gebhart/patrepeval huggingface dataset:
Fully Automated Detection and Quantification of T1 Hypointense Lesions in Multiple Sclerosis (P6.119) (2014)

OBJECTIVE: We present a fully automated and hence user independent technique for detection and quantification of T1-hypointense white matter (WM) lesions in multiple sclerosis (MS) patients. BACKGROUND: T1 hypointense lesion detection and volumetry are increasingly being used for prediction of disability in MS patients. To date T1 hypointense lesion detection is performed manually or semi-automatically. DESIGN/METHODS: A novel method for fully automatic detection of T1 hypointense lesions in 3D high-resolution T1-weighted gradient echo MR (MPRAGE) images was recently proposed (Spies et al. 2013). The method exploits the fact that hypointense WM lesions, which appear darker than the surrounding normal appearing WM tissue in MPRAGE images, are partly misclassified as grey matter (GM) by standard intensity-based segmentation engines. To quantify misclassified WM on voxel-level voxel-based morphometry was deployed. The method is limited to deep WM regions. Here, we extend the algorithm to cover also juxtacortical regions. Due to a higher fraction of voxels with partial volume effect juxtacortical regions are prone to false positive findings. We developed a method to reduce false positive findings using region growing in combination with front line assessment. For a cohort of 21 well-characterized relapsing-remitting MS (RRMS) patients a T1 and T2 lesion database was created using manual and semi-automated lesion contouring. The extended algorithm was characterized against this database. RESULTS: For T1-hypointense lesions of 0.1 ml and larger the extended algorithm produced a sensitivity of almost 100% at a false positive rate of 4 lesions per patient dataset. CONCLUSIONS: The extended algorithm demonstrates a high sensitivity at an acceptable rate of false positive findings. It thus has potential to become a valuable tool for lesion detection and quantification in clinical MS trials to assess the risk of disability.
Tumor-Infiltrating Lymphocyte Therapy and Neoantigens (2017)

The adoptive cell transfer (ACT) of autologous tumor-infiltrating lymphocytes has been shown to be effective at mediating tumor regression in more than half of patients with metastatic melanoma and in mediating long-term complete regression in approximately one fourth of all patients with this cancer. The success of this approach in patients with cholangiocarcinoma and colon cancer supports efforts to expand ACT therapies to treatment of patients bearing a wide array of cancer types. Recent improvements in deep sequencing of the patient cancers, combined with extensive immunological testing of autologous tumor-infiltrating lymphocytes, indicate that T cells targeting epitopes arising from nonsynonymous somatic mutations, termed neoantigens, play important roles in mediating many of the effective cancer immunotherapies seen in response to ACT.
Peptide Mass Fingerprinting (PMF) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Decreased hospital charges and postoperative pain in septoplasty by application of enhanced recovery after surgery (2018)

Our study indicated ERAS application can reduce hospital charges and postoperative pain in septoplasty, thereby improving patient quality of life and hospital expenses at the same time.
Developing population health research priorities in Asian city state: Results from a multi-step participatory community engagement (2019)

This study illuminates that greater community engagement in research priority setting for population health can facilitate the formulation of evidence-based research agendas that matter to the care providers and service users in the community. The outcomes derived from this exercise will help focus researchers' efforts through which meaningful gains can be made for population health.
Reliable multiplex generation of pooled induced pluripotent stem cells for genetic testing (2022)

Abstract Inducing somatic cells into pluripotent stem cells (iPSCs) provides an excellent model for studying systems in-vitro . Understanding the impact of individual donor genetic backgrounds on reprogramming ability would allow researchers to harness these genetic differences and increase the efficiency of the reprogramming process. To better understand the genetic basis of reprogramming cells into iPSCs, we present Induction of Pluripotency from Pooled Cells (iPPC) - an efficient, scalable, and reliable reprogramming procedure. Using our deconvolution algorithm that employs low-coverage pooled sequencing and single nucleotide polymorphisms (SNPs), we estimate individual donor proportions of cell lines within large cohorts. With iPPC, we concurrently reprogrammed over one hundred donor LCLs into iPSCs and found strong correlations of individual donors’ reprogramming ability across multiple experiments. We note that individual donors’ reprogramming ability remains consistent across both same-day replicates and multiple experimental runs, and that the expression of certain immunoglobulin precursor genes (IGLV10-54, IGLV3-9, IGLV1-17, IGLV1-6, and IGLV3-1) may impact reprogramming ability. Our process enables a multiplex framework to study the reprogramming ability of different donor cells into iPSCs and also provides a reliable method along with a pooled library of donor iPSCs for downstream research and investigation of other in-vitro phenotypes.
Performance Improvement of Space-Division Multiplexed 128-Gb/s PDM-QPSK Signals by Constructive Superposition in a Single-Input-Multiple-Output Configuration (2012)

