gebhart/patrepeval huggingface dataset:
Two novel and correlated CF-causing insertions in the (TG)mTn tract of the CFTR gene (2019)

Two novel and related pathogenic variants of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene were structurally and functionally characterized. These alterations have not been previously described in literature. Two patients with diagnosis of Cystic Fibrosis (CF) based on the presence of one mutated allele, p.Phe508del, pathological sweat test and clinical symptoms were studied. To complete the genotypes of both patients, an extensive genetic and functional analysis of the CFTR gene was performed. Extensive genetic characterization confirmed the presence of p.Phe508del pathogenic variant and revealed, in both patients, the presence of an insertion of part of intron 10 in intron 9 of the CFTR gene, within the (TG)m repeat, with a variable poly-T stretch. The molecular lesions resulted to be very similar in both patients, with only a difference in the number of T in the poly-T stretch. The functional characterization at RNA level revealed a complete anomalous splicing, without exon 10, from the allele with the insertion of both patients. Consequently, the alleles with the insertions are expected not to contribute to the formation of a functional CFTR protein. Molecular and functional features of these alterations are compatible with the definition of novel CF-causing variants of the CFTR gene. This also allowed the completion of the genetic characterization of both patients.
Fluid and Solute Transfer Characteristics in a Dialyzer with a High-Performance Membrane (2011)

To date, many types of high-flux dialyzers with high-performance membranes have been developed. They seem to have a higher internal filtration flow rate (Q(IF)) because of a higher ultrafiltration coefficient. In the health reimbursement system in Japan, commercially available dialyzers are categorized into five types based on their β(2)-microglobulin clearance (K(BMG)) values. Although the K(BMG) value was not correlated strongly with the Q(IF) value for 26 types of commercially available dialyzers, almost all the dialyzers with a higher Q(IF) value had a higher KBMG value. These dialyzers seem to have a higher convective transport because of internal filtration in addition to diffusive transport. We measured the blood flow velocity in a cross-sectional plane of the dialyzer using pulse Doppler ultra-sonography to evaluate QIF. It is a useful method for the bedside monitoring because it is noninvasive to the patient and produces reliable data with a higher reproducibility. On the other hand, membrane fouling occurs more easily in higher Q(IF) dialyzers, compared with conventional dialyzers, because of the higher degree of membrane fouling. Internal filtration-enhanced hemodialysis (IFEHD) using these dialyzers, therefore, has the advantage of increasing solute removal efficiency by enhancing convective transport and the simultaneous disadvantage of decreasing solute removal efficiency by causing membrane fouling. Thus, IFEHD treatment should be performed using a dialyzer with a high-performance membrane to ensure that the advantage is superior to the disadvantage.
Advanced information processing system: Authentication protocols for network communication (1994)

In safety critical I/O and intercomputer communication networks, reliable message transmission is an important concern. Difficulties of communication and fault identification in networks arise primarily because the sender of a transmission cannot be identified with certainty, an intermediate node can corrupt a message without certainty of detection, and a babbling node cannot be identified and silenced without lengthy diagnosis and reconfiguration . Authentication protocols use digital signature techniques to verify the authenticity of messages with high probability. Such protocols appear to provide an efficient solution to many of these problems. The objective of this program is to develop, demonstrate, and evaluate intercomputer communication architectures which employ authentication. As a context for the evaluation, the authentication protocol-based communication concept was demonstrated under this program by hosting a real-time flight critical guidance, navigation and control algorithm on a distributed, heterogeneous, mixed redundancy system of workstations and embedded fault-tolerant computers.
Comparison of contrast-enhanced digital mammography and contrast-enhanced digital breast tomosynthesis for lesion assessment (2019)

