gebhart/patrepeval huggingface dataset:
Lentiviral standards to determine the sensitivity of assays that quantify lentiviral vector copy numbers and genomic insertion sites in cells (2022)

With an increasing number of gene therapy clinical trials and drugs reaching the market, it becomes important to standardize the methods that evaluate the efficacy and safety of gene therapy. We herein report the generation of lentiviral standards which are stable, cloned human cells prepared from the diploid HCT116 cell line and which carry a known number of lentiviral vector copies in their genome. These clones can be used as reference cellular materials for the calibration or qualification of analytical methods that quantify vector copy numbers in cells (VCN) or lentiviral vector genomic integration sites (IS). Cellular standards were used to show the superior precision of digital droplet PCR (ddPCR) over quantitative PCR (qPCR) for VCN determination. This enabled us to develop a new sensitive and specific VCN ddPCR method specific for the integrated provirus and not recognizing the transfer plasmid. The cellular standards, were also useful to assess the sensitivity and limits of a ligation-mediated PCR (LM-PCR) method to measure IS showing that at least 1% abundance of a single IS can be detected in a polyclonal population but that not all IS can be amplified with similar efficiency. Thus, lentiviral standards should be systematically used in all assays that assess lentiviral gene therapy efficacy and safety.
Lanthanides post-functionalized nanocrystalline metal–organic frameworks for tunable white-light emission and orthogonal multi-readout thermometry (2015)

We demonstrate tunable white-light emission and multi-readout thermometry in two respective nanocrystalline luminescent metal-organic frameworks (MOFs), which are prepared via postsynthetic functionalization with lanthanide cations of a robust UiO type MOF bearing the 2,2'-bipyridyl moiety (UiO-67-bpydc, 1). The white-light emitting framework Eu(3+)@1 can be conveniently applied as a thin film onto a commercial UV-LED chip for practical white lighting applications. The multi-readout orthogonal thermometry is illustrated in relation to the emission intensity ratio as well as the decay time and luminescence color of Eu(3+)/Tb(3+)@1 nanocrystals. This work highlights the opportunity for designing white-light emitters and nanothermometers based on lanthanide functionalized MOFs.
To Rb or Not to Rb: Uncovering Unique Subsets of Small Cell Lung Carcinoma (2022)

The use of IHC as a surrogate for specific underlying genomic alterations has allowed for increasingly comprehensive and accurate diagnosis of small cell lung carcinoma (SCLC). This is especially relevant in light of the increasing recognition of the biologic heterogeneity of this aggressive and difficult-to-treat lung tumor. Integrated genomic and IHC profiling of Rb status in SCLC yields new diagnostic insights and has translational implications. See related article by Febres-Aldana et al., p. 4702.
General groundwater session (1988)

The session on general groundwater at the AGU 1987 Fall Meeting included several interesting presentations. In this report, the papers have been grouped into four categories for the ease of discussion: groundwater management, aquifer compaction, field approaches, and modeling.
ATP analogues with modified phosphate chains and their selectivity for rat P2X2 and P2X2/3 receptors (2003)

1. Heteromeric P2X2/3 receptors are much more sensitive than homomeric P2X2 receptors to alphabeta-methylene-ATP, and this ATP analogue is widely used to discriminate the two receptors on sensory neurons and other cells. 2. We sought to determine the structural basis for this selectivity by synthesising ADP and ATP analogues in which the alphabeta and/or betagamma oxygen atoms were replaced by other moieties (including -CH2-, -CHF-, -CHCl-, -CHBr-, -CF2-, -CCl2-, -CBr2-, -CHSO3-, -CHPO3-, -CFPO3-, -CClPO3-, -CH2-CH2-, C triple bond C, -NH-, -CHCOOH-). 3. We tested their actions as agonists or antagonists by whole-cell recording from human embryonic kidney cells expressing P2X2 subunits alone (homomeric P2X2 receptors), or cells expressing both P2X2 and P2X3 subunits, in which the current through heteromeric P2X2/3 receptors was isolated. 4. ADP analogues had no agonist or antagonist effect at either P2X2 or P2X2/3 receptors. All the ATP analogues tested were without agonist or antagonist activity at homomeric P2X2 receptors, except betagamma-difluoromethylene-ATP, which was a weak agonist. 5. At P2X2/3 receptors, betagamma-imido-ATP, betagamma-methylene-ATP, and betagamma-acetylene-ATP were weak agonists, whereas alphabeta,betagamma- and betagamma,gammadelta-bismethylene-AP4 were potent full agonists. betagamma-Carboxymethylene-ATP and betagamma-chlorophosphonomethylene-ATP were weak antagonists at P2X2/3 receptors (IC50 about 10 microm). 6. The results indicate (a). that the homomeric P2X2 receptor presents very stringent structural requirements with respect to its activation by ATP; (b). that the heteromeric P2X2/3 receptor is much more tolerant of alphabeta and betagamma substitution; and (c). that a P2X2/3-selective antagonist can be obtained by introduction of additional negativity at the betagamma-methylene.
Composable controllers for physics-based character animation (2001)

