gebhart/patrepeval huggingface dataset:
Generation of human alveolar epithelial type I cells from pluripotent stem cells (2023)

In the distal lung, alveolar epithelial type I cells (AT1s) comprise the vast majority of alveolar surface area and are uniquely flattened to allow the diffusion of oxygen into the capillaries. This structure along with a quiescent, terminally differentiated phenotype has made AT1s particularly challenging to isolate or maintain in cell culture. As a result, there is a lack of established models for the study of human AT1 biology, and in contrast to alveolar epithelial type II cells (AT2s), little is known about the mechanisms regulating their differentiation. Here we engineer a human in vitro AT1 model system through the directed differentiation of induced pluripotent stem cells (iPSC). We first define the global transcriptomes of primary adult human AT1s, suggesting gene-set benchmarks and pathways, such as Hippo-LATS-YAP/TAZ signaling, that are enriched in these cells. Next, we generate iPSC-derived AT2s (iAT2s) and find that activating nuclear YAP signaling is sufficient to promote a broad transcriptomic shift from AT2 to AT1 gene programs. The resulting cells express a molecular, morphologic, and functional phenotype reminiscent of human AT1 cells, including the capacity to form a flat epithelial barrier which produces characteristic extracellular matrix molecules and secreted ligands. Our results indicate a role for Hippo-LATS-YAP signaling in the differentiation of human AT1s and demonstrate the generation of viable AT1-like cells from iAT2s, providing an in vitro model of human alveolar epithelial differentiation and a potential source of human AT1s that until now have been challenging to viably obtain from patients.
A novel strategy to initiate a peroral endoscopic myotomy program† (2017)

The excellent results of laparoscopic myotomy with partial fundoplication are challenging to duplicate during the initial adoption of a POEM approach. We present a program developed to steepen the learning curve and enhance patient safety while implementing this new procedure.
Low Power Unsupervised Anomaly Detection by Non-Parametric Modeling of\n Sensor Statistics (2020)

This work presents AEGIS, a novel mixed-signal framework for real-time\nanomaly detection by examining sensor stream statistics. AEGIS utilizes Kernel\nDensity Estimation (KDE)-based non-parametric density estimation to generate a\nreal-time statistical model of the sensor data stream. The likelihood estimate\nof the sensor data point can be obtained based on the generated statistical\nmodel to detect outliers. We present CMOS Gilbert Gaussian cell-based design to\nrealize Gaussian kernels for KDE. For outlier detection, the decision boundary\nis defined in terms of kernel standard deviation ($\\sigma_{Kernel}$) and\nlikelihood threshold ($P_{Thres}$). We adopt a sliding window to update the\ndetection model in real-time. We use time-series dataset provided from Yahoo to\nbenchmark the performance of AEGIS. A f1-score higher than 0.87 is achieved by\noptimizing parameters such as length of the sliding window and decision\nthresholds which are programmable in AEGIS. Discussed architecture is designed\nusing 45nm technology node and our approach on average consumes $\\sim$75 $\\mu$W\npower at a sampling rate of 2 MHz while using ten recent inlier samples for\ndensity estimation. \\textcolor{red}{Full-version of this research has been\npublished at IEEE TVLSI}\n
Single‐Atom Gold Catalysis in the Context of Developments in Parahydrogen‐Induced Polarization (2015)

A highly isolated monoatomic gold catalyst, with single gold atoms dispersed on multiwalled carbon nanotubes (MWCNTs), has been synthesized, characterized, and tested in heterogeneous hydrogenation of 1,3-butadiene and 1-butyne with parahydrogen to maximize the polarization level and the contribution of the pairwise hydrogen addition route. The Au/MWCNTs catalyst was found to be active and efficient in pairwise hydrogen addition and the estimated contributions from the pairwise hydrogen addition route are at least an order of magnitude higher than those for supported metal nanoparticle catalysts. Therefore, the use of the highly isolated monoatomic catalysts is very promising for production of hyperpolarized fluids that can be used for the significant enhancement of NMR signals. A mechanism of 1,3-butadiene hydrogenation with parahydrogen over the highly isolated monoatomic Au/MWCNTs catalyst is also proposed.
Rezension von: Rheinheimer, Joachim; Hassler, Michael, Die Blattkäfer Baden-Württembergs (2021)

