gebhart/patrepeval huggingface dataset:
Theory of transformation-invariant compact process modeling (2019)

Modern one-digit technological nodes demand strict reproduction of the optical proximity corrections (OPC) for repeatable congruent patterns. To ensure this property the optical and process simulations must be invariant to the geometrical transformations of the translation, rotation, and reflection. Simulators must support invariance both in theory, mathematically, and in practice, numerically. In the first part of this study we aim to examine manner and conditions under which optical approximations, such as Sum of Coherent Systems (SOCS) and Abbe decomposition, preserve or violate intrinsic invariances of exact imaging. In this age of asymmetrical pixelated sources, complex Jones pupils, and tilted chief rays, the full rotational invariance is observed only in some cases of annular illuminations; otherwise, it is rare in contemporary optics. In the second part we consider more important topic: invariances of compact process modeling (CPM) operators. Translational, rotational, and reflectional invariances are obligatory in CPM, because photoresist processing effects do not have preferential lateral direction, origin, or reflectional axis. The invariance of CPM operators has never been scrutinized before. We fill this gap by expanding generic translationally-invariant CPM operator into Volterra series, and then examine linear, quadratic, and high-order terms. Contrary to the straightforward invariance conditions for linear operators, the morphology of invariance for the second and high order operators is non-trivial. We found necessary and sufficient conditions for the invariance to take place, and provide examples of non-linear Volterra operators that can be used as atomic construction blocks in neural networks for CPM.
3D-NAND Flash Solid-State Drive (SSD) for Deep Neural Network Weight Storage of IoT Edge Devices with 700x Data-Retention Lifetime Extention (2018)

3D-TLC (triple-level cell) NAND flash-based solid-state drive (SSD) for deep neural network (DNN) weight storage is proposed. The data-retention lifetime of 3D-TLC NAND flash memory is extended by 700-times to achieve over 10-year lifetime of IoT edge devices such as automobiles and infrastructures. Proposed SSD combines reliability enhancement techniques for 3D-TLC NAND flash memories with unique characteristics of DNN weights, which have values of near 0. This paper proposes two techniques for SSD controller. The 1st proposal, One-State Error Recovery, removes all of 1-state errors of important bits in DNN weights even when error-correcting code (ECC) cannot correct errors. The 2nd proposal, DNN Weight Data Mapping, assigns frequently used "0" to the highly reliable VTH-state of memory cells. Due to error tolerance of DNN weights, acceptable bit error rate (BER) increases by 9.8-times.
Synthesis and High‐Throughput Screening of N‐Acetyl‐β‐hexosaminidase Inhibitor Libraries Targeting Osteoarthritis. (2004)

C1 Nitrogen iminocyclitols are potent inhibitors of &lt;i&gt;N&lt;/i&gt;-acetyl-β-hexosaminidases. Given hexosaminidases' important roles in osteoarthritis, we developed two straightforward and efficient syntheses\nof C1 nitrogen iminocyclitols from two readily available starting materials, d-mannosamine\nhydrochloride and the microbial oxidation product of fructose. A diversity-oriented synthetic strategy\nwas then performed by coupling these core structures with various aldehydes, carboxylic acids,\nand alkynes to generate three separate libraries. High-throughput screening of the generated\nlibraries with human &lt;i&gt;N&lt;/i&gt;-acetyl-β-hexosaminidases produced only moderate inhibitory activities.\nHowever, the synthetic approach and screening strategy for these compounds will be applied to\ndevelop new potent inhibitors of human &lt;i&gt;N&lt;/i&gt;-acetyl-β-hexosaminidases, particularly when combined\nwith the structural information of these enzymes.
Speaker normalization and adaptation using second-order connectionist networks (1993)

A method for speaker normalization and adaption using connectionist networks is developed. A speaker-specific linear transformation of observations of the speech signal is computed using second-order network units. Classification is accomplished by a multilayer feedforward network that operates on the normalized speech data. The network is adapted for a new talker by modifying the transformation parameters while leaving the classifier fixed. This is accomplished by backpropagating classification error through the classifier to the second-order transformation units. This method was evaluated for the classification of ten vowels for 76 speakers using the first two formant values of the Peterson-Barney data. The results suggest that rapid speaker adaptation resulting in high classification accuracy can be accomplished by this method.
Novel Compact Hybrid Monopole ASA Antenna (2018)

