gebhart/patrepeval huggingface dataset:
Estimating patient-specific treatment advantages in the ‘Treatment for Adolescents with Depression Study’ (2018)

The ‘Treatment for Adolescents with Depression Study’ (TADS, ClinicalTrials.gov, identifier: NCT00006286) was a cornerstone, randomized controlled trial evaluating the effectiveness of standard treatment options for major depression in adolescents. Whereas previous TADS analyses examined primarily effect modifications of treatment-placebo differences by various patient characteristics, less is known about the modification of inter-treatment differences, and hence, patient characteristics that might guide treatment selection. We sought to fill this gap by estimating patient-specific inter-treatment differences as a function of patients’ baseline characteristics. We did so by applying the ‘model-based random forest’, a recently-introduced machine learning-based method for evaluating effect heterogeneity that allows for the estimation of patient-specific treatment effects as a function of arbitrary baseline characteristics. Treatment conditions were cognitive-behavioural therapy (CBT) alone, fluoxetine (FLX) alone, and the combination of CBT and fluoxetine (COMB). All inter-treatment differences (CBT vs. FLX; CBT vs. COMB; FLX vs. COMB) were evaluated across 23 potential effect modifiers extracted from previous studies. Overall, FLX was superior to CBT, while COMB was superior to both CBT and FLX. Evidence for effect heterogeneity was found for the CBT-FLX difference and the FLX-COMB difference, but not for the CBT-COMB difference. Baseline depression severity modified the CBT-FLX difference; whereas baseline depression severity, patients’ treatment expectations, and childhood trauma modified the FLX-COMB difference. All modifications were quantitative rather than qualitative, however, meaning that the differences varied only in magnitude, but not direction. These findings imply that combining CBT with fluoxetine may be superior to either therapy used alone across a broad range of patients.
Two-Dimensional MXenes Mo2Ti2C3Tz and Mo2TiC2Tz: Microscopic Conductivity and Dynamics of Photoexcited Carriers (2020)

MXenes are a recently discovered family of two-dimensional transition metal carbides, nitrides, and carbonitrides with electronic properties that can be tuned by their chemistry and structure. Herein THz spectroscopy was used to investigate the microscopic conductivity and photoexcited charge carrier dynamics in two Mo-based MXenes: Mo2Ti2C3Tz and Mo2TiC2Tz. We find that both have high intrinsic carrier densities (∼1020 cm–3 in Mo2Ti2C3Tz and ∼1019 cm–3 in Mo2TiC2Tz) and mobilities and exhibit high conductivities within individual nanosheets. Optical excitations result in a transient conductivity increase in both compositions, in stark contrast with the most studied member of the MXene family, Ti3C2Tz, where photoexcitation suppresses the conductivity for nanoseconds. Deintercalation of water, and other species, from between the nanosheets by mild vacuum annealing at 200 °C further improves the long-range, internanosheet transport of the photoexcited carriers and increases their lifetime. High, and long-lived, photoinduced conductivity that can be engineered by substituting Mo for Ti renders these Mo-based MXenes attractive for a variety of optoelectronic, sensing, and photoelectrochemical applications.
Comparison of Purified Alpha-Toxins from Various Strains of Staphylococcus aureus (1974)

Alpha-toxin from five strains of Staphylococcus aureus, including Wood 46, was purified by isoelectric focusing. The alpha-toxins obtained from different strains were similar. The isoelectric point of the purified toxins was 8.65 +/- 0.15. Sharp concentration peaks were not always obtained. In the ultracentrifuge the alpha-toxins migrated usually as three peaks which could be dissociated with propionic acid to yield one peak. A single line of identity was obtained in immunoelectrophoresis when a heterologous antiserum was reacted with the five purified toxins. It was concluded that the widespread use of the Wood 46 strain for the production of alpha-toxin is justified.
Graded Coatings for Light Gas Gun Flyer Plate Applications (2006)

