gebhart/patrepeval huggingface dataset:
Species Specificity of Thimet Oligopeptidase (EC 3.4.24.15) (1996)

The recombinant rat testes metallo-endooligopeptidase (EC 3.4.24.15) and the rabbit brain endooligopeptidase A (formerly EC 3.4.22.19) were compared, side-by-side, in view of their striking similarities in both the physicochemical features and the specificities for oligopeptides. Concerning the tissue distribution in rat and rabbit, no relation between the levels of enzyme activity in cytosol and the levels of metallo-endooligopeptidase 24.15 mRNA could be established. The results suggest that the predominant neuropeptide-metabolizing activity attributed to the metallo-endooligopeptidase 24.15 is performed by, at least, two distinct cytosolic enzymes, one predominant in rat testes and the other in rabbit brain and testes, and possibly also in rat brain. Both enzymes are activated by dithiothreitol and irreversibly inhibited by a SH-affinity labeling dynorphin-related compound, but they are not inhibited by EDTA in a concentration dependent manner. Both enzymes exhibit the same specificity toward several bioactive peptides, except for LH-RH and substance P, which are only hydrolysed by the rat testes enzyme. Taken together, these results lead us to conclude that it is unlikely that the recombinant rat testes metallo-endooligopeptidase 24.15 and the rabbit brain endooligopeptidase A are the same molecule although they might belong to the same family of oligopeptidases.
Increased efficiency of direct nanoimprinting on planar and curved bulk titanium through surface modification (2013)

In this work the direct transfer of nanopatterns into titanium is demonstrated. The nanofeatures are imprinted at room temperature using diamond stamps in a single step. We also show that the imprint properties of the titanium surface can be altered by anodisation yielding a significant reduction in the required imprint force for pattern transfer. The anodisation process is also utilised for curved titanium surfaces where a reduced imprint force is preferable to avoid sample deformation and damage. We finally demonstrate that our process can be applied directly to titanium rods.
Learning mixtures of spherical Gaussians: moment methods and spectral decompositions (2012)

This work provides a computationally efficient and statistically consistent moment-based estimator for mixtures of spherical Gaussians. Under the condition that component means are in general position, a simple spectral decomposition technique yields consistent parameter estimates from low-order observable moments, without additional minimum separation assumptions needed by previous computationally efficient estimation procedures. Thus computational and information-theoretic barriers to efficient estimation in mixture models are precluded when the mixture components have means in general position and spherical covariances. Some connections are made to estimation problems related to independent component analysis.
Rapid and Extraction-Free Detection of SARS-CoV-2 from Saliva by Colorimetric Reverse-Transcription Loop-Mediated Isothermal Amplification (2020)

Rapid and extraction-free detection of SARS-CoV-2 from saliva by colorimetric RT-LAMP is a simple, sensitive, and cost-effective approach with broad potential to expand diagnostic testing for the virus causing COVID-19.
Extended Photo-Conversion Spectrum in Low-Toxic Bismuth Halide Perovskite Solar Cells (2016)

Lead-based perovskites show very promising properties for use in solar cells; however, the toxicity of lead is a potential inhibitor for large-scale application of these solar cells. Here, a low-toxic bismuth halide, CsBi3I10, is synthesized from solution and the optical properties and crystal structure are compared with previously reported Cs3Bi2I9 perovskite, and the photovoltaic properties are also investigated. The XRD pattern suggests that the CsBi3I10 film has a layered structure with a different dominating crystal growth direction than the Cs3Bi2I9 perovskite. A band gap of 1.77 eV is obtained for the CsBi3I10 film, which is smaller than the band gap of Cs3Bi2I9 at 2.03 eV, and an extended visible light absorption spectrum is therefore obtained. The solar cell device with CsBi3I10 shows a photocurrent up to 700 nm, and this work shows therefore the possibility for increased light absorption and higher photocurrents in solar cells based on bismuth halide perovskites.
Analysis of high efficiency multistage matching networks with volume constraint (2017)

Matching networks have useful applications in transforming voltages and impedances in resonant inverters and dc-dc converters. Stacking multiple stages of matching networks can, in some cases, increase the efficiency because each stage is responsible for smaller transformation, but it also reduces the available inductor volume for each stage which can increase the loss. We present optimization of matching networks with volume constraints to determine the optimum number of stages and other design choices for various transformation ratios, volumes and impedances. Scaling models of inductor performance with size are presented and their effect on the efficiency of single-stage and multistage matching networks is analyzed. The analytical results are verified by an experiment using 1- and 2-stage matching networks with a total volume constraint and a voltage transformation ratio of 4. Simple design rules for designing matching networks are presented for voltage transformation ratios lower than 20.
Software Power Measurement (2005)

