gebhart/patrepeval huggingface dataset:
Characterization and modeling of BiCMOS logic for low temperature operation (2003)

The results of using a closed-form analytic model for the transient response of a BiCMOS inverter to determine bipolar device requirements for acceptable BiCMOS operation at low temperatures are presented. Measurements of bipolar device parameters versus temperature for bipolar devices fabricated in a BiCMOS process are presented and combined with model predictions of gate delay dependence on these key parameters to predict how gate delay varies with temperature. The predictions are compared to BiCMOS ring oscillator measurements over the temperature range of 77 K to 350 K. It is shown that, although BiCMOS gate delay does not substantially increase until far below room temperature, operation of present BiCMOS gates at low temperatures does not yield speed advantages similar to those seen in CMOS gates. However, since this is due to poor bipolar device performance at low temperatures, it is concluded that careful optimization of critical device parameters, such as B/sub f/, for low-temperature operation holds significant promise.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Operating characteristics of modes in an A6 relativistic magnetron with a stepped cavity (2013)

Summary form only given. The possibility of using a one-step cavity to replace the common tapered cavity to extend the interaction volume to enhance the beam-wave interaction in an A6 relativistic magnetron with axial extraction for ease of manufacture for future experiments is studied using the particle-in-cell (PIC) code UNIPIC. In the stepped cavity A6 relativistic magnetron driven by a transparent cathode, the efficiency can be as high as 78% with GW output power in optimized configurations. When a voltage of 400 kV is applied, the PIC simulations show that the energetic electrons emitted from the cathode strike the anode block wall such that secondary electron and backscattering electron emission occur.
Editorial: Non Genomic Actions of Thyroid Hormones in Cancer (2019)

EDITORIAL article Front. Endocrinol., 04 December 2019Sec. Cancer Endocrinology Volume 10 - 2019 | https://doi.org/10.3389/fendo.2019.00847
Visual Recognition using a Combination of Shape and Color Features (2013)

We develop and implement a new approach to utilizing color information for object and scene recognition that is inspired by the characteristics of color-and object-selective neurons in the high-level inferotemporal cortex of the primate visual system.In our hierarchical model, we introduce a new dictionary of features representing visual information as quantized color blobs that preserve coarse, relative spatial information.We run this model on several datasets such as Caltech101, Outdoor Scenes and Underwater Images.The combination of our color features with (grayscale) shape features leads to significant increases in performance over shape or color features alone.Using our model, performance is significantly higher than using color naively, i.e. concatenating the channels of various color spaces.This indicates that usage of color information per se is not enough to produce good performance, and that it is specifically our biologically-inspired approach to color that results in significant improvement.
RELIABILITY SENSITIVITY ANALYSIS BASED ON ADAPTIVE IMPORTANCE SAMPLING METHOD (2007)

For reliability model of implicit limit state equation with small failure probability,a reliability sensitivity algorithm is presented on the basis of adaptive importance sampling.The appropriate sampling points are selected from those of the importance sampling.Hereby the regression and the derivative rule for implicit function are employed to obtain the sensitivity of the failure probability to the distribution parameters of the basic variables.The precision of the presented method is illustrated by examples with accurate solution of sensitivity,and the presented method is then applied to an engineering example.Compared with the sensitivity analysis based on Monte Carlo method,the presented method has closer precision and cheaper computational cost,and these advantages are more significant for the sensitivity analysis with small failure probability.
Peptide retention prediction applied to proteomic data analysis (2007)

A retention prediction model was developed for peptides separated in reversed-phase chromatography. The model was utilized to identify and exclude the false positive (FP) peptide identifications obtained via database search. The selected database included human proteins, as well as decoy sequences of random proteins. The FP peptide detection rate was defined either as number of retention time outliers, or random decoy sequence identifications. The FP rate for various MASCOT scores was calculated. The peptides identified in one-dimensional (1D) and two-dimensional (2D) liquid chromatography/mass spectrometry (LC/MS) experiments were validated by prediction models. Multi-dimensional LC was based on two orthogonal reversed-phase chromatography modes; prediction models were successfully applied for data filtering in both separation dimensions.
Ligand-induced oligomerization of the human GPCR neurotensin receptor 1\n monitored in living HEK293T cells (2019)

