gebhart/patrepeval huggingface dataset:
Draft Genome Sequence of Pandoraea sp. Strain SD6-2, Isolated from Lindane-Contaminated Australian Soil (2013)

Pandoraea sp. strain SD6-2 is a δ-hexachlorocyclohexane-degrading bacterial strain isolated from lindane-contaminated soil in Queensland, Australia. The genome of SD6-2 was sequenced to investigate its ability to degrade δ-hexachlorocyclohexane. Here we report the annotated genome sequence of this strain.
Pharmacokinetic and pharmacodynamic tomography (2021)

This is a brief introduction to the Visualizing and Quantify Drugs in Tissue Conference. It will briefly review the conference and its schedule and invite participation during the day.
Minireview Blocks Apoptosis (1997)

. In vitro, this lipid can beMontreal Neurological Institute producedby thep170/mCpk-typePI3K that phosphory-McGill University lates PtdIns-4-P at the D-3 position (Figure 1) or by aMontreal, Quebec H3A 2B4 kinase that phosphorylates PtdIns-3-P at the D-4 posi-Canada tion (not shown). Thus, the relative levels of PtdIns-3,4-
Controller for an Axial Flow Blood Pump (1996)

A rotary blood pump inherently provides only one noninvasive "observable'" parameter (motor current) and allows for only one "controllable" parameter (pump speed). To maintain the systemic circulation properly, the pump speed must be controlled to sustain appropriate outlet Hows and perfusion pressure while preventing pulmonary damage caused by extremes in preload. Steady-state data were collected at repeated intervals during chronic trials of the Nimbus AxiPump (Nimbus, Inc., Rancho Cordova, California, U.S.A.) in sheep (n = 7) and calves (n = 12). For each data set, the pump speed was increased at increments of 500 rpm until left ventricular and left atrial emptying was observed by left atrial pressure diminishing to zero. The effect of decreasing preload was evaluated perioperatively by inferior vena cava occlusion at a constant pump speed. Fourier analysis established a relationship between changes in the pump preload and the power spectra of the pump current waveform. Based on these results, a control method was devised to avoid ventricular collapse and maintain the preload within a physiologic range. The objective of this controller is the minimization of the second and third harmonic of the periodic current waveform. This method is intended to provide a noninvasive regulation of the pump by eliminating the need for extraneous transducers.
Integrative genetic and genomic networks identify microRNA associated with COPD and ILD (2022)

ABSTRACT Chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD) are clinically and molecularly heterogeneous diseases. We utilized clustering and integrative network analyses to elucidate roles for microRNAs (miRNAs) and miRNA isoforms (isomiRs) in COPD and ILD pathogenesis. Short RNA sequencing was performed on 351 lung tissue samples of COPD (n=145), ILD (n=144) and controls (n=64). Five distinct subclusters of samples were identified including 1 COPD-predominant cluster and 2 ILD-predominant clusters which associated with different clinical measurements of disease severity. Utilizing 262 samples with gene expression and SNP microarrays, we built disease-specific genetic and expression networks to predict key miRNA regulators of gene expression. Members of miR-449/34 family, known to promote airway differentiation by repressing the Notch pathway, were among the top connected miRNAs in both COPD and ILD networks. Genes associated with miR-449/34 members in the disease networks were enriched among genes that increase in expression with airway differentiation at an air-liquid interface. A highly expressed isomiR containing a novel seed sequence was identified at the miR-34c-5p locus. 47% of the anticorrelated predicted targets for this isomiR were distinct from the canonical seed sequence for miR-34c-5p. Overexpression of the canonical miR-34c-5p and the miR-34c-5p isomiR with an alternative seed sequence down-regulated NOTCH1 and NOTCH4. However, only overexpression of the isomiR down-regulated genes involved in Ras signaling such as CRKL and GRB2. Overall, these findings elucidate molecular heterogeneity inherent across COPD and ILD patients and further suggest roles for miR-34c in regulating disease-associated gene-expression.
AR costumes (2018)

