gebhart/patrepeval huggingface dataset:
Identification of glycoproteins associated with different histological subtypes of ovarian tumors using quantitative glycoproteomics (2011)

Ovarian cancer is the most lethal gynecologic malignancy in adult women. The origin of epithelial ovarian tumors is both morphologically and biologically heterogeneous, and different subtypes of ovarian tumors have different clinical outcomes. In spite of the heterogeneous nature of ovarian carcinoma, the current biomarkers and treatments for this disease are not subtype-specific. To discover the molecular basis of the ovarian tumor subtypes, we analyzed extracellular glycoproteins of seven common subtypes and normal ovary tissues using quantitative glycoproteomic analysis. Glycoproteins for different ovarian tumor subtypes were identified by liquid chromatography-tandem mass spectrometry and quantitated by spectral counting and then verified by iTRAQ labeling and Western blotting. Glycoproteins uniquely expressed in different subtypes of ovarian tumors or commonly expressed in most subtypes were identified. Using Western blots, we verified that mesothelin was overexpressed in serous carcinoma and transitional-cell carcinoma, CEA5 and CEA6 were overexpressed only in mucinous carcinoma, while versican and periostin were overexpressed in most subtypes of ovarian tumors. This study presents the first proteomic characterization of different ovarian tumor subtypes. The identified glycoproteins for histological subtypes of ovarian tumors will facilitate the understanding of the molecular basis, diagnosis of ovarian tumor subtypes, and predictions for treatment responses to therapeutic agents.
Gut mucosa alterations and loss of segmented filamentous bacteria in type 1 diabetes are associated with inflammation rather than hyperglycaemia (2021)

Our results demonstrate that gut mucosa alterations and dysbiosis in T1D are primarily linked to inflammation rather than hyperglycaemia. Anti-inflammatory treatment preserves gut homeostasis and protective commensal flora reducing T1D incidence.
Understanding and eliminating the detrimental effect of endogenous thiamine auxotrophy on metabolism of the oleaginous yeast Yarrowia lipolytica (2019)

ABSTRACT Thiamine is an essential vitamin that functions as a cofactor for key enzymes in carbon and energy metabolism for all living cells. While most plants, fungi and bacteria can synthesize thiamine de novo , the oleaginous yeast, Yarrowia lipolytica , cannot. In this study, we used proteomics together with physiological characterization to understand key metabolic processes influenced and regulated by thiamine availability and identified the genetic basis of thiamine auxotrophy in Y. lipolytica . Specifically, we found thiamine depletion results in decreased protein abundance of the lipid biosynthesis pathways and energy metabolism (i.e., ATP synthase), attributing to the negligible growth and poor sugar assimilation observed in our study. Using comparative genomics, we identified the missing gene scTHI13, encoding the 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase for the de novo thiamine synthesis in Y. lipolytica, and discovered an exceptional promoter, P3, that exhibits strong activation or tight repression by low and high thiamine concentrations, respectively. Capitalizing on the strength of our thiamine-regulated promoter (P3) to express the missing gene, we engineered the first thiamine-prototrophic Y. lipolytica reported to date. By comparing this engineered strain to the wildtype, we unveiled the tight relationship linking thiamine availability to lipid biosynthesis and demonstrated enhanced lipid production with thiamine supplementation in the engineered thiamine-prototrophic Y. lipolytica . IMPORTANCE Thiamine plays a crucial role as an essential cofactor for enzymes in carbon and energy metabolism of all living cells. Thiamine deficiency has detrimental consequences on cellular health. Yarrowia lipolytica , a non-conventional oleaginous yeast with broad biotechnological applications, is a native thiamine auxotroph, whose effects on cellular metabolism are not well understood. Therefore, Y. lipolytica is an ideal eukaryotic host to study thiamine metabolism, especially as mammalian cells are also thiamine-auxotrophic and thiamine deficiency is implicated in several human diseases. This study elucidates the fundamentals of thiamine deficiency on cellular metabolism of Y. lipolytica and identifies genes and novel thiamine-regulated elements that eliminate thiamine auxotrophy in Y. lipolytica . Furthermore, discovery of thiamine-regulated elements enables development of thiamine biosensors with useful applications in synthetic biology and metabolic engineering.
Microfluidic Supercritical Antisolvent Continuous Processing of Poly(3-hexylthiophene) Nanoparticles (2015)

