gebhart/patrepeval huggingface dataset:
A large Turkish kindred with syndactyly type II (synpolydactyly). 2. Homozygous phenotype? (1995)

Syndactyly type II (synpolydactyly (SPD)) is an autosomal dominant condition with typical abnormalities of the distal parts of both upper and lower limbs. We report here a previously undescribed phenotypic feature of people with severe hand and foot deformities who were born to two affected parents. This is the first example of SPD subjects manifesting a very distinctive phenotype, suggesting that they must be homozygous for this condition. The typical characteristic clinical features in these subjects are as follows: (1) short hands with wrinkled fatty skin and short feet; (2) complete soft tissue syndactyly involving all four limbs; (3) polydactyly of the preaxial, mesoaxial, and postaxial digits of the hands; (4) loss of the normal tubular shape of the carpal, metacarpal, and phalangeal bones, so as to give polygonal structures; (5) loss of the typical structure of the cuboid and all three cuneiform bones while the talus calcaneus and navicular bones remain intact; (6) large bony islands instead of metatarsals, most probably because of cuboid-metatarsal and cuneiform-metatarsal fusions; and (7) severe middle phalangeal hypoplasia/aplasia as well as fusion of some phalangeal structures that are associated with the loss of normal phalangeal pattern. We report seven subjects with this phenotype from three different branches of a very large SPD pedigree exhibiting the same phenotype with minimal variation. In mice, the Polysyndactyly (Ps) mutation shows a pattern of synpolydactyly very similar to that of human SPD, suggesting that they may well be homologous mutations. A molecular genetic study is currently under way to determine the chromosomal location of the SPD locus in humans and to identify the corresponding homologous region in mice.
Design of a Cold Plate Tester for Accurate Measurement of Thermal Performance (2005)

With the continuing industry trends towards smaller, faster and higher power devices, thermal management has become an extremely important element in the development of computer products. The primary goal of a good thermal design is to ensure that the chip can function at its rated frequency, while maintaining its junction temperature below the specified limit, to ensure reliable operation. The use of a heat sink or cold plate to manage the external thermal resistance has been well documented in the literature. However, the measurement of thermal performance of today state-of-the-art cold plates is challenging because of the low value of thermal resistance that they offer to heat dissipation. In this paper, the design of a tester apparatus for such high performance cold plates is presented. The expected performance of the tester is modeled numerically for a heat flux of 250 W/cm2, and for a range of footprint areas of 100-400 mm2. The analysis study is supported by a detailed uncertainty analysis that utilizes a Monte Carlo simulation approach. It was observed that the sum of random and repeatable errors could be controlled to within ±7.5% even for a very high performance cold plate with an effective heat transfer coefficient of 200,000 W/m2-K dissipating 250 W/cm2, with assumed errors in other relevant parameters.
Evaluation of the 12-Gene Molecular Score and the 21-Gene Recurrence Score as Predictors of Response to Neo-adjuvant Chemotherapy in Estrogen Receptor-Positive, HER2-Negative Breast Cancer (2020)

In this microarray study, two commercial breast cancer prognostic scores were significant predictors of response to NaCT. In direct comparison, the 12-gene MS outperformed the 21-gene RS as a predictive marker for NaCT. Considering pCR as surrogate for improved survival, these results support the ability of both scores to predict chemotherapy sensitivity.
Elimination of Spurious Loss in Euler Equation Computations (2000)

The accuracy of a standard implicit conservative Euler equation solver is greatly improved by incorporation of an entropy-conservation equation, used in lieu of the streamwise momentum equation in all regions of the e ow except at shock waves. A slight modie cation is also required at stagnation points to maintain a well-posed nature. The overall method eliminates spurious entropy errors and, thus, reduces the grid density required to achieve any particular level of accuracy. Results arepresented for subsonic and transonicairfoil e ows. Although thederivation and resultsareforsteady,two-dimensionalEulerequations, theapproach hasno inherent limitationsthatpreclude extension to unsteady, three-dimensional, or viscous e ows. A brief discussion of these extensions is presented. Nomenclature c = speed of sound D/Dt = substantial derivative (@/ @t + q¢ r ) E = total energy f = momentum-conservation trigger g = stagnation trigger H = total enthalpy h = static enthalpy ` = cell size M = Mach number p = pressure Q = enthalpy e ux q = speed,j qj q = velocity vector R = residual S = entropy t = time u, v = velocity components a = angle of attack c = specie c-heat ratio ±( ) = upwinding change e = viscous dissipation k = characteristic speed q = mass density s¯ = shear stress tensor
COACH-based Shack-Hartmann wavefront sensor (2021)

