gebhart/patrepeval huggingface dataset:
The mRNA-destabilizing protein Tristetraprolin targets “meiosis arrester” Nppc mRNA in mammalian preovulatory follicles (2021)

C-natriuretic peptide (CNP) and its receptor guanylyl cyclase, natriuretic peptide receptor 2 (NPR2), are key regulators of cyclic guanosine monophosphate (cGMP) homeostasis. The CNP-NPR2-cGMP signaling cascade plays an important role in the progression of oocyte meiosis, which is essential for fertility in female mammals. In preovulatory ovarian follicles, the luteinizing hormone (LH)-induced decrease in CNP and its encoding messenger RNA (mRNA) natriuretic peptide precursor C (<i>Nppc</i>) are a prerequisite for oocyte meiotic resumption. However, it has never been determined how LH decreases CNP/<i>Nppc</i> In the present study, we identified that tristetraprolin (TTP), also known as zinc finger protein 36 (ZFP36), a ubiquitously expressed mRNA-destabilizing protein, is the critical mechanism that underlies the LH-induced decrease in <i>Nppc</i> mRNA. <i>Zfp36</i> mRNA was transiently up-regulated in mural granulosa cells (MGCs) in response to the LH surge. Loss- and gain-of-function analyses indicated that TTP is required for <i>Nppc</i> mRNA degradation in preovulatory MGCs by targeting the rare noncanonical AU-rich element harbored in the <i>Nppc</i> 3' UTR. Moreover, MGC-specific knockout of <i>Zfp36</i>, as well as lentivirus-mediated knockdown in vivo, impaired the LH/hCG-induced <i>Nppc</i> mRNA decline and oocyte meiotic resumption. Furthermore, we found that LH/hCG activates <i>Zfp36</i>/TTP expression through the EGFR-ERK1/2-dependent pathway. Our findings reveal a functional role of TTP-induced mRNA degradation, a global posttranscriptional regulation mechanism, in orchestrating the progression of oocyte meiosis. We also provided a mechanism for understanding CNP-dependent cGMP homeostasis in diverse cellular processes.
Outstanding challenges in protein–ligand docking and structure‐based virtual screening (2011)

Abstract With an ever‐increasing number of protein structures being solved by X‐ray crystallography, the use of protein–ligand docking algorithms to assess candidate ligands for a binding site has become commonplace. In particular, over the last decade, high‐throughput docking has been widely applied to the virtual screening of large chemical databases for supporting hit‐finding programs in drug discovery. However, the techniques and practice of protein–ligand docking in general, and of structure‐based virtual screening in particular, are still evolving and significant limitations remain to be addressed. In this review, we seek to highlight some of the active areas of research and debate in this promising, but challenging, field. © 2011 John Wiley &amp; Sons, Ltd. WIREs Comput Mol Sci 2011 1 229–259 DOI: 10.1002/wcms.18 This article is categorized under: Structure and Mechanism &gt; Computational Biochemistry and Biophysics
In-Situ Study of Dynamic Structural Rearrangements During Stress Relaxation (1994)

Abstract We have conducted in-situ, real-time x-ray diffraction experiments to probe the dynamic structural changes occurring in copper during loading and then on relaxation. The 331 Kα I , Kα II peaks were used to monitor the development of elastic strains during loading, and their response during relaxation. The peak width was studied to better understand the structural changes that occur during loading, and more importantly on relaxation, since it is these structural rearrangements that reduce the overall strain in the system and allow the stress to relax. The results revealed that the structure is highly mobile immediately following the start of stress relaxation. The mobility decreases with time, scales with the magnitude of the applied strain and is highly dependent upon the applied strain rate. In addition, it was apparent that the Kα I and Kα II peaks do not respond in the same way to the elastic strains and that they also show different structural rearrangements. This suggests an in homogeneous distribution of displacements within the sample.
An ethoxylated surfactant enhances the penetration of the sulfated laminarin through leaf cuticle and stomata, leading to increased induced resistance against grapevine downy mildew (2015)

