gebhart/patrepeval huggingface dataset:
Inactivation of porcine interleukin-1β results in failure of rapid conceptus elongation (2017)

Conceptus expansion throughout the uterus of mammalian species with a noninvasive epitheliochorial type of placentation is critical establishing an adequate uterine surface area for nutrient support during gestation. Pig conceptuses undergo a unique rapid morphological transformation to elongate into filamentous threads within 1 h, which provides the uterine surface to support development and maintain functional corpora lutea through the production of estrogen. Conceptus production of a unique interleukin 1β, IL1B2, temporally increases during the period of trophoblast remodeling during elongation. CRISPR/Cas9 gene editing was used to knock out pig conceptus <i>IL1B2</i> expression and the secretion of IL1B2 during the time of conceptus elongation. Trophoblast elongation occurred on day 14 in wild-type (IL1B2<sup>+/+</sup>) conceptuses but did not occur in ILB2-null (IL1B2<sup>-/-</sup>) conceptuses. Although the morphological transition of IL1B2<sup>-/-</sup> conceptuses was inhibited, expression of a number of conceptus developmental genes was not altered. However, conceptus aromatase expression and estrogen secretion were decreased, indicating that IL1B2 may be involved in the spatiotemporal increase in conceptus estrogen synthesis needed for the establishment of pregnancy in the pig and may serve to regulate the proinflammatory response of endometrium to IL1B2 during conceptus elongation and attachment to the uterine surface.
Computational Modeling and Analysis of Iron Release from Macrophages (2014)

A major process of iron homeostasis in whole-body iron metabolism is the release of iron from the macrophages of the reticuloendothelial system. Macrophages recognize and phagocytose senescent or damaged erythrocytes. Then, they process the heme iron, which is returned to the circulation for reutilization by red blood cell precursors during erythropoiesis. The amount of iron released, compared to the amount shunted for storage as ferritin, is greater during iron deficiency. A currently accepted model of iron release assumes a passive-gradient with free diffusion of intracellular labile iron (Fe2+) through ferroportin (FPN), the transporter on the plasma membrane. Outside the cell, a multi-copper ferroxidase, ceruloplasmin (Cp), oxidizes ferrous to ferric ion. Apo-transferrin (Tf), the primary carrier of soluble iron in the plasma, binds ferric ion to form mono-ferric and di-ferric transferrin. According to the passive-gradient model, the removal of ferrous ion from the site of release sustains the gradient that maintains the iron release. Subcellular localization of FPN, however, indicates that the role of FPN may be more complex. By experiments and mathematical modeling, we have investigated the detailed mechanism of iron release from macrophages focusing on the roles of the Cp, FPN and apo-Tf. The passive-gradient model is quantitatively analyzed using a mathematical model for the first time. A comparison of experimental data with model simulations shows that the passive-gradient model cannot explain macrophage iron release. However, a facilitated-transport model associated with FPN can explain the iron release mechanism. According to the facilitated-transport model, intracellular FPN carries labile iron to the macrophage membrane. Extracellular Cp accelerates the oxidation of ferrous ion bound to FPN. Apo-Tf in the extracellular environment binds to the oxidized ferrous ion, completing the release process. Facilitated-transport model can correctly predict cellular iron efflux and is essential for physiologically relevant whole-body model of iron metabolism.
Volumetric MRI Differences in Treatment Naïve and Chronically Treated Adolescents With ADHD-Combined Type (2012)

These findings suggest that aberrant prefrontal and caudate volumes in ADHD-C may compromise functioning of the frontostriatal circuitry.
Muscle biopsies in children—an evaluation of histopathology and clinical value during a 5-year period (2009)

Muscle biopsy is an important diagnostic tool in the investigation of children with neuromuscular disorders. This report presents the experience with paediatric muscle biopsies during a 5-year period at a routine pathology laboratory. A total number of 58 cases were included, and indications, microscopical findings, and final histopathological diagnoses were recorded. A total of 21 biopsies were from females (36%) and 37 biopsies from males (64%); 53% of the cases were from children under 2 years of age. Major pathological findings were found in 30% comprising muscular dystrophy, neurogenic atrophy, and congenital and metabolic disorders, even in cases with vague clinical manifestations. These findings confirm the high diagnostic yield of muscle biopsies, especially as new techniques have been introduced such as immunohistochemistry. Muscle pathology is difficult and emphasizes the importance of this service being undertaken by specialized laboratories with an experienced staff. Microscopical examination of muscle biopsies should be based on adequate clinical information, demonstrating the necessity of close contact between pathologists and referring physicians.
Catalytic reactivity of surfaces: in recognition of François Gault (2017)