We describe a method to automatically augment a watertight digital costume onto a person's body from a monocular RGB image. When overlaying a digital costume onto a body using pose matching, several parts of the person's cloth or skin remain visible due to differences in shape and proportions. In this paper, we present a practical solution to these artifacts which requires minimal costume parameterization work, and a straightforward inpainting approach. To our knowledge, our approach is the first to deliver plausible watertight costumes from RGB imagery only, and is compatible with mobile devices. We show successful results at high resolution in our video and project web page, as well as defects in the discussion section of paper, which can serve as comparison for future improvements.
MIMO Precoding With X- and Y-Codes (2011)

We consider a slow fading nt x nr multiple-input multiple-output (MIMO) system with channel state information (CSI) at both the transmitter and receiver. Since communication in such scenarios is subject to block fading, reception reliability, quantified in terms of the achievable diversity gain, is of importance. A simple and well known precoding scheme is based upon the singular value decomposition (SVD) of the channel matrix, which transforms the MIMO channel into parallel subchannels. Despite having low maximum likelihood decoding (MLD) complexity, this SVD based precoding scheme provides a diversity gain which is limited by the diversity gain of the weakest subchannel. We therefore propose X- and YCodes, which improve the diversity gain of the SVD precoding scheme, by jointly coding information across a pair of subchannels (i.e., pairing subchannels). In particular, subchannels with high diversity gain are paired with those having low diversitygain. A pair of subchannels is jointly encoded using a 2 x 2 real matrix, which is fixed a priori and does not change with each channel realization. For X-Codes, these matrices are 2-dimensional rotation matrices parameterized by a single angle, while for Y-Codes, these matrices are 2-dimensional upper left triangular matrices. Also, since joint coding is performed only across a pair of subchannels, the joint MLD complexity remains low. In particular, the MLD complexity of Y-Codes is even lower than that of X-Codes, and is equivalent to symbol by symbol detection. Moreover, we propose X-, Y-Precoders with the same structure as X-, Y-Codes, but with encoding matrices adapted to each channel realization. With respect to the error probability performance, the optimal encoding matrices for X-, YCodes/ Precoders are derived analytically and numerically. Whencompared to other precoding schemes reported in the literature, it is observed that X-Codes/Precoders perform better in wellconditioned channels, while Y-Codes/Precoders perform better in ill-conditioned channels.
Impact of Relocations on Mental Health and School Functioning of Adolescents from Canadian Military Families (2020)

The study aim was to explore the impact of one aspect of military lifestyle, frequent relocations, on the adjustment of youth from Canadian military families. In all, 134 parents completed online questionnaires about their 13- to 18-year-old adolescents. Internalized and externalized problems, school functioning, and prosocial behaviors were assessed. Parental perceived stress levels were also measured. Analyses revealed that the mobility rate (i.e., the number of relocations/adolescent age) was not related to youth academic performance, greater suspensions/expulsions from school, or internalized problems. Conversely, mobility rate correlated positively with the presence of externalized problems and negatively with prosocial behaviors. Although these associations were not significant when relocation recency (measured by living in the same community for less than 12 months) was taken into account, they remained a trend, suggesting that adjustment issues were not completely resolved after the transition period. Relocation recency, rather than mobility rate, was a better predictor of adolescent adjustment. Furthermore, parental perceived stress was the variable most associated with adolescent internalized/externalized problems and prosocial behaviors. These results indicate that greater attention should be given to adolescent adjustment in the year following a relocation, because this is the period in which adolescents are at greater risk of developing difficulties. Additionally, the substantial influence of parental stress on youth well-being indicates the importance of services to help parents alleviate their own stress.
Selective formation of lactate by oxidation of 1,2-propanediol using gold palladium alloy supported nanocrystals (2009)

