gebhart/patrepeval huggingface dataset:
Two-Step Semi-Supervised Denoising for Low-field Diffusion MRI (2023)

In clinical low-field MRI, prolonged data acquisition is impractical, limiting the achievable SNR during imaging. In the absence of ground truth, unsupervised denoising is desirable, but many of them underperform on correlated noise structure of reconstructed MR images. In this work, we present an effective two step training framework for removing correlated MR noise without ground truth. We demonstrate that the proposed approach outperforms the existing denoising methods when applied to the low-field (64mT) diffusion-weighted images and demonstrate that significant noise reduction is possible. 82.5% of processed images were expertly rated clearly/far better overall.
A Dry-format Field-deployable Quantitative Reverse Transcriptase-polymerase Chain Reaction Assay for Diagnosis of Dengue Infections (2008)

We have systematically evaluated a dry-format, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assay developed by Tetracore Inc. for the Cepheid SmartCycler platform to facilitate rapid diagnosis of dengue virus infections. A panel of related flaviviruses was used to evaluate the clinical specificity of the assay, and it was found to be specific to dengue. Eighty-one clinical samples previously confirmed dengue positive by virus isolation, along with 25 dengue negative control specimens were used to validate this new diagnostic assay. Using these clinical samples, the assay exhibited 98.77% sensitivity and 100% specificity. Over 85% of the clinical specimen exhibited viral loads ranging from 10(3) to 10(7) plaque-forming units per milliliter (PFU/mL). In addition, this dry-format assay is stable at ambient temperatures and requires minimal technical expertise to perform in a small thermocycler platform. These characteristics make it a promising candidate for diagnosis of dengue in mobile laboratories in the field.
Message from the Editors to our Reviewers (2019)

Neurology ® manuscript submissions continue to increase. The journal received 3,336 new and 597 revised manuscripts between April 1, 2019, and September 30, 2019 (compared to 2,673 new and 681 revised manuscripts during the same period in 2018). We received 4,455 peer reviews evaluating these papers. Our reviewers play a crucial role in enhancing the quality of what we publish.
Dependence receptor UNC5A restricts luminal to basal breast cancer plasticity and metastasis (2018)

The majority of estrogen receptor-positive (ERα+) breast cancers respond to endocrine therapies. However, resistance to endocrine therapies is common in 30% of cases, which may be due to altered ERα signaling and/or enhanced plasticity of cancer cells leading to breast cancer subtype conversion. The mechanisms leading to enhanced plasticity of ERα-positive cancer cells are unknown. We used short hairpin (sh)RNA and/or the CRISPR/Cas9 system to knockdown the expression of the dependence receptor UNC5A in ERα+ MCF7 and T-47D cell lines. RNA-seq, quantitative reverse transcription polymerase chain reaction, chromatin immunoprecipitation, and Western blotting were used to measure the effect of UNC5A knockdown on basal and estradiol (E2)-regulated gene expression. Mammosphere assay, flow cytometry, and immunofluorescence were used to determine the role of UNC5A in restricting plasticity. Xenograft models were used to measure the effect of UNC5A knockdown on tumor growth and metastasis. Tissue microarray and immunohistochemistry were utilized to determine the prognostic value of UNC5A in breast cancer. Log-rank test, one-way, and two-way analysis of variance (ANOVA) were used for statistical analyses. Knockdown of the E2-inducible UNC5A resulted in altered basal gene expression affecting plasma membrane integrity and ERα signaling, as evident from ligand-independent activity of ERα, altered turnover of phosphorylated ERα, unique E2-dependent expression of genes effecting histone demethylase activity, enhanced upregulation of E2-inducible genes such as BCL2, and E2-independent tumorigenesis accompanied by multiorgan metastases. UNC5A depletion led to the appearance of a luminal/basal hybrid phenotype supported by elevated expression of basal/stem cell-enriched ∆Np63, CD44, CD49f, epidermal growth factor receptor (EGFR), and the lymphatic vessel permeability factor NTN4, but lower expression of luminal/alveolar differentiation-associated ELF5 while maintaining functional ERα. In addition, UNC5A-depleted cells acquired bipotent luminal progenitor characteristics based on KRT14+/KRT19+ and CD49f+/EpCAM+ phenotype. Consistent with in vitro results, UNC5A expression negatively correlated with EGFR expression in breast tumors, and lower expression of UNC5A, particularly in ERα+/PR+/HER2− tumors, was associated with poor outcome. These studies reveal an unexpected role of the axon guidance receptor UNC5A in fine-tuning ERα and EGFR signaling and the luminal progenitor status of hormone-sensitive breast cancers. Furthermore, UNC5A knockdown cells provide an ideal model system to investigate metastasis of ERα+ breast cancers.
Quantitative <i>in-situ</i> scanning electron microscope pull-out experiments and molecular dynamics simulations of carbon nanotubes embedded in palladium (2014)

