gebhart/patrepeval huggingface dataset:
Gigaxonin E3 ligase governs ATG16L1 turnover to control autophagosome production (2019)

Autophagy is an essential self-digestion machinery for cell survival and homoeostasis. Membrane elongation is fundamental, as it drives the formation of the double-membrane vesicles that engulf cytosolic material. LC3-lipidation, the signature of autophagosome formation, results from a complex ubiquitin-conjugating cascade orchestrated by the ATG16L1 protein, whose regulation is unknown. Here, we identify the Gigaxonin-E3 ligase as the first regulator of ATG16L1 turn-over and autophagosome production. Gigaxonin interacts with the WD40 domain of ATG16L1 to drive its ubiquitination and subsequent degradation. Gigaxonin depletion induces the formation of ATG16L1 aggregates and impairs LC3 lipidation, hence altering lysosomal fusion and degradation of the main autophagy receptor p62. Altogether, we demonstrate that the Gigaxonin-E3 ligase controls the production of autophagosomes by a reversible, ubiquitin-dependent process selective for ATG16L1. Our findings unveil the fundamental mechanisms of the control of autophagosome formation, and provide a molecular switch to fine-tune the activation of autophagy.
Smooth and Striated Muscle Development in the Intrinsic Urethral Sphincter (1997)

Development of the intrinsic urethral sphincter is characterized by sequential expression of well characterized muscle marker proteins. The co-expression of smooth and striated muscle markers by developing sphincter myotubule suggests the possibility that trans-differentiation of smooth to striated muscle occurs in the developing genitourinary tract.
Screening study of nerve growth factor's and brain-derived neurotrophic factor's mimetics effects at the experimental depression model (2020)

At the Zakusov Institute of Pharmacology designed and synthesized dimeric dipeptide mimetics of the 1st (GK-6) and 4th (GK-2) nerve growth factor loops, 1st (GSB-214), 2nd (GTS-201) and 4th (GSB -106, GSB-106Ac) brain-derived neurotrophic factor loops. Antidepressant activity of GSB-106 has already been established by oral and intraperitoneal administration in 0.1-5.0 mg/kg doses. Newly synthesized mimetics were studied in comparison with GSB-106 for antidepressant-like activity in the forced swim test on male Balb/c mice with a single intraperitoneal administration. It was found that only mimetic of the fourth brain-derived neurotrophic factor loop GSB-106Ac, varied from GSB-106 by replace monosuccinyl fragment to acetyl, has antidepressant activity in doses of 1.0 mg / kg and 5.0 mg / kg.
[Val 5]-angiotensin II and atrial natriuretic peptide binding sites in the kidney of Xenopus laevis (1987)

Angiotensin II (AII) has potent vasoactive properties, not only in mammals but also in lower vertebrates like amphibia. The active biological form of the octapeptide in these animals is [Val5]-AII. Recently, many studies in mammals, including man, have focused on the action of a potent physiological antagonist of All, the atrial natriuretic peptide (ANP). In mammals, the kidneys are the main target sites for both peptides. In amphibian kidneys (ophistonephros), binding sites for All and ANP have not been demonstrated so far. We investigated their distribution and properties in the kidney of the clawed toad (Xenopus laevis) by quantitative in vitro receptor autoradiography.
A critical role for Lyn kinase in strengthening endothelial integrity and barrier function (2013)

The Src family kinases (SFKs) c-Src and Yes mediate vascular leakage in response to various stimuli including lipopolysaccharide (LPS) and vascular endothelial growth factor (VEGF). Here, we define an opposing function of another SFK, Lyn, which in contrast to other SFKs, strengthens endothelial junctions and thereby restrains the increase in vascular permeability. Mice lacking Lyn displayed increased mortality in LPS-induced endotoxemia and increased vascular permeability in response to LPS or VEGF challenge compared with wild-type littermates. Lyn knockout mice repopulated with wild-type bone marrow-derived cells have higher vascular permeability than wild-type mice, suggesting a role of endothelial Lyn in the maintenance of the vascular barrier. Small interfering RNA-mediated down-regulation of Lyn disrupted endothelial barrier integrity, whereas expression of a constitutively active mutant of Lyn enhanced the barrier. However, down-regulation of Lyn did not affect LPS-induced endothelial permeability. We demonstrate that Lyn association with focal adhesion kinase (FAK) and phosphorylation of FAK at tyrosine residues 576/577 and 925 were required for Lyn-dependent stabilization of endothelial adherens junctions. Thus, in contrast to c-Src and Yes, which increase vascular permeability in response to stimuli, Lyn stabilizes endothelial junctions through phosphorylation of FAK. Therefore, therapeutics activating Lyn kinase may strengthen the endothelial barrier junction and hence have anti-inflammatory potential.
Photochromic materials for holography: issues and constraints (2012)