Joachim Rheinheimer und Michael Hassler: Die Blattkäfer Baden-Württembergs. Kleinsteuber Books Karlsruhe 2018. 928 Seiten mit über 1000 Abbildungen. Gebunden € 79,80. ISBN 978-3-9818110-2-5
Minimization of System-Level Losses in VSI-Based Induction Motor Drives: Offline Strategies (2016)

Applications of motor drives, ranging from automotive traction to more-electric aircraft, have widely varying speed and torque demands. With extensive use of inverter-fed drives, loss minimization techniques for such applications have evolved over the past few decades. Previous work on loss minimization has mainly focused on specific drive components. Component-level loss minimization, however, will not guarantee minimum total loss in the drive system. In this paper, a system-level loss minimization method is developed using a comprehensive loss model, to achieve true minimum total loss in the system. The total loss obtained is lower for the proposed system-based minimization than the component-based methods such as machine loss minimization, torque maximization per stator ampere, and dc-link loss minimization. Simulation and experimental results for a sample drive cycle are presented to verify the benefits of the proposed scheme for an induction motor drive. Results suggest system loss reduction of about 7%, when compared to machine-based optimization, in high-variability applications.
Development of Personalized Cancer Therapy for Men with Advanced Prostate Cancer (2015)

Abstract : The purpose of this study is to develop a strategy to identify molecular markers of response of advanced prostate cancer to specific therapies using clinically relevant prostate cancer patient-derived xenografts (PDXs) that are responders and nonresponders to these therapies. We will identify genomic alterations via integrative genomic analysis of these PDXs. The MD Anderson and Michigan teams will interact closely to analyze results and generate a responder ID profile hypothesis. The validity of the responder ID profiles will be assessed in clinical trials. When we were in the process of performing our studies at the MD Anderson site, we were informed that there was a miscommunication between MD Anderson and USAMRMC Animal Care and Use Review Office (ACURO) and that the animal protocols had not been reviewed by ACURO. Thus we were asked to stop all studies and to return all funds utilized for the project as this could not be executed until the animal protocol is approved by ACURO. In May2016, we had our animal protocol approved and we started our studies.
Supplementary Table 1 from Systems Analysis of the NCI-60 Cancer Cell Lines by Alignment of Protein Pathway Activation Modules with “-OMIC” Data Fields and Therapeutic Response Signatures (2023)

&lt;p&gt;PDF file - 107K, List of antibodies against total-, phospho- and cleaved-proteins, with dilutions used for RPPA analysis.&lt;/p&gt;
VEGF-C receptor binding and pattern of expression with VEGFR-3 suggests a role in lymphatic vascular development (1996)

The vascular endothelial growth factor family has recently been expanded by the isolation of two new VEGF-related factors, VEGF-B and VEGF-C. The physiological functions of these factors are largely unknown. Here we report the cloning and characterization of mouse VEGF-C, which is produced as a disulfide-linked dimer of 415 amino acid residue polypeptides, sharing an 85% identity with the human VEGF-C amino acid sequence. The recombinant mouse VEGF-C protein was secreted from transfected cells as VEGFR-3 (Flt4) binding polypeptides of 30–32x10(3) Mr and 22–23x10(3) Mr which preferentially stimulated the autophosphorylation of VEGFR-3 in comparison with VEGFR-2 (KDR). In in situ hybridization, mouse VEGF-C mRNA expression was detected in mesenchymal cells of postimplantation mouse embryos, particularly in the regions where the lymphatic vessels undergo sprouting from embryonic veins, such as the perimetanephric, axillary and jugular regions. In addition, the developing mesenterium, which is rich in lymphatic vessels, showed strong VEGF-C expression. VEGF-C was also highly expressed in adult mouse lung, heart and kidney, where VEGFR-3 was also prominent. The pattern of expression of VEGF-C in relation to its major receptor VEGFR-3 during the sprouting of the lymphatic endothelium in embryos suggests a paracrine mode of action and that one of the functions of VEGF-C may be in the regulation of angiogenesis of the lymphatic vasculature.
ALD Enabled Nickel MEMS Switches for Digital Logic (2011)

