gebhart/patrepeval huggingface dataset:
C1q binding to surface-bound IgG is stabilized by C1r 2 s 2 proteases (2021)

Abstract Complement is an important effector mechanism for antibody-mediated clearance of infections and tumor cells. Upon binding to target cells, the antibody’s constant (Fc) domain recruits complement component C1 to initiate a proteolytic cascade that generates lytic pores and stimulates phagocytosis. The C1 complex (C1qr 2 s 2 ) consists of the large recognition protein C1q and a heterotetramer of proteases C1r and C1s (C1r 2 s 2 ). While interactions between C1 and IgG-Fc’s are believed to be mediated by the globular heads of C1q, we here find that C1r 2 s 2 proteases affect the capacity of C1q to form an avid complex with surface-bound IgG molecules (on various DNP-coated surfaces and pathogenic Staphylococcus aureus ). The extent to which C1r 2 s 2 contribute to C1q-IgG stability strongly differs between human IgG subclasses. Using antibody engineering of monoclonal IgG we reveal that hexamer-enhancing mutations improve C1q-IgG stability, both in absence and presence of C1r 2 s 2 . In addition, hexamer-enhanced IgGs targeting S. aureus mediate improved complement-dependent phagocytosis by human neutrophils. Altogether, these molecular insights into complement binding to surface-bound IgGs could be important for optimal design of antibody therapies.
Local Non-Affine Deformations and Fiber Kinematics of Elastomeric Electrospun Scaffolds (2007)

For most tissue engineering applications that seek to generate tissue de novo, the scaffold is the first step in a series of important developmental considerations. Whether synthetic or natural, scaffolds developed for immediate in vivo use must have mechanical properties comparable to the native tissue for at least the minimum time necessary for the accompanying seeded cells, and eventual cells that migrate in, to lay down an equivalent supporting matrix. Scaffolds developed for the purpose of growing a tissue in vitro, with eventual in vivo use, need not necessarily meet these mechanical requirements. However, to better develop new tissues in bioreactors or in vivo, it is pertinent to understand how the fiber network changes under some regimen of mechanical load, in essence to understand what the cell witnesses within the scaffold. Extending our previous work, which focused on measuring and modeling the mechanical response of electrospun poly ester urethane urea (es-PEUU) scaffolds [1], we investigated the intricate and detailed es-PEUU fiber networks that are created during scaffold synthesis and how these networks change under various levels of strain. Specifically, we focused on several scaffold responses to strain: 1) Characteristics of fiber tortuosity, which when increased can yield delayed onset of scaffold stiffness as well as other varying mechanical responses. 2) Fiber splay, which determines the orientation of the all fibers within the scaffold. 3) Local vs global strain analysis to determine whether the scaffolds follow affine or non-affine deformations. 4) Fiber strain, to investigate how increasing levels of scaffold strain are transmitted to local fibers. 5) Changes in fiber tortuosity and overall fiber directions under strain.
Effects of Pylon-Aided Fuel Injection on Mixing in a Supersonic Flowfield (2010)

Previous analyses have shown that mixing can be enhanced using thin pylons that have only a negligible impact on pressure losses. In this study, helium and argon have been transversely injected into a Mach 1.6 airflow simulating a light and a heavy fuel injection behind a thin triangular pylon placed upstream, in the isolator. Penetration and mixing in the test section were observed at three cross-sections including the recirculation region and beyond with planar laser-induced fluorescence (PLIF). Results were compared to the no-pylon cases. The presence of the pylon resulted in improving both penetration and spreading of the jet and, at the same time, in lowering the concentration gradients in the recirculation region , an indication of improved flameholding ability.
Iodomethylzinc Iodide (2001)