The human neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor that\ncan be expressed in HEK293T cells by stable transfection. Its ligand is a\n13-amino-acid peptide that binds with nanomolar affinity from the extracellular\nside to NTSR1. Ligand binding induces conformational changes that trigger the\nintracellular signaling processes. Recent single-molecule studies revealed a\ndynamic monomer - dimer equilibrium of the receptor in vitro. Here we report on\nthe oligomerization state of the human NTSR1 in the plasma membrane of HEK293T\ncells in vivo. We fused different fluorescent marker proteins mRuby3 or\nmNeonGreen to the C-terminus of NTSR1 and mutated a tetracysteine motif into\nintracellular loop 3 (ICL3) for subsequent FlAsH labeling. Oligomerization of\nNTSR1 was monitored before and after stimulation of the receptor with its\nligand by FLIM and homoFRET microscopy (i.e. Forster resonance energy transfer\nbetween identical fluorophores detected by fluorescence anisotropy), by\ncolocalization microscopy and by time-lapse imaging using structured\nillumination microscopy (SIM).\n
LONGITUDINAL GAIT ALTERATIONS OF ACL-INJURED INDIVIDUALS RECONSTRUCTED WITH THE HAMSTRING GRAFT (2001)

The double loop semitendinosus-gracilis graft (DLSTG) is now common in ACL-reconstruction surgery. Anecdotally, these patients recover faster, particularly early in the rehabilitation phase, compared to B-PT-B patients. Despite widespread use, gait alterations of DLSTG patients have not been presented. The purpose of this study was to quantify joint kinematics of DLSTG reconstructed patients when walking at 6 and 12 weeks post-surgery. Eight DLSTG patients and eight healthy subjects walked at a self-selected pace and at 1.5 m/s, respectively. Video data were collected (60 Hz) to compute hip, knee, and ankle joint kinematics. The appropriate t-test (p ≤ 0.05) was used for specific planned comparisons. At 6 weeks, the DLSTG group exhibited reduced knee joint and greater ankle joint ROM. By 12 weeks, kinematics of the DLSTG group were similar to the controls, except for ankle angle at contact. Results indicate that most gait kinematics of DLSTG patients return to near normal values by 12 weeks. Future study of joint energetics is warranted to evaluate NMS changes underlying the kinematic changes.Table
Comparing Wi-Fi 6 and 5G Downlink Performance for Industrial IoT (2021)

The use of wireless communications in Industrial Internet of Things (IIoT) enables unparalleled levels of flexibility and instantaneous reconfiguration for autonomous industrial processes. In this paper, the focus is on optimizing and evaluating Wi-Fi 6 and 5G New Radio (NR) licensed and unlicensed wireless networks for meeting the packet latency and reliability requirements of critical IIoT applications. The study is based on extensive system simulations using a 3GPP-defined IIoT indoor factory framework and application traffic models. Each radio technology is individually optimized leveraging the pros and cons of that technology to maximize the carried load in the network while fulfilling the delay requirements at a specified reliability level of 99.999 %. In addition to a performance comparison, the paper also provides deployment guidance for applying each radio technology in the considered IIoT setting. With proposed latency aware scheduling and when operated in interference free spectrum, Wi-Fi 6 can support <; 1 ms applications at a very low load, whereas the performance gap with respect to 5G NR reduces as delay requirements are relaxed to 10-100 ms. Conditioned on the fulfilment of the application latency and reliability requirements, unlicensed 5G NR shows nearly 2× the spectral efficiency of Wi-Fi 6 in all available configurations. Licensed 5G NR shows generally the best performance, especially for delay requirement <; 1 ms, supporting 2-4 × the spectral efficiency achievable by unlicensed technologies.
PRKAR1A and Thyroid Tumors (2021)