This paper presents a novel compact hybrid monopole- Annular Slot Antenna (ASA). The proposed antenna combines the advantages of an ASA with the broadband feature of a wideband monopole. The antenna simulated performance is thoroughly analyzed and validated via measurements.
Figure S4 from TRK Fusions Are Enriched in Cancers with Uncommon Histologies and the Absence of Canonical Driver Mutations (2023)

&lt;p&gt;Supplemental Figure 4. Pathologic and preclinical characterization of melanoma with concurrent GON4L-NTRK1 and NRAS Q61R mutations.&lt;/p&gt;
Compact and low-loss silicon TM-pass polarizer using a subwavelength-grating based asymmetrical directional coupler (2020)

A low-loss and compact TM-pass polarizer on silicon is proposed using an asymmetrical directional coupler (ADC) consisted of a silicon wire waveguide and a sub-wavelength-grating (SWG) waveguide. To reduce the reflection loss and improve the extinction ratio (ER), tapered structure and sharp bending are introduced at the input and output port of the SWG waveguide, respectively. The TE input-mode is coupled into the SWG waveguide through the ADC, and then filtered out and absorbed by the Chromium wires located at two sides of the end of the bending. By properly selecting the structure parameters, the TM mode is cut-off in the SWG waveguide and thus directly passes through the silicon wire waveguide. Results show that a compact device length of 9.6μm with an ER of 18.3 dB and insertion loss of 0.16 dB is obtained at the wavelength of 1.55μm. To further improve the performance of the device, a cascaded scheme is constructed and analyzed. The total device length of the scheme is 40μm with an operating bandwidth of ~62nm for ensuring ER&gt; 30dB. Similar concepts can also be used to produce a TE-pass polarizer by simply constructing a vertical ADC.
Monoclonal antibodies to Pseudomonas aeruginosa ferripyochelin-binding protein (1986)

Hybridomas secreting specific monoclonal antibodies against the Pseudomonas aeruginosa ferripyochelin-binding protein (FBP) were isolated. These monoclonal antibodies reacted with FBP in immunoblots of outer membrane preparations from all serotypes of P. aeruginosa. Two of the monoclonal antibodies also reacted with FBP in strains of P. putida, P. fluorescens, and P. stutzeri. These antibodies did not react with outer membranes of P. cepacia, "P. multivorans," P. maltophilia, or other gram-negative organisms. The monoclonal antibodies were opsonophagocytic and blocked the binding of [59Fe]ferripyochelin to isolated outer membranes of strain PAO. By indirect immunofluorescence techniques, the monoclonal antibodies were used to demonstrate that FBP is present on the cell surface of P. aeruginosa cells grown in low-iron but not high-iron medium. These observations were confirmed by using 125I in surface-labeling techniques.
Trismus‐pseudocamptodactyly syndrome is caused by recurrent mutation of MYH8 (2006)

Trismus-pseudocamptodactyly syndrome (TPS) is a rare autosomal dominant distal arthrogryposis (DA) characterized by an inability to open the mouth fully (trismus) and an unusual camptodactyly of the fingers that is apparent only upon dorsiflexion of the wrist (i.e., pseudocamptodactyly). TPS is also known as Dutch-Kentucky syndrome because a Dutch founder mutation is presumed to be the origin of TPS cases in the Southeast US, including Kentucky. To date only a single mutation, p.R674Q, in MYH8 has been reported to cause TPS. Several individuals with this mutation also had a so-called "variant" of Carney complex, suggesting that the pathogenesis of TPS and Carney complex might be shared. We screened MYH8 in four TPS pedigrees, including the original Dutch family in which TPS was reported. All four TPS families shared the p.R674Q substitution. However, haplotype analysis revealed that this mutation has arisen independently in North American and European TPS pedigrees. None of the individuals with TPS studied had features of Carney complex, and p.R674Q was not found in 49 independent cases of Carney complex that were screened. Our findings show that distal arthrogryposis syndromes share a similar pathogenesis and are, in general, caused by disruption of the contractile complex of muscle.
Generation of SARS-CoV-2 escape mutations by monoclonal antibody therapy (2023)

