gebhart/patrepeval huggingface dataset:
A distributed temperature sensor based on liquid-core optical fibers (1983)

The principles of operation, the design, and performance of a fiber-optic temperature-distribution sensor are discussed. The sensor uses optical time-domain reflectometry (OTDR) to detect temperature-induced changes of backscatter power at many separate locations in the fiber. In liquid-core fibers, a sensitivity of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2.3 \times 10^{-2}</tex> dB/°C (0.54 percent° C <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> ) was observed. A measurement accuracy of 1°C with a spatial resoltuion of 1 m is attainable over a fiber length of 100 m.
Direct-from-sputum rapid phenotypic drug susceptibility test for mycobacteria (2020)

We demonstrated "proof of principle" that (a) live mycobacteria can be isolated from sputum using MNPs with high efficiency (almost all the bacteria that survive decontamination) and (b) that the efficacy of candidate drugs on the mycobacteria thus isolated (in suspensions containing MNPs) could be tested in real-time using m-EIS.
Genomewide association study of Parkinson's disease clinical biomarkers in 12 longitudinal patients' cohorts (2019)

We identified novel genetic factors associated with heterogeneity of Parkinson's disease. The results can be used for validation or hypothesis tests regarding Parkinson's disease. © 2019 International Parkinson and Movement Disorder Society.
Supervised adaptation of MCE-trained CDHMMS using minimum classification error linear regression (2002)

In this paper, we present a formulation of minimum classification error linear regression (MCELR) for adaptation of Gaussian mixture continuous density HMM (CDHMM) parameters. We demonstrate that the MCELR can be used to adapt the MCE-trained HMM parameters under a consistent criterion. In a supervised speaker adaptation application, we observe that such adapted models perform better than the ones adapted using MLLR from the ML-trained seed models. We also observe that the MCELR performs consistently better than the MLLR for either sets of seed models.
Strong constraints on the $b \to s\gamma$ photon polarisation from $B^0 \to K^{*0}e^+e^-$ decays (2020)

Abstract: An angular analysis of the B0 → K*0e+e− decay is performed using a data sample corresponding to an integrated luminosity of 9 fb−1 of pp collisions collected with the LHCb experiment. The analysis is conducted in the very low dielectron mass squared (q2) interval between 0.0008 and 0.257 GeV2, where the rate is dominated by the B0 → K*0γ transition with a virtual photon. The fraction of longitudinal polarisation of the K*0 meson, FL, is measured to be FL = (4.4 ± 2.6 ± 1.4)%, where the first uncertainty is statistical and the second systematic. The ATRe observable, which is related to the lepton forward-backward asymmetry, is measured to be ATRe = −0.06 ± 0.08 ± 0.02. The AT2 and ATIm transverse asymmetries, which are sensitive to the virtual photon polarisation, are found to be AT2 = 0.11 ± 0.10 ± 0.02 and ATIm = 0.02 ± 0.10 ± 0.01. The results are consistent with Standard Model predictions and provide the world’s best constraint on the b → sγ photon polarisation.
Sialic acid feeding aged rats rejuvenates stimulated salivation and colon enteric neuron chemotypes (2009)

Old age is linked to numerous changes of body functions such as salivation, gastrointestinal motility, and permeability all linked to central and enteric nervous system decline. Thus, gut motility and barrier functions suffer. Sialic acid plays a key role in the nervous system at large and for many receptor functions specifically. Decreased sialylation in the elderly suggests an endogenous sialic acid deficit. We used a rat model of aging, to ask whether sialic acid feeding would affect (i) stimulated salivation, (ii) gut functions, and (iii) sialic acid levels and neuronal markers in brain and gut. We observed reduced levels of pilocarpine-stimulated salivation in old versus young rats and restored this function by sialic acid feeding. Brain ganglioside bound sialic acid levels were found lower in aged versus young rats, and sialic acid feeding partly restored the levels. The hypothalamic expression of cholinergic and panneuronal markers was reduced in aged rats. The expression of the nitrergic marker nNOS was increased upon sialic acid feeding in aged rats. Neither fecal output nor gut permeability was different between young and aged rats studied here, and sialic acid feeding did not alter these parameters. However, the colonic expression of specific nervous system markers nNOS and Uchl1 and the key enzyme for sialic acid synthesis GNE were differentially affected in young and aged rats by sialic acid feeding indicating that regulatory mechanisms change with age. Investigation of sialic acid supplementation as a functional nutrient in the elderly may help those who suffer from disorders of reduced salivation. Further research is needed to understand the differential effects of sialic acid feeding in young and aged rats.
Strontium Ranelate Reduces the Risk of Vertebral and Nonvertebral Fractures in Women Eighty Years of Age and Older (2006)