We propose digital constructive-superposition to improve the performance of space-division-multiplexed (SDM) signals, and demonstrate a Q2-factor improvement of 2.2 (3.6) dB by constructively-superimposing 2 (3) SDM copies of a 128-Gb/s PDM-QPSK signal after 2688-km transmission over a seven-core-fiber.
H2 Suboptimal Estimation and Control for Nonnegative Dynamical Systems (2007)

Linear matrix inequalities provide a powerful design framework for linear control problems. In this paper, we use linear matrix inequalities to develop H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (sub)optimal estimators and controllers for nonnegative dynamical systems. Specifically, we formulate a series of generalized eigenvalue problems subject to a set of linear matrix inequality constraints for designing H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> suboptimal estimators, static controllers, and dynamic controllers for nonnegative dynamical systems.
Image collapse issues in photoresist (2001)

The continued shrinkage of line widths below 150nm has not been without concerns of the mechanical stability of the resist structure. The development of the exposed resist undergoes many phase changes such as solid solubilization into a liquid followed by drying by volatilization. In the development of features especially with aspect ratio (AR) &gt;3 and for lines/spaces (l/s)&lt;1:2, the phase changes create interfacial tensions at the liquid/solid and gas/liquid/solid surfaces that can cause image collapse (IC). Aqueous based resist are particularly susceptible to collapse due to the high surface tension of the rinse water (72 mN/m). Two major steps to reduce or eliminate the IC are to strengthen the mechanical stability of the resist or to reduce the surface tension of the drying/rinse liquid. We have investigated various methods to reduce the surface tension of the water rinse either by lowering the surface tension of the rinse liquid or by removal of the rinse water prior to drying. Positive ArF and KrF resist and negative resist have been investigated. To reduce the surface tension of rinse liquid, the addition of surfactant followed by drying is a direct method which may be used. Indirectly, the prior removal of water by solvents or emulsification with inert components followed by drying in the supercritical fluid of CO<SUB>2</SUB> can maintain high aspect ratio images at AR&gt;3. Negative resist are more applicable to process as they can tolerate a wider variety of co- solvents of CO<SUB>2</SUB> phillic surfactants.
Practice patterns in the management of acute renal failure in the critically ill patient: an international survey (2005)

New classifications such as RIFLE criteria might improve well-known uncertainty about ARF definition. Different RRT techniques are available in most centres, but a general lack of treatment dose standardization is noted by our survey. Non-renal indications to RRT still need to find a definitive role in routine practice.
Main-chain engineering of polymer photocatalysts with hydrophilic non-conjugated segments for visible-light-driven hydrogen evolution (2022)

Photocatalytic water splitting is attracting considerable interest because it enables the conversion of solar energy into hydrogen for use as a zero-emission fuel or chemical feedstock. Herein, we present a universal approach for inserting hydrophilic non-conjugated segments into the main-chain of conjugated polymers to produce a series of discontinuously conjugated polymer photocatalysts. Water can effectively be brought into the interior through these hydrophilic non-conjugated segments, resulting in effective water/polymer interfaces inside the bulk discontinuously conjugated polymers in both thin-film and solution. Discontinuously conjugated polymer with 10 mol% hexaethylene glycol-based hydrophilic segments achieves an apparent quantum yield of 17.82% under 460 nm monochromatic light irradiation in solution and a hydrogen evolution rate of 16.8 mmol m<sup>-2</sup> h<sup>-1</sup> in thin-film. Molecular dynamics simulations show a trend similar to that in experiments, corroborating that main-chain engineering increases the possibility of a water/polymer interaction. By introducing non-conjugated hydrophilic segments, the effective conjugation length is not altered, allowing discontinuously conjugated polymers to remain efficient photocatalysis.
And then there were none (2013)

short-paper And then there were none: a stall-free real-time garbage collector for reconfigurable hardware Authors: David F. Bacon IBM T.J. Watson Research Center, NY IBM T.J. Watson Research Center, NYView Profile , Perry Cheng IBM T.J. Watson Research Center, NY IBM T.J. Watson Research Center, NYView Profile , Sunil Shukla IBM T.J. Watson Research Center, NY IBM T.J. Watson Research Center, NYView Profile Authors Info & Claims Communications of the ACMVolume 56Issue 12December 2013 pp 101–109https://doi.org/10.1145/2534706.2534726Published:01 December 2013Publication History 7citation5,251DownloadsMetricsTotal Citations7Total Downloads5,251Last 12 Months4,035Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Integrated Microreactor System for Gas-Phase Catalytic Reactions. 2. Microreactor Packaging and Testing (2007)

