gebhart/patrepeval huggingface dataset:
Sub-Space Modeling: An Enrollment Solution for XOR Arbiter PUF using Machine Learning (2022)

Summary form only given. In this work we present sub-space modeling of XOR Arbiter PUF as a cost efficient solution for enrollment for the designers’ community. Our goal is to demonstrate a method which can reduce the overall cost in terms of number of CRPs required for training, training time and memory. Here we propose to reduce the complexity of the modeling target by dividing the PUF into smaller sub-components and model each sub-component of the PUF independently. Our early experimental assessment show that our sub-space modeling can significantly reduce the cost of training compared to some of the latest works, thus it is potentially a cost-efficient solution to enroll strong PUF with high complexity.
Supplementation of native grass hay with cowpea (Vigna unguiculata) hay, wilted leucaena (Leucaena leucocephala) forage, wilted tagasaste (Chamaecytisus palmensis) forage or a wheat middling for young Friesian x Zebu (Boran) crossbred steers (1992)

A 100-day experiment of a randomized block design was conducted with forty Friesian x Zebu (Boran) crossbred growing steers to compare the value of wheat middling, an agro-industrial by-product (diet W), cowpea (Vigna unguiculata) hay (diet C), and wilted forages of leucaena (Leucaena leucocephala, diet L) and tagasaste (Chamaecytisus palmensis, diet T) as cattle feed. These feeds were fed daily at a level of 1.5 kg (on an air dry basis) to supplement the basal diet (diet H) of native hay. A mineral supplement containing 50 g bone meal and 10 g common salt was also given daily. The steers were group-fed, but during the last two weeks at the end of the experiment the animals were housed individually in feeding pens to estimate the feed intake and apparent digestibilities of the diets. The animals were weighed at the beginning of the experiment, thereafter every two weeks, and finally at the end of the experiment. The animals consumed all the offered supplements, except for tagasaste forage, of which one third remained unconsumed. The mean daily total dry matter intake during the individual feeding period ranged from 4.0 to 5.0 kg between the diets (P
Synthesis of Isoreticular Zinc(II)‐Phosphonocarboxylate Frameworks and Their Application in the Friedel–Crafts Benzylation Reaction (2011)

Three isoreticular zinc(II)-phosphonocarboxylate frameworks, namely {[Zn(3)(pbdc)(2)]·2H(3)O}(n) (ZnPC-2), {[Zn(3)(pbdc)(2)]·Hpd·H(3)O·4H(2)O}(n) (Hpd@ZnPC-2) and {[Co(1.5)Zn(1.5)(pbdc)(2)]·2H(3)O}(n) (CoZnPC-2) (H(4)pbdc=5-phosphonobenzene-1,3-dicarboxylic acid, pd=pyrrolidine), were solvothermally synthesized. ZnPC-2 has a 3D structure based on trinuclear Zn(II) clusters (Zn(3)-SBU) showing 3D interconnected channels. Hpd@ZnPC-2 contains an isoreticular framework of ZnPC-2 with small channels blocked by Hpd molecules. In CoZnPC-2, Zn(II) ions in ZnPC-2 are partially substituted by Co(II) ions. The Friedel-Crafts benzylation reactions were carried out over these isoreticular porous materials. The catalytic results reveal that ZnPC-2 is an excellent heterogeneous Lewis acid catalyst with a high selectivity (>90%) towards less bulky para-oriented products. The catalytic reaction has been proved to occur inside the pore of ZnPC-2, and the immobilized Zn(3)-SBUs are the active sites.
A single strain of Mycobacterium bovis bacillus Calmette-Guérin (BCG) grown in two different media evokes distinct humoral immune responses in mice (2001)

