gebhart/patrepeval huggingface dataset:
Targeted high-resolution chromosome conformation capture at genome-wide scale (2020)

ABSTRACT Chromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at up to several hundred loci. All 3C methods are affected to varying degrees by inefficiency, bias and noise. As such, generation of reproducible high-resolution interaction profiles has not been achieved at scale. To overcome this barrier, we systematically tested and improved upon current methods. We show that isolation of 3C libraries from intact nuclei, as well as shortening and titration of enrichment oligonucleotides used in high-resolution methods reduces noise and increases on-target sequencing. We combined these technical modifications into a new method Nuclear-Titrated (NuTi) Capture-C, which provides a &gt;3-fold increase in informative sequencing content over current Capture-C protocols. Using NuTi Capture-C we target 8,061 promoters in triplicate, demonstrating that this method generates reproducible high-resolution genome-wide 3C interaction profiles at scale.
The development, safety and efficacy of pacritinib for the treatment of myelofibrosis (2016)

Dysregulation of janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway has been described in myelofibrosis (MF). Currently, there is an unmet need for agents that have the benefit of JAK inhibition, yet also are safe and effective in patients with thrombocytopenia. Areas covered: We discuss the various preclinical and clinical studies describing pacritinib, a selective JAK2/FLT3 inhibitor. So far, it has shown promising results, without significant thrombocytopenia. A PubMed search, using keywords 'pacritinib', 'SB 1518' and 'myelofibrosis' was conducted. Published abstracts from recent national and international meetings were also reviewed for unpublished data. Expert commentary: Currently, pacritinib is on hold by Food and Drugs Administration. It would be imperative to understand if there is a treatment related toxicity that would limit its use. If a safe path is found for this agent, it could have a significant benefit in various settings, based on the data so far.
Strategies for Gasoline Particulate Emission Control - A “Foresight Vehicle” Project (2002)

&lt;div class="htmlview paragraph"&gt;The health threat from sub-100 nm particulates, emitted in significant numbers from gasoline vehicles, and anticipated changes in legislation to address this, have prompted investigation of techniques capable of trapping and oxidizing particulates from gasoline engines. Numerical studies have indicated that cooling to encourage particle capture by thermophoresis is less effective than use of electrostatic fields. A laboratory wire-cylinder electrostatic trap is under development, showing promising initial results. As an alternative trapping technique, the effectiveness of a cordierite wall-flow filter has been demonstrated, in simulation experiments and on a GDI-engined vehicle. Catalysts have been identified for particulate oxidation at typical exhaust temperatures, using water vapour and carbon dioxide as the oxygen source and retaining activity after short-term high-temperature aging.&lt;/div&gt;
A high-average power femtosecond laser for synchrotron light source applications (2007)

We describe a 60W, 70fs, 20kHz Ti:sapphire CPA laser system using cryogenically-cooled amplifiers, currently operating at the Advanced Light Source at LBNL. The system consists of an oscillator, a 20 kHz regenerative preamplifier, and two power amplifiers to produce two output beams, each at 30W. Each power amp can be pumped by two 90 Watt, 10 kHz, diode-pumped, doubled YLF lasers simultaneously (for 10 kHz) or interleaved in time (for 20 kHz). The regen is pumped at 20 kHz and 60W, producing 8W output which is split between the power amps. To maintain the crystals near the thermal conductivity peak at ~50°K, we used 300 Watt cryorefrigerators mechanically decoupled from the optical table. Pulses are compressed in a quartz transmission grating compressor, to minimize thermal distortions of the phase front typical of gold coated gratings at high power density. Transmission through the compressor is >80%, using a single 100 x 100mm grating. One of the 30W output beams is used to produce 70fs electron bunches in the synchrotron light source. The other is delayed by 300ns in a 12-pass Herriot cell before amplification, to be synchronized with the short light pulse from the synchrotron.
Transcranial Magnetic Stimulation Following a Paired Associative Stimulation Protocol Based on a Video Game Neuromodulates Cortical Excitability and Motor Behavior (2022)

