gebhart/patrepeval huggingface dataset:
Cistromic and genetic evidence that the vitamin D receptor mediates susceptibility to latitude-dependent autoimmune diseases (2016)

The vitamin D receptor (VDR) is a ligand-activated transcription factor that regulates gene expression in many cell types, including immune cells. It requires binding of 1,25 dihydroxy vitamin D3 (1,25D3) for activation. Many autoimmune diseases show latitude-dependent prevalence and/or association with vitamin D deficiency, and vitamin D supplementation is commonly used in their clinical management. 1,25D3 is regulated by genes associated with the risk of autoimmune diseases and predominantly expressed in myeloid cells. We determined the VDR cistrome in monocytes and monocyte-derived inflammatory (DC1) and tolerogenic dendritic cells (DC2). VDR motifs were highly overrepresented in ChIP-Seq peaks in stimulated monocyte (40%), DC1 (21%) and DC2 (47%), P<E(-100) for all. Of the nearly 11 000 VDR-binding peaks identified across the genome in DC1s, 1317 were shared with DC2s (91% of DC2 sites) and 1579 with monocytes (83% of monocyte sites). Latitude-dependent autoimmune disease risk polymorphisms were highly overrepresented within 5 kb of the peaks. Several transcription factor recognition motifs were highly overrepresented in the peaks, including those for the autoimmune risk gene, BATF. This evidence indicates that VDR regulates hundreds of myeloid cell genes and that the molecular pathways controlled by VDR in these cells are important in maintaining tolerance.
SU‐FF‐J‐107: Tumor‐Delineation Uncertainties in FDG‐PET and FMISO‐PET Images and the Effect On Radiation Therapy Plans (2005)

Purpose: To quantify the uncertainties in tumor boundary delineation in head and neck and lung cancer patients using FDG‐PET and FMISO‐PET images and evaluate the dosimetric impact on radiotherapy plans. Method and Materials: We contoured FDG‐PET and FMISO‐PET based tumor volumes using images from the GE Advance PET scanner. We use the autocontour function of the ADAC/Pinnacle radiation planning system to delineate tumor boundaries at successively higher PET signal levels. CT‐based tumor volumes are also contoured by a physician on coregistered PET/CT images. We generated intensity‐modulated radiotherapy (IMRT) plans for head and neck patients treating 66 Gy to CT‐based gross disease and 54 Gy to nodal regions at risk, followed by a boost to the PET‐based tumor. Results: The volumes of PET‐based tumors are a sensitive function of threshold intensity level for all patients. For FDG‐based volumes, a 10% decrease in threshold translates into an approximately 200% increase in volume. Lesions smaller than approximately 8 cm 3 display a more pronounced threshold‐volume dependence. The threshold‐volume dependence in FMISO scans is significantly more sensitive than in FDG scans. Lung cancer patients show a similar trend to head and neck patients with a possible overall shift in sensitivity. IMRT planning results on head and neck patients show that the boost dose limit of FDG‐based volumes depends on the threshold level chosen for contouring. In one patient the D95 of the planning target volume decreased from 7770 cGy to 7230 cGy when the contour level changed from 42% to 55%. Conclusion: PET‐based tumor volumes are strongly affected by the choice of threshold level which has a direct dosimetric impact. Further validation and refinement of delineation methods, including a determination of the proper threshold level, should reduce PET‐related delineation uncertainties for radiotherapy applications.
ChemInform Abstract: Enantioselective Synthesis of Phosphinyl Peptidomimetics via an Asymmetric Michael Reaction of Phosphinic Acids with Acrylate Derivatives. (2002)

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.
Nanosurgery with Femtosecond Lasers (2009)

Femtosecond laser pulses make it possible to ablate cell structures at the submicrometer scale. We apply this technique to study biological processes in living cells and to help identify the function of neurons in nematodes.
Fast error simulation of optical 3D measurements at translucent objects (2012)