Abstract Use of graded coatings is a well-known strategy for creating materials with continuously changing physical properties. The stiffness (modulus of elasticity) and density of flyer plates used in light gas gun testing directly influences the shape of the shock wave produced by the flyer plate. Many strategies exist for creating flyer plates that produce variable shock profiles, including stacked foils and powder compaction. We have investigated graded thermal spray coatings as an alternative method for creating flyer plates that produce variable shock profiles. An initial proof of concept demonstration has been completed by air plasma spraying a graded coating of Cu &amp; Al onto a copper substrate. This composite flyer plate was tested in a light gas gun to demonstrate that a non-linear shock profile can be created. The plasma spray strategies used to create a group of similar graded density impactors are discussed. Initial light gas gun testing shows that graded density impactors can be created using thermal spray coatings.
Continuing the Reformation: Essays on Modern Religious Thought [review] / B.A. Gerrish. (1997)

only through yieldedness.No. 12, Regarding the , was very popular, being issued in four original editions (from Jena, Augsburg, Strasbourg, and Constance) as well as at least three known reprint editions.Of the booklet's 13 sections, seven address the basic theology and spirituality of the Sabbath rest, five describe aspects of how the Sabbath should be celebrated or may be desecrated (3 18), one considers "Which Day of the Week Must be Celebrated" (333-334), and one is a polemic against "Designated Feast Days for Saints and Angels," (336-337).No. 15, O n the Incarnation of Christ is Carlstadt's farewell sermon to his Zurich congregation in 1534, on accepting the professorship at Basel.It contains traces of the warm, emphatic spirituality seen in the earlier works, but is more notable for its "orthodox Christology" (387).
Campylobacter coli Clade 3 Isolates Induce Rapid Cell Death In Vitro (2018)

<i>Campylobacter</i> bacteria are major human enteropathogens. <i>Campylobacter coli</i> shows less genetic diversity than <i>C. jejuni</i> and clusters into three clades, of which clade 1 includes most human and farm animal isolates, while environmental <i>C. coli</i> isolates mainly belong to clades 2 and 3. Recently, we sequenced the whole genomes of eight <i>C. coli</i> clade 2 and 3 isolates cultivated from water, and here we studied their interaction with human HT-29 colon cancer cells compared to that of clinical clade 1 isolates. All <i>C. coli</i> clade 3 isolates already caused cell necrosis 1 to 2 h after inoculation, whereas none of the clade 1 and 2 isolates analyzed induced cell death. Isolates from clades 2 and 3 adhered to epithelial cells better than clade 1 isolates, but all isolates induced similar levels of interleukin-8 (IL-8). Alignment and phylogenetic analysis of the translated putative virulence genes <i>cadF</i>, <i>flpA</i>, <i>iamA</i>, <i>ciaB</i>, and <i>ceuE</i> revealed clade-specific protein sequence variations, with clade 1 and 2 sequences being more closely related and clade 3 sequences being further apart, in general. Moreover, when RNA levels were measured, clade 3 isolates showed significantly lower levels of expression of <i>cadF</i>, <i>iamA</i>, and <i>ceuE</i> than clade 2 isolates, while <i>flpA</i> expression levels were higher in clade 3 isolates. The cytolethal distending toxin genes were also expressed in clades 2 and 3, although there was no difference between clades. Our findings demonstrate differences between the effects of <i>C. coli</i> clade 1, 2, and 3 isolates on human cells and suggest that <i>C. coli</i> clade 3 might be more virulent than clade 2 due to the observed cytotoxicity.<b>IMPORTANCE</b><i>Campylobacter coli</i> is a common zoonotic cause of gastroenteritis in humans worldwide. The majority of infections are caused by <i>C. coli</i> clade 1 isolates, whereas infections due to clade 2 and 3 isolates are rare. Whether this depends on a low prevalence of clade 2 and 3 isolates in reservoirs important for human infections or their lower ability to cause human disease is unknown. Here, we studied the effects of <i>C. coli</i> clade 2 and 3 isolates on a human cell line. These isolates adhered to human cells to a higher degree than clinical clade 1 isolates. Furthermore, we could show that <i>C. coli</i> clade 3 isolates rapidly induced cell death, suggesting differences in the virulence of <i>C. coli</i> The exact mechanism of cell death remains to be revealed, but selected genes showed interesting clade-specific expression patterns.
Primary versus radiation‐associated craniofacial osteosarcoma (2006)

