gebhart/patrepeval huggingface dataset:
Capillary electrophoresis of synthetic peptide standards varying in charge and hydrophobicity (2003)

A mixture of eight structurally closely related synthetic peptides as capillary electrophoretic (CE) standards is introduced. The almost identical mass-to-charge ratio of the standards, coupled with their random-coil (i.e., no secondary structure) nature, offer a potent analytical test for CE to separate peptides varying only subtly in hydrophobicity. Parameters varied to effect a separation included background electrolyte concentration, temperature, applied voltage in capillary zone electrophoresis (CZE in uncoated capillaries), as well as the introduction of hydrophobic mechanisms to the separation either through the use of micelles or C8-coated capillaries. Our step-by-step approach culminated in an optimized combination of a CZE mechanism for separation of differently charged peptide groups (based on common mass-to-charge ratio) and an ion-pairing mechanism (effecting a separation within each group of identically charged peptides), which we have termed ion-interaction CZE or II-CZE. The study clearly shows how the peptide standards allow an excellent assessment of the resolving power of CE.
Radical and ionic nucleophilic substitution reactions on α-Alkyl-γ-(p-nitrophenyl)allyl derivatives (1983)

The nature of the reaction between a-alkyl-?-(p-nitrophenyl)allyl chlorides (1)-(3), which have the general form p -O2NC6H4CH=CHCH(Cl)R, and a variety of nucleophiles depends on the alkyl group R and the nucleophile. The chloride (1) (R = Me) undergoes ionic (SN2 and subsequent Michael addition) processes with the salt (7) of 2-nitropropane to give products (15) and (16) whereas the chloride (2) (R = Pr1) gives a mixture of products (17) and (18) which are shown to arise by a radical-chain nucleophilic substitution process, with allylic rearrangement-an SRNl' reaction-and ionic processes respectively. The chloride (3) (R = But) gives the SRN1' product (25) with the salt (7). Other nucleophiles with (2) and (3) appear to react by ionic (SN2 and SN2') and/or SRNl' processes; e.g. (3) gives an excellent yield of the malononitrile (32) by an SN2' process when treated with the sodium salt (9).
Bayesian Analysis of an Epidemiologic Model of Plasmodium falciparum Malaria Infection in Ndiop, Senegal (2000)

Plasmodium falciparum has a complex transmission cycle. Public health planning and research would benefit from the ability of a calibrated model to predict the epidemiologic characteristics of populations living in areas of malaria endemicity. This paper describes the application of Bayesian calibration to a malaria transmission model using longitudinal data gathered from 176 subjects in Ndiop, Senegal, from July 1, 1993, to July 31, 1994. The model was able to adequately predict P. falciparum parasitemia prevalence in the study population. Further insight into the dynamics of malaria in Ndiop was provided. During the dry season, the estimated fraction of nonimmune subjects goes down to 20% and then increases up to 80%. The model-predicted time-weighted average incidences contributed by nonimmune and immune individuals are 0.52 cases per day and 0.47 cases per day, respectively. The median times needed to acquire infection (conversion delay) for nonimmune and immune individuals are estimated at 39 days and 285 days, respectively.
CO<sub>2</sub>-Responsive polymer materials (2016)

This paper reviews the chemical fundamentals of CO<sub>2</sub>-responsive polymers as well as the latest reported “smart” material systems switched by CO<sub>2</sub>.
Isothermally Sensitive Detection of Serum Circulating miRNAs for Lung Cancer Diagnosis (2013)

Tumor-derived miRNAs in serum are emerging as the new noninvasive biomarkers for the diagnosis of human cancers, especially at their early stage. An ideal method with high sensitivity, excellent selectivity, a simple procedure, and small amounts of starting materials is imperative for the detection of clinic circulating miRNAs. Here, we develop a new method for isothermally sensitive detection of serum miRNAs using hairpin probe-based rolling circle amplification (HP-RCA). This method exhibits ultrahigh sensitivity toward lung cancer-related miR-486-5p with a detection limit of as low as 10 fM and a large dynamic range of 6 orders of magnitude, and it can even discriminate miR-486-5p from both miRNAs with high sequence homology and its precursors (pre-miRNAs). More importantly, this method can directly and accurately distinguish the expression of serum miR-486-5p among six nonsmall-cell lung carcinoma (NSCLC) patients and six healthy persons, holding a great potential for further applications in the clinical diagnosis of lung cancers.
Self-contained indoor positioning on off-the-shelf mobile devices (2010)