Contrast-enhanced digital mammography (CEDM) reveals neovasculature of breast lesions in a two-dimensional contrast enhancement map. Contrast-enhanced digital breast tomosynthesis (CEDBT) provides contrast enhancement in three dimensions, which may improve lesion characterization and localization. We aim to compare CEDM and CEDBT for lesion assessment. Women with breast imaging-reporting and data system 4 or 5 suspicious breast lesion(s) were recruited in our study and were imaged with CEDM and CEDBT in succession under one breast compression. Two radiologists assessed CEDM and CEDBT with both images displayed side-by-side and compared (1) contrast enhancement of lesions and (2) lesion margin using a five-point scale ranging from <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>-</mml:mo> <mml:mn>2</mml:mn></mml:mrow> </mml:math> (CEDM much better) to <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>+</mml:mo> <mml:mn>2</mml:mn></mml:mrow> </mml:math> (CEDBT much better). Biopsy identified 19 malignant lesions with contrast enhancement. Our results show that CEDBT provides better lesion margins than CEDM with limited reduction in contrast enhancement. CEDBT delivers less radiation dose compared to CEDM + DBT. Synthetic CEDM can be generated from CEDBT data and provides lesion contrast enhancement comparable to CEDM. CEDBT has potential for clinical applications, such as treatment response monitoring and guidance for biopsy.
A new method for labelling enkephalins and LC/LIF/MS studies (2006)

communication orale
1,3-Dithianes as Acyl Anion Equivalents in Pd-Catalyzed Asymmetric Allylic Substitution (2016)

A Pd-catalyzed asymmetric allylic substitution with 1,3-dithianes as acyl anion equivalents has been developed in high yields and excellent enantioselectivities. The reaction was performed on a gram scale, and the corresponding alkylated products were conveniently converted into several biologically active products. This work provides an alternative strategy utilizing electrophilic carbonyl compounds as nucleophilic species in a Pd-catalyzed allylic substitution.
Novel High-Performance Analog Devices for Advanced Low-Power High-k Metal Gate Complementary Metal–Oxide–Semiconductor Technology (2011)

High performance analog (HPA) devices in high- k metal gate (HKMG) scheme with innovative halo engineering have been successfully demonstrated to produce superior analog and digital performance for low power applications. HPA device was processed “freely” with no extra mask, no extra litho, and no extra process step. This paper details a comprehensive study of the analog and digital characteristics of these HPA devices in comparison with analog control (conventional digital devices with matched geometry). Analog properties such as output voltage gain (also called self-gain), trans-conductance G m , conductance G ds , G m / I d , mismatching (MM) behavior, flicker noise (1/ f noise) and current linearity have clearly reflected the advantage of HPA devices over analog control, while DC performance (e.g., I on – I off , I off – V tsat , DIBL, C jswg ) and reliability (HCI) have also shown the comparability of HPA devices over control.
The Impact of Soil Sampling Errors on Variable Rate Fertilization (2004)

Variable rate fertilization of an agricultural field is done taking into account spatial variability in the soil’s characteristics. Most often, spatial variability in the soil’s fertility is the primary characteristic used to determine the differences in fertilizers applied from one point to the next. For several years the Idaho National Engineering and Environmental Laboratory (INEEL) has been developing a Decision Support System for Agriculture (DSS4Ag) to determine the economically optimum recipe of various fertilizers to apply at each site in a field, based on existing soil fertility at the site, predicted yield of the crop that would result (and a predicted harvest-time market price), and the current costs and compositions of the fertilizers to be applied. Typically, soil is sampled at selected points within a field, the soil samples are analyzed in a lab, and the lab-measured soil fertility of the point samples is used for spatial interpolation, in some statistical manner, to determine the soil fertility at all other points in the field. Then a decision tool determines the fertilizers to apply at each point. Our research was conducted to measure the impact on the variable rate fertilization recipe caused by variability in the measurement of the soil’s fertility at the sampling points. The variability could be laboratory analytical errors or errors from variation in the sample collection method. The results show that for many of the fertility parameters, laboratory measurement error variance exceeds the estimated variability of the fertility measure across grid locations. These errors resulted in DSS4Ag fertilizer recipe recommended application rates that differed by up to 138 pounds of urea per acre, with half the field differing by more than 57 pounds of urea per acre. For potash the difference in application rate was up to 895 pounds per acre and over half the field differed by more than 242 pounds of potash per acre. Urea and potash differences accounted for almost 87% of the cost difference. The sum of these differences could result in a $34 per acre cost difference for the fertilization. Because of these differences, better analysis or better sampling methods may need to be done, or more samples collected, to ensure that the soil measurements are truly representative of the field’s spatial variability.
Impact of Electronic Modification of the Chelating Benzylidene Ligand in cis-Dichloro-Configured Second-Generation Olefin Metathesis Catalysts on Their Activity (2014)