Craniofacial radiation-associated osteosarcomas are high-grade tumors that behave more aggressively than most primary craniofacial osteosarcomas. In addition, they demonstrate higher expression rates of adverse prognostic indicators, further highlighting the distinction.
Metabolic reprogramming of the myeloid lineage by Schistosoma mansoni infection persists independently of antigen exposure (2021)

Macrophages have a defined role in the pathogenesis of metabolic disease and cholesterol metabolism where alternative activation of macrophages is thought to be beneficial to both glucose and cholesterol metabolism during high fat diet induced disease. It is well established that helminth infection protects from metabolic disease, but the mechanisms underlying protection are not well understood. Here, we investigated the effects of Schistosoma mansoni infection and cytokine activation in the metabolic signatures of bone marrow derived macrophages using an approach that integrated transcriptomics, metabolomics, and lipidomics in a metabolic disease prone mouse model. We demonstrate that bone marrow derived macrophages (BMDM) from S. mansoni infected male ApoE-/- mice have dramatically increased mitochondrial respiration compared to those from uninfected mice. This change is associated with increased glucose and palmitate shuttling into TCA cycle intermediates, increased accumulation of free fatty acids, and decreased accumulation of cellular cholesterol esters, tri and diglycerides, and is dependent on mgll activity. Systemic injection of IL-4 complexes is unable to recapitulate either reductions in systemic glucose AUC or the re-programing of BMDM mitochondrial respiration seen in infected males. Importantly, the metabolic reprogramming of male myeloid cells is transferrable via bone marrow transplantation to an uninfected host, indicating maintenance of reprogramming in the absence of sustained antigen exposure. Finally, schistosome induced metabolic and bone marrow modulation is sex-dependent, with infection protecting male, but not female mice from glucose intolerance and obesity. Our findings identify a transferable, long-lasting sex-dependent reprograming of the metabolic signature of macrophages by helminth infection, providing key mechanistic insight into the factors regulating the beneficial roles of helminth infection in metabolic disease.
Efficient Joint Image Reconstruction of Multi-Patch Data Reusing a Single System Matrix in Magnetic Particle Imaging (2018)

Due to peripheral nerve stimulation, the magnetic particle imaging (MPI) method is limited in the maximum applicable excitation-field amplitude. This in turn leads to a limitation of the size of the covered field of view (FoV) to few millimeters. In order to still capture a larger FoV, MPI is capable to rapidly acquire volumes in a multi-patch fashion. To this end, the small excitation volume is shifted through space using the magnetic focus fields. Recently, it has been shown that the individual patches are preferably reconstructed in a joint fashion by solving a single linear system of equations taking the coupling between individual patches into account. While this improves the image quality, it is computationally and memory demanding since the size of the linear system increases in the best case quadratically with the number of patches. In this paper, we will develop a reconstruction algorithm for MPI multi-patch data exploiting the sparsity of the joint system matrix. A highly efficient implicit matrix format allows for rapid on-the-fly calculations of linear algebra operations involving the system matrix. Using this approach, the computational effort can be reduced to a linear dependence on the number of used patches. The algorithm is validated on 3-D multi-patch phantom data sets and shown to reconstruct large data sets with 15 patches in less than 22 s.
Quantification of Uncertainties in OCO-2 Measurements of XCO 2 : Simulations and Linear Error Analysis (2016)

Abstract. We present an analysis of uncertainties in global measurements of the column averaged dry-air mole fraction of CO2 ('XCO2') by the NASA Orbiting Carbon Observatory-2, ('OCO-2'). The analysis is based on our best estimates for uncertainties in the OCO-2 operational algorithm and its inputs, and uses simulated spectra calculated for the actual flight and sounding geometry, with measured atmospheric analyses. The simulations are calculated for land nadir and ocean glint observations. We include errors in measurement, smoothing, interference, and forward model parameters. All types of error are combined to estimate the uncertainty in XCO2 from single soundings, before any attempt at bias correction has been made. From these results we also estimate the 'variable error' which differs between soundings, to infer the error in the difference of XCO2 between any two soundings. The most important error sources are aerosol interference, spectroscopy, and instrument calibration. Aerosol is the largest source of variable error. Variable errors are usually
On the design of perturbation-resilient atomic commit protocols for mobile transactions (2011)

