gebhart/patrepeval huggingface dataset:
BASIC—LIVER, PANCREAS, AND BILIARY TRACT Loss of the Acinar-Restricted Transcription Factor Mist1 Accelerates Kras-Induced Pancreatic Intraepithelial Neoplasia (2009)

Background & Aims: Invasive pancreatic ductal adenocarcinoma is thought to originate from duct-like lesions called pancreatic intraepithelial neoplasia (PanIN). PanINs progress from low grade (PanIN-1) to high grade (PanIN-3) as the cells attain molecular alterations to key regulatory genes, including activating mutations in the KRAS protooncogene. Despite a well-documented progression model, our knowledge of the initiator cells of PanINs and the transcriptional networks and signaling pathways that impact PanIN formation remains incomplete. Methods: In this study, we examined the importance of the acinarrestricted transcription factor Mist1 to Kras G12D -induced mouse PanIN (mPanIN) formation in 3 different mouse models of pancreatic cancer. Results: In the absence of Mist1 (Mist1 KO ), Kras G12D -expressing mice exhibited severe exocrine pancreatic defects that were rescued by ectopic expression of Mist1 in acinar cells. mPanIN development was greatly accelerated in Mist1KO /Kras G12D/ pancreata, and in vitro assays revealed that Mist1 KO acinar cells were predisposed to convert to a ductal phenotype and activate epidermal growth factor receptor (EGFR) and Notch-signaling pathways. Conclusions: We propose that convergence of EGFR, Notch, and Kras pathways in acinar cells lacking Mist1 leads to enhanced mPanIN formation.
Rare missense variant (R251G) on APOE counterbalances the Alzheimer’s disease risk associated with APOE‐ε4 (2022)

Abstract Background Despite decades of research, the mechanisms linking APOE to Alzheimer’s disease (AD) remain poorly understood. Finding additional risk variants at the APOE locus, beyond the common APOE ‐ε2 and APOE ‐ε4 alleles, may help elucidate how APOE is involved in the disease. Method Association with case‐control status was tested in a sequenced discovery sample (Stage 1) and followed‐up in several microarray imputed cohorts as well as the UK Biobank whole‐exome sequencing resource using a proxy‐AD phenotype (Stages 2+3) ( Table 1 ). Stage 1 included 37,409 non‐unique participants of European or Admixed‐European ancestry, with 11,868 cases and 11,934 controls passing analysis inclusion criteria. In Stages 2+3, 475,473 participants were considered across 8 cohorts, of which 56,029 cases, 28,484 proxy‐AD cases, and 328,372 healthy‐controls passed inclusion criteria, and were of European ancestry. Result Two missense variants were associated with a two to three‐fold decreased AD risk: R251G (odds ratio, 0.44; 95% confidence interval [CI], 0.33‐0.59; P = 4.7×10‐8) and V236E (odds ratio, 0.37; 95% CI, 0.25‐0.56; P = 1.9×10‐6) ( Table 2, Figures 1, 2) . Additionally, the cumulative incidence of AD in carriers of these variants was found to grow more slowly with age compared to non‐carriers ( Table 3 ). Conclusion We identified a novel variant associated with AD, R251G, which mitigates the ε4 associated AD risk, and confirmed the protective effect of the V236E variant. The location of the variants confirms that the carboxyl‐terminal portion of apoE plays an important role in AD pathogenesis. The large risk reductions reported here, suggest that protein chemistry and functional assays of these variants have the potential to identify novel pathways for drug development.
An Environmentally Friendly Process for Electroplating Copper on Zinc (2012)

Abstract not Available.
'IFilinearity 01 'lhree Yerspect ive (1995)

It has been established that certain trilinear froms of three perspective views give rise to a tensor of 27 intrinsic coefficients [ll]. We show in this paper that a permutation of the the trilinear coefficients produces three homograph y matrices (projective t ransfonn at ions of planes) of three distinct intrinsic planes, respectively. This, in turn, yields the result that 30 invariants are recovered directly - simply by appropriate arrangement of the tensor’s coefficients. On a secondary level, we show new relations between fundamental matrix, epipoles, Euclidean structure and the trilinear tensor. On the practical side, the new results extend the existing envelope of methods of 30 recovery from 20 views -for example, new linear methods that cut through the epipolar geometry, and new methods for computing epipolar geometry using redundancy available across many views.
A New Classification of Diabetic Gait Pattern Based on Cluster Analysis of Biomechanical Data (2010)

