gebhart/patrepeval huggingface dataset:
Scaling up Dynamic Topic Models (2016)

Dynamic topic models (DTMs) are very effective in discovering topics and capturing their evolution trends in time series data. To do posterior inference of DTMs, existing methods are all batch algorithms that scan the full dataset before each update of the model and make inexact variational approximations with mean-field assumptions. Due to a lack of a more scalable inference algorithm, despite the usefulness, DTMs have not captured large topic dynamics. This paper fills this research void, and presents a fast and parallelizable inference algorithm using Gibbs Sampling with Stochastic Gradient Langevin Dynamics that does not make any unwarranted assumptions. We also present a Metropolis-Hastings based $O(1)$ sampler for topic assignments for each word token. In a distributed environment, our algorithm requires very little communication between workers during sampling (almost embarrassingly parallel) and scales up to large-scale applications. We are able to learn the largest Dynamic Topic Model to our knowledge, and learned the dynamics of 1,000 topics from 2.6 million documents in less than half an hour, and our empirical results show that our algorithm is not only orders of magnitude faster than the baselines but also achieves lower perplexity.
Viewpoint: A long-distance quantum repeater gets one step closer (2011)

Researchers demonstrate a robust, high-fidelity, broadband quantum memory that could be used to realize a long-distance quantum repeater for secure communication.
Managemental influences on the selective proliferation of two strains of haemolyticEscherichia coliin weaned pigs (1988)

In an experimental study on a piggery it was found that haemolytic Escherichia coli of O-serotypes 138 or 139 proliferated in the intestinal tracts of pigs following weaning, with E. coli of the O-138 type also being occasionally recovered from unweaned pigs, and once from a sow. Organisms of the O-138 type produced heat labile enterotoxin and their presence in weaned pigs was associated with the development of severe post-weaning diarrhoea. E. coli of O-139 type produced a vero cell cytotoxin and were associated with a milder diarrhoea in weaned pigs. Under various managemental circumstances the O-138 type E. coli almost invariably proliferated after weaning. The O-139 strain of E. coli did however proliferate rather than the O-138 strain following the movement of weaned pigs to new accommodation, after weaned pigs were returned to their sow and then weaning again 5 days later, and very occasionally in pigs weaned at 5 weeks of age. In all these cases earlier proliferation of the O-138 E. coli had been detected, suggesting that this may be a prerequisite for proliferation of the O-139 strain.
GENESYS - A Cross-Domain Architecture for Dependable Embedded Systems (2011)

Recognizing the strategic importance of embedded computing for industry and society, the European Commission formed, together with industry, academia, and national governments, the European technology platform ARTEMIS (Advanced Research and Technology for Embedded Intelligence and Systems) in 2004. It is one goal of ARTEMIS to develop a cross-domain embedded system architecture, supported by design methods and tools, to significantly improve the functionality, dependability, and cost-effectiveness of embedded systems. The GENESYS (Generic Embedded Systems) project, carried out by a consortium of twenty industrial and academic partners coming from different embedded system domains, developed a blueprint for such an architecture that should be applicable in the industrial domain as well as in the multimedia domain. This blueprint (GENESYS) has been strongly influenced by the concepts of and the experience with the time-triggered architecture. It is the objective of this contribution to give an overview of the cross-domain architecture GENESYS.
Variation in sclerophylly among Iberian populations of Quercus coccifera L. is associated with genetic differentiation across contrasting environments (2009)

Evergreen oaks are an emblematic element of the Mediterranean vegetation and have a leaf phenotype that seems to have remained unchanged since the Miocene. We hypothesise that variation of the sclerophyll phenotype among Iberian populations of Quercus coccifera is partly due to an ulterior process of ecotypic differentiation. We analysed the genetic structure of nine Iberian populations using ISSR fingerprints, and their leaf phenotypes using mean and intracanopy plasticity values of eight morphological (leaf angle, area, spinescence, lobation and specific area) and biochemical traits (VAZ pool, chlorophyll and beta-carotene content). Climate and soil were also characterised at the population sites. Significant genetic and phenotypic differences were found among populations and between NE Iberia and the rest of the populations of the peninsula. Mean phenotypes showed a strong and independent correlation with both genetic and geographic distances. Northeastern plants were smaller, less plastic, with smaller, spinier and thicker leaves, a phenotype consistent with the stressful conditions that prevailed in the steppe environments of the refugia within this geographic area during glaciations. These genetic, phenotypic, geographic and environmental patterns are consistent with previously reported palaeoecological and common evidence. Such consistency leads us to conclude that there has been a Quaternary divergence within the sclerophyllous syndrome that was at least partially driven by ecological factors.
High temperature superconductivity space experiment (HTSSE): Passive millimeter wave devices (1991)