Effective system-level power management requires cheap, accurate and finegrained power measurement and accounting. Unfortunately current portable hardware does not provide this capability. We advocate software power measurement: estimation of power consumption by modelling it as a function of device state. The approach requires no additional hardware, and allows fine-grained, per-device and per-application power measurement. We describe a design and implementation of software power measurement, and a feasibility study showing significantly better accuracy than power profiling based on time averaging. We conclude with design recommendations for OS designers and portable hardware vendors to improve the ease and accuracy of power measurement.
A microfluidic concentration-gradient droplet array generator for the production of multi-color nanoparticles (2013)

A microfluidic concentration-gradient droplet array generator (CDrAG) with parallel multi-channels and multi-layers was developed with 64 outlet channels producing 33 droplet gradient concentrations. A droplet production rate of 5 × 10(4) min(-1) was obtained, and the RSD value of droplet diameters in 64 groups is 5.5% (n = 64). Using the concentration gradient droplet array as parallel microreactors, 33 Au/Ag ratio nanoparticles were synthesized. The absorption spectra of the Au/Ag nanoparticles shifted from the spectrum of pure gold to one of pure silver. This demonstrates the CDrAG platform's promising potential to produce specific nanoparticle barcodes for high-throughput screening in chemistry, biology and a broad range of life science applications.
Family resemblance for fasting blood glucose: the Jerusalem Lipid Research Clinic (1987)

Familial aggregation of fasting plasma glucose was studied in a sample of families examined at the Jerusalem Lipid Research Clinic. We first examined homogeneity of familial correlations across major origin groups in the Israeli sample. Correlations were generally homogeneous across origin groups, except for mother-son pairs. The pooled familial correlations were relatively low for unadjusted blood glucose values, and somewhat higher upon adjustment for sex, age, ethnicity, education, seasonality, body mass, cigarette smoking, alcohol consumption and dietary intake. Genetic and cultural determinants of blood glucose were estimated utilizing a path model with 10 parameters to be estimated from a total of 16 correlations. Under a reduced model genetic heritability (h2) was estimated to be 0.18 +/- 0.08 and cultural heritability (c2) was 0.10 +/- 0.02. However, within this population the additive variation could be explained by a cultural model of inheritance without introducing genetic parameters, and most of the variance is due to "random" unmeasured environmental factors. Commingling analysis was also performed, and our findings imply that there is no evidence for admixture in the distribution of fasting blood glucose in this Israeli population sample.
Impact of COVID-19 Pandemic on Sleep Including HRV and Physical Activity as Mediators: A Causal ML Approach (2023)

Abstract Sleep quality is crucial to both mental and physical well-being. The COVID-19 pandemic, which has notably affected the population’s health worldwide, has been shown to deteriorate people’s sleep quality. Numerous studies have been conducted to evaluate the impact of the COVID-19 pandemic on sleep efficiency, investigating their relationships using correlation-based methods. These methods merely rely on learning spurious correlation rather than the causal relations among variables. Furthermore, they fail to pinpoint potential sources of bias and mediators and envision counterfactual scenarios, leading to a poor estimation. In this paper, we develop a Causal Machine Learning method, which encompasses causal discovery and causal inference components, to extract the causal relations between the COVID-19 pandemic (treatment variable) and sleep quality (outcome) and estimate the causal treatment effect, respectively. We conducted a wearable-based health monitoring study to collect data, including sleep quality, physical activity, and Heart Rate Variability (HRV) from college students before and after the COVID-19 lockdown in March 2020. Our causal discovery component generates a causal graph and pinpoints mediators in the causal model. We incorporate the strongly contributing mediators (i.e., HRV and physical activity) into our causal inference component to estimate the robust, accurate, and explainable causal effect of the pandemic on sleep quality. Finally, we validate our estimation via three refutation analysis techniques. Our experimental results indicate that the pandemic exacerbates college students’ sleep scores by 8%. Our validation results show significant p-values confirming our estimation.
Epithelial Mesenchymal Transition in Tumor Metastasis (2018)

Metastasis is the major cause of cancer-related deaths; therefore, the prevention and treatment of metastasis are fundamental to improving clinical outcomes. Epithelial mesenchymal transition (EMT), an evolutionarily conserved developmental program, has been implicated in carcinogenesis and confers metastatic properties upon cancer cells by enhancing mobility, invasion, and resistance to apoptotic stimuli. Furthermore, EMT-derived tumor cells acquire stem cell properties and exhibit marked therapeutic resistance. Given these attributes, the complex biological process of EMT has been heralded as a key hallmark of carcinogenesis, and targeting EMT pathways constitutes an attractive strategy for cancer treatment. However, demonstrating the necessity of EMT for metastasis in vivo has been technically challenging, and recent efforts to demonstrate a functional contribution of EMT to metastasis have yielded unexpected results. Therefore, determining the functional role of EMT in metastasis remains an area of active investigation. Studies using improved lineage tracing systems, dynamic in vivo imaging, and clinically relevant in vivo models have the potential to uncover the direct link between EMT and metastasis. This review focuses primarily on recent advances in and emerging concepts of the biology of EMT in metastasis in vivo and discusses future directions in the context of novel diagnostic and therapeutic opportunities.
Stress and the hypothalamo-pituitary-adrenal axis: acute, chronic and immunological activation (1992)