Background: The diabetic foot, one of the most serious complications of diabetes mellitus and a major risk factor for plantar ulceration, is determined mainly by peripheral neuropathy. Neuropathic patients exhibit decreased stability while standing as well as during dynamic conditions. A new methodology for diabetic gait pattern Classification based on cluster analysis has been proposed that aims to identify groups of subjects with similar patterns of gait and verify if three-dimensional gait data are able to distinguish diabetic gait patterns from one of the control subjects. Method: The gait of 20 nondiabetic individuals and 46 diabetes patients with and without peripheral neuropathy was analyzed [mean age 59.0 (2.9) and 61.1(4.4) years, mean body mass index (BMI) 24.0 (2.8), and 26.3 (2.0)]. K-means cluster analysis was applied to classify the subjects' gait patterns through the analysis of their ground reaction forces, joints and segments (trunk, hip, knee, ankle) angles, and moments. Results: Cluster analysis Classification led to definition of four well-separated clusters: One aggregating just neuropathic subjects, one aggregating both neuropathics and non-neuropathics, one including only diabetes patients, and one including either controls or diabetic and neuropathic subjects. Conclusions: Cluster analysis was useful in grouping subjects with similar gait patterns and provided evidence that there were subgroups that might otherwise not be observed if a group ensemble was presented for any specific variable. In particular, we observed the presence of neuropathic subjects with a gait similar to the controls and diabetes patients with a long disease duration with a gait as altered as the neuropathic one.
Pairing devices for social interactions (2011)

When users wish to establish wireless radio communication between/among their devices, the channel has to be bootstrapped first. The process of setting up a secure communication channel between two previously unassociated devices is referred to as "Secure Device Pairing". The focus of prior research on this topic has mostly been limited to "personal pairing" scenarios, whereby a single user controls both the devices. In this paper, we instead consider "social pairing" scenarios, whereby two different users establish pairing between their respective devices. We present a comprehensive study to identify methods suitable for social pairing, and comparatively evaluate the usability and security of these methods. Our results identify methods best-suited for users, in terms of efficiency, error-tolerance and of course, usability. Our work provides insights on the applicability and usability of methods for emerging social pairing scenarios, a topic largely ignored so far.
Study of Different Substituted Cyclic and Acyclic Benzylpronucleotides of d4T Relative to Their Hydrolytic Stability and Antiviral Activity (2003)

CycloSal-d4TMP and two different bis(benzyl) phosphate triesters of the antivirally active nucleoside analog d4T were studied with regard to their chemical hydrolysis behavior at pH 7.3, in CEM/0 cell extracts, and their anti-HIV activity. In contrast to triesters 2-4, bis-(o-AB)-d4TMP 1 was found to be chemically exquisitely stable. All compounds led to the formation of d4TMP in cell extracts and all triesters achieved the TK-bypass.
Creation efficiency of nitrogen-vacancy centres in diamond (2010)

Nitrogen-vacancy (NV) colour centres in diamond are attracting growing attention due to potential applications in solid-state quantum information processing and magnetometry. Although proof-of-principle experiments have been demonstrated, further development requires the controllable production of defects with a high yield. In this paper, we experimentally show that the production efficiency of NV defects strongly depends on the ion implantation energy. This can be explained in terms of the number of vacancies produced per implanted ion and surface proximity. The dependence on ion fluence is also underlined, revealing a nonlinear regime and showing how the diamond lattice is damaged at higher fluences.
Role of ovarian sympathetic nerves and cholinergic local system during cold stress (2019)