This special issue of Catalysis Science &amp; Technology pays tribute to the scientific work of François Gault.
Simple integrated single-atom detector (2009)

We present a reliable and robust integrated fluorescence detector capable of detecting single atoms. The detector consists of a tapered lensed single-mode fiber for precise delivery of excitation light and a multimode fiber to collect the fluorescence. Both are mounted in lithographically defined SU-8 holding structures on an atom chip. 87Rb atoms propagating freely in a magnetic guide are detected with an efficiency of up to 66%, and a signal-to-noise ratio in excess of 100 is obtained for short integration times.
Supplementary Methods from Oncogenic Deregulation of EZH2 as an Opportunity for Targeted Therapy in Lung Cancer (2023)

&lt;p&gt;Supplementary Methods&lt;/p&gt;
Extended Compositional Range for the Synthesis of SWIR and LWIR Ge1–ySny Alloys and Device Structures via CVD of SnH4 and Ge3H8 (2021)

A chemical vapor deposition (CVD) strategy is presented for the synthesis of Ge1–ySny alloys on Si wafers with band gaps in the short-wave infrared (SWIR) range of 1.8–2.6 μm, as well as in the long-wave infrared (LWIR) at 12 μm and beyond. This broad compositional versatility is achieved by CVD reactions of Ge3H8 and SnH4 as Ge and Sn precursors, respectively. The use of conventional SnH4 instead of the previously used SnD4 is found to be critical in synthesizing alloys with Sn contents between 30 and 36%, suggesting that at very low temperatures required to grow these supersaturated alloys, the incorporation of Sn is reaction-rate-dependent. The SnD4 precursor was historically preferred to SnH4 due to its longer lifetime at room temperature. However, the difference is found not to be significant from a practical perspective, and the fact that SnH4 can be synthesized from cheap and readily available starting materials represents a significant cost reduction and portends feasibility for commercial applications. The subtle differences between SnD4 and SnH4 that may explain why alloys with Sn incorporation higher than 30% can only be achieved with the latter are discussed in detail. Optical experiments indicate that such concentrations may be sufficient to cover much of the LWIR range. Device structures containing SWIR Ge1–ySny alloys were grown with the SnH4 precursor to demonstrate its suitability as a viable Sn source. The fabricated heterostructure pin diodes display excellent structural properties and a clear rectifying behavior, providing evidence that SnH4 is a practical and versatile CVD source of Sn at all concentrations of practical interest.
Housing, spatial patterns and social cohesion (2011)

Abstract This chapter explores how housing policy should be evaluated in relation to the cohesion debate. It also reorientates housing-policy debates around the core theme of social, as distinct from ‘community’, cohesion. The significance of housing quality and the built environment is explained. The dominant social-policy focus on ethnic segregation, infused with the suggestion that communities have begun to exhibit ‘parallel lives’, is a relatively recent phenomenon. The chapter then addresses the key questions: how can access to good-quality housing can be improved?; and how can more stable and cohesive neighbourhoods be promoted? In addition, it elaborates the increasing access to social housing, the problem of ‘racial steering’, and deploying regeneration policy so as to promote greater ‘social mix’. There is some evidence that mixed-tenure developments may enhance interaction between residents from different backgrounds.
Demonstration of a Scalable Microfabrication Process for Arrayed Electrowetting Microprisms (2010)

A challenging non-planar scalable microfabrication process of arrayed electrowetting microprisms is reported. And an ~1500 element array of ~150 μm- size electrowetting microprisms is demonstrated.
MIF Promotes B Cell Chemotaxis through the Receptors CXCR4 and CD74 and ZAP-70 Signaling (2014)

Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine with chemokine-like functions that plays a pivotal role in the pathogenesis of inflammatory diseases by promoting leukocyte recruitment. We showed that MIF promotes the atherogenic recruitment of monocytes and T cells through its receptors CXCR2 and CXCR4. Effects of MIF on B cell recruitment have not been addressed. In this study, we tested the involvement of MIF in B cell chemotaxis and studied the underlying mechanism. We show that MIF promotes primary murine B cell chemotaxis in a dose-dependent manner, comparable to the B cell chemokines CXCL13 and CXCL12. Splenic B cells express CXCR4 and the receptor CD74 but not CXCR2. Inhibition of CXCR4 or CD74 or a genetic deficiency of Cd74 in primary B cells fully abrogated MIF-mediated B cell migration, implying cooperative involvement of both receptors. MIF stimulation of B cells resulted in a rapid increase in intracellular Ca(2+) mobilization and F-actin polymerization. Intriguingly, the tyrosine kinase ZAP-70 was activated upon MIF and CXCL12 treatment in a CXCR4- and CD74-dependent manner. Pharmacological inhibition of ZAP-70 resulted in abrogation of primary B cell migration. Functional involvement of ZAP-70 was confirmed by small interfering RNA-mediated knockdown in Ramos B cell migration. Finally, primary B cells from ZAP-70 gene-deficient mice exhibited ablated transmigration in response to MIF or CXCL12. We conclude that MIF promotes the migration of B cells through a ZAP-70-dependent pathway mediated by cooperative engagement of CXCR4 and CD74. The data also suggest that MIF may contribute to B cell recruitment in vivo (e.g., in B cell-related immune disorders).
In Vitro Performance of Published Glypican 3-Targeting Peptides TJ12P1 and L5 Indicates Lack of Specificity and Potency (2019)

<b><i>Background:</i></b> Glypican 3 (GPC3), a plasma membrane heparan sulfate proteoglycan, is overexpressed on human hepatocellular carcinoma and may represent a promising biomarker. Several studies have reported peptides that selectively bind to GPC3 and could serve as scaffolds for imaging or therapeutic agents. <b><i>Materials and Methods:</i></b> We synthesized variants of two previously published peptides, DHLASLWWGTEL (TJ12P1) and RLNVGGTYFLTTRQ (L5), and evaluated their <i>in vitro</i> binding performance in paired isogenic cell lines, A431(GPC3<sup>-</sup>) and A431-GPC3<sup>+</sup> (G1), as well as the liver cancer cell line HepG2. Using flow cytometry and biolayer interferometry (BLI), we compared the binding of the TJ12P1 and L5 peptide variants to the binding of corresponding scrambled peptides having the same amino acid composition, but in random sequence. <b><i>Results:</i></b> While both peptides bound to G1 and HepG2, they also bound to A431. The corresponding scrambled peptides demonstrated greater apparent binding to both G1 and A431 than their specific counterparts. BLI confirmed lack of binding at 0.5-1 μM for both peptides. <b><i>Conclusions:</i></b> We conclude that neither TJ12P1 nor L5 variant demonstrates selectivity for GPC3 at concentrations near the reported <i>K</i><sub>D</sub>, and that the peptides lack potency or are nonspecific, making them inadequate for use as imaging agents.
Deformation behaviour of the cross-section of a heat-sealed area in plastic film used for liquid package bags (1997)

Displacements on a cross-section of a heat-sealed area in laminated plastic film used for liquid package bags are measured by a digital image correlation. All the specimens used for obtaining the images necessary to measure the displacements are cut into the required shape from heat-sealed package bags. The images are recorded by an 8mm video camera via a microscope, and digitized by an image-processing device. Twenty-six images are used for obtaining the displacements between the no-load condition and failure of the specimens. As a result, a characteristic displacement is found in the heat-sealed area.
Identification of Proteins Associated with Spatial-Specific Phytochrome- Mediated Light Signaling in Arabidopsis thaliana by Liquid Chromatography-Tandem Mass Spectrometry (2011)

Photosensory phytochromes perceive mainly red and far-red light and utilize a linear tetrapyrrole chromophore, phytochromobilin, for their photoactivity in plants. Although phytochromes have been extensively studied for light-dependent regulation of numerous developmental processes, our understanding of the molecular mechanisms responsible for distinct organ- and tissue-specific phytochrome responses is still limited. Recent studies using transgenic Arabidopsis thaliana plants expressing a gene that encodes the biliverdin IXα reductase (BVR) enzyme, which reduces the biosynthesis and accumulation of phytochromobilin, and thus inactivates phytochromes, have led to advances in probing tissue-specific roles of phytochromes in plant development. We performed one-dimensional SDS-PAGE, followed by protein identification and peptide quantification using liquid chromatography-tandem mass spectrometry (LC/MSMS) to identify proteins that accumulate differentially in transgenic Arabidopsis lines with mesophyll specific phytochrome deficiencies (i.e., CAB3::pBVR2 plants) compared to wild-type (WT). We identified the large subunit of Rubisco (RbcL) and small subunit of Rubisco (RbcS), which accumulated to lower levels in CAB3::pBVR2 relative to WT under continuous far-red light. We found that Beta-glucosidase proteins (BGLUs) accumulated highly in the CAB3::pBVR2 line under these conditions. RT-PCR and microarray analyses showed a positive correlation between the expression of the target genes and the accumulation of their products in BVR lines. We conclude that RbcL, RbcS, and BGLU18 are targets of mesophyll-specific phytochrome-mediated light signaling under far-red conditions.
PEDF Promotes Biosynthesis of a Novel Anti-inflammatory and Anti-apoptotic Mediator NPD1 in Retinal Pigment Epithelial Cells. (2008)

