gebhart/patrepeval huggingface dataset:
Dynamic conformal arcs for lung stereotactic body radiation therapy: A comparison with volumetric‐modulated arc therapy (2019)

This study constitutes a feasibility assessment of dynamic conformal arc (DCA) therapy as an alternative to volumetric-modulated arc therapy (VMAT) for stereotactic body radiation therapy (SBRT) of lung cancer. The rationale for DCA is lower geometric complexity and hence reduced risk for interplay errors induced by respiratory motion. Forward planned DCA and inverse planned DCA based on segment-weight optimization were compared to VMAT for single arc treatments of five lung patients. Analysis of dose-volume histograms and clinical goal fulfillment revealed that DCA can generate satisfactory and near equivalent dosimetric quality to VMAT, except for complex tumor geometries. Segment-weight optimized DCA provided spatial dose distributions qualitatively similar to those for VMAT. Our results show that DCA, and particularly segment-weight optimized DCA, may be an attractive alternative to VMAT for lung SBRT treatments if the patient anatomy is favorable.
A new electrowetting lab-on-a-chip platform based on programmable and virtual wall-less channels (2011)

Microscale liquid handling based on electrowetting has been previously demonstrated by several groups. Such liquid manipulation however is limited to control of individual droplets, aptly termed digital microfluidics. The inability to form continuous channels thus prevents conventional microfluidic sample manipulation and analysis approaches, such as electroosmosis and electrophoresis. In this paper, we discuss our recent progress on the development of electrowettingbased virtual channels. These channels can be created and reconfigured on-demand and preserve their shape without external stimulus. We also discuss recent progress towards demonstrating electroosmotic flows in such microchannels for fluid transport. This would permit a variety of basic functionalities in this new platform including sample transport and mixing between various functional areas of the chip.
T cell receptor repertoires associated with control and disease progression following Mycobacterium tuberculosis infection (2023)

Antigen-specific, MHC-restricted αβ T cells are necessary for protective immunity against Mycobacterium tuberculosis, but the ability to broadly study these responses has been limited. In the present study, we used single-cell and bulk T cell receptor (TCR) sequencing and the GLIPH2 algorithm to analyze M. tuberculosis-specific sequences in two longitudinal cohorts, comprising 166 individuals with M. tuberculosis infection who progressed to either tuberculosis (n = 48) or controlled infection (n = 118). We found 24 T cell groups with similar TCR-β sequences, predicted by GLIPH2 to have common TCR specificities, which were associated with control of infection (n = 17), and others that were associated with progression to disease (n = 7). Using a genome-wide M. tuberculosis antigen screen, we identified peptides targeted by T cell similarity groups enriched either in controllers or in progressors. We propose that antigens recognized by T cell similarity groups associated with control of infection can be considered as high-priority targets for future vaccine development.
Focused Hierarchical RNNs for Conditional Sequence Processing (2018)

Recurrent Neural Networks (RNNs) with attention mechanisms have obtained state-of-the-art results for many sequence processing tasks. Most of these models use a simple form of encoder with attention that looks over the entire sequence and assigns a weight to each token independently. We present a mechanism for focusing RNN encoders for sequence modelling tasks which allows them to attend to key parts of the input as needed. We formulate this using a multi-layer conditional sequence encoder that reads in one token at a time and makes a discrete decision on whether the token is relevant to the context or question being asked. The discrete gating mechanism takes in the context embedding and the current hidden state as inputs and controls information flow into the layer above. We train it using policy gradient methods. We evaluate this method on several types of tasks with different attributes. First, we evaluate the method on synthetic tasks which allow us to evaluate the model for its generalization ability and probe the behavior of the gates in more controlled settings. We then evaluate this approach on large scale Question Answering tasks including the challenging MS MARCO and SearchQA tasks. Our models shows consistent improvements for both tasks over prior work and our baselines. It has also shown to generalize significantly better on synthetic tasks as compared to the baselines.
Image-sensor-based visible light communication for automotive applications (2014)