COVID-19 patients at risk of severe disease may be treated with neutralising monoclonal antibodies (mAbs). To minimise virus escape from neutralisation these are administered as combinations e.g. casirivimab+imdevimab or, for antibodies targeting relatively conserved regions, individually e.g. sotrovimab. Unprecedented genomic surveillance of SARS-CoV-2 in the UK has enabled a genome-first approach to detect emerging drug resistance in Delta and Omicron cases treated with casirivimab+imdevimab and sotrovimab respectively. Mutations occur within the antibody epitopes and for casirivimab+imdevimab multiple mutations are present on contiguous raw reads, simultaneously affecting both components. Using surface plasmon resonance and pseudoviral neutralisation assays we demonstrate these mutations reduce or completely abrogate antibody affinity and neutralising activity, suggesting they are driven by immune evasion. In addition, we show that some mutations also reduce the neutralising activity of vaccine-induced serum.
Straightforward Methodology for the Enantioselective Synthesis of Benzo[a]- and Indolo[2,3-a]quinolizidines (2007)

An enantioselective two-step route to substituted benzo[a]- and indolo[2,3-a]quinolizidines has been developed. It consists of (i) a stereoselective cyclocondensation of a racemic or prochiral delta-oxo(di)ester with either (S)-(3,4-dimethoxyphenyl)alaninol or (S)-tryptophanol in a process involving a dynamic kinetic resolution and/or the differentiation of enantiotopic or diastereotopic ester groups, and (ii) a subsequent stereocontrolled cyclization on the aromatic ring taking advantage of the masked N-acyl iminium ion present in the resulting oxazolopiperidone lactams.
Sensitive resonant gas sensor operating in air with metal organic frameworks coating (2017)

We report a practical resonant gas sensor that is uniformly coated with metal organic frameworks (MOFs) and excited near the higher order modes for a higher attained sensitivity. The resonator is based on an electrostatically excited clamped-clamped microbeam. The microbeam is fabricated from a polyimide layer coated from the top with Cr/Au and from the bottom with Cr/Au/Cr layer. The geometry of the resonator is optimized to reduce the effect of the squeeze film damping, thereby allowing operation under atmospheric pressure. The electrostatic force electrode is designed to enhance the excitation of the second mode of vibration with the minimum power required. Significant frequency shift (kHz) is demonstrated for the first time upon water vapor, acetone, and ethanol exposure due to the MOFs functionalization and the higher order modes excitation. Also, the adsorption dynamics and MOF selectivity is investigated by studying the decaying time constants of the response upon gas exposure.
A High-Affinity Peptide Ligand Targeting Syntenin Inhibits Glioblastoma (2021)

Despite the recent advances in cancer therapeutics, highly aggressive cancer forms, such as glioblastoma (GBM), still have very low survival rates. The intracellular scaffold protein syntenin, comprising two postsynaptic density protein-95/discs-large/zona occludens-1 (PDZ) domains, has emerged as a novel therapeutic target in highly malignant phenotypes including GBM. Here, we report the development of a novel, highly potent, and metabolically stable peptide inhibitor of syntenin, KSL-128114, which binds the PDZ1 domain of syntenin with nanomolar affinity. KSL-128114 is resistant toward degradation in human plasma and mouse hepatic microsomes and displays a global PDZ domain selectivity for syntenin. An X-ray crystal structure reveals that KSL-128114 interacts with syntenin PDZ1 in an extended noncanonical binding mode. Treatment with KSL-128114 shows an inhibitory effect on primary GBM cell viability and significantly extends survival time in a patient-derived xenograft mouse model. Thus, KSL-128114 is a novel promising candidate with therapeutic potential for highly aggressive tumors, such as GBM.
Handling-Oriented Stiffness Control of a Multichamber Suspension (2023)

This paper deals with the development of a handling-oriented stiffness control strategy using multichamber suspensions. Indeed, being this technology capable of stiffness variability, it is particularly indicated for improving the vehicle handling performance, here intended as the reduction of roll and pitch angles during maneuvers. The proposed strategy exploits the multichamber's inner features in order to enhance the performance: simulation results show improvements up to 12% compared to the best passive stiffness configuration, still preventing deterioration of the driving comfort.
Doxorubicin Cardiotoxicity: Assessment of Late Left Ventricular Dysfunction By Radionuclide Cineangiography (1981)