Here we demonstrate that pigment epithelium derived factor is an activator of neuroprotectin D1 synthesis in ARPE-19 cells exposed to oxidative stress. A major action of pigment epithelium derived factor-stimulated neuroprotectin D1 synthesis shown here is retinal pigment epithelial cytoprotection. Since the retinal pigment epithelial cell is impaired in retinal degeneration, these novel mechanisms potentially may be targeted in macular degeneration and other retinal degenerative diseases as a new therapeutic avenue and may be applicable for neuroprotection in glaucoma and in other neurodegenerative diseases.
The Dependency of Bioactive Follicle-Stimulating Hormone Secretion on Gonadotropin-Releasing Hormone in Hypogonadal and Cycling Women (1989)

KESSEL, B.; DAHL, K. D.; KAZER, R. R.; LIU, C. -H.; RIVIER, J.; VALE, W.; HSUEH, A. J. W.; YEN, S. S. C. Author Information
Outer Retinal Assessment Using Spectral-Domain Optical Coherence Tomography in Patients With Alzheimer's and Parkinson's Disease (2018)

There were no identifiable differences in the outer retinal metrics across neurodegenerative disease groups and controls. The relationship between the degree of cognitive impairment and ellipsoid zone to retinal pigment epithelium volume warrants further study.
Evidence that Resorption of Bone by Rat Peritoneal Macrophages Occurs in an Acidic Environment (1985)

Skeletal loss in space, like any form of osteoporosis, reflects a relative imbalance of the activities of cells resorbing (degrading) or forming bone. Consequently, prevention of weightlessness induced bone loss may theoretically be accomplished by (1) stimulating bone formation or (2) inhibiting bone resorption. This approach, however, requires fundamental understanding of the mechanisms by which cells form or degrade bone, information not yet at hand. An issue central to bone resorption is the pH at which resorption takes place. The pH dependent spectral shift of a fluorescent dye (fluorescein isothiocyanate) conjugated to bone matrix was used to determine the pH at the resorptive cell bone matrix interface. Devitalized rat bone was used as the substrate, and rat peritoneal macrophages were used as the bone resorbing cells. The results suggest that bone resorption is the result of generation of an acidic microenvironment at the cell matrix junction.
Transverse mode discrimination in long-wavelength wafer-fused vertical-cavity surface-emitting lasers by intra-cavity patterning (2013)

Transverse mode discrimination is demonstrated in long-wavelength wafer-fused vertical-cavity surface-emitting lasers using ring-shaped air gap patterns at the fused interface between the cavity and the top distributed Bragg reflector. A significant number of devices with varying pattern dimensions was investigated by on-wafer mapping, allowing in particular the identification of a design that reproducibly increases the maximal single-mode emitted power by about 30 %. Numerical simulations support these observations and allow specifying optimized ring dimensions for which higher-order transverse modes are localized out of the optical aperture. These simulations predict further enhancement of the single-mode properties of the devices with negligible penalty on threshold current and emitted power.
ChemInform Abstract: Nagelamides Q and R, Novel Dimeric Bromopyrrole Alkaloids from Sponges Agelas sp. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Inhibition of angiogenesis and breast cancer xenograft tumor growth by vegi, a novel cytokine of the tnf superfamily (1999)