In this paper, we present our results of experimental and numerical pull-out tests on carbon nanotubes (CNTs) embedded in palladium. We prepared simple specimens by employing standard silicon wafers, physical vapor deposition of palladium and deposition of CNTs with a simple drop coating technique. An AFM cantilever with known stiffness connected to a nanomanipulation system was utilized inside a scanning electron microscope (SEM) as a force sensor to determine forces acting on a CNT during the pull-out process. SEM-images of the cantilever attached to a CNT have been evaluated for subsequent displacement steps with greyscale correlation to determine the cantilever deflection. We compare the experimentally obtained pull-out forces with values of numerical investigations by means of molecular dynamics and give interpretations for deviations according to material impurities or defects and their influence on the pull-out data. We find a very good agreement of force data from simulation and experiment, which is 17 nN and in the range of 10–61 nN, respectively. Our findings contribute to the ongoing research of the mechanical characterization of CNT-metal interfaces. This is of significant interest for the design of future mechanical sensors utilizing the intrinsic piezoresistive effect of CNTs or other future devices incorporating CNT-metal interfaces.
Binding of Pili from Uropathogenic <i>Escherichia coli</i> to Membranes Secreted by Human Colonocytes and Enterocytes (1999)

PapG adhesins mediate the binding of uropathogenic Escherichia coli. Although receptors for these adhesins have not been demonstrated in intestinal epithelia, the colonic microflora includes strains of uropathogenic E. coli. We now report that surfactant-like particles secreted by the human intestine contain receptors for PapG adhesins and may provide an intestinal habitat for uropathogenic bacteria.
A power side-channel-based digital to analog converterfor Xilinx FPGAs (2014)

A novel Digital to Analog Converter (DAC) modulates the overall power consumption of an FPGA by disabling/enabling short circuits programmed into the interconnect. The power pin of the FPGA serves as the output of the DAC. The DAC achieves high linearity and can be used to implement applications in communications, security, etc. The shortcircuit-based DAC consumes 1/3 the area of an alternative shift-register-based DAC that is presented for the sake of comparison.
Cocktail party training induces increased speech intelligibility and decreased cortical activity in bilateral inferior frontal gyri. A functional near-infrared study (2022)