Organic electronic devices are promising alternatives to conventional inorganic technologies. Ink-based processes can easily be used to obtain active films, e.g. by spray-drying or roll-to-roll techniques. But their industrial development might be limited by the use of chlorinated solvents. An alternative consists in using solvent-dispersed NPs of organic semi-conductor. Previous work have demonstrated that it was possible to obtain organic semi-conducting dispersions of P3HT and/or [6,6]-Phenyl C61-Butyric acid Methyl ester (PCBM) NPs using an antisolvent approach. For organic photovoltaic devices, the nano-morphology has to be controlled in order to have donor and acceptor domains size in the range of the exciton diffusion length (10 nm). However, conventional synthesis approaches are based on slow solvent / antisolvent mixing process, whereas strong mixing is required to access small sizes and narrow size distributions. Admittedly, micromixing has a significant effect over particles size and size distribution since homogeneous concentration distribution and high degree of supersaturation can only be reached by intense micromixing. This can be achieved by performing antisolvent processes at microscale using microfluidic devices and/or by using supercritical fluids as antisolvents.By coupling both, we will present in here the first demonstration of a supercritical antisolvent process performed within a microsystem, so called µSAS. The µSAS process was applied to the processing of P3HT NPs as small as 36 ± 8 nm. The designed set-up includes a spraying nozzle at the outlet of the back pressure regulator allowing depositing P3HT NPs films onto a substrate. The µSAS process benefits from both the advantages of supercritical antisolvent approaches and microscale processes (fast mixing, high supersaturation, etc.) and can be successfully used to synthesize semi-conducting polymeric NPs, which size are compatible with the diffusion-length of excitons in active layer of photovoltaic devices.
HFO‐1234yf as a CF 3 Building Block: Synthesis of Trifluoromethyl Quinoline and Chromene Derivatives from Trifluoromethyl‐ynones (2023)

Abstract Trifluoromethyl ynones derived from the refrigerant gas HFO‐1234yf (2,3,3,3‐tetrafluoropropene) react with nucleophiles via a Michael‐type addition process and the allenolate intermediate formed reacts intramolecularly with a carbonyl group to form heterocyclic derivatives. Thus, reaction of 2‐amino and 2‐hydroxyl benzaldehyde or ketone substrates with trifluoromethyl ynone derivatives gives trifluoromethyl quinoline and chromene products by a one‐pot tandem ring closing sequence, forming pharmaceutically relevant structures from an inexpensive starting material without the need for transition metals or column chromatography. The 2‐trifluoromethylquinoline products also show unusual fluxional behaviour, which was explored through 2‐D NMR and X‐ray crystallographic studies.
Camphor modulates TRPV3 cation channels activity by interacting with critical pore-region cysteine residues. (2013)

TRPV3 ion channels mediate thermo-transduction, nociception, inflammation and dermatitis in mammals. TRPV1-4 proteins have been shown to have conserved cysteine-residues in the pore-forming regions. These residues participate in channel activation via S-nitrosylation of channel proteins. Camphor is a commonly used ligand for TRPV3 channels. Thus the knowledge about the potential binding/interacting site(s) for camphor will help to design effective and potent analgesic compounds. In an overlap-extension PCR method, following primer-pairs were used to mutate conserved cysteine-residues in the pore-region of TRPV3 channels; GATTGAGAATcCTCCAAGGACAAAAAGGAC, TRPV3-C612S-Fw and GTCCTTGGAGgACTTCTCAATCAGTCAGTGAGG, TRPV3-C612S-Rv primers pair. And for TRPV3-C619S: GGACTCcAGTTCCTATGGCCAGC, TRPV3-C619S-Fw and GCTGGCCATAgGAACTGGAGTCC, TRPV3-C619S-Rv respectively. All cDNA constructs were confirmed by DNA-sequencing and used to make cRNAs. Oocytes expressing mTRPV3-C619S and mTRPV3-C612S mutant channels were challenged with 2-APB (1 mM), camphor (10 mM) and dihydrocarveol (10 mM) either at -40 mV or +40 mV holding potentials in voltage-clamp experiments. Responses of both mutants to 2-APB were similar to wild-type mTRPV3. Interestingly, responses to camphor were totally lost in mTRPV3-C619S mutant, while responses to dihydrocarveol remained intact. In contrast mTRPV3-C612S displayed slightly altered (16±2 % reduction) phenotype with respect to camphor sensitivity. It is concluded that pore-region cysteines play critical role in camphor sensitivity of TRPV3 ion channels.
Genome‐wide binding analysis of AtGNC and AtCGA1 demonstrates their cross‐regulation and common and specific functions (2017)