We introduce a novel self-contained seamless positioning solution for indoor and outdoor environments, well suited for and designed to be operated on off-the-shelf mobile phones. Position information is deduced from a combination of GNSS where available, combined with Pedestrian Dead Reckoning (PDR) utilizing inertial measurements and context-aware activity based map matching. The proposed system heavily exploits different types of human movement, such as walking, running, ascending or descending stairs, to improve the employed positioning model. In remaining independent from any external infrastructure, accurate localization is also possible in environments, where the installation and maintenance of such infrastructure does not make sense or is simply not affordable - as for example in a parking garage to guide a user to the next exit or back to his car. Concerning this particular use case we have also implemented an interface for the synchronization of location information between the mobile positioning solution and the car.
A Prospective 9-Month Human Clinical Evaluation of Laser-Assisted New Attachment Procedure (LANAP) Therapy (2014)

This investigation was designed and implemented as a single-center, prospective study to evaluate the clinical response to the Laser-Assisted New Attachment Procedure (LANAP). Eight patients with advanced periodontitis were enrolled and treated with full-mouth LANAP therapy and monitored for 9 months. Fullmouth clinical measurements, including clinical attachment level (CAL), probing depth (PD), and recession, were provided at baseline and after 9 months of healing by a single calibrated examiner, including a total of 930 sites and 444 sites with initial PD equal to or greater than 5 mm. Clinical results for the 930 sites measured pre- and postoperatively revealed that mean PD was reduced from 4.62 ± 2.29 mm to 3.14 ± 1.48 mm after 9 months (P < .05). CAL decreased from 5.58 ± 2.76 mm to 4.66 ± 2.10 mm (P < .05) and recession increased from 0.86 ± 1.31 mm to 1.52 ± 1.62 after 9 months (P < .05). For the subset of 444 sites with initial PD greater than or equal to 5 mm, the PD decreased from 6.50 ± 2.07 mm to 3.92 ± 1.54 mm (P < .05) and CAL decreased from 7.42 ± 2.70 mm to 5.78 ± 2.06 mm (P < .05). As demonstrated by the clinical evaluation, the majority of treated sites demonstrated clinical improvement. LANAP therapy should be further investigated with long-term clinical trials to compare the stability of clinical results with conventional therapy.
A monolithic 10-bit A/D using I/sup 2/L and LWT thin-film resistors (1978)

Describes the function, circuit details, and performance of a monolithic 10-bit A/D converter. The converter is a successive approximation type using linear compatible I/SUP 2/L for the SAR. The converter is completely self-contained, including both clock and voltage reference. Biasing is arranged to take advantage of naturally occurring interfaces in the circuitry, simplifying the overall circuit in comparison to discrete or hybrid approaches. The processing also includes on-chip thin-film resistors which are laser-wafer-trimmed (LWR) for overall accuracy and temperature stability. The finished circuits operate with no missing codes over the -55/spl deg/ to +125/spl deg/C temperature range.
Direct Observation of Ferroelectric Domains in Solution-Processed CH<sub>3</sub>NH<sub>3</sub>PbI<sub>3</sub> Perovskite Thin Films (2014)

A new generation of solid-state photovoltaics is being made possible by the use of organometal-trihalide perovskite materials. While some of these materials are expected to be ferroelectric, almost nothing is known about their ferroelectric properties experimentally. Using piezoforce microscopy (PFM), here we show unambiguously, for the first time, the presence of ferroelectric domains in high-quality β-CH3NH3PbI3 perovskite thin films that have been synthesized using a new solution-processing method. The size of the ferroelectric domains is found to be about the size of the grains (∼100 nm). We also present evidence for the reversible switching of the ferroelectric domains by poling with DC biases. This suggests the importance of further PFM investigations into the local ferroelectric behavior of hybrid perovskites, in particular in situ photoeffects. Such investigations could contribute toward the basic understanding of photovoltaic mechanisms in perovskite-based solar cells, which is essential for the further enhancement of the performance of these promising photovoltaics.
Distributed visualization at Los Alamos National Laboratory (1989)