A series of electronically modified second-generation cis-dichloro ruthenium ester chelating benzylidene complexes was prepared, characterized, and benchmarked in a typical ring-opening metathesis polymerization (ROMP) experiment. The electronic tuning of the parent chelating benzylidene ligand (2-ethyl ester benzylidene) was achieved by substitution at the 4- and 5-positions with electron-withdrawing nitro or electron-donating methoxy groups. The effect of the electronic tuning on the cis-trans isomerization process was studied experimentally and theoretically. Density functional theory calculations clearly revealed the influence of electronic modification on the relative stability between the cis and trans isomers, which is decisive for the activity of the studied compounds as initiators in ROMP. © 2014 American Chemical Society.
A Critical Assessment of the Quality of Reporting of Randomized, Controlled Trials in the Urology Literature (2007)

This formal review suggests that randomized, controlled trial reporting in the urology literature has improved since the publication of the Consolidated Standards of Reporting Trials statement in 1996. Certain areas, such as reporting of trial methods, continue to meet Consolidated Standards of Reporting Trials criteria in fewer than half of publications. Ongoing graduate and postgraduate education in trial design and evidence based practice may result in further improvement in randomized, controlled trial reporting.
High speed phase modulator driver unit in 55 nm SiGe BiCMOS for a single-channel 100 Gb/s NRZ silicon photonic modulator (2015)

In this paper, a silicon integrated driver unit, intended for a single-channel NRZ 3D heterogeneous silicon photonic modulator is proposed. It allows data rate of up to 100 Gb/s, which is beyond the current state of the art. It directly controls 160 GHz bandwidth high speed phase modulator (HSPM) segment of a Mach Zehnder Interferometer (MZI). It is fabricated in 55 nm SiGe BiCMOS technology with fT of up to 300 GHz. It features a 300 mW of dc power consumption and delivers a 2.5 Vpp single-ended output swing at 100 Gb/s.
TAS-Seq: a robust and sensitive amplification method for bead-based scRNA-seq (2021)

Abstract Single-cell RNA-sequencing (scRNA-seq) is valuable for analyzing cellular heterogeneity. Cell composition accuracy is critical for analyzing cell–cell interaction networks from scRNA-seq data. We developed terminator-assisted solid-phase cDNA amplification and sequencing (TAS-Seq) for scRNA-seq based on a terminator, terminal transferase, and nanowell/bead-based scRNA-seq platform; TAS-Seq showed high tolerance to variations in the terminal transferase reaction, which complicate the handling of existing terminal transferase-based scRNA-seq methods. In murine and human lung samples, TAS-Seq yielded scRNA-seq data that were highly correlated with flow-cytometric data, showing higher gene-detection sensitivity and more robust detection of important cell–cell interactions and expression of growth factors/interleukins in cell subsets than 10X Chromium v2 and Smart-seq2. Expanding TAS-Seq application will improve understanding and atlas construction of lung biology at the single-cell level.
Lithium enhances growth of human leukaemia cells in vitro (1982)

Lithium is known to cause leucocytosis in normal humans, and lithium salts have been used therapeutically in attenuating leucopenia in patients undergoing chemotherapy. Recent reports also described leukaemia development during lithium treatment. We have investigated the effect of lithium chloride on the proliferation of human myeloid, erythroblastic, and T- and B-lymphoblast leukaemia cells in vitro. Colony formation by cells of the myeloid leukaemia lines HL-60 and KG-1 was enhanced by lithium chloride, and maximal stimulation was seen at 5 X 10(-4) M. Lithium also increased the proliferation of KG-1a cells, a subline of KG-1 cells that does not respond to colony-stimulating factor, indicating a direct growth-promoting effect on myeloid leukaemia cells. Lithium was found to enhance colony formation by the T-lymphoblast cell line MOLT 4 and the B-lymphoblast line IM-9 at concentrations between 10(-6) and 10(-3) M. The addition of lithium chloride to murine Friend or human K-562 erythroleukaemia cells also caused an augmentation in colony formation. These observations may have relevance to the therapeutic use of lithium in patients with haematological malignancies.
Bone morphogenetic protein signaling in the murine distraction osteogenesis model. (2009)