The scan results of optical 3D measurements at translucent objects deviate from the real objects surface. This error is caused by the fact that light is scattered in the objects volume and is not exclusively reflected at its surface. A few approaches were made to separate the surface reflected light from the volume scattered. For smooth objects the surface reflected light is dominantly concentrated in specular direction and could only be observed from a point in this direction. Thus the separation either leads to measurement results only creating data for near specular directions or provides data from not well separated areas. To ensure the flexibility and precision of optical 3D measurement systems for translucent materials it is necessary to enhance the understanding of the error forming process. For this purpose a technique for simulating the 3D measurement at translucent objects is presented. A simple error model is shortly outlined and extended to an efficient simulation environment based upon ordinary raytracing methods. In comparison the results of a Monte-Carlo simulation are presented. Only a few material and object parameters are needed for the raytracing simulation approach. The attempt of in-system collection of these material and object specific parameters is illustrated. The main concept of developing an error-compensation method based on the simulation environment and the collected parameters is described. The complete procedure is using both, the surface reflected and the volume scattered light for further processing.
Pharmacokinetics and In Vivo Fate of Intra-Articularly Transplanted Human Bone Marrow-Derived Clonal Mesenchymal Stem Cells (2014)

In this study, we report the pharmacokinetics and in vivo fate of intra-articularly transplanted human mesenchymal stem cells (MSCs) in comparison with those of intravenously administered cells. Bone marrow-derived human clonal mesenchymal stem cells (hcMSCs) were transplanted to nude mice through intravenous or intra-articular routes. The numbers of hcMSCs in blood and tissue samples were measured by the quantitative real-time-polymerase chain reaction (qPCR) with human Alu (hAlu) as a detection marker. Following intra-articular transplantation, the blood levels of hcMSCs peaked 8 h postdose and gradually diminished, showing a 95-fold higher mean residence time than hcMSCs delivered through the intravenous route. Unlike intravenously administered hcMSCs, intra-articularly injected hcMSCs were mainly retained at injection joint sites where their levels 8 h postdose were 116-fold higher than those in muscle tissues. Regardless of injection routes, biodistribution patterns did not significantly differ between normal and osteoarthritis-induced mice. Quantitative analysis using hAlu-specific qPCR revealed that hcMSC levels in joint tissues were significantly higher than those in muscle tissues 120 days postdose. These dramatic differences in kinetic behavior and fate of intra-articularly transplanted hcMSCs compared with intravenously administered hcMSCs may provide insights useful for the development of human MSCs for arthritis therapeutics.
Lateral Connectivity in the Olfactory Bulb is Sparse and Segregated (2011)

Lateral connections in the olfactory bulb were previously thought to be organized for center-surround inhibition. However, recent anatomical and physiological studies showed sparse and distributed interactions of inhibitory granule cells (GCs) which tended to be organized in columnar clusters. Little is known about how these distributed clusters are interconnected. In this study, we use transsynaptic tracing viruses bearing green or red fluorescent proteins to further elucidate mitral- and tufted-to-GC connectivity. Separate sites in the glomerular layer were injected with each virus. Columns with labeling from both viruses after transsynaptic spread show sparse red or green GCs which tended to be segregated. However, there was a higher incidence of co-labeled cells than chance would predict. Similar segregation of labeling is observed from dual injections into olfactory cortex. Collectively, these results suggest that neighboring mitral and tufted cells receive inhibitory inputs from segregated subsets of GCs, enabling inhibition of a center by specific and discontinuous lateral elements.
Proton sponge hydrofluoride as a soluble fluoride ion source (1993)

Proton Sponge (PS) hydrofluoride has been prepared and is totally soluble in acetonitrile; this system was used to generate carbanions from hexafluoropropene and to form carbon–fluorine bonds by reaction with 2,4,6-trichloropyrimidine and by reaction with benzoyl chloride (Proton Sponge hydrochloride is insoluble in acetonitrile).
Data from ABCG2/BCRP Expression Modulates d-Luciferin–Based Bioluminescence Imaging (2023)

