gebhart/patrepeval huggingface dataset:
MP598 ROLE OF HFR CARTRIDGE IN THE REMOVALOF MEDIATORS OF INFLAMMATION IN HEMODIALYSIS PATIENTS (2013)

Introduction and Aims: Elevated white blood cell (WBC) count associates with an increased mortality risk in hemodialysis (HD) patients. The prognostic value of trends (increase or decrease) of neutrophil and lymphocyte count is unclear. We aimed to analyze the relationship of changes in neutrophil and lymphocyte count and mortality in HD patients. Methods: Incident HD patients treated in RRI clinics who had their first in-center treatment between 1/2000 and 12/2010 and survived a minimum of 12 months were included. Slopes of neutrophil and lymphocyte counts (as proportions of WBC) were computed for each patient using linear regression of all available values between months 4 and 12 from the start of treatment. Patients were stratified based on (a) the average rate of change in neutrophil % (declined: 7 points/yr) and (b) the average rate of change in lymphocyte % (declined: 5.5 points/yr); which resulted in 9 groups. Survival was then analyzed in months 13 to 18 following HD initiation using a Cox hazards model adjusted for age, gender, race, ethnicity, diabetes, access type, BMI, albumin, systolic blood pressure, body temp, nPCR, eKt/V, interdialytic weight gain, urea distribution volume, and slope of neutrophils and lymphocytes. Results: A total of 2809 patients were studied. The median (IQR) age at the start of HD was 62.9 (51.7-72.7) yrs, 55.1% were male, 44.7% were white and 46.5% of patients were black. The Cox Hazards model showed that simultaneous increases in neutrophil and lymphocyte counts (HR=12.3; 95% C.I=1.3-113.5, P=0.03) or decrease of neutrophil and lymphocyte counts (HR=4.7; 95% CI=0.6-38.4, P=0.14) were associated with an increased risk of mortality as compared to reference group (stable neutrophil and stable lymphocyte). Declines in lymphocyte count and increases in neutrophil count were at increased death risk (HR=1.8; 95% CI=1.2-2.6, P=0.003) whereas increase in lymphocyte count with stable or decrease neutrophil count exert a protective effect on survival (HR=0.3; 95% CI=0.07-1.13, P=0.07 & HR=0.8; 95% CI = 0.5-1.3, respectively). Conclusions: Our results shows survival advantage for patients with stable neutrophil and lymphocyte counts. HD patients with high neutrophil count and low lymphocyte count are associated with increased mortality risk. This relationship may be partially explained by the presence of protein-energy malnutrition and acute inflammation. Further studies are required to understand the roles of neutrophil and lymphocyte counts, their temporal trends and the prognostic significance of these trends.
SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools (2006)

With SinicView, users can use their own data sequences to compare various alignment tools or scoring systems and select the most suitable one to perform alignment in the initial stage of sequence analysis.
Performance of proportional fair frequency and time domain scheduling in LTE uplink (2009)

Channel-aware scheduling is one of the advanced features introduced in the uplink of long term evolution (LTE) in order to improve the system spectral efficiency. In the uplink of LTE channel-aware scheduling is possible thanks to the transmission of sounding reference signals. In this paper the performance of frequency and time domain scheduling in LTE uplink is investigated. In particular, we focus on the performance impact of various scheduling metrics which try to achieve proportional fairness in throughput or resource allocation. Our analysis shows that a combination of a throughput-based metric in the time domain and an SINR-based metric in the frequency domain is able to provide the highest performance. For example, in a noise-limited propagation environment with high inter-site distance the sector throughput gain compared to performing throughput-based proportional fair scheduling in both time and frequency domain is above 20%.
Dihydropyridine-like effects of amiodarone and desethylamiodarone on thyrotropin secretion and intracellular calcium concentration in rat pituitary (1995)