A murine distraction osteogenesis model was standardized to allow analysis of the molecular pathways associated with postnatal de novo bone formation. The authors examined the presence and expression of Bone Morphogenetic Proteins (BMPs) -2, -3, -4, -6 and -7, and the BMP receptors Alk3 and Alk6 at different stages. Strong signals were detected for BMP-4 at the end of the distraction period and for BMP-6 during the entire experimental period. Signals for BMP-7 (Osteogenic Protein-1) were very low, suggesting a less important role during the normal process of distraction bone healing. Immunohistochemical staining revealed the presence of BMP-4 in the early chondroblasts, while BMP-6 was detected in the more mature cartilage cells. The data indicate a BMP molecular profile reminiscent of the embryonic maturation process in endochondral bone formation.
Short‐term interleukin‐37 treatment improves vascular endothelial function, endurance exercise capacity, and whole‐body glucose metabolism in old mice (2019)

Aging is associated with vascular endothelial dysfunction, reduced exercise tolerance, and impaired whole-body glucose metabolism. Interleukin-37 (IL-37), an anti-inflammatory cytokine of the interleukin-1 family, exerts salutary physiological effects in young mice independent of its inflammation-suppressing properties. Here, we assess the efficacy of IL-37 treatment for improving physiological function in older age. Old mice (26-28 months) received daily intraperitoneal injections of recombinant human IL-37 (recIL-37; 1 µg/200 ml PBS) or vehicle (200 ml PBS) for 10-14 days. Vascular endothelial function (ex vivo carotid artery dilation to increasing doses of acetylcholine, ACh) was enhanced in recIL-37 vs. vehicle-treated mice via increased nitric oxide (NO) bioavailability (all p < .05); this effect was accompanied by enhanced ACh-stimulated NO production and reduced levels of reactive oxygen species in endothelial cells cultured with plasma from IL-37-treated animals (p < .05 vs. vehicle plasma). RecIL-37 treatment increased endurance exercise capacity by 2.4-fold, which was accompanied by a 2.9-fold increase in the phosphorylated AMP-activated kinase (AMPK) to AMPK ratio (i.e., AMPK activation) in quadriceps muscle. RecIL-37 treatment also improved whole-body insulin sensitivity and glucose tolerance (p < .05 vs. vehicle). Improvements in physiological function occurred without significant changes in plasma, aortic, and skeletal muscle pro-inflammatory proteins (under resting conditions), whereas pro-/anti-inflammatory IL-6 was greater in recIL-37-treated animals. Plasma metabolomics analysis revealed that recIL-37 treatment altered metabolites related to pathways involved in NO synthesis (e.g., increased L-arginine and citrulline/arginine ratio) and fatty acid metabolism (e.g., increased pantothenol and free fatty acids). Our findings provide experimental support for IL-37 therapy as a novel strategy to improve diverse physiological functions in old age.
Holographic particle image velocimetry using Bacteriorhodopsin (2006)