&lt;div&gt;Abstract&lt;p&gt;Bioluminescence imaging (BLI) is becoming indispensable to the study of transgene expression during development and, in many &lt;i&gt;in vivo&lt;/i&gt; models of disease such as cancer, for high throughput drug screening &lt;i&gt;in vitro&lt;/i&gt;. Because reaction of d-luciferin with firefly luciferase (fLuc) produces photons of sufficiently long wavelength to permit imaging in intact animals, use of this substrate and enzyme pair has become the method of choice for performing BLI &lt;i&gt;in vivo&lt;/i&gt;. We now show that expression of the ATP-binding cassette (ABC) family transporter ABCG2/BCRP affects BLI signal output from the substrate d-luciferin. &lt;i&gt;In vitro&lt;/i&gt; studies show that d-luciferin is a substrate for ABCG2/BCRP but not for the &lt;i&gt;MDR1&lt;/i&gt; P-glycoprotein (ABCB1/Pgp), multidrug resistance protein 1 (MRP1/ABCC1), or multidrug resistance protein 2 (MRP2/ABCC2). d-Luciferin uptake within cells is shown to be modulated by ABC transporter inhibitors, including the potent and selective ABCG2/BCRP inhibitor fumitremorgin C. Images of xenografts engineered to express transgenic ABCG2/BCRP, as well as xenografts derived from the human prostate cancer cell line 22Rv1 that naturally express ABCG2/BCRP, show that ABCG2/BCRP expression and function within regions of interest substantially influence d-luciferin–dependent bioluminescent output &lt;i&gt;in vivo&lt;/i&gt;. These findings highlight the need to consider ABCG2/BCRP effects during d-luciferin–based BLI and suggest novel high throughput methods for identifying new ABCG2/BCRP inhibitors. [Cancer Res 2007;67(19):9389–97]&lt;/p&gt;&lt;/div&gt;
Supplementary Figure 4 from Anti-DLL4 Inhibits Growth and Reduces Tumor-Initiating Cell Frequency in Colorectal Tumors with Oncogenic <i>KRAS</i> Mutations (2023)

Supplementary Figure 4 from Anti-DLL4 Inhibits Growth and Reduces Tumor-Initiating Cell Frequency in Colorectal Tumors with Oncogenic &lt;i&gt;KRAS&lt;/i&gt; Mutations
Compact and Accurate Models of Large Single-Wall Carbon-Nanotube Interconnects (2011)

Single-wall carbon nanotubes (SWCNTs) have been proposed for very large scale integration interconnect applications and their modeling is carried out using the multiconductor transmission line (MTL) formulation. Their time-domain analysis has some simulation issues related to the high number of SWCNTs within each bundle, which results in a highly complex model and loss of accuracy in the case of long interconnects. In recent years, several techniques have been proposed to reduce the complexity of the model whose accuracy decreases as the interconnection length increases. This paper presents a rigorous new technique to generate accurate reduced-order models of large SWCNT interconnects. The frequency response of the MTL is computed by using the spectral form of the dyadic Green's function of the 1-D propagation problem and the model complexity is reduced using rational-model identification techniques. The proposed approach is validated by numerical results involving hundreds of SWCNTs, which confirm its capability of reducing the complexity of the model, while preserving accuracy over a wide frequency range.
Identification of novel single amino acid changes that result in hyperactivation of the unique GTPase, Rheb, in fission yeast (2005)

Rheb GTPase is a key player in the control of growth, cell cycle and nutrient uptake that is conserved from yeast to humans. To further our understanding of the Rheb pathway, we sought to identify hyperactivating mutations in the Schizosaccharomyces pombe Rheb, Rhb1. Hyperactive forms of Rhb1 were found to result from single amino acid changes at valine-17, serine-21, lysine-120 or asparagine-153. Expression of these mutants confers resistance to canavanine and thialysine, phenotypes which are similar to phenotypes exhibited by cells lacking the Tsc1/Tsc2 complex that negatively regulates Rhb1. The thialysine-resistant phenotype of the hyperactive Rhb1 mutants is suppressed by a second mutation in the effector domain. Purified mutant proteins exhibit dramatically decreased binding of GDP, while their GTP binding is not drastically affected. In addition, some of the mutant proteins show significantly decreased GTPase activities. Thus the hyperactivating mutations are expected to result in an increase in the GTP-bound/GDP-bound ratio of Rhb1. By using the hyperactive mutant, Rhb1(K120R), we have been able to demonstrate that Rhb1 interacts with Tor2, one of the two S. pombe TOR (Target of Rapamycin) proteins. These fission yeast results provide the first evidence for a GTP-dependent association of Rheb with Tor.
Partial Hydrothermal Oxidation of High Molecular Weight Unsaturated Carboxylic Acids for Upgrading of Biodiesel Fuel (2007)