Several approaches to visualizing simulated data are described. It is noted that a centralized video animation facility represents the state of the art in scientific visualization, but is too expensive to replicate widely. Methods used at LANL for connecting supercomputers with display units, ranging from dumb terminals to powerful workstations, are also described. Of particular interest is the Scientific Visualization Workbench, an inexpensive and effective way of using 'televisualization' to move data from supercomputer to user and to modify the user's display. The implication of higher speed networks are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Conjugated Polymers for Optoelectronic Applications (2008)

Abstract Novel conjugated polymers containing carbazole, phenothiazine or triphenylamine units in the main chain were designed and synthesized via Wittig, Knovenagel or Heck condensations respectively. A majority of them have good solubility in common organic solvents, high thermal stability and good hole‐injection ability. Their diluted solutions in THF showed strong absorption with the absorption maximum in the range of 294∼470 nm and the optic band gaps located in the range of 1.90∼2.75 eV. When irradiated by ultraviolet or visible light, the diluted solutions in THF of the polymers emitted light from purple to yellow color with the emission maximum in the range of 347∼597 nm and the full width at half maximum located in the range of 59∼119 nm. Several polymeric light‐emitting diodes (PLEDs) devices were fabricated using these polymers as light‐emitting materials, and a double‐layer device composed of ITO/PEDOT:PSS/PQTN/Mg:Ag showed a good performance, in which the maximum brightness was measured as 2434.0 cd/m 2 under a 11.0 V forward bias voltage. Photovoltaic devices were also investigated using these polymers as an active layer, and a device composed of ITO/PNB/PTCDI‐C 13 /Al showed a good performance, which was estimated to have external quantum efficiency at around 1% at 330 nm. From these preliminary experimental results, we may infer that these polymers are good light‐emitting materials for PLEDs; while for photovoltaic applications, their absorption spectra need to be further improved to match the solar illumination.
Fully-Adaptive Feature Sharing in Multi-Task Networks with Applications in Person Attribute Classification (2017)

Multi-task learning aims to improve generalization performance of multiple prediction tasks by appropriately sharing relevant information across them. In the context of deep neural networks, this idea is often realized by hand-designed network architectures with layers that are shared across tasks and branches that encode task-specific features. However, the space of possible multi-task deep architectures is combinatorially large and often the final architecture is arrived at by manual exploration of this space, which can be both error-prone and tedious. We propose an automatic approach for designing compact multi-task deep learning architectures. Our approach starts with a thin multi-layer network and dynamically widens it in a greedy manner during training. By doing so iteratively, it creates a tree-like deep architecture, on which similar tasks reside in the same branch until at the top layers. Evaluation on person attributes classification tasks involving facial and clothing attributes suggests that the models produced by the proposed method are fast, compact and can closely match or exceed the state-of-the-art accuracy from strong baselines by much more expensive models.
Olfactory epithelium amyloid‐β and paired helical filament‐tau pathology in Alzheimer disease (2009)

These data demonstrate that AD pathology in the OE is present in the majority of cases with pathologically verified AD and correlates with brain pathology. Future work may assess the utility of amyloid-beta and PHFtau measurement in OE as a biomarker for AD.
Swirling Flow Through Venturi Tubes of Convergent Angle 10.5° and 21° (2006)

Computational Fluid Dynamics (CFD) was used to compute the effect of two bends in perpendicular planes on the performance of 4-inch Venturi tubes with β = 0.4, 0.6 and 0.75 for water at a Reynolds number of 350,000 and at various distances from the bend. Two types of Venturi tubes were analysed, the first having a standard convergent angle of 21°, the second having a non-standard convergent angle of 10.5°. Good agreement with experiment was obtained. Swirling axisymmetric flows were computed to help interpret experimental data.
Oxidative stress causes enhanced endothelial cell injury in human heme oxygenase-1 deficiency (1999)