The present article introduces VLC for automotive applications using an image sensor. In particular, V2I-VLC and V2V-VLC are presented. While previous studies have documented the effectiveness of V2I and V2V communication using radio technology in terms of improving automotive safety, in the present article, we identify characteristics unique to image-sensor-based VLC as compared to radio wave technology. The two primary advantages of a VLC system are its line-of-sight feature and an image sensor that not only provides VLC functions, but also the potential vehicle safety applications made possible by image and video processing. Herein, we present two ongoing image-sensor-based V2I-VLC and V2VVLC projects. In the first, a transmitter using an LED array (which is assumed to be an LED traffic light) and a receiver using a high-framerate CMOS image sensor camera is introduced as a potential V2I-VLC system. For this system, real-time transmission of the audio signal has been confirmed through a field trial. In the second project, we introduce a newly developed CMOS image sensor capable of receiving highspeed optical signals and demonstrate its effectiveness through a V2V communication field trial. In experiments, due to the high-speed signal reception capability of the camera receiver using the developed image sensor, a data transmission rate of 10 Mb/s has been achieved, and image (320 × 240, color) reception has been confirmed together with simultaneous reception of various internal vehicle data, such as vehicle ID and speed.
RCT Abstract - The effect of inhaled hypertonic saline on lung structure in preschool children with cystic fibrosis (2021)

<b>Background:</b> Inhaled 7% hypertonic saline(HS) is used to improve mucociliary clearance for Cystic Fibrosis (CF) lung disease. It is unclear if HS maintenance therapy can slow progression of CF structural lung changes in preschool children with CF (pCwCF). <b>Objective:</b> To investigate the efficacy of inhaled HS for 48 weeks on quantitative chest CT score in pCwCF <b>Methods:</b> pCwCF aged 3-6 years were enrolled in a multicentre, randomised, double-blind, controlled trial. pCwCF were randomised to 7% HS or 0.9% isotonic saline(IS) inhalation twice daily for 48 weeks. CTs were obtained at baseline and 48 weeks and were scored using PRAGMA-CF method to quantify % of lung volume occupied by Bronchiectasis (%BE), Mucus Plugging (%MP) and Airway Wall Thickening (%AWT) on inspiratory scans and Trapped Air(%TA) on expiratory scans. Primary outcome was %Dis which is the sum of airway-related abnormalities (%BE+%MP+%AWT). Regression analysis was used to investigate the difference in %Dis at 48 weeks between groups. <b>Results:</b> 116 pCwCF (56 HS, 60 IS), median age 55.0 months (range 36.2-71.7 months) were enrolled at 23 sites in Europe, North America, and Australia. Mean(95%CI) estimated %Dis at 48 weeks was 0.93 (0.63,1.23) in the HS and 1.60(1.31,1.88) in the IS(mean difference 0.67,95%CI, 0.25 to 1.09; p=0.019). Similar differences between groups were found in %BE and %TA (p=0.016 and p=0.005, respectively). <b>Conclusion:</b> Inhaled HS for 48 weeks had a significant positive and clinically relevant impact on structural lung changes on chest CT in pCwCF relative to IS. This is the first demonstration of an intervention that alters the progressive trajectory of structural disease&nbsp;in young children with CF (Funded by CFFT).
Long‐range acoustic transmission in the northwest Atlantic (1980)

An acoustic propagation experiment conducted west of Bermuda during the fall of 1978 demonstrated that individual acoustic arrivals at 900‐km range were stable and identifiable over a 48‐day period. The observed arrival pattern is interpreted by geometric ray theory and by comparison with a ‘synthetic sofargram’ (equivalent to a synthetic seismogram) constructed from WKBJ theory. Using geometric ray theory, we examine the expected generation and annihilation of ray paths as a result of the seasonal erosion of the autumnal thermocline. Many rays are converted from purely refracted to surface reflected/refracted rays. The ultimate goal of this work is to interpret variability in acoustic transmission in terms of ocean variability.
Sorting nexin 1 loss results in increased oxidative stress and hypertension (2020)