Two attenuated bacillus Calmette-Guérin (BCG) preparations derived from the same Moreau strain, Copenhagen but grown in Sauton medium containing starch and bacto-peptone (onco BCG, O-BCG), or asparagine (intradermal BCG, ID-BCG), exhibited indistinguishable DNA sequences and bacterial morphology. The number of viable bacilli recovered from spleen, liver and lungs was approximately the same in mice inoculated with the vaccines and was similarly reduced (over 90%) in mice previously immunized with either BCG vaccine. The humoral immune response evoked by the vaccines was, however, distinct. Spleen cell proliferation accompanying the growth of bacilli in tissue was significantly higher in mice inoculated with O-BCG. These cells proliferated in vitro upon challenge with the corresponding BCG extract. Previous cell treatment with mAb anti-CD4 T cells abolished this effect. Anti-BCG antibodies, as assayed either in serum by ELISA or by determining the number of antibody-producing spleen cells by the spot-ELISA method, were significantly higher in mice inoculated with ID-BCG. Anti-BCG antibodies were detected in all immunoglobulin classes, but they were more prevalent in IgG with the following distribution among its isotypes: IgG1>(IgG2a = IgG2b)>IgG3. When some well-characterized Mycobacterium tuberculosis antigens were used as substitutes for BCG extracts in ELISA, although antibodies against the 65-kDa and 96-kDa proteins were detected significantly, antibodies against the 71-kDa, 38-kDa proteins and lipoarabinomannan were only barely detected or even absent. These results indicate that BCG bacilli cultured in Sauton-asparagine medium permitted the multiplication of bacilli, tending to induce a stronger humoral immune response as compared with bacilli grown in Sauton-starch/bacto-peptone-enriched medium.
Integration of microRNA miR-122 in hepatic circadian gene expression (2009)

In liver, most metabolic pathways are under circadian control, and hundreds of protein-encoding genes are thus transcribed in a cyclic fashion. Here we show that rhythmic transcription extends to the locus specifying miR-122, a highly abundant, hepatocyte-specific microRNA. Genetic loss-of-function and gain-of-function experiments have identified the orphan nuclear receptor REV-ERBalpha as the major circadian regulator of mir-122 transcription. Although due to its long half-life mature miR-122 accumulates at nearly constant rates throughout the day, this miRNA is tightly associated with control mechanisms governing circadian gene expression. Thus, the knockdown of miR-122 expression via an antisense oligonucleotide (ASO) strategy resulted in the up- and down-regulation of hundreds of mRNAs, of which a disproportionately high fraction accumulates in a circadian fashion. miR-122 has previously been linked to the regulation of cholesterol and lipid metabolism. The transcripts associated with these pathways indeed show the strongest time point-specific changes upon miR-122 depletion. The identification of Pparbeta/delta and the peroxisome proliferator-activated receptor alpha (PPARalpha) coactivator Smarcd1/Baf60a as novel miR-122 targets suggests an involvement of the circadian metabolic regulators of the PPAR family in miR-122-mediated metabolic control.
Plastids Contain a Second Sec Translocase System with Essential Functions (2010)

Proteins that are synthesized on cytoplasmic ribosomes but function within plastids must be imported and then targeted to one of six plastid locations. Although multiple systems that target proteins to the thylakoid membranes or thylakoid lumen have been identified, a system that can direct the integration of inner envelope membrane proteins from the stroma has not been previously described. Genetics and localization studies were used to show that plastids contain two different Sec systems with distinct functions. Loss-of-function mutations in components of the previously described thylakoid-localized Sec system, designated as SCY1 (At2g18710), SECA1 (At4g01800), and SECE1 (At4g14870) in Arabidopsis (Arabidopsis thaliana), result in albino seedlings and sucrose-dependent heterotrophic growth. Loss-of-function mutations in components of the second Sec system, designated as SCY2 (At2g31530) and SECA2 (At1g21650) in Arabidopsis, result in arrest at the globular stage and embryo lethality. Promoter-swap experiments provided evidence that SCY1 and SCY2 are functionally nonredundant and perform different roles in the cell. Finally, chloroplast import and fractionation assays and immunogold localization of SCY2-green fluorescent protein fusion proteins in root tissues indicated that SCY2 is part of an envelope-localized Sec system. Our data suggest that SCY2 and SECA2 function in Sec-mediated integration and translocation processes at the inner envelope membrane.
Localization of Hidden Insulinomas with 68Ga-DOTA-Exendin-4 PET/CT: A Pilot Study (2015)

These preliminary data suggest that the use of (68)Ga-DOTA-exendin-4 PET/CT in detecting hidden insulinomas is feasible.
A note on irrotational viscous flow (2005)

This Brief Communication describes features of steady irrotational flow in a viscous fluid. The aim is to illustrate, in a simple manner, the different roles played by viscous forces (which are identically zero) and viscous stresses (which are not), the differences in behavior of stagnation pressure (which is constant along a streamline even in the presence of viscous dissipation) and stagnation enthalpy (which changes through the flow), and the role of viscous stresses on the boundary in creating these behaviors.
Quantitative Assessment of the SR Ca 2+ Leak-Load Relationship (2002)

