gebhart/patrepeval huggingface dataset:
Data from Voxel Forecast for Precision Oncology: Predicting Spatially Variant and Multiscale Cancer Therapy Response on Longitudinal Quantitative Molecular Imaging (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Prediction of spatially variant response to cancer therapies can inform risk-adaptive management within precision oncology. We developed the “Voxel Forecast” multiscale regression framework for predicting spatially variant tumor response to chemoradiotherapy on fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) imaging.&lt;/p&gt;Experimental Design:&lt;p&gt;Twenty-five patients with locally advanced non–small cell lung cancer, enrolled on the FLARE-RT phase II trial (NCT02773238), underwent FDG PET/CT imaging prior to (PETpre) and during week 3 (PETmid) of concurrent chemoradiotherapy. Voxel Forecast was designed to predict tumor voxel standardized uptake value (SUV) on PETmid from baseline patient-level and voxel-level covariates using a custom generalized least squares (GLS) algorithm. Matérn covariance matrices were fit to patient- specific empirical variograms of distance-dependent intervoxel correlation. Regression coefficients from variogram-based weights and corresponding standard errors were estimated using the jackknife technique. The framework was validated using statistical simulations of known spatially variant tumor response. Mean absolute prediction errors (MAEs) of Voxel Forecast models were calculated under leave-one-patient-out cross-validation.&lt;/p&gt;Results:&lt;p&gt;Patient-level forecasts resulted in tumor voxel SUV MAE on PETmid of 1.5 g/mL while combined patient- and voxel-level forecasts achieved lower MAE of 1.0 g/mL (&lt;i&gt;P&lt;/i&gt; &lt; 0.0001). PETpre voxel SUV was the most important predictor of PETmid voxel SUV. Patients with a greater percentage of under-responding tumor voxels were classified as PETmid nonresponders (&lt;i&gt;P&lt;/i&gt; = 0.030) with worse overall survival prognosis (&lt;i&gt;P&lt;/i&gt; &lt; 0.001).&lt;/p&gt;Conclusions:&lt;p&gt;Voxel Forecast multiscale regression provides a statistical framework to predict voxel-wise response patterns during therapy. Voxel Forecast can be extended to predict spatially variant response on multimodal quantitative imaging and may eventually guide optimized spatial–temporal dose distributions for precision cancer therapy.&lt;/p&gt;&lt;/div&gt;
Strain Sensing Using a Single Silicon Vacancy Center in a Diamond Cantilever (2022)

The 53rd Annual Meeting of the APS Division of Atomic, Molecular and Optical Physics will take place from May 30 – June 3, 2022 in Orlando, Fl, USA. <a href="https://morressier.zoom.us/j/89880865272?pwd=SWxTRGhra1ZOSDBrSkhVZDBzVDR6UT09/">Virtual Presenter Help Desk</a>
Machine efficiency optimization using ripple correlation control (2002)

It is well known that when DC and field-oriented-controlled induction machines are under-loaded they experience unnecessary losses because of excessive field excitation. Present methods to provide an adaptive flux reference involve extensive calculation based on machine models, or intentionally perturb the rotor flux to obtain gradient information. This paper presents a straightforward and convenient method of optimization based on ripple correlation control. Exact parameter knowledge is not needed and the method has small computational requirements.
Neutrophil products that inhibit cell proliferation: relation to granulocytic "chalone" (1978)

