gebhart/patrepeval huggingface dataset:
Performance analysis of cooperative networks with optimum combining and Co-channel interference (2015)

This paper analyzes the performance of optimum combining (OC) cooperative interference-limited systems in the presence of co-channel interference (CCI). In particular, we investigate a dual-hop decode-and-forward relaying system comprising a pair of source-destination, multiple relays and multiple interferers affecting the relays as well as the destination. Under this scenario, we first derive the probability density function (PDF) and the cumulative distribution function (CDF) of the signal-to-interference ratio (SIR) at the destination. Based on the results of the CDF and PDF, closed-form expressions for the outage probability and average error probability are derived over Rayleigh fading channels. To investigate the impact of the CCI on the system performance, an asymptotic average error expression is derived to get insights on the diversity and coding gains. Numerical and simulation results are presented to validate our analysis. Results demonstrate that the interference-limited systems achieve the diversity gain of the relaying system.
Rhodium‐Catalyzed Addition—Cyclization Reactions of 5‐Yn‐1‐ones with Arylboronic Acids. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Reducing Inter-Channel Coherence In Stereophonic Acoustic Echo Cancellation Using Partial Update Adaptive Filters (2004)

Publication in the conference proceedings of EUSIPCO, Viena, Austria, 2004
Recent development in reconfigurable reflectors (1990)

A new concept in shaped reflector technology in which the antenna pattern can be reconfigured under motor control is described. In a spacecraft application it will be possible to prescribe coverage, synthesize the corresponding rigid reflector surface, determine the control string lengths to ensure the best fit, aid drive through telemetry, the control motors to achieve the desired pattern. However, considerable work must be done before a flight model can be built, and many fundamental problems of both an electrical and mechanical nature remain to be solved. Measured H-plane radiation patterns obtained using the compact antenna range are given. The pattern with the antenna configured as a paraboloid is shown, together with the pattern with the antenna configured as an elliptically shaped beam. There is excellent agreement with theoretical predictions. Examples of patterns achievable with this reflector system are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Pulse erasure technology in a high-density magneto-optic disk drive (1993)

We present the pulse erasure experimental results on a 5.25-in. (130 mm) 645-megabyte/side sampled servo magneto-optic disk drive. The effect of the relative delay between the erasure pulse and the write pulse on the erase residue is studied.
Relaxation of Isolated Ventricular Cardiomyocytes by a Voltage-Dependent Process (1988)

Cell contraction and relaxation were measured in single voltage-clamped guinea pig cardiomyocytes to investigate the contribution of sarcolemmal Na+-Ca2+ exchange to mechanical relaxation. Cells clamped from -80 to 0 millivolts displayed initial phasic and subsequent tonic contractions; caffeine reduced or abolished the phasic and enlarged the tonic contraction. The rate of relaxation from tonic contractions was steeply voltage-dependent and was significantly slowed in the absence of a sarcolemmal Na+ gradient. Tonic contractions elicited in the absence of a Na+ gradient promptly relaxed when external Na+ was applied, reflecting activation of Na+-Ca2+ exchange. It appears that a voltage-dependent Na+-Ca2+ exchange can rapidly mechanically relax mammalian heart muscle.
Chromosome painting in acute monocytic leukemia (1993)

An Alu polymerase chain reaction (PCR) probe specific for chromosome 11 prepared from the somatic cell hybrid J1 was used to analyze karyotypes of eight patients with acute monocytic leukemia (AML-M5). Chromosome painting confirmed the t(9;11) in one patient and a der(1)t(1;6)t(6;11) in another and allowed the identification of a complex rearrangement involving chromosomes 9, 11, and 17, previously classified as del(11)(q23), in a third patient. An analysis of five patients with AML-M5 and a normal karyotype did not detect abnormalities of chromosome 11. The usefulness of chromosome painting combined with in situ hybridization with probes previously located on particular chromosomes is emphasized.
Is Secure Coding Education in the Industry Needed? An Investigation Through a Large Scale Survey (2021)