Radionuclide cineangiography was used to evaluate 32 patients who sustained long-term remission of soft tissue sarcoma after adjuvant therapy with a cumulative doxorubicin dose from 480 to 550 mg/m body surface area. Left ventricular ejection fraction at rest was below normal (less than 45%) in eight of 32 patients. The abnormal response of ejection fraction to exercise identified an additional 12 patients with diminished left ventricular functional reserve. Ejection fraction determined at rest or during exercise did not differ 1 to 9 months) and those studied 30 months (range, 21 to 43 months) after completing doxorubicin treatment. Sequential studies in 13 patients, done 6 to 15 months after initial post-doxorubicin evaluation also showed persistent depression of average ejection fraction at rest and with exercise, with the continued deterioration of left ventricular function in six patients. Left ventricular dysfunction, evident in over half of asymptomatic patients even long after "acceptable" cumulative doses of doxorubicin, may persist for years.
Link between the conductivity and elastic moduli of composite materials (1993)

We derive relations linking the conductivity ${\mathrm{\ensuremath{\sigma}}}_{\mathrm{*}}$ and elastic moduli of any two-dimensional, isotropic composite material. Specifically, upper and lower bounds are derived on the effective bulk modulus ${\mathrm{\ensuremath{\kappa}}}_{\mathrm{*}}$ in terms of ${\mathrm{\ensuremath{\sigma}}}_{\mathrm{*}}$ and on the effective shear modulus ${\mathrm{\ensuremath{\mu}}}_{\mathrm{*}}$ in terms of ${\mathrm{\ensuremath{\sigma}}}_{\mathrm{*}}$. In some cases the bounds are attainable by certain microgeometries and thus optimal. Knowledge of the conductivity can yield sharp estimates of the elastic moduli (and vice versa) even for infinite phase contrast.
Identification of BST2 as a conjunctival epithelial stem/progenitor cell marker (2023)

The conjunctival epithelium consists of conjunctival epithelial cells and goblet cells derived from conjunctival epithelial stem/progenitor cells. However, the source of these cells is not well known because no specific markers for conjunctival epithelial stem/progenitor cells have been discovered. Therefore, to identify conjunctival epithelial stem/progenitor cell markers, we performed single-cell RNA sequencing of a conjunctival epithelial cell population derived from human-induced pluripotent stem cells (hiPSCs). The following conjunctival epithelial markers were identified: BST2, SLC2A3, AGR2, TMEM54, OLR1, and TRIM29. Notably, BST2 was strongly positive in the basal conjunctival epithelium, which is thought to be rich in stem/progenitor cells. Moreover, BST2 was able to sort conjunctival epithelial stem/progenitor cells from hiPSC-derived ocular surface epithelial cell populations. BST2-positive cells were highly proliferative and capable of successfully generating conjunctival epithelial sheets containing goblet cells. In conclusion, BST2 has been identified as a specific marker of conjunctival epithelial stem/progenitor cells.
Functional characterization of the manganese transporter smf2 homologue gene, PsMnt, of Phanerochaete sordida YK-624 via homologous overexpression (2018)

A homologue gene of the yeast natural resistance-associated macrophage protein (Nramp) family transporter smf2 was identified in the white-rot fungus Phanerochaete sordida YK-624. Relative expression levels of the homologue, designated PsMnt, were roughly equivalent in cultures containing 0 to 1000 μM Mn(II), a concentration non-toxic to the fungus. In the PsMnt-overexpressing mutant, cellular Mn accumulation and manganese peroxidase (MnP) activity increased significantly in 4-day cultures containing 10 μM MnSO4. Compared with the wild-type strain, MnP activity in the overexpressing mutants was higher at lower Mn concentrations (specifically 10-15 times higher). These results suggest that PsMnt is a high-affinity Mn transporter involved in cellular Mn accumulation under Mn-deficient conditions. This is the first report of an smf2 homologue in wood rot fungi.
Gene expression patterns in livers of Hispanic patients infected with hepatitis C virus (2011)