CMOS transistor based digital logic technology has delivered spectacular levels of device integration and processing capability since its advent. However, traditional CMOS device performance remains limited in harsh environments, such as high temperature or irradiated environments. Electrostatically actuated MEMS/NEMS switches offer improved performance in these environments. In this work, out-of-plane three terminal microswitches suitable for digital logic are presented. Each switch consists of a suspended fixed-fixed bowtie shaped electroplated nickel beam (300μm × 250μm × ∼2μm) buckled out-of-plane over a 10μm wide gold electrode on a LPCVD nitride coated low resistance Si substrate, which acts as a common gate electrode. Atomic layer deposited (ALD) alumina (100nm thick) is incorporated as a sacrificial layer to keep the fabrication processing low temperature and provide precise gap uniformity across chip. Steady-state I-V performance results are presented showing contact voltages between 17–36V. Mechanical modeling of the beam deformation is performed using commercial FEA software and compared to the actual measured beam response. These devices offer a valid approach for simple MEMS based logic circuitry with proper film stress management and geometry scaling.
Rates for inductive learning of compositional models (2013)

Compositional Models are widely used in Computer Vision as they exhibit strong expressive power by generating a combinatorial number of configurations with a small number of components. However, the literature is still missing a theoretical understanding of why compositional models are better than flat representations, despite empirical evidence as well as strong arguments that compositional models need fewer training examples. In this paper we try to give some theoretical answers in this direction, focusing on AND/OR Graph (AOG) models used in recent literature for representing objects, scenes and events, and bringing the following contributions. First, we analyze the capacity of the space of AND/OR graphs, obtaining PAC (Probably Approximately Correct) bounds for the number of training examples sufficient to guarantee with a given certainty that the model learned has a given accuracy. Second, we propose an algorithm for supervised learning AND/OR Graphs that has theoretical performance guarantees based on the dimensionality and number of training examples. Finally, we observe that part localization, part noise tolerance and part sharing leads to a reduction in the number of training examples required.
Analysis of adenomatous polyposis coli promoter hypermethylation in human cancer. (2000)

Germ-line mutations in the tumor suppressor gene APC are associated with hereditary familial adenomatous polyposis (FAP), and somatic mutations are common in sporadic colorectal tumors. We now report that methylation in the promoter region of this gene constitutes an alternative mechanism for gene inactivation in colon and other tumors of the gastrointestinal tract. The APC promoter is hypermethylated in 18% of primary sporadic colorectal carcinomas (n = 108) and adenoma (n = 48), and neoplasia with APC methylation fails to express the APC transcript. Methylation affects only wild-type APC in 95% of cases and is not observed in tumors from FAP patients who have germ-line APC mutations. As with APC mutation, aberrant APC methylation occurs early in colorectal carcinogenesis. When other tumor types are analyzed (n = 208), methylation of the APC promoter is not restricted to the colon but is present in tumors originating elsewhere in the gastrointestinal tract but rarely in other tumors. Our data suggest that hypermethylation of APC provides an important mechanism for impairing APC function and further underscores the importance of the APC pathway in gastrointestinal tumorigenesis.
Recurrent DICER1 hotspot mutations in endometrial tumours and their impact on microRNA biogenesis (2015)

DICER1 plays a critical role in microRNA (miRNA) biogenesis. Recurrent somatic 'hotspot' mutations at the four metal-binding sites within the RNase IIIb domain of DICER1 were identified in ovarian sex cord-stromal tumours and have since been described in other paediatric tumours. In this study, we screened the RNase IIIb domain of DICER1 in 290 endometrial tumours and identified six cases with hotspot mutations, including two cases affected by an atypical G1809R mutation directly adjacent to a metal-binding site. Using Illumina and Sanger targeted resequencing, we observed and validated biallelic DICER1 mutations in several cases with hotspot mutations. Through in vitro DICER1 cleavage assays, small RNA deep sequencing and real-time PCR, we demonstrated that mutations adding a positively charged side chain to residue 1809 have similar detrimental effects on 5p miRNA production to mutations at the metal-binding sites. As expected, 5p miRNAs were globally reduced in tumours and cell lines with hotspot mutations. Pathway analysis of gene expression profiles indicated that genes de-repressed due to loss of 5p miRNAs are strongly associated with pathways regulating the cell cycle. Using a Dicer1-null mouse cell line model, we found that expression of DICER1 hotspot mutants promoted cell proliferation, whereas wild-type (WT) DICER1 inhibited cell proliferation. Furthermore, targets of let-7 family miRNAs are enriched among the up-regulated genes, suggesting that loss of let-7 may be impacting downstream pathways. Our results reveal that DICER1 hotspot mutations are implicated in common malignancies and may constitute a unique oncogenic pathway.
Joint fixed beamforming and eigenmode precoding for super high bit rate massive MIMO systems using higher frequency bands (2014)