The Naval Research Laboratory (NRL) is exploring the feasibility of deploying high temperature superconductivity (HTS) devices and components in space. A variety of devices, primarily passive microwave and millimeter wave component, have been procured and well integrated with a cryogenic refrigerator system and data acquistion system to form the space package, which will be launched late in 1992. This Space Experiment will demonstrate that this technology is sufficiently robust to survive the space environment and has the potential to significantly improve space communications systems. The devices for the initial launch (HTSSE‐I) have been received by NRL and evaluated electrically, thermally and mechanically and will be integrated into the final space package early in 1991. The performance of the devices will be summarized and some potential applications of HTS technology in space system will be outlined.
Abstract 2911: The CEA-targeted ISAC, BDC-2034, shows preclinical efficacy associated with innate immune activation, phagocytosis, and myeloid reprogramming (2022)

Abstract Introduction: Immune-stimulating antibody conjugates (ISACs) direct a TLR7/8 agonist into tumors through engagement of cell surface antigens to activate tumor-associated myeloid cells and initiate a broad innate and adaptive anti-tumor immune response. We are developing the ISAC BDC-2034 to target the tumor antigen, CEA (CEACAM5), which is expressed in many solid tumors. BDC-2034 comprises our proprietary antibody, CEA1, covalently conjugated to a potent TLR7/8 agonist via a non-cleavable linker. The strong pro-phagocytic capacity and slow internalization rate of CEA1 makes it an ideal antibody for the ISAC approach. Methods: The ability of BDC-2034 to induce the secretion of pro-inflammatory cytokines was evaluated in vitro using co-cultures of tumor cells and primary immune cells (including monocytes and dendritic cells). Anti-tumor efficacy was demonstrated in vivo with xenograft and syngeneic mouse tumor models. In parallel studies, the mechanism of BDC-2034 action was assessed by quantifying intratumoral immune infiltration, cytokine levels, and transcript profile. Results: In co-cultures of CEA-expressing tumor cells and immune cells, BDC-2034 induced the secretion of cytokines and chemokines that are essential for a broad anti-tumor immune response, including IL-12p70, CXCL10, and TNFα. These effects were accompanied by myeloid cell activation as demonstrated by elevation in costimulatory surface markers such as CD40. In vivo, BDC-2034 inhibited tumor growth in multiple xenograft and syngeneic mouse tumor models having CEA expression comparable to human cancers. Consistent with the proposed mechanism of action, BDC-2034 induced intratumoral immune cell infiltration, inflammatory cytokine secretion, and myeloid re-programming in a dose-dependent and CEA-dependent fashion. The constellation of BDC-2034 effects translated to durable therapeutic activity. Conclusions: These preclinical findings demonstrate the potential of BDC-2034 to generate anti-tumor activity in CEA-expressing cancers through direct innate immune activation and the induction of adaptive anti-tumor immunity. Citation Format: Lisa K. Blum, Cecelia I. Pearson, Laughing Bear Torrez Dulgeroff, Rishali Gadkari, Angela Luo, Andrew Luo, Jennifer E. Melrose, Jess L. Nolin, Hai Li, Arthur Lee, Matthew N. Zhou, Puneet Anand, Ganapathy Sarma, Karla A. Henning, Steven J. Chapin, Shelley E. Ackerman, Romas Kudirka, Yuyi Shen, Bruce Hug, Edith A. Perez, Marcin Kowanetz, Michael N. Alonso, Brian S. Safina, David Dornan, William G. Mallet. The CEA-targeted ISAC, BDC-2034, shows preclinical efficacy associated with innate immune activation, phagocytosis, and myeloid reprogramming [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2911.
ChemInform Abstract: Competing Phases, Complex Structure, and Complementary Diffraction Studies of R3‐δFeAl4‐xMgxTt2 Intermetallics (R: Y, Dy, Er, Yb; Tt: Si or Ge; x < 0.5). (2013)

