gebhart/patrepeval huggingface dataset:
A timing methodology considering within-die clock skew variations (2008)

Timing margining is a key component of timing sign-off. Insufficient margin can lead to silicon failure and excessive pessimistic margin will entail unnecessary design optimization effort. Timing margin is intended to cover the uncertainty in clock arrival times and clock skews arising from within-die process variations. In highly scaled technologies, the increased process variations tend to enforce an overestimation of timing margins making it difficult for the designs to achieve the target performance. In this paper, we present a more efficient margining methodology to account for clock-skew variations arising due to within-die variations. The proposed methodology fits well within current corner based timing sign-off framework and allows for significant reduction in margin pessimism. We present the results and observations on a low power processor for hold-time margin correction. Evaluation of the proposed methodology for hold analysis on a low power processor shows, on average, ~67% reduction in the original margin. Further the margin correction decreases the number of hold-time violations significantly and effectively achieves 10times reduction in hold-violation fixing effort.
Data from Vaccine-Induced Memory CD8<sup>+</sup> T Cells Provide Clinical Benefit in HER2 Expressing Breast Cancer: A Mouse to Human Translational Study (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Immune-based therapy for metastatic breast cancer has had limited success, particularly in molecular subtypes with low somatic mutations rates. Strategies to augment T-cell infiltration of tumors include vaccines targeting established oncogenic drivers such as the genomic amplification of HER2. We constructed a vaccine based on a novel alphaviral vector encoding a portion of HER2 (VRP-HER2).&lt;/p&gt;Patients and Methods:&lt;p&gt;In preclinical studies, mice were immunized with VRP-HER2 before or after implantation of hHER2&lt;sup&gt;+&lt;/sup&gt; tumor cells and HER2-specific immune responses and antitumor function were evaluated. We tested VRP-HER2 in a phase I clinical trial where subjects with advanced HER2-overexpressing malignancies in cohort 1 received VRP-HER2 every 2 weeks for a total of 3 doses. In cohort 2, subjects received the same schedule concurrently with a HER2-targeted therapy.&lt;/p&gt;Results:&lt;p&gt;Vaccination in preclinical models with VRP-HER2 induced HER2-specific T cells and antibodies while inhibiting tumor growth. VRP-HER2 was well tolerated in patients and vaccination induced HER2-specific T cells and antibodies. Although a phase I study, there was 1 partial response and 2 patients with continued stable disease. Median OS was 50.2 months in cohort 1 (&lt;i&gt;n&lt;/i&gt; = 4) and 32.7 months in cohort 2 (&lt;i&gt;n&lt;/i&gt; = 18). Perforin expression by memory CD8 T cells post-vaccination significantly correlated with improved PFS.&lt;/p&gt;Conclusions:&lt;p&gt;VRP-HER2 increased HER2-specific memory CD8 T cells and had antitumor effects in preclinical and clinical studies. The expansion of HER2-specific memory CD8 T cells in vaccinated patients was significantly correlated with increased PFS. Subsequent studies will seek to enhance T-cell activity by combining with anti-PD-1.&lt;/p&gt;&lt;/div&gt;
730-P: Effects of Obstructive Sleep Apnea Treatment on Whole-Body and Adipose Tissue Insulin Sensitivity—Role of Senescence and Mitigation by Adjuvant Metformin Therapy (2023)