Amiodarone (AM) and its major metabolite desethylamiodarone (DEA) are structurally similar to biologically active thyroid hormones. Amiodarone therapy is frequently associated with impairment of thyrotropic function, whose mechanisms are still controversial. Besides its effect on nuclear thyroid hormone binding. AM is able to displace dihydropyridine (DH) binding on membrane preparations from several tissues. By perifusing rat pituitary fragments and measuring thyrotropin (TSH) release we examined: the effect of AM on Ca(2+)-dependent and DHP-sensitive potentiation of the TSH response to thyrotropin-releasing hormone (TRH) induced by either triiodothyronine (T3, perifused for only 30 min before a TRH pulse) or by the prepro-TRH peptide 160-169 (PS4); and the effect of DEA on TRH-induced TSH response in the presence or absence of the DHP nifedipine. We show that AM reverses T3 or PS4 potentiation of the TSH response to TRH; this effect is specific because AM does not modify ionomycin potentiation of that response. In contrast, DEA significantly potentiates the TSH response to TRH and the DHP nifedipine reverses that potentiation. We also tested whether AM would change the acute T3-induced increase in intracellular Ca2+ concentration by measuring intracellular Ca2+ ([Ca2+])i with fura-2 imaging on primary cultures of pituitary cells. We show that AM reverses the effect of T3 on [Ca2+]i as well as the PS4-induced increase in [Ca2+]i. In contrast, DEA increases [Ca2+]i and nifedipine reverses this effect. Our results suggest that AM and DEA display DHP-like effects on TRH-induced TSH release, behaving either as a Ca2+ channel blocker (AM) or as a Ca2+ channel agonist (DEA).
Pulmonary Hypertension (1995)

Administration of iopromide for pulmonary angiography in patients with pulmonary hypertension resulted in no appreciable hemodynamic alterations associated with the observed changes in atrial natriuretic peptide, antidiuretic hormone, and renin. No allergy-mediated reactions were observed in these patients.
On the sum of chemical reactions (2022)

It is standard in chemistry to represent a sequence of reactions by a single overall reaction, often called a complex reaction in contrast to an elementary reaction. Photosynthesis $6 \text{CO}_2+6 \text{H}_2\text{O} \longrightarrow \text{C}_6\text{H}_{12}\text{O}_6 + 6 \text{O}_2$ is an example of such complex reaction. We introduce a mathematical operation that corresponds to summing two chemical reactions. Specifically, we define an associative and non-communicative operation on the product space ${\mathbb{N}}_0^n\times {\mathbb{N}}_0^n$ (representing the reactant and the product of a chemical reaction, respectively). The operation models the overall effect of two reactions happening in succession, one after the other. We study the algebraic properties of the operation and apply the results to stochastic reaction networks (RNs), in particular to reachability of states, and to reduction of RNs.
PREOPERATIVE PROSTATE NEEDLE BIOPSY p27 CORRELATES WITH SUBSEQUENT RADICAL PROSTATECTOMY p27, GLEASON GRADE AND PATHOLOGICAL STAGE (2000)

Expression of p27 in prostate biopsies can be used to predict the degree of expression in radical prostatectomy specimens. As loss of p27 protein expression in prostatectomy specimens has been shown to correlate with biochemical recurrence and shortened prostate specific survival, these results suggest that biopsy p27 may help identify high risk patients preoperatively.
Digital nanoliter to milliliter flow rate sensor with in vivo demonstration for continuous sweat rate measurement (2018)

Microfluidic flow rate sensors have constraints in both detection limits and dynamic range, and are not often easily integrated into lab-on-chip or wearable sensing systems. We constructed a flow rate sensor that easily couples to the outlet of a microfluidic channel, and measures the flow rate by temporarily shorting periodic droplets generated between two electrodes. The device was tested in a dynamic range as low as 25 nL min-1 and as high as 900 000 nL min-1 (36 000× range). It was tested to continuously operate up to ∼200 hours. The device is also simple to fabricate, requiring inexpensive parts, and is small enough to be integrated into wearable devices. The required input pressure is as low as 370 Pascals. An ultra-low flow rate application was demonstrated for wearable sweat biosensing where sweat generation rates (nL min-1 per gland) were accurately measured in human subjects. The digital nanoliter device provides real-time flow rates for sweat rates and may have other applications for low flow rates in microfluidic devices.
A Convenient Method for the Preparation of 3-Azetidinylidene Acetic Acid (1999)

Abstract A facile route to novel 3-azetidinylidene acetic acid from commercially available epichlorohydrin is described.
ChemInform Abstract: Direct Arylation of Dithienylperfluorocyclopentenes via Palladium‐Catalyzed C—H Bond Activation: A Simpler Access to Photoswitches. (2012)

