gebhart/patrepeval huggingface dataset:
Data from Chemopreventive and Chemotherapeutic Actions of mTOR Inhibitor in Genetically Defined Head and Neck Squamous Cell Carcinoma Mouse Model (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; To assess the efficacy of rapamycin treatment in chemoprevention and chemotherapy of tumorigenesis in a genetically defined mouse model of head and neck squamous cell carcinoma (HNSCC).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental design:&lt;/b&gt; Knockdown of Tgfbr1 and/or Pten using siRNA-mediated RNA interference was carried out in human HNSCC cell lines to analyze molecular changes in the mTOR pathway&lt;i&gt;. Tgfbr1&lt;/i&gt;&lt;sup&gt;flox/flox&lt;/sup&gt;; &lt;i&gt;Pten&lt;/i&gt;&lt;sup&gt;flox/flox&lt;/sup&gt;; K14-CreER&lt;sup&gt;tam&lt;/sup&gt; mice were treated with oral gavage of tamoxifen for the conditional deletion of &lt;i&gt;Tgfbr1&lt;/i&gt; and &lt;i&gt;Pten&lt;/i&gt; in oral mucosa, resulting in HNSCC. &lt;i&gt;Tgfbr1&lt;/i&gt; and &lt;i&gt;Pten&lt;/i&gt; conditonal deletion (2cKO) mice were treated with rapamycin before or after the onset of HNSCC, and the efficacy of this treatment was assessed by determining tumor burden, longevity, and molecular analysis of the mTOR pathway. Molecular changes observed in human HNSCC cell lines and 2cKO mice were compared to identify key alterations in the mTOR pathway.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Knockdown of Tgfbr1 and/or Pten in human HNSCC cell lines resulted in activation of mTOR activity complex 1 and increased levels of survivin. Furthermore, we observed similar changes in HNSCC of the 2cKO mouse. In the human HNSCC tissue array, a loss of Tgfbr1 expression correlated with increased survivin levels. Chemopreventive rapamycin treatment significantly delayed the onset of the HNSCC tumors and prolonged survival in 2cKO mice. In addition, we also found that rapamycin had a therapeutic effect on squamous cell carcinomas in these mice. In 2cKO HNSCC tongue tumors, rapamycin treatment induced apoptosis, inhibited cell proliferation and phosphorylation of Akt and S6, and decreased survivin expression.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These findings indicate that tumorigenesis in 2cKO HNSCC is associated with activation of the Akt/mTOR/survivin pathway, and inhibition of this pathway by rapamycin treatment successfully ameliorates the onset and progression of tumorigenesis. &lt;i&gt;Clin Cancer Res; 18(19); 5304–13. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
A new RTD-FET logic family (1999)

We describe a new family of clocked logic gates based on the resonant-tunneling diode (RTD). Pairs of RTDs form storage latches, and these are connected by networks consisting of field-effect transistors (FETs), saturated resistors, and RTDs. The design, operation, and expected performance of both a shift register and a matched filter using this logic are discussed. Simulations show that the RTD circuits can achieve higher performance in terms of speed and power in many signal processing applications. Compared to circuits using III-V FETs alone, the RTD circuits are expected to run nearly twice as fast at the same power or at the same speed with reduced power. Compared to circuits using Lincoln Laboratory's fully depleted silicon-on-insulator CMOS, implementation using state-of-the-art RTDs should operate five times faster when both technologies follow the CMOS design rules.
ClearT: a detergent- and solvent-free clearing method for neuronal and non-neuronal tissue (2013)

We describe a clearing method for enhanced visualization of cell morphology and connections in neuronal and non-neuronal tissue. Using Clear(T) or Clear(T2), which are composed of formamide or formamide/polyethylene glycol, respectively, embryos, whole mounts and thick brain sections can be rapidly cleared with minimal volume changes. Unlike other available clearing techniques, these methods do not use detergents or solvents, and thus preserve lipophilic dyes, fluorescent tracers and immunohistochemical labeling, as well as fluorescent-protein labeling.
Characterization of polyurethane resins by FTIR, TGA, and XRD (2009)