Introduction: Obstructive sleep apnea (OSA) is a prevalent sleep disorder linked to high type 2 diabetes risk. Positive airway pressure (PAP) therapy is the standard of care for OSA, but it inconsistently improves glucose homeostasis. Senescent cells are common in adipose tissue (AT) of patients with OSA and may impair insulin signaling. However, the effects of PAP therapy on AT senescence are not known. Addition of metformin, an insulin-sensitizer with anti-senescent effects, may be a good adjuvant therapeutic strategy to improve glycemic control in patients with OSA. Methods: We randomly assigned 16 nondiabetic participants with OSA (Mean± SD; age: 50.9 ± 6.7 y, BMI: 36.5 ± 2.9 kg/m2) in a 1:1 ratio to receive either 2g metformin or placebo daily along with PAP therapy for 3 months in a double-blind pilot study. Whole body and AT insulin sensitivity was determined by 2h oral glucose tolerance test (OGTT). AT biopsy was obtained to estimate tissue insulin signaling and senescence. Results: The metformin and placebo groups had comparable age, BMI and OSA severity at baseline. PAP compliance was 38% and 75% in the metformin and placebo groups, respectively. Matsuda Index, glucose area under the curve (2h AUC), and free-fatty acid suppression at baseline and follow-up were not different in metformin or placebo treated groups. Compared to baseline, insulin AUC and insulin to glucose AUC ratio during OGTT was unchanged in the metformin but increased in the placebo group. Metformin, but not placebo, was associated with increased insulin mediated AKT phosphorylation and decreased senescence biomarkers (p21 and MCP1) in AT during the follow-up visit. Conclusion: Metformin, as adjunct to PAP therapy, attenuated insulin rises during OGTT, improved AT insulin signaling, and lowered senescence biomarkers in OSA patients. Larger trials of longer treatment duration are needed to determine if metformin can prevent diabetes in OSA patients. Disclosure S. Rodrigues: None. W.S. Dantas: None. R.A. Beyl: None. R.C. Hebert: None. I. Griffith: None. M. Tanksley: None. E.C. Mader: None. J.P. Kirwan: None. C.L. Axelrod: None. E. Ravussin: Research Support; Eli Lilly and Company, Novartis AG. Advisory Panel; Novartis. P. Singh: None. Funding National Institutes of Health (P30DK072476, U54GM104940); CAPES (88887.470405/2019-00 to S.R.)
Reliability Gain of Network Coding in Lossy Wireless Networks (2008)

The capacity gain of network coding has been extensively studied in wired and wireless networks. Recently, it has been shown that network coding improves network reliability by reducing the number of packet retransmissions in lossy networks. However, the extent of the reliability benefit of network coding is not known. This paper quantifies the reliability gain of network coding for reliable multicasting in wireless networks, where network coding is most promising. We define the expected number of transmissions per packet as the performance metric for reliability and derive analytical expressions characterizing the performance of network coding. We also analyze the performance of reliability mechanisms based on rateless codes and automatic repeat request (ARQ), and compare them with network coding. We first study network coding performance in an access point model, where an access point broadcasts packets to a group of K receivers over lossy wireless channels. We show that the expected number of transmissions using ARQ, compared to network coding, scales as ominus (log K) as the number of receivers becomes large. We then use the access point model as a building block to study reliable multicast in a tree topology. In addition to scaling results, we derive expressions for the expected number of transmissions for finite multicast groups as well. Our results show that network coding significantly reduces the number of retransmissions in lossy networks compared to an ARQ scheme. However, rateless coding achieves asymptotic performance results similar to that of network coding.
A plea to stop using the case‐control design in retrospective database studies (2019)

The case-control design is widely used in retrospective database studies, often leading to spectacular findings. However, results of these studies often cannot be replicated, and the advantage of this design over others is questionable. To demonstrate the shortcomings of applications of this design, we replicate two published case-control studies. The first investigates isotretinoin and ulcerative colitis using a simple case-control design. The second focuses on dipeptidyl peptidase-4 inhibitors and acute pancreatitis, using a nested case-control design. We include large sets of negative control exposures (where the true odds ratio is believed to be 1) in both studies. Both replication studies produce effect size estimates consistent with the original studies, but also generate estimates for the negative control exposures showing substantial residual bias. In contrast, applying a self-controlled design to answer the same questions using the same data reveals far less bias. Although the case-control design in general is not at fault, its application in retrospective database studies, where all exposure and covariate data for the entire cohort are available, is unnecessary, as other alternatives such as cohort and self-controlled designs are available. Moreover, by focusing on cases and controls it opens the door to inappropriate comparisons between exposure groups, leading to confounding for which the design has few options to adjust for. We argue that this design should no longer be used in these types of data. At the very least, negative control exposures should be used to prove that the concerns raised here do not apply.
Novel lignin as natural‐biodegradable binder for various sectors—A review (2021)