Transcranial Magnetic Stimulation (TMS) can be used to modulate cortico-spinal excitability following a paired associative stimulation (PAS) protocol. Movement-related cortical stimulation (MRCS) is a PAS protocol based on the synchronization of a single-pulse TMS with a movement task. However, plasticity and motor performance potentiation due to MRCS has been related exclusively to single-movement tasks. In order to unveil the effects of an MRCS protocol in complex movements, we applied PAS synchronized with a movement-related dynamic task (MRDT) with a customized video game. In 22 healthy subjects, we measured the reaction time (RT), trajectory error (TE), and the number of collected and avoided items when playing the custom video game to evaluate the task motor performance. Moreover, we assessed the recruitment curve of Motor Evoked Potentials (MEPs) with five different intensities to evaluate the motor corticospinal excitability. MEPs were recorded in <i>Abductor Pollicis Brevis</i> (APB) and <i>Abductor Digiti Minimi</i> (ADM), before, right after, and 30 min after the PAS intervention, in an active versus sham experimental design. The MRCS PAS intervention resulted in RT reduction, and motor corticospinal excitability was modulated, reflected as significant MEP amplitude change at 110% RMT intensity in ADM and at 130% RMT intensity in APB. RTs and ADM MEP amplitudes correlated positively in specific time and intensity assessments. We conclude that the proposed PAS protocol facilitated RT performance in a complex task. This phenomenon might be useful to develop neurorehabilitation strategies with complex movements, similar to activities of daily living.
Methods for DNA Strand Breaks Detection (2012)

The study of Deoxyribonucleic Acid (DNA) damage holds a wide interest within both basic and applied fields of research. Elucidating the mechanisms involved in the generation of DNA damage and the consequences of this damage, will have an enormous impact on multiple fields of scientific research and will ultimately lead to a better understanding of human disease. In this review article, a variety of experimental molecular biology techniques will be described.
Change of insulin action with aging in conscious rats determined by euglycemic clamp (1988)

To clarify the mechanism responsible for age-related changes in insulin action, the euglycemic clamp technique was performed with graded doses of insulin in conscious rats aged 2, 4, 10, and 20 mo. Insulin binding (IB) to muscle membranes was also studied. Maximal response of insulin-induced glucose disappearance rate (Rd) was decreased significantly between 2 and 4 mo of age. Dose-response curves shifted to the right progressively up to 20 mo of age. However, IB to the muscle membrane diminished between 1 and 4 mo of age without a decrease thereafter. When Rd was plotted against insulin bound to the membranes, the resulting curves shifted to the right with aging, suggesting a coupling defect between the binding and effector unit. In conclusion, insulin action alters in rats between 2 and 20 mo of age. The most pronounced impairment in IB and maximal response of insulin-induced Rd occurs during early life stage (through maturation) and then a coupling defect seems to be superimposed with further aging. However, we cannot exclude the possibility that these changes may be secondary to obesity or reduced physical activity, rather than aging per se.
Complicações da tireoidectomia (1960)

de difcil acesso.
Comparison of mailed vs. Internet applications of the Delphi technique in clinical informatics research. (2000)

The Delphi technique provides a means of assessing the judgments of groups of experts without the necessity of having these experts meet together. The technique has been used in health care since the mid-1970s, and has just recently become more common in clinical informatics research. As informatics develops as a specialty, it is logical to consider information technology solutions to research as well as clinical practice problems. The overall purpose of this methodology presentation is to compare a mailed vs. Internet application of the Delphi technique for clinical informatics research. Specifically, this presentation will provide: 1) an overview of the Delphi technique, and 2) a methodological comparison of two research applications of the Delphi technique. Results of the studies will be presented elsewhere.
An inductorless injection-locked PLL with 1/2- and 1/4-integral subharmonic locking in 90 nm CMOS (2012)

