimeters were dosed with effluent from a septic tank for 24 mo at a rate of 12 cm d(-1) and subsequently for 2 mo at 4 cm d(-1). LEACH lysimeters had developed a clogging mat, or biomat, 20 mo before the beginning of our study. The level of aeration in the AIR treatment was held constant regardless of loading rate. No conventional biomat developed in the AIR treatment, whereas a biomat was present in the LEACH lysimeters. The headspace of LEACH lysimeters was considerably depleted in O(2) and enriched in CH(4), CO(2), and H(2)S relative to AIR lysimeters. Drainage water from AIR lysimeters was saturated with O(2) and had significantly lower pH, five-day biological oxygen demand (BOD(5)), and ammonium, and higher levels of nitrate and sulfate than LEACH lysimeters regardless of dosing rate. By contrast, significantly lower levels of total N and fecal coliform bacteria were observed in AIR than in LEACH lysimeters only at the higher dosing rate. No significant differences in total P removal were observed. Our results suggest that aeration may improve the removal of nitrogen, BOD(5), and fecal coliforms in leachfield soil, even in the absence of a biomat.
Using microprojectiles to study the ballistic limit of polymer thin films (2020)

The dynamic impact between a particle and a planar material is important in many high impact events, and there is a growing need to characterize the mechanical properties of light-weight polymeric materials at dynamic loading conditions. Here, a laser-induced projectile impact test (LIPIT) is employed to investigate the ballistic limit (V0) and materials properties at impact velocities ranging from 40 m s-1 to 70 m s-1. An analytical expression describing the various energy dissipation mechanisms is established to estimate the yield stress and elasticity for polycarbonate thin films. This measurement approach demonstrates the utility of using low sample mass for discovery of materials for impact mitigation, as well as high-throughput mechanical characterization at dynamic loading rates.
Factors Associated with Prescriptions for an Orexin Receptor Antagonist Among Japanese Patients with Insomnia: Analysis of a Nationwide Japanese Claims Database (2023)

This is the first study to determine the factors associated with ORA prescriptions in Japan. Our findings could help guide appropriate insomnia treatment using ORAs.
Effective desynchronization with a resetting pulse train followed by a single pulse (2001)

A combined pulse train, single-pulse stimulation technique is presented here which makes it possible to effectively desynchronize a cluster of globally coupled phase oscillators in the presence of noise. Such a composite stimulus consists of a resetting short periodic high-frequent pulse train followed by a desynchronizing single pulse. The pulse train entrains and, thus, restarts the collective oscillation independently of its initial dynamic state. With a fixed delay after the pulse train, a single pulse is delivered which desynchronizes the cluster by hitting it in a vulnerable state. After the desynchronization the cluster wants to become synchronized again since the incoherent state is unstable. Nevertheless, repeated administration of the same composite stimulus blocks the resynchronization. Compared to double-pulse phase resetting and with regard to neurological applications, this method is particularly mild and can be applied to effectively maintain incoherency in a population of oscillatory neurons that tend to synchronize their firing. The composite stimulation approach sheds new light on the mechanism of standard deep brain stimulation and suggests an improved, milder and demand-controlled deep brain stimulation technique for patients with Parkinson's disease or essential tremor.
Erratum: Potts Ferromagnets on Coexpressed Gene Networks: Identifying Maximally Stable Partitions [Phys. Rev. Lett.90, 158102 (2003)] (2003)

Received 28 April 2003DOI:https://doi.org/10.1103/PhysRevLett.90.229901©2003 American Physical Society
Optimal downlink beamforming with additional constraints (2004)

This work addresses the problem of joint downlink beamforming and power control with general quality of service (QoS) constraints. Previous work on downlink beamforming does not provide a framework to handle the additional constraints in a straightforward fashion. Herein, it is shown that the QoS requirements can be formulated as quadratic constraints to a convex optimization problem. An efficient algorithm for solving the problem, based on semidefinite optimization is presented. To demonstrate the performance of the proposed approach, we present an example using quadratic constraints to greatly decrease the probability of a low instantaneous signal to interference and noise ratio (SINR) for a receiver equipped with a RAKE combiner.
pH-responsive micelles an vesicles nanocapsules based on polypeptode diblock copolymers (2007)