A new Shack-Hartmann wavefront sensor (SHWS) based on the principle of coded aperture correlation holography is used to achieve higher precision. Coded phase masks are employed to create sparse dot patterns in the sensor plane.
Photonic devices enabled by waveguide-mode resonance effects in periodically modulated films (2003)

The chief properties and possible applications of periodic waveguides and their leaky modes are presented in this paper. After summarizing the basic physics of the guided-mode resonance, computed leaky-mode field patterns are provided to illustrate their structure and the high local focal field enhancement obtainable. An example fabricated bandstop filter is found to exhibit 90% efficiency, 1 nm linewidth, and low sidebands. Computed spectra for a single-layer bandpass filter operating at 1.55 &mu;m wavelength yield low sidebands, extending 100 nm, and an angular aperture of ~1.7&deg;. Resonant vertical-cavity surface-emitting lasers (VCSEL) are presented in which multilayer Bragg-stack mirrors are replaced with leaky-mode resonance layers. The use of guided-mode resonance mirrors provides optical power flow across and laterally along the laser active region. The round-trip gain is thereby increased resulting in high laser efficiency and relaxed mirror reflectivity constraints. As the GMR mirror achieves high reflectivity at resonance, the laser wavelength is locked at the resonance wavelength principally defined by the period. Example resonant VCSEL embodiments are shown along with their computed characteristics. Resonant biosensors are addressed last. The high parametric sensitivity of the guided-mode resonance effect, a potential limitation in filter applications, can be exploited for sensors as illustrated by several examples.
Aberrant FHIT transcripts in Merkel cell carcinoma. (1996)

Merkel cell carcinoma is a rare neuroendocrine carcinoma of the skin which shares several features with small cell lung carcinoma. In a previous study, we reported a high frequency of abnormalities of the FHIT gene, located at 3p14.2, in small cell lung tumors. To determine the role of the FHIT gene in small cell neuroendocrine malignancies, 14 cases of Merkel cell carcinoma were analyzed by reverse transcription of FHIT mRNA followed by PCR amplification and sequencing of products. Eight of 14 tumors (57%) displayed abnormal FHIT products that lacked three or more exons of the FHIT gene. The pattern of abnormal transcripts was similar to that observed in small cell lung tumors, suggesting that FHIT abnormalities might be a common genetic marker of these two types of neuroendocrine tumors.
A Caged Lanthanide Complex as a Paramagnetic Shift Agent for Protein NMR (2004)

A lanthanide complex, named CLaNP (caged lanthanide NMR probe) has been developed for the characterisation of proteins by paramagnetic NMR spectroscopy. The probe consists of a lanthanide chelated by a derivative of DTPA (diethylenetriaminepentaacetic acid) with two thiol reactive functional groups. The CLaNP molecule is attached to a protein by two engineered, surface-exposed, Cys residues in a bidentate manner. This drastically limits the dynamics of the metal relative to the protein and enables measurements of pseudocontact shifts. NMR spectroscopy experiments on a diamagnetic control and the crystal structure of the probe-protein complex demonstrate that the protein structure is not affected by probe attachment. The probe is able to induce pseudocontact shifts to at least 40 A from the metal and causes residual dipolar couplings due to alignment at a high magnetic field. The molecule exists in several isomeric forms with different paramagnetic tensors; this provides a fast way to obtain long-range distance restraints.
Magnetic Nanoparticles Applications for Amyloidosis Study and Detection: A Review (2018)