Some β-1,3-glucans and particularly sulfated laminarin (PS3) are known as resistance inducers (RIs) in grapevine against the downy mildew. However, their efficacy in vineyard is still often too low, which might be caused by a limited penetration through the leaf cuticle following spray application. We used (14) C-sucrose uptake experiments with grapevine leaves in order to select a surfactant as saccharide penetration enhancer. Our results showed that although sucrose foliar uptake was low, it was strongly enhanced by Dehscofix CO125 (DE), a highly ethoxylated surfactant. Fluorescent saccharides were then produced and laser scanning microscopy was used to analyze their foliar diffusion pattern in Arabidopsis thaliana and grapevine. Interestingly, sucrose and PS3 were seemingly able to penetrate the leaf cuticle only when formulated with DE. Diffusion could preferentially occur via stomata, anticlinal cell walls and trichomes. In grapevine, PS3 penetration rate was much higher on the stomateous abaxial surface of the leaf than on the adaxial surface. Finally, using DE allowed a higher level of downy mildew control by PS3, which corroborated diffusion observations. Our results have practical consequences for the improvement of treatments with saccharidic inducers on grape. That is, formulation of such RIs plays a critical role for their cuticular diffusion and consequently their efficacy. Also, spray application should preferentially target the abaxial surface of the leaves in order to maximize their penetration.
Bariatric Procedures in Older Adults in the United States: Analysis of a Multicenter Database (2019)

Background<i>:</i> Bariatric procedures help reduce obesity-related comorbidities and thus improve survival. Clinical characteristics and outcomes after bariatric procedures in older adults were investigated. Methods<i>:</i> A multi-institutional Nationwide Inpatient Sample (NIS) database was queried from years 2005 through 2012. Older adults >60 years of age with procedure codes for bariatric procedures and a diagnosis of obesity/morbid obesity were selected to compare clinical characteristics/outcomes between those undergoing closed versus open procedures and identify risk factors associated with in-hospital mortality and increased hospital length of stay (LOS). Results<i>:</i> Over the study period, 79,122 bariatric procedures were performed. Those undergoing open procedures compared to closed procedures had a higher in-hospital mortality (0.8% vs. 0.2%) and a longer hospital LOS (4.8 days vs. 2.2 days). Risk factors significantly associated with in-hospital mortality were open procedures, the Western region, and the Elixhauser comorbidity index. Risk factors associated with increased LOS were Medicaid insurance type, an open procedure, a higher Elixhauser comorbidity score, a required skilled nursing facility (SNF) discharge, and died in hospital. Conclusion<i>:</i> Closed bariatric procedures are increasingly being preferred in older adults, with a four-fold lower mortality compared to open procedures. Besides choice of procedure, the presence of specific comorbidities is associated with increased mortality in older adults.
Fermi level unpinning in ex situ Schottky contacts on n-GaAs capped with low-temperature-grown GaAs (2002)

The Schottky barrier behavior of a GaAs layer structure consisting of a thick n-GaAs layer, capped by a thin (3.5 nm) layer of as-grown unintentionally or Be-doped low-temperature-grown GaAs (LTG:GaAs), both grown by molecular beam epitaxy, has been studied. Nonalloyed, ex situ Schottky contacts using three different metals were fabricated on the LTG:GaAs-capped layers and on n-GaAs control samples, in order to study the interface barrier height (φb) versus the metal work function (φm). High frequency capacitance–voltage measurements, along with simulations that incorporate a complete description of the defect states in LTG:GaAs, were used to extract the φb values. The variation in φb with the metal work function is nearly six times greater in the LTG:GaAs capped contacts than in uncapped n-GaAs samples. This direct observation of Fermi level unpinning is consistent with earlier measurements that indicated the inhibited oxidation of LTG:GaAs layers in comparable structures for short air exposure times.
Natural Drag-Reducing Polymers: Discovery, Characterization and Potential Clinical Applications (2016)