Abstract The use of cyclopentyl methyl ether as the solvent is found to be crucial to avoid decomposition of the reactants and the products.
Importance of Preferential Flow and Soil Management in Vertical Transport of a Biocontrol Strain of Pseudomonas fluorescens in Structured Field Soil (1996)

The large-scale release of wild-type or genetically modified bacteria into the environment for control of plant diseases or for bioremediation entails the potential risk of groundwater contamination by these microorganisms. For a model study on patterns of vertical transport of bacteria under field conditions, the biocontrol strain Pseudomonas fluorescens CHA0, marked with a spontaneous resistance to rifampin (CHA0-Rif), was applied to a grass-clover ley plot (rotation grassland) and a wheat plot. Immediately after bacterial application, heavy precipitation was simulated by sprinkling, over a period of 8 h, 40 mm of water containing the mobile tracer potassium bromide and the dye Brilliant Blue FCF to identify channels of preferential flow. One day later, a 150-cm-deep soil trench was dug and soil profiles were prepared. Soil samples were extracted at different depths of the profiles and analyzed for the number of CHA0-Rif cells and the concentration of bromide and Brilliant Blue FCF. Dye coverage in the soil profiles was estimated by image analysis. CHA0 was present at 10(sup8) CFU/g in the surface soil, and 10(sup6) to 10(sup7) CFU/g of CHA0 was detected along macropores between 10 and 150 cm deep. Similarly, the concentration of the tracer bromide along the macropores remained at the same level below 20 cm deep. Dye coverage in lower soil layers was higher in the ley than in the wheat plot. In nonstained parts of the profiles, the number of CHA0-Rif cells was substantially smaller and the bromide concentration was below the detection limit in most samples. We conclude that after heavy rainfall, released bacteria are rapidly transported in large numbers through the channels of preferential flow to deeper soil layers. Under these conditions, the transport of CHA0-Rif is similar to that of the conservative tracer bromide and is affected by cultural practice.
Analysis of middle ear mechanics and application to diseased and reconstructed ears. (1997)

Sound can be transmitted from the car canal to the cochlea via two mechanisms: the tympano-ossicular system (ossicular coupling) and direct acoustic stimulation of the oval and round windows (acoustic coupling). Acoustic coupling is negligibly small in normal ears, but can play a significant role in some diseased and reconstructed ears. In the normal ear, middle ear pressure gain (which is the result of ossicular coupling) is frequency-dependent and less than generally believed. The severity of conductive hearing loss due to middle-ear disease or after tympanoplasty surgery can be predicted by the degree to which ossicular coupling, acoustic coupling, and stapescochlear input impedance are altered. Hearing after type IV and V tympanoplasty is determined solely by acoustic coupling. The difference in magnitude between the oval- and round-window pressures is more important than the difference in phase in determining cochlear input. In tympanoplasty types I, II, and III, adequate middle-ear and round-window aeration is necessary and the tympanic membrane-ossicular configuration may be less crucial.
Continuously variable W-band phase shifters based on MEMS-actuated conductive fingers (2013)

This paper presents four continuously variable W-band phase shifters in terms of design, fabrication, and radiofrequency (RF) characterization. They are based on low-loss ridge waveguide resonators tuned by electrostatically actuated highly conductive rigid fingers with measured variable deflection between 0.3° and 8.25° (at a control voltage of 0–27.5 V). A transmission-type phase shifter based on a tunable highly coupled resonator has been manufactured and measured. It shows a maximum figure of merit (FOM) of 19.5°/dB and a transmission phase variation of 70° at 98.4 GHz. The FOM and the transmission phase shift are increased to 55°/dB and 134°, respectively, by the effective coupling of two tunable resonances at the same device with a single tuning element. The FOM can be further improved for a tunable reflective-type phase shifter, consisting of a transmission-type phase shifter in series with a passive resonator and a waveguide short. Such a reflective-type phase shifter has been built and tested. It shows a maximum FOM of 101°/dB at 107.4 GHz. Here, the maximum phase shift varied between 0° and 377° for fingers deflections between 0.3° and 8.25°.
Voxel-based Viterbi Active Speaker Tracking (V-VAST) with best view selection for video lecture post-production (2011)