The first known human case of heme oxygenase-1 (HO-1) deficiency is presented in this report. The patient is a six-year-old boy with severe growth retardation. He has been suffering from persistent hemolytic anemia characterized by marked erythrocyte fragmentation and intravascular hemolysis, with paradoxical increase of serum haptoglobin and low bilirubin. An abnormal coagulation/fibrinolysis system, associated with elevated thrombomodulin and von Willebrand factor, indicated the presence of severe, persistent endothelial damage. Electron microscopy of renal glomeruli revealed detachment of endothelium, with subendothelial deposition of an unidentified material. Iron deposition was noted in renal and hepatic tissue. Immunohistochemistry of hepatic tissue and immunoblotting of a cadmium-stimulated Epstein-Barr virus-transformed lymphoblastoid cell line (LCL) revealed complete absence of HO-1 production. An LCL derived from the patient was extremely sensitive to hemin-induced cell injury. Sequence analysis of the patient's HO-1 gene revealed complete loss of exon-2 of the maternal allele and a two-nucleotide deletion within exon3 of the paternal allele. Growth retardation, anemia, iron deposition, and vulnerability to stressful injury are all characteristics observed in recently described HO-1 targeted mice. This study presents not only the first human case of HO-1 deficiency but may also provide clues to the key roles played by this important enzyme in vivo.
Common problems in the management of hypertriglyceridemia. (2002)

Case 

A 41-year-old man presents for assessment of severe hypertriglyceridemia. He has previously been well. His lipid levels were checked because his serum appeared milky on screening for dyslipidemia. He has no history of abdominal pains, his medical history is unremarkable (in particular, no
Differential CD4 T Cell Activation in Measles (1993)

Measles is associated with a vigorous antibody response without production of significant measles virus-specific delayed type hypersensitivity. Generalized disruption of immune responses also occurs during measles, including depressed skin test responses and decreased in vitro lymphocyte proliferation to mitogens. To determine if preferential activation of a subset of CD4 cells might explain these observations, the patterns of cytokines produced in vivo and in vitro during measles were determined. Soluble CD4 was elevated in plasma at all times. Interleukin (IL)-2 was increased in plasma during and shortly after the clearance of the rash and then declined. Plasma IL-4 became elevated after resolution of the rash and remained elevated in some patients through the 7-week study period. Mononuclear cells proliferated poorly in response to stimulation with anti-CD3 and produced low levels of IL-2 and interferon-gamma and high levels of IL-4 and IL-6 in vitro. The defect in lymphoproliferation during convalescence was partially corrected by in vitro neutralization of IL-4. Preferential activation of type 2 cells late during measles may explain the predominant humoral immune response and the generalized suppression of cellular immune responses.
All-Optical Interrogation of Neural Circuits (2015)

This review describes the nexus of dramatic recent developments in optogenetic probes, genetically encoded activity sensors, and novel microscopies, which together allow the activity of neural circuits to be recorded and manipulated entirely using light. The optical and protein engineering strategies that form the basis of this "all-optical" approach are now sufficiently advanced to enable single-neuron and single-action potential precision for simultaneous readout and manipulation from the same functionally defined neurons in the intact brain. These advances promise to illuminate many fundamental challenges in neuroscience, including transforming our search for the neural code and the links between neural circuit activity and behavior.
Downregulation of MiR-199a Derepresses Hypoxia-Inducible Factor-1α and Sirtuin 1 and Recapitulates Hypoxia Preconditioning in Cardiac Myocytes (2009)

MicroRNAs are posttranscriptional gene regulators that are differentially expressed during various diseases and have been implicated in the underlying pathogenesis. We report here that miR-199a is acutely downregulated in cardiac myocytes on a decline in oxygen tension. This reduction is required for the rapid upregulation of its target, hypoxia-inducible factor (Hif)-1alpha. Replenishing miR-199a during hypoxia inhibits Hif-1alpha expression and its stabilization of p53 and, thus, reduces apoptosis. On the other hand, knockdown of miR-199a during normoxia results in the upregulation of Hif-1alpha and Sirtuin (Sirt)1 and reproduces hypoxia preconditioning. Sirt1 is also a direct target of miR-199a and is responsible for downregulating prolyl hydroxylase 2, required for stabilization of Hif-1alpha. Thus, we conclude that miR-199a is a master regulator of a hypoxia-triggered pathway and can be exploited for preconditioning cells against hypoxic damage. In addition, the data demonstrate a functional link between 2 key molecules that regulate hypoxia preconditioning and longevity.
Electron scattering interaction with coupled plasmon-polar-phonon modes in degenerate semiconductors (1978)