Thyroid cancer is the most common type of endocrine malignancy and the incidence is rapidly increasing. Follicular (FTC) and papillary thyroid (PTC) carcinomas comprise the well-differentiated subtype and they are the two most common thyroid carcinomas. Multiple molecular genetic and epigenetic alterations have been identified in various types of thyroid tumors over the years. Point mutations in <i>BRAF</i>, <i>RAS</i> as well as <i>RET/PTC</i> and <i>PAX8/PPARγ</i> chromosomal rearrangements are common. Thyroid cancer, including both FTC and PTC, has been observed in patients with Carney Complex (CNC), a syndrome that is inherited in an autosomal dominant manner and predisposes to various tumors. CNC is caused by inactivating mutations in the tumor-suppressor gene encoding the cyclic AMP (cAMP)-dependent protein kinase A (PKA) type 1α regulatory subunit (<i>PRKAR1A</i>) mapped in chromosome 17 (17q22-24). Growth of the thyroid is driven by the TSH/cAMP/PKA signaling pathway and it has been shown in mouse models that PKA activation through genetic ablation of the regulatory subunit <i>Prkar1a</i> can cause FTC. In this review, we provide an overview of the molecular mechanisms contributing to thyroid tumorigenesis associated with inactivation of the <i>RRKAR1A</i> gene.
Treatment of Thoracic Pseudarthrosis in the Adult: Is Combined Surgery Necessary? (2003)

In deformity surgery in adults, pseudarthrosis remains an important cause of progressive deformity and postoperative pain. Revision surgery for pseudarthrosis in the lumbar spine is a difficult challenge with failure rates of as much as 50% using posterior surgery alone. Treatment of pseudarthrosis of the thoracic spine has not been well-described. The purpose of the current study was to review the long-term clinical and radiographic results of posterior-only surgery for the treatment of pseudarthrosis in the thoracic spine. Using a posterior extension osteotomy through the identified pseudarthrosis with reinstrumentation and autogenous bone grafting, an improvement of regional sagittal balance was shown and reliable clinical outcomes were obtained. A single-stage posterior revision surgery with extension osteotomies through the regions of pseudarthrosis coupled with rigid internal fixation and autogenous bone grafting is an effective technique for treatment of pseudarthrosis of the thoracic spine. This technique improves regional sagittal deformity and leads to reliable arthrodesis. Combined anterior and posterior surgery was not necessary for effective treatment of thoracic pseudarthrosis in this series.
The MISDEF2 algorithm: an updated algorithm for patient selection in minimally invasive deformity surgery (2019)

The MISDEF2 algorithm was found to have substantial inter- and intraobserver agreement. The MISDEF2 algorithm incorporates recent advances in MIS surgery. The use of the MISDEF2 algorithm provides reliable guidance for surgeons who are considering either an MIS or an open approach for the treatment of patients with adult spinal deformity.
The Vasopressin V1b Receptor as a Therapeutic Target in Stress-related Disorders (2003)

The complexity of the stress response would appear to provide multiple opportunities for intervention, but treatment strategies are often centered on the improvement of symptoms rather than attempting to "treat" the stress response. However, recent efforts have begun to focus on the development of pharmacological agents that can attenuate the stress response itself, rather than the symptoms associated with stress. Although CRF, which is the main regulator of the stress system, is the focus of current interest, there is an accumulating body of evidence suggesting that the vasopressinergic system may play an equal role in the regulation of the stress response, and that V(1b) receptor antagonists may be of potential therapeutic benefit. The availability of SSR149415, the first selective antagonist for the V(1b) receptor has allowed us to evaluate this hypothesis. SSR149415 is able to attenuate some but not all stress-related behaviors in rodents. While the antidepressant-like activity of the compound was comparable to that of reference antidepressants, the overall profile displayed in anxiety tests was different from that of classical anxiolytics, such as benzodiazepines. The latter were active in a wide range of anxiety models, whereas the V(1b) receptor antagonist showed clear-cut effects only in particularly stressful situations. It is important to note that SSR149415 is devoid of central depressant effects, even at high doses, and does not affect cognitive processes, suggesting a large therapeutic window. Altogether, these findings suggest that V(1b) receptor antagonists might be useful as a treatment for major depression and stress disorders that result from traumatic events.
A Learning OCR System Using Short/Long-term Memory Approach and Hardware Implementation in FPGA (2006)