GATA transcription factors are involved in multiple processes in plant growth and development. Two GATA factors, <i>NITRATE-INDUCIBLE</i>,<i>CARBON METABOLISM-INVOLVED</i> (<i>GNC</i>) and <i>CYTOKININ-RESPONSIVE GATA FACTOR 1</i> (<i>CGA1</i>, also named <i>GNL</i>), are important regulators in greening, flowering, senescence, and hormone signaling. However, their direct target genes related to these biological processes are poorly characterized. Here, GNC and CGA1 are shown to be transcription activators and by using chromatin immunoprecipitation sequencing (ChIP-seq), 1475 and 638 genes are identified to be associated with GNC and CGA1 binding, respectively. Enrichment of diverse motifs in the peak binding regions for GNC and CGA1 suggests the possibility that these two transcription factors also interact with other transcription factors and in addition genes coding for DNA-binding proteins are highly enriched among GNC- and CGA1-associated genes. Despite the fact that these two GATA factors are known to share a large portion of co-expressed genes, our analysis revealed a low percentage of overlapping binding-associated genes for these two homologues. This suggests a possible cross-regulation between these, which is verified using ChIP-qPCR. The common and specific biological processes regulated by GNC and CGA1 also support this notion. Functional analysis of the binding-associated genes revealed that those encoding transcription factors, E3 ligase, as well as genes with roles in plant development are highly enriched, indicating that GNC and CGA1 mediate complex genetic networks in regulating different aspects of plant growth and development.
Faseroptisches Sensorray zur Untersuchung von Gas/Flüssig‐Mehrphasenströmungen (2003)

Abstract No abstracts.
Adequacy Guidelines for High Permeability Membranes (1989)

A Ktl V of 1.0 or greater has been oflered as a guideline for adequate dialysis treatment, independ‐ ent of the time of dialysis. Most of these studies have been performed with cellulosic‐based membranes, and recently the necessity for a KtlV of this magnitude has been questioned for membranes with high middle molecular clearances. Do you feel that diflerent Ktl V standards should apply for diflerent mem‐ brane materials? Are there any formal studies looking at Ktl V with noncellulosic membranes?
Preparation of Covalently Functionalized Graphene Using Residual Oxygen-Containing Functional Groups (2010)

When fabricated by thermal exfoliation, graphene can be covalently functionalized more easily by applying a direct ring-opening reaction between the residual epoxide functional groups on the graphene and the amine-bearing molecules. Investigation by X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, and transmission electron microscopy (TEM) all confirm that these molecules were covalently grafted to the surface of graphene. The resulting dispersion in an organic solvent demonstrated a long-term homogeneous stability of the products. Furthermore, comparison with traditional free radical functionalization shows the extent of the defects characterized by TEM and Raman spectroscopy and reveals that direct functionalization enables graphene to be covalently functionalized on the surface without causing any further damage to the surface structure. Thermogravmetric analysis (TGA) shows that the nondestroyed graphene structure provides greater thermal stability not only for the grafted molecules but also, more importantly, for the graphene itself, compared to the free-radical grafting method.
Common mode frequency instability in internally phase-locked terahertz quantum cascade lasers (2011)

Feedback from a diode mixer integrated into a 2.8 THz quantum cascade laser (QCL) was used to phase lock the difference frequencies (DFs) among the Fabry-Perot (F-P) longitudinal modes of a QCL. Approximately 40% of the DF power was phase locked, consistent with feedback loop bandwidth of 10 kHz and phase noise bandwidth ~0.5 MHz. While the locked DF signal has ≤ 1 Hz linewidth and negligible drift over ~30 min, mixing measurements between two QCLs and between a QCL and molecular gas laser show that the common mode frequency stability is no better than a free-running QCL.
Optimization of Location Management for PCS Networks with CTRW Mobility Model (2008)