Recently, we reported a novel protein of the tumor necrosis factor (TNF) superfamily, named vascular endothelial cell growth inhibitor (VEGI), which is expressed predominantly in endothelial cells. When a secreted form of this new protein was overexpressed in mouse colon cancer cells, the growth of tumors formed by these cells in black mice was inhibited. We now report that recombinant VEGI inhibits the proliferation of endothelial cells but not that of other types of cells examined. The protein also inhibits formation of capillary-like structures by endothelial cells in collagen gels, and the growth of capillaries into collagen gels placed on the chick chorioallantoic membrane. The anticancer potential of VEGI was examined in a breast cancer xenograft tumor model in which the cancer cells were co-injected with Chinese hamster ovary cells overexpressing a secreted form of the protein. The co-injection resulted in potent inhibition of xenograft tumor growth. Our findings are consistent with the view that VEGI is an endothelial cell-specific negative regulator of angiogenesis. Int. J. Cancer 82:131–136, 1999. © 1999 Wiley-Liss, Inc.
<title>Experiments in virtual-endoscopic guidance of bronchoscopy</title> (2001)

Transbronchial needle biopsy is a common procedure for early detection of lung cancer. In practice, accurate results are difficult to obtain, since the bronchoscopy procedure requires a blind puncture into a region hidden behind the airway walls. This paper presents an image-guided endoscopy system for procedure preplanning and for guidance during bronchoscopy. Before the bronchoscopy, a 3D CT scan is analyzed to define guidance paths through the major airways to suspect biopsy sites. During subsequent bronchoscopy, the paths give the physician step-by-step guidance to each suspect site location. At a suspect site, a virtual CT image is registered to the bronchoscopic video. Then, the predefined biopsy site, from the prior CT analysis, is rendered onto the registered video. This gives the physician a reference for performing the needle biopsy. This paper focuses on our recent experiments with this system. These experiments involve a rubber phantom model of the human airway tree and in vivo animal tests. The experiments demonstrate the promise of our approach.
Identification of Protective Brucella Antigens and their Expressions in Vaccinia Virus to Prevent Disease in Animals and Humans. (1996)

Abstract : Vaccinia-Brucella recombinants expressing the Brucella GroEL, HtrA and Cu/Zn SOD proteins were used to immunize mice and the animals were tested for protection against a virulent B. abortus challenge. The Wyeth vaccinia strain expressing GroEL recombinant was unable to proliferate in mice and did not protect. The Western Reserve vaccinia strain expressing HtrA or SOD were able to replicate in mice but did not protect after 1 or 2 vaccinations. It was not possible to detect a CMI response to HtrA or SOD in these mice which may account for lack of protection. A synthetic early-late promoter is now being used to generate vaccinia constructs in order to overcome this problem. Homologs of the E. coli YajC and SecD were identified in Brucella and vaccinia recombinants are being generated nsing the corresponding genes. Genes for the Brucella 18kDa lipoprotein and a 14kDa protein have been cloned to create vaccinia recombinants with them. The Baculovirus expression system is being employed to produce large quantities of Brucella antigens for in vitro and in vivo testing. Fractionation of Brucella lysates is being used as an alternative method to find protective antigens; 4 additional antigens have been identified by this method.
DEVELOPMENT OF A MICROFLUIDIC PLATFORM AND DETECTION SYSTEM FOR PLATELET FUNCTION ANALYSIS (2008)

We have developed a prototype point-of-care diagnostic tool for early warning of platelet related disorders. The system objectively quantifies early-stage, shearmediated platelet-surface interactions for well characterized protein surfaces. The hybrid microfluidic platform significantly reduces sample volume (from ~ 5000 µL to ~150 μL) relative to current laboratory systems, while the detection system utilises low-cost optical components for fluorescence detection of platelet-surface interactions in whole blood.
A Synthetic Route to the MT1-MMP Inhibitor Ancorinoside D (2018)

A methyl ester of ancorinoside D, a 3-acyltetramic acid metabolite of a sponge Penares sollasi, was synthesised in ten steps starting from a protected β-d-glucopyranosyl-(1→4)-d-galactopyranosyltrichloroacetimidate donor. Its attachment to the left half of the 3-acyl spacer by a Schmidt glycosylation, 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO)-mediated oxidation to the uronic acid, introduction of the Z-alkene via Wittig reaction, and functionalisation of the spacer terminus with Meldrum’s acid gave a β-keto ester that reacted with dimethyl N-methyl-d-aspartate under neutral conditions to afford a fully protected ancorinoside D as the product of an unusual domino N-acylation–Dieckmann condensation. Global deprotection left a methyl ester of ancorinoside D, which resisted all saponification attempts.