gebhart/patrepeval huggingface dataset:
Assembly of Lampbrush Chromosomes from Sperm Chromatin (1998)

We have examined the behavior of demembranated sperm heads when injected into the germinal vesicle (GV) of amphibian oocytes. Xenopus sperm heads injected into Xenopus GVs swelled immediately and within hours began to stain with an antibody against RNA polymerase II (Pol II). Over time each sperm head became a loose mass of chromosome-like threads, which by 24-48 h resolved into individually recognizable lampbrush chromosomes (LBCs). Although LBCs derived from sperm are unreplicated single chromatids, their morphology and immunofluorescent staining properties were strikingly similar to those of the endogenous lampbrush bivalents. They displayed typical transcriptionally active loops extending from an axis of condensed chromomeres, as well as locus-specific "landmarks. " Experiments with [3H]GTP and actinomycin D demonstrated that transcription was not necessary for the initial swelling of the sperm heads and acquisition of Pol II but was required for maintenance of the lampbrush loops. Splicing was not required at any stage during formation of sperm LBCs. When Xenopus sperm heads were injected into GVs of the newt Notophthalmus, the resulting sperm LBCs displayed very long loops with pronounced Pol II axes, like those of the endogenous newt LBCs; as expected, they stained with antibodies against newt-specific proteins. Other heterologous injections, including sperm heads of the frog Rana pipiens and the zebrafish Danio rerio in Xenopus GVs, confirm that LBCs can be derived from taxonomically distant organisms. The GV system should help identify both cis- and trans-acting factors needed to convert condensed chromatin into transcriptionally active LBCs. It may also be useful in producing cytologically analyzable chromosomes from organisms whose oocytes do not go through a typical lampbrush phase or cannot be manipulated by current techniques.
DeBERTa: Decoding-enhanced BERT with Disentangled Attention (2020)

Recent progress in pre-trained neural language models has significantly improved the performance of many natural language processing (NLP) tasks. In this paper we propose a new model architecture DeBERTa (Decoding-enhanced BERT with disentangled attention) that improves the BERT and RoBERTa models using two novel techniques. The first is the disentangled attention mechanism, where each word is represented using two vectors that encode its content and position, respectively, and the attention weights among words are computed using disentangled matrices on their contents and relative positions, respectively. Second, an enhanced mask decoder is used to incorporate absolute positions in the decoding layer to predict the masked tokens in model pre-training. In addition, a new virtual adversarial training method is used for fine-tuning to improve models' generalization. We show that these techniques significantly improve the efficiency of model pre-training and the performance of both natural language understanding (NLU) and natural langauge generation (NLG) downstream tasks. Compared to RoBERTa-Large, a DeBERTa model trained on half of the training data performs consistently better on a wide range of NLP tasks, achieving improvements on MNLI by +0.9% (90.2% vs. 91.1%), on SQuAD v2.0 by +2.3% (88.4% vs. 90.7%) and RACE by +3.6% (83.2% vs. 86.8%). Notably, we scale up DeBERTa by training a larger version that consists of 48 Transform layers with 1.5 billion parameters. The significant performance boost makes the single DeBERTa model surpass the human performance on the SuperGLUE benchmark (Wang et al., 2019a) for the first time in terms of macro-average score (89.9 versus 89.8), and the ensemble DeBERTa model sits atop the SuperGLUE leaderboard as of January 6, 2021, out performing the human baseline by a decent margin (90.3 versus 89.8).
Microcontaminants in Pentachlorophenol Synthesis. 3. Effect of Temperature and Chlorine Flow Rate at End of Run (2006)