The self-assembly of well-defined polypeptide-based diblock copolymers into micelles and vesicles is presented. The stimuli-responsive behavior of polypeptides to pH and ionic strength is used to produce stimuli-responsive nanoparticles with controlled size and shape. Results focusing on micelles and vesicles obtained from polypeptide-based diblock copolymers that are particularly promising for biomedical applications are detailed by means of static and dynamic light scattering analysis, UV circular dichroism, NMR and small angle neutron scattering experiments. Also systems able to form vesicles with a narrow size distribution at basic and acid pH going through a single molecule intermediate state are presented. These nanoparticles are particularly interesting for encapsulation and delivery purpose at a controlled pH. (c) 2006 Elsevier B.V. All rights reserved.
Immunotherapy with enhanced self immune cells. (2004)

Extract: Immunotherapy with empowered self immune cells, also called adoptive immunotherapy, has emerged as an exciting therapeutic modality for the treatment of cancer and infectious diseases over the past decade. Adoptive immunotherapy can be defined as the ex vivo (outside the body) generation and expansion of antigen-specific T cells over a short time period and infusion back into the patients. Currently, it has been evaluated for the treatment of infections with viruses such as cytomegalovirus (CMV), Epstein-Barr virus (EBV), and human immunodeficiency virus (HIV), along with a variety of malignancies, including malignant melanoma and multiple myeloma.
Identification of a novel protein in the genome sequences of Leptospira interrogans with the ability to interact with host's components (2019)

This novel leptospiral protein may function as an adhesin at the colonization steps and may help the invasion process by plasmin generation at the bacterial cell surface.
Synthesis and anti-bacterial activities of novel 5-isonicotinoyl-1,2,3,4-tetrahydropyrimidines and bis-(5-isonicotinoyl-1,2,3,4-tetrahydropyrimidines) (2009)

Novel 5-isonicotinoyl-1,2,3,4-tetrahydropyrimidines 4a-i have been synthesized in good yields by the reaction of enaminones 3a-c, primary amines and formaldehyde. 4a-i have been screened for their antibacterial properties. Enaminones 3a-c have also been reacted with diamines and formaldehyde to give hitherto unreported bis-tetrahydropyrimidines 5a-l in good yields. The structures of 4a-i and 5a-l have been established with the help of spectral and analytical data.
Construction of plasmids for gp64-VP1 expression by baculovirus. (2015)

&lt;p&gt;The VP1 gene was incorporated between gp64 signal peptide and gp64 mature domain by overlapping PCR. The recombinant gene gp64-VP1 was then inserted into pFastBac HT A. The resultant plasmids were designated pFast-Pph-gp64-VP1. The polyhedrin promoter (Pph) was later replaced by WSSV ie1 promoter which is active in both Sf9 and mammalian cells. Like gp64 protein, the recombinant protein gp64-VP1 should be transported to the surface of the infected Sf9 cells, and incorporated into the surface of recombinant baculoviruses.&lt;/p&gt;
Compute Solution for Tesla's Full Self-Driving Computer (2020)

Tesla's full self-driving (FSD) computer is the world's first purpose-built computer for the highly demanding workloads of autonomous driving. It is based on a new System on a Chip (SoC) that integrates industry standard components such as CPUs, ISP, and GPU, together with our custom neural network accelerators. The FSD computer is capable of processing up to 2300 frames per second, a 21× improvement over Tesla's previous hardware and at a lower cost, and when fully utilized, enables a new level of safety and autonomy on the road.
Shape recovery of rotating object using weighted voting of spacio-temporal images (2002)

We propose a method to recover the 3D shape of an object rotating on a turnable. A spacio-temporal image is made of the sequential images taken by a single camera. Then, the trajectories which correspond to the 3D points on the surface are extracted in the spacio-temporal image by using "weighted voting" of all intensity values on a constrained surface. Since the method consequently utilize intensity information as it is, the method can recover dense 3D positions compared with the one using feature extraction and tracking. Also, it can recover concave shapes unlike the one using silhouettes of the object. The experimental results with real images show the effectiveness of our method.