An integrated packaging system is developed for the multilayer laminate gas-phase microreactor die whose design and fabrication was described in Part 1 of this series. A commercial plastic socket used for integrated circuit testing was adapted so the reactor chip could be easily installed while maintaining consistent alignment with all electrical contacts. A heated fluidics interface was developed that connects the nonmetallic feed and product gas ports on the microreactor chip to metal tubing. Thermal experiments and 3-D finite-element heat transfer simulations of the combined socket-fluidics assembly showed that the plastic reactor socket could be safely operated up to 250 °C. Other tests showed that the microreactor heaters were capable of achieving membrane temperatures in excess of 600 °C. Step-response tests demonstrated that temperature changes of ca. 100 °C could be achieved in less than 10 ms. Testing of the electrical leads on the reactor chip verified that the device resistance on a single reactor chip was uniform within a few percentage points. The packaged system developed here is used in Part 3 of this series to create a modular reactor board for incorporation into an integrated process system.
Improved remote gaze estimation using corneal reflection-adaptive geometric transforms (2014)

Recently, the remote gaze estimation (RGE) technique has been widely applied to consumer devices as a more natural interface. In general, the conventional RGE method estimates a user’s point of gaze using a geometric transform, which represents the relationship between several infrared (IR) light sources and their corresponding corneal reflections (CRs) in the eye image. Among various methods, the homography normalization (HN) method achieves state-of-the-art performance. However, the geometric transform of the HN method requiring four CRs is infeasible for the case when fewer than four CRs are available. To solve this problem, this paper proposes a new RGE method based on three alternative geometric transforms, which are adaptive to the number of CRs. Unlike the HN method, the proposed method not only can operate with two or three CRs, but can also provide superior accuracy. To further enhance the performance, an effective error correction method is also proposed. By combining the introduced transforms with the error-correction method, the proposed method not only provides high accuracy and robustness for gaze estimation, but also allows for a more flexible system setup with a different number of IR light sources. Experimental results demonstrate the effectiveness of the proposed method.
ChemInform Abstract: Highly Enantioselective Epoxidation of 1,1‐Disubstituted Alkenes Catalyzed by Chloroperoxidase. (1995)

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.
LARGE SCALE STRUCTURE OF TURBULENT BOUNDARY LAYER SUBJECTED TO AN ADVERSE PRESSURE GRADIENT (2009)

The effects of adverse pressure gradients on turbulent structures were investigated by carrying out direct numerical simulations of turbulent boundary layers subjected to adverse pressure gradients. The equilibrium adverse pressure gradient flows were established by using a power law free-stream distribution U∞ ~ xm.. Estimates of the conditionally averaged velocity fields associated with the spanwise vortical motion were obtained by using linear stochastic estimation. These results confirm that the outer region of the adverse pressure gradient boundary layer is populated with streamwise-aligned vortex organizations.
Integration of Pseudorange Measurements from Multiple Base Stations For Asset Mapping (1995)

Abstract Differential GPS surveys can routinely yield position accuracy of better than five metres. There are a significant number of applications requiring such an accuracy level, one of which is the collection of assets such as fire hydrants, telecommunications utilities, light poles and street furniture. Processing of the double difference pseudorange observable provides an effective solution for achieving the accuracy required for asset mapping. One potential weakness of differential GPS techniques is the requirement for a continuously tracking base station. Greater survey insurance and integrity can be achieved by collecting data using multiple base sites established at different locations. This paper introduces a technique for merging the measurements acquired at roving sites and multiple base sites in a single estimation process. Double differences are generated between each rover-base station combination and are combined to yield a least squares position estimate of the rover station. Results of a field test highlight the ability of the procedure to increase survey integrity by effectively reducing errors caused by data collected at noisy base station sites.
Treatment of early rectal tumours by transanal endoscopic microsurgery in Hong Kong: prospective study. (2004)

Transanal endoscopic microsurgery is a safe procedure and can achieve good local tumour control. It is ideal in the management of rectal villous adenomas at stages pT0 and pTis. Its application is now extended to the treatment of early rectal carcinoma at stage pT1 with curative intent. For tumours at stage pT2 or later, it can also serve as a good option for local palliation.
High Reflectivity Broadband Photonic Crystal Mirror MEMS Scanner (2007)