Successful existence depends on the ability to cope with an immense variety of complex challenges or stressors and to mount an 'appropriate' response to any particular situation. While the concept of stress is readily understood, a definition acceptable to more than a handful of individuals remains elusive. It is necessary therefore at the outset to clarify the context within which we have written the current review. We will utilize a simple definition based on the neuroendocrine response to stressors and for this purpose we shall limit our discussion to those events resulting in the activation of the hypothalamo-pituitary-adrenal (HPA) axis. The final stage of this activation is the secretion of glucocorticoids from the adrenal cortex. Glucocorticoids have a wide range of actions affecting many aspects of bodily function including metabolism, inflammation and immunity. Glucocorticoids also control their own synthesis and release by completing a negative feedback loop at the level
Coronary evaginations and peri-scaffold aneurysms following implantation of bioresorbable scaffolds: incidence, outcome, and optical coherence tomography analysis of possible mechanisms (2015)

Optical coherence tomography-detected evaginations are relatively common after BVS implantation, but, as for modern drug-eluting metallic stents, major evaginations are very rare. Optical coherence tomography evidence of immature neointima and strut fractures were associated with more severe development of evaginations.
Intelligence trajectories in individuals at ultra-high risk for psychosis: An 8-year longitudinal analysis (2021)

Background: Cognitive impairment is a well-documented predictor of transition to a full-threshold psychotic disorder amongst individuals at ultra-high risk (UHR) for psychosis. However, less is known about whether change in cognitive functioning differs between those who do and do not transition to a psychotic disorder. Studies to date have not examined trajectories in intelligence constructs (e.g., acquired knowledge and fluid intelligence), which have demonstrated marked impairments in individuals with schizophrenia. This study aimed to examine intelligence trajectories using longitudinal data from three time-points, spanning an average of eight years.Methods: Participants (N=139) at UHR for psychosis completed the Wechsler Abbreviated Scale of Intelligence (WASI) at each follow-up. Linear mixed-effects models mapped changes in WASI Full-Scale IQ (FSIQ) and T-scores on Vocabulary, Similarities, Block Design, and Matrix Reasoning subtests.Results: The sample showed stable and improving trajectories for FSIQ and all subtests. There were no significant differences in trajectories between those who did and did not transition to psychosis and between individuals with good and poor functional outcomes. However, although not significant, the trajectories of the acquired knowledge subtests diverged between transitioned and non-transitioned individuals (β=−0.12, 95% CI [−0.29, 0.05] for Vocabulary and β=−0.14, 95% CI [−0.33, 0.05] for Similarities). Conclusions: There was no evidence for long-term deterioration in intelligence trajectories in this UHR sample. As the small sample of individuals who transitioned may have limited our ability to detect subtle differences, future studies with larger sample sizes are needed to explore potential differences in intelligence trajectories between UHR transition groups.
A Dynamic Residual Self-Attention Network for Lightweight Single Image Super-Resolution (2021)

Deep learning methods have shown outstanding performance in many applications, including single-image super-resolution (SISR). With residual connection architecture, deeply stacked convolutional neural networks provide a substantial performance boost for SISR, but their huge parameters and computational loads are impractical for real-world applications. Thus, designing lightweight models with acceptable performance is one of the major tasks in current SISR research. The objective of lightweight network design is to balance a computational load and reconstruction performance. Most of the previous methods have manually designed complex and predefined fixed structures, which generally required a large number of experiments and lacked flexibility in the diversity of input image statistics. In this paper, we propose a dynamic residual self-attention network (DRSAN) for lightweight SISR, while focusing on the automated design of residual connections between building blocks. The proposed DRSAN has dynamic residual connections based on dynamic residual attention (DRA), which adaptively changes its structure according to input statistics. Specifically, we propose a dynamic residual module that explicitly models the DRA by finding the interrelation between residual paths and input image statistics, as well as assigning proper weights to each residual path. We also propose a residual self-attention (RSA) module to further boost the performance, which produces 3-dimensional attention maps without additional parameters by cooperating with residual structures. The proposed dynamic scheme, exploiting the combination of DRA and RSA, shows an efficient trade-off between computational complexity and network performance. Experimental results show that the DRSAN performs better than or comparable to existing state-of-the-art lightweight models for SISR.
Production and characterization of polymer microcantilevers (2004)