Magnetic nanoparticles (MNPs) have great potential in biomedical and clinical applications because of their many unique properties. This contribution provides an overview of the MNPs mainly used in the field of amyloid diseases. The first part discusses their use in understanding the amyloid mechanisms of fibrillation, with emphasis on their ability to control aggregation of amyloidogenic proteins. The second part deals with the functionalization by various moieties of numerous MNPs' surfaces (molecules, peptides, antibody fragments, or whole antibodies of MNPs) for the detection and the quantification of amyloid aggregates. The last part of this review focuses on the use of MNPs for magnetic-resonance-based amyloid imaging in biomedical fields, with particular attention to the application of gadolinium-based paramagnetic nanoparticles (AGuIX), which have been recently developed. Biocompatible AGuIX nanoparticles show favorable characteristics for in vivo use, such as nanometric and straightforward functionalization. Their properties have enabled their application in MRI. Here, we report that AGuIX nanoparticles grafted with the Pittsburgh compound B can actively target amyloid aggregates in the brain, beyond the blood⁻brain barrier, and remain the first step in observing amyloid plaques in a mouse model of Alzheimer's disease.
Report of a Problem with a New Spinal Needle (1987)

Morris, Richard MB, BS, FFARACS; Allen, Paul MD; Van Rensburg, Marie MD; Philip, James ME(E), MD Author Information
Characterizing satellite‐derived soil moisture and its relationship with rainfall over India (2019)

Abstract Understanding the spatial and temporal variations of soil moisture is important since the feedback between soil moisture and precipitation is a key control of the climate. This is also important as soil moisture data is a key input in regional climate models. The inter‐annual and inter‐decadal variability of soil moisture has been investigated here using the European Space Agency's Climate Change Initiative active and passive combined soil moisture product over different climate regimes of India. The observed soil moisture and rainfall are positively correlated and their relationship in this study suggests that both positive and negative feedback occur. The analysis showed an increasing soil moisture trend with a significant increase in the monsoon and autumn seasons for the past two decades over central India, where the frequency of extreme precipitation increased in the same period. An overall increase in soil moisture over the western arid region is also significant. A decreasing trend in soil moisture prevailed throughout the monsoon season over eastern India, where monsoon depressions make landfall, signalling the recent climate trends over the Indian subcontinent.
Formula G1: Cell cycle in the driver's seat of stem cell fate determination (2016)

Cell cycle dynamics has emerged as a key regulator of stem cell fate decisions. In particular, differentiation decisions are associated with the G1 phase, and recent evidence suggests that self-renewal is actively regulated outside of G1. The mechanisms underlying these phenomena are largely unknown, but direct control of gene regulatory programs by the cell cycle machinery is heavily implicated. A recent study sheds important mechanistic insight by demonstrating that in human embryonic stem cells (hESCs) the Cyclin-dependent kinase CDK2 controls a wide-spread epigenetic program that drives transcription at differentiation-related gene promoters specifically in G1. Here, we discuss this finding and explore whether similar mechanisms are likely to function in multipotent stem cells. The implications of this discovery toward our understanding of stem cell-related disease are discussed, and we postulate novel mechanisms that position the cell cycle as a regulator of cell fate gene networks at epigenetic, transcriptional and post-transcriptional levels.
Optimal Operation of Energy Storage Systems Considering Forecasts and Battery Degradation (2016)

Energy storage systems have the potential to deliver value in multiple ways, and these must be traded off against one another. An operational strategy that aims to maximize the returned value of such a system can often be significantly improved with the use of forecasting - of demand, generation, and pricing - but consideration of battery degradation is important too. This paper proposes a stochastic dynamic programming approach to optimally operate an energy storage system across a receding horizon. The method operates an energy storage asset to deliver maximal lifetime value, by using available forecasts and by applying a multi-factor battery degradation model that takes into account operational impacts on system degradation. Applying the method to a dataset of a residential Australian customer base demonstrates that an optimally operated system returns a lifetime value which is 160% more, on average, than that of the same system operated using a set-point-based method applied in many settings today.
Effect of Processing Additive on the Nanomorphology of a Bulk Heterojunction Material (2010)