The use of bio-renewable resources, such as glycerol, a by-product from bio-diesel manufacture, can provide a viable way to make valuable products using greener technology. In particular, glycerol can be reduced to give 1,2-propanediol that can then be selectively oxidised to lactate, which has immense potential as a monomer for the synthesis of biodegradable polymers. We show that gold-palladium alloy catalysts can be very effective for the selective oxidation of 1,2-propanediol to lactate. Two supports, TiO2 and carbon, and two preparation methods, wet impregnation and sol-immobilisation, are contrasted. The addition of palladium to gold significantly enhances the activity and retains the high selectivity to lactate using O2 as oxidant (we observe 96% lactate selectivity at 94% conversion). Use of hydrogen peroxide is also possible but lower activities are observed as a result of the reaction conditions, but in this case no marked enhancement is observed on addition of palladium to gold. Comparison of the activity for C3 alcohols shows that the reactivity decreases in the order: glycerol > 1,2-propanediol > 1,3-propanediol ∼ 1-propanol > 2-propanol. The use of a sol-immobilisation preparation method as compared to impregnation leads to alloy catalysts with the highest activity for lactate formation from the oxidation of 1,2-propanediol; the origins of these activity trends are discussed.
Controlled Synthesis of Metal–Organic Frameworks in Scalable Open-Porous Contactor for Maximizing Carbon Capture Efficiency (2021)

Metal-organic frameworks (MOFs) are a class of microporous materials that have been highlighted with fast and selective sorption of gas molecules; however, they are at least partially unstable in the scale-up process. Here, we report a rational shaping of MOFs in a scalable architecture of fiber sorbent. The long-standing stability challenge of MOFs was resolved by using stable metal oxide precursors that are subject to controlled surface oxide dissolution-growth chemistry during the Mg-based MOF synthesis. Highly uniform MOF crystals are synthesized along with the open-porous fiber sorbents networks, showing unprecedented cyclic CO<sub>2</sub> capacities in both flue gas and direct air capture (DAC) conditions. The same chemistry enables an in situ flow synthesis of Mg-MOF fiber sorbents, providing a scalable pathway for MOF synthesis in an inert condition with minimal handling steps. This modular approach can serve both as a reaction stage for enhanced MOF fiber sorbent synthesis and as a "process-ready" separation device.
DrosophilaMuller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution (2015)

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25-50%) than euchromatic reference regions (3-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4-3.6 vs. 8.4-8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.
Electrical Properties of the La<sub>2</sub>O<sub>3</sub>/4H-SiC Interface Prepared by Atomic Layer Deposition Using La(iPrCp)<sub>3</sub> and H<sub>2</sub>O (2006)

The La2O3 and Al2O3/La2O3 layers were grown on 4H-SiC by atomic layer deposition (ALD) method. The electrical properties of La2O3 on 4H-SiC were examined using metal-insulator-semiconductor (MIS) structures of Pt/La2O3(18nm)/4H-SiC and Pt/Al2O3(10nm)/La2O3(5nm)/4H-SiC. For the Pt/La2O3(18nm)/4H-SiC structure, even though the leakage current density was slightly reduced after the rapid thermal annealing at 500 oC, accumulation capacitance was gradually increased with increasing bias voltage due to a high leakage current. On the other hand, since the leakage current in the accumulation regime was decreased for the Pt/Al2O3/La2O3/4H-SiC MIS structure owing to the capped Al2O3 layer, the capacitance was saturated. But the saturation capacitance was strongly dependent on frequency, indicating a leaky interfacial layer formed between the La2O3 and SiC during the fabrication process of Pt/Al2O3(10nm)/ La2O3(5nm)/ 4H-SiC structure.
Understanding the Interactions of Seawater Ions with Amidoxime through X-Ray Crystallography (2019)