Abstract Yb 2.77 FeAl 3.72 Mg 0.28 Si 2 , Dy 3‐δ FeAl 4‐x Mg x Si 2 , Y 3‐δ FeAl 4‐x Mg x Ge 2 , Er 3‐δ FeAl 4‐x Mg x Ge 2 , and Yb 5 Fe 4 Al 17 Si 6 are synthesized from the elements using an equimolar Mg/Al reactive flux (950 °C, 5 h).
Emergence of Brachyspira species and strains: reinforcing the need for surveillance (2015)

This short review discusses the increasing complexity that has developed around the understanding of <i>Brachyspira</i> species that infect pigs, and their ability to cause disease. It describes the recognition of new weakly haemolytic <i>Brachyspira</i> species, and the growing appreciation that <i>Brachyspira pilosicoli</i> and some other weakly haemolytic species may be pathogenic in pigs. It discusses swine dysentery (SD) caused by the strongly haemolytic <i>Brachyspira hyodysenteriae</i>, particularly the cyclical nature of the disease whereby it can largely disappear as a clinical problem from a farm or region, and re-emerge years later. The review then describes the recent emergence of two newly described strongly haemolytic pathogenic species, "<i>Brachyspira suanatina</i>" and "<i>Brachyspira hampsonii</i>" both of which appear to have reservoirs in migratory waterbirds, and which may be transmitted to and between pigs. "<i>B. suanatina</i>" seems to be confined to Scandinavia, whereas "<i>B. hampsonii</i>" has been reported in North America and Europe, causes a disease indistinguishable from SD, and has required the development of new routine diagnostic tests. Besides the emergence of new species, strains of known <i>Brachyspira</i> species have emerged that vary in important biological properties, including antimicrobial susceptibility and virulence. Strains can be tracked locally and at the national and international levels by identifying them using multilocus sequence typing (MLST) and comparing them against sequence data for strains in the PubMLST databases. Using MLST in conjunction with data on antimicrobial susceptibility can form the basis for surveillance programs to track the movement of resistant clones. In addition some strains of <i>B. hyodysenteriae</i> have low virulence potential, and some of these have been found to lack the <i>B. hyodysenteriae</i> 36 kB plasmid or certain genes on the plasmid whose activity may be associated with colonization. Lack of the plasmid or the genes can be identified using PCR testing, and this information can be added to the MLST and resistance data to undertake detailed surveillance. Strains of low virulence are particularly important where they occur in high health status breeding herds without causing obvious disease: potentially they could be transmitted to production herds where they may colonize more effectively and cause disease under stressful commercial conditions.
Probing elastic properties of graphene and heat conduction in graphene bubbles above 1000∘C (2023)

The elastic and thermal properties of graphene were investigated by illuminating graphen bubbles with a laser spot. Tempertures above $1000{\phantom{\rule{0.16em}{0ex}}}^{\ensuremath{\circ}}\mathrm{C}$ were obtained in large ($&gt;10\phantom{\rule{0.28em}{0ex}}\textmu{}\mathrm{m}$) graphene bubbles. The formation of standing optical waves lead to laser heating depending on the height of the garphene bubble, which results in Raman band oscillations when scanning the laser spot across the bubble. The profile of the bubble under laser illumination can be deduced from the Raman G band oscillations. A distinct swelling at the center of the bubble is observed which is attributed to the strong softening of graphene above $1000{\phantom{\rule{0.16em}{0ex}}}^{\ensuremath{\circ}}\mathrm{C}$. From the size and height of the swelling it is deduced that the elastic modulus is reduced by at least $40%$ at $1000{\phantom{\rule{0.16em}{0ex}}}^{\ensuremath{\circ}}\mathrm{C}$. On solving the heat equation for the heat dissipation through the graphene only, analytical expressions are obtained for the isotherms on the bubble for both symmetrical and asymmetrical positions of the laser spot. It was found that a large fraction of the absorbed heat dissipates through the gas in the bubble using the finite volume method. Analytical expressions for the temperature distribution in the bubble are deduced from the numerical results. Heat conduction through the gas in the bubble influences the temperature distribution and needs to be taken into account in the heat dissipation in graphene bubbles.
Techniques for determining physical zones of influence (2023)