Increased diastolic SR Ca2+ leak (J(leak)) could depress contractility in heart failure, but there are conflicting reports regarding the J(leak) magnitude even in normal, intact myocytes. We have developed a novel approach to measure SR Ca2+ leak in intact, isolated ventricular myocytes. After stimulation, myocytes were exposed to 0 Na+, 0 Ca2+ solution +/-1 mmol/L tetracaine (to block resting leak). Total cell [Ca2+] does not change under these conditions with Na+-Ca2+ exchange inhibited. Resting [Ca2+]i declined 25% after tetracaine addition (126+/-6 versus 94+/-6 nmol/L; P<0.05). At the same time, SR [Ca2+] ([Ca2+](SRT)) increased 20% (93+/-8 versus 108+/-6 micromol/L). From this Ca2+ shift, we calculate J(leak) to be 12 micromol/L per second or 30% of the SR diastolic efflux. The remaining 70% is SR pump unidirectional reverse flux (backflux). The sum of these Ca2+ effluxes is counterbalanced by unidirectional forward Ca2+ pump flux. J(leak) also increased nonlinearly with [Ca2+](SRT) with a steeper increase at higher load. We conclude that J(leak) is 4 to 15 micromol/L cytosol per second at physiological [Ca2+](SRT). The data suggest that the leak is steeply [Ca2+](SRT)-dependent, perhaps because of increased [Ca2+]i sensitivity of the ryanodine receptor at higher [Ca2+](SRT). Key factors that determine [Ca2+](SRT) in intact ventricular myocytes include (1) the thermodynamically limited Ca2+ gradient that the SR can develop (which depends on forward flux and backflux through the SR Ca2+ ATPase) and (2) diastolic SR Ca2+ leak (ryanodine receptor mediated).
Enhanced Photocatalytic Performance of Brookite TiO2 Macroporous Particles Prepared by Spray Drying with Colloidal Templating (2007)

Macroporous particle photocatalysts can be produced using polystyrene latex (PSL) colloidal templating (see figure), which can be used for organic waste degradation. The rate of degradation is similar to that of nanoparticles. Macroporous particles have lower mechanical mobilities than nanoparticles and can be easily collected and recovered for repeated use.
Overview of the Development of Solid Oxide Fuel Cells at Forschungszentrum Juelich (2005)

The SOFC group at FZJ has assembled and tested more than 190 SOFC stacks during the last 10 years, rated between 100 W and 15 kW. The topics of high performance materials, corrosion, materials matching and cost-effectiveness, including manufacturing processes etc. are being continuously addressed. Use of the ferritic steel JS-3 that was developed at FZJ has resulted in reduced degradation rates around 1% per 1000 hours over stack lifetimes of more than 8000 hours. However, the target of the development is directed towards 0.25%/1000 h for commercial operation in stationary applications. Large stacks of 5 kW and above have been operated since 2002 and also been successfully delivered and operated in Finland and Korea. In parallel, light-weight stacks are being developed in the so-called 'cassette design' line for SOFC-APU. Several 1 to 20 kW SOFC laboratory systems are in preparation, partly using the integrated stack concept which combines all hot parts of the balance of plant into one single module.
Integrated analysis reveals distinct molecular, clinical, and immunological features of B7‐H3 in acute myeloid leukemia (2021)

The role of B7-H3 in acute myeloid leukemia (AML) is not fully understood. Two previous studies investigating its expression and significances in AML are partially different. In this study, we aimed to systematically characterize the genomic and immune landscape in AML patients with altered B7-H3 expression using multi-omics data in the public domain. We found significantly increased B7-H3 expression in AML compared to either other hematological malignancies or healthy controls. Clinically, high B7-H3 expression was associated with old age, TP53 mutations, wild-type WT1 and CEBPA, and the M3 and M5 FAB subtypes. Moreover, we observed that increased B7-H3 expression correlated significantly with a poor outcome of AML patients in four independent datasets. Gene set enrichment analysis (GSEA) revealed the enrichment of the "EMT" oncogenic gene signatures in high B7-H3 expressers. Further investigation suggested that B7-H3 was more likely to be associated with immune-suppressive cells (macrophages, neutrophils, dendritic cells, and Th17 cells). B7-H3 was also positively associated with a number of checkpoint genes, such as VISTA (B7-H5), CD80 (B7-1), CD86 (B7-2), and CD70. In summary, we uncovered distinct genomic and immunologic features associated with B7-H3 expression in AML. This may lead to a better understanding of the molecular mechanisms underlying B7-H3 dysregulation in AML and to the development of novel therapeutic strategies.
Role of the D arm and the anticodon arm in tRNA recognition by eubacterial and eukaryotic RNase P enzymes (1993)

