gebhart/patrepeval huggingface dataset:
Single cell analysis to dissect molecular heterogeneity and disease evolution in metastatic melanoma (2019)

Originally described as interpatient variability, tumour heterogeneity has now been demonstrated to occur intrapatiently, within the same lesion, or in different lesions of the same patient. Tumour heterogeneity involves both genetic and epigenetic changes. Intrapatient heterogeneity is responsible for generating subpopulations of cancer cells which undergo clonal evolution with time. Tumour heterogeneity develops also as a consequence of the selective pressure imposed by the immune system. It has been demonstrated that tumour heterogeneity and different spatiotemporal interactions between all the cellular compontents within the tumour microenvironment lead to cancer adaptation and to therapeutic pressure. In this context, the recent advent of single cell analysis approaches which are able to better study tumour heterogeneity from the genomic, transcriptomic and proteomic standpoint represent a major technological breakthrough. In this review, using metastatic melanoma as a prototypical example, we will focus on applying single cell analyses to the study of clonal trajectories which guide the evolution of drug resistance to targeted therapy.
A Microprism Array for Large-Scale, Wide-Band Interconnection of Optoelectronic Systems (1992)

In contrast to any existing means of interconnection for a large-scale, high-speed optoelectronic system, Physical Optics Corporation (POC) proposes fabricating and using a microprism (-100 um in size,) array (MPA) as a wide-band coupler for two-dimensional and three-dimensional system integration. The flexibility of MPA's angles allows implementation of the MPA to any point to point interconnects. Realizing that the major bottle neck of hologram-based interconnection is the intrinsic limitation of coupling bandwidth (-10 um), we demonstrated a microprism coupler (MPA) with larger than 200 um bandwidth from free space to optical data bus (ODB). For example, LED-based transmission from a single-mode guide to a multimode fiber can be solved only by using the MPA. Unlike the conventional prism which has a dimension of -mm to -cm, the MPA has miniscule dimensions. An MPA with -100 Jim in size as demonstrated. The proposed MPA is immune from electromagnetic interference (EMI). Furthermore, the cost of the microprism is less than S1 a piece in mass production, significantly less than holograms. In Phase 1, fabrication of the MPA will be upgraded followed by a demonstration of large-scale board-to-board MAP-based 3-D interconnection.
Widely Tunable SOA-Based OTDR Employing a Cost-Effective Source Configuration (2012)

We describe an SOA-based tunable pulsed optical source employing a novel topology, which provides pulses of variable duration and rapid rise time for OTDR measurements. Applications to spectral attenuation and CD characterization are illustrated.
Axonal damage accumulates in the progressive phase of multiple sclerosis: three year follow up study (2005)

The increase in NfH during the progressive phase of the disease together with the correlation of NfH(SMI35) with all clinical scales at follow up suggests that cumulative axonal loss is responsible for sustained disability and that high NfH(SMI35) levels are a poor prognostic sign.
Comparison of Automated and Traditional Western Blotting Methods (2023)

Traditional Western blotting is one of the most used analytical techniques in biological research. However, it can be time-consuming and suffer from a lack of reproducibility. Consequently, devices with different degrees of automation have been developed. These include semi-automated techniques and fully automated devices that replicate all stages downstream of the sample preparation, including sample size separation, immunoblotting, imaging, and analysis. We directly compared traditional Western blotting with two different automated systems, iBind™ Flex, which is a semi-automated system designed to perform the immunoblotting, and JESS Simple Western™, a fully automated and capillary-based system performing all steps downstream of sample preparation and loading, including imaging and image analysis. We found that a fully automated system can save time and importantly offer valuable sensitivity. This is particularly beneficial for limited sample amounts. The downside of automation is the cost of devices and reagents. Nevertheless, automation can be a good option to increase output and facilitate sensitive protein analyses.
Monitoring coronary artery stent deployment in living human patients with optical coherence tomography (2001)