Polychlorinated dibenzodioxins (PCDDs) and dibenzofurans (PCDFs) are undesired byproducts that form as microcontaminants during the synthesis of pentachlorophenol. In temperature-programmed, laboratory-scale synthesis, most of the microcontaminant toxicity forms near the end of the run and while the molten pentachlorophenol product cools and solidifies. Terminating the chlorine feed to the reactor before the end of the run, where some tetrachlorophenol remains, prevented the formation of microcontaminants in high concentrations in the final product. Therefore, it appears that the microcontaminant-forming reactions that occur near the end of the run are inhibited by creating chlorine starvation conditions in the reaction system. In a commercial implementation of this strategy, it may also be beneficial to purge the reactor contents with an inert gas after stopping the chlorine flow to remove the residual chlorine.
Multidimensional screening yields channelrhodopsin variants having improved photocurrent and order-of-magnitude reductions in calcium and proton currents (2019)

Channelrhodopsins (ChRs) are light-gated ion channels in widespread use in neuroscience for mediating the genetically targetable optical control of neurons (optogenetics). ChRs pass multiple kinds of ions, and although nonspecific ChR-mediated conductance is not an issue in many neuroscience studies, conductance of calcium and protons, which can mediate diverse cellular signals, may be undesirable in some instances. Here, we turned our attention to the creation of ChRs that have high cation photocurrent but pass fewer calcium ions and protons. We developed an automated, time-resolved screening method capable of rapidly phenotyping channelrhodopsin-2 (ChR2) variants. We found substitution mutations throughout ChR2 that could boost current while altering ion selectivity and observed that the mutations that reduced calcium or proton conductance have additive effects. By combining four mutations, we obtained a ChR, ChromeQ, with improved photocurrent that possesses order-of-magnitude reductions in calcium and proton conductance and high fidelity in driving repetitive action potentials in neurons. The approach presented here offers a viable pathway toward customization of complex physiological properties of optogenetic tools. We propose that our screening method not only enables elucidation of new ChR variants that affect microbial opsin performance but may also reveal new principles of optogenetic protein engineering.
Efficient Channel Quality Feedback Schemes For OFDMA Systems With Different Schedulers (2009)

In orthogonal frequency division-multiple access (OFDMA) systems, the available downlink frequency is divided into subbands which are shared among users. The transmitter determines the users that are scheduled on each subband, and the data rate for each user. To enable these transmitter choices, each user feeds back a channel quality indicator (CQI), giving a compressed version of its observed signal-to-interference-noise ratio (SINR) on all subbands. In this paper, we classify existing CQI compression schemes into symmetric and asymmetric schemes. Symmetric schemes aim to accurately represent the CQI on all subbands, and are shown to be suitable when the receiver cannot accurately predict the subbands on which it will be scheduled. This happens, for instance, when the receiver is fast-moving, or when a round- robin scheduler is employed, or during low load conditions. Asymmetric schemes, on the other hand, greedily achieve accuracy only in high-SINR subbands, and are shown to perform well in high-load cellular networks with proportional fair scheduling and low-speed users. We propose one new scheme in each category. Simulation results for a 3GPP LTE cellular network show that our proposed schemes achieve similar or better performance than the current best-M feedback scheme used in LTE, with 30% less overhead.
A high strength nickel-base alloy with improved oxidation resistance up to 2200 deg F. (1968)

High tensile strength nickel base alloy with improved oxidation resistance up to 2200 degrees Farenheit
Measurements of rheological fluid properties with the falling needle viscometer (1988)

The use of data from the falling needle viscometer to determine the rheological properties of purely viscous non-Newtonian fluids is described. From the solution of the basic flow equation, which is given in tabular and graphical form, a method is presented to determine rheological flow curves for both power law and more generalized rheological fluids. The use of the instrument to determine the zero shear rate viscosity is also described and a method of fitting appropriate constitutive equations to the data is discussed and illustrated by examples. Finally, a technique for measuring fluid densities using the falling needle viscometer is presented that is applicable to both Newtonian and power law fluids.
<title>Restoration services for the optical Internet</title> (2000)