Various investigators have proposed the existence of a “chalone” or product of mature granulocytes which inhibits the replication of granulocytic progenitors in a tissue-specific, species-nonspecific regulatory system. We tested this system utilizing purified populations of human leukocytes and a variety of proliferating target cell populations. Granulocyte-conditioned medium potently inhibited 3Hthymidine incorporation in normal mouse bone marrow, in mouse erythroid precursors from spleens of phenylhydrazinetreated animals, and in human leukemic myeloblasts. This effect occurred without demonstrable cytotoxicity. Human marrow was only slightly inhibited and mitogen-stimulated proliferating lymphocytes were unaffected. Granulocyte-conditioned medium was also inhibitory in colony-forming assays for erythroid precursors but not for granulocyte precursors. It also reduced the mitotic index of proliferating erythroid progenitors in mouse spleen. Inhibitory activity was separable into at least two components on the basis of stability during heating and ultrafiltration, and in susceptibility to digestion by proteolytic enzymes. On the basis of these observations, we concluded that human granulocytes contain potent inhibitors of growth and 3H-thymidine uptake of some proliferating hematopoietic cells, but these are not true granulocyte “chalones.” I N 1960, Bullough and Lawrence provided experimental evidence for the control of epidermal cell mitosis by products of mature cells in culture in vitro.’ They evolved the concept of a tissue-specific product of differentiated cells that served as a mitotic inhibitor of early cells of the same line. They termed the inhibitor a “chalone” (from the Greek, “to loosen” or “make slack”). Since then, a number of experimenters have suggested the existence of chalones specific for various tissues.2 More recently, various investigators have emphasized theoretical reasons why granulopoiesis should be under negative feedback control and have adduced evidence for the existence of granulocyte chalones.38 However, the diversity of model systems, methodologic limitations, and frequently inadequate experimental design have made interpretations difficult. RytOmaa and Kiviniemi,7’8 Paukovitz,5’6 and Bateman3 have presented evidence suggesting that rat and calf serum solutions “conditioned” by granulocyte-rich cell suspensions and spleen homogenates inhibit DNA synthesis in developing myeloid precursors in short-term cultures of rat bone marrow cells. This “chalone” material has been partially purified by gel filtration, ultrafiltration, and electrophoresis.57 It is reported to be a polypeptide of a molecular weight of approximately 4000-5000 daltons, which is unstable at 4#{176}C,8 with
Ultra-low Jitter Frequency Stabilized Mode-locked Laser (2009)

We report a low noise, frequency stabilized, semiconductor based, 10.287 GHz actively mode- locked laser with 1000 finesse intracavity etalon, with a timing jitter (1Hz – 100MHz) of 3 fs and optical linewidth &lt;1 kHz.
Macrovascular contributions to high-resolution balanced SSFP- and GE-EPI-based fMRI at 9.4T evaluated using surface-based cortical depth analyses in human visual cortex (2017)

Several strategies have been proposed for maximizing neuronal specificity of fMRI by utilizing pulse sequences that are primarily sensitive to signal changes within microvasculature. Here we compare the microvascular sensitivity of high-resolution balanced SSFP and gradient-echo EPI at 9.4T using cortical depth analyses within human visual cortex. Because of the large draining vessels lying along the pial surface, the behavior of fMRI signals as a function of cortical depth can provide helpful insights into the vascular contributions. Our preliminary analyses suggest that, for the protocols used here, both balanced SSFP and EPI show similar cortical depth profiles of BOLD responses.
Carbonyl(pyridine)iron(II) Tetrabenzporphyrin π‐Radical Cation (1978)

“Oxidation state isomerism” exists between porphyrins which differ only in the localization of their electrons. Such a system is that of the title compound [Fe II (TBP + )(CO)(py)]⊕, in which one electron is removed from the porphyrin ring, and the corresponding (unknown) Fe III porphyrin.
P1‐258: Genome‐Wide Analysis of Large Rare Copy Number Variations in Alzheimer Disease Among Caribbean Hispanics (2011)