(1; ICH2ZnI) [4109-94-8] CH2I2Zn (MW 333.22) (2; BrCH2ZnBr) [4109-95-9] CH2Br2Zn (MW 239.22) (3; (ICH2)2Zn) [14399-53-2] C2H4I2Zn (MW 347.25) (4; (ICH2)2Zn·DME) [131457-21-1] C6H14I2O2Zn (MW 437.39) (5; (BrCH2)2Zn) [92601-82-6] C2H4Br2Zn (MW 253.25) (6; (ClCH2)2Zn·DME) [131457-22-2] C6H14Cl2O2Zn (MW 254.49) (methylene transfer reagent: cyclopropanates alkenes,1 a1/d1 multicoupling reagent,2 transmetalation with various metal halides affords other iodomethylmetal compounds3) Alternate Name: Simmons–Smith reagent. Physical Data: an X-ray crystal structure of (ICH2)2Zn complexed to a glycol bis-ether is known;4 DME complexes of (ICH2)2Zn and (ClCH2)2Zn and an acetone complex of (ICH2)2Zn/ZnI2 have been characterized by NMR spectroscopy;4 1H NMR spectra attributed to THF complexes of BrCH2ZnBr and (BrCH2)2Zn have been reported.5 Solubility: ICH2ZnI generated from either CH2I2/Zn–Cu couple or EtZnI/CH2I2 is generally prepared in ethereal solvents (Et2O, DME). The Et2Zn/CH2I2 method of reagent generation can utilize noncoordinating solvents (CH2Cl2, ClCH2CH2Cl, toluene, etc.). Preparative Methods: the two most widely used methods of preparing halomethylzinc reagents are the Simmons–Smith and Furukawa procedures, utilizing Diiodomethane/Zinc/Copper Couple and CH2I2/Diethylzinc (or Chloroiodomethane/Et2Zn),6 respectively. The reagent is often prepared in the presence of the substrate (usually an alkene). Various methods of reagent preparation are discussed below. The precursors are widely available.
Supplementary Figure 3 from Dysregulation of EGFR Pathway in EphA2 Cell Subpopulation Significantly Associates with Poor Prognosis in Colorectal Cancer (2023)

&lt;p&gt;Supplementary Figure 3 - Clinical characteristics of EphA2high and EphA2low patients in cohort 1 to 6&lt;/p&gt;
High-power, high-brightness, high-reliability laser diodes emitting at 800-1000 nm (2007)

In this paper we report the development of high power high brightness semiconductor laser chips using a combination of quantum well intermixing (QWI) and novel laser designs including laterally unconfined non-absorbing mirrors (LUNAM). We demonstrate both multi-mode and single-mode lasers with increased power and brightness and reliability performance for the wavelengths of 980 nm, 940 nm, 830 nm and 808 nm.
Implanted Antennas and RF Transmission in Through-Body Communications (2016)

This chapter focuses on radio frequency (RF) transmission characterization as well as the antenna designs for wireless capsule endoscopy and neural motor prosthetic devices. It reviews the key issues of RF or microwave signal propagation through body/head and implanted/external antennas of implanted medical devices. The key performances of the implanted/external antennas such as the impedance matching and antenna efficiency are affected by the lossy, inhomogeneous, and dispersive surrounding tissues. The chapter shows that the co-design of antenna with its surrounding tissues and biocompatible casing is needed in order to achieve optimum efficiency. It shows that to reduce the specific absorption rate (SAR) and enhance the transmission with the external receiver, an antenna with directional radiation is preferred. The system consists of three 32-channel implantable probe units for neural signal acquisition, a wearable head unit for neural signal acquisition, wireless telemetry, and wireless power transfer as well as an external base station.
Low-dose endotoxin elicits variability in the inflammatory response in healthy volunteers (2005)

Endotoxin has been implicated as a cause of sepsis, inflammation and organ dysfunction after surgery. Patients differ in their response to endotoxin, and this may account for differences in outcome. The traditional human model of endotoxin challenge (2-4 ng/kg) is not associated with significant inter-individual variability in systemic inflammation and may not be suitable for studying variability in the inflammatory response. We examined whether low-dose regimens of endotoxin cause significant variability in inflammation. Volunteers (n = 30) were randomised in a double-blinded ('double-dummy') study to one of 6 dosing regimens: saline (placebo) or Escherichia coli O:113 endotoxin as a 4 ng/kg bolus (positive control), 0.25 ng/kg (bolus), 0.25 ng/kg (30 min infusion), 0.75 ng/kg (bolus) or 0.75 ng/kg (30 min infusion). Temperature, white cell count, platelet count, C-reactive protein and cytokine changes from baseline were measured. In contrast to subjects receiving placebo, those randomised to 4 ng/kg endotoxin exhibited significant systemic inflammation during the 10-h observation period. The four low-dose regimens elicited variability in most markers of inflammation. We conclude that low-dose endotoxin elicits inter-individual variability in inflammation and could be used to test factors that may affect the human response to endotoxin.
Expression of hypoxia-inducible factors in human renal cancer: relationship to angiogenesis and to the von Hippel-Lindau gene mutation. (2002)