Techniques for analyzing flow of a quantity in a given domain are provided. In one aspect, a method for modeling regions in a domain affected by a flow of a quantity is provided which includes the following steps. A physical representation of the domain is provided. A grid that contains a plurality of grid-points in the domain is created. Sources are identified in the domain. Given a vector field that defines a direction of flow of the quantity within the domain, a boundary value problem is defined for each of one or more of the sources identified in the domain. Each of the boundary value problems is solved numerically to obtain a solution for the boundary value problems at each of the grid-points. The boundary problem solutions are post-processed to model the regions affected by the flow of the quantity on the physical representation of the domain.
Identification of Reference Genes for Quantitative Real-Time PCR in Date Palm (Phoenix dactylifera L.) Subjected to Drought and Salinity (2016)

Date palm is an important crop plant in the arid and semi-arid regions supporting human population in the Middle East and North Africa. These areas have been largely affected by drought and salinity due to insufficient rainfall and improper irrigation practices. Date palm is a relatively salt- and drought-tolerant plant and more recently efforts have been directed to identifying genes and pathways that confer stress tolerance in this species. Quantitative real-time PCR (qPCR) is a promising technique for the analysis of stress-induced differential gene expression, which involves the use of stable reference genes for normalizing gene expression. In an attempt to find the best reference genes for date palm's drought and salinity research, we evaluated the stability of 12 most commonly used reference genes using the geNorm, NormFinder, BestKeeper statistical algorithms and the comparative ΔCT method. The comprehensive results revealed that HEAT SHOCK PROTEIN (HSP), UBIQUITIN (UBQ) and YTH domain-containing family protein (YT521) were stable in drought-stressed leaves whereas GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPDH), ACTIN and TUBULIN were stable in drought-stressed roots. On the other hand, SMALL SUBUNIT RIBOSOMAL RNA (25S), YT521 and 18S ribosomal RNA (18S); and UBQ, ACTIN and ELONGATION FACTOR 1-ALPHA (eEF1a) were stable in leaves and roots, respectively, under salt stress. The stability of these reference genes was verified by using the abiotic stress-responsive CYTOSOLIC Cu/Zn SUPEROXIDE DISMUTASE (Cyt-Cu/Zn SOD), an ABA RECEPTOR, and a PROLINE TRANSPORTER 2 (PRO) genes. A combination of top 2 or 3 stable reference genes were found to be suitable for normalization of the target gene expression and will facilitate gene expression analysis studies aimed at identifying functional genes associated with drought and salinity tolerance in date palm.
Stereo Imaging with Spaceborne Radars (1983)

Stereo viewing is a valuable tool in photointerpretation and is used for the quantitative reconstruction of the three dimensional shape of a topographical surface. Stereo viewing refers to a visual perception of space by presenting an overlapping image pair to an observer so that a three dimensional model is formed in the brain. Some of the observer's function is performed by machine correlation of the overlapping images - so called automated stereo correlation. The direct perception of space with two eyes is often called natural binocular vision; techniques of generating three dimensional models of the surface from two sets of monocular image measurements is the topic of stereology.
Coherent Combining with Imperfect Beams (2011)

Coherent combining efficiency losses from spatially and temporally mismatched input fields are quantified in terms of normalized variances of the field parameters. We derive expressions for Gaussian beams relevant for coherent fiber arrays.
Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI (2019)

