gebhart/patrepeval huggingface dataset:
Supplementary Table S2 from Bispecific Antibodies and Antibody–Drug Conjugates (ADCs) Bridging HER2 and Prolactin Receptor Improve Efficacy of HER2 ADCs (2023)

&lt;p&gt;In vitro Potency of HER2 ADC, PRLR ADC and HER2xPRLRbs ADC in a Panel of Breast Cancer Cell Lines&lt;/p&gt;
Iron-Catalyzed Carbomagnesiation of Propargylic Alcohols (2007)

The addition of organometallic reagents to alkynes is an important method for forming a new C-C bond. The authors report here a novel Fe-catalyzed carbomagnesiation of propargylic and homopropargylic alcohols. It offers a simple preparation of a broad variety of polysubstituted allylic and homoallylic alcohols, using environmentally benign reagents and catalysts. The products are obtained with excellent regio- andE/Z selectivity and in good yields. Enantiopure propargylic alcohols react with retention of chirality.
Fracture Energy of an Aligned Porous Silicon Nitride (2000)

The fracture energy of a porous silicon nitride with aligned fibrous grains was investigated, using a chevron‐notched‐beam technique. A crack was constrained to propagate normal to the grain alignment. The obtained fracture energy was ∼500 J/m 2 , which was ∼7 times larger than that of a dense silicon nitride with randomly oriented fibrous grains. The large fracture energy was attributable primarily to the sliding resistance associated with interlocking grains.
Artificial Intelligence to Aid Early Detection of Heart Failure With Preserved Ejection Fraction (2023)

[Figure: see text]
Stabilization of zinc-blende cubic AlN in AlN/W superlattices (2001)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation I. W. Kim, A. Madan, M. W. Guruz, V. P. Dravid, S. A. Barnett; Stabilization of zinc-blende cubic AlN in AlN/W superlattices. J. Vac. Sci. Technol. A 1 September 2001; 19 (5): 2069–2073. https://doi.org/10.1116/1.1372897 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAVS: Science & Technology of Materials Interfaces and ProcessingJournal of Vacuum Science & Technology A Search Advanced Search |Citation Search
Region based searching for early terminated motion estimation algorithm of H.264/AVC video coding standard (2009)

H.264/AVC is the newest international video coding standard which shows extremely higher coding efficiency compared to any other previous standards, but it brings high computational complexity. The variable block size motion estimation process is the most time consuming part of the H.264/AVC encoder. In order to reduce the computation of the full search motion estimation method, this paper presents a region based search algorithm. The entire search window is divided into several search regions based on the orientation of the previously calculated motion vector. The experimental results show that the proposed method reduced about 77% of motion estimation time with ignorable degradation of rate-distortion performance.
Two distinct structures of α‐conotoxin GI in aqueous solution (1998)

The detailed analysis of conformational space of alpha-conotoxin GI in aqueous solution has been performed on the basis of two-dimensional NMR spectroscopy data using multiconformational approach. As the result, two topologically distinct interconvertible sets of GI conformations (populations of 78% and 22%) have been found. A common feature of the two sets is the Asn4-Cys7 beta-turn. The Gly8 to Tyrll region has a structure of right-handed helical turn in the major set and two sequential bends in the minor one. N-terminus and C-terminus also have different orientations, anti-parallel in the major conformational set and parallel in the minor one. An average pairwise rmsd for backbone heavy atoms is 0.56 A in the major set, 0.23 A in the minor, and 1.85 A between the structures of the two sets. The X-ray structure of GI [Guddat, L. W., Martin, J. A., Shan, L., Edmundson, A. B. & Gray, W. R. (1996) Biochemistry 35, 11329 - 11335] has the same folding pattern as the major NMR set, the average backbone rmsd between the two structures being 0.77 A.
Identification of Radiation-Responsive GenesIn VitroUsing a Gene Trap Strategy Predicts for Modulation of Expression by RadiationIn Vivo (2002)