Acute renal depletion of sorting nexin 1 (SNX1) in mice results in blunted natriuretic response and hypertension due to impaired dopamine D<sub>5</sub> receptor (D<sub>5</sub> R) activity. We elucidated the molecular mechanisms for these phenotypes in Snx1<sup>-/-</sup> mice. These mice had increased renal expressions of angiotensin II type 1 receptor (AT<sub>1</sub> R), NADPH oxidase (NOX) subunits, D<sub>5</sub> R, and NaCl cotransporter. Basal reactive oxygen species (ROS), NOX activity, and blood pressure (BP) were also higher in Snx1<sup>-/-</sup> mice, which were normalized by apocynin, a drug that prevents NOX assembly. Renal proximal tubule (RPT) cells from hypertensive (HT) Euro-American males had deficient SNX1 activity, impaired D<sub>5</sub> R endocytosis, and increased ROS compared with cells from normotensive (NT) Euro-American males. siRNA-mediated depletion of SNX1 in RPT cells from NT subjects led to a blunting of D<sub>5</sub> R agonist-induced increase in cAMP production and decrease in Na<sup>+</sup> transport, effects that were normalized by over-expression of SNX1. Among HT African-Americans, three of the 12 single nucleotide polymorphisms interrogated for the SNX1 gene were associated with a decrease in systolic BP in response to hydrochlorothiazide (HCTZ). The results illustrate a new paradigm for the development of hypertension and imply that the trafficking protein SNX1 may be a crucial determinant for hypertension and response to antihypertensive therapy.
Synthesis of chemically reactive analogues of AZT and their biological evaluation against HIV (1988)

Several 3'-deoxythymidine analogues were prepared and tested against HIV. The choice of analogues was based on their possible covalent binding to the enzyme reverse transcriptase.
Proactive call drop avoidance in UMTS networks (2013)

The rapid advancement of smartphones has instigated tremendous data applications for cell phones. Supporting simultaneous voice and data services in a cellular network is not only desirable but also becoming indispensable. However, if the voice and data are serviced through the same antenna (like the 3G UMTS network), a voice call with data sessions requires better radio connection than a voice-only call. In this paper, we systematically study the coordination between the voice and data transmissions in UMTS networks. From analyzing a large carrier's UMTS network recording data, we first identify the most relevant network measurements/features indicating a potential call drop, then propose a drop-call predictor based on AdaBoost. Moreover, we develop an intelligent call management strategy to voluntarily block data sessions when the voice is predicted to be dropped. Our analysis utilizing real service provider's data sets shows that our proposed scheme can not only predict drop calls with a very high accuracy but also achieve the highest user satisfaction compared to the other existing call management strategies.
Natural Antioxidants as a Component of an Egg Albumen Film in the Reduction of Lipid Oxidation in Cooked and Uncooked Poultry (2002)

ABSTRACT: Egg albumen coatings with natural antioxidants fenugreek, rosemary, and vitamin E were evaluated for their antioxidant activity in diced raw and diced cooked poultry breast meat. Coatings were applied using a vacuum tumbling and a boiling method. Coated samples and uncoated controls were evaluated for their malondialdehyde and reactive substances content as a measure of lipid oxidation via the thiobarbituric acid test. Cooked egg albumen‐coated samples showed reactive compound changes of 1.56 × 10 −7 M for 4 d of refrigeration, compared to 1.59 × 10 −6 M change in the cooked control. Raw control changed by 1.97 × 10 −6 M versus 1.67 × 10 −6 M for raw rosemary coated samples. In raw and cooked studies EAS coating showed most effective against lipid oxidation.
Dreiklang - the one, two, three in photoswitching. (2012)

The green fluorescent protein and its homologues have become essential tools for the visualization of protein distributions and of dynamic processes in living cells and organisms. In the last decade members of a new subclass of fluorescent proteins, namely the reversibly switchable fluorescent proteins (RSFPs) have attracted widespread attention for their unique property that they may be repeatedly photoswitched between a fluorescent and a non-fluorescent state by irradiation with light of two distinct wavelengths. However, the full potential of these conventional RSFPs has been curtailed for many applications since switching and fluorescence read-out in these proteins is strictly coupled. To overcome this limitation we generated the RSFP Dreiklang, which enables reversible photoswitching independently from fluorescence excitation. In Dreiklang, fluorescence is excited at ~515 nm, whereas reversible on- and off- switching is accomplished at illumination wavelengths of ~365 nm and ~405 nm, respectively. High resolution X-ray analysis of single Dreiklang protein crystals in the photoswitched off- and on-states demonstrate that switching in Dreiklang is based on a reversible hydration/dehydration reaction of the chromophore. This molecular reversible switching mechanism was further supported by mass spectrometry data. The unique switching properties of Dreiklang enabled far-field fluorescence super-resolution microscopy in living mammalian cells using both an ensemble and a single molecule based switching approach. Dreiklang represents a new class of RSFPs opening up new possibilities in light microscopy.
Enantioselective Catalysis in Water: Mukaiyama‐Aldol Condensation Promoted by Copper Complexes of Bisoxazolines Supported on Poly(ethylene glycol). (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Clonal hematopoiesis and therapy-related myeloid neoplasms following neuroblastoma treatment (2021)