Abstract Fourier Transformed Infrared Spectroscopy, Thermogravimetric Analysis, and X‐ray Diffractometry have been used to investigate the rigid, semi rigid, and soft polyurethane (PU) forms, which were developed by the Group of Analytic Chemistry and Technology of Polymers ‐ USP ‐ São Carlos. The –NCO/–OH ratios were 0.6, 0.5, and 0.3% for rigid, semi rigid, and soft PUs, respectively, showing that different ratios cause differences in thermal behaviors and crystalline structures of the synthesized PU resins. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Floral Phenology and Morphology of Black Cottonwood, Populus trichocarpa (Salicaceae) (1994)

Seasonal changes in the development of reproductive structures are documented for Populus trichocarpa Torr. and Gray. Buds were collected and studied from several trees for a 2-yr period, but to maintain a congruous phenology, representative structures from only one male and one female tree are presented. Collected tissues were fixed, dehydrated, embedded in wax, sectioned, and differentially stained. The development of reproductive meristems begins early in the spring, before leaves emerge. However, the anatomy of male and female flowers is virtually indistinguishable until late spring. The structures of the gynoecium develop in about 2 wk, then continue to enlarge through the summer and autumn until the trees become dormant. The unilocular ovary consists of usually three, but sometimes four carples. Stamen development begins in the center of a disk-shaped meristematic region and proceeds centrifugally. Megasporogenesis and microsporogenesis take place late in the winter, approximately 2 wk before anthesis. Dissection of mature flowers revealed 30–50 seeds per capsule on female trees and 40–60 stamens on male trees. When compared to most other Populus species, P. trichocarpa has a relatively large number of reproductive structures.
Recent insights into the genotype–phenotype relationship from massively parallel genetic assays (2019)

With the molecular revolution in Biology, a mechanistic understanding of the genotype-phenotype relationship became possible. Recently, advances in DNA synthesis and sequencing have enabled the development of deep mutational scanning assays, capable of scoring comprehensive libraries of genotypes for fitness and a variety of phenotypes in massively parallel fashion. The resulting empirical genotype-fitness maps pave the way to predictive models, potentially accelerating our ability to anticipate the behaviour of pathogen and cancerous cell populations from sequencing data. Besides from cellular fitness, phenotypes of direct application in industry (<i>e.g</i>. enzyme activity) and medicine (<i>e.g</i>. antibody binding) can be quantified and even selected directly by these assays. This review discusses the technological basis of and recent developments in massively parallel genetics, along with the trends it is uncovering in the genotype-phenotype relationship (distribution of mutation effects, epistasis), their possible mechanistic bases and future directions for advancing towards the goal of predictive genetics.
Distributed integrated circuits: an alternative approach to high-frequency design (2002)

Distributed integrated circuits are presented as a methodology to design high-frequency communication building blocks. Distributed circuits operate based on multiple parallel signal paths working in synchronization that can be used to enhance the frequency of operation, combine power, and enhance the robustness of the design. These multiple signal paths usually result in strong couplings inside the circuit that necessitate a treatment spanning architecture, circuits, devices, and electromagnetic levels of abstraction.
What Should/Do/Can LSTMs Learn When Parsing Auxiliary Verb\n Constructions? (2019)

There is a growing interest in investigating what neural NLP models learn\nabout language. A prominent open question is the question of whether or not it\nis necessary to model hierarchical structure. We present a linguistic\ninvestigation of a neural parser adding insights to this question. We look at\ntransitivity and agreement information of auxiliary verb constructions (AVCs)\nin comparison to finite main verbs (FMVs). This comparison is motivated by\ntheoretical work in dependency grammar and in particular the work of Tesni\\`ere\n(1959) where AVCs and FMVs are both instances of a nucleus, the basic unit of\nsyntax. An AVC is a dissociated nucleus, it consists of at least two words, and\nan FMV is its non-dissociated counterpart, consisting of exactly one word. We\nsuggest that the representation of AVCs and FMVs should capture similar\ninformation. We use diagnostic classifiers to probe agreement and transitivity\ninformation in vectors learned by a transition-based neural parser in four\ntypologically different languages. We find that the parser learns different\ninformation about AVCs and FMVs if only sequential models (BiLSTMs) are used in\nthe architecture but similar information when a recursive layer is used. We\nfind explanations for why this is the case by looking closely at how\ninformation is learned in the network and looking at what happens with\ndifferent dependency representations of AVCs. We conclude that there may be\nbenefits to using a recursive layer in dependency parsing and that we have not\nyet found the best way to integrate it in our parsers.\n
Non-Localized Ligand-to-Metal Charge Transfer Excited States in (Cp)2Ti(IV)(NCS)2 (2003)