An inductorless PLL with 1/2- and 1/4-integral as well as integral subharmonic injection locking is realized, which can solve tradeoff between the selectable frequency step and phase noise of injection-locked PLLs (ILPLLs). The proposed ILPLL was fabricated in 90 nm CMOS process (PLL area: 0.083 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , tuning range: 1.1-2.0 GHz). For a 80 MHz reference, it shows that the 1-MHz-offset phase noise is -106 dBc/Hz at 1.8 GHz (= 11.25 × 160 MHz) with injection. A 15-dB reduction is achieved, compared with that in the case without injection.
Development of an Efficient Method for Preparation of 1,3,5‐Trihydroxyisocyanuric Acid (THICA) and Its Use as Aerobic Oxidation Catalyst. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Fine-grained Concept Linking using Neural Networks in Healthcare (2018)

To unlock the wealth of the healthcare data, we often need to link the real-world text snippets to the referred medical concepts described by the canonical descriptions. However, existing healthcare concept linking methods, such as dictionary-based and simple machine learning methods, are not effective due to the word discrepancy between the text snippet and the canonical concept description, and the overlapping concept meaning among the fine-grained concepts. To address these challenges, we propose a Neural Concept Linking (NCL) approach for accurate concept linking using systematically integrated neural networks. We call the novel neural network architecture as the COMposite AttentIonal encode-Decode neural network (COM-AID). COM-AID performs an encode-decode process that encodes a concept into a vector and decodes the vector into a text snippet with the help of two devised contexts. On the one hand, it injects the textual context into the neural network through the attention mechanism, so that the word discrepancy can be overcome from the semantic perspective. On the other hand, it incorporates the structural context into the neural network through the attention mechanism, so that minor concept meaning differences can be enlarged and effectively differentiated. Empirical studies on two real-world datasets confirm that the NCL produces accurate concept linking results and significantly outperforms state-of-the-art techniques.
Analysis of Cuticular Lipids of the Pharaoh Ant (Monomorium pharaonis) and Their Selective Adsorption on Insecticidal Zeolite Powders (2018)

The pharaoh ant is a notorious and hard to eradicate pest, which poses a threat in hospitals, spreading pathogens and contaminating sterile equipment. When applied on ants, zeolites adsorb part of their epicuticular wax layer. The ants are then vulnerable to desiccation, since this layer regulates water exchange. We analyzed the chemical composition of this wax layer using GC-MS (Gas Chromatography-Mass Spectrometry). A hexane wash of <i>M. pharaonis</i> foragers resulted in the identification of 53 components, four of which were not previously defined in <i>Monomorium</i> species. Selective adsorption of specific compounds on zeolites assisted in the identification of compounds which could not be separated on the GC column and allowed for the identification of three additional compounds. Zeolites show different affinities for the wax compounds depending on pore structure and chemical composition. Selective adsorption of alkanes on zeolites is also investigated in the fields of refinery processes and catalysis. Pore mouth and key lock adsorption mechanisms and selectivity according to molecular weight and branching, investigated in these fields, are also involved in adsorption processes of epicuticular waxes. The insecticidal activity of a zeolite is related to adsorption selectivity rather than capacity. One of the best adsorbing zeolites showed limited insecticidal activity and can be considered as a non-lethal alternative for epicuticular wax sampling.
Verbundstrangpressen von Titan‐Aluminium‐Verbindungen (2009)

Abstract Durch die Kombination von unterschiedlichen metallischen Werkstoffen lassen sich maßgeschneiderte Konstruktionen mit optimierten Eigenschaften herstellen. Die Herstellung von Werkstoffverbunden ist jedoch häufig mit hohen Anforderungen an die Fertigungstechnik verbunden. Schwerpunkt dieser Untersuchung ist das Verbundstrangpressen von Aluminium und Titan. Neben den mechanischen Eigenschaften des Verbundes wurden die Ausbildung der Bindungszone sowie die beim Haftungsaufbau wirksamen Bindungsmechanismen untersucht. Hierbei war neben dem Einfluss der Probenvorbereitung vor allem die Wirksamkeit von unterschiedlichen Haftvermittlerschichten von Interesse. Während Schichten aus Kupfer oder Nickel den Haftungsaufbau aufgrund von Oxidschichtbildung verhindern, können durch Umformung eingegossener Titankerne Festigkeiten von über 100 MPa erreicht werden. Im Vergleich zu alternativen Fügeverfahren tritt eine Beeinträchtigung des Werkstoffgefüges in Form von Wärmeeinflusszonen, Porenbildung oder Grobkornbildung hier nicht auf.
Recovery of B-cell homeostasis after rituximab in chronic graft-versus-host disease (2010)