Abstract Lignin functions as an essential polymer in plants that forms the plant body's structural framework. The natural glue holds the cellulosic fibers together in the plant body, thereby providing rigidity and strength. Despite this, lignin shows promising relevance for biomaterial production due to its abundance, nontoxic nature and biodegradability. Considerably, adhesive components were derived from petroleum, which is increasingly more expensive. Hence, lignin, the natural glue in plant materials, gained much popularity because of its phenolic nature, making it an attractive substitute for adhesives. Lignin‐based binders are produced through phenols substitution in phenol‐formaldehyde resins with lignin due to their similar structural framework. Many researchers have confirmed the multifunctional applications of lignin, such as wood adhesive in fiber board, plywood and particleboard, a binder in printed wiring boards, abrasive tools, epoxy asphalts, epoxy wood composites, 3D printing, adhesive hydrogels, soil suppressants, lignocellulosic paper and coatings. This review presents a comprehensive description of the utilization of lignin‐based binders for different applications. The present work highlights the discussion on the various methods by which lignin can be used to replace synthetic binders. This review focuses on global research work introducing lignin in different chemical adhesives for a more cost‐effective and less harmful alternative.
Training Stochastic Grammars From Unlabelled Text Corpora (1992)

The paper describes various aspects and prac-ticalities of applying the &amp;quot;Hidden Markov &amp;quot; ap-proach to train parameters of regular and context-free stochastic grammars. The approach enables grammars to be trained from unlabelled text cor-pora, providing flexibility in the choice of syntac-tic categories and text domain. Part-of-speech tagging and parsing are discussed as applica-tions. Linguistic considerations can be used to de-velop constrained grammars, providing appropri-ate higher-order context for disamhiguation. Un-constrained grammars provide the opportunity to capture patterns that are not covered by a specific grammar. Experimental results are discussed for these alternatives.
Synthese und Struktur von pentakoordinierten spirocyclischen Derivaten des Phosphors und Arsens (1981)

Synthesis and Structure of Pentacoordinated Spirocyclic Derivatives of Phosphorus and Arsenic Phosphorus ( 2a , b ) and arsenic 4 containing spirocyclic compounds have been synthesised from substituted ureas and halides of phosphorus and arsenic. On the basis of an X‐ray analysis of 2b it is demonstrated that λ 5 ‐P compounds and not phosphonium salts were obtained.
Educating Students with Learning Disabilities in Inclusive Classrooms (2013)

There is great debate over including students with disabilities, in particular students with learning disabilities, in inclusive classrooms. Several strategies are available to support educating students with learning disabilities in inclusive classrooms including: co-teaching, differentiated instruction, and peer-mediated instruction and interventions. Theory suggests the practice of inclusion is congruent with social justice, but evidence suggests mixed results regarding academic achievement typically occur. However, results of providing separate pullout instructional services are not necessarily more likely to achieve desired results. Therefore, educators will need to make placement decisions considering the resources available in their school, in addition to the skill level of the students they work with, in order to make proper decisions regarding least restrictive environment. Doing so puts the student at the center of educational planning rather than ideological belief.
Nasopharyngeal carcinoma super-enhancer–driven ETV6 correlates with prognosis (2017)

Nasopharyngeal carcinoma (NPC) most frequently occurs in southern China and southeast Asia. Epidemiology studies link NPC to genetic predisposition, Epstein-Barr virus (EBV) infection, and environmental factors. Genetic studies indicate that mutations in chromatin-modifying enzymes are the most frequent genetic alterations in NPC. Here, we used H3K27ac chromatin immune precipitation followed by deep sequencing (ChIP-seq) to define the NPC epigenome in primary NPC biopsies, NPC xenografts, and an NPC cell line, and compared them to immortalized normal nasopharyngeal or oral epithelial cells. We identified NPC-specific enhancers and found these enhancers were enriched with nuclear factor κB (NF-κB), IFN-responsive factor 1 (IRF1) and IRF2, and ETS family members ETS1 motifs. Normal cell-specific enhancers were enriched with basic leucine zipper family members and TP53 motifs. NPC super-enhancers with extraordinarily broad and high H3K27ac signals were also identified, and they were linked to genes important for oncogenesis including ETV6. ETV6 was also highly expressed in NPC biopsies by immunohistochemistry. High ETV6 expression correlated with a poor prognosis. Furthermore, we defined the EBV episome epigenetic landscapes in primary NPC tissue.
Conical Second Harmonic Generation in Two-dimensional Nonlinear Photonic Structures (2010)