About seven decades ago, it was discovered that special long-chain soluble polymers added to fluid at nanomolar concentrations significantly reduce resistance to turbulent flow (Toms effect). These so-called drag-reducing polymers (DRPs) do not affect resistance to laminar flow. While the flow parameters associated with the Toms effect do not occur in the cardiovascular system, many later studies demonstrated that intravenous injections of DRPs given to experimental animals produced significant hemodynamic effects, such as increasing tissue perfusion, suggesting potential clinical use of these polymers. Moreover, it was found that the specific viscoelastic properties of these polymers make them capable of modifying traffic of blood cells in microvessels and beneficially redistributing them in the blood capillary system—a phenomenon related to rheological properties of DRPs and not related to their specific chemistry. The domain of drag reducing polymers includes many organic and water-soluble, synthetic and natural long-chain molecules. The study presented here employed chemical and rheological methods, as well as macro and microfluidic tests, to characterize the DRP that we discovered in the Aloe vera plant, which was found to be a more powerful drag reducer and less fragile than many synthetic DRPs. The drag-reducing component of aloe gel was purified and chemically identified, which helped to standardize preparation and made this polymer a strong candidate for clinical use. Examples of successful testing of the aloe-derived DRP in animal models are described.
Generation of a Comprehensive Transcriptome Atlas and Transcriptome Dynamics in Medicinal Cannabis (2019)

Cannabinoids are the main medicinal compounds of interest in the plant Cannabis sativa, that are primarily synthesised in the glandular trichomes; found on female floral buds. The content, composition and yield of secondary metabolites (cannabinoids and terpenoids) is influenced by the plant's genetics and environment. Some initial gene expression experiments have been performed from strains of this plant species that contrasted in cannabinoid production, however the present knowledge about detailed trichome transcriptomics in this species is limited. An extensive transcriptome atlas was generated by RNA sequencing using root, shoot, flower and trichome tissues from a female plant strain (Cannbio-2) and was enhanced with the addition of vegetative and reproductive tissues from a male cannabis plant. Differential gene expression analysis identified genes preferentially expressed in different tissues. Detailed trichomics was performed from extractions specifically from glandular trichomes as well as female floral tissues at varying developmental stages, to identify stage-specific differentially expressed genes. Candidate genes involved in terpene and cannabinoid synthesis were identified and the majority were found to have an abundant expression in trichomes. The comprehensive transcriptome is a significant resource in cannabis for further research of functional genomics to improve the yield of specialised metabolites with high pharmacological value.
Observation of Crystalline Imperfections in Supercritical Thickness Strained Silicon on Insulator Wafers by Synchrotron X-ray Topography (2008)

A commercial supercritical thickness strained Si-on-insulator (SC-sSOI) wafer was characterized by large-area synchrotron x-ray topography at the glancing incident condition. Several kinds of contrast showing crystalline imperfections were observed all over the wafers, such as macule and crosshatch patterns. Similar crosshatch patterns were also observed in the x-ray topographs of a conventional strained Si-on-insulator (sSOI) wafer and a strained Si wafer that has the strained Si layer epitaxially grown on the relaxed SiGe layer on the insulator (SGOI) structure. This indicates that the crosshatch pattern of the SC-sSOI wafer originates from the lattice distortion in the original SiGe substrate of the strained Si layer.
Prognostic and Predictive Biomarkers in Patients With Coronavirus Disease 2019 Treated With Tocilizumab in a Randomized Controlled Trial* (2021)

Multiple biomarkers prognostic for clinical outcomes were confirmed in COVACTA. Ferritin was identified as a predictive biomarker for the effects of tocilizumab in the COVACTA patient population; high ferritin levels were associated with better clinical outcomes for tocilizumab compared with placebo at day 28.
Effects of a single 10mg dose of empagliflozin on postprandial insulin kinetics in patients with postbariatric hypoglycaemia (2021)