Photochromic materials can find application in holography, thanks to the peculiar possibility to change reversibly their transparency in the visible (amplitude holography) and their refractive index in the near infrared region (phase holography). The main advantages of such materials are rewritability and self-development. A large change of the key property is crucial to obtain efficient devices and some strategies are followed, accordingly. Production of the holograms have open important issues regarding the film thickness and the nonlinear response to light, because of the strong absorption of the writing light by the material. Results related to these topics, mainly focused on diarylethene-based materials, are reported.
An extension of ECA architecture and its application to HTML document browsing (2003)

We propose a new agent architecture which is represented by extended ECA (XECA) rules. Conventional ECA rules which consist of descriptors such as "event", "condition" and "action" are employed in the field of active databases. We propose new descriptors in order to represent the agents' behavior by ECA rules. These descriptors enable to specify the time constraint of a rule, and express a complex combination of some pairs of condition-action with simple script. In this paper, we show concrete examples of XECA rules to realize Web browsing assistance agents. We discuss two kinds of assistance agents. One is a user profile management agent which constructs the user profile represented by the characteristic keywords and their weights in the Web pages. The other is an information collection agent which automatically collects related information with the user profile. We also show the configuration of a user adaptive browsing system based on the proposed agents.
ChemInform Abstract: The Synthesis of Heterocycles via Addition‐Elimination Reactions of 4‐ and 5‐Aminoimidazoles. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ConnectBoard: Enabling Genuine Eye Contact and Accurate Gaze in Remote Collaboration (2011)

Conventional telepresence systems allow remote users to see one another and interact with shared media, but users cannot make eye contact, and gaze awareness with respect to shared media and documents is lost. In this paper, we describe a remote collaboration system based on a see-through display to create an experience where local and remote users are seemingly separated only by a vertical sheet of glass. Users can see each other and media displayed on the shared surface. Face detectors are applied on the local and remote video streams to introduce an offset in the video display so as to bring the local user's face, the local camera, and the remote user's face image into collinearity. This ensures that, when the local user looks at the remote user's image, the camera behind the see-through display captures an image with the “Mona Lisa effect,” where the eyes of an image appears to follow the viewer. Experiments show that, for one-on-one meetings, our system is capable of capturing and delivering realistic, genuine eye contact as well as accurate gaze awareness with respect to shared media.
Balloon-occluded retrograde transvenous obliteration of gastric varix with multiple drainage veins performed with temporal occlusion of the pericardiacophrenic vein with a micro-balloon (2015)

We encountered a case with a gastric varix that drained into the gastro-renal shunt, left pericardiacophrenic vein, and several other dilated collateral veins. This patient had a circumaortic venous ring. For this case we successfully performed balloon-occluded retrograde transvenous obliteration in which sclerotic agents were infused from the balloon catheter advanced to the left pre-aortic renal vein and the tip was wedged into the end of the gastro-renal shunt. Before injection of sclerotic agents, collateral veins other than the left pericardiacophrenic vein were embolized with micro-coils. During the injection, the left pericardiacophrenic vein was occluded temporarily with a micro-balloon catheter coaxially advanced from the catheter inserted from the femoral vein to the left pericardiacophrenic vein through the left brachiocephalic vein.
Focused ion beams for microfabrication (1997)