This paper considers the design of the optimal locationupdate area (LA) of the distance-based scheme for personal communication service (PCS) networks. We focus on the optimization of two design parameters associated with the LA: 1) initial position upon LA update; 2) distance threshold for triggering of LA update. Based on the popular continuous-time random walk (CTRW) mobility model, we propose a novel analytical framework that uses a diffusion equation to minimize the location management cost. In this framework, a number of measurable physical parameters, such as length of road section, angle between road sections, and road section crossing time, can be integrated into the system design. This framework allows us to easily evaluate the total cost under general call arrival distributions and LA of different shapes. For the particular case of circular LA and small Poisson call-arrival rate, we prove the following: (1) When the drift is weak, the optimal initial position approaches the center of the LA; when the drift is strong, it approaches the boundary of the LA. (2) Comparing the optimal initial-position and center-initial-position solutions (which is assumed in most prior work), when the drift is weak, the optimal distance threshold and the minimum total cost are roughly equal; when the drift is strong, the optimal distance threshold in the later is about 1.260 times that in the former, and the minimum total cost in the later is about 1.587 times that in the former. That is, optimizing on initial position, which previous work did not consider, has the potential of reducing the cost measure by 37%.
Pathophysiology of Diuretic Resistance and Its Implications for the Management of Chronic Heart Failure (2020)

Diuretic resistance implies a failure to increase fluid and sodium (Na<sup>+</sup>) output sufficiently to relieve volume overload, edema, or congestion, despite escalating doses of a loop diuretic to a ceiling level (80 mg of furosemide once or twice daily or greater in those with reduced glomerular filtration rate or heart failure). It is a major cause of recurrent hospitalizations in patients with chronic heart failure and predicts death but is difficult to diagnose unequivocally. Pharmacokinetic mechanisms include the low and variable bioavailability of furosemide and the short duration of all loop diuretics that provides time for the kidneys to restore diuretic-induced Na<sup>+</sup> losses between doses. Pathophysiological mechanisms of diuretic resistance include an inappropriately high daily salt intake that exceeds the acute diuretic-induced salt loss, hyponatremia or hypokalemic, hypochloremic metabolic alkalosis, and reflex activation of the renal nerves. Nephron mechanisms include tubular tolerance that can develop even during the time that the renal tubules are exposed to a single dose of diuretic, or enhanced reabsorption in the proximal tubule that limits delivery to the loop, or an adaptive increase in reabsorption in the downstream distal tubule and collecting ducts that offsets ongoing blockade of Na<sup>+</sup> reabsorption in the loop of Henle. These provide rationales for novel strategies including the concurrent use of diuretics that block these nephron segments and even sequential nephron blockade with multiple diuretics and aquaretics combined in severely diuretic-resistant patients with heart failure.
Rapid 3D modelling from live video (2010)

Off-line model reconstruction relies on an image collection phase and a slow reconstruction phase, requiring a long time to verify a model obtained from an image sequence is acceptable. Our reconstruction system, ProFORMA, generates 3D models on-line as the input sequence is being collected. As the user rotates the object in front of a stationary camera, generated partial models aid view planning and are also used by the system to robustly track the pose of the object. Models are rapidly produced through a Delaunay tetrahedralisation of points obtained from on-line structure from motion estimation, followed by a probabilistic tetrahedron carving step to obtain a textured surface mesh of the object.
On the Influence of Impedance Matching for the Sensitivity of Reflection Phase Measurements with Resonant Sensors (2022)

In this contribution, the influence of impedance matching for sensors that incorporate phase measurements in a one-port reflection setup is elaborated in detail. The developed theoretical basis is validated by three-dimensional electromagnetic simulations that are corroborated by reflection measurements of a metamaterial-based, resonant near-field sensor with varying impedance matching conditions.
Closed-tube genotyping of apolipoprotein E by isolated-probe PCR with multiple unlabeled probes and high-resolution DNA melting analysis (2007)

Isolated-probe PCR (IP-PCR) is a method that combines asymmetric PCR, unlabeled probes, and high-resolution DNA melting while maintaining a closed tube system. A double-stranded DNA (dsDNA) dye LCGreen® I was used to detect the unlabeled probes. LCGreen I is also used to detect the 277-base pair PCR product peak as an internal amplification control. To accomplish this, IP-PCR separates the asymmetric PCR amplification step and the detection step of the unlabeled probes. This prevents the probes from interfering with the amplification of the DNA target. The samples are then melted using a high-resolution DNA melting instrument: the HR-I™. The closed tube system virtually eliminates PCR product contamination or sample carryover. The target apolipoprotein E (APOE) was chosen to test the IP-PCR technique. APOE contains two single nucleotide polymorphisms (SNPs) located 139 base pairs apart in a GC-rich region of the human genome. The results from this study show that the IP-PCR technique was able to determine the correct APOE genotype for each of the 101 samples. The IP-PCR technique should also be useful in detecting SNPs in other high-GC regions of the human genome.
Efficacy of porcine reproductive and respiratory syndrome virus vaccine and porcine interleukin-12. (2001)