The bulk heterojunction (BHJ) material Si-PDTBT:PC(70)BM is sensitive to the use of a small amount of 1-chloronaphthalene (CN) as a processing additive; CN as a cosolvent (e.g., 4% in chlorobenzene) causes in a factor of 2 increase in the power conversion efficiency of BHJ solar cells. The morphology of the BHJ material, prepared with and without the CN additive is studied with top-down transmission electron microscopy, cross-sectional transmission electron microscopy, and atomic force microscopy. The improved performance is the result of changes in the nanoscale morphology. Field-effect transistor measurements are consistent with the observed changes in morphology.
ChemInform Abstract: Thermolysis of Bis[2‐[(trimethylsilyl)oxy]prop‐2‐yl]furoxan (TOP‐furoxan). (1986)

Abstract Thermolyse der Titelverbindung, des Dimeren (II), erzeugt in situ das Nitriloxid (III), welches unter der optimierten Bedingung A) mit einer Reihe von 1,2‐di‐ oder trisubstituierten Olefinen regioselektiv unter Bildung der Isoxazoline (IV), (VII), (VIII) und (XI) reagiert (Diskussion des Reaktionsmechanismus).
Synchrotron X-Ray Microdiffraction Investigation of Scaling Effects on Plasticity and the Correlation to TSV Extrusion (2017)

The reliability of copper through-silicon vias (TSVs) has been shown to be largely determined by the microstructure and extrusion statistics, and the mechanism for this requires further investigation. Synchrotron x-ray microdiffraction is an advantageous technique for TSV measurements due to its high beam intensity, which allows for full stress derivation with submicron resolution, and its nondestructive sample preparation. Since copper is highly elastically anisotropic, the grain structure and corresponding mechanical properties are crucial in determining the thermomechanical response. In this paper, microdiffraction is used to investigate the TSV scaling effect on plastic deformation and its correlation to the grain growth and extrusion behavior. Electron backscatter diffraction results indicate that the grain growth mechanism is not largely affected by scaling in the range of 10µm to 2µm diameter TSVs. However, the magnitude and statistical spread of the via extrusion for the 2µm TSVs is higher than that of the 5µm TSVs. Microdiffraction results reveal that the magnitude and variation of the plasticity is also higher for the 2µm TSVs, and that the plastic deformation is correlated to the microstructure. These results, validated by thermomechanical simulation, demonstrate that scaling TSV dimensions does not improve stress and reliability for the via middle process, where further annealing beyond the post-plating anneal is required.
Carbon nanotube interconnects (2007)

Based on physical models, circuit models are presented for SWNTs, SWNT-bundles and MWNTs. These models can be used for circuit simulations and compact modeling. It is demonstrated that by customizing CNT interconnects at the local, semiglobal and global levels several major challenges facing GSI systems can potentially be addressed. For local interconnects, mono- or few-layer SWNT interconnects can offer up to 50% reduction in capacitance and power dissipation with considerable improvements in latency if they are short enough (
An irreducible delay in manual and saccadic reaction time in amblyopia (2015)