Focused ion beam (FIB) techniques are commonly used in microelectronics for prototyping, failure analysis and process control. With the growing interest in MEMS (Micro-Electro-Mechanical Systems) the importance of FIB in this field has to be established for FIB to be considered for production. The milling time is crucial. We show with the fabrication of a microaccelerometer structure that there is scope for FIB in prototyping and production of micromechanical structures leading to novel sensors. (6 pages)
Associations Between Anxiety Disorder Diagnoses and Body Mass Index Differ by Age, Sex and Race: A Population Based Study (2016)

Our results suggest that anxiety may have heterogeneous associations with BMI in the population. Further research on potential mechanisms contributing to these findings will help direct efforts in anxiety and obesity management across diverse population groups.
Ambient ionisation mass spectrometry for lipid profiling and structural analysis of mammalian oocytes, preimplantation embryos and stem cells (2015)

Lipids play fundamental roles in mammalian embryo preimplantation development and cell fate. Triacylglycerol accumulates in oocytes and blastomeres as lipid droplets, phospholipids influence membrane functional properties, and essential fatty acid metabolism is important for maintaining the stemness of cells cultured in vitro. The growing impact that lipids have in the field of developmental biology makes analytical approaches to analyse structural information of great interest. This paper describes the concept and presents the results of lipid profiling by mass spectrometry (MS) of oocytes and preimplantation embryos, with special focus on ambient ionisation. Based on our previous experience with oocytes and embryos, we aim to convey that ambient MS is also valuable for stem cell differentiation analysis. Ambient ionisation MS allows the detection of a wide range of lipid classes (e.g. free fatty acids, cholesterol esters, phospholipids) in single oocytes, embryos and cell pellets, which are informative of in vitro culture impact, developmental and differentiation stages. Background on MS principles, the importance of underused MS scan modes for structural analysis of lipids, and statistical approaches used for data analysis are covered. We envisage that MS alone or in combination with other techniques will have a profound impact on the understanding of lipid metabolism, particularly in early embryo development and cell differentiation research.
Synthetic peptide immunogens eliciting antibodies to Plasmodium falciparum sporozoite and merozoite surface antigens in H-2b and H-2k mice. (1990)

Peptides representing conserved (MSA2/1A and MSA2/1B) and variant (MSA2/2, MSA2/6 and MSA2/7) regions of the merozoite surface Ag 2 (MSA2) of Plasmodium falciparum (FCQ-27/PNG isolate) were coupled to either peptide NP(NANP)5NA or peptide C(NANP)6 both of which contained the core sequence (NANP)n. The coupling was done via the N-terminus of one peptide and a cysteine residue on either terminus of the other. BL/10 (H-2b) and B10.BR (H-2k) mice were immunized with these MSA2-(NANP)n conjugates. The mice were also immunized with the unconjugated MSA2 peptides and with NP(NANP)5NA and C(NANP)6. Antibody responses were evaluated by 1) ELISA, in which the MSA2 peptides and C(NANP)6 were used as Ag; 2) immunofluorescence assays (IFAT) against intact sporozoites and merozoites; and 3) immunoblotting experiments against solubilized P. falciparum blood stage proteins. High titer antibodies to (NANP)n were elicited in both BL/10 and B10.BR mice after immunization with all the conjugates except MSA2/7-(NANP)n which gave only a very limited response in B10.BR mice. These antibodies recognized unfixed sporozoites. The conjugates also elicited antibodies to MSA2 as shown by ELISA, IFAT, and immunoblotting except for mice immunized with MSA2/1B-(NANP)n where an anti-MSA2 response was only detectable by immunoblotting. Immunization with unconjugated MSA2 peptides showed that MSA2/2 was immunogenic in both BL/10 and BR.10 mice, with MSA2/6 and MSA2/7 being immunogenic only in BL/10 mice. The antibodies elicited recognized both merozoites and the MSA2 protein. However, the antibody titers were lower overall than those seen when these peptides were used in the conjugated form. No anti-MSA2 antibodies were detected after immunization with MSA2/1A and MSA2/1B. Immunization of mice with the peptide NP(NANP)5NA produced antibodies in BL/10 (H-2b) mice only, and the immunogenicity of this preparation was poor. In contrast, C(NANP)6 produced a strong antibody response in both mouse strains. The antibodies elicited by NP(NANP)5NA and C(NANP)6 recognised sporozoites in IFAT. The MSA2 peptides studied (or their derivatives) were previously shown to be recognized by human T cells. Their immunogenic potential shows promise in that complex anti-P. falciparum responses can be elicited with simple synthetic immunogens based on these peptides.
Ultrafast two-bit all-optical analog-to-digital conversion based on femtosecond soliton sequence sampling (2011)