The Department of Homeland Security in the United States estimates that 90% of software vulnerabilities can be traced back to defects in design and software coding. The financial impact of these vulnerabilities has been shown to exceed 380 million USD in industrial control systems alone. Since software developers write software, they also introduce these vulnerabilities into the source code. However, secure coding guidelines exist to prevent software developers from writing vulnerable code. This study focuses on the human factor, the software developer, and secure coding, in particular secure coding guidelines. We want to understand the software developers' awareness and compliance to secure coding guidelines and why, if at all, they aren't compliant or aware. We base our results on a large-scale survey on secure coding guidelines, with more than 190 industrial software developers. Our work's main contribution motivates the need to educate industrial software developers on secure coding guidelines, and it gives a list of fifteen actionable items to be used by practitioners in the industry. We also make our raw data openly available for further research.
Abstract 6775: Combination of spatial transcriptomics and multiplex IHC as valuable multi-omics tool for biomarker discovery (2023)

Abstract Colorectal cancer (CRC) is one of the most common cancers worldwide and shows heterogenous molecular subtypes making personalized medicine as well as identifying new targets highly important to provide individual patients with the most appropriate treatment. To gain more insight into the visualization of potential molecules or pathways for targeting CRC we used a multi-omics approach for the simultaneous analysis of gene and protein expression within a sample. In this study we combined fluorescent multiplex immunohistochemistry (mIHC) for the detection of proteins (4-plex panel) with the Visium Spatial Transcriptomics technology (10x Genomics) that enables the detection of the whole transcriptome in the histological context. A formalin-fixed paraffin-embedded (FFPE) tumor tissue sample from a patient diagnosed with CRC was selected according to our quality standards. For this multi-omics approach, serial sections were prepared. The first section was used for fluorescent mIHC staining visualizing the protein expression of Ki67 (proliferation marker), p53 and p21 (both tumor suppressor genes). The second section was stained for hematoxylin and eosin (H&amp;E) to evaluate the tissue morphology. On the third section the Visium FFPE Spatial Gene Expression workflow was applied, and gene expression patterns were analyzed by using the software Space Ranger and Loupe Browser. Our data showed on the one hand a good correlation of protein and gene expression of Ki67, p53 and p21 within the analyzed sample and on the other hand a clear difference of expression patterns between tumor cell areas and regions with corresponding normal mucosa cells. Moreover, by comparing Spatial Transcriptomics gene expression patterns of tumor cell and corresponding normal mucosa cell areas, we also identified genes that were linked to other cancer types and/or are still only poorly described in cancer, especially for CRC. Corresponding protein expression will be verified by chromogenic IHC in the next steps. The combination of fluorescent mIHC and Spatial Transcriptomics has been shown to be a valuable approach not only to visualize already described relations as proof of principle, but more importantly to enable the discovery of new biomarkers or pathways predominantly linked to colorectal tumor tissue that may serve as new targets for cancer treatment. Citation Format: Nicole Kerstedt, Monika Schoeppler, Bita Motamedi-Baniassad, Antonia Hirt, Julia Ploetzky, Mirja Kastein, Laura Thoms, Malik Khenkhar, Hartmut Juhl, Kerstin A. David. Combination of spatial transcriptomics and multiplex IHC as valuable multi-omics tool for biomarker discovery. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6775.
Autophosphorylation of rat brain Ca2+-activated and phospholipid-dependent protein kinase. (1986)