We report conical second harmonic generation in two-dimensional nonlinear photonic structures with fundamental beam of linear, circular, and elliptical polarizations, respectively. We develop a theoretical model for describing this phenomenon and explore its physical origin.
Supplementary Figure 3 from Ubiquitination and Downregulation of BRCA1 by Ubiquitin-Conjugating Enzyme E2T Overexpression in Human Breast Cancer Cells (2023)

Supplementary Figure 3 from Ubiquitination and Downregulation of BRCA1 by Ubiquitin-Conjugating Enzyme E2T Overexpression in Human Breast Cancer Cells
Outer membrane protein OmpQ of Bordetella bronchiseptica is required for mature biofilm formation (2015)

Bordetella bronchiseptica, an aerobic Gram-negative bacterium, is capable of colonizing the respiratory tract of diverse animals and chronically persists inside the hosts by forming biofilm. Most known virulence factors in Bordetella species are regulated by the BvgAS two-component transduction system. The Bvg-activated proteins play a critical role during host infection. OmpQ is an outer membrane porin protein which is expressed under BvgAS control. Here, we studied the contribution of OmpQ to the biofilm formation process by B. bronchiseptica. We found that the lack of expression of OmpQ did not affect the growth kinetics and final biomass of B. bronchiseptica under planktonic growth conditions. The ΔompQ mutant strain displayed no differences in attachment level and in early steps of biofilm formation. However, deletion of the ompQ gene attenuated the ability of B. bronchiseptica to form a mature biofilm. Analysis of ompQ gene expression during the biofilm formation process by B. bronchiseptica showed a dynamic expression pattern, with an increase of biofilm culture at 48 h. Moreover, we demonstrated that the addition of serum anti-OmpQ had the potential to reduce the biofilm biomass formation in a dose-dependent manner. In conclusion, we showed for the first time, to the best of our knowledge, evidence of the contribution of OmpQ to a process of importance for B. bronchiseptica pathobiology. Our results indicate that OmpQ plays a role during the biofilm development process, particularly at later stages of development, and that this porin could be a potential target for strategies of biofilm formation inhibition.
Prions (2015)

Prions are infectious proteins that have been described in both mammals and fungi. That prions are composed solely of proteins makes them unprecedented infectious pathogens. Prions are composed of proteins that can misfold and are prone to aggregation, and multiply by forcing the precursor protein to acquire the corrupted conformation. Different conformations of proteins in the prion state encipher distinct strains with specific patterns of pathology. In mammals, prions accumulate to high levels in the nervous system, where they cause dysfunction and fatal degeneration. Both, mammalian and fungal prions have been produced in cell-free systems. Synthetic prion protein (PrP) peptides and recombinant PrP fragments have been used to form mammalian prions, while N-terminal regions – called prion domains – that are rich in glutamine and asparagine have been used to form fungal prions. Mammalian prions cause a group of invariably fatal, neurodegenerative diseases. Prion diseases may present as genetic, infectious, or sporadic disorders, all of which involve the modification of PrPs. The tertiary and quaternary structures of PrPs are profoundly altered as prions are formed and, as such, prion diseases represent disorders of protein conformation. Prion diseases are present in humans and farmed animals. Cross-species transmission of prions can occur; indeed, dietary exposure of the human population to the prions responsible for bovine spongiform encephalopathy (BSE) have led to the emergence of variant Creutzfeldt–Jakob disease (vCJD). Prions can persist in the environment for years and are extremely difficult to inactivate, thus posing a threat to animal and human health.
Identification of Latent Variables in a Semantic Odor Profile Database Using Principal Component Analysis (2006)