Investigation of the effects of rituximab (anti-CD20) on B-cell-activating factor of the tumor necrosis factor family (BAFF) and B cells would better define the significance of B-cell homeostasis in chronic graft-versus-host disease (cGVHD) pathophysiology. We studied 20 cGVHD patients at a median of 25 months after rituximab treatment when most patients had recovered total B-cell numbers. A total of 55% of patients had stable/improved cGVHD, and total B-cell numbers in these patients were significantly higher compared with rituximab-unresponsive patients. Although total B-cell number did not differ significantly between cGVHD groups before rituximab, there was a proportional increase in B-cell precursors in patients who later had stable/improved cGVHD. After rituximab, BAFF levels increased in all patients. Coincident with B-cell recovery in the stable/improved group, BAFF/B-cell ratios and CD27(+) B-cell frequencies decreased significantly. The peripheral B-cell pool in stable/improved cGVHD patients was largely composed of naive IgD(+) B cells. By contrast, rituximab-unresponsive cGVHD patients had persistent elevation of BAFF and a predominance of circulating B cells possessing an activated BAFF-R(Lo)CD20(Lo) cell surface phenotype. Thus, naive B-cell reconstitution and decreased BAFF/B-cell ratios were associated with clinical response after rituximab in cGVHD. Our findings begin to delineate B-cell homeostatic mechanisms important for human immune tolerance.
Air-compatible Broadband Angular Selective Material Systems (2015)

An optical broadband angular selective filter achieved by stacking of one-dimensional photonic crystals has promising potential in various applications. In this report, we demonstrate the first experimental realization of an optical broadband angular selective filter capable of operation in air, in contrast to our previous demonstration in index matching liquid.
Quantification of tumour budding, lymphatic vessel density and invasion through image analysis in colorectal cancer (2014)

We demonstrate methodology through image analysis which can standardise the quantification of TB, LVD and LVI from a single tissue section while decreasing observer variability. We suggest this technology is capable of stratifying a high risk Dukes B CRC subpopulation and we show the three histopathological features to be of prognostic significance.
Practical Considerations in Quantitative Short Extension Strategies (2008)

This article analyzes short extension strategies under realistic scenarios in portfolio construction, where the portfolio strategy includes constraints such as tracking error, industry bets, asset level bounds, and turnover. Further, it considers a systematic tool, called Constraint Attribution, to analyze the impact of these constraints on the realized active returns of portfolios in a historical backtest study. For example, the article compares a 130/30 strategy to its long-only counterpart in backtest studies using two different expected return data as well as varying tracking error limits. It further studies the effect of using a fixed leverage ratio versus a dynamic strategy where the leverage can change over time. Finally, the article analyzes the effect of transaction costs, namely in the form of leverage costs (which may be a combination of borrow costs, short rebate costs, and short-selling costs). It concludes that the appropriate leverage ratio varies through time and depends largely on the 
underlying risk of the market, the tracking error limit, the forecasted returns, and the distribution of the information contained in them.
Evolution of microstructure in amorphous hydrogenated silicon (1982)

Hydrogenated α-Si films prepared by rf sputtering were investigated as a function of film thickness (150 Å to 10 μm) and substrate type and roughness. The physical structure was shown to evolve with film thickness as a result of the nucleation, growth, and incomplete coalescence of ’’island’’-like structures which lead to a supernetwork of larger voids. At least four different supernetwork structures of increasing size were identified in the present study. The structural evolution was essentially unaffected by substrate type for this material in which low adatom mobility is the controlling factor. This evolutionary model is expected to have general application to all vapor-deposition processes including glow-discharge decomposition of silane.
Detection of Lymph Node Involvement in Hematologic Malignancies Using Micromagnetic Resonance Lymphangiography with a Gadolinum-Labeled Dendrimer Nanoparticle (2005)