3D histology, slice-based connectivity atlases, and diffusion MRI are common techniques to map brain wiring. While there are many modality-specific tools to process these data, there is a lack of integration across modalities. We develop an automated resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling the analysis of histological features across multiple fiber tracts and networks, and their correlation with in-vivo biomarkers. We apply our pipeline in a murine stroke model, demonstrating not only strong correspondence between MRI abnormalities and CLARITY-tissue staining, but also uncovering acute cellular effects in areas connected to the ischemic core. We provide improved maps of connectivity by quantifying projection terminals from CLARITY viral injections, and integrate diffusion MRI with CLARITY viral tracing to compare connectivity maps across scales. Finally, we demonstrate tract-level histological changes of stroke through this multimodal integration. This resource can propel investigations of network alterations underlying neurological disorders.
Relationship Among Initial Serum Prostate Specific Antigen, Prostate Specific Antigen Progression and Prostate Cancer Detection at Repeat Screening Visits (2006)

The proposed retesting schedule using current PSA and age decreases the number of visits by 38.1%, while delaying the detection of only 2.4% of CaPs that would have been detected using annual PSA testing.
Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample (2021)

Information about the scripts and data used in this study: Sahraeian SME, et al., Achieving Robust Somatic Mutation Detection with Deep Learning Models Derived from Reference Data Sets of a Cancer Sample, Genome Biology, 2022.
Studies in Bicyclo[3.1.0]hexane Methanolysis. Ring Opening of Activated Cyclopropanes under Acidic and Basic Conditions. (2003)

A bicyclo[3.1.0]hexane, with one cyclopropane\ncarbon flanked by a ketone and an ester or an aldehyde,\nundergoes methanolysis with cleavage of one of the two\nactivated cyclopropane bonds, depending on the reaction\nconditions. Acidic conditions yield primarily or exclusively\na 4-methoxycyclohexane, while basic conditions yield a\n3-methoxymethylcyclopentanone.
Low-loss, InP-based integrated optical isolators (2008)

We discuss the development of a monolithically integratable optical isolator. The device is a semiconductor optical amplifier with a magnetized ferromagnetic metal contact. 12.7 dB of isolation combined with optical transparency has been demonstrated.
Mechanism-based analysis of enzyme inhibitors of amide bond hydrolysis. (1989)

Biochemical information regarding the mechanism of amide bond hydrolysis offers insight into the possible chemical groups in the enzyme active site responsible for hydrolysis. Assuming that these groups have a relatively fixed geometry in accord with their functional role, then their three-dimensional position in space can be determined if sufficient structural diversity exists within the data set of compounds with known affinities. Each compound which binds can be augmented by additional chemical groups to represent the receptor's functional groups. For each compound, the set of geometrical arrangements of these groups which would show optimal binding to the compound can be determined by systematic search. A common geometric arrangement representing the active site geometry should be present for each compound. In studies of the binding of mechanism-based inhibitors of chymotrypsin, Naruto et al. (1985) showed some movement of active site residues to accommodate different ligands. Nevertheless, this procedure found a unique active site geometry for ACE which compared favorably with that of carboxypeptidase A, an enzyme of analogous function.
Ask the Experts: The Future of Neurodegenerative Diseases: Emerging Targets, Treatments and Technologies (2012)

The field of medicinal chemistry applied to the discovery of novel and efficacious therapy for neurodegenerative diseases is ever changing as new molecular targets, compounds and technologies are discovered. Isaac Bruce, Commissioning Editor, spoke to six experts and discussed why they became involved in the field, the future of the area and the challenges it faces.
Toll‐like receptors’ two‐edged sword: when immunity meets apoptosis (2007)

Toll-like receptors (TLR) have emerged as key players in the detection of pathogens and the induction of anti-microbial immune response. TLR recognize pathogen-associated molecular patterns, and trigger anti-microbial innate immune responses ranging from the secretion of pro-inflammatory mediators to the increase of natural killer cell cytotoxicity. Besides activating the innate immune response, TLR engagement also shapes the adaptive immune response. Indeed, the broad diversity of signaling pathways initiated by TLR is progressively unraveled. Recent reports suggested that among the anti-microbial defenses they initiate, members of the TLR family can induce apoptosis. This review focuses on this newly described function of TLR, and emphasizes the similarities and differences between the different apoptosis-signaling pathways described downstream of TLR. The functional relevance of TLR-triggered apoptosis is also discussed, as therapeutic applications are likely to ensue in the near future.