Truncated precursor tRNAs lacking the D arm or anticodon arm were studied in vitro as substrates for RNase P enzymes from Escherichia coli, Thermus thermophilus (eubacteria), and HeLa. Deletion of the D arm still allowed 5'-processing by E. coli RNase P, but strongly impaired maturation by T. thermophilus and HeLa extracts. In contrast, deletion of the anticodon arm had no influence on processing by RNase P activities from all three organisms. Inhibition kinetics and gel retardation studies showed that deletion of the D arm leads to low-affinity binding to E. coli RNase P RNA (M1 RNA). However, the E. coli enzyme appears to form sufficiently strong contacts in the region of the T arm, acceptor stem, and CCA terminus to still allow productive enzyme-substrate interaction even in the absence of the structural contribution provided by the D arm. Pb(2+)-induced hydrolysis of a tRNAGly from T. thermophilus gave identical cleavage patterns in the D arm and anticodon loop in the absence and presence of E. coli M1 RNA, whereas lead hydrolysis was strongly reduced at the CUCCAA 3'-terminus due to the presence of the enzyme.
PMU Placement Optimization for Efficient State Estimation in Smart Grid (2019)

This paper investigates phasor measurement unit (PMU) placement for informative state estimation in smart grid by incorporating various constraints for observability. Observability constitutes an important property for PMU placement to characterize the depth of the buses' reachability by the placed PMUs, but addressing it solely by binary linear programming as in many works still does not guarantee a good estimate for the grid state. Some existing works have considered optimization of some estimation indices by ignoring the observability requirements for computational ease and thus potentially lead to trivial results such as acceptance of the estimate for an unobserved state component as its unconditional mean. In this work, the PMU placement optimization problem is considered by minimizing the mean squared error or maximizing the mutual information between the measurement output and grid state subject to observability constraints, which incorporate operating conditions such as presence of zero injection buses, contingency of measurement loss, and limitation of communication channels per PMU. The proposed design is thus free from the fundamental shortcomings in the existing PMU placement designs. The problems are posed as large scale binary nonlinear optimization problems involving thousands of binary variables, for which this paper develops efficient algorithms for computational solutions. Their performance is analyzed in detail through numerical examples on large scale IEEE power networks. The solution method is also shown to be extendable to AC power flow models, which are formulated by nonlinear equations.
Die Reibung, Wärmeleitung und Diffusion in Gasmischungen. XXVI. Die innere Reibung von Propylen und β‐Butylen und von ihren Mischungen mit He oder H2 (1934)

Abstract I. Messungsverfahren. ‐ II. Ergebnisse: a) Reingase; b) Gemische. ‐ III. Zusammenfassung.
HiHi fMRI: a data-reordering method for measuring the hemodynamic response of the brain with high temporal resolution and high SNR (2022)

There is emerging evidence that sampling the blood-oxygen-level-dependent (BOLD) response with high temporal resolution opens up new avenues to study the in vivo functioning of the human brain with functional magnetic resonance imaging. Because the speed of sampling and the signal level are intrinsically connected in magnetic resonance imaging via the T1 relaxation time, optimization efforts usually must make a trade-off to increase the temporal sampling rate at the cost of the signal level. We present a method, which combines a sparse event-related stimulus paradigm with subsequent data reshuffling to achieve high temporal resolution while maintaining high signal levels (HiHi). The proof-of-principle is presented by separately measuring the single-voxel time course of the BOLD response in both the primary visual and primary motor cortices with 100-ms temporal resolution.
Time-dependent genetic effects on gene expression implicate aging processes (2017)

Gene expression is dependent on genetic and environmental factors. In the last decade, a large body of research has significantly improved our understanding of the genetic architecture of gene expression. However, it remains unclear whether genetic effects on gene expression remain stable over time. Here, we show, using longitudinal whole-blood gene expression data from a twin cohort, that the genetic architecture of a subset of genes is unstable over time. In addition, we identified 2213 genes differentially expressed across time points that we linked with aging within and across studies. Interestingly, we discovered that most differentially expressed genes were affected by a subset of 77 putative causal genes. Finally, we observed that putative causal genes and down-regulated genes were affected by a loss of genetic control between time points. Taken together, our data suggest that instability in the genetic architecture of a subset of genes could lead to widespread effects on the transcriptome with an aging signature.
Large B-Cell Lymphomas in the 5th Edition of the WHO-Classification of Haematolymphoid Neoplasms—Updated Classification and New Concepts (2023)