The bent d(0) titanium metallocene (Cp)(2)Ti(NCS)(2) exhibits an intense phosphorescence from a ligand-to-metal charge transfer triplet excited state at 77 K in an organic glass substrate and a poly(methyl methacrylate) plastic substrate. Quantum chemical calculations and spectroscopic studies show that the orbital parentage of this triplet state arises from the promotion of an electron from an essentially nonbonding symmetry adapted pi molecular orbital located on the NCS(-) ligands to a d(z)2-(y)2 orbital located on the Ti metal. Standard infrared spectroscopy of (Cp)(2)Ti(NCS)(2) in its ground electronic state at 77 K reveals a pair of closely spaced absorptions at (2072 cm(-1), 2038 cm(-1))(glass) and (2055 cm(-1), 2015 cm(-1))(plastic) that are assigned, respectively, to the symmetric and antisymmetric CN stretching modes of the two coordinated NCS(-) ligands. Low-temperature (77 K) time-resolved infrared spectroscopy that accesses the phosphorescing triplet excited state on the ns time scale shows an IR bleach that is coincident with the two ground state CN stretching bands and an associated grow-in of a pair of new IR bands at slightly lower energies (2059 cm(-1), 2013 cm(-1))(glass) and (2049 cm(-1), 1996 cm(-1))(plastic) that are assigned, respectively, to the symmetric and antisymmetric CN stretches in the emitting triplet state. These transient IR bands decay with virtually identical lifetimes to those observed for the phosphorescence decays when measured under identical experimental conditions. Singular value decomposition analysis of the time-resolved infrared data shows that the observed transient IR features arise from the same electronic manifold as measured through luminescence studies. The close similarity between the ground state and excited-state CN stretching bands in (Cp)(2)Ti(NCS)(2) indicates that symmetry breaking does not occur in forming the charge-transfer triplet excited-state manifold; i.e., electron density is withdrawn from a delocalized pi MO spread across both NCS(-) ligands. Calculations at several levels of theory reveal a delocalized ligand-to-metal charge transfer excited triplet manifold. These calculations closely reproduce the relative intensity ratios and frequencies of the symmetric and antisymmetric transient infrared vibrations in the CN region. This study is the first time-resolved infrared investigation of a ligand-to-metal charge-transfer excited state and the first to be performed at cryogenic temperatures in thin-film organic glass and plastic substrates.
Transport in a Grooved Perfusion Flat-Bed Bioreactor for Cell Therapy Applications (1998)

This study considers the transport of oxygen (a growth-associated solute) and lactate (a metabolic byproduct) in a flat-bed perfusion chamber modified to retain cells through the addition of grooves, perpendicular to the direction of flow, at the chamber bottom. The chamber has been successfully applied to hematopoietic cell culture and may be useful for other basic and applied biomedical applications. The objective of this study is to characterize the culture environment in terms of solute transport under various operational conditions. This will allow one to improve the design and operating strategy of the perfusion system for maximizing cell numbers. The system is numerically simulated using the finite element package FIDAP. The reaction kinetics describing oxygen uptake by cells are simplified to zero order to give an upper bound for the oxygen consumption. A flat-bed chamber without grooves is considered here as a benchmark. We show that the growth environment is not oxygen limited (local oxygen concentration above 10 microM) for a variety of flow rates and culture conditions (qO2 = 0.1 micromol/(10(6) cells h)). With a medium flow rate of 2.5 mL/min through the reactor, the model predicts that the 29-cm2 reactor can support at least 33.4 x 10(6) total cells when the inlet medium is in equilibrium with high (20%) oxygen concentration. The culture becomes oxygen limited however for the same flow rate for low (5%) oxygen concentration and can only support 7.2 x 10(6) total cells. Comparison of grooved vs nongrooved chambers reveals that the presence of grooves only affects solute transport on a local scale. This result is attributed to the small size (200 microgram) of the cavities relative to the chamber dimensions. The comparison also yields an empirical relation that allows for rapid estimation of oxygen and lactate concentrations in the grooves using only the numerical simulation of the simpler nongrooved chamber. Finally, our investigation shows that, while decreasing the spacing between cavities decreases the total number of cells the reactor can support, the efficiency of the reactor is increased by 25% (on an area basis) without growth restriction.
Si/a-Si Core/Shell Nanowires as Nonvolatile Crossbar Switches (2008)