An increase in the sympathetic tone in the rat ovary induces a polycystic ovary (PCOS-like) phenotype. No information exists about its impact on fertility. In contrast, increased follicular development and improved fertility in rats were found after pharmacological inhibition of acetylcholinesterase, which increased intraovarian acetylcholine (ACh). Now, we studied the impact of sympathetic stress, followed by a recovery period without stress, on the cholinergic and noradrenergic systems of the rat ovary and on fertility. To activate ovarian sympathetic nerves, female Sprague-Dawley rats were exposed to cold stress (4°C/3 h day for 28 days; first period), followed by a 28-day period without cold stress (second period). No changes in estrous cyclicity during the first period was found. At the end of this period, ovarian levels of NA and ACh were increased. Morphometric analysis showed lower numbers of secondary and antral follicles, enhanced follicular atresia and fewer corpora lutea. Plasma progesterone was lower and testosterone was higher than that in controls. At end of the second period, ovarian ACh levels had returned to control levels, but NA levels remained elevated. The second period was also characterized by the presence of cystic follicles in the ovary, by elevated plasma testosterone and estradiol levels, while progesterone levels were decreased. Estrous cyclicity and ovulation during that period were irregular and fertility decreased. Thus, cold stress initially activated both ovarian noradrenergic and cholinergic system. After stress, the ovary did not fully recover and activation of the noradrenergic system persisted and correlated with cystic ovarian morphology and decreased fertility.
An Ankle-Foot Prosthesis Emulator Capable of Modulating Center of Pressure (2019)

This emulator system will enable rapid development of controllers designed to enhance user balance and reduce user energy expenditure. Experiments conducted using this emulator could identify beneficial control behaviors that can be implemented on autonomous devices, thus improving mobility and quality of life of individuals with amputation.
Synthesis of Tetracyclic Heterocompounds as Selective Estrogen Receptor Modulators. Part 1. Process Development for Scale-up of 2,5,8-Substituted 5,11-Dihydrochromeno[4,3-c]chromene Derivatives (2007)

Unsymmetrical benzopyranobenzopyran compounds are novel selective estrogen receptor modulators (SERMs). A reproducible and nonchromatographic process was developed to prepare multihundred gram quantities of 5-(4-(2-(piperidin-1-yl)ethoxy)phenyl)-5,11-dihydrochromeno[4,3-c]chromene-2,8-diyl-bis(2,2-dimethylpropanoate) (14). The overall yield of this 11-step synthesis was improved from 0.17% to 7.1% after three scale-up campaigns.
Microbiome Toolbox: methodological approaches to derive and visualize microbiome trajectories (2022)

Supplementary data are available at Bioinformatics online.
Retroviral DNA Methylation and Epigenetic Repression Are Mediated by the Antiviral Host Protein Daxx (2012)

Integrated retroviral DNA is subject to epigenetic transcriptional silencing at different frequencies. This process is mediated by repressive DNA methylation and histone modifications on viral chromatin. However, the detailed mechanisms by which retroviral silencing is initiated and maintained are not well understood. Using a model system in which avian sarcoma virus (ASV) DNA is epigenetically repressed in mammalian cells, we previously found that a cellular scaffolding protein, Daxx, acts as an antiretroviral factor that promotes epigenetic repression through recruitment of histone deacetylases (HDACs). Here we show that human Daxx protein levels are increased in response to retroviral infection and that Daxx acts at the time of infection to initiate epigenetic repression. Consistent with a rapid and active antiviral epigenetic response, we found that repressive histone marks and long terminal repeat (LTR) DNA methylation could be detected within 12 h to 3 days postinfection, respectively. Daxx was also found to be required for long-term ASV silencing maintenance and full viral DNA methylation, and it was physically associated with both viral DNA and DNA methyltransferases (DNMTs). These findings support a model in which incoming retroviral protein-DNA complexes are detected by Daxx, and the integrated provirus is rapidly chromatinized and repressed by DNA methylation and histone modification as part of an antiviral response. These results uncover a possible direct and active antiviral mechanism by which DNMTs can be recruited to retroviral DNA.
Antifertility effects of luteinizing hormone-releasing hormone (LHRH) agonists. (1981)