Summary form only given. In this preliminary study, we have demonstrated that intravascular OCT imaging following stent deployment is feasible and permits the high resolution visualization of detailed vessel wall structure within and adjacent to stents. The data obtained from imaging eleven stents in ten patients indicates that with OCT: (1) stent strut apposition to the vessel lumen can be accurately determined, (2) superficial calcium can be identified within stents, (3) the detailed structure of the vessel wall can be visualized within stents, (4) dissections within and adjacent to stents can be identified, and (5) even small protrusions of tissue through stent struts can be quantified. The improved ability of OCT to visualize vessel and stent structure may provide a new tool for accurately monitoring stent deployment and understanding in-stent restenosis.
The complete sequence of a human genome (2021)

Abstract In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of the human genome, which revolutionized the field of genomics. While these drafts and the updates that followed effectively covered the euchromatic fraction of the genome, the heterochromatin and many other complex regions were left unfinished or erroneous. Addressing this remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium has finished the first truly complete 3.055 billion base pair (bp) sequence of a human genome, representing the largest improvement to the human reference genome since its initial release. The new T2T-CHM13 reference includes gapless assemblies for all 22 autosomes plus Chromosome X, corrects numerous errors, and introduces nearly 200 million bp of novel sequence containing 2,226 paralogous gene copies, 115 of which are predicted to be protein coding. The newly completed regions include all centromeric satellite arrays and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies for the first time.
Accounting for the effects on residual deformations due to torsional response (2006)

Recent developments in performance-based seismic design and assessment&#13;\napproaches have emphasised the importance of properly assessing and limiting the&#13;\nresidual (permanent) deformations typically sustained by a structure after a seismic event,&#13;\neven when designed according to current code provisions.&#13;\nIn this contribution, the performance-based design framework for residual deformations,&#13;\npreviously developed by the authors for 2-D regular structures, is further extended to the&#13;\nbehaviour of 3-D irregular (asymmetric in-plan) buildings. The seismic response of a set&#13;\nsingle storey systems, comprising of seismic resisting frames, and made of alternative&#13;\nmaterials (concrete or steel), is investigated under uni-directional earthquake loading&#13;\nexcitations. Different layouts in plan, leading to either torsionally unrestrained or&#13;\nrestrained systems, are considered.&#13;\nSensitivity analyses are carried out in order to identify the influence of varying levels of&#13;\ntorsional restraint on the residual deformations/displacements in the response of a 3-D&#13;\nirregular building, the irregularity being given by an imposed mass eccentricity.
GPS receiver sensitivity enhancement in wireless applications (1999)

A major concern in using GPS is satellite visibility, especially in urban canyons and indoor applications. We demonstrate techniques to use the communication link to enhance the sensitivity of GPS receivers in wireless applications. We analyze the performance of the different sensitivity enhancement schemes. Receiver operating characteristics (ROC) and improvements in sensitivity are presented and discussed.
TccP2 of O157:H7 and Non-O157 Enterohemorrhagic Escherichia coli (EHEC): Challenging the Dogma of EHEC-Induced Actin Polymerization (2006)

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 and enteropathogenic E. coli (EPEC) trigger actin polymerization at the site of bacterial adhesion by inducing different signaling pathways. Actin assembly by EPEC requires tyrosine phosphorylation of Tir, which subsequently binds the host adaptor protein Nck. In contrast, Tir(EHEC O157) is not tyrosine phosphorylated and instead of Nck utilizes the bacterially encoded Tir-cytoskeleton coupling protein (TccP)/EspF(U), which mimics the function of Nck. tccP is carried on prophage CP-933U/Sp14 (TccP). Typical isolates of EHEC O157:H7 harbor a pseudo-tccP gene that is carried on prophage CP-933 M/Sp4 (tccP2). Here we report that atypical, beta-glucuronidase-positive and sorbitol-fermenting, strains of EHEC O157 harbor intact tccP and tccP2 genes, both of which are secreted by the LEE-encoded type III secretion system. Non-O157 EHEC strains, including O26, O103, O111, and O145, are typically tccP negative and translocate a Tir protein that encompasses an Nck binding site. Unexpectedly, we found that most clinical non-O157 EHEC isolates carry a functional tccP2 gene that encodes a secreted protein that can complement an EHEC O157:H7 DeltatccP mutant. Using discriminatory, allele-specific PCR, we have demonstrated that over 90% of tccP2-positive non-O157 EHEC strains contain a Tir protein that can be tyrosine phosphorylated. These results suggest that the TccP pathway can be used by both O157 and non-O157 EHEC and that non-O157 EHEC can also trigger actin polymerization via the Nck pathway.
High-power Femtosecond Thin-disk Oscillators for Mid-infrared and Extreme Ultraviolet Generation (2016)