ABSTRACT Introduction Postbariatric hypoglycaemia (PBH) is an increasingly recognized late metabolic complication of Roux-en-Y gastric bypass (GB) surgery. PBH typically manifests with a fact occurring post-meal hyperglycaemic peak, followed by a disproportionately exaggerated insulin response leading to low glucose levels. On this basis, we evaluated the effect of a single dose of empagliflozin 10mg vs. placebo on parameters of insulin kinetics. Materials and methods Insulin secretion, hepatic insulin extraction and total insulin clearance were evaluated after a single of empagliflozin 10mg vs. placebo followed by a standardized liquid mixed meal were evaluated in 11 subjects with confirmed PBH after GB over 3h. Parameters of interest were calculated using established mathematical models. Indices were compared between the groups using the Wilcoxon signed-rank test. Results Total beta-cell responsiveness tends to be lower with empagliflozin vs. placebo (24.83±11.00 vs. 27.15±9.68 [10 −9 min -1 ], p=0.150). Total first-pass hepatic insulin extraction increased after empagliflozin compared to placebo (49.6±14.2 vs. 39.7±12.1 %, p=0.006), while no significant effect of empaglizflozin on basal first-pass hepatic insulin extraction was observed (79.7±7.1 vs. 81.1±6.6 %, p=0.521). Total insulin clearance resulted to be significantly lower after empagliflozin compared to placebo (3.91±1.58 vs. 3.00±1.27 l/min, p=0.002). Conclusion The present analysis suggests that the hypoglycaemia-attenuating effect of SGLT2-inhibition in patients with PBH is mainly mediated by an increment in insulin clearance, with also a tendency to a reduction in insulin secretion.
Sizing, Integration and Characterization of an Active Flow Control System (2023)

View Video Presentation: https://doi.org/10.2514/6.2023-2493.vid The sizing of an Active Flow Control (AFC) system involves a wide design space and multiple variables including the target flight conditions, air source characteristics, AFC actuator selection, and optimizing the air distribution system. This design space is explored by using empirical and analytical models and validation with full-scale bench tests. Steady state and dynamic test points were performed to characterize the AFC system, capturing the mass flow, pressure, and temperature behavior under various system conditions. Designing a fully integrated AFC system for the Defense Advanced Research Projects Agency (DARPA) X-plane revealed additional integration challenges such as structural integration of the air distribution network, temperature implications, and control bandwidth requirements of the system when operating dynamically. The balance between optimizing the AFC system for performance and vehicle integration constraints was critical for a successful design. This engineering space is being addressed with the presented work.
Three-color photonic crystal demultiplexer based on ultralow-refractive-index metamaterial technology (2005)

We numerically demonstrate the operation of a novel class of wavelength-division demultiplexing circuit based on photonic crystal waveguides that are entirely synthesized by ultralow-refractive-index metallic nanopillars. The operational principle of the newly proposed device is based on the phenomenon of total external reflections in ultralow-refractive-index metallic photonic crystal structures (metamaterials). In addition we provide detailed design guidelines for optimum device performance. The low propagation losses and compact size, as well as temperature-insensitive operation over a wide temperature range, are only a few of the advantages of the proposed technology, making this new type of demultiplexer an excellent candidate for applications in the visible spectrum.
Sign and pseudo-sign of Leser-Trélat: case reports and a review of the literature. (2013)

This review updates the existing SLT literature and emphasizes the presence of PLT. Clinicians should be aware that SK eruptions may be early manifestations of an internal malignancy or other pathology. To our knowledge, this is the first review examining both SLT and PLT.
Collaboration meets Fitts' law : Passing virtual objects with and without haptic force feedback (2003)

Abstract: Handing over objects is a common event during collaboration in face-to-face interaction. We investigate how such an event can be supported when the interaction takes place in virtual space. In a formal experiment, subjects passed a series of cubic objects to each other and tapped them at target areas. Their performance with and without haptic force feedback was evaluated. Furthermore, we placed our study in the framework of Fitts ’ law and hypothesized that object hand off constituted a collaboratively performed Fitts ’ law task. Our results showed that task completion time indeed linearly increased with Fitts ’ index of difficulty, both with and without force feedback. The time required for passing objects did not differ significantly between the haptic and nonhaptic condition. However, the error rate was significantly lower with haptic feedback than without.
Orbital angular momentum division multiplexing in optical fibre (2013)