In this paper we introduce a MEMS scanner with a highly reflective broadband photonic crystal mirror. These mirrors achieve higher reflectivity than metal reflectors and can tolerate higher processing temperatures. Photonic crystal mirrors can be made of a single dielectric material and hence are much simpler to fabricate than multi-layer dielectric stacks. Our photonic crystal mirror shows broadband high reflectivity in the wavelength spectrum from 1300 nm to 1500 nm. The single-axis MEMS scanner is fabricated on a SOI wafer and actuated by electrostatic combdrives on resonance. Dynamic deflection measurements show that the scanner achieves 20deg total scan angle with an input square wave of 40 V and up to 120deg total scan angle with 190 V at a resonance frequency of 2.03 kHz.
Experimental Observations of Soliton Wave Trains in Electron Beams (2013)

The first experimental observation of a Korteweg-de Vries-type soliton wave train in intense electron beams is reported. A narrow, large-amplitude perturbation on a long-pulse beam is observed to steepen and spawn a soliton wave train. The pulse width and amplitude of each peak remain unchanged over a long propagation distance, and the amplitude is inversely proportional to the square of the width. Two such pulses are seen to pass through each other, emerging from the collision unchanged. The experimental results are reproduced by particle-in-cell simulations.
CHARACTERIZATION OF MHC ALLOPEPTIDE REACTIVE T CELL CLONES FROM HUMAN RENAL ALLOGRAFT RECIPIENTS (1998)

382 We have recently demonstrated that T cells obtained from patients with chronic renal allograft dysfunction are primed to recognize and respond to specific donor-derived class II MHC allopeptides in vitro. In experimental animal models, class II MHC allopeptide-specific Th1 clones generated from rejecting animals express restricted TCR Vß repertoire and transfer delayed type hypersensitivity responses in vivo. In this study we generated T cell clones from PBMCs of two human renal transplant recipients; the first patient has chronic allograft dysfunction and the second control patient has stable graft function. Patient 1 received a HLA-DR*0101 mismatched living donor renal allograft and currently has chronic allograft dysfunction (creatinine: 2.9mg/dl) with typical histopathological features of chronic rejection. We have previously demonstrated T cell reactivity to peptide (42-62) of HLA-DR*0101 in this patient. Patient 2 received a HLA-DR*1501 mismatched cadaver renal allograft and currently has stable renal function (creatinine: 1.6mg/dl). Allopeptide reactivity was not detectable to any of 5 HLA-DR*1501 allopeptides on each of three separate occasions in this patient. T cell lines were generated from PBMCs of both patients by repeated stimulation with self APC pulsed allopeptide; peptide (42-62) of HLA-DR*0101 was used for patient 1 and peptide (1-21) of HLA-DR*1501 was used for patient 2. T cell clones were then generated by limiting dilution and were phenotyped using flow cytometric analysis. Culture supernatants were analyzed for cytokine production by ELISA, and the TCR Vß expression was characterized by RT-PCR. T cell clones from patient 1 were found to be CD4+ cells which specifically proliferated to peptide (42-62) of HLA-DR*0101 and which produced IL-2 and IFN-γ after re-stimulation with the peptide. Clones from patient 2 proliferated weakly, yet specifically to peptide (1-21) of HLA-DR*1501 and were found to be CD4+ cells which produced IL-4 and IL-10 after re-stimulation with the peptide. RT-PCR transcript analysis with specific human TCR Vß primers showed that the clones from both patients expressed a restricted TCR Vß repertoire: 5.2, 8, 9, 13.1 and 13.2 for patient 1, and Vß 4, 6, 13.1, 13.1 and 13.1 for patient 2. The is the first demonstration, at the clonal level, that chronic allograft rejection in humans is associated with the presence of CD4+ MHC allopeptide-specific T cell clones that express a Th1 phenotype. In contrast, MHC allopeptide-specific T cell clones generated in the absence of rejection are associated with a (? protective) Th2 phenotype. Expanding these studies and understanding the mechanisms of immune deviation in humans should yield relevant information on the pathogenesis of chronic allograft rejection, the major clinical problem in organ transplantation.
Flame: Simplifying Topology Extension in Federated Learning (2023)

Distributed machine learning approaches, including a broad class of federated learning (FL) techniques, present a number of benefits when deploying machine learning applications over widely distributed infrastructures. The benefits are highly dependent on the details of the underlying machine learning topology, which specifies the functionality executed by the participating nodes, their dependencies and interconnections. Current systems lack the flexibility and extensibility necessary to customize the topology of a machine learning deployment. We present Flame, a new system that provides flexibility of the topology configuration of distributed FL applications around the specifics of a particular deployment context, and is easily extensible to support new FL architectures. Flame achieves this via a new high-level abstraction Topology Abstraction Graphs (TAGs). TAGs decouple the ML application logic from the underlying deployment details, making it possible to specialize the application deployment with reduced development effort. Flame is released as an open source project, and its flexibility and extensibility support a variety of topologies and mechanisms, and can facilitate the development of new FL methodologies.