Radial core/shell nanowires (NWs) represent an important class of nanoscale building blocks with substantial potential for exploring fundamental electronic properties and realizing novel device applications at the nanoscale. Here, we report the synthesis of crystalline silicon/amorphous silicon (Si/a-Si) core/shell NWs and studies of crossed Si/a-Si NW metal NW (Si/a-Si x M) devices and arrays. Room-temperature electrical measurements on single Si/a-Si x Ag NW devices exhibit bistable switching between high (off) and low (on) resistance states with well-defined switching threshold voltages, on/off ratios greater than 10(4), and current rectification in the on state. Temperature-dependent switching experiments suggest that rectification can be attributed to barriers to electric field-driven metal diffusion. Systematic studies of Si/a-Si x Ag NW devices show that (i) the bit size can be at least as small as 20 nm x 20 nm, (ii) the writing time is <100 ns, (iii) the retention time is >2 weeks, and (iv) devices can be switched >10(4) times without degradation in performance. In addition, studies of dense one-dimensional and two-dimensional Si/a-Si x Ag NW devices arrays fabricated on crystalline and plastic substrates show that elements within the arrays can be independently switched and read, and moreover that bends with radii of curvature as small as 0.3 cm cause little change in device characteristics. The Si/a-Si x Ag NW devices represent a highly scalable and promising nanodevice element for assembly and fabrication of dense nonvolatile memory and programmable nanoprocessors.
The Effect of Ni Doping on the Performance and Electronic Structure of LSCF Cathodes Used for IT-SOFCs (2017)

We investigated the effect of nickel doping on the electronic structure and performance of nanostructured La0.6Sr0.4Co0.2Fe0.8–0.03Ni0.03O3−δ prepared by the one-pot sol–gel method. The commercial undoped La0.6Sr0.4Co0.2Fe0.8O3−δ (LSCF0.8) was used as reference. Moreover, for comparison, Ni (3 mol %) was deposited by wetness impregnation over the La0.6Sr0.4Co0.2Fe0.8O3−δ. We show by in situ X-ray absorption spectroscopy at 900 °C under air flow that nickel enters the B perovskite site of the material and favors the stabilization of the cobalt oxidation state, as evidenced by the delay in the decrease of the average Co valence with respect to undoped samples. Our results are further supported by in situ X-ray Raman spectroscopy (XRS) that allowed us to monitor the temperature evolution of the O K-edge. XRS evidences that nickel-doped LSCF shows unmodified O2p-TM3d density of states, which proves that the Co oxidation state is preserved. Electrochemical impedance spectroscopy measurements were carried out over half-cell systems consisting of LSCF-based materials deposited onto a Ce0.8Gd0.2O2−δ electrolyte. The improvement of the electrochemical performances of the Ni-doped La0.6Sr0.4Co0.2Fe0.8–0.03Ni0.03O3−δ sample with respect to a reference Ni-impregnated LSCF is attributed to the stabilization of the TM-O6 structural units, which were recently proposed as the functional units for oxygen reduction.
Better classifier calibration for small datasets (2020)

Classifier calibration does not always go hand in hand with the classifier’s ability to separate the classes. There are applications where good classifier calibration, i.e., the ability to produce accurate probability estimates, is more important than class separation. When the amount of data for training is limited, the traditional approach to improve calibration starts to crumble. In this article, we show how generating more data for calibration is able to improve calibration algorithm performance in many cases where a classifier is not naturally producing well-calibrated outputs and the traditional approach fails. The proposed approach adds computational cost but considering that the main use case is with small datasets this extra computational cost stays insignificant and is comparable to other methods in prediction time. From the tested classifiers, the largest improvement was detected with the random forest and naive Bayes classifiers. Therefore, the proposed approach can be recommended at least for those classifiers when the amount of data available for training is limited and good calibration is essential.
Common Properties of Interspike Interval Distributions of Simple and Realistic Model Neurons Driven by White Noise Modulated by a Two-state Markov Process (2019)

Recently, firing statistics of integrate-and-fire (IF) neurons driven by a two-state Markov process or white noise modulated by a two-state Markov process has been studied. Although IF neurons are analytically tractable, they are not a detailed model such as a Hodgkin–Huxley (HH) neuron. In contrast to constant input, for fluctuating input, the relation between the dynamics of IF neurons and that of the HH neuron is not obvious. In a previous study [Phys. Rev. E 98, 032416 (2018)], we derived a common formula for ISI distributions of leaky integrate-and-fire (LIF) and HH neurons driven by white noise modulated by a symmetric two-state Markov process, and clarified the commonalities between ISI distributions of those neurons. In this study, by deriving a formula that holds even for the input of white noise modulated by an asymmetric two-state Markov process, we fully clarify the commonalities between ISI distributions of the LIF and HH neurons. The results are helpful in interpreting the analytical expressions of ISI distributions of IF neurons driven by a two-state input.
Cholesteric Carbohydrate Liquid Crystals Incorporating an Intact Glucopyranose Moiety (1997)