Recently, candidate gene and genome-wide association studies in large cohorts of cases and controls have identified associations of sporadic late-onset AD with SNPs in the CLU, PICALM, BIN1, CR1, ABCA7, and SORL1 genes. However, the disease variants in these genes have not yet been found. We analyzed signal intensity data from a SNP genotyping array in order to estimate genome-wide contribution of copy number variants (CNVs) to the risk of AD in our Caribbean Hispanic dataset. CNVs were identified using SNP-array intensity files from the GWAS: 549 AD cases and 544 controls genotyped on the Illumina 650Y v2 array. Raw array data was normalized using the Illumina's BeadStudio software v.3.3.7. In order to obtain high-confidence CNV calls, we applied three CNV prediction algorithms: QuantiSNP, iPattern, and PennCNV. Stringent CNVs were called by two or more prediction algorithms and had sizes of 100 Kb or greater (= 5 consecutive probes). Quality control steps retained 392 cases and 357 controls for subsequent analyses. Global burden analyses for rare CNVs (=1%) were performed with PLINK v1.07 and genome-wide P-values were estimated by permutation (one-sided, 100,000 permutations). A total of 734 rare CNVs were observed in our dataset, including 277 deletions and 457 duplications. None of these CNVs affected well-confirmed AD-associated genes. AD cases did not show a higher global burden for rare CNVs when compared to controls, even when considering deletion-only and duplication-only subsets. For instance, case/control ratio for all rare CNV events was 1.03 (empirical P = 0.35); and no significant differences between cases and controls were detected for size or number of deletions/duplications. Also, no evidence of global enrichment was observed for rare genic CNVs in cases vs controls. In the Caribbean Hispanic dataset we found no significant genome-wide differences between cases and controls in the CNV rate, total or average CNV size, and the number of genes affected by rare large CNVs. Our study highlights the general challenges in the field of genetics of complex diseases, such as a need for thee valuation of large datasets in order to accurately assess association with rare disease-related variations.
Investigation of switch designs for a prolate-spheroidal impulse radiating antenna (2010)

Summary form only given. The prolate-spheroidal impulse radiating antenna (PSIRA) is used to focus a fast (100 ps), high voltage (> 100 kV) pulse launched from the first focal point onto targets located at the second focal point. These fast electromagnetic pulses with high amplitude are used in various biological applications such as skin cancer treatment and gene insertion. For these fast, high voltage pulses a switch system is desired to radiate spherical TEM waves from the first focal point. The switch system consists of the switch cones, gas (hydrogen) chamber and the pressure vessel. We have investigated various switch cone geometries which deviate from previous designs used in the prototype IRA system. Impedance considerations play an important role in the design of such a switch system. The use of 100 ps pulses also presents the interesting possibility of reducing the feed arms from the PSIRA. The waves radiated from the switch/source and the focal impulse waveforms for each design are explored using numerical simulations. The hydrogen chamber and pressure vessel are required to avoid dielectric breakdown when the switch is subjected to input voltages of greater than 100 kV. The design of the pressure vessel involves optimizing the dimensions and determining suitable dielectric material so that a spherical TEM wave emanates from the first focal point. The design must also be easy to fabricate. Numerical simulations to investigate the pressure vessel design are presented in this paper. The possibility of using the pressure vessel as a lens is also explored.
Altered Processing of Pro-Orphanin FQ/Nociceptin and Pro-Opiomelanocortin-Derived Peptides in the Brains of Mice Expressing Defective Prohormone Convertase 2 (2001)

The bioactivity of neuropeptides can be regulated by a variety of post-translational modifications, including proteolytic processing. Here, gene-targeted mice producing defective prohormone convertase 2 (PC2) were used to examine the post-translational processing of two neuroendocrine prohormones, pro-opiomelanocortin (POMC) and pro-orphanin FQ (pOFQ)/nociceptin (N), in the brain. Reversed-phase HPLC and gel-exclusion chromatography were combined with specific radioimmunoassays to analyze the processing patterns of these two prohormones in the hypothalamus and the amygdala. In the case of POMC, the lack of PC2 activity completely prevented carboxy-shortening of beta-endorphins and greatly diminished conversion of beta-lipotropin to gamma-lipotropin and beta-endorphin. Although conversion of beta-lipotropin to beta-endorphin decreased, the lack of PC2 activity caused an increase in beta-lipotropin and beta-endorphin levels in the mutant animals, but no increases in POMC or biosynthetic intermediates were seen. The extent of OFQ/N production was significantly lower in PC2-deficient mice and there was an accumulation of relatively large amounts of pOFQ/N and biosynthetic intermediates. These results demonstrate that PC2 is directly involved in the biogenesis of two brain neuropeptides in vivo and suggest that the specific prohormone and cellular context influences neuropeptide processing by PCs.
Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP‐independent amino acid racemases (2002)