Treatment with strontium ranelate safely reduces the risk of vertebral and nonvertebral fractures in women with osteoporosis > or = 80 years of age. Even in the oldest old, it is not too late to reduce fracture risk.
Molecular cloning of cDNA that encode MHC class I molecules from a New World primate ( Saguinus oedipus ). Natural selection acts at positions that may affect peptide presentation to T cells. (1990)

To investigate the evolutionary pressures that drive the generation of polymorphism in primate MHC class I molecules, three cDNA that encode MHC class I alleles from a New World monkey, the cotton-top tamarin (Saguinus oedipus), were cloned and sequenced. These tamarin MHC class I alleles contained amino acid substitutions not found in any of the previously sequenced human MHC class I alleles. Moreover, the majority of these unique amino acid substitutions was located in the Ag recognition site at positions that have been shown to be critical in the presentation of viral peptides to T cells in mice and humans. These data suggest that selective pressures on MHC class I molecules preferentially act on the Ag recognition site and that the peptide binding or presenting functions of these molecules may drive the generation of MHC class I polymorphism. The novel Ag recognition sites of the tamarin MHC class I molecules, in addition to their restricted polymorphism, might account for the unusual susceptibility of the cotton-top tamarin to human pathogens.
Realization of regular arrays of nanoscale resistive switching blocks in thin films of Nb-doped SrTiO3 (2008)

We report on the realization of short-range-ordered arrays of nanoscale resistive switching blocks in epitaxial Nb-doped SrTiO3 thin films. These blocks can be individually addressed by the tip of a conductive tip atomic force microscope and reversibly switched between a high and a low resistance state reaching an Roff to Ron ratio of up to 50. Scanning micrometer-scale areas with an appropriately biased tip, all blocks within the scanned area can be switched between the two resistive states. We suggest a connection between these nanoscale switching blocks and defect-rich nanoclusters which were detected with high resolution transmission electron microscopy.
Supplementary Figure 1 from Resistance to Irreversible EGF Receptor Tyrosine Kinase Inhibitors through a Multistep Mechanism Involving the IGF1R Pathway (2023)

&lt;p&gt;PDF file - 578K, PI3K inhibition restores sensitivity to PF299804 and WZ4002&lt;/p&gt;
TGFβ signaling regulates the choice between pluripotent and neural fates during reprogramming of human urine derived cells (2016)

Human urine cells (HUCs) can be reprogrammed into neural progenitor cells (NPCs) or induced pluripotent stem cells (iPSCs) with defined factors and a small molecule cocktail, but the underlying fate choice remains unresolved. Here, through sequential removal of individual compound from small molecule cocktail, we showed that A8301, a TGFβ signaling inhibitor, is sufficient to switch the cell fate from iPSCs into NPCs in OSKM-mediated HUCs reprogramming. However, TGFβ exposure at early stage inhibits HUCs reprogramming by promoting EMT. Base on these data, we developed an optimized approach for generation of NPCs or iPSCs from HUCs with significantly improved efficiency by regulating TGFβ activity at different reprogramming stages. This approach provides a simplified and improved way for HUCs reprogramming, thus would be valuable for banking human iPSCs or NPCs from people with different genetic background.
miR-26a regulates extracellular vesicle secretion from prostate cancer cells via targeting SHC4, PFDN4 and CHORDC1 (2019)