Recent advances in the development of femtosecond thin-disk oscillators are reported. A novel mode-locking technique relying on distributed Kerr-lenses is presented. The generation of W-level mid-infrared frequency comb is described.
1A1-E10 Prediction Method Based on State Estimation for the Moving Objects Grasping(Manufacturing System and Manufacturing Machinery Mechatronics) (2011)

This paper describes about a control scheme that enables industrial robots to grasp moving objects. In the developed control system, the target position is measured at a constant frequency by processing images acquired from two cameras. To consider the delay of image acquisition and robot motion, the move destination of the target object is predicted by using the state of movement estimated based on the Extended Kalman Filter (EKF). Results of the experiment that estimates the state of movement of a pendulum target are provided in order to validate the developed system to predict the move destination, and to detect the sudden change of target motion that affects the final accuracy of grasping.
Crossflow Vortices of a Jet Injected into a Supersonic Crossflow (1997)

Numerous investigations of the fluid mechanics of the transverse jet injected into a supersonic flow (TJISF) flowfield have been motivated by the study of supersonic combustor fuel injection, thrust vector control of rocket nozzles, and jet reaction force prediction. Early studies presented detailed qualitative discussions of the structure of the TJISF flowfield. A few studies have provided either quantitative or semiquantitative measurements of the velocity fields of underexpanded jets injected into a supersonic flow. Despite these investigations, there is a dearth of nonintrusive, quantitative mean velocity and turbulence measurements in the TJISF flowfield. This note uses laser Doppler velocimetry (LDV) measurements of the mean velocity fields to study development of the crossflow vortices of a sonic, underexpanded transverse jet injected into a Mach 1.6 crossflow.
Structure and conformation of the calcium complex of cyclo(Ala‐Leu‐Pro‐Gly)2 in two crystal forms (1993)

Crystal structures of two different forms of the calcium perchlorate complex of cyclo(Ala-Leu-Pro-Gly)2 have been determined and refined using X-ray crystallographic techniques. Orthorhombic form: C32H52N8O8.Ca(ClO4)2.7H2O.2CH3OH, space group C222(1), a = 14.366, b = 18.653, c = 19.824 A, Z = 4, R = 0.068 for 2208 observed reflections. Monoclinic form: C32H52N8O8.Ca(ClO4)2.4H2O, space group C2, a = 21.096, b = 10.182, c = 11.256 A, beta = 103.33 degrees, Z = 2, R = 0.075 for 2165 observed reflections. The cyclic peptide molecule in both the structures has the form of a twofold symmetric, slightly elongated bowl. Type II' beta-turns, involving Gly and Ala at the corners, exist at the two ends of the molecule. The interior of the molecule is substantially hydrophilic, and the external surface of the bowl is largely hydrophobic. The calcium ion is located at the centre of the mouth of the bowl-like molecule. In both crystal forms, four peptide carbonyl oxygens from the cyclic peptide and two solvent oxygens coordinate to the metal ion. The mode of complexation may be described as incomplete encapsulation as, for example, in the case of metal complexes of antamanide. In the crystal structures the complex ions are held together by hydrogen bonds involving perchlorate ions and water molecules. The molecular structure observed in the crystals is entirely consistent with the results of solution studies, which also indicate the conformation of the cyclic peptide in the complex to be similar to that of the uncomplexed molecule.
Controlled-release Particulate Cytokine Adjuvants for Cancer Therapy (2007)