An ambitious goal in the area of physics-based computer animation is the creation of virtual actors that autonomously synthesize realistic human motions and possess a broad repertoire of lifelike motor skills. To this end, the control of dynamic, anthropomorphic figures subject to gravity and contact forces remains a difficult open problem. We propose a framework for composing controllers in order to enhance the motor abilities of such figures. A key contribution of our composition framework is an explicit model of the “pre-conditions” under which motor controllers are expected to function properly. We demonstrate controller composition with pre-conditions determined not only manually, but also automatically based on Support Vector Machine (SVM) learning theory. We evaluate our composition framework using a family of controllers capable of synthesizing basic actions such as balance, protective stepping when balance is disturbed, protective arm reactions when falling, and multiple ways of standing up after a fall. We furthermore demonstrate these basic controllers working in conjunction with more dynamic motor skills within a prototype virtual stunt-person. Our composition framework promises to enable the community of physics-based animation practitioners to easily exchange motor controllers and integrate them into dynamic characters.
THE METABOLISM OF L-THREONINE AND GLYCINE BY Escherichia coli (1957)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
The Effect on Tumor Response of Adding Sequential Preoperative Docetaxel to Preoperative Doxorubicin and Cyclophosphamide: Preliminary Results From National Surgical Adjuvant Breast and Bowel Project Protocol B-27 (2003)

The addition of four cycles of preoperative docetaxel after four cycles of preoperative AC significantly increased clinical and pathologic response rates for operable breast cancer.
Some general observations on Ph.D. production in computer science (1976)

Based on remarks made as a participant of Panel on the Ph.D. Production Rate, Meeting of Heads of Ph.D. Computer Science Departments, Snowbird, Utah, July 1-2, 1974.
Multi-agent based intrusion prevention and mitigation architecture for software defined networks (2017)

Software Defined Networking (SDN) has proved to be a promising approach for creating next generation software based network ecosystems. It has provided us with a centralized network provision, a holistic management plane and a well-defined level of abstraction. But, at the same time brings forth new security and management challenges. Research in the field of SDN is primarily focused on reconfiguration, forwarding and network management issues. However in recent times the interest has moved to tackling security and maintenance issues. This work is based on providing a means to mitigate security challenges in an SDN environment from a DDoS attack based point of view. This paper introduces a Multi-Agent based intrusion prevention and mitigation architecture for SDN. Thus allowing networks to govern their behavior and take appropriate measures when the network is under attack. The architecture is evaluated against filter based intrusion prevention architectures to measure efficiency and resilience against DDoS attacks and false policy based attacks.
Osteogenic differentiation of hypertrophic chondrocytes involves asymmetric cell divisions and apoptosis. (1995)

We have investigated the early cellular events that take place during the change in lineage commitment from hypertrophic chondrocytes to osteoblast-like cells. We have induced this osteogenic differentiation by cutting through the hypertrophic cartilage of embryonic chick femurs and culturing the explants. Immunocytochemical characterization, [3H]thymidine pulse-chase labeling, in situ nick translation or end labeling of DNA breaks were combined with ultrastructural studies to characterize the changing pattern of differentiation. The first responses to the cutting, seen after 2 d, were upregulation of alkaline phosphatase activity, synthesis of type I collagen and single-stranded DNA breaks, probably indicating a metastable state. Associated with the change from chondrogenic to osteogenic commitment was an asymmetric cell division with diverging fates of the two daughter cells, where one daughter cell remained viable and the other one died. The available evidence suggests that the viable daughter cell then divided and generated osteogenic cells, while the other daughter cell died by apoptosis. The results suggest a new concept of how changes in lineage commitment of differentiated cells may occur. The concepts also reconcile previously opposing views of the fate of the hypertrophic chondrocyte.
Arsenic contamination in groundwater: a global perspective with emphasis on the Asian scenario. (2006)

The incidence of high concentrations of arsenic in drinking-water has emerged as a major public-health problem. With newer-affected sites discovered during the last decade, a significant change has been observed in the global scenario of arsenic contamination, especially in Asian countries. This communication presents an overview of the current scenario of arsenic contamination in countries across the globe with an emphasis on Asia. Along with the present situation in severely-affected countries in Asia, such as Bangladesh, India, and China, recent instances from Pakistan, Myanmar, Afghanistan, Cambodia, etc. are presented.
Deep Discriminant Analysis for i-vector Based Robust Speaker Recognition (2018)