The X-ray crystal structure has revealed two similar alpha/beta domains of aspartate racemase (AspR) from Pyrococcus horikoshii OT3, and identified a pseudo mirror-symmetric distribution of the residues around its active site [Liu et al. (2002) J. Mol. Biol. 319, 479-489]. Structural homology and functional similarity between the two domains suggested that this enzyme evolved from an ancestral domain by gene duplication and gene fusion. We have expressed solely the C-terminal domain of this AspR and determined its three-dimensional structure by X-ray crystallography. The high structural stability of this domain supports the existence of the ancestral domain. In comparison with other amino acid racemases (AARs), we suggest that gene duplication and gene fusion are conventional ways in the evolution of pyridoxal 5'-phosphate-independent AARs.
Development of an Fn14 agonistic antibody as an anti-tumor agent (2011)

TWEAK, a TNF family ligand with pleiotropic cellular functions, was originally described as capable of inducing tumor cell death in vitro. TWEAK functions by binding its receptor, Fn14, which is up-regulated on many human solid tumors. Herein, we show that intratumoral administration of TWEAK, delivered either by an adenoviral vector or in an immunoglobulin Fc-fusion form, results in significant inhibition of tumor growth in a breast xenograft model. To exploit the TWEAK-Fn14 pathway as a therapeutic target in oncology, we developed an anti-Fn14 agonistic antibody, BIIB036. Studies described herein show that BIIB036 binds specifically to Fn14 but not other members of the TNF receptor family, induces Fn14 signaling, and promotes tumor cell apoptosis in vitro. In vivo, BIIB036 effectively inhibits growth of tumors in multiple xenograft models, including colon (WiDr), breast (MDA-MB-231), and gastric (NCI-N87) tumors, regardless of tumor cell growth inhibition response observed to BIIB036 in vitro. The anti-tumor activity in these cell lines is not TNF-dependent. Increasing the antigen-binding valency of BIB036 significantly enhances its anti-tumor effect, suggesting the contribution of higher order cross-linking of the Fn14 receptor. Full Fc effector function is required for maximal activity of BIIB036 in vivo, likely due to the cross-linking effect and/or ADCC mediated tumor killing activity. Taken together, the anti-tumor properties of BIIB036 validate Fn14 as a promising target in oncology and demonstrate its potential therapeutic utility in multiple solid tumor indications.
Analog programmable chips for implementing ANNs using capacitive weight storage (2002)

The design approach for fully multiplexed 32*32 and 128*64 programmable analog vector-matrix multipliers utilizing capacitive weight storage is described. A fully differential design has been used throughout the signal path for cancellation of common-mode noise feedthroughs and reduction of multiplier and multiplexer offsets. The 32*32 vector-matrix multiplier circuit has been fabricated using the MOSIS 2- mu m P-well CMOS technology. A method to increase dynamic range and a method to reduce power dissipation by an order of magnitude are described. Results showing operation of the 32*32 vector-matrix multiplier circuit are reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
On the origin of the redshift in the emission wavelength of InGaN/GaN blue light emitting diodes grown with a higher temperature interlayer (2012)

A redshift of the peak emission wavelength was observed in the blue light emitting diodes of InGaN/GaN grown with a higher temperature interlayer that was sandwiched between the low-temperature buffer layer and high-temperature unintentionally doped GaN layer. The effect of interlayer growth temperature on the emission wavelength was probed and studied by optical, structural, and electrical properties. Numerical studies on the effect of indium composition and quantum confinement Stark effect were also carried out to verify the experimental data. The results suggest that the redshift of the peak emission wavelength is originated from the enhanced indium incorporation, which results from the reduced strain during the growth of quantum wells.
A compact, low resolution, wavelength monitor applied to Raman pump power monitoring (2004)

We demonstrate an ultra-compact, low cost coarse wavelength monitor. Wavelength resolution of 7 nm is achieved through core-radiation mode coupling of a tilted grating in photosensitive clad fiber. We applied the device to measure the powers of a multiwavelength source.
Supplementary Figures Legends from Pharmacological Inhibition of the Protein Kinase MRK/ZAK Radiosensitizes Medulloblastoma (2023)

&lt;p&gt;Legends to Supplementary Figures&lt;/p&gt;
A new type of demountable optical device for coupling single-mode planar waveguides to a multifiber array using passive alignment (1995)