Insoluble polymer substrates functionalized with the amidoxime (R-C(NH2)=NOH) functional group have been demonstrated as a technically feasible platform for extracting uranium from seawater, a potential source of extremely abundant uranium for use as nuclear fuel. While it is possible to isolate macroscopic amounts of uranium from the ocean with a positive energy return on investment using these materials, both the economic and energetic costs are many times greater than those of terrestrial uranium mining. Currently, the major contribution to this cost is the production of the sorbent itself, so being able to recycle the sorbent even a small number of times will have a huge impact on lowering the cost of their use. However, amidoxime resins show capacity fading when stripped by strong acids, presently limiting their recyclability. Both alternative extractants and alternative elution chemistries are under development with promising results but are yet at too early a stage to make predictions about their ultimate success. Given the potentially huge impact of a successful recycling process on the viability of seawater extraction of uranium, there is a strong need to pursue additional routes to elution chemistry. During the course of this project, we studied the interactions of amidoxime-containing small molecules with the abundant metal ions in seawater, including Li, Na, K, Mg, Ca, Fe, Cu, and V, to understand the interactions of [UO2]2+ with amidoxime. By using small molecules with multiple adjacent functional groups, we crystallized the resulting metal complexes and used single crystal X-ray diffraction (SCXRD) as our primary tool for structural characterization. We also investigated the use of solutions of hydroxylammonium salts in weak acids as eluents for stripping and recycling amidoxime-based sorbents. The replacement of strong acids, which react with and destroy the amidoxime functional groups, with weak acids based on hydroxylammonium, a reagent that is actually used to make the amidoxime groups, is expected to avoid capacity loss on recycling and possibly even regenerate functionality that was lost due to exposure to the marine environment.
Drying of Potato Tissue Pretreated by Ohmic Heating (2006)

The influence of the ohmic heating pretreatment on convective drying of potato tissue was investigated. The degree of material damage Z under the different modes of electrical treatment is studied and the electroporation phenomena is assumed to be the main reason of material disintegration. The relations between Z, electric field strength E, energy input W, and temperature of ohmic heating T are analyzed. Two different damage stages, short and long, are revealed in this study. It is shown that ohmic treatment at relatively low fields (E < 100 V/cm) results in incomplete damage of material, but allows to obtain material with high disintegration degree Z ≈ 0.7 at E > 70 V/cm. The electric field strength E and the total electric energy input W influence considerably the drying rate. The highest drying rates are always observed for more energy consuming freeze-thawed pretreatment, but the AC pretreatment seems to be promising for enhancing the air drying processes.
Non-uniform sampling point selection in orthogonal frequency division multiplexing receiver with fractional sampling (2011)

To achieve diversity with a single antenna, a fractional sampling (FS) scheme in OFDM has been proposed. FS achieves path diversity with a higher sampling rate and multiple demodulation branches. In the previous literatures for FS, the sampling interval is fixed even though the initial phase selection of the sampling has been investigated. The fixed sampling interval limits the diversity gain through FS. Thus, in this study, a non-uniform sampling point selection scheme according to the frequency response of a channel is proposed. Numerical results through computer simulation show that the proposed scheme improves the BER performance by about 2 dB when the number of the demodulation branches is 2. While the proposed scheme further improves bit error rate (BER) performance it requires a larger rate and more computational complexity for the selection of the sampling points. Therefore the complexity reduction for the sampling point selection is also investigated. The complexity reduction scheme eliminates the specific sets of the sampling points and reduces the computational complexity of the sampling point selection for the proposed scheme by a factor of 2. Computer simulation also shows that the low complexity version of the proposed scheme even achieves the equivalent BER compared to the original proposed scheme.
MEMS Based Paramagnetic Oxygen Measurement (2007)

This paper describes a novel micromechanical sensor chip that is used to measure the concentration of oxygen in gases by exploiting their physical rather than chemical properties. The so-called magneto-mechanical measurement principle that has been used for oxygen concentration measurements for more than 40 years in classical, precision-mechanical setups has been transferred to the MEMS world. This leads to a new sensor which offers improved performance mainly due to a largely reduced sensor volume, but brings in all the "normal" advantages of batch processing where manual assembly was used up to now.
Abstract B012: Preclinical study of Kiatomab, a novel monoclonal antibody to the cancer stem cell surface marker KIAA1114, for anti-cancer therapy in colorectal carcinoma (2016)