To gain better insight into the behaviour of turbulent flow there is a demand for a practical measurement instrument to perform three-dimensional flow measurements. Holography is a three-dimensional imaging technique, and as such is ideally suited for this purpose. Because flow media (such as water and air) are generally transparent, optical measurements in such media are enabled by adding small particles to the flow of interest. When the position of such a particle is known at two instances (by recording two holograms of the particle field), the local flow vector may be deduced. The holographic system that has been developed throughout this research uses the light-sensitive protein bacteriorhodopsin (BR) as the recording medium. We studied the properties of BR, with a focus on the practical applicability of this material and the development of new techniques. The BR molecule has the special property that it is sensitive to the polarization of the illuminating light. This allows the storage of two independent holograms inside a single BR film. Our concept of polarization multiplexing gives our system a number of distinct advantages over other recently demonstrated holographic measurement systems. It makes our system inherently more robust and accurate. To demonstrate the capabilities of the system, a number of measurements were performed on a multiphase jet. In such a measurement we determined the displacement of more than one thousand particles in a volume of less than 0.1 cm^3. Using our system, it was possible for one person to perform thirty multiphase jet measurements within eight hours. This would have been impossible with any other holographic measurement system. As such, this research has made a significant step towards holography becoming a standard research tool in fluid dynamics.
Low-fat, plant-based diet in multiple sclerosis: A randomized controlled trial (2016)

While a very-low fat, plant-based diet was well adhered to and tolerated, it resulted in no significant improvement on brain MRI, relapse rate or disability as assessed by EDSS scores in subjects with RRMS over one year. The diet group however showed significant improvements in measures of fatigue, BMI and metabolic biomarkers. The study was powered to detect only very large effects on MRI activity so smaller but clinically meaningful effects cannot be excluded. The diet intervention resulted in a beneficial effect on the self-reported outcome of fatigue but these results should be interpreted cautiously as a wait-list control group may not completely control for a placebo effect and there was a baseline imbalance on fatigue scores between the groups. If maintained, the improved lipid profile and BMI could yield long-term vascular health benefits. Longer studies with larger sample sizes are needed to better understand the long-term health benefits of this diet.
A tractable DDN-POMDP Approach to Affective Dialogue Modeling for General Probabilistic Frame-based Dialogue Systems (2006)

We propose a new approach to developing a tractable affective dialogue model for general probabilistic frame-based dialogue systems. The dialogue model, based on the Partially Observable Markov Decision Process (POMDP) and the Dynamic Decision Network (DDN) techniques, is composed of two main parts, the slot level dialogue manager and the global dialogue manager. It has two new features: (1) being able to deal with a large number of slots and (2) being able to take into account some aspects of the user's affective state in deriving the adaptive dialogue strategies. Our implemented dialogue manager prototype can handle hundreds of slots; each slot might have many values. A first evaluation of the slot level dialogue manager (1-slot case) showed that with a 95% confidence level the DDN-POMDP dialogue strategy outperforms three handcrafted dialogue strategies when the user's action error is induced by stress.
HCC in Living Donor Liver Transplantation: Can We Expand the Milan Criteria? (2007)

Application of serum AFP level to selection of HCC for LT affords better patient selection criteria.
Peripheral nerve stimulation informed design of a high‐performance asymmetric head gradient coil (2023)

Augmenting the design phase of a new high-performance head gradient coil by PNS modeling dramatically improved the usable image-encoding performance by raising PNS thresholds.
Phytophthora palmivora establishes tissue-specific intracellular infection structures in the earliest divergent land plant lineage (2018)

The expansion of plants onto land was a formative event that brought forth profound changes to the earth's geochemistry and biota. Filamentous eukaryotic microbes developed the ability to colonize plant tissues early during the evolution of land plants, as demonstrated by intimate, symbiosis-like associations in >400 million-year-old fossils. However, the degree to which filamentous microbes establish pathogenic interactions with early divergent land plants is unclear. Here, we demonstrate that the broad host-range oomycete pathogen <i>Phytophthora palmivora</i> colonizes liverworts, the earliest divergent land plant lineage. We show that <i>P. palmivora</i> establishes a complex tissue-specific interaction with <i>Marchantia polymorpha</i>, where it completes a full infection cycle within air chambers of the dorsal photosynthetic layer. Remarkably, <i>P. palmivora</i> invaginates <i>M. polymorpha</i> cells with haustoria-like structures that accumulate host cellular trafficking machinery and the membrane syntaxin MpSYP13B, but not the related MpSYP13A. Our results indicate that the intracellular accommodation of filamentous microbes is an ancient plant trait that is successfully exploited by pathogens like <i>P. palmivora</i>.