A novel demountable optical device is developed for coupling single-mode waveguides to a multifiber array using passive alignment. This device is fabricated by forming V-grooves on a waveguide chip and precisely molding both end portions of the chip. The 1/spl times/8 coupling device exhibits a low insertion loss of 10.7 dB and a small loss change of /spl plusmn/0.2 dB for 100 reconnections.
Supposedly identical microplastic particles substantially differ in their material properties influencing particle-cell interactions and cellular responses (2021)

Microplastics and its putative adverse effects on environmental and human health increasingly gain scientific and public attention. Systematic studies on the effects of microplastics are currently hampered by using rather poorly characterised particles, leading to contradictory results for the same particle type. Here, surface properties and chemical composition of two commercially available nominally identical polystyrene microparticles, frequently used in effect studies, were characterised. We show distinct differences in monomer content, ζ-potentials and surface charge densities. Cells exposed to particles showing a lower ζ-potential and a higher monomer content displayed a higher number of particle-cell-interactions and consequently a decrease in cell metabolism and proliferation, especially at higher particle concentrations. Our study emphasises that no general statements can be made about the effects of microplastics, not even for the same polymer type in the same size class, unless the physicochemical properties are well characterised.
The Spectrum of Clinical and Laboratory Findings Resulting from Human Herpesvirus-6 (HHV-6) in Patients with Mononucleosis-Like Illnesses not Resulting from Epstein-Barr Virus or Cytomegalovirus (1990)

Recently, the morphologic, immunologic, and molecular makeup of a new virus designated human herpesvirus-6 (HHV-6) has been described. Because cell cultures of HHV-6-infected mononuclear cells showed prominent lymphocytic changes, it could be anticipated that mononucleosis-like illnesses or lymphoproliferative disorders would turn out to be manifestations of active HHV-6 infection. In the present study, blood samples from 27 patients previously categorized as having non-Epstein-Barr virus (non-EBV)/noncytomegalovirus (non-CMV) heterophil-negative mononucleosis-like illnesses were tested for IgM and IgG antibodies to HHV-6. Eight of these patients (30%) had serologic evidence of active HHV-6 infection. The clinical spectrum includes a short-lived febrile illness, mild cervical lymphadenopathy, laboratory data suggestive of active viral hepatitis in two patients, and a prolonged febrile illness in a single patient with previously documented positive anti-HIV serology. The viral studies revealed the presence of fourfold HHV-6-specific IgG titer increases by immunofluorescent assay (IFA) in seven serially studied cases and positive IgM serology on one or more samples tested by IFA or enzyme-linked immunosorbent assay (ELISA) in all eight cases. The authors could not determine whether the illnesses represented primary HHV-6 infections in susceptible individuals or reactivation of latent virus. HHV-6 serologic studies may be indicated in patients with mononucleosis-like illnesses with atypical lymphocytosis when EBV and CMV test results are nondiagnostic.
Buffer Requirements at ECN-Capable RED Gateways to Minimize Packet Losses (2006)

Explicit congestion notification (ECN) used with random early detection (RED) is known to reduce delays for low-bandwidth delay-sensitive transport control protocol (TCP) connections by avoiding unnecessary packet drops and retransmissions. However, choosing the optimum values for buffer size and RED parameters is still an ongoing research topic. In this paper, we present a model to determine the buffer size and RED parameters to minimize packet losses at a RED gateway
Classical analysis of microcavity lasers (1993)

Antenna theory is developed for the study of spontaneous emission by atomic dipoles in microcavity lasers.
Spectroscopic measurement of packaging-induced strains in quantum-well laser diodes (1999)

Packaging-induced strain is studied in high-power semiconductor lasers by a noninvasive optical technique. Fourier-transform photocurrent measurements with intentionally strained laser array devices for 808 nm emission reveal spectral shifts of optical transitions within the active region. These shifts by up to 10 meV serve as a measure for the strain status within the active layer of the devices and are compared with model calculations. For different packaging architectures we quantify the strain portion which is transmitted to the optically active region of the semiconductor device.