Abstract Extracellular vesicles (EVs) are known to be involved in intercellular communication during cancer progression; thus, elucidating the detailed mechanism will contribute to the development of a novel strategy for EV-targeted cancer treatment. However, the biogenesis of EVs in cancer cells is not completely understood. MicroRNAs (miRNAs) regulate a variety of physiological and pathological phenomena; thus, miRNAs could regulate EV secretion. Here, we performed high-throughput miRNA-based screening to identify the regulators of EV secretion using an ExoScreen assay. By using this miRNA-based screening, we identified miR-26a, which was reported as a tumor suppressive miRNA, as a miRNA involved in EV secretion from prostate cancer (PCa) cells. In addition, we found that the SHC4, PFDN4, and CHORDC1 genes regulate EV secretion in PCa cells. Suppression of these genes by siRNAs significantly inhibited the secretion of EVs in PCa cells. Furthermore, the progression of PCa cells was inhibited in an in vivo study. On the other hand, injection of EVs isolated from PCa cells partially rescued this suppressive effect on tumor growth. Taken together, our findings suggest that miR-26a regulates EV secretion via targeting SHC4, PFDN4, and CHORDC1 in PCa cells, resulting in the suppression of PCa progression.
High‐Responsivity Near‐Infrared Photodetector Using Gate‐Modulated Graphene/Germanium Schottky Junction (2019)

Abstract A high‐responsivity near‐infrared photodetector is demonstrated using a transparent ZnO top gate‐modulated graphene/Ge Schottky junction. The responsivity of a graphene/Ge junction photodetector characterized with a scanning photocurrent microscopy system is improved to 0.75 A W −1 . This result is 5 to 35 times higher than the previously reported graphene/Ge photodetectors that did not use gate modulation. The detectivity is also improved to 2.53 × 10 9 cm Hz 1/2 W −1 at V g = −10 V from 0.43 × 10 9 cm Hz 1/2 W −1 at V g = 0 V. The performance of this gate‐modulated graphene/Ge Schottky junction base infrared (IR) detector is comparable to a commercially available IR photodetector, but the fabrication process is much simpler and compatible with glass or flexible substrates.
Shifts in the epitopes of myelin basic protein recognized by Lewis rat T cells before, during, and after the induction of experimental autoimmune encephalomyelitis. (1993)

An epitope present in the 71-90 sequence of basic protein (BP) has been identified as the dominant epitope recognized by most Lewis rat encephalitogenic T cells isolated during experimental autoimmune encephalomyelitis (EAE). In the present study, we investigated the BP epitopes recognized by Lewis rat T cells in naive rats, in rats suffering from acute EAE, and in recovered rats. T cells isolated from the spinal cord lesions and from the lymph nodes were studied using T cell lines and bulk cultures. Virulence of the T cells was assayed by adoptive transfer. We now report that naive and recovered Lewis rats are populated with T cells reactive to a variety of BP epitopes and only a minority are specific for the 71-90 epitope. In contrast, the induction of EAE was associated with a predominance of T cells reactive to the 71-90 epitope. T cells recovered from naive, diseased, or recovered rats were found to be virulent upon passive transfer. Some of these virulent T cells were specific to BP epitopes other than the 71-90 epitope. There was no major difference in the BP specificities of T cells isolated from the lesions and from the lymph nodes. Thus, natural T cell reactivity to BP is heterogeneous and pathogenicity is not confined to one particular epitope, active disease is characterized by a dominant response to the 71-90 epitope, and recovery is marked by a return to heterogeneity.
Using Wearable Sensors to Monitor Physical Activities of Patients with COPD: A Comparison of Classifier Performance (2009)