In order to tackle rapidly increasing traffic, the 5th generation (5G) mobile communication system will introduce small cells using higher frequency bands with wider bandwidth to achieve super high bit rate transmission of several tens Gbps. Massive MIMO beamforming (BF) is one of promising technologies to compensate for larger path-loss in the higher frequency bands. Joint analog fixed BF and digital precoding has been proposed to reduce the cost of a Massive MIMO transceiver. However, the conventional scheme assumes the transmission of a few streams using well-known codebook-based precoding as the digital precoding, and both a selection method of the fixed BF weights and a digital precoder design, which are suitable for the super high bit rate transmission using multiple streams, have not been studied. This paper proposes a joint fixed BF and CSI-based precoding (called FBCP) scheme for the 5G Massive MIMO systems. FBCP first selects the analog fixed BF weights based on maximum total received power criterion, and then it calculates eigenmode (EM) precoding matrix exploiting CSI. This paper targets a 5G system achieving 20 Gbps in 20 GHz band as one example, and throughput performances of the proposed FBCP are evaluated by link level simulation and compared with those of the fixed BF and those of the EM precoding.
Circularly polarized stacked patch antenna array with enhanced bandwidth for S‐band applications (2019)

In this article, a circularly polarized coupled slot 1 × 4 stacked patch antenna array with enhanced bandwidth is proposed for S-band applications. Initially, a patch antenna radiating at 2.79 GHz is designed and maximum energy from feedline to patch element is coupled using two rectangular slots. Whereas, a parallel feedline structure is designed to provide polarization flexibility by creating 0, 90, and 180o phase differences. Then, a truncated patch element is vertically stacked in the design to achieve broader bandwidth of 600 MHz over frequency range from 2.4 to 3.0 GHz. Finally, a coupled slot 1 × 4 array stacked antenna array having feedline line structure to provide 90o phase difference for circular polarization is designed and fabricated for measurements. It is observed that the final design achieved target specification having impedance matching (|S11| (dB) < −10 dB over 2.4 to 3.0 GHz, broad band circular polarization, and 11.5 dBic total gain. Overall, a good agreement between simulated and measurement results is observed.
Clinical Analysis of 70 Patients with Tubal Pregnancy Undergoing Laparoscopic Surgery (2011)

Objective To investigate the effects of laparoscopic salpingostomy and salpingectomy on the tubal pregnancy,and evaluate the outcome of the subsequent pregnancy.Methods The clinical data of 70 patients with tubal pregnancy undergoing laparoscopic surgery from April 2004 to December 2008 were analyzed retrospectively.28 patients in the group Ⅰ received the laparoscopic salpingostomy,and 42 patients in the group Ⅱ received the laparoscopic salpingectomy.The operative time,bleeding volume,outcomes of surgery and subsequent pregnancy were compared between the two groups.Results The operative time and bleeding volume in group Ⅰ were higher than those in group Ⅱ(P0.05);The incidence of persistent ectopic pregnancy in group Ⅰ was higher than that in group Ⅱ;The incidence of the subsequent pregnancy and ectopic pregnancy in the group Ⅰ was higher than that in the group Ⅱ,but it was not statistical significant P0.05).Conclusion The degree of difficulty,incidence of subsequent pregnancy and ectopic pregnancy in the laparoscopic salpingostomy group were higher than that in the laparoscopic salpingectomy.The incidence of subsequent pregnancy depends on the status of contralateral tube.When the contralateral fallopian tube is normal,the laparoscopic salpingectomy should be performed for the severe injured tube.
A HIGH-MASS, EIGHT-FOLD SYMMETRIC SILICON CARBIDE MEMS GYROSCOPE (2018)