Linear Discriminant Analysis (LDA) has been used as a standard post-processing procedure in many state-of-the-art speaker recognition tasks. Through maximizing the inter-speaker difference and minimizing the intra-speaker variation, LDA projects i-vectors to a lower-dimensional and more discriminative sub-space. In this paper, we propose a neural network based compensation scheme(termed as deep discriminant analysis, DDA) for i-vector based speaker recognition, which shares the spirit with LDA. Optimized against softmax loss and center loss at the same time, the proposed method learns a more compact and discriminative embedding space. Compared with the Gaussian distribution assumption of data and the learnt linear projection in LDA, the proposed method doesn't pose any assumptions on data and can learn a non-linear projection function. Experiments are carried out on a short-duration text-independent dataset based on the SRE Corpus, noticeable performance improvement can be observed against the normal LDA or PLDA methods.
Injection temperature effects using On‐column and split sampling in capillary gas chromatography (1983)

Abstract The effect of sample injection temperature on quantitation is examined for on‐column and conventional split modes of sampling in capillary gas chromatography. Discrimination effects can be observed even with on‐column injection if the injection temperature is too far above the boiling point of the solvent (or that of a major low boiling constituent(. This is attributed to higher boiling components being left behind in the syringe needle, and a set of simulation experiments are described to illustrate this effect. Various discrimination patterns using conventional split injection were observed, depending on temperature of injection. Apart from syringe needle effects, discrimination is probably due to the preferential venting of higher boiling components as liquid sample droplets, which can have a lifetime greater than the time of transit to the splitter. With such a two‐phase system, involving variable droplet size, the flow distribution in the splitter will be critical to uniform sampling. The use of combination on‐column/split sampling, with the appropriate temperature control to provide sample uniformity to the splitter is discussed as an advantageous alternative to conventional split sampling.
Low-Temperature Crystallization Enables 21.9% Efficient Single-Crystal MAPbI3 Inverted Perovskite Solar Cells (2020)

Lead halide perovskite solar cells (PSCs) have advanced rapidly in performance over the past decade. Single-crystal PSCs based on micrometers-thick grain-boundary-free films with long charge carrier diffusion lengths and enhanced light absorption (relative to polycrystalline films) have recently emerged as candidates for advancing PSCs further toward their theoretical limit. To date, the preferred method to grow MAPbI3 single-crystal films for PSCs involves solution processing at temperatures ≳120 °C, which adversely affects the films’ crystalline quality, especially at the surface, primarily because of methylammonium iodide loss at such high temperatures. Here we devise a solvent-engineering approach to reduce the crystallization temperature of MAPbI3 single-crystal films (<90 °C), yielding better quality films with longer carrier lifetimes. Single-crystal MAPbI3 inverted PSCs fabricated with this strategy show markedly enhanced open-circuit voltages (1.15 V vs 1.08 V for controls), leading to power conversion efficiencies of up to 21.9%, which are among the highest reported for MAPbI3-based devices.
Human Pose Estimation with Iterative Error Feedback (2016)

Hierarchical feature extractors such as Convolutional Networks (ConvNets) have achieved impressive performance on a variety of classification tasks using purely feedforward processing. Feedforward architectures can learn rich representations of the input space but do not explicitly model dependencies in the output spaces, that are quite structured for tasks such as articulated human pose estimation or object segmentation. Here we propose a framework that expands the expressive power of hierarchical feature extractors to encompass both input and output spaces, by introducing top-down feedback. Instead of directly predicting the outputs in one go, we use a self-correcting model that progressively changes an initial solution by feeding back error predictions, in a process we call Iterative Error Feedback (IEF). IEF shows excellent performance on the task of articulated pose estimation in the challenging MPII and LSP benchmarks, matching the state-of-the-art without requiring ground truth scale annotation.
Synergies of Variable Valve Actuation and Direct Injection (2002)

&lt;div class="htmlview paragraph"&gt;The main goal in the development of new automobile SI engines is to significantly reduce fuel consumption. To this end both, variable valve actuation and direct gasoline injection, are being pursued as new engine concepts. Both approaches appear to offer approximately the same potential to reduce fuel consumption. The development so far is creating the impression of two competing technical concepts with no obvious way to combine them [&lt;span class="xref"&gt;1&lt;/span&gt;].&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The two engine concepts, however, can be combined, although it is often objected that their combination would only yield marginal additional potential. That is true to the extent that the advantages of dethrottling offered by both of the concepts can only be counted once in terms of overall potential. But there is a number of additional effects to be taken into account.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This Paper represents an analysis of the individual potential of the two approaches as well as an estimation of their combined potential. The synergetic effects are discussed and evaluated on the basis of computational and experimental analysis.&lt;/div&gt;
Iodine/Palladium Approaches to the Synthesis of Polyheterocyclic Compounds (2010)