Abstract Most targeted therapy drugs block the growth of cancer cells by targeting specific molecules needed for tumor growth. Among targeted therapy drugs, cetuximab, the monoclonal antibody which binds to epidermal growth factor receptor (EGFR) and inhibits downstream signaling of EGFR, has greatly improved the median survival of patients with metastatic colorectal cancer (CRC). Yet, cetuximab showed limited therapeutic effect in CRC patients who carry certain mutation in the KRAS, which emphasizes the necessity of developing new targeted therapy drugs for CRC. KIA1114 is a full-length protein of the trophinin gene and is localized on the cell surface. In our previous research, we identified the role of KIA1114 as a novel surface marker of tumor initiating cells of hepatocellular carcinoma (HCC) by developing Kiatomab, KIA1114-specific monoclonal antibody. Here, we show that KIA1114 is also highly expressed in various CRC cells with mouse or human origin. Kiatomab treatment inhibits tumor growth in a syngeneic graft CRC mouse model in antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC) dependent manner. In the metastatic CRC model, Kiatomab therapy suppresses metastasis, with a significant increase of survival. Of note, the anticancer efficacy of Kiatomab is further improved by combinatorial treatment with the standard chemotherapeutic agent cyclophosphamide (CTX), in both metastatic and solid tumor models. In summary, our findings suggest that KIAA1114 is a new target for CRC and its monoclonal antibody Kiatomab might have a potential for anticancer therapy. Citation Format: Young Min Kim, Sae Won Kim, Seungwon Lee, Hyekang Kim, Ji-Hae Kim, Han Wook Park, Young Chul Sung, Seung-Woo Lee. Preclinical study of Kiatomab, a novel monoclonal antibody to the cancer stem cell surface marker KIAA1114, for anti-cancer therapy in colorectal carcinoma [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr B012.
Ultra-wideband communications: an idea whose time has come (2003)

Summary form only given. Ultra-wideband (UWB) refers to bandwidths in excess of 2 GHz, whose utilization by radar systems dates back to the late '60s. The renewed and rapidly growing interest for UWB was sparked by the spectral mask released by FCC in February 2002, and is well motivated by the attractive features UWB brings to commercial communications: low-power carrier-free transmissions, ample multipath diversity, enhanced penetration capability, low-complexity transceivers, ability to overlay existing systems, and a potential for increase in capacity. This article outlines features and challenges unique to UWB, with emphasis on timely signal processing issues that focus on synchronization, channel estimation, multiple access, and suppression of interference UWB systems cause to (and suffer from) co-existing narrowband systems. Application areas include shortrange indoor wireless links at home, and in the workplace for low-cost multimedia communications and storage, as well as secure connectivity for ranging, and covert communications.
SaaS: Speed as a Supervisor for Semi-supervised Learning (2018)

We introduce the SaaS Algorithm for semi-supervised learning, which uses learning speed during stochastic gradient descent in a deep neural network to measure the quality of an iterative estimate of the posterior probability of unknown labels. Training speed in supervised learning correlates strongly with the percentage of correct labels, so we use it as an inference criterion for the unknown labels, without attempting to infer the model parameters at first. Despite its simplicity, SaaS achieves state-of-the-art results in semi-supervised learning benchmarks.
TWO-STAGE KNEE ARTHRODESIS FOR COMPLEX, FAILED, INFECTED TKA: RELIABLE LIMB SALVAGE AT THE COST OF HIGH INITIAL COMPLICATION RATE (2019)

Introduction While knee arthrodesis is a salvage option for recalcitrant total knee arthroplasty (TKA) periprosthetic joint infection (PJI) it is used relatively uncommonly and contemporary data ar...