The efficacy of porcine recombinant interleukin-12 (prIL-12) as an adjuvant to stimulate immunity was investigated in pigs vaccinated against porcine reproductive and respiratory syndrome virus (PRRSV). Porcine recombinant IL-12 was cloned and expressed in the insect baculovirus system. Thirty pigs were randomly allocated to five groups, and individual pigs were injected with PRRSV modified live virus with and without coadministration of prIL2; PRRSV killed virus with and without coadministration of prIL-12; or prIL-12 only (control). The effect of prIL-12 was evaluated through monitoring of humoral and cell-mediated immune (CMI) responses. Results indicated that the killed virus given in conjunction with prlL-12 induced humoral and CMI responses of similar magnitude to those of the modified live virus. However, without prIL-12, the immunologic response to vaccination with the killed virus vaccine was poor and similar to that of controls.
Oxygen concentration imaging in a single living cell using phosphorescence lifetime of Pt-porphyrin (2007)

An oxygen concentration imaging system inside a single living cell, based on the phosphorescence lifetime, under a microscope was developed. A fluorescence microscope equipped with a pulsed Nd : YAG laser (532 nm) and a CCD camera equipped with a gated imaging intensifier was used. When the cell was incubated with the phosphorescent compound, platinum tetra-(carboxyphenyl)-porphyrin ( PtTCPP ) was incorporated and localized in the cell. As the phosphorescence intensity depends not only on the concentration of a quencher such as oxygen but also on the concentration of phosphorescent molecules, the oxygen concentration was measured by the phosphorescence lifetime. To measure the oxygen concentration image, the time dependence of the phosphorescence intensity was observed under a microscope. The phosphorescence intensity decay obeyed first order kinetics and the oxygen concentration imaging in the single cell was obtained by the lifetime of a single exponential decay curve.
Hematopoietic and Nonhematopoietic p66Shc Differentially Regulates Stem Cell Traffic and Vascular Response to Ischemia in Diabetes (2021)

<b><i>Aims:</i></b> Peripheral artery disease (PAD) is a severe complication of diabetes, characterized by defective traffic of hematopoietic stem/progenitor cells (HSPCs). We examined the hematopoietic <i>versus</i> nonhematopoietic role of p66Shc in regulating HSPC traffic and blood flow recovery after ischemia in diabetic mice. <b><i>Results:</i></b> Using streptozotocin-induced diabetes, chimeric mice with green fluorescent protein (GFP)<sup>+</sup> bone marrow (BM), and the hind limb ischemia model, we found that the physiologic mobilization and homing of HSPCs were abolished by diabetes, along with impaired vascular recovery. Hematopoietic deletion of <i>p66Shc</i>, obtained by transplanting <i>p66Shc</i><sup>-/-</sup> BM cells into wild-type (Wt) recipients, but not nonhematopoietic deletion, constrained hyperglycemia-induced myelopoiesis, rescued postischemic HSPC mobilization, and improved blood flow recovery in diabetic mice. In Wt diabetic mice transplanted with BM cells from <i>GFP</i><sup>+</sup><i>p66Shc</i><sup>-/-</sup> mice, the amount of HSPCs homed to ischemic muscles was greater than in mice transplanted with <i>GFP</i><sup>+</sup><i>p66Shc</i><sup>+/+</sup> cells, with recruited cells displaying higher expression of adhesion molecules and <i>Vegf</i>. In 40 patients with diabetes, <i>p66Shc</i> gene expression in mononuclear cells was correlated with myelopoiesis and elevated in the presence of PAD. In 13 patients with diabetes and PAD, <i>p66Shc</i> expression in HSPC-mobilized peripheral blood cells was inversely correlated with <i>VEGF</i> expression. <b><i>Innovation:</i></b> For the first time, we dissect the role of hematopoietic <i>versus</i> nonhematopoietic p66Shc in regulating HSPC traffic and ischemic responses. <b><i>Conclusion:</i></b> Hematopoietic deletion of <i>p66Shc</i> was sufficient to rescue HSPC mobilization and homing in diabetes after ischemia and improved blood flow recovery. Inhibiting p66Shc in blood cells may be a novel strategy to counter PAD in diabetes. <i>Antioxid. Redox Signal</i>. 36, 593-607. Clinical Trial No.: NCT02790957.