Realization of two-bit all-optical analog-to-digital conversion for an analog signal sampled by a femtosecond soliton sequence is investigated. Two approaches are suggested. The first one is based on filtering the broadened soliton spectrum after evolution over half of the soliton period in a standard single-mode fiber. In the second approach, the pulse is temporally sampled at the specified times after propagating through one soliton period. The sampled soliton sequence must be amplified to achieve an initial peak power of between 0 and 75 kW for the first method and between 0 and 66 kW for the second method. The soliton pulse-width is 50 fs. Based on the resulted peak power, the "0" or "1" bit is generated with reference to the threshold values. Subsequently, the digital gray code is produced at the outputs. The effect of inaccuracy in filter frequency and fiber length are also studied in this paper. The first method is sensitive to variations in the filter frequency, whereas the second method is affected by the fiber length inaccuracy.
Enabling Reproducibility and Meta-learning Through a Lifelong Database of Experiments (LDE) (2022)

Artificial Intelligence (AI) development is inherently iterative and experimental. Over the course of normal development, especially with the advent of automated AI, hundreds or thousands of experiments are generated and are often lost or never examined again. There is a lost opportunity to document these experiments and learn from them at scale, but the complexity of tracking and reproducing these experiments is often prohibitive to data scientists. We present the Lifelong Database of Experiments (LDE) that automatically extracts and stores linked metadata from experiment artifacts and provides features to reproduce these artifacts and perform meta-learning across them. We store context from multiple stages of the AI development lifecycle including datasets, pipelines, how each is configured, and training runs with information about their runtime environment. The standardized nature of the stored metadata allows for querying and aggregation, especially in terms of ranking artifacts by performance metrics. We exhibit the capabilities of the LDE by reproducing an existing meta-learning study and storing the reproduced metadata in our system. Then, we perform two experiments on this metadata: 1) examining the reproducibility and variability of the performance metrics and 2) implementing a number of meta-learning algorithms on top of the data and examining how variability in experimental results impacts recommendation performance. The experimental results suggest significant variation in performance, especially depending on dataset configurations; this variation carries over when meta-learning is built on top of the results, with performance improving when using aggregated results. This suggests that a system that automatically collects and aggregates results such as the LDE not only assists in implementing meta-learning but may also improve its performance.
Eradication of Biofilm-Forming Staphylococcus epidermidis (RP62A) by a Combination of Sodium Salicylate and Vancomycin (2001)

Staphylococcus epidermidis is a major cause of infections associated with indwelling medical devices. Biofilm production is an important virulence attribute in the pathogenesis of device-related infections. Therefore, elimination of these biofilms is an ideal treatment. Salicylate (5 mM) combined with 1 microg of vancomycin per ml inhibited biofilm formation by S. epidermidis (RP62A) by >or=99.9%. When biofilm-coated polystyrene beads were exposed to 5 mM sodium salicylate and 4 microg of vancomycin per ml (one-half the minimum biofilm eradication concentration), there was a >99.9% reduction in viable count.
Performance analysis of an iSCSI-based unified storage network. (2004)

In this paper, we introduced a novel storage architecture "Unified Storage Network", which merges NAC(Network Attached Channel) and SAN(Storage Area Network), and provides the file I/O services as NAS devices and provides the block I/O services as SAN. To overcome the drawbacks from FC, we employ iSCSI to implement the USN(Unified Storage Network). To evaluate whether iSCSI is more suitable for implementing the USN, we analyze iSCSI protocol and compare it with FC protocol from several components of a network protocol which impact the performance of the network. From the analysis and comparison, we can conclude that the iSCSI is more suitable for implementing the storage network than the FC under condition of the wide-area network. At last, we designed two groups of experiments carefully.
Worst-case analysis of target localization errors in fiducial-based rigid body registration (2009)