Distributed mobile transactions utilize commit protocols to achieve atomicity and consistent decisions. This is challenging, as mobile environments are typically characterized by frequent perturbations such as network disconnections and node failures. On one hand environmental constraints on mobile participants and wireless links may increase the resource blocking time of fixed participants. On the other hand frequent node and link failures complicate the design of atomic commit protocols by increasing both the transaction abort rate and resource blocking time. Hence, the deployment of classical commit protocols (such as two-phase commit) does not reasonably extend to distributed infrastructure-based mobile environments driving the need for perturbation-resilient commit protocols. In this article, we comprehensively consider and classify the perturbations of the wireless infrastructure-based mobile environment according to their impact on the outcome of commit protocols and on the resource blocking times. For each identified perturbation class a commit solution is provided. Consolidating these subsolutions, we develop a family of fault-tolerant atomic commit protocols that are tunable to meet the desired perturbation needs and provide minimized resource blocking times and optimized transaction commit rates. The framework is also evaluated using simulations and an actual testbed deployment.
Iterative scalar algorithm for the rapid design of wide-angle diffraction Fourier elements (2013)

International audience
Performance evaluation of MEMS piezoelectric inertial energy generator (2011)

Vibration based inertial energy generators have become significantly popular due to the growing demand of wireless sensor networks which need miniature, portable, long lasting and easily recharged sources of power. Usage of hazardous batteries is an unacceptable solution to power up the densely populated nodes due to their bulky sizes and high battery replacement cost. As such, the viability of ‘green’ microelectromechanical (MEMS) vibration based inertial energy generator has become even more dominant. This paper reports the design and simulation of a cantilever piezoelectric inertial energy generator based on bulk silicon micromachining for wireless condition monitoring in power plants. Power plants generate ambient vibrations in the low kHz range which can be harvested to power the wireless condition monitoring circuits. Output power of the system will be enhanced when it is operated at the ambient resonance frequency. This paper discusses the effect of various lengths, shapes and volume of the cantilever beam, to its natural resonant frequency. The effect of different piezoelectric material with the maximum output power produced is also highlighted. The design and finite element modeling was conducted using MEM PZE module in Coventorware™.
POH1 deubiquitylates and stabilizes E2F1 to promote tumour formation (2015)

Hyperactivation of the transcriptional factor E2F1 occurs frequently in human cancers and contributes to malignant progression. E2F1 activity is regulated by proteolysis mediated by the ubiquitin-proteasome system. However, the deubiquitylase that controls E2F1 ubiquitylation and stability remains undefined. Here we demonstrate that the deubiquitylase POH1 stabilizes E2F1 protein through binding to and deubiquitylating E2F1. Conditional knockout of Poh1 alleles results in reduced E2F1 expression in primary mouse liver cells. The POH1-mediated regulation of E2F1 expression strengthens E2F1-downstream prosurvival signals, including upregulation of Survivin and FOXM1 protein levels, and efficiently facilitates tumour growth of liver cancer cells in nude mice. Importantly, human hepatocellular carcinomas (HCCs) recapitulate POH1 regulation of E2F1 expression, as nuclear abundance of POH1 is increased in HCCs and correlates with E2F1 overexpression and tumour growth. Thus, our study suggests that the hyperactivated POH1-E2F1 regulation may contribute to the development of liver cancer.
Antigenotoxic Effect of Piperine in Broiler Chickens Intoxicated with Aflatoxin B1 (2016)