The human brain networks responsible for selectively listening to a voice amid other talkers remain to be clarified. The present study aimed to investigate relationships between cortical activity and performance in a speech-in-speech task, before (Experiment I) and after training-induced improvements (Experiment II). In Experiment I, 74 participants performed a speech-in-speech task while their cortical activity was measured using a functional near infrared spectroscopy (fNIRS) device. One target talker and one masker talker were simultaneously presented at three different target-to-masker ratios (TMRs): adverse, intermediate and favorable. Behavioral results show that performance may increase monotonically with TMR in some participants and failed to decrease, or even improved, in the adverse-TMR condition for others. On the neural level, an extensive brain network including the frontal (left prefrontal cortex, right dorsolateral prefrontal cortex and bilateral inferior frontal gyri) and temporal (bilateral auditory cortex) regions was more solicited by the intermediate condition than the two others. Additionally, bilateral frontal gyri and left auditory cortex activities were found to be positively correlated with behavioral performance in the adverse-TMR condition. In Experiment II, 27 participants, whose performance was the poorest in the adverse-TMR condition of Experiment I, were trained to improve performance in that condition. Results show significant performance improvements along with decreased activity in bilateral inferior frontal gyri, the right dorsolateral prefrontal cortex, the left inferior parietal cortex and the right auditory cortex in the adverse-TMR condition after training. Arguably, lower neural activity reflects higher efficiency in processing masker inhibition after speech-in-speech training. As speech-in-noise tasks also imply frontal and temporal regions, we suggest that regardless of the type of masking (speech or noise) the complexity of the task will prompt the implication of a similar brain network. Furthermore, the initial significant cognitive recruitment will be reduced following a training leading to an economy of cognitive resources.
Morphology Optimization via Side Chain Engineering Enables All-Polymer Solar Cells with Excellent Fill Factor and Stability (2018)

All-polymer solar cells (all-PSCs) composed of conjugated polymers as both donor and acceptor components in bulk heterojunction photoactive layers have attracted increasing attention. However, it is a big challenge to achieve optimal morphology in polymer:polymer blends. In response, we report herein a new strategy to adjust the nanoscale organization for all-PSCs. Specifically, side chain engineering of the well-known naphthalene diimide (NDI)-based polymer N2200 is modulated by introducing a fraction of linear oligoethylene oxide (OE) side chains to replace branched alkyl chains on the NDI units and by synthesizing a series of NDI-based polymer acceptors NOE x, where x is the percentage of OE chain substituted NDI units relative to total NDI units. Compared to the reference polymer NOE0, OE-chain-containing polymer NOE10 offers a much higher power conversion efficiency (PCE) of 8.1% with a record high fill factor (FF) of 0.75 in all-PSCs. Moreover, the NOE10-based all-PSC exhibits excellent long-term and thermal stabilities with >97% of the initial PCE being maintained after 300 h of aging at 65 °C. This work demonstrates an effective morphology optimization strategy to achieve highly efficient and stable all-PSCs and shows the excellent potential of NOE10 as an alternative to commercially available acceptor polymers N2200.
Crystallization and preliminary X-ray analysis of the NAD<sup>+</sup>-reducing [NiFe] hydrogenase from<i>Hydrogenophilus thermoluteolus</i>TH-1 (2014)

NAD+-reducing [NiFe] hydrogenases catalyze the oxidoreduction of dihydrogen concomitant with the interconversion of NAD+ and NADH. Here, the isolation, purification and crystallization of the NAD+-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus TH-1 are reported. Crystals of the NAD+-reducing [NiFe] hydrogenase were obtained within one week from a solution containing polyethylene glycol using the sitting-drop vapour-diffusion method and micro-seeding. The crystal diffracted to 2.58 Å resolution and belonged to space group C2, with unit-cell parameters a=131.43, b=189.71, c=124.59 Å, β=109.42°. Assuming the presence of two NAD+-reducing [NiFe] hydrogenase molecules in the asymmetric unit, VM was calculated to be 2.2 Å3 Da(-1), which corresponds to a solvent content of 43%. Initial phases were determined by the single-wavelength anomalous dispersion method using the anomalous signal from the Fe atoms.
Supplementary Data 1 from Pilot Study of ONCOS-102 and Pembrolizumab: Remodeling of the Tumor Microenvironment and Clinical Outcomes in Anti–PD-1–Resistant Advanced Melanoma (2023)

&lt;p&gt;Immunologic pathway genes&lt;/p&gt;
Enzymes as Biodevelopers for Nano- And Micropatterned Bicomponent Biopolymer Thin Films (2016)