Ca2+-activated and phospholipid-dependent protein kinase (protein kinase C) isolated from rat brain cytosol undergoes autophosphorylation in the presence of Mg2+, ATP, Ca2+, phosphatidylserine, and diolein. Approximately 2-2.5 mol of phosphate were incorporated per mol of the kinase. After sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography, the phosphorylated kinase showed a single protein band of Mr = 82,000 compared to the Mr = 80,000 of the nonphosphorylated enzyme. Analysis of the 32P-labeled tryptic peptides derived from the autophosphorylated kinase by peptide mapping revealed that multiple sites were phosphorylated. Both serine and threonine residues were found to be labeled with 32P. Limited proteolysis of the autophosphorylated kinase with trypsin resulted in the conversion of the kinase into a phospholipid- and Ca2+-independent form. Two major 32P-labeled fragments, Mr = 48,000 and 38,000, were formed as a result of proteolysis, suggesting that the catalytic domain and possibly the Ca2+- and phospholipid-binding region were both phosphorylated. Protein kinase C autophosphorylation has a Km for ATP (1.5 microM) about 10-fold lower than that for phosphorylation of exogenous substrates. The kinetically preferred autophosphorylation appears to be an intramolecular reaction. The autophosphorylated protein kinase C, unlike the protease-degraded enzyme, still depends on Ca2+ and phospholipid for maximal activity. However, the autophosphorylated form of the kinase has a lower Ka for Ca2+ and a higher affinity for the binding of [3H]phorbol-12, 13-dibutyrate. These findings suggest that autophosphorylation of protein kinase C may be important in the regulation of the enzymic activity subsequent to signal transduction.
Faculty Opinions recommendation of High progression-free survival after intermediate intensity double unit cord blood transplantation in adults. (2021)

Cord blood transplantation (CBT) after high intensity or nonmyeloablative conditioning has limitations. We investigated cyclosporine-A/mycophenolate mofetil-based intermediate intensity (cyclophosphamide 50 mg/kg, fludarabine 150 mg/m2, thiotepa 10 mg/kg, total body irradiation 400 cGy) unmanipulated double-unit CBT (dCBT) with prioritization of unit quality and CD34+ cell dose in graft selection. Ninety adults (median age, 47 years [range, 21-63]; median hematopoietic cell transplantation comorbidity index, 2 [range, 0-8]; 61 [68%] acute leukemia) received double-unit grafts (median CD34+ cell dose, 1.3 × 105/kg per unit [range, 0.2-8.3]; median donor-recipient human leukocyte antigen (HLA) match, 5/8 [range 3-7/8]). The cumulative incidences of sustained CB engraftment, day 180 grade III-IV acute, and 3-year chronic graft-versus-host disease were 99%, 24%, and 7%, respectively. Three-year transplant-related mortality (TRM) and relapse incidences were 15% and 9%, respectively. Three-year overall survival (OS) is 82%, and progression-free survival (PFS) is 76%. Younger age and higher engrafting unit CD34+ cell dose both improved TRM and OS, although neither impacted PFS. Engrafting unit-recipient HLA match was not associated with any outcome with a 3-year PFS of 79% in 39 patients engrafting with 3-4/8 HLA-matched units. In 52 remission acute leukemia patients, there was no association between minimal residual disease (MRD) and 3-year PFS: MRD negative of 88% vs MRD positive of 77% (P = .375). Intermediate intensity dCBT is associated with high PFS. Use of highly HLA mismatched and unmanipulated grafts permits wide application of this therapy, and the low relapse rates support robust graft-versus-leukemia effects even in patients with MRD.© 2020 by The American Society of Hematology. PMID: 33290545 Funding information This work was supported by: NHLBI NIH HHS, United States Grant ID: K08 HL143189
Rash and fever in a kidney transplant recipient (2020)