A large number of genes are known to be responsive to ionizing radiation, and there is strong evidence for the existence of inducible radiation resistance in mammalian cells. We have developed a gene trap insertional mutagenesis strategy to identify novel genes involved in responses to radiation. Using this approach, we have isolated four gene-trap integrations in embryonic stem cells. In three cases (9A, 3E and 9H) the trapped genes are radiation-inducible, and in one (7D) the gene is down-regulated. Sequence analysis of fusion transcripts from three of the integrations indicate one novel gene (3E), the mouse homologue (9A) of a known but uncharacterized human gene that encodes a protein with significant homology to several GTPase-activating proteins and a murine locus, Mym (9H). The embryonic stem cell clone with the 9A insertion was introduced into the mouse germline, and the in vivo expression pattern of 9A was studied in detail. A unique, spatially restricted pattern of expression in embryos and adult animals was observed. There is tissue-specific in vivo induction of the 9A gene in adult mice by radiation. This study demonstrates the potential of the gene trap approach for the identification and functional analysis of novel radiation-regulated genes. Similar strategies may facilitate the discovery and characterization of genes involved in other cellular stress responses.
Mutation analysis of hypoxia-inducible factors HIF1A and HIF2A in renal cell carcinoma. (2009)

The detection of a loss-of-function HIF1A mutation in a primary RCC is consistent with HIF-1 and HIF-2 having different roles in renal tumourigenesis, However, somatic mutations of HIF1A are not frequently implicated in the pathogenesis of RCC.
Botulinum Toxin to Treat Neurogenic Bladder (2016)

Alteration in neural control from suprapontine areas to the nerves innervating the bladder can lead to bladder dysfunction and the development of a neurogenic bladder (NGB). Patients with NGB often suffer from urinary incontinence, which can lead to adverse events such as urinary tract infections and decubiti, in addition to creating a large care burden for family members or healthcare providers and significantly impairing patient quality of life. The common failure of anticholinergic medications has spurned the development of second-line treatments, including the use of botulinum toxin. OnabotulinumtoxinA (onaBoNT-A; BOTOX, Allergan, Inc.) was approved by the U.S. Food and Drug Administration (FDA) in 2011 to treat neurogenic detrusor overactivity in patients with urinary incontinence resulting from a NGB. In this review the authors summarize pertinent results from key trials leading to FDA approval of onaBoNT-A as well as more recent long-term data.
Intentional defect array wafers: their practical use in semiconductor control and monitoring systems (2003)

In the competitive world of semiconductor manufacturing today, control of the process and manufacturing equipment is paramount to success of the business. Consistent with the need for rapid development of process technology, is a need for development wiht respect to equipment control including defect metrology tools. Historical control methods for defect metrology tools included a raw count of defects detected on a characterized production or test wafer with little or not regard to the attributes of the detected defects. Over time, these characterized wafers degrade with multiple passes on the tools and handling requiring the tool owner to create and characterize new samples periodically. With the complex engineering software analysis systems used today, there is a strong reliance on the accuracy of defect size, location, and classification in order to provide the best value when correlating the in line to sort type of data. Intentional Defect Array (IDA) wafers were designed and manufacturered at International Sematech (ISMT) in Austin, Texas and is a product of collaboration between ISMT member companies and suppliers of advanced defect inspection equipment. These wafers provide the use with known defect types and sizes in predetermined locations across the entire wafer. The wafers are designed to incorporate several desired flows and use critical dimensions consistent with current and future technology nodes. This paper briefly describes the design of the IDA wafer and details many practical applications in the control of advanced defect inspection equipment.
Self-regulating soliton domain walls in microresonators (2021)