In this paper we propose a new approach for optical layer restoration management in a dynamically reconfigurable optical network. The optical network consists of Optical Layer Cross-connects (OLXCs) which have the ability to convert the wavelength of any incoming channel to any outgoing wavelength (i.e. have wavelength conversion). Recently, there has been intense interest within the optical networking community and in standards bodies on bandwidth management in a dynamically reconfigurable optical networks [e.g. 1,2,3,4]. In these networks, it is assumed that the physical hardware is deployed, but that network connectivity is not defied until high bandwidth connections referred to as linghtpaths are established within the network. The lightpaths are provisioned by choosing a route through the network with sufficient available capacity. The lightpaths are established by allocating capacity on each link along the chose route, and appropriately configuring the OLXCs. Restoration is provided by reserving capacity on routes that are physically diverse to the primary lightpath. In this paper we present a new approach to restoration for the future optical Internet, employing distributed restoration bandwidth measurement, failure detection and failure handling.
Bioengineered tumors (2015)

Three-dimensional (3D) tumor models generated in vitro using methods of tissue engineering are just starting to show potential for predictive studies of therapeutic targets and screening of anticancer drugs. By mimicking some of the key features of the in vivo tumor environment, these models allow us to grow physiologically relevant tumors and study the initiation, progression and metastasis. Using a recent report on how to engineer bone tumors, we comment on the state-of-the-art in bioengineered bone tumors, with focus on the components required for recapitulating the in vivo milieu of bone tumor development.
Predicting slice loss distortion in H.264/AVC video for low complexity data prioritization (2012)

We propose a low complexity Generalized Linear Model (GLM) for prioritizing slices during real-time H.264/AVC compressed video streaming. We train the GLM over a video database to predict the Cumulative Mean Square Error (CMSE) corresponding to individual slice losses by using a combination of efficient video parameters which can be easily extracted during the encoding of a frame. We prioritize the slices generated within a Group of Pictures (GOP) based on the predicted CMSE by using a Quartile Based Prioritization (QBP) scheme. For comparison, we also perform QBP on measured CMSE values from individual pre-encoded slice losses and analyze the priority misclassifications of the slices. We validate our model by applying Unequal Error Protection (UEP) using RCPC codes to the different prioritized bitstreams and evaluating their performance over noisy channels. Simulation results show that predicted CMSE schemes achieve PSNR performance close to that of the measured CMSE schemes for different slice sizes, video bitrates and over different channel SNRs.
Fast algorithms for GS-model-based image reconstruction in data-sharing fourier imaging (2003)

Many imaging experiments involve acquiring a time series of images. To improve imaging speed, several "data-sharing" methods have been proposed, which collect one (or a few) high-resolution reference(s) and a sequence of reduced data sets. In image reconstruction, two methods, known as "Keyhole" and reduced-encoding imaging by generalized-series reconstruction (RIGR), have been used. Keyhole fills in the unmeasured high-frequency data simply with those from the reference data set(s), whereas RIGR recovers the unmeasured data using a generalized series (GS) model, of which the basis functions are constructed based on the reference image(s). This correspondence presents a fast algorithm (and two extensions) for GS-based image reconstruction. The proposed algorithms have the same computational complexity as the Keyhole algorithm, but are more capable of capturing high-resolution dynamic signal changes.
An unsupervised boosting technique for refiningword alignment (2010)

Translation rules extracted from automatic word alignment form the basis of statistical machine translation (SMT) systems. An unsupervised expectation-maximization (EM) algorithm is typically used to obtain a word alignment from parallel corpora. Being statistically-driven, the alignments produced by this technique are often erroneous. In this paper, we propose an unsupervised boosting strategy for refining automatic word alignment with the goal of improving SMT performance. The proposed approach results in fewer unaligned words, a significant reduction in the number of extracted translation phrase pairs, a corresponding improvement in SMT decoding speed, and a consistent improvement in translation accuracy, as measured by BLEU, across multiple language pairs and test sets. The reduction in storage and processing requirements coupled with improved accuracy make the proposed technique ideally suited for interactive translation services, facilitating applications such as mobile speech-to-speech translation.
<i>BEAM-ish</i>: a graphical user interface for the physical characterization of macromolecular crystals (2000)