A 59-year-old man was admitted to the hospital with a 2-day history of rash and high fever. He reported malaise and myalgia but denied itchiness and respiratory, gastrointestinal, and urinary symptoms. He had received a living-donor kidney transplant 6 years previously; his primary renal disease was IgA nephropathy. His past medical history included hypertension, diverticular disease, and osteopenia. Two months prior to this presentation, he experienced acute allograft dysfunction due to intragraft posttransplant lymphoproliferative disorder (PTLD) with associated Epstein–Barr virus (EBV) viremia. The allograft dysfunction had resolved with valganciclovir treatment. Tacrolimus and mycophenolate mofetil were stopped and prednisolone (10 mg daily) was commenced as the sole immunosuppressive agent. EBV had then become undetectable by polymerase chain reaction (PCR). Two weeks prior to the current presentation, azathioprine (50 mg daily) was added to his immunosuppressive regimen. Other medications included ramipril and vitamin D. On examination, his heart rate was 108 bpm and his blood pressure was 140/86 mmHg. His temperature was 40°C/104°F. No focal infective signs were present, and no lymphadenopathy was detected. The renal graft was nontender on palpation. He had a rash (Figure 1) localized to the chest, abdomen, back, and legs. The neck, face, scalp, and mucous membranes were unaffected. Blood tests revealed stable allograft function (a creatinine level of 1.5 mg/dL), a C-reactive protein level of 350 mg/L, and a white blood cell count of 13.2 × 109/L with 90% neutrophils. Other hematological and biochemical parameters were within normal limits, and chest radiograph was normal. Urinalysis demonstrated protein + only. Multiple blood cultures were negative for bacterial and fungal growth. 1What is the most appropriate initial investigation?aComputed tomography (CT) scan of the chest, abdomen, and pelvisbSerum IgA titercRenal allograft biopsydSkin biopsyeVaricella zoster virus (VZV) PCR2What does the skin biopsy light microscopy (Figure 2) show?aEpidermal keratinocyte necrosisbEpidermal thickeningcIgA deposition in superficial capillariesdLeukocytoclastic vasculitiseNeutrophilic folliculitis3What is the diagnosis?aAzathioprine hypersensitivity syndromebHenoch–Schönlein purpuracPTLDdSweet’s syndromeeVZV infection4What is the best course of management?aStart acyclovirbStart broad-spectrum antibioticscStart high-dose corticosteroidsdStart plasma exchangeeStop azathioprine
A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture (2011)

Incorporating gene regulation into the model of solvent production by C. acetobutylicum enables an accurate representation of the pH-induced switch to solvent production to be obtained and theoretical investigations of possible synthetic-biology approaches to be pursued. Steady-state analyses suggest that, to increase butanol yield, alterations in the expression of single solvent-associated genes are insufficient; a more complex approach targeting two or more genes is required.
Enlarged cisterna magna and the Dandy-Walker malformation: factors associated with chromosome abnormalities. (1991)

Thirty-three fetuses with an enlarged cisterna magna (10 mm or more) were evaluated to determine factors that might be associated with an underlying chromosome abnormality. Eighteen fetuses (55%) proved to have a chromosome abnormality, including trisomy 18 or trisomy 18 variant (12), trisomy 13 (three), Turner syndrome (one), or other rearrangements (two). Among various risk factors analyzed, the absence of ventricular dilatation correlated most strongly with a chromosome abnormality. Chromosome abnormalities were found in 17 of 22 fetuses (77%) lacking ventricular dilatation, compared with only one of 11 fetuses (9%) with ventricular dilatation (P less than .001). Other factors statistically associated (P less than .01) with an underlying chromosome abnormality included mild enlargement of the cisterna magna (10-14 mm), concurrent anomalies detected sonographically, and fetal growth retardation. However, stepwise logistic regression showed that only the absence of ventricular dilatation and the presence of concurrent anomalies were significant when multiple factors were evaluated. These observations support the utility of evaluating the cisterna magna as part of a routine anatomical survey.
The Application of Next Generation Sequencing to the Understanding of Antibody Repertoires (2013)

In the decade since the human genome sequence was declared complete, the development of next generation sequencing (NGS) or "deep" sequencing to deliver cost-effective genomic sequencing has influenced advances beyond its primary application and changed the research landscape in many other areas. This review will survey recent applications of NGS which have broadened the understanding of natural antibody repertoires (the "antibodyome") and how these evolve in response to viral infection. We will also report examples where deep sequencing of binding populations, derived from both natural and synthetic repertoires, have been used to benefit antibody engineering. This knowledge will ultimately lead to the design of more effective biological drugs and vaccines.
Topological signatures and stability of hexagonal close packing and Barlow stackings (2021)

Two common representations of close packings of identical spheres consisting of hexagonal layers, called Barlow stackings, appear abundantly in minerals and metals. These motifs, however, occupy an identical portion of space and bear identical first-order topological signatures as measured by persistent homology. Here we present a novel method based on <i>k</i>-fold covers that unambiguously distinguishes between these patterns. Moreover, our approach provides topological evidence that the FCC motif is the more stable of the two in the context of evolving experimental sphere packings during the transition from disordered to an ordered state. We conclude that our approach can be generalised to distinguish between various Barlow stackings manifested in minerals and metals.
Ion-Ion Proton Transfer and Parallel Ion Parking for the Analysis of Mixtures of Intact Proteins on a Modified Orbitrap Mass Analyzer (2019)