This work describes the production of microcantilever beams via a solvent casting technique. The beams produced had dimensions of roughly 500 by 50 by 2 μm (length, width, and thickness, respectively). A subset of the beams produced were characterized and were shown to have comparable dynamic mechanical behavior as that of existing ceramic and photopolymer microcantilevers.
Structures and mechanism of dipeptidyl peptidases 8 and 9, important players in cellular homeostasis and cancer (2018)

Dipeptidyl peptidases 8 and 9 are intracellular N-terminal dipeptidyl peptidases (preferentially postproline) associated with pathophysiological roles in immune response and cancer biology. While the DPP family member DPP4 is extensively characterized in molecular terms as a validated therapeutic target of type II diabetes, experimental 3D structures and ligand-/substrate-binding modes of DPP8 and DPP9 have not been reported. In this study we describe crystal and molecular structures of human DPP8 (2.5 Å) and DPP9 (3.0 Å) unliganded and complexed with a noncanonical substrate and a small molecule inhibitor, respectively. Similar to DPP4, DPP8 and DPP9 molecules consist of one β-propeller and α/β hydrolase domain, forming a functional homodimer. However, they differ extensively in the ligand binding site structure. In intriguing contrast to DPP4, where liganded and unliganded forms are closely similar, ligand binding to DPP8/9 induces an extensive rearrangement at the active site through a disorder-order transition of a 26-residue loop segment, which partially folds into an α-helix (R-helix), including R160/133, a key residue for substrate binding. As vestiges of this helix are also seen in one of the copies of the unliganded form, conformational selection may contributes to ligand binding. Molecular dynamics simulations support increased flexibility of the R-helix in the unliganded state. Consistently, enzyme kinetics assays reveal a cooperative allosteric mechanism. DPP8 and DPP9 are closely similar and display few opportunities for targeted ligand design. However, extensive differences from DPP4 provide multiple cues for specific inhibitor design and development of the DPP family members as therapeutic targets or antitargets.
Magnetic Susceptibility of α-Phase Cu-Al and Cu-Al(Fe) (1974)

The magnetic susceptibilities of α‐phase Cu‐Al and dilute Cu‐Al(Fe) alloys have been measured over the temperature range of 1.5 K to 300 K. The alloys had Al concentrations of about 0, 2.4, 5.0, and 10.0 at. % and the samples with magnetic additions had Fe concentrations of about 0.07 at. %. The measurements were conducted for fields in the range of 3.95 kOe to 12.75 kOe. In addition to the temperature dependence characteristic of Kondo alloys, the susceptibility of the Fe‐containing samples exhibited a magnetic field dependence which became pronounced below 10 K. The susceptibility was compared to a very simple model which includes the effects of Fe impurities and pairs of parallel‐spin coupled impurities with a small Kondo temperature. The results suggest that, for our Fe concentrations, interactions between pairs and possibly other magnetic entities are important in the Cu(Fe) system; but that these correlations are substantially reduced by Al additions. Further, from the fits of the data to our simple model, one finds that the number of pairs increases with increasing Al concentration which suggests nonrandomness in the distribution of Fe impurities.
Serine protease LACTB – a component of filament-shaped structures in the mitochondrial intracristal compartments (2005)

Paracrystalline inclusions in the mitochondrial matrix or intermembrane compartment occur in several biochemically unrelated disorders such as myopathies, paragangliomas and steatohepatitis, and in various cell types under normal conditions, as well. However, little is known about the composition of the inclusions, the mechanism of their formation and their relation to disease processes. In this study we have described the helix-shaped structures in the intracristal compartments of rat liver mitochondria that have undergone Ca2+-induced permeability transition. The filaments are anchored in opposing parts of the mitochondrial membranes and appear to support the cristae mechanically. A protein, that apparently is a component of these helical filaments, has been identified as serine protease LACTB. This protein shows close sequence similarity to the class C bacterial beta-lactamases and is the only member of this class in animals. Since LACTB has not been studied previously we cloned its cDNA for expression in E. coli as C-terminal His-tagged fusion protein. LACTB underwent proteolytic processing in both E. coli and in isolated mitochondria resulting in several protein fragments. This is likely to be due to auto-cleavage and may be an activation/maturation process. 2D blue native gel electrophoresis indicated that LACTB was part of a >600 kDa protein supercomplex. In summary, the presence of the serine protease motive in LACTB and its supposed ability to form helical filaments suggest that LACTB might function not only as a component of ‘mitoskeleton’ in maintaining and rearranging the mitochondrial ultrastructure under certain conditions, but also might take part in apoptotic processes.
Elementary-Body Virus Isolated from Clinical Trachoma in California (1959)

From an adult white resident of California with clinically typical early trachoma a virus was isolated by growth in embryonated eggs. Morphologically and serologically the virus belongs in the psittacosis-lymphogranuloma group. When it is instilled into monkey eyes it produces acute follicular conjunctivitis with typical inclusion bodies.