Therapy-related myeloid neoplasms (TMN) constitute one of the most challengingcomplications of cancer treatment.1 Whilst understanding of TMN pathogenesis remains fragmentary, genomic studies in adults have thus far refuted the notion that TMN simply result from cytotoxin-induced DNA damage.2–4 Analysis of the preclinical evolution of a limited number of adult TMN have retraced the majority of cases to clonal haematopoiesis (CH) that predates cytotoxic treatment and lacks the mutational footprint of genotoxic therapies.2–6 Balanced translocations, generally attributed to treatment with topoisomerase II inhibitors, are implicated in a minority of TMN.1 TMN is a leading cause of premature death in childhood cancer survivors, and affects 7-11% of children treated for high-risk neuroblastoma and sarcoma.7,8 However, the origin of pediatric TMN remains unclear. Targeted sequencing of known cancer genes detects CH in ~4% of children following cytotoxic treatment,6,9 whereas CH is vanishingly rare in young individuals in the general population.10,11 Moreover, to our knowledge, no cases of childhood TMN have been retraced to pretreatment CH. In light of these observations, we asked whether a broader driver landscape had eluded targeted CH screens in pediatric cancer patients and/or whether therapy-induced mutagenesis may be an under-recognised catalyst of CH and TMN in this patient group.
Optical Spectral Surveillance of Breast Tissue Landscapes for Detection of Residual Disease in Breast Tumor Margins (2013)

We demonstrate a strategy to "sense" the micro-morphology of a breast tumor margin over a wide field of view by creating quantitative hyperspectral maps of the tissue optical properties (absorption and scattering), where each voxel can be deconstructed to provide information on the underlying histology. Information about the underlying tissue histology is encoded in the quantitative spectral information (in the visible wavelength range), and residual carcinoma is detected as a shift in the histological landscape to one with less fat and higher glandular content. To demonstrate this strategy, fully intact, fresh lumpectomy specimens (n = 88) from 70 patients were imaged intra-operatively. The ability of spectral imaging to sense changes in histology over large imaging areas was determined using inter-patient mammographic breast density (MBD) variation in cancer-free tissues as a model system. We discovered that increased MBD was associated with higher baseline β-carotene concentrations (p = 0.066) and higher scattering coefficients (p = 0.007) as measured by spectral imaging, and a trend toward decreased adipocyte size and increased adipocyte density as measured by histological examination in BMI-matched patients. The ability of spectral imaging to detect cancer intra-operatively was demonstrated when MBD-specific breast characteristics were considered. Specifically, the ratio of β-carotene concentration to the light scattering coefficient can report on the relative amount of fat to glandular density at the tissue surface to determine positive margin status, when baseline differences in these parameters between patients with low and high MBD are taken into account by the appropriate selection of threshold values. When MBD was included as a variable a priori, the device was estimated to have a sensitivity of 74% and a specificity of 86% in detecting close or positive margins, regardless of tumor type. Superior performance was demonstrated in high MBD tissue, a population that typically has a higher percentage of involved margins.
An Analysis of Hierarchical Genetic Programming (1995)

Hierarchical genetic programming (HGP) approaches rely on the discovery, modification, and use of new functions to accelerate evolution. This paper provides a qualitative explanation of the improved behavior of HGP, based on an analysis of the evolution process from the dual perspective of diversity and causality. From a static point of view, the use of an HGP approach enables the manipulation of a population of higher diversity programs. Higher diversity increases the exploratory ability of the genetic search process, as demonstrated by theoretical and experimental fitness distributions and expanded structural complexity of individuals. From a dynamic point of view, this report analyzes the causality of the crossover operator. Causality relates changes in the structure of an object with the effect of such changes, i.e. changes in the properties or behavior of the object. The analyses of crossover causality suggests that HGP discovers and exploits useful structures in a bottom-up, hier...
Phase I and pharmacokinetic study of farletuzumab in solid tumors. (2012)