Dissipative soliton Kerr frequency combs in microresonators have recently been demonstrated with the self-injection locking process. They have the advantage of turnkey deterministic comb generation and simplifying dark soliton generation in the normal dispersion regime. Here, the formation process of dark pulses triggered by self-injection locking is studied by regarding them as a pair of domain walls that connect domains having different intracavity powers. The self-injection locking mechanism allows the domain walls to self-regulate their position so that a wide range of dark comb states can be accessed, and the duty cycle is controlled by the feedback phase. Direct imaging of the dark pulse shape using the electro-optic sampling technique is used to verify the theory. The results provide new physical insights as well as a new operational modality for this important class of nonlinear waves.
Analytic solution for separating spectra into illumination and surface reflectance components (2007)

The measured light spectrum is the result of an illuminant interacting with a surface. The illuminant spectral power distribution multiplies the surface spectral reflectance function to form a color signal--the light spectrum that gives rise to our perception. Disambiguation of the two factors, illuminant and surface, is difficult without prior knowledge. Previously [IEEE Trans. Pattern Anal. Mach. Intell.12, 966 (1990); J. Opt. Soc. Am. A21, 1825 (2004)], one approach to this problem applied a finite-dimensional basis function model to recover the separate illuminant and surface reflectance components that make up the color signal, using principal component bases for lights and for reflectances. We introduce the idea of making use of finite-dimensional models of logarithms of spectra for this problem. Recognizing that multiplications turn into additions in such a formulation, we can replace the original iterative method with a direct, analytic algorithm with no iteration, resulting in a speedup of several orders of magnitude. Moreover, in the new, logarithm-based approach, it is straightforward to further design new basis functions, for both illuminant and reflectance simultaneously, such that the initial basis function coefficients derived from the input color signal are optimally mapped onto separate coefficients that produce spectra that more closely approximate the illuminant and the surface reflectance for any given dimensionality. This is accomplished by using an extra bias correction step that maps the analytically determined basis function coefficients onto the optimal coefficient set, separately for lights and surfaces, for the training set. The analytic equation plus the bias correction is then used for unknown input color signals.
Topology optimization for transient response of photonic crystal structures (2010)

An optimization scheme based on topology optimization for transient response of photonic crystal structures is developed. The system response is obtained by a finite-element time-domain analysis employing perfectly matched layers as an absorbing boundary condition. As an example a waveguide-side-coupled microcavity is designed. The gradient-based optimization technique is applied to redistribute the material inside the microcavity such that the Q factors of a monopole and a dipole mode are improved by 375% and 285%, respectively, while maintaining strong coupling. This is obtained by maximizing the stored energy inside the microcavity in the decaying regime of the transient response. Manufacturable designs are achieved by filtering techniques capable of controlling minimum length scales of the design features.
Data from Pathology-Driven Comprehensive Proteomic Profiling of the Prostate Cancer Tumor Microenvironment (2023)

&lt;div&gt;Abstract&lt;p&gt;Prostate cancer is the second most common cancer in men worldwide. Gleason grading is an important predictor of prostate cancer outcomes and is influential in determining patient treatment options. Clinical decisions based on a Gleason score of 7 are difficult as the prognosis for individuals diagnosed with Gleason 4+3 cancer is much worse than for those diagnosed with Gleason 3+4 cancer. Laser capture microdissection (LCM) is a highly precise method to isolate specific cell populations or discrete microregions from tissues. This report undertook a detailed molecular characterization of the tumor microenvironment in prostate cancer to define the proteome in the epithelial and stromal regions from tumor foci of Gleason grades 3 and 4. Tissue regions of interest were isolated from several Gleason 3+3 and Gleason 4+4 tumors using telepathology to leverage specialized pathology expertise to support LCM. Over 2,000 proteins were identified following liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of all regions of interest. Statistical analysis revealed significant differences in protein expression (&gt;100 proteins) between Gleason 3 and Gleason 4 regions—in both stromal and epithelial compartments. A subset of these proteins has had prior strong association with prostate cancer, thereby providing evidence for the authenticity of the approach. Finally, validation of these proteins by immunohistochemistry has been obtained using an independent cohort of prostate cancer tumor specimens.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Implications:&lt;/b&gt; This unbiased strategy provides a strong foundation for the development of biomarker protein panels with significant diagnostic and prognostic potential. &lt;i&gt;Mol Cancer Res; 15(3); 281–93. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Pseudo Distance for Trellis Coded Modulation in Overloaded MIMO OFDM with Sphere Decoding (2016)