An automated system is presented for reducing a multi-view lecture recording into a single view video containing a best view summary of active speakers. The system uses skin color detection and voxel-based analysis in locating likely speaker locations. Using time-delay estimates from multiple micro phones, speech activity is analyzed for each speaker position. The Viterbi algorithm is then used to estimate a track of the active speaker which maximizes the observed speech activity. This novel approach is termed Voxel-based Viterbi Active Speaker Tracking (V-VAST) and is shown to track speakers with an accuracy of 0.23m. Using the tracking information, the system then extracts from the available camera views the most frontal face view of the active speaker to display.
The Transcriptional Regulator Sin3A Contributes to the Oncogenic Potential of STAT3 (2019)

Epigenetic silencing of promoter and enhancer regions is a common phenomenon in malignant cells. The transcription factor STAT3 is aberrantly activated in several tumors, where its constitutive acetylation accounts for the transcriptional repression of a number of tumor suppressor genes (TSG) via molecular mechanisms that remain to be understood. Using nucleophosmin-anaplastic lymphoma kinase-positive (NPM-ALK<sup>+</sup>) anaplastic large-cell lymphoma (ALCL) as model system, we found in cells and patient-derived tumor xenografts that STAT3 is constitutively acetylated as a result of ALK activity. STAT3 acetylation relied on intact ALK-induced PI3K- and mTORC1-dependent signaling and was sensitive to resveratrol. Resveratrol lowered STAT3 acetylation, rescued TSG expression, and induced ALCL apoptotic cell death. STAT3 constitutively bound the Sin3A transcriptional repressor complex, and both STAT3 and Sin3A bound the promoter region of silenced TSG via a resveratrol-sensitive mechanism. Silencing SIN3A caused reexpression of TSG, induced ALCL apoptotic cell death <i>in vitro</i>, and hindered ALCL tumorigenic potential <i>in vivo</i>. A constitutive STAT3-Sin3A interaction was also found in breast adenocarcinoma cells and proved critical for TSG silencing and cell survival. Collectively, these results suggest that oncogene-driven STAT3 acetylation and its constitutive association with Sin3A represent novel and concomitant events contributing to STAT3 oncogenic potential. SIGNIFICANCE: This study delineates the transcriptional regulatory complex Sin3A as a mediator of STAT3 transcriptional repressor activity and identifies the STAT3/Sin3A axis as a druggable target to antagonize STAT3-addicted tumors. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/79/12/3076/F1.large.jpg.<i>See related commentary by Monteleone and Poli, p. 3031</i>.
Preparation of graphene with few defects using expanded graphite and rose bengal (2012)

We report an easy exfoliation technique using expanded graphite and rose bengal that requires shorter sonication time compared to that of currently reported methods in order to produce an aqueous graphene dispersion and high-quality graphene sheets with few defects. This is a simple method for graphene preparation using expanded graphite and rose bengal (RB) with amphiphilic properties as a surfactant in a short reaction time. RB with a hydrophilic carboxyl group and a hydrophobic aromatic group helps to separate the expanded graphite (EG) layers and prevents reformation of the exfoliated graphene layersvia electrostatic repulsion. The obtained graphene flakes showed oxygenated sp3carbon on the sheet edge and consisted mostly of mono- and few-layer graphene with lateral dimensions of a few hundred nanometres. This method facilitates graphene preparation for various applications.
The halogen bond in crystal chemistry and beyond (2017)