Cytokine therapy can induce tumor regression in cancer patients but systemic administration of cytokines is accompanied with severe toxicity. Loco-regional delivery represents an effective and less toxic alternative to systemic injection. However; the requirement for frequent repeated injections of recombinant cytokine or the logistical difficulties associated with gene-modification have limited wide-spread use of loco-regional therapy. A simpler alternative local delivery strategy involves the use of controlled-release cytokine depot formulations. These formulations provide the advantage that physiological doses of cytokines are directly released to the tumor microenvironment in a sustained manner. Anti-tumor efficacy of IL-2; IL-12; GM-CSF or TNFalpha-encapsulated polymer microspheres has been evaluated in syngeneic murine and human tumor /SCID mouse xenograft models. A single intra-tumoral injection of these formulations; particularly that of IL-12 in combination with GM-CSF or TNFalpha; promoted the regression of established primary tumors; induced systemic anti-tumor T- and NK-cell responses and achieved complete eradication of disseminated disease. Cellular and molecular analysis of post-therapy tumor microenvironment demonstrated that treatment promoted the activation of tumor-associated T-effector/memory cells; the elimination of CD4+ CD25+ Foxp3+ T-suppressors and the de novo priming of tumor-specific CD8+ T-effector cells. Long-term monitoring of post-therapy tumors revealed that reversal of intra-tumoral immune suppression was transient and that T-suppressor cells rapidly re-infiltrated tumors. Repeated treatment resurrected anti-tumor activity; however, therapeutic efficacy declined with each treatment cycle. The observed loss of therapeutic efficacy was associated with a progressive intensification of the post-treatment T-suppressor cell rebound. In contrast; depletion of T-suppressor cells with low dose chemotherapy prior to each cycle of treatment resulted in a dramatic enhancement of long-term therapeutic efficacy leading to complete remissions. Clinical implications of these findings are discussed herein.
Stability and Generalization of Bilevel Programming in Hyperparameter\n Optimization (2021)

The (gradient-based) bilevel programming framework is widely used in\nhyperparameter optimization and has achieved excellent performance empirically.\nPrevious theoretical work mainly focuses on its optimization properties, while\nleaving the analysis on generalization largely open. This paper attempts to\naddress the issue by presenting an expectation bound w.r.t. the validation set\nbased on uniform stability. Our results can explain some mysterious behaviours\nof the bilevel programming in practice, for instance, overfitting to the\nvalidation set. We also present an expectation bound for the classical\ncross-validation algorithm. Our results suggest that gradient-based algorithms\ncan be better than cross-validation under certain conditions in a theoretical\nperspective. Furthermore, we prove that regularization terms in both the outer\nand inner levels can relieve the overfitting problem in gradient-based\nalgorithms. In experiments on feature learning and data reweighting for noisy\nlabels, we corroborate our theoretical findings.\n
High-resolution transmission electron microscopy of Fe-Al powder particles (1999)

Sections of a few μm-sized particles of Fe1−xAlx (x = 0.35–0.42) powders, produced by the atomizing method, were prepared for transmission electron microscopy (TEM) using new specimen supporting methods and ion thinning. As-atomized paramagnetic particles, the particles magnetized by cold milling for several hours and those demagnetized by ageing for 1 min at 200°C have been observed in cross-sectional high-resolution TEM images.
Neutral-beam injection calculations for torsatrons (1980)

A numerical investigation of the effectiveness of neutral-beam heating in two torsatron-type devices has been undertaken. A modified version of a well-known deposition and orbit code was used for this purpose. It was found that, for beam currents within the applicable range of the model, neutral beams can efficiently heat either a 'classical' torsatron or an 'ultimate' torsatron plasma provided the injection is tangential to the magnetic axis. These results were obtained by following ionized test particles down to thermalization. Efficiency of the injection drops as the angle approaches perpendicular, because of relatively poor containment of helically trapped orbits within the assumed plasma volume.
TiO2 surface engineering with multifunctional oligomeric polystyrene coadsorbent for dye-sensitized solar cells (2015)

Oligomeric, hydrophobic coadsorbents based on polystyrene (<italic>M</italic><sub>n</sub> = 2400) terminated by a carboxylic acid exhibit dual functions in dye-sensitized solar cells: passivation of the TiO<sub>2</sub> surface, and promotion of the strongly-anchored N719 dyes.
Prolyl‐isomerase Pin1 controls normal and cancer stem cells of the breast (2013)