Abstract Recently, the first monosaccharide derivatives containing a fully intact monosaccharide and two vicinal OH-groups which display thermotropic chiral mesophases were synthesized. These liquid crystals have a rigid core, with a trans-decalin-like skeleton incorporating the D-glucopyranose ring, substituted with an alkoxylated polarizable aromatic group, e.g. a phenyl 4-octyloxybenzoate, on one side and an alkoxyphenyl group at the anomeric centre. On the basis of the focal-conic fan-like texture displayed and the existence of a blue phase in the UV, we expected the cholesteric helix to have a very short pitch. The compounds possessed an exceptionally high helical twisting power. Extrapolation of these data to dopant concentrations of 100 % also indicates a very short pitch (30–90 nm).
Background Subtraction with Real-time Semantic Segmentation (2018)

Accurate and fast foreground object extraction is very important for object tracking and recognition in video surveillance. Although many background subtraction (BGS) methods have been proposed in the recent past, it is still regarded as a tough problem due to the variety of challenging situations that occur in real-world scenarios. In this paper, we explore this problem from a new perspective and propose a novel background subtraction framework with real-time semantic segmentation (RTSS). Our proposed framework consists of two components, a traditional BGS segmenter $\mathcal{B}$ and a real-time semantic segmenter $\mathcal{S}$. The BGS segmenter $\mathcal{B}$ aims to construct background models and segments foreground objects. The real-time semantic segmenter $\mathcal{S}$ is used to refine the foreground segmentation outputs as feedbacks for improving the model updating accuracy. $\mathcal{B}$ and $\mathcal{S}$ work in parallel on two threads. For each input frame $I_t$, the BGS segmenter $\mathcal{B}$ computes a preliminary foreground/background (FG/BG) mask $B_t$. At the same time, the real-time semantic segmenter $\mathcal{S}$ extracts the object-level semantics ${S}_t$. Then, some specific rules are applied on ${B}_t$ and ${S}_t$ to generate the final detection ${D}_t$. Finally, the refined FG/BG mask ${D}_t$ is fed back to update the background model. Comprehensive experiments evaluated on the CDnet 2014 dataset demonstrate that our proposed method achieves state-of-the-art performance among all unsupervised background subtraction methods while operating at real-time, and even performs better than some deep learning based supervised algorithms. In addition, our proposed framework is very flexible and has the potential for generalization.
Aerobic training decreases bronchial hyperresponsiveness, serum chemokines and symptoms in asthmatic patients: Randomized controlled trial (2013)

Background: Bronchial hyperresponsiveness (BHR) is a hallmark in asthma and related with airway inflammation and asthma symptoms. Although aerobic training (AT) has been shown to reduce airway inflammation in asthmatics, its effect on BHR and systemic inflammation remains unknown. Objective : To evaluate the effect of AT on BHR, serum chemokine, and asthma symptoms in patients with moderate or severe asthma. Methods: Third-six patients (42±10years; FEV 1 =76.8±21.4% predicted) clinically well-controlled were randomly assigned to either control (CG, n=18) or trained group (TG, n=18). Patients in the CG (educational program+breathing exercises) and TG (similar to CG+AT) were followed 2x/week for 3 - month period with no change in corticosteroid consumption. All patients underwent broncoprovocation test, serum chemokines analysis (MCP-1, IP-10, and MIG), and filled in a daily symptoms diary . Results : At baseline the groups were similar in all outcomes. After 3 months, only TG increased PC 20 (0.7±1.8 vs. 1.9±4.0 mg/mL, p&lt;0.01), reduced MCP-1 (25.4±16.2 vs. 20.4±12.2pg/mL, p&lt;0.01) and enhanced days without asthma symptoms (12±10 vs. 16±12days, p=0.02) compared with baseline data. Conclusions: Our results show for the first time that aerobic training reduces BHR, serum chemokines and symptoms in asthmatic patients. Supported by FAPESP.