Crystal mosaicity is determined from the measurement of the reflection angular width and can be used as an indicator of crystal perfection. A new method has been developed that combines the use of unfocused synchrotron radiation, super-fine phi slicing and a CCD area detector to simultaneously measure the mosaicity of hundreds of reflections . The X-ray beam characteristics and Lorentz correction are deconvoluted from the resulting reflection widths to calculate the true crystal mosaicity.
Inter-core cooperative TLB for chip multiprocessors (2010)

Translation Lookaside Buffers (TLBs) are commonly employed in modern processor designs and have considerable impact on overall system performance. A number of past works have studied TLB designs to lower access times and miss rates, specifically for uniprocessors. With the growing dominance of chip multiprocessors (CMPs), it is necessary to examine TLB performance in the context of parallel workloads.
A New Glycan-Dependent CD4-Binding Site Neutralizing Antibody Exerts Pressure on HIV-1 In Vivo (2015)

The CD4 binding site (CD4bs) on the envelope glycoprotein is a major site of vulnerability that is conserved among different HIV-1 isolates. Many broadly neutralizing antibodies (bNAbs) to the CD4bs belong to the VRC01 class, sharing highly restricted origins, recognition mechanisms and viral escape pathways. We sought to isolate new anti-CD4bs bNAbs with different origins and mechanisms of action. Using a gp120 2CC core as bait, we isolated antibodies encoded by IGVH3-21 and IGVL3-1 genes with long CDRH3s that depend on the presence of the N-linked glycan at position-276 for activity. This binding mode is similar to the previously identified antibody HJ16, however the new antibodies identified herein are more potent and broad. The most potent variant, 179NC75, had a geometric mean IC80 value of 0.42 μg/ml against 120 Tier-2 HIV-1 pseudoviruses in the TZM.bl assay. Although this group of CD4bs glycan-dependent antibodies can be broadly and potently neutralizing in vitro, their in vivo activity has not been tested to date. Here, we report that 179NC75 is highly active when administered to HIV-1-infected humanized mice, where it selects for escape variants that lack a glycan site at position-276. The same glycan was absent from the virus isolated from the 179NC75 donor, implying that the antibody also exerts selection pressure in humans.
Identification of calreticulin as a nuclear matrix protein associated with human colon cancer (2003)

Colon cancer is one of the most common malignancies among populations in the United States and Western Europe, and one of the leading causes of worldwide morbidity and mortality due to cancer. The early detection of colon cancer is central to the effective treatment of this disease and early detection markers are needed. We have demonstrated that high-resolution two-dimensional gel analysis of nuclear matrix proteins (NMPs) demonstrated a specific oncological fingerprint of colon cancer. Utilizing this approach, four proteins specific for colon cancer was identified. Additionally, one protein was expressed much more strongly in colon cancer compared to adjacent and normal donor tissue. The amino acid composition of this protein revealed sequence similarity with calreticulin. The multi-functional protein, calreticulin, is normally found in the lumen of the endoplasmic reticulum although some reports have described a nuclear localization of the protein. The aim of this study was to confirm the identity of the protein as calreticulin as well as to evaluate the localization of calreticulin in the nuclear matrix of colon cancer tissue.
Potential for bioremediating using constructed mixed microbial mats (1994)