The scattering interaction of Bloch electrons with the coupled systems of electrons and longitudinal-optical phonons in degenerate polar semiconductors is investigated. At degenerate carrier concentrations (${10}^{17}$-${10}^{18}$ ${\mathrm{cm}}^{\ensuremath{-}3}$ in IV-VI and III-V compounds) the free-carrier plasma frequency is comparable to the LO-phonon frequency. This gives rise to electron scattering by strongly coupled plasmon-LO-phonon modes whose resonance frequencies are highly broadened in the particle-hole excitation (Landau damping) region. A generalized expression for the scattering lifetime taking these effects into account is derived in terms of a dielectric response formalism within the random-phase approximation. The factor $\mathrm{Im}(\frac{1}{{\ensuremath{\epsilon}}_{T}})$ appearing in this treatment, where ${\ensuremath{\epsilon}}_{T}$ is the coupled-system dielectric function, modifies the bare Coulomb potential, and together they determine the effective scattering strength of the coupled modes. In the Landau-damping region the scattering strength is highly dispersive with respect to energy and momentum transfers. Calculations that illustrate these interaction effects are performed for PbTe and GaAs.
Concomitant epigenetic targeting of LSD1 and HDAC synergistically induces mitochondrial apoptosis in rhabdomyosarcoma cells (2017)

The lysine-specific demethylase 1 (LSD1) is overexpressed in several cancers including rhabdomyosarcoma (RMS). However, little is yet known about whether or not LSD1 may serve as therapeutic target in RMS. We therefore investigated the potential of LSD1 inhibitors alone or in combination with other epigenetic modifiers such as histone deacetylase (HDAC) inhibitors. Here, we identify a synergistic interaction of LSD1 inhibitors (i.e., GSK690, Ex917) and HDAC inhibitors (i.e., JNJ-26481585, SAHA) to induce cell death in RMS cells. By comparison, LSD1 inhibitors as single agents exhibit little cytotoxicity against RMS cells. Mechanistically, GSK690 acts in concert with JNJ-26481585 to upregulate mRNA levels of the proapoptotic BH3-only proteins BMF, PUMA, BIM and NOXA. This increase in mRNA levels is accompanied by a corresponding upregulation of BMF, PUMA, BIM and NOXA protein levels. Importantly, individual knockdown of either BMF, BIM or NOXA significantly reduces GSK690/JNJ-26481585-mediated cell death. Similarly, genetic silencing of BAK significantly rescues cell death upon GSK690/JNJ-26481585 cotreatment. Also, overexpression of antiapoptotic BCL-2 or MCL-1 significantly protects RMS cells from GSK690/JNJ-26481585-induced cell death. Furthermore, GSK690 acts in concert with JNJ-26481585 to increase activation of caspase-9 and -3. Consistently, addition of the pan-caspase inhibitor N-benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone (zVAD.fmk) significantly reduces GSK690/JNJ-26481585-mediated cell death. In conclusion, concomitant LSD1 and HDAC inhibition synergistically induces cell death in RMS cells by shifting the ratio of pro- and antiapoptotic BCL-2 proteins in favor of apoptosis, thereby engaging the intrinsic apoptotic pathway. This indicates that combined treatment with LSD1 and HDAC inhibitors is a promising new therapeutic approach in RMS.
Right and Left Atrial Radiofrequency Catheter Therapy of Paroxysmal Atrial Fibrillation (1996)

Successful radiofrequency catheter ablation of drug-refractory daily paroxysmal AF is feasible using linear atrial lesions complemented by focal ablation targeted at arrhythmogenic foci. Ablation only in the right atrium is a safe technique providing limited success, whereas linear lesions in the left atrium significantly increase the incidence of stable restoration of sinus rhythm, the inability to induce sustained AF, and the final success rate. The described technique is promising but must be considered preliminary because significant improvements are required to optimize lesion characteristics and shorten total procedure duration.
Scaling of copper seed layer thickness using plasma-enhanced ALD and an optimized precursor (2011)

A recently developed precursor, AbaCus, has been evaluated for use in ultra-low temperature copper deposition by PEALD. Film adhesion, platability and process window evaluation demonstrate a strong capability of this precursor to overcome current metallization challenges.