Mammary epithelial stem cells are fundamental to maintain tissue integrity. Cancer stem cells (CSCs) are implicated in both treatment resistance and disease relapse, and the molecular bases of their malignant properties are still poorly understood. Here we show that both normal stem cells and CSCs of the breast are controlled by the prolyl-isomerase Pin1. Mechanistically, following interaction with Pin1, Notch1 and Notch4, key regulators of cell fate, escape from proteasomal degradation by their major ubiquitin-ligase Fbxw7α. Functionally, we show that Fbxw7α acts as an essential negative regulator of breast CSCs' expansion by restraining Notch activity, but the establishment of a Notch/Pin1 active circuitry opposes this effect, thus promoting breast CSCs self-renewal, tumor growth and metastasis in vivo. In human breast cancers, despite Fbxw7α expression, high levels of Pin1 sustain Notch signaling, which correlates with poor prognosis. Suppression of Pin1 holds promise in reverting aggressive phenotypes, through CSC exhaustion as well as recovered drug sensitivity carrying relevant implications for therapy of breast cancers.
Hole relaxation inp-typeInxGa1−xAs/AlyGa1−yAs quantum wells observed by ultrafast midinfrared spectroscopy (1995)

We have performed midinfrared pump-probe transmission measurements in p-type strained ${\mathrm{In}}_{0.5}$${\mathrm{Ga}}_{0.5}$As/${\mathrm{Al}}_{0.5}$${\mathrm{Ga}}_{0.5}$As quantum wells at room temperature. The laser source was a midinfrared free-electron laser generating subpicosecond pulses and tuned on resonance between the heavy-hole and the light-hole subbands. The relaxation time is \ensuremath{\sim}1 ps, which is shorter than for electrons in the conduction band. Interactions between the optical phonons and holes account for the measured relaxation.
Comparative Study of positional efficiency between Chinese bashetball team and the top 3 teams in the 16th FIBA World Championship (2012)

The essay researches the positional efficiency of China and the top 3 teams in the 16th FIBA World Championship with the following approaches: literature and data,live observation,questionnaire,expert interview,mathematical statistics.The research result is to provide the direction to stable,continual and effective development of China basketball.
Dual-Microring Resonator Based 8×8 Silicon Photonic Switch (2019)

First demonstration of a dual-microring 8×8 silicon-photonic switch in a compact 4 mm2 footprint shows 4.4–8.4 dB end-to-end on-chip loss, −16.75 dB first-order switching crosstalk, and 40 GHz switching bandwidth capable of high-data-rate datacenter transmissions.
Cover Feature: The Impact of Halogenated Phenylalanine Derivatives on NFGAIL Amyloid Formation (ChemBioChem 24/2020) (2020)

As shown for the model peptide NFGAIL, the introduction of different fluorinated phenylalanine derivatives leads to specific amyloid-folding kinetics through an alteration in hydrophobicity and changes in their α-frameworks. This is represented by the clock, as its hand (the “F” for fluorine) determines the self-assembly process. The extent of fluorination, illustrated as potential plots, acts as a dimension of change not only for aggregation kinetics, but also for the morphology of resulting fibrils, as revealed by TEM micrographs. More information can be found in the full paper by B. Koksch et al. The picture was created by S.C., Helmut Fouquet, J.M., M.B., R.R.N. and B.K.
Scheduling in Mobile Ad Hoc Networks With Topology and Channel-State Uncertainty (2012)

We study throughput-optimal scheduling in mobile ad hoc networks with time-varying (fading) channels. Traditional back-pressure algorithms (based on the work by Tassiulas and Ephremides) require instantaneous network state (topology, queues-lengths, and fading channel-state) in order to make scheduling/routing decisions. However, such instantaneous network-wide (global) information is hard to come by in practice, especially when mobility induces a time-varying topology. With information delays and a lack of global network state, different mobile nodes have differing “views” of the network, thus inducing uncertainty and inconsistency across mobile nodes in their topology knowledge and network state information. In such a setting, we first characterize the throughput-optimal rate region and develop a back-pressure-like scheduling algorithm, which we show is throughput-optimal. Then, by randomly partitioning the geographic region spatially into disjoint and interference-free sub-areas, and sharing delayed topology and network state information only among nearby mobile nodes, we develop a localized low-complexity scheduling algorithm. The algorithm uses instantaneous local information (the queue length, channel state and current position at a mobile node) along with delayed network state information from nearby nodes (i.e., from nodes that were within a nearby geographic region as opposed to network-wide information). The proposed algorithm is shown to be near-optimal, where the geographic distance over which delayed network-state information is shared determines the provable lower bound on the achievable throughput.