We investigate the feasibility of the orbital angular momentum division multiplexing in optical fibre. Two optical vortices carrying well-definite values of orbital angular momentum, with topological charges equal to 0 and 1, respectively, are multiplexed in a few-mode fibre and then demultiplexed after a propagation of 200 m. The two vortices are discriminated by means of a Mach-Zehnder interferometer with mutually 90°-rotated Dove prisms in the two different arms, showing an inter-modal crosstalk lower than -10 dB. This demultiplexing scheme can be generalized to a higher number of vortices and it is all-optical, without the need of electronic post-processing. The proposed orbital angular momentum division multiplexing technique is very promising for increasing the capacity of the fibre-optic transmission systems in an energy-saving efficient way.
Implementation Guide for the ETSI AFI GANA model: A Standardized Reference Model for Autonomic Networking, Cognitive Networking and Self-Management (2013)

This paper describes an Implementation Guide for an emerging standard for autonomic management &control of networks and services, namely the ETSI AFI GANA Reference Model for Autonomic Networking, Cognitive Networking and Self-Management (an emerging standard from ETSI). The implementation guide also takes into consideration the impact of emerging paradigms such as SDN and Virtualization. This is because as the standardized Reference Model has been published, it becomes important to provide an associated Implementation Guide that can be followed in implementing autonomic management & control in network architectures.
Circumnavigation using distance measurements (2009)

Consider a stationary agent A at an unknown location and a mobile agent B that must move to the vicinity of and then circumnavigate A at a prescribed distance from A. In doing so, B can only measure its distance from A, and knows its own position in some reference frame. This paper considers this problem, which has applications to surveillance or maintaining an orbit. In many of these applications it is difficult for B to directly sense the location of A, e.g. when all that B can sense is the intensity of a signal emitted by A. This intensity does, however provide a measure of the distance. We propose a nonlinear periodic continuous time control law that achieves the objective. Fundamentally, B must exploit its motion to estimate the location of A, and use its best instantaneous estimate of where A resides, to move itself to achieve the ultimate circumnavigation objective. The control law we propose marries these dual goals and is globally exponentially convergent. We show through simulations that it also permits B to approximately achieve this objective when A experiences slow, persistent and potentially nontrivial drift.
MTD−PLS:  A PLS Variant of the Minimal Topologic Difference Method. III. Mapping Interactions between Estradiol Derivatives and the Alpha Estrogenic Receptor (2005)

A homogeneous collection of 45 estrogen agonist derivatives with relative binding affinities measured to the estrogen receptor from Ratus norvegicus was used. The quantitative structure−activity relationships were derived using an improved minimal topologic difference (MTD) method in a partial least-squares (PLS) variant. The spatially assigned analysis of fragment properties can provide receptor site maps, within the limits of the existing series. A steric misfit was found for the steroidal position 2; benefic hydrophobic and van der Waals (enhanced by high polarizability) interactions were found for the 17α−CHCH−X group. MTD-PLS mapping results are confirmed by the experimentally derived estradiol−estrogen receptor binding site contacts (based on X-ray crystallography). Our results suggest that this MTD-PLS method can yield useful results for interactions with receptors of unknown 3D structure and, generally, for the steric rigidity of receptor sites.
VISUAL RESULTS AND COMPLICATIONS AFTER RETINAL REATTACHMENT IN THE ACUTE RETINAL NECROSIS SYNDROME (1989)

The authors compare the complications and visual results encountered in a consecutive series of 16 eyes undergoing retinal reattachment surgery for retinal detachment associated with the acute retinal necrosis syndrome. Eight eyes were treated with scleral buckling, vitrectomy, and cryotherapy with or without gas injection. Eight consecutive eyes (with one exception) were treated by the combination of vitrectomy, gas injection and laser photocoagulation with or without primary lensectomy and not subjected to scleral buckling as a primary procedure. The final reattachment rate was 93.8% (15 of 16 eyes) with no significant difference between the primary scleral buckle group (87.5%) and the non-buckle group (100%). Retinal reoperation and complication rates were higher in the primary buckle group and final visual acuities better in the non-buckle group despite comparable preoperative characteristics. RETINA 9:170-174, 1989