In this paper we propose a learning OCR system which is based on taking a short and long-term memory and a ranking mechanism which manages the transition of reference patterns between two memories. Also, an optimization algorithm is used to optimize the reference vectors magnitude as well as their distribution, continuously. The system was implemented in the FPGA platform and was tested with some real test data of Roman fonts and the classification results found acceptable. LSI architecture Comparing to other learning models like neural networks or A-means, the main advantage of the proposed algorithm is its simple design which makes it implementable in the hardware especially LSI architecture with no need to a large amount of resources.
Asymmetric synthesis of secondary alcohols from primary alcohols via intramolecular carbenoid C–H insertion catalyzed by rhodium(ii) 3-phenylcholestane-2-carboxylate (2004)

Chiral secondary alcohols may be prepared from primary alcohols via asymmetric C-H insertion reactions of alpha'-alkoxy-alpha-diazoketones catalyzed by rhodium(II)(2R,3R)-3-phenylcholestane-2-carboxylate.
Activation State of the M3 Muscarinic Acetylcholine Receptor Modulates Mammalian Odorant Receptor Signaling (2011)

A diverse repertoire of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) enables cells to sense their environment. Mammalian olfaction requires the activation of odorant receptors (ORs), the largest family of GPCRs; however, whether ORs functionally interact with other families of GPCRs is unclear. We show that the interaction of ORs with the type 3 muscarinic acetylcholine receptor (M3-R), which is found in olfactory sensory neurons (OSNs), modulated OR responses to cognate odorants. In human embryonic kidney-293T cells, ORs and the M3-R physically interacted, and the M3-R increased the potency and efficacy of odorant-elicited responses of several ORs. Selective M3-R antagonists attenuated odorant-dependent activation of OSNs, and, when the M3-R and ORs were expressed in transfected cells, OR activation was enhanced by muscarinic agonists and inhibited by muscarinic antagonists. Furthermore, M3-R-dependent potentiation of OR signaling synergized with that of receptor transporting protein 1S (RTP1S), an accessory factor required for the efficient membrane targeting of ORs. However, the M3-R did not enhance the abundance of ORs at the cell surface, suggesting that the M3-R acted through a distinct mechanism independent of RTP1S. Finally, the activation of ORs by cognate odorants transactivated the M3-R in the absence of its agonist. The crosstalk between ORs and the M3-R suggests that the functional coupling of ORs and the M3-R is required for robust OR activation.
Transmissive Nanohole Arrays for Massively-Parallel Optical Biosensing (2014)

A high-throughput optical biosensing technique is proposed and demonstrated. This hybrid technique combines optical transmission of nanoholes with colorimetric silver staining. The size and spacing of the nanoholes are chosen so that individual nanoholes can be independently resolved in massive parallel using an ordinary transmission optical microscope, and, in place of determining a spectral shift, the brightness of each nanohole is recorded to greatly simplify the readout. Each nanohole then acts as an independent sensor, and the blocking of nanohole optical transmission by enzymatic silver staining defines the specific detection of a biological agent. Nearly 10000 nanoholes can be simultaneously monitored under the field of view of a typical microscope. As an initial proof of concept, biotinylated lysozyme (biotin-HEL) was used as a model analyte, giving a detection limit as low as 0.1 ng/mL.
Into the Wild with AudioScope: Unsupervised Audio-Visual Separation of On-Screen Sounds (2020)

Recent progress in deep learning has enabled many advances in sound separation and visual scene understanding. However, extracting sound sources which are apparent in natural videos remains an open problem. In this work, we present AudioScope, a novel audio-visual sound separation framework that can be trained without supervision to isolate on-screen sound sources from real in-the-wild videos. Prior audio-visual separation work assumed artificial limitations on the domain of sound classes (e.g., to speech or music), constrained the number of sources, and required strong sound separation or visual segmentation labels. AudioScope overcomes these limitations, operating on an open domain of sounds, with variable numbers of sources, and without labels or prior visual segmentation. The training procedure for AudioScope uses mixture invariant training (MixIT) to separate synthetic mixtures of mixtures (MoMs) into individual sources, where noisy labels for mixtures are provided by an unsupervised audio-visual coincidence model. Using the noisy labels, along with attention between video and audio features, AudioScope learns to identify audio-visual similarity and to suppress off-screen sounds. We demonstrate the effectiveness of our approach using a dataset of video clips extracted from open-domain YFCC100m video data. This dataset contains a wide diversity of sound classes recorded in unconstrained conditions, making the application of previous methods unsuitable. For evaluation and semi-supervised experiments, we collected human labels for presence of on-screen and off-screen sounds on a small subset of clips.
Superior In Vitro Stimulation of Human CD8+ T-Cells by Whole Virus versus Split Virus Influenza Vaccines (2014)