This paper reviews the mechanisms responsible for the antifertility effects of luteinizing hormone-releasing hormone (LHRH) agonists. Large doses of the LHRH agonist LHRH-EA lead to a marked reduction of testicular and secondary sex organ weight, LH receptor levels, and plasma testosterone concentration. A marked inhibition of basal testicular and testosterone concentrations is obtained after daily administration of the LHRH agonists at doses greater than 10 ng. Treatment with low doses of the LHRH agonist can lead to an increased steroidogenic response to LH. Treatment with low doses of LHRH agonists could stimulate Leydig cell function while high doses are history. A study of the effects of longterm treatment with an LHRH agonsist on spermatogenesis revelaed that testis, prostate, and seminal vesicle weight decreased and plasma LH and FSH levels increased over 12 weeks. Comparison of the effects of increasing doses of LHRH agonist on testicular and ovarian gonadotropin receptors and steroidogenesis in male rats indicates that single or repeated administration of LHRH agonists can lead to loss of testicular LH receptors in the absence of the pituitary gland. The loss of ovarian gonadotropin receptors in female rats is also investigated. Antifertility effects of LHRH ethylamide are accompanied by a marked loss of LH/hCG and FSH receptors in ovarian tissue. The injection of 1,3, or 10 ng LHRH-EA in intact rats has no significant effect on ovarian LH receptor levels. A study of the direct action of LHRH agonists at the ovarian level demonstrates a close relationship between the binding activity of a large series of LHRH agonists and antagonists in the anterior pituitary gland and the ovary. Inhibition of testicular steroidogenesis in man by treatment with a potent LHRH agonist is also demonstrated. Intranasal administration of LHRH ethylamide has luteolytic effects in normal women. Daily administration of LHRH-EA inhibited ovulation in all but 2 of 89 treatment cycles in the normal women studied. These studies demonstrate a luteolytic action of LHRH and its agonists in women. LRHR agonists may be used as a new and near-physiological approach to contraception as inhibitors of ovulation or for the induction of menses and as an alternative to the postcoital estrogenic pill.
Cytotoxic Effects of 2-Methoxyestradiol in the Hepatocellular Carcinoma Cell Line HepG2 (2009)

2ME2 exerts cytotoxic activity in the HepG2 cell line by preferential cell blocking at the G(2)/M phase as well as induction of apoptosis as evidenced by increased caspase 9 enzymatic activity and observed DNA laddering in 2ME2-treated HepG2 cells. In addition, a reduction in hypervascularity is an important postulated mechanism as indicated by the significant reduction in the expression of VGEF, one of the most important angiogenic factors.
Soil Water Measurements Relevant to Agronomic and Environmental Functions of Chemically Treated Soil (2008)

Abstract Modern agricultural, turf, and landscape management routinely apply and depend upon chemical applications to optimize system function for specific outcomes. The effectiveness of these applied chemicals to achieve desired outcomes usually depends upon their interaction with and transport by water. To fully and accurately assess the role of water as a chemical delivery and activation system requires a good understanding of how the applied chemicals, soil, and water interact, the scale at which a phenomenon is important, the nature of soil variability, and which of the three dominant soil water properties (content, movement, or potential energy) is most suited to assessing water’s role. The science of this assessment process is extensive and its literature is voluminous. For the uninitiated, however, it is worth being aware at least of the basics of soil water assessment and where some of the pitfalls lie. This presentation describes soil as a three-phase system (solids, liquid, and gases) and highlights some of the key measurements and measurement considerations necessary to appropriately characterize treatment efficacy for specific, and especially, non-intuitive effects. The presentation cannot be comprehensive or substitute for requisite university-level courses in soil physics and soil chemistry, but can, perhaps, alert applicators to situations and considerations that demand more than mere cursory assessment for proper evaluation and interpretation.
Model-Free Generative Replay for Lifelong Reinforcement Learning: Application to Starcraft-2 (2022)

One approach to meet the challenges of deep lifelong reinforcement learning (LRL) is careful management of the agent's learning experiences, to learn (without forgetting) and build internal meta-models (of the tasks, environments, agents, and world). Generative replay (GR) is a biologically inspired replay mechanism that augments learning experiences with self-labelled examples drawn from an internal generative model that is updated over time. We present a version of GR for LRL that satisfies two desiderata: (a) Introspective density modelling of the latent representations of policies learned using deep RL, and (b) Model-free end-to-end learning. In this paper, we study three deep learning architectures for model-free GR, starting from a naïve GR and adding ingredients to achieve (a) and (b). We evaluate our proposed algorithms on three different scenarios comprising tasks from the Starcraft-2 and Minigrid domains. We report several key findings showing the impact of the design choices on quantitative metrics that include transfer learning, generalization to unseen tasks, fast adaptation after task change, performance wrt task expert, and catastrophic forgetting. We observe that our GR prevents drift in the features-to-action mapping from the latent vector space of a deep RL agent. We also show improvements in established lifelong learning metrics. We find that a small random replay buffer significantly increases the stability of training. Overall, we find that "hidden replay" (a well-known architecture for class-incremental classification) is the most promising approach that pushes the state-of-the-art in GR for LRL and observe that the architecture of the sleep model might be more important for improving performance than the types of replay used. Our experiments required only 6% of training samples to achieve 80-90% of expert performance in most Starcraft-2 scenarios.
Block- vs. Symbol-wise Differential Encoding in Spectrally Efficient Digital Subcarrier Multiplexing for Direct Detection (2010)