Despite normal motor control, saccadic latencies are delayed in the non-preferred eye of patients with amblyopia (≈25-100ms1,2). This delay extends to manual reaction time when responding to targets with the amblyopic eye (≈50-100ms1,3,4). Previous researchers have shown a positive correlation between the delay and the magnitude of visual acuity impairment in the amblyopic eye5. This delay may be due to a difference in effective stimulus strength of the targets, since reaction times to weak stimuli are prolonged, decreasing as stimulus strength increases, until reaching a plateau6. Here, we measure saccadic and manual reaction times of normal and amblyopic subjects to the abrupt appearance of a Gabor patch at 5 degrees to the left or right of fixation, while varying the contrast of the patch. Even after adjusting for differences in effective stimulus strength, we find significant delays in both saccadic and manual response times when viewing with the amblyopic eye. We speculate that this irreducible delay may be a consequence of impaired ability to rapidly direct spatial attention with the amblyopic eye. 1 Mackensen, G. (1958). Reaktionszeitmessungen bei Amblyopia. Graefes Arch Ophthalmol 159:636 – 642. 2 Ciuffreda, K.J., Kenyon R.V. Stark L. (1978). Increased saccadic latencies in amblyopic eyes. Invest Ophthalmol Vis Sci 17: 697-702. 3 Von Noorden, G.K. (1961). Reaction time in normal and amblyopic eyes. Arch Ophthalmol 66:695-699. 4 Levi, D.M., Harwerth, R.S., and Manny, R.E. (1979). Suprathreshold spatial frequency detection and binocular interaction in strabismic and anisometropic amblyopia. Invest Ophthalmol Vis Sci 18:714-725. 5 Hamasaki, D.I. and Flynn, J.T. (1981). Amblyopic eyes have longer reaction times. Invest Ophthalmol Vis Sci 21:846-853. 6 Pieron, H. (1952). The Sensations: Their Functions, Processes and Mechanisms. London: Frederick Muller Ltd. Meeting abstract presented at VSS 2015
Complementary studies of lipid membrane dynamics using iSCAT and super-resolved fluorescence correlation spectroscopy (2018)

Observation techniques with high spatial and temporal resolution, such as single-particle tracking based on interferometric scattering (iSCAT) microscopy, and fluorescence correlation spectroscopy applied on a super-resolution STED microscope (STED-FCS), have revealed new insights of the molecular organization of membranes. While delivering complementary information, there are still distinct differences between these techniques, most prominently the use of fluorescent dye tagged probes for STED-FCS and a need for larger scattering gold nanoparticle tags for iSCAT. In this work, we have used lipid analogues tagged with a hybrid fluorescent tag-gold nanoparticle construct, to directly compare the results from STED-FCS and iSCAT measurements of phospholipid diffusion on a homogeneous supported lipid bilayer (SLB). These comparative measurements showed that while the mode of diffusion remained free, at least at the spatial (>40 nm) and temporal (50 ⩽ t ⩽ 100 ms) scales probed, the diffussion coefficient was reduced by 20- to 60-fold when tagging with 20 and 40 nm large gold particles as compared to when using dye tagged lipid analogues. These FCS measurements of hybrid fluorescent tag-gold nanoparticle labeled lipids also revealed that commercially supplied streptavidin-coated gold nanoparticles contain large quantities of free streptavidin. Finally, the values of apparent diffusion coefficients obtained by STED-FCS and iSCAT differed by a factor of 2-3 across the techniques, while relative differences in mobility between different species of lipid analogues considered were identical in both approaches. In conclusion, our experiments reveal that large and potentially cross-linking scattering tags introduce a significant slow-down in diffusion on SLBs but no additional bias, and our labeling approach creates a new way of exploiting complementary information from STED-FCS and iSCAT measurements.
High performance bulk thermoelectrics via a panoscopic approach (2013)

One of the intellectual challenges for next generation thermoelectric materials revolves around the synthesis and fabrication of hierarchically organized microstructures that do not appreciably compromise the innate high power factor of the chosen thermoelectric system, but significantly reduce lattice thermal conductivity to enhance the overall figure of merit, ZT. An effective emerging strategy is to introduce nanostructures into bulk thermoelectric materials, which allow for diverse phonon scattering mechanisms to reduce thermal conductivity. In this review, we present key examples to show the intricate but tractable relationship across all relevant length-scales between various microstructural attributes (point, line, interfacial and mesoscale defects; as well as associated elastic and plastic strain) and lattice thermal conductivity in systems based on PbTe matrices. We emphasize the need for an overarching panoscopic approach that enables specific design strategies for the next generation of thermoelectric materials.
Via first dual damascene integration of nanoporous ultra low-k material (2003)

In this paper, ISMT reports on the first successful integration of a porous ultra low-k dielectric in a via first/trench last dual damascene structure. The porous dielectric was a spin on siloxane based material with k/spl sim/2.2. Cap layer optimization for CMP, resist strip, clean, and electrical results from single and dual damascene integration are discussed.