Fiducial-based rigid registration is the preferred method for aligning the preoperative image with the intra-operative physical anatomy in existing image-guided surgery systems. After registration, the targets locations usually cannot be measured directly, so the Target Registration Error (TRE) is often estimated with the Fiducial Registration Error (FRE), or with Fitzpatrick TRE (FTRE) estimation formula. However, large discrepancies between the FRE and the TRE have been exemplified in hypothetical setups and have been observed in the clinic. In this paper, we formally prove that in the worst case the FRE and the TRE, and the FTRE and the TRE are independent, regardless of the target location, it location, the number of fiducials, and their configuration. The worst case occurs when the unknown Fiducial Localization Error (FLE) is modeled as an affine anisotropic inhomogeneous bias. Our results generalize previous examples, contribute to the mathematical understanding of TRE estimation in fiducial-based rigid-body registration, and strengthen the need for realistic and reliable FLE models and effective TRE estimation methods.
Survival Advantage With Adjuvant Chemotherapy for Locoregionally Advanced Rectal Cancer: A Veterans Health Administration Analysis (2020)

In this population of patients with LARC treated with neoadjuvant CRT and surgery, OS and DSS were improved among those treated with AC versus OBS. DSS benefits were seen with ≥4 months of AC. No additional benefit was observed with multiagent therapy. In the absence of phase III data, these findings support the use of AC for LARC.
Interaction of β2-Glycoprotein-I with Human Blood Platelets: Influence Upon the ADP-Induced Aggregation (1985)

The interaction of beta 2-glycoprotein-I (beta 2-G-I), a plasma constituent of unknown function, with blood platelets was studied. The following results were obtained: 1) beta 2-G-I binds to washed human platelets isolated by centrifugation (WP) at one kind of specific, saturable binding sites. The dissociation constant was found to be approx. 1 X 10(-6) M. In the presence of physiological concentrations of Ca++ (2.5 mM), this specific binding is markedly reduced. Unspecific binding of beta 2-G-I to platelets, however, is not influenced by Ca++. Platelets prepared by gel filtration (GFP), differing in their in vitro aggregability from WP, exhibit no specific binding of beta 2-G-I. Binding to GFP is also not induced by activation with thrombin, collagen or ADP. beta 2-G-I causes significant alteration of the ADP-induced aggregation of GFP. Aggregation induced by thrombin, collagen, arachidonic acid or PAF-acether, however is not altered by beta 2-G-I. It is suggested, that pelleting during centrifugation causes irreversible rearrangements in the membrane of platelets.
SYNTHESIS OF (2-BUTYL-3-BENZOFURANYL)[4-[2-(DIETHYLAMINO)ETHOXY]-3,5-DIIODOPHENYL)METHANE DERIVATIVES (1989)

(1989). SYNTHESIS OF (2-BUTYL-3-BENZOFURANYL)[4-[2-(DIETHYLAMINO)ETHOXY]-3,5-DIIODOPHENYL)METHANE DERIVATIVES. Organic Preparations and Procedures International: Vol. 21, No. 3, pp. 348-351.
Synthesis and Water Splitting Activity of NaTaO3 Photocatalyst by Hydrothermal Method and Solvothermal Method (2011)

We prepared NaTaO3 by hydrothermal method and solvothermal method. Na2Ta2O6 was obtained by hydrothermal treatment of water soluble tantalum complex and NaOH. On the other hand NaTaO3 was obtained by solvothermal treatment of TaCl5 and NaOH in methanol. Many samples were synthesized in various hydrothermal condition, however all samples were Na2Ta2O6 or amorphous. Primary particle size of samples obtained by solvothermal method was 10 nm. Primary particles aggregated and formed 20-50 nm secondly particles. Moreover, specific surface area of NaTaO3 synthesized by the solvothermal method was 109 m2/g. Therefore we succeeded in obtaining NaTaO3 fine particles with high specific surface area. NaTaO3 sample loaded NiO of 6 wt% produced H2 of 600 μmol/h. When solvothermal treatment time was extended from 5 hours to 10 hours and stirring in solvothermal treatment, water splitting activity of NaTaO3 was improved.