Many classifications of odors have been proposed, but none of them have yet gained wide acceptance. Odor sensation is usually described by means of odor character descriptors. If these semantic profiles are obtained for a large diversity of compounds, the resulting database can be considered representative of odor perception space. Few of these comprehensive databases are publicly available, being a valuable source of information for fragrance research. Their statistical analysis has revealed that the underlying structure of odor space is high dimensional and not governed by a few primary odors. In a new effort to study the underlying sensory dimensions of the multivariate olfactory perception space, we have applied principal component analysis to a database of 881 perfume materials with semantic profiles comprising 82 odor descriptors. The relationships identified between the descriptors are consistent with those reported in similar studies and have allowed their classification into 17 odor classes.
Structural history of the Terang and Sirasun fields and the impact upon timing of charge and reservoir performance, Kangean PSC, East Java Sea, Indonesia (2018)

Abstract Detailed seismic structural analysis of the Terang-Sirasun feature, offshore Bali, has revealed a complex history of alternating long-term subsidence and episodic uplift. These fluctuations have had a significant impact on gas volume expansion and gas producibility due to differences in drainage rather than imbibition reservoir saturation history. A drainage rather than imbibition saturation history should significantly improve total ultimate production from this reservoir. The Sirasun structure was charged very late and is filled with biogenically sourced gas. The bulk of the gas volume entered the trap since the initiation of the ongoing period of uplift, and charge continues at present. Although the structure overall has subsided since the Late Cretaceous, this subsidence has been punctuated by periods of pronounced uplift, with the initial phase of uplift occurring in the early Miocene, and additional phases in the Plio-Pleistocene and present. Mapping of truncated seismic reflections around the crest of the Terang-Sirasun structure indicates that more than 1,000 feet of uplift has occurred during the last 1.5 mybp (million years before present) and that the bulk of that uplift is due to the current phase of inversion. The current uplift is causing the biogenic gas to expand and displace water within the transition zone and at the gas water contact (GWC). Because the expanding gas is displacing water, the reservoir's saturation history is due to drainage conditions. A gas pool which has experienced a drainage saturation history will result in reduced water production, a higher initial gas saturation, and larger recoverable gas volumes as compared to a pool that has experienced an imbibition saturation history. ARCO's previous reservoir model was calibrated to imbibition, consistent with a depositional model that involved continuous subsidence over the life of the gas volumes. ARCO's new depositional model that involves episodic uplift and a drainage saturation history therefore should result in improved reservoir performance.
Cooperative manipulation and transportation with aerial robots (2009)

In this paper we consider the problem of controlling multiple robots manipulating and transporting a payload in three dimensions via cables. We develop robot configurations that ensure static equilibrium of the payload at a desired pose while respecting constraints on the tension and provide analysis of payload stability for these configurations. We demonstrate our methods on a team of aerial robots via simulation and experimentation.
Influence of Processing and of Material Defects on the Electrical Characteristics of SiC-SBDs and SiC-MOSFETs (2010)

The influences of processing and material defects on the electrical characteristics of large-capacity (approximately 100A) SiC-SBDs and SiC-MOSFETs have been investigated. In the case of processing defects, controlled activation annealing is the most important factor. On the other hand for material defects, the number of epitaxial defects must be decreased to zero for both SBDs and MOSFETs. The dislocation defects in SiC wafers are dangerous for the breakdown voltage of MOSFETs. However, they are not killer defects. If the epitaxial defect density is sufficiently low and the dislocation density is in the order of 10000cm-2, the long- term reliability of the gate oxide at the electric field of 3MV/cm can be guaranteed.
BUILDING ELECTRONIC BURSTERS WITH THE MORRIS–LECAR NEURON MODEL (2006)

We propose a method for the design of electronic bursting neurons, based on a simple conductance neuron model. A burster is a particular class of neuron that displays fast spiking regimes alternating with resting periods. Our method is based on the use of an electronic circuit that implements the well-known Morris–Lecar neuron model. We use this circuit as a tool of analysis to explore some regions of the parameter space and to contruct several bifurcation diagrams displaying the basic dynamical features of that system. These bifurcation diagrams provide the initial point for the design and implementation of electronic bursting neurons. By extending the phase space with the introduction of a slow driving current, our method allows to exploit the bistabilities which are present in the Morris–Lecar system to the building of different bursting models.