We report a gene expression study aimed at the identification of genes differentially expressed in the livers of Hispanic patients infected with hepatitis C virus (HCV). Six uninfected controls were compared with 14 HCV(+) patients in which the liver biopsies were obtained at the time of diagnosis. Among the latter, five patients were also analyzed 4 weeks after the onset of standard anti-HCV therapy (pegylated interferon-α + ribavirin). We identified many genes up- or down-regulated by the infection with HCV in the human livers. When these genes were subjected to pathway analysis, several prominent pathways were revealed including many interferon (IFN)-inducible pathways as well as immune cell trafficking, inflammation, anti-microbial responses, and even cancer. We detected expression of many genes that have previously been associated with HCV infection, as well as several novel genes including CD47. The genes induced by HCV infection showed large expression changes, whereas the genes induced by the IFN-α combination therapy were relatively few (including MX2, ORMDL3, GPAM, KOPX18, TMEM56, and HBP1) and they reflected relatively small expression changes. This is the first study to identify changes in gene expression in livers of HCV(+) Hispanic patients and the first to identify genes induced by anti-HCV combination therapy in the human liver.
Supplementary figures from IL1 Receptor Antagonist Controls Transcriptional Signature of Inflammation in Patients with Metastatic Breast Cancer (2023)

&lt;p&gt;Figure S1. Cytokines screening from breast tumor tissue Figure S2. IL-1β induces TSLP production from breast cancer cells. Figure S3. IL-1β production in DCs is caspase-1 dependent. Figure S4. IL-1β production requires TAK1-dependent caspase-1 activation. Figure S5. IL-1 and TGF-β mediate tumor-promoting type 2 cytokines in humanized mouse model. Figure S6. Cells component in blood from patients in clinical trial. Anakinra signature clustered breast cancer patients in TCGA dataset.&lt;/p&gt;
Presence of epidermal growth factor during in vitro maturation of pig oocytes and embryo culture can modulate blastocyst development after in vitro fertilization (1998)

The present study examined the effect of epidermal growth factor (EGF) during in vitro maturation (IVM) and embryo culture on blastocyst development in the pig. In experiment 1, cumulus oocyte complexes were cultured in North Carolina State University (NCSU) 23 medium containing porcine follicular fluid, cysteine, hormonal supplements, and with or without EGF (0–40 ng/ml) for 20–22 hr. They then were cultured for an additional 20–22 hr without hormones. After maturation, cumulus-free oocytes were co-incubated with frozen-thawed spermatozoa for 5–6 hr. Putative embryos were transferred to NCSU 23 containing 0.4% BSA and cultured for 144 hr. In experiment 2, oocytes were matured in medium containing 10 ng/ml EGF, inseminated, and putative embryos were cultured in the presence of 0–40 ng/ml EGF. In experiment 3, oocytes were cultured in the presence of 0, 10 and 40 ng/ml EGF to examine the kinetics of meiotic maturation. In experiment 4, 2- to 4-cell and 8-cell to morula stage embryos derived from oocytes matured with 10 ng/ml EGF were transferred to the oviduct and uterus, respectively, of each of three recipient gilts (3 and 4 days post-estrus, respectively). The presence or absence of EGF during IVM did not affect cumulus expansion, nuclear maturation, fertilization parameters, or cleavage rate. However, compared to no addition (21%), presence of 1 (33%) and 10 ng/ml EGF (42%) during IVM increased (P < 0.01) the rate of blastocyst development in a concentration-dependent manner. Compared to 10 ng/ml EGF, higher concentrations (20 and 40 ng/ml) reduced (P < 0.01) blastocyst development in a concentration-dependent manner (35% and 24%, respectively). No difference was observed between no addition and 40 ng/ml EGF (22%). Compared to no addition and 10 ng/ml EGF, a significantly (P < 0.001) higher proportion (25% vs. 55%) of oocytes reached metaphase II stage 33 hr after IVM with 40 ng/ml EGF. However, no difference was observed at 44 hr. Transfer of embryos to six recipient gilts resulted in three pregnancies and birth of 18 piglets. The results show that EGF at certain concentrations in IVM medium can influence the developmental competence of oocytes. However, addition of EGF during the culture of pig embryos derived from oocytes matured in the presence of EGF is without effect. Birth of piglets provides evidence that embryos derived from oocytes matured in a medium containing EGF are viable. Mol. Reprod. Dev. 51:395–401, 1998. © 1998 Wiley-Liss, Inc.