Efficient detection schemes for an overloaded multiple-input multiple-output (MIMO) system have been investigated recently. The literature shows that trellis coded modulation (TCM) is able to enhance a system's capability to separate signal streams in the detection process of MIMO systems. However, the computational complexity remains high as a maximum likelihood detection (MLD) algorithm is used in the scheme. Thus, a sphere decoding (SD) algorithm with a pseudo distance (PD) is proposed in this paper. The PD maintains the coding gain advantage of the TCM by keeping some potential paths connected unlike conventional SD which truncates them. It is shown that the proposed scheme can reduce the number of distance calculations by about 98% for the transmission of 3 signal streams. In addition, the proposed scheme improves the performance by about 2dB at the bit error rate of 10-2.
On Greedy Methods for EXIT Chart Based Transmission Power Allocation (2010)

This paper addresses the problem of power allocation for single carrier point-to-point multiple input multiple output (MIMO) systems with iterative frequency-domain (FD) soft cancellation (SC) minimum mean squared error (MMSE) equalization. Two novel heuristic power allocation methods are proposed. The proposed methods explicitly take into account the convergence properties of the iterative equalizer while transmission power is minimized. The proposed heuristic schemes are based on, convergence constraint power allocation (CCPA), technique that decouples the spatial interference between streams using singular value decomposition (SVD), and minimize the transmission power while achieving the target mutual information for each stream after iterations at the receiver side. The proposed heuristic transmission schemes are inspired by well-known greedy algorithm resulting in a simple and efficient solutions to the power allocation problem. Numerical results show that the proposed heuristic schemes can achieve close to optimal performance in the terms of equalizer convergence as well as the total transmission power.
Structure of the Hepatitis B virus capsid quasi-6-fold with a trapped C-terminal domain reveals capsid movements associated with domain exit (2023)

Many viruses undergo transient conformational change to surveil their environments for receptors and host factors. In Hepatitis B virus (HBV) infection, after the virus enters the cell, it is transported to the nucleus by interaction of the HBV capsid with an importin α/β complex. The interaction between virus and importins is mediated by nuclear localization signals on the capsid protein's C-terminal domain (CTD). However, CTDs are located inside the capsid. In this study, we asked where does a CTD exit the capsid, are all quasi-equivalent CTDs created equal, and does the capsid structure deform to facilitate CTD egress from the capsid? Here, we used Impβ as a tool to trap transiently exposed CTDs and examined this complex by cryo-electron microscopy. We examined an asymmetric reconstruction of a T = 4 icosahedral capsid and a focused reconstruction of a quasi-6-fold vertex (3.8 and 4.0 Å resolution, respectively). Both approaches showed that a subset of CTDs extended through a pore in the center of the quasi-6-fold complex. CTD egress was accompanied by enlargement of the pore and subtle changes in quaternary and tertiary structure of the quasi-6-fold. When compared to molecular dynamics simulations, structural changes were within the normal range of capsid flexibility. Although pore diameter was enlarged in the Impβ-bound reconstruction, simulations indicate that CTD egress does not exclusively depend on enlarged pores. In summary, we find that HBV surveillance of its environment by transient exposure of its CTD requires only modest conformational change of the capsid.
Quasi Passive Optical Switch Based on Transition Metal Oxide Device (2011)

We propose optical switch architecture based on transition metal oxide material. It use electrical field to change oxygen vacancy distribution and its optical property such as absorption coefficient. We demonstrate the absorption coefficient of such device can be latched in binary state, which is useful for optical networking and interconnect applications.
2-Methyl-1-propenyl Trifluoromethanesulfonate (2001)