A novel MEMS gyroscope is presented, which blends the best aspects of traditional tuning fork gyroscopes with modern wholeangle capable designs such as rings and disks. The gyroscopes were fabricated in both silicon and silicon carbide. The resonators were measured to have quality factors of 120,000 (SiC) and 260,000 (Si), and frequency splits of 0.08% (SiC) and 0.24% (Si). Open loop rate mode gyroscope operation was demonstrated on both gyroscopes.
A pulse regenerating circuit with two Esaki diodes (1967)

A new pulse regenerating circuit is developed, which has no reflection and transmits pulses unidirectionally, when it is inserted in a transmission line. The circuit consists of a pair of Esaki diodes connected face to face and a transformer.
Group velocity independent coupling into slow light photonic crystal waveguide on silicon nanophotonic integrated circuits (2011)

Slow light in photonic crystal waveguide can significantly enhance the light-matter interaction, which is a promising approach toward building ultra-compact photonic devices. However, optical coupling from strip waveguide to slow light photonic crystal waveguide is challenging due to the group velocity mismatch between these waveguides. This issue can be addressed by designing a photonic crystal taper that allows the defect guided mode in photonic crystal waveguide to slow down gradually when it enters the photonic crystal waveguide from strip waveguide, thereby minimizing the group velocity mismatch. By using the photonic crystal taper design, experimental results show coupling efficiency can be enhanced by more than 20dB in normal group velocity region with 5dB less fluctuation as compared to the control group, which does not have photonic crystal taper. Enhancement right before photonic bandgap cutoff can be up to 28dB. Measurement results show excellent agreement with two-dimensional (2D) finite-difference time domain (FDTD) simulation.
Kingfisher: Cost-aware elasticity in the cloud (2011)

In this paper we present Kingfisher, a cost-aware system that provides efficient support for elasticity in the cloud by (i) leveraging multiple mechanisms to reduce the time to transition to new configurations, and (ii) optimizing the selection of a virtual server configuration that minimizes the cost. We have implemented a prototype of Kingfisher and have evaluated its efficacy on a laboratory cloud platform. Our experiments with varying application workloads demonstrate that Kingfisher is able to (i) decrease the cost of virtual server resources by as much as 24% compared to the current cost-unaware approach, (ii) reduce by an order of magnitude the time to transition to a new configuration through multiple elasticity mechanisms in the cloud, and (iii), illustrate the opportunity for further design alternatives which trade-off the cost of server resources with the time required to scale the application.
Modeling the 802.11 Protocol Under Different Capture and Sensing Capabilities (2007)

Decentralized medium access control schemes for wireless networks based on CSMA/CA, such as the 802.11 protocol, are known to be unfair. In multi-hop networks, they can even favor some connections to such an extent that the others suffer from virtually complete starvation. This observation has been reported in quite a few works, but the factors causing it are still not well understood. We find that the capture effect and the relative values of the receiving and carrier sensing ranges play a crucial role in the unfairness of these protocols. We show that an idealized 802.11 protocol does suffer from starvation when the receiving and sensing ranges are equal, but quite surprisingly this unfairness is reduced or even disappears when these two ranges are sufficiently different. Using a Markovian model, we explain why apparently benign variations in these ranges have such a dramatic impact on the 802.11 protocol performance.
Synthesis and in vivo behavior of a copper‐64‐labeled dithiosemicarbazone derivative coupled to a dihydropyridine carrier (1993)

Abstract The dihyropyridine ⇄ pyridinium salt redox delivery system was used to develop a perfusion agent that could be labeled with a generator‐produced positron emitter 62 Cu. A 64 Cu‐labeled dithiosemicarbazone (DTS) molecule attached to a dihyropyridine carrier (PDTS‐DHC) was synthesized by the simple mixing of 64 Cu acetate and Zn‐PDTS‐DHC. The latter was prepared by dithionite reduction of the Zn complex of a corresponding pyridinum precursor (PDTS‐QC + ). When injected into mice, 64 Cu‐PDTS‐DHC showed a high myocardial uptake and high heart‐to‐blood and heart‐to‐lung ratios. These results demonstrate that it may be possible to develop 62 Cu‐PDTS‐DHC compounds as radiopharmaceuticals for myocardial perfusion studies using positron emission tomography.