Digital Subcarrier Multiplexing allows simple direct detection of multicarrier signals. We show, by means of simulations, that by differentially encoding in symbol-wise manner, the tolerance to both, nonlinearities and dispersion, is remarkably improved.
Superelastic NiTi honeycombs: fabrication and experiments (2007)

In this paper we demonstrate a new class of superelastic NiTi honeycomb structures. We have developed a novel brazing technique that has allowed us to fabricate Nitinol-based cellular structures with relative densities near 5%. Commercially available nickel-rich Nitinol strips were shape-set into corrugated form, stacked, and bonded at high temperature by exploiting a contact eutectic melting reaction involving pure niobium. After heat treatment to restore transformational superelastic response, prototype honeycomb structures were subjected to severe in-plane compression loading at room temperature. The specimens exhibited good specific strength, high specific stiffness, and enhanced shape recovery compared to monolithic shape memory alloys (SMAs). Compressive strains of over 50% could be recovered upon unloading. The demonstrated architectures are simple examples of a wide variety of possible built-up topologies, enabled by the bonding method, that can be engineered for customizable net section properties, arbitrary shape, and kinematically enhanced thermomechanical shape-memory and superelastic response.
Selecting an Accessory Device with a Metered-Dose Inhaler: Variable Influence of Accessory Devices on Fine Particle Dose, Throat Deposition, and Drug Delivery with Asynchronous Actuation from a Metered-Dose Inhaler (2001)

Accessory devices reduce common problems with metered-dose inhalers (MDIs), namely high oropharyngeal deposition of aerosol and incoordination between actuation and inhalation by the patient. The objective of this study was to systematically compare the performance of various accessory devices in vitro. MDIs were tested alone or in combination with four spacers (Toilet paper roll, Ellipse, Optihaler, Myst Assist) and five holding chambers (Aerochamber, Optichamber, Aerosol Cloud Enhancer, Medispacer, and Inspirease). An Anderson cascade impactor was used to measure aerosol mass median aerodynamic diameter (MMAD) and fine particle dose (MMAD < 4.7 microm). In separate experiments, the influence of asynchronous MDI actuation on drug delivery was determined with a simulated spontaneous breathing model. Compared with the MDI alone, all of the accessory devices reduced aerosol MMAD and increased lung-throat ratio (fine particle dose/throat impaction; p < 0.05 for both parameters). The fine particle dose of albuterol was 40% higher with the Ellipse (p < 0.01), was equivalent with the Toilet Paper Roll, Aerochamber, Optichamber, and Medispacer, and was 33-56% lower with the Optihaler, Myst Assist, Aerosol Cloud Enhancer, and Inspirease (p < 0.03). MDI actuation in synchrony with inspiration produced highest drug delivery; when MDI actuation occurred 1-sec before inspiration or during exhalation, decrease in drug delivery with holding chambers (10-40% reduction) was less than that with spacers (40-90% reduction). Accessory device selection is complicated by variability in performance between devices, and in the performance of each device in different clinical settings. In vitro characterization of a MDI and accessory device could guide appropriate device selection in various clinical settings.
Digital Holographic Microscopy for Comparative Metrology in Micro-Optics and MOEMs (Digitale holografische Mikroskopie für vergleichende Messungen von mikro-optischen Komponenten und MOEMs) (2006)

Summary Digital holographic microscopy (DHM) is an imaging technique, which can be applied to the visualisation and metrology of microscopic objects. It has been established in the frame of the DISCO project that DHM can be considered as an efficient method for direct comparison of the shape or deformations of two objects. “Comparison DHM” allows a straight comparison with a gauge provided by a manufacturer or customer. The phase subtraction between ideal and actual wavefront of the object provides data equivalent to those given by a Twyman–Green or a Mach–Zehnder interferometer.