With increasing environmental awareness and crude oil price, biodiesel fuel (BDF) is gaining recognition as a renewable fuel which may be used as an alternative diesel fuel without any modification to the engine. The cold flow and viscosity of BDF, however, is a major drawback that limited its use in cold area. In this study, therefore, we investigated that partial oxidation of high molecular weight unsaturated carboxylic acids in subcritical water, which major compositions in BDF, to upgrade biodiesel fuel. Oleic acid, (HOOC(CH2)7CH=CH(CH2)7CH3), was selected as a model compound of high molecular weight unsaturated carboxylic acids. All experiments were performed with a batch reactor made of SUS 316 with an internal volume of 5.7 cm3. Oleic acid was oxidized at 300 °C with oxygen supply varying from 1–10 %. Results showed that a large amount of carboxylic acids and aldehydes having 8–9 carbon atoms were formed. These experimental results suggest that the hydrothermal oxidative cleavage may mainly occur at double bonds and the cleavage of double bonds could improve the cold flow and viscosity of BDF.
Synthesis, crystal structure and some derivatives of the chlorotris(tetramethylphospholyl)uranium (1992)

Reaction of UCl4 with the potassium salt of the tetramethylphospholyl anion afforded the title compound, which has been transformed into the derivatives [U(η-C4Me4P)3X](X = H, Me, OPri); the trigonal crystal structure revealed that the three phospholyl ligands are pentahapto bonded to the uranium.
Spectrum assignment and fairness in femtocell networks (2013)

In heterogeneous networks, frequency resources can be allocated to different tiers in a co-channel (shared-spectrum) or dedicated channel (split-spectrum) manner, or through a hybrid technique, which is a combination of the two approaches. In the co-channel approach shown in Figure 15.1(a), while the spectrum resources are fully reused in different tiers, cross-tier interference may cause crucial setbacks to the system. For example, macrocell users in the vicinity of closed subscriber group (CSG) femtocells are not allowed to connect to the femtocells, even if their link quality with these femtocells is good. Therefore, such macrocell users receive strong downlink interference from CSG femtocells and may fall into outage.
Multi-wavelength Digital Colposcopy to Aid Early Detection of Cervical Cancer (1998)

The incidence and mortality of invasive cervical cancer in North America has decreased by 70% over the last fifty years, because of early detection through screening efforts (1,2). The test characteristics of the Papanicolaou smear have never been proven through rigorous sensitivity and specificity trials and range widely depending on the study population used to derive them (3). False positive and false negative results cause unnecessary morbidity, and in some cases, mortality.
Straightforward Methodology for the Enantioselective Synthesis of Benzo[a]‐ and Indolo[2,3‐a]quinolizidines. (2007)

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, please click on HTML or PDF.
Harnessing the open-circuit voltage via a new series of Ru(ii) sensitizers bearing (iso-)quinolinyl pyrazolate ancillaries (2013)