The creation of nano- and micropatterned polymer films is a crucial step for innumerous applications in science and technology. However, there are several problems associated with environmental aspects concerning the polymer synthesis itself, cross-linkers to induce the patterns as well as toxic solvents used for the preparation and even more important development of the films (e.g., chlorobenzene). In this paper, we present a facile method to produce micro- and nanopatterned biopolymer thin films using enzymes as so-called biodevelopers. Instead of synthetic polymers, naturally derived ones are employed, namely, poly-3-hydroxybutyrate and a cellulose derivative, which are dissolved in a common solvent in different ratios and subjected to spin coating. Consequently, the two biopolymers undergo microphase separation and different domain sizes are formed depending on the ratio of the biopolymers. The development step proceeds via addition of the appropriate enzyme (either PHB-depolymerase or cellulase), whereas one of the two biopolymers is selectively degraded, while the other one remains on the surface. In order to highlight the enzymatic development of the films, video AFM studies have been performed in real time to image the development process in situ as well as surface plasmon resonance spectroscopy to determine the kinetics. These studies may pave the way for the use of enzymes in patterning processes, particularly for materials intended to be used in a physiological environment.
Yet Another Robot Application? [From the Guest Editors] (2016)

The articles in this special section is to find out what lies beyond the fascination toward robots that we have inherited from popular culture, the pleasure of learning with robots derived from the gamification of learning, and the strong appeal for robotics technologies given by its aura of innovation. Are there authentic ways in which robotics can improve education, and what affordances does robotics, in particular, provide for such educational transformation? Indeed, one of the biggest gray areas of educational robotics concerns the lack of empirical evidence on the educational (pedagogical as well as psychological) effectiveness of robots that is related to both the lack of standardized evaluation criteria and the methodological difficulties in conducting sound scientific tests.
Neutral atom imaging of the magnetospheric cusps (2011)

The magnetospheric cusps separate closed dayside magnetospheric field lines from open field lines of the magnetotail mantle and lobes. All magnetospheric field lines that map to the magnetopause also pass through the cusp regions. Thus whenever magnetic reconnection occurs at the magnetopause, magnetosheath plasma can enter one or both of the cusp regions and charge exchange with the geocorona. The resulting energetic neutral atoms (ENAs) resulting from this charge exchange process propagate away from the cusps and are observed remotely by the Interstellar Boundary Explorer (IBEX). The asymmetry of the ENA intensities between the northern and southern cusps are strongly dependent upon the Earth's dipole tilt angle and are consistent with in situ cusp observations. These asymmetric fluxes in the cusp regions are suggested to be explained by the regions at the magnetopause where magnetic reconnection is expected.
Performances of fast frequency hopping, binary frequency shift keying (FFH-BFSK) spread spectrum multiple access communications over fading channels (1988)

A fast-frequency-hopping spread-spectrum multiple-access (FFH-SSMA) system with a binary frequency-shift-keying (BFSK) modulation scheme is studied. Interference from undesired users and multipath are analyzed. Improvement due to the use of equal gain diversity is studied in terms of bit error rate (BER). Expressions for the BER are evaluated when a maximum-likelihood decision criterion is used to show the advantages of frequency hopping in selective fading channels.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Regulation of prolactin and its role in gallinaceous bird reproduction (1984)

There are major changes in circulating luteinizing hormone (LH), prolactin (PRL), estrogens (E), and progesterone (P) in relation to the onset of reproduction, egg laying, incubation, and care of young. LH levels increase in the prelaying period, followed some days later by increased circulating levels of E, P, and PRL. Levels of these hormones tend to stabilize during egg laying with periodic ovulatory cycle changes. Around the onset of incubation PRL levels increase, while LH, E, and P levels fall. During incubation PRL reaches very high levels, falling sharply when incubation is terminated. Stimulatory effects of hypothalamic neurotransmitters, peptides, and ovarian steroids on PRL secretion have been shown. The prelaying increase is dependent on E and P and the high levels of incubation require a functional serotonergic system. The causal relationships and roles of PRL in incubation of gallinaceous birds are, however, still unclear.
Local aortic histamine metabolism and albumin accumulation. Differences between blue and white areas. (1981)