According to the recommendation recently issued by an IUPAC Committee, the halogen bond is the net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity [1]. Two distinctive features of the halogen bond are its directionality and the tunability of its strength. There is in fact a remarkable tendency of nucleophilic species to enter the elongation of the carbon-halogen covalent bond as this is the region of the halogen where the electrostatic potential is most positive. The strength of halogen bonds increases with the polarizability of the halogen atom, namely moving from fluorine to chlorine, to bromine, to iodine and with the electron withdrawing ability of groups neighboring the halogen. Thanks to these two features described above, the halogen bond impacts in all fields where molecular recognition and selfassembly processes have a role. In this lecture it will be discussed how haloperfluorocarbon residues are particularly good halogen bond donors and how halogen bond driven self-assembly processes allow for the preparation of two-, three-, and four-component co-crystals by design. The obtained systems may contain zero-dimensional adducts or one-, two-, or three-dimensional networks. A nice control of the metric and topology of the crystalline solids can be obtained. It will be described, for instance, how a library of halogen bonded Borromean networks was obtained by design [2]. It will be presented how the XB is robust enough from the structural point of view to control the packing of molecular materials in the solid and their organization in the liquid and it will be shown how the interaction can be used to turn on, to turn off, and/or to tune useful functional properties [3]. For instance, the formation of supramolecular gels and liquid crystals will be described and the effectiveness of the interaction in driving the self-assembly and performances of lightresponsive supramolecular polymers will be considered [3]. Finally, we will discuss how the halogen bond is robust enough from the conceptual point of view to enable for the collective understanding of the general ability of various groups in the Periodic Table, in addition to halogens, to form attractive interactions with nucleophiles. The mindset developed in relation to the halogen bond studies favored the rationalization that the elements of the chalcogen, pnictogen, and tetrel groups can all form attractive interactions with nucleophiles as the result of an overlooked anisotropic distribution of the electron density around the atoms. Same crystals where tetrel and chalcogen bonds control the lattice will be briefly presented.
A click chemistry approach to C3 symmetric, G-quadruplex stabilising ligands (2010)

Described is the structure-based design and synthesis of a series of tris-triazole G-quadruplex binding ligands utilising the copper catalysed azide-alkyne 'click' reaction. The results of G-quadruplex stabilisation by the ligands are reported and discussed.
Identification of SCL and LMO Oncogenes as Transcriptional Repressors of HEB/E2A in the Thymus through Functional Genomic/Genetic Approaches. (2007)

Abstract The SCL and LMO oncogenes are frequently activated in childhood T cell acute leukemia (T-ALL). SCL is a bHLH transcription factor that forms heterodimers with other members, specifically HEB and E2A. SCL can either activate or repress transcription but its mechanism of action as an oncogene remains to be clarified. Ectopic expression of SCL and LMO in transgenic mice causes thymocyte differentiation arrest during the preleukemic phase with aberrant differentiation at the DN3–DN4 stage, prior to the acquisition of CD4 and CD8. We therefore took several approaches to define the mechanism underlying this differentiation arrest. Using a CD3e-deficient background to eliminate preTCR signaling effects, an event that is not essential for leukemogenesis, we first analyzed global gene expression of pre-leukemic SCLtg/LMOtg DN3 thymocytes against their non-transgenic littermates via the Affymetrix platform. In this context, SCL/LMO globally affects the expression of both positive and negative targets of E2A/HEB. These results were confirmed by real-time quantitative PCR, showing that SCL/LMO repress E2A/HEB activity. Second, bioinformatic analysis of genes significantly affected by SCL/LMO allowed us to identify phylogenetically conserved HEB/E2A binding sites within the promoter regions of half of these genes. E2A/HEB binding was directly assessed through chromatin immunoprecipitation of primary thymocytes, confirming known target genes and revealing novel ones. This assay also showed that SCL associates with HEB and/or E2A on DNA. Moreover, structure function analysis indicate that transcription inhibition by SCL depends on its HLH domain but not on LMO interaction. We therefore conclude that SCL inhibits thymocyte differentiation by inhibiting E2A/HEB targets that include genes required for thymocyte differentiation, cell signalling, DNA repair and replication. Finally, using a genetic approach we show that SCL/LMO collaborates with HEB haploinsufficiency in inducing leukemia. Our observations therefore reveal that the repression of HEB/E2A by SCL/LMO is a crucial step in T cell transformation. Support from CIHR and FRSQ.
The effect of passivation on different GaAs surfaces (2013)

The surface passivation of semiconductors on different surface orientations results in vastly disparate effects. Experiments of GaAs/poly(3,4-ethylenedioxythiophene/indium tin oxide solar cells show that sulfur passivation results in threefold conversion efficiency improvements for the GaAs (100) surface. In contrast, no improvements are observed after passivation of the GaAs (111B) surface, which achieves 4% conversion efficiency. This is explained by density-functional theory calculations, which find a surprisingly stable (100) surface reconstruction with As defects that contains midgap surface states. Band structure calculations with hybrid functionals of the defect surface show a surface state on the undimerized As atoms and its disappearance after passivation.