3084 Background: Farletuzumab (F) is a humanized monoclonal antibody against folate receptor α (FRA). Expression of FRA is reported to be 90% and 40% in ovarian cancer (OC) and gastric cancer (GC), respectively. The purpose of the study is to assess tolerability, pharmacokinetic profile and preliminary antitumor effect in solid tumors. Methods: Patients with OC or FRA expressing solid tumor who are resistant to standard treatments are eligible in the study. After pharmacokinetic (PK) run-in, F was administered by IV injection repeating every week until disease progression. PK profile was analyzed on day1 to day 10 in PK run-in and on day 22 to 29 in cycle 1. Dose limiting toxicities (DLTs) were defined as G4 hematological and G3/4 non-hematological toxicities by NCI-CTCAE. Dose escalation was planed in 4 cohorts (50, 100, 200 and 400mg/m 2 ). Results: Sixteen patients (14 OC and 2GC) received F infusion. Neither DLTs nor G3/4 toxicities were reported in all cohorts. As adverse events, G1/2 infusion reaction (44%), headache (44%), cytokine release syndrome (38%), nausea (31%) and appetite loss (31%) were observed and medically managed. AUC and C max. were increased dose-dependently and linear PK profiles were identified with median clearance between 6.02 and 10.54 mL/hr/m 2 in each cohort. No tumor shrinkage was recorded, but long-term disease stabilization for 22+ mos. and 10+ mos. were observed in one patient with clear cell OC (100mg/m 2 ) and one patient with GC (400 mg/m 2 ), respectively. No cumulative toxicities were observed in these 2 patients. Conclusions: The toxicities of F in Japanese patients were manageable with similar PK profile as compared with the US population (Konner et al. Clin Cancer Res 2010: 16; 5288-95). Long term disease stabilization is observed in subpopulation of clear cell OC and GC.
Fidelity Decay Saturation Level for Initial Eigenstates (2002)

We show that the fidelity decay between an initial eigenstate state evolved under a unitary chaotic operator and the same eigenstate evolved under a perturbed operator saturates well before the 1/N limit, where $N$ is the size of the Hilbert space, expected for a generic initial state. We provide a theoretical argument and numerical evidence that, for intermediate perturbation strengths, the saturation level depends quadratically on the perturbation strength.
Effect of Fabricating Temperature and Volume Fraction of Nb Sheet on Impact Properties of Nb/MoSi<SUB>2</SUB>-ZrO<SUB>2</SUB> Laminate Composites (2000)

Nb/MoSi2-ZrO2 laminate composites have been successfully fabricated by alternately stacking MoSi2-ZrO2 powder layer and Nb sheet, followed by hot pressing in a graphite mould. The selected fabricating parameters were hot press temperature and volume fraction of Nb sheet. The instrumented Charpy impact test was carried out at the room temperature in order to investigate the relationship between impact properties and fabricating conditions. The interfacial shear strength between MoSi2-ZrO2 and Nb, which is associated with the fabricating temperature and the growth of interfacial reaction layer, is also discussed. The plastic deformation of Nb sheet and the interfacial delamination were macroscopically observed. The Nb/MoSi2-ZrO2 laminate composites had the maximum impact value when fabricated at 1623 K, accompanying the increase of fracture displacement and crack propagation energy. The impact value of Nb/MoSi2-ZrO2 laminate composites dramatically increased with increasing the volume fraction of Nb sheet and showed 64.9 kJ/m2 for Nb content of 15 vol%. The interfacial shear strength of Nb/MoSi2-ZrO2 laminate composites increased with the growth of interfacial reaction layer, which resulted from the increase of fabricating temperature. It is useful to promote an appropriate interfacial shear strength for the enhancement of impact value of Nb/MoSi2-ZrO2 laminate composites. A large increase of interfacial shear strength restrains the plastic deformation of Nb sheet.
Neutron Dark-Field Tomography (2008)

We report how a grating interferometer yields neutron dark-field scatter images for tomographic investigations. The image contrast is based on ultrasmall-angle scattering. It provides otherwise inaccessible spatially resolved information about the distribution of micrometer and submicrometer sized structural formations. Three complementary sets of tomographic data corresponding to attenuation, differential phase, and small-angle scattering can be obtained from one measurement. The method is compatible with conventional imaging and provides significantly higher efficiency than existing techniques.