Chronic obstructive pulmonary disease (COPD) is a major public health problem. Early detection and treatment of an exacerbation in the outpatient setting are important to prevent worsening of clinical status and need for emergency room care or hospital admission. In this study we use accelerometers to capture motion data; and heart rate and respiration rate to capture physiological responses from patients with COPD as they perform a range of Activities of Daily Living (ADL) and physical exercises. We present a comparative analysis of classification performance of a set of different classification techniques and factors that affect classification performance for activity recognition based on accelerometer data. This is the first step towards building a wearable sensor monitoring system for tracking changes in physiological responses of patients with COPD with respect to their physical activity level.
Non-figurative coloured arrangements, towards a new tool to visually facilitate odour imagery? (2022)

Abstract Odour imagery, the ability to experience smell when an appropriate stimulus is absent, has widely been documented as being particularly difficult. However, previous studies have shown the beneficial effect of visual cues ( e.g. pictures or words) to facilitate performance in numerous tasks of olfactory nature. Therefore, the use of visual cues to evoke odours seems relevant. In this study, our interest is directed towards non-figurative coloured arrangements, which result from a patented technology and aim at chromatically representing any smell from its chemical composition. We recorded and compared hemodynamic responses during odour imagery facilitated by non-figurative coloured arrangements and pictures using functional magnetic resonance imaging. Our findings reveal that the use of non-figurative coloured arrangements during odour imagery solicits olfactory and non-olfactory brain regions which have roles mainly in olfactory processing, multimodal integration. Moreover, very similar cortical activity was found between the use of non-figurative coloured arrangements and pictures during odour imagery. Overall, non-figurative coloured arrangements could become a robust tool to visually evoke odours without requiring prior familiarity with the depicted odour. Future studies are needed to determine the relationships between brain activation and vividness of the generated odour images as well as the necessary mental workload.
Binding of 3-o-acetyl-4"-o-isovaleryltylosin to ribosomes from a macrolide-resistant strain of Staphylococcus aureus. (1982)

The resistance of Staphylococcus aureus MS-9610 to tylosin and 3-O-acetyltylosin was due to the decreased affinity of its ribosome system to these macrolides. However, 3-O-acetyl-4"-O-isovaleryltylosin was found to bind to ribosomes of the strain about three times more than 3-O-acetyltylosin. This binding was not interfered by tylosin and 3-O-acetyltylosin. The 4"-O-acyl group and the mycinose moiety were suggested to have an important role in the binding of tylosin derivatives to ribosomes of resistant strains.
PPDF‐based method to account for atmospheric light scattering in observations of carbon dioxide from space (2008)

We present an original method that accounts for thin clouds in carbon dioxide retrievals from space‐based reflected sunlight observations in near‐infrared regions. This approach involves a reasonable, simple parameterization of effective transmittance using a set of parameters that describe the path‐length modification caused by clouds. The complete retrieval scheme included the following: estimation of cloud parameters from the 0.76‐ μ m O 2 A‐band and from the H 2 O‐saturated absorption area of the 2.0‐ μ m band; a necessary correction to utilize these parameters at the target CO 2 1.58‐ μ m band using estimated ground surface albedo outside of gas absorption lines in this band; and retrieval of CO 2 amount at the 1.58‐ μ m band using a maximum a posteriori method of inversion. The primary retrieved parameters refer to the CO 2 volume mixing ratio vertical profile that is then transformed to an averaged‐column amount under a pre‐defined increment of pressure. A set of numerical simulations with synthetic radiance spectra particular to Greenhouse Gases Observing Satellite (GOSAT) observations showed that the proposed method provides acceptably accurate CO 2 retrievals from an atmosphere that includes thin cirrus clouds. Efficiency of the aerosol and cloud corrections was demonstrated by comparing it with a modified iterative maximum a posteriori‐DOAS (IMAP‐DOAS) that neglects path length modifications due to the scattering effects.
Emergency department care-related causal factors of in-patient deterioration (2021)