Relationships between histamine metabolism, histamine content, and albumin accumulation were examined in Evans blue dye stained areas (blue) and unstained (white) areas of normal canine aortas. Results indicated that, while no differences existed in histamine methyltransferase-mediated catabolism, both histidine decarboxylase-mediated histamine synthesis and the histamine content of blue regions were significantly greater (p less than 0.005) than in contiguous white areas. Blue areas also showed significantly higher fluorescein-labeled albumin accumulation than white areas. By multiple regression analysis, a significant relationship (r = 0.81) was obtained between local aortic albumin accumulation and combined influences of local histidine decarboxylase activity and histamine content. The best predictor in this case was the local histidine decarboxylase activity. These data indicate that blue areas, believed to represent areas of spontaneous hemodynamic-induced vascular injury, have a larger nascent histamine pool than do contiguous white areas and that the distribution of histamine and histamine synthesis in the aorta is highly variable depending on the region examined. The data also suggest that local aortic histamine synthesis in blue areas may play a significantly role in mediation of the increased albumin accumulation observed in these regions.
Hyperplacentosis: A Novel Cause of Hyperthyroidism (2001)

Human chorionic gonadotropin (hCG), which is capable of thyrotropic activity, is believed responsible for the hyperthyroidism of gestational trophoblastic disease and hyperemesis gravidarum. Hyperplacentosis is a condition of heightened trophoblastic activity characterized by increased placental weight and circulating hCG levels higher than those associated with normal pregnancy. We report the first case of hyperthyroidism associated with hyperplacentosis. Correction of the hyperthyroidism occurred after hysterotomy and correlated with declining hCG levels. Hyperplacentosis should be included among the causes of hCG-mediated hyperthyroidism.
Performance of Nonlinear Compensation Techniques in a 71.64 Tb/s Capacity Demonstration Over 6970 km (2017)

We show the benefits of using a combination of DSP algorithms to compensate transmission nonlinearities. We measure an average total benefit of 1.4dBQ at nominal power using digital back propagation together with adaptive linear filters aided by coded modulation decisions.
ChemInform Abstract: Efficient Synthesis of Triazoles from D‐Arabinose and L‐Fucose. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Evolving mean-update selection methods for CMA-ES (2019)

This paper details an investigation of the extent to which performance can be improved for the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) by tuning the selection of individuals used for the mean-update algorithm. A hyper-heuristic is employed to explore the space of algorithms which select individuals from the population. We show the increase in performance obtained with a tuned selection algorithm, versus the unmodified CMA-ES mean-update algorithm. Specifically, we measure performance on instances from several real-valued benchmark function classes to demonstrate generalization of the improved performance.
Assessment of dynamic autonomic changes with posture using instantaneous entropy measures (2014)

Dynamic analysis provides a powerful methodological framework for characterizing physiological systems. In particular, complex heartbeat dynamics related to autonomic control mechanisms are known to change at each moment in time, and complexity measures have been proven to have prognostic value in both health and disease. Nevertheless, an instantaneous measure of complexity for cardiovascular time series (or any other series of stochastic physiological "events ") is still missing. In this study we introduce a mathematical framework serving instantaneous complex estimates of heartbeat dynamics to characterize different activities, tasks, and/or pathological states. In particular we propose new definitions of inhomogeneous point-process approximate and sample entropy where the discrete events are modeled by probability density functions characterizing and predicting the time until the next event occurs as a function of past history. These definitions are built on our previous work employing Laguerre expansions of the Wiener-Volterra autoregressive terms to account for long-term memory. We demonstrate an exemplary study on heartbeat data gathered from healthy subjects undergoing postural changes such as stand-up, slow tilt, and fast tilt. Results show that instantaneous complexity is able to effectively track the complex autonomic changes as they are affected by different postural changes.