Piperine is an abundant amide extracted from black pepper seeds which has been shown to have protective effects against cytotoxic and genotoxic carcinogenesis induced by certain chemical carcinogens and aflatoxin B1 (AFB1) in vitro. The aim of this work was to study, in vivo, the antigenotoxic potential of feed-added piperine on broiler chickens experimentally intoxicated with AFB1, using micronucleus and comet assays. The antigenotoxicity assessment of 9-day-old chicks was performed on a total of 60 chickens divided into four groups of 15 broilers each: (C) control, (P) 60 mg·piperine kg−1 feed, (A) 0.5 mg·AFB1·kg−1 body weight, (daily by oral route), and (P + A) co-treatment with piperine and AFB1. The experiment was conducted for 26 days. Chicks intoxicated with AFB1 showed significant genotoxic effects in the first 24 h post intoxication, and the effects remained in the other periods analyzed (48, 72, and 96 h and 26 days of treatment). The DNA damage in peripheral blood cells, the number of erythrocytes with micronuclei, and polychromatic-to-normochromatic erythrocyte ratio were significantly reduced or absent in the piperine/AFB1 group. No significant differences were observed between the group piperine/AFB1 and the control and piperine-alone groups. The addition 60 mg·kg−1 of piperine to the diet of the broiler chicks was safe, promoting beneficial effects in poultry health with respect to the toxic effects 0.5 mg·AFB1·kg−1 body weight.
Nucleotide sequences of goose circovirus isolated in Taiwan (2003)

We report the complete nucleotide (nt) sequences of eleven goose circovirus (GoCV) isolated in Taiwan. Nine out of the eleven isolates had a genome size of 1821 nt, whereas the remaining two isolates have a size of 1820 nt. Sequence comparisons of the eleven Taiwanese GoCV isolates and a German isolate revealed that these viruses could be divided into three distinct genetic groups. Group I contains the German isolate, group II contains three Taiwanese isolates, and group III contains eight Taiwanese isolates. Nucleotide differences between viruses of different genetic groups ranged from 7.0-7.7%, whereas the differences within the same group were only 0.2-1.0%. The most diversified sequences were found at a region between nt 27-72 of the viral genome, which corresponded to the right one-third of the 5' intergenic region. Open reading frame analysis shows that the genome of all Taiwanese GoCV isolates could encode four proteins: V1 (Rep, 293 amino acids), V2 (37 amino acids), C1 (capsid, 250 amino acids), and C2 (99 amino acids). The sizes of V1, C1 and C2 proteins of all Taiwanese isolates and the German GoCV isolates were identical. However, the size of V2 protein (37 amino acids), although identical in all Taiwanese isolates, was much smaller than that of the German isolate (120 amino acids). Moreover, the initiation codon of the V2 ORF of three Taiwanese isolates was ATA rather than ATG. Our result indicates that GoCV of multiple genetic groups might have been circulating in Europe and Asia, and these viruses differ in their nucleotide sequences, sizes of the genome, and sizes of the V2 ORFs.
A General Route to 4-Imidazolyl-Containing Multidentate Ligands for Biomimetic Studies (1999)

[formula: see text] 4-iodo-1-tritylimidazole undergoes magnesium-iodine exchange with a Grignard reagent to give selectively the 4-magnesioimidazole derivative, which reacts with esters to form a variety of poly-4-imidazolyl carbinol compounds in 40-79% yields. A wide range of bi-, tri-, and pentadentate ligands featuring 4-substituted imidazole units have been efficiently synthesized.
Collaborative tele-directing (2001)

The Tele-Direction interface allows a physically remote and geographically distributed audience to collaboratively control a shared remote resource. It features contextualized user-driven goal setting and voting, an economy, and chat. In this paper we discuss the design considerations that led to this interface and describe our initial implementation.
2,2′-Bipyridinium(1+) bromide monohydrate (2004)

In the crystal structure of 2,2'-bipyridinium(1+) bromide monohydrate, C(10)H(9)N(2)(+).Br(-).H(2)O, the cation has a cisoid conformation with an intramolecular N-H.N hydrogen bond. The cation also forms an N-H.O hydrogen bond to an adjacent water molecule, which in turn forms O-H.Br(-) hydrogen bonds to adjacent Br(-) anions. In this way, a chain is formed extending along the b axis. Additional interactions (C-H.Br(-) and pi-pi) serve to stabilize the structure further.
Performance of Screening Questionnaires and Risk Scores for Undiagnosed Diabetes (2005)

Currently proposed questionnaires yielded low validity when applied to a new population, most likely due to differences in population characteristics. Performance of diabetes risk questionnaires or scores must be assessed in the target population where they will be applied.