Objective The aim of this study was to determine factors related to emergency department (ED) care causing in-patient deterioration. Methods This retrospective cohort study examined in-patient records using the human factors classification framework for patient safety in a regional health service in New South Wales, Australia, between March 2016 and February 2017. Deterioration was defined as either the initiation of a medical emergency team call, cardiac arrest or unplanned admission to the intensive care unit. Results Of the 1074 patients who deteriorated within 72 hours of admission via the ED, the care received in the ED was a contributing factor for 101 patients (9%). The most common human causal factors were poor communication between staff, medical management errors, delayed treatment, medical documentation errors, nursing management errors and unclear policies or guidelines. Communication issues occurred the most when patients had more comorbidities (P = 0.039) and were more likely to occur in the presence of a medical documentation error (odds ratio 4.4; 95% confidence interval 1.7-11.3). Unclear policies or guidelines as a factor was most frequent with a surgical diagnosis (34.5% vs 15.7% for surgical vs medical, respectively; P = 0.038) and in patients ≥80 years of age (30.0% vs 21.8% for age ≥80 vs <80 years, respectively; P = 0.027). Conclusion Quality monitoring and interventions that consider human factors are required to address preventable in-patient deterioration. What is known about the topic? The ED represents the hospital's point of contact for potentially life-threatening conditions. Adverse event rates for emergency admissions are more than double those of non-emergency admissions. Patients are at particular risk of deterioration on discharge from the ED to the ward in the first 72 hours. Predicting which patients will deteriorate following transfer to the ward remains challenging, with care in the ED hypothesised to play a role. What does this paper add? This paper reveals that in-patient deterioration relating to ED care could be reduced through the routine identification of causal factors within a human factors framework in any patient deterioration event and subsequent evidence-informed interventions to address these factors. It is also extrapolated that the implementation of any intervention should be informed by behaviour-change principles. What are the implications for practitioners? It is implied that there is a need for the clarification and revision of policies and guidelines pertaining to the management of elderly patients, education regarding the critical importance of the often clinically masked vital sign deviations in younger patients and improved communication between staff, especially regarding patients with more comorbidities. Reviews of adverse events, such as patient deterioration, should incorporate a human factors analysis. Regular collation of data following adverse events should occur, with interventions considering all aspects of the factors that led to the event.
Multiscale Centerline Detection (2015)

Finding the centerline and estimating the radius of linear structures is a critical first step in many applications, ranging from road delineation in 2D aerial images to modeling blood vessels, lung bronchi, and dendritic arbors in 3D biomedical image stacks. Existing techniques rely either on filters designed to respond to ideal cylindrical structures or on classification techniques. The former tend to become unreliable when the linear structures are very irregular while the latter often has difficulties distinguishing centerline locations from neighboring ones, thus losing accuracy. We solve this problem by reformulating centerline detection in terms of a regression problem. We first train regressors to return the distances to the closest centerline in scale-space, and we apply them to the input images or volumes. The centerlines and the corresponding scale then correspond to the regressors local maxima, which can be easily identified. We show that our method outperforms state-of-the-art techniques for various 2D and 3D datasets. Moreover, our approach is very generic and also performs well on contour detection. We show an improvement above recent contour detection algorithms on the BSDS500 dataset.
Large Margin Learning of Upstream Scene Understanding Models (2018)

Upstream supervised topic models have been widely used for complicated scene understanding. However, existing maximum likelihood estimation (MLE) schemes can make the prediction model learning independent of latent topic discovery and result in an imbalanced prediction rule for scene classification. This paper presents a joint max-margin and max-likelihood learning method for upstream scene understanding models, in which latent topic discovery and prediction model estimation are closely coupled and well-balanced. The optimization problem is efficiently solved with a variational EM procedure, which iteratively solves an online loss-augmented SVM. We demonstrate the advantages of the large-margin approach on both an 8-category sports dataset and the 67-class MIT indoor scene dataset for scene categorization.
Microprocessor Chip with Photonic I/O (2017)

In this work, we provide an overview of the technology and architecture of a microprocessor chip with optical I/O. Zero-change photonics integration enabled the chip to be fabricated in a commercial electronics CMOS foundry.