A simple, straightforward strategy for the synthesis of polyheterocyclic compounds (PHCs) is reported, which involves iterative cycles of palladium-catalyzed Sonogashira coupling, followed by iodocyclization using I(2) or ICl. A variety of heterocyclic units, including benzofurans, benzothiophenes, indoles, and isocoumarins, can be efficiently incorporated under mild reaction conditions. In addition, variations of this strategy afford a variety of linked and fused PHCs.
Frameshift mutation in codon 176 of the p53 gene in rat esophageal epithelial cells transformed by benzo[a]pyrene dihydrodiol (1995)

Mutations in the p53 tumor suppressor gene have been associated with exposure to environmental chemical carcinogens. Cultured rat esophageal epithelial cells were transformed in vitro by treatment with benzo[a]pyrene dihydrodiol (BP-DHD). A BP-DHD-transformed cell line and control cell lines were analyzed for mutations in the p53 gene and in the Ha-ras gene by single-strand conformation polymorphism analysis of polymerase chain reaction-amplified products and direct DNA sequencing. The deletion of one cytosine in codons 174-176 (TGCCCCCAC-->TGCCCCAC) of the p53 gene was found only in the BP-DHD-transformed cell line. The BP-DHD-transformed cells were highly invasive and tumorigenic when transplanted into syngeneic rats, whereas control lines either were nontumorigenic or formed epithelial cysts. BP-DHD-transformed cells and control lines were negative for mutations in the Ha-ras gene. Our results suggest that the tumorigenic potential of the BP-DHD-transformed cell line is associated with a frameshift mutation in codon 176 of the p53 gene but not with mutations in the Ha-ras gene. The G/C-rich codons 174-176 in the rat p53 gene may be specific targets for BP-DHD.
Antenna Proximity Effects for Talk and Data Modes in Mobile Phones (2010)

Based on a recent study of the ways a phone is held (a grip study), CAD models of the human hand have been generated, and antenna proximity effects for both talk and data modes in mobile phones have been investigated using an FDTD code. The simulation results showed that the hand, and especially the index finger, exhibited a major contribution in determining the total loss when compared to the upper torso alone. The influence of the position of the fingers on the handset was found to be more important when close to the antenna. The palm-handset gap and the index-finger location were the main factors for both absorption and mismatch loss. Different data-mode hand phantoms and configurations were investigated, showing that both “overlapped” and “interlaced” grip styles similarly influenced the antenna's communication performance.
Assessing the need for flexibility technologies in decarbonized power systems: A new model applied to Central Europe (2020)

The increasing use of renewable energy leads to a higher share of intermittent and volatile electricity generation. In this paper, we develop FLEXIES, a new open-source power system optimization model to determine the cost-efficient deployment of renewable electricity generation technologies and flexibility technologies. We apply FLEXIES in a case study of power systems in Central Europe (Switzerland, Austria, France, Germany, and Italy) in 2030, 2040, and 2050. The case study indicates that low-carbon electricity generation, batteries, and power-to-gas, consisting of multiple gas storages, are cost-efficient in 2050 – rather than burning natural gas in gas turbines. Such decarbonized power systems could be cost-efficient earlier assuming sufficiently high carbon prices. Furthermore, we find that onshore wind is prioritized over highly volatile solar generation due to a lower need for electricity storage. Interconnections enable higher shares of uniform generation technologies (on– and offshore wind, nuclear, biomass-waste) and reduce the need for solar and storage. Hence, compared to a case in which countries are isolated, interconnections reduce total electricity generation by up to 8.2%, system costs by up to 16.3%, and carbon equivalent emissions by up to 9.0%. Finally, we observe that decarbonized power systems entail a cost shift from the operational to the investment phase and total normalized costs could be higher than power market prices. Thus, new mechanisms may be needed to incentivize decarbonized power systems.
Ecosystem effects of integrating human-made runoff-harvesting systems into natural dryland watersheds (2017)

Runoff-harvesting systems (RHSs) design to collect runoff water and nutrients from small rocky watersheds into ponds bounded by soil dikes (termed limans) that are used as an afforestation grove. Our study aimed at quantifying the influence of RHSs using two indicators: soil quality (SQ) and aboveground net primary productivity (ANPP) in a small watershed scale. The SQ index was estimated by 13 physical, chemical, and biological soil properties. ANPP was evaluated by a spaceborne-derived vegetation index of total biomass (woody and annual) and field measurements of annuals. The study was conducted in four small RHS watersheds, as well as in a reference watershed without a liman, located in the Negev Desert, Israel. Our findings are: (1) there is a significantly higher soil organic matter, total water content, and phosphorus values in all the limans than in the other locations (upstream and downstream area); and (2) significantly higher SQ and total ANPP values in the limans than in the downstream areas, amplifying the overall watershed fertility and enhance ecosystem services. We conclude that integrating RHS as a fertility island, be adjusted their size and location, can be essential techniques to sustain ecosystem services and maintain the natural ecosystem in the watershed.