Microbial mats are natural heterotrophic and autotrophic communities dominated by cyanobacteria (blue-green algae). They are self-organized laminated structures annealed tightly together by slimy secretions from various Microbial components. The surface slime of the mats effectively immobilizes the ecosystem to a variety of substrates, thereby stabilizing the most efficient internal microbial structure. Constructed microbial mats can be generated rapidly by enriching a water surface with ensiled grass clippings. These constructed mats are durable, tolerant to a variety of toxins and resilient under changing environmental conditions. The mats can he designed for specific tasks by inoculating the cyanobacteria/silage with selected microorganisms. Mats constructed with specific microbial components have been developed for various bioremediation applications: removal of metals, organic degradation, treatment of mixed contaminants, biological treatment ponds, and soil remediation. Constructed mats offer a broad range of mechanisms related to the sequestration of heavy metals, the biodegradation of recalcitrant organic compounds, and the remediation of mixed organic/inorganic contaminants such as TCE and carbofuran with heavy metals.
Stimulation of the sensory pudendal nerve increases bladder capacity in the rat (2017)

Pudendal nerve stimulation is a promising treatment approach for lower urinary tract dysfunction, including symptoms of overactive bladder. Despite some promising clinical studies, there remain many unknowns as to how best to stimulate the pudendal nerve to maximize therapeutic efficacy. We quantified changes in bladder capacity and voiding efficiency during single-fill cystometry in response to electrical stimulation of the sensory branch of the pudendal nerve in urethane-anesthetized female Wistar rats. Increases in bladder capacity were dependent on both stimulation amplitude and rate. Stimulation that produced increases in bladder capacity also led to reductions in voiding efficiency. Also, there was a stimulation carryover effect, and increases in bladder capacity persisted during several nonstimulated trials following stimulated trials. Intravesically administered PGE<sub>2</sub> reduced bladder capacity, producing a model of overactive bladder (OAB), and sensory pudendal nerve stimulation again increased bladder capacity but also reduced voiding efficiency. This study serves as a basis for future studies that seek to maximize the therapeutic efficacy of sensory pudendal nerve stimulation for the symptoms of OAB.
Effect of matrix metalloproteinase-2 on antitumor immunity. (2012)

2570 Background: Cancer cells, including melanoma, can be highly resistant to traditional treatments such as chemotherapy and radiotherapy. As a result, a lot of effort has been put into developing immune therapies to treat cancer patients. The main barrier to design effective immunotherapies is the immunosuppression induced by the tumor. Matrix metalloproteinase-2 (MMP-2) is over-expressed in most cancers including melanoma, and its expression is associated with increased dissemination and poorer survival/prognosis. Here, we uncovered an immunosuppressive role of MMP-2 in inducing ineffective/detrimental T H 2 immune responses and its underlying mechanisms. Methods: Human dendritic cells (DCs) were cultured in the presence of MMP-2 or various TLR agonists. DCs responses were monitored using immunostaining, ELISA or cytometric bead array methods. Autologous CD4+ T cells were stimulated using these conditioned tumor-associated antigen (TAA)-pulsed DCs. TAA-specific CD4+ T cells were cloned and characterized using the same techniques as for DCs. Results: Herewe showed that MMP-2-conditioned human DCs primed naïve CD4+ T cells into an inflammatory T H 2 phenotype, i.e. mainly secreting TNFα, IL-4 and IL-13 and expressing GATA3. Accordingly, we detected MMP-2-specific CD4+ T cells displaying the same inflammatory T H 2 profile in tumor-infiltrating lymphocytes from melanoma patients. We revealed the underlying mechanisms: on the one hand, MMP-2 was found to degrade the type-I IFN receptor IFNAR1, thereby preventing STAT1 phosphorylation, which is necessary for IL-12 production. On the other hand, MMP-2 triggers the Toll-like receptor (TLR)-2 on DCs, which leads to NF-kB activation and OX40L expression. Both lack of IL-12 and over-expression of OX40L were found responsible for skewing T cell responses towards a detrimental T H 2 phenotype. Conclusions: MMP-2, therefore, acts as an endogenous T H 2 "conditioner" and may underlie the prevalence of detrimental T H 2 responses in cancer. Our findings also described the responsible MMP-2-dependent mechanisms, which open the way to novel therapeutic strategies and/or targets to skew anti-tumor CD4+ T cell responses towards a more efficient anti-tumor T H 1 phenotype to treat cancer patients.