Pandemic and seasonal influenza viruses cause considerable morbidity and mortality in the general human population. Protection from severe disease may result from vaccines that activate antigen-presenting DC for effective stimulation of influenza-specific memory T cells. Special attention is paid to vaccine-induced CD8+ T-cell responses, because they are mainly directed against conserved internal influenza proteins thereby presumably mediating cross-protection against circulating seasonal as well as emerging pandemic virus strains. Our study showed that influenza whole virus vaccines of major seasonal A and B strains activated DC more efficiently than those of pandemic swine-origin H1N1 and pandemic-like avian H5N1 strains. In contrast, influenza split virus vaccines had a low ability to activate DC, regardless which strain was investigated. We also observed that whole virus vaccines stimulated virus-specific CD8+ memory T cells much stronger compared to split virus counterparts, whereas both vaccine formats activated CD4+ Th cell responses similarly. Moreover, our data showed that whole virus vaccine material is delivered into the cytosolic pathway of DC for effective activation of virus-specific CD8+ T cells. We conclude that vaccines against seasonal and pandemic (-like) influenza strains that aim to stimulate cross-reacting CD8+ T cells should include whole virus rather than split virus formulations.
Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds (2011)

Despite the importance of migratory birds in the ecology and evolution of avian influenza virus (AIV), there is a lack of information on the patterns of AIV spread at the intra-continental scale. We applied a variety of statistical phylogeographic techniques to a plethora of viral genome sequence data to determine the strength, pattern and determinants of gene flow in AIV sampled from wild birds in North America. These analyses revealed a clear isolation-by-distance of AIV among sampling localities. In addition, we show that phylogeographic models incorporating information on the avian flyway of sampling proved a better fit to the observed sequence data than those specifying homogeneous or random rates of gene flow among localities. In sum, these data strongly suggest that the intra-continental spread of AIV by migratory birds is subject to major ecological barriers, including spatial distance and avian flyway.
NIM811, a cyclophilin inhibitor without immunosuppressive activity, is beneficial in collagen VI congenital muscular dystrophy models (2014)

Ullrich congenital muscular dystrophy (UCMD) and Bethlem myopathy (BM) are inherited muscle diseases due to mutations in the genes encoding the extracellular matrix protein collagen (Col) VI. Opening of the cyclosporin A-sensitive mitochondrial permeability transition pore (PTP) is a causative event in disease pathogenesis, and a potential target for therapy. Here, we have tested the effect of N-methyl-4-isoleucine-cyclosporin (NIM811), a non-immunosuppressive cyclophilin inhibitor, in a zebrafish model of ColVI myopathy obtained by deletion of the N-terminal region of the ColVI α1 triple helical domain, a common mutation of UCMD. Treatment with antisense morpholino sequences targeting col6a1 exon 9 at the 1-4 cell stage (within 1 h post fertilization, hpf) caused severe ultrastructural and motor abnormalities as assessed by electron and fluorescence microscopy, birefringence, spontaneous coiling events and touch-evoked responses measured at 24-48 hpf. Structural and functional abnormalities were largely prevented when NIM811--which proved significantly more effective than cyclosporin A--was administered at 21 hpf, while FK506 was ineffective. Beneficial effects of NIM811 were also detected (i) in primary muscle-derived cell cultures from UCMD and BM patients, where the typical mitochondrial alterations and depolarizing response to rotenone and oligomycin were significantly reduced; and (ii) in the Col6a1(-/-) myopathic mouse model, where apoptosis was prevented and muscle strength was increased. Since the PTP of zebrafish shares its key regulatory features with the mammalian pore, our results suggest that early treatment with NIM811 should be tested as a potential therapy for UCMD and BM.
Supplementary Figure 5 from The Gut Microbiome Associates with Immune Checkpoint Inhibition Outcomes in Patients with Advanced Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Supplementary Figure 5&lt;/p&gt;