[53282-30-7] C5H7F3O3S (MW 204.19)





InChI = 1S/C5H7F3O3S/c1-4(2)3-11-12(9,10)5(6,7)8/h3H,1-2H3



InChIKey = ZBMXEMUYHOPIKB-UHFFFAOYSA-N



(precursor to dimethylvinylidene carbene,1 2-methyl-1-propenyl ethers,1 isopropylidenecyclopropanes,2 isopropylidenecyclopropenes,2 3-isopropylindazoles,3 and 2-methyl-1-propenyltriphenylphosphonium triflates4)



Physical Data: bp 65–66 °C/70 mmHg.



Solubility: sol most organic solvents.



Preparative Method: prepared in a single step from 2-methylpropionaldehyde, Trifluoromethanesulfonic Anhydride, and a hindered pyridine in 1,2-dichloroethane at reflux (eq 1). Distillation gives the product in 45% yield.5

(1)
Predicting conformational entropy of bond vectors in proteins by networks of coupled rotators (2008)

In this article, a formal expression for the conformational entropy of a bond vector in a protein is derived using the networks of coupled rotators model for the description of internal dynamics. Analytical relationships between NMR order parameters and conformational entropies are derived, and the possibility to extract the latter from NMR experiments is discussed. These results are illustrated in the case of the calcium-binding protein calbindin.
Viruses and human breast cancer. (1972)

There are well-established risk factors for breast cancer, most of which relate to estrogens and growth hormones in females. These include early-age menarche, late-age menopause, postmenopausal obesity and use of hormone therapy. However, these factors do not account for the sixfold difference in breast cancer incidence and mortality between countries and the fact that these differences dramatically lessen after migration; nor do they account for male breast cancer. Accordingly, hormone-responsive viruses have become major suspects as etiological agents for human breast cancer. Human papillomaviruses, mouse mammary tumor virus and Epstein-Barr virus are the prime candidate viruses as causes of human breast cancer. Human papillomaviruses and the mouse mammary tumor virus have hormone responsive elements that appear to be associated with enhanced replication of these viruses in the presence of corticosteroid and other hormones. This biological phenomenon is particularly relevant because of the hormone dependence of breast cancer. Viral genetic material for each of these candidate viruses has been identified by polymerase chain reaction in breast tumors but rarely in normal breast tissue controls. Pooled data from controlled studies show substantial odds ratios for the presence of viral genetic material in breast tumors compared with normal controls. These and additional data provide substantial, but not conclusive, evidence that human papillomavirus, the mouse mammary tumor virus and Epstein-Barr virus may have a role in the etiology of human breast cancer. If conclusive evidence for a role of these viruses in breast carcinogenesis can be developed, there is a practical possibility of primary prevention.
Supplementary Materials and Methods, Figures 1 - 2, Table 1 from Effect of Small-Molecule Modification on Single-Cell Pharmacokinetics of PARP Inhibitors (2023)

&lt;p&gt;PDF file - 401KB, Supplemental file containing a mathematical model description, Figure S1 showing the modeling approach, Table S1 with model parameters, and Figure S2 graphing cellular clearance.&lt;/p&gt;
Dielectrophoretic Characterization of SnO2 Nanobelts (2007)

In the present work we report the results of AC dielectrophoresis experiments on ethanol suspended SnO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> nanobelts. AC field (frequency ~ 5 Hz - 10 MHz) was applied between microelectrodes, and detailed and direct observations of the nanobelt motion were performed. It revealed a wide variety of nanobelt motions induced by the dielectrophoretic forces, which include attraction and repulsion depending on the signal frequency range. These forces caused rigid body motion and deformation in long nanobelts, and pearl chain formation in short nanobelts and particles. The presence of negative (repulsion) dielectrophoresis is unusual in SnO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , since bulk material properties dictate positive dielectrophoresis in the frequency range studied.