The family/class of the large B-cell lymphomas (LBCL) in the 5th edition of the World Health Organization (WHO) classification of haematolymphoid tumors (WHO-HAEM5) features only a few major changes as compared to the 4th edition. In most entities, there are only subtle changes, many of them only representing some minor modifications in diagnostic terms. Major changes have been made in the diffuse large B-cell lymphomas (DLBCL)/high-grade B-cell lymphomas (HGBL) associated with <i>MYC</i> and <i>BCL2</i> and/or <i>BCL6</i> rearrangements. This category now consists of <i>MYC</i> and <i>BCL2</i> rearranged cases exclusively, while the <i>MYC/BCL6</i> double hit lymphomas now constitute genetic subtypes of DLBCL, not otherwise specified (NOS) or of HGBL, NOS. Other major changes are the conceptual merger of lymphomas arising in immune-privileged sites and the description of LBCL arising in the setting of immune dysregulation/deficiency. In addition, novel findings concerning underlying biological mechanisms in the pathogenesis of the different entities are provided.
Converting networks to predictive logic models from perturbation signalling data with CellNOpt (2020)

Abstract Motivation The molecular changes induced by perturbations such as drugs and ligands are highly informative of the intracellular wiring. Our capacity to generate large data-sets is increasing steadily as new experimental approaches are developed. A useful way to extract mechanistic insight from the data is by integrating them with a prior knowledge network of signalling to obtain dynamic models. Logic models scale better with network size than alternative kinetic models, while keeping the interpretation of the model simple, making them particularly suitable for large datasets. Results CellNOpt is a collection of Bioconductor R packages for building logic models from perturbation data and prior knowledge of signalling networks. We have recently developed new components and refined the existing ones. These updates include (i) an Integer Linear Programming (ILP) formulation which guarantees efficient optimisation for Boolean models, (ii) a probabilistic logic implementation for semi-quantitative datasets and (iii) the integration of MaBoSS, a stochastic Boolean simulator. Furthermore, we introduce Dynamic-Feeder, a tool to identify missing links not present in the prior knowledge. We have also implemented systematic post-hoc analyses to highlight the key components and parameters of our models. Finally, we provide an R-Shiny tool to run CellNOpt interactively. Availability R-package(s): https://github.com/saezlab/cellnopt Contact julio.saez@bioquant.uni-heidelberg.de Supplementary information Supplemental Text.
Cardiomyopathy phenotypes in human-induced pluripotent stem cell-derived cardiomyocytes—a systematic review (2018)

Human-induced pluripotent stem cells (hiPSC) can be differentiated to cardiomyocytes at high efficiency and are increasingly used to study cardiac disease in a human context. This review evaluated 38 studies on hypertrophic (HCM) and dilated cardiomyopathy (DCM) of different genetic causes asking to which extent published data allow the definition of an in vitro HCM/DCM hiPSC-CM phenotype. The data are put in context with the prevailing hypotheses on HCM/DCM dysfunction and pathophysiology. Relatively consistent findings in HCM not reported in DCM were larger cell size (156 ± 85%, n = 15), more nuclear localization of nuclear factor of activated T cells (NFAT; 175 ± 65%, n = 3), and higher β-myosin heavy chain gene expression levels (500 ± 547%, n = 8) than respective controls. Conversely, DCM lines showed consistently less force development than controls (47 ± 23%, n = 9), while HCM forces scattered without clear trend. Both HCM and DCM lines often showed sarcomere disorganization, higher NPPA/NPPB expression levels, and arrhythmic beating behaviour. The data have to be taken with the caveat that reporting frequencies of the various parameters (e.g. cell size, NFAT expression) differ widely between HCM and DCM lines, in which data scatter is large and that only 9/38 studies used isogenic controls. Taken together, the current data provide interesting suggestions for disease-specific phenotypes in HCM/DCM hiPSC-CM but indicate that the field is still in its early days. Systematic, quantitative comparisons and robust, high content assays are warranted to advance the field.
New soliton solutions of dissipative (2+1)-dimensional AKNS equation (2013)

We employ the idea of Hirota's bilinear method, to obtain some new exact soliton solutions for high nonlinear form of dissipative (2+1)-dimensional AKNS equation. Multiple singular soliton solutions were obtained by this method. Moreover, multiple singular soliton solutions were also derived.