We have enabled parallel ion parking on a modified Orbitrap Elite™ as a way to control ion-ion proton transfer reactions via selective activation of a range of ions. The result is the concentration of the majority of ion current from multiple charge states of each precursor proteoform into a single charge state, maximizing signal intensity and increasing effective sensitivity compared to conventional MS1 spectra. These techniques were applied in an on-line HPLC, data-dependent MS/MS analysis of intact E. coli ribosomal proteins with HCD fragmentation. With one injection, all but two ribosomal proteins were selected for fragmentation and subsequently identified. The techniques described facilitate rapid identification of intact proteins in complex mixtures and an enhanced ability to observe proteins of low abundance.
Changing trends in antimicrobial susceptibility and hospital acquired infections over an 8 year period in a tertiary care hospital in relation to introduction of an infection control programme. (2010)

Resistance among Gram negative pathogens (especially ESBL production in Enterobacteriaceae and carbapenem resistance in Pseudomonas and Acinetoacter) is a major problem in our tertiary care hospital. On the other hand C.difficile and VRE are rarely encountered. Infection control measures were modestly effective in reducing CRBSI/ VAP rates but resistance rates among Gram negative pathogens were not significantly lowered.
Brief Communication Impact of a Phosphorothioate Oligodeoxynucleotide MCP-1 on NF-kB, AP-1, SP1 and NF- kB, and AP-1 Subunit Composition in Human Pulmonary Endothelial Cells (2001)

Phosphorothioate oligodeoxynucleotides (PS-ODN) are widely used prototypic antisense oligomers for sequence-specific suppression of normal and diseased gene expression. As polyanionic molecules, however, PSODN may also evoke nonsequence-specific side effects. The objective of the present study was to evaluate the impact of PS-ODN treatment of human pulmonary artery endothelial cells (HPAEC) and microvascular endothelial cells of the lung (HMVEC-L) on the cellular pool of the transcription factors nuclear factor- kB (NFkB) and activator protein-1 (AP-1) as well as Sp1, using gel shift assays. In addition, by performing supershift assays, we investigated whether antisense treatment of endothelial cells affected the subunit composition of NFkB and AP-1. Our data show that pretreatment of HPAEC and HMVEC-L with PS-ODN doses ranging from 50 to 5000 nM did not affect the total NF- kB, AP-1, or Sp1 pool in tumor necrosis factor- a (TNF-a)-activated endothelial cells (EC) or the subunit composition of the transcription factors NF- kB and AP-1. These findings suggest that putative nonsequence-specific effects of PS-ODN are not due to interactions of these oligomers with the transcription factors NF- kB, AP-1, or Sp1, at least in the EC type, a common target in transfection studies.
Layout constrained body-biasing for thermal clock-skew compensation (2012)

In this work we investigate on the actual capability of adaptive body bias to be applied on Clock Distribution Networks (CDNs) for dynamic compensation of thermally-induced skews. Selectively applying different bulk polarizations to the clock buffers, i.e., Forward Body Bias (FBB) to speed-up, or Reverse Body Bias (RBB) to slow down, it is possible to recover the timing phase shifts which accumulate along the clock tree paths due to on-chip thermal gradients. However, the physical implementation of such technique is not trivial: While a fine tuning of the clock buffers would require to apply a cell-by-cell biasing, design constraints due to semi-custom layout rules impose a higher granularity, that is, a physical cluster of cells, i.e., a layout row. We therefore propose a row-based ILP formulation that considers the aforementioned physical constraints and that provides optimal body bias assignment for thermal clock skew minimization. As will shown for a set of realistic benchmarks mapped into an industrial 40nm technology, our solution allows real skew compensation under different thermal profiles while avoiding unfeasible conditions where buffers placed in the same row require different bulk polarizations.
One-step and eco-friendly modification of cellulose membranes by polymer grafting (2014)

Cellulose sheets were grafted with several acrylic polymers, first globally through a dipping procedure and then locally by inkjet printing.