A novel class of Ru(II) sensitizers (TFRS-51–TFRS-54) with a 4,4′-dicarboxy-2,2′-bipyridine anchoring ligand and two trans-oriented isoquinolinyl (or quinolinyl) pyrazolate ancillaries were designed, characterized and used to fabricate dye sensitized solar cell (DSC) devices. In sharp contrast to Ru(II) sensitizers that employ functionalized thiophene appendages in their ancillary bipyridal ligands, the extended π-conjugation introduced by the isoquinolinyl or quinolinyl groups improves the optical absorptivity, particularly for the absorption located at ∼500 nm when compared with the parent sensitizer TFRS-1 possessing less conjugated 5-pyrid-2-yl pyrazolate ancillaries. As a result, DSCs incorporated with these dyes show much improved JSC compared with the reference device. Moreover, the use of bulky t-butyl substituents on the ancillary ligands improves the cell performance with excellent VOC of up to 830 mV recorded. Also, the addition of tetra-n-butyl ammonium deoxycholate [TBA][DOC] as co-adsorbent to the dye solution further improves the power conversion efficiency (η). The best solar cell parameters recorded were JSC = 16.3 mA cm−2, VOC = 860 mV, FF = 0.72, and η = 10.1% for a device sensitized with TFRS-52. The markedly high open-circuit voltage is confirmed by the longer electron lifetime revealed in transient photovoltage (TPV) measurement versus the TFRS-1 sensitizer, and is probably derived from a combination of the higher conduction band edge of TiO2 induced by the in situ metathesis of carboxylate anchors and the reduced recombination contributed by the bulky sensitizer.
Loss of the VEGF164 and VEGF188 Isoforms Impairs Postnatal Glomerular Angiogenesis and Renal Arteriogenesis in Mice (2002)

Vascular endothelial growth factor (VEGF) is transcribed in the VEGF(120), VEGF(164), or VEGF(188) isoforms, which differ in receptor binding, matrix association, and angiogenic activity. This vascular growth factor has been implicated in the development of the renal vasculature, but the role of the distinct VEGF isoforms remains unknown. In the present report, renal angiogenesis and arteriogenesis were studied in VEGF(120/120) mice, expressing only the short VEGF(120) isoform. In VEGF(120/120) mice, ingrowth and survival of capillaries in glomeruli, remodeling of peritubular capillaries, vascular coverage by pericytes, and branching of renal arteries were all severely impaired, causing abnormal glomerular filtration and impairing renal function. The arterial branching defect might be related to a reduced expression of renin, a presumed renal arterial branching factor. Glomerulosclerosis and tubular dilation possibly resulted from renal ischemia caused by vascular defects. Thus, VEGF(164) and VEGF(188) not only mediate angiogenesis, but they also play an essential role in renal branching arteriogenesis.
Thickness Effects on Physical and Ferroelectric Properties of Bi3.35La0.85Ti3O12(BLT) Films withc-axis-Preferred and Random Orientations (2003)

Thickness effects on dependences of physical and ferroelectric properties were investigated for two kinds of Bi3.35La0.85Ti3O12 (BLT) film with c-axis-preferred and random orientations. BLT films were prepared on Pt/TiOx/SiO2/Si substrates by the metalorganic decomposition (MOD) method, and their crystalline orientation was controlled by baking and rapid thermal annealing (RTA) conditions. When scaling down thickness from 210 to 70 nm, the c-axis-oriented film showed a big reduction in switching polarization (P*-P∧) from 13 to 6 µC/cm2 due to the predominant negative effect of the increased degree in c-axis-preferred orientation rather than the positive effect of increased grain size. However, the randomly oriented film showed no physical change such that it maintained a large polarization of 15–16 µC/cm2 in spite of the thickness reduction. Coercive field (2Ec) and fatigue-free property showed no significant thickness dependence for both BLT films.
A Safety Valve for the Pediatric Rees System (1976)

RAMANATHAN, SIVAM MD; CHALON, JACK MD; TURNDORF, HERMAN MDEditor(s): MUNSON, EDWIN S.; STOELTING, ROBERT K. Author Information
Direct Evidence of High Spatial Localization of Hot Spots in Surface‐Enhanced Raman Scattering (2009)

Hot and cold: The high degree of localization in SERS hot spots is demonstrated directly by a selective deposition of Raman analytes inside and outside the field-enhanced regions in a plasmonic cavity (see picture). The localization is demonstrated by measurements of both the absolute SERS intensities and the kinetics for photoinduced degradation at different positions. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.