Animal models of lymphoma should reflect their counterparts in humans; however, it can be difficult to ascertain whether an induced disease is intralymphatic or extralymphatic based on direct visualization. Current imaging methods are insufficient for identifying lymphatic and intralymphatic involvement. To differentiate intralymphatic from extralymphatic involvement, we have developed a magnetic resonance imaging-based lymphangiography method and tested it on two animal models of lymphoma. A gadolinium (Gd)-labeled dendrimer nanoparticle (generation-6; approximately 220 kDa/ approximately 10 nm) was injected interstitially into mice bearing hematologic malignancies to perform dynamic micromagnetic resonance lymphangiography (micro-MRL). Both a standard T1-weighted 3D fast spoiled gradient echo and a T2/T1-weighted 3D fast imaging employing steady-state acquisition (3D-FIESTA-C) were compared in an imaging study to differentiate intralymphatic from extralymphatic involvement of tumors. The lymphatics and lymph nodes were visualized with both methods in all cases. In addition, 3D-FIESTA-C depicted both the lymphatic system and the extralymphatic tumor. In an animal model, 3D-FIESTA-C demonstrated that the bulk of the tumor thought to be intralymphatic was actually extralymphatic. In conclusion, micro-MRL, using Gd-labeled dendrimer nanoparticles with the combined method, can define both the normal and abnormal lymphatics and can distinguish intralymphatic from extralymphatic diseases in mouse models of malignant lymphoma.
Results from Kentucky’s 10-year Bobwhite Recovery Plan (2022)

The northern bobwhite (Colinus virginianus; hereafter, bobwhite) has experienced a precipitous population decline through almost all its historical range over the last 6 decades. We initiated a 10-year restoration plan in Kentucky, USA in 2008 and reported on it through 3 published “Road to Recovery” reports along with 30 peer-reviewed articles and abstracts, 2 technical documents, 7 theses or dissertations, and 11 popular literature pieces. Seven Quail Focus Areas were selected across the state based on site personnel, geographic position (east to west), and land ownership (e.g., private, public, state, federal) for monitoring and habitat management. The focus areas averaged 11,895 acres and area managed for quail on an annual basis ranged from 9% to 42%. Management took the form of herbicide applications, disking, fire, planting, grazing, control of woody vegetation, and mowing. Hierarchical distance sampling models using time-of-removal information to inform detection processes were used to assess bobwhite density on each focus area. Models were based on spring breeding bird point counts in which a suite of grassland songbirds were recorded and fall covey counts in which only bobwhite were recorded. Roadside surveys (direct observation) and hunter harvest information were also used for statewide comparisons of focus areas and statewide trends. Across all years and focus areas a 40% increase in the quail population was observed in 20 years (38%) of the possible 53 years of survey data. Stable to increasing trends were also observed in focal area populations of dickcissel (Spiza americana), eastern meadowlark (Sturnella magna), eastern kingbird (Tyrannus tyrannus), field sparrow (Spizella pusilla), prairie warbler (Setophaga discolor), and Bell’s vireo (Vireo bellii). A focus on habitat management and associated monitoring on relatively small (<20,000 acres) areas was shown to be successful on an individual area, as determined by increases in bird numbers across years and challenges completed in the Quail Plan but did not result in an observed increase in statewide quail indices. Future quail restoration plans in Kentucky should be directed more toward open production land, which is made up of 6 million acres of pastureland, hay land, row crop agriculture, reverting fields, reclaimed mineland, and grasslands. This work will be completed by utilizing working lands, such as field borders in row crop systems and grazing native warm-season grasses in pasture or hay systems, for wildlife activities. Monitoring systems on these production lands will be in the breeding season only and autonomous recording devices will be