The von Hippel-Lindau tumor suppressor protein acts as the substrate recognition component of a ubiquitin E3 ligase that targets hypoxia-inducible factor (HIF)-alpha subunits for proteolysis. Stabilization of HIF-alpha subunits has been described in VHL-defective cell lines, leading to HIF activation and up-regulation of hypoxia-inducible mRNAs. Mutations of the von Hippel-Lindau tumor suppressor protein are found in most clear cell renal cell carcinomas (CC-RCCs) but not other renal tumors, raising a question about the importance of activation of the HIF pathway in CC-RCC development. To address this question, we have examined the expression of HIF-alpha subunits in 45 primary renal tumors and related this to tumor subtype, the presence of VHL mutations, and measures of angiogenesis. We show that HIF-alpha is up-regulated in the majority of CC-RCCs, and that the pattern of expression is biased toward the HIF-2alpha isoform. Expression of HIF-alpha proteins was associated significantly with up-regulation of VEGF mRNA and protein and increased microvessel density. Up-regulation of HIF-alpha in CC-RCC was found to involve increased mRNA as well as protein expression, suggesting that both VHL-dependent and VHL-independent mechanisms are involved. These results suggest that activation of the HIF pathway is functionally important in CC-RCC development and might provide a new therapeutic target.
Metabolic Changes in Mesenchymal Stem Cells in Osteogenic Medium Measured by Autofluorescence Spectroscopy (2006)

The purpose of this study was to measure metabolic changes in mesenchymal stem cells (MSCs) placed in osteogenic medium by autofluorescence spectroscopy. MSCs were plated in stem cell-supporting or osteogenic medium and imaged. Shift from the basic growth environment to the inductive osteogenic environment was confirmed by reverse transcription-polymerase chain reaction. Reduced pyridine nucleotides were detected by exciting near 366 nm and measuring fluorescence at 450 nm, and oxidized flavoproteins were detected by exciting at 460 nm and measuring fluorescence at 540 nm. The ratio of these fluorescence measurements, reduction-oxidation (redox) fluorometry, is a noninvasive measure of the cellular metabolic state. The detected pyridine nucleotide to flavoprotein ratio decreased upon transitioning from the stem cell to the differentiated state, as well as with increasing cell density and cell-cell contact. MSC metabolism increased upon placement in differentiating medium and with increasing cell density and contact. Redox fluorometry is a feasible, noninvasive technique for distinguishing MSCs from further differentiated cells.
Enhancing the Convergence Speed of a Multi-Modulus Blind Equalization Algorithm (2006)

In this paper, some methods are examined for accelerating the convergence time of a recently proposed blind equalization algorithm [Abrar et al. (2004)]. It is shown that, as in conventional equalizers, the adaptive self-or pre-orthogonalization methods can be exploited to enhance the convergence of a blind equalization algorithm. An improvement in convergence time is reported.
Oligomeric α-Synuclein Is Increased in Basal Tears of Parkinson’S Patients (2019)

<b>Aim:</b> Secretion of proteins into basal tears of Parkinson's disease (PD) patients may be altered by changes in nerve function. <b>Materials & methods:</b> Oligomeric α-Syn<sub>Oligo</sub> and total α-Syn<sub>Total</sub>, CCL-2, DJ-1, LF and MMP-9 were measured in basal tears from 93 PD patients and 82 age- and sex-equivalent healthy controls. <b>Results:</b> α-Syn<sub>Total</sub> was decreased (p = 0.0043), whereas α-Syn<sub>Oligo</sub> (p < 0.0001) and the ratio of α-Syn<sub>Oligo</sub>/α-Syn<sub>Total</sub> (p < 0.0001) were increased in basal tears from PD patients compared with healthy controls. Area under receiver-operating curves of α-Syn<sub>Oligo</sub> and α-Syn<sub>Oligo</sub>/α-Syn<sub>Total</sub> contents were 0.70 (95% confidence limits: 0.621-0.774) and 0.72 (95% confidence limits: 0.642-0.792). <b>Conclusion:</b> PD patient basal tears may contain biomarkers that can be assayed noninvasively and inexpensively.
Synthetic Studies on Ceratospongamides, Cyclic Heptapeptides Containing Thiazole and Oxazoline Units: Total Synthesis of cis,cis-Ceratospongamide (2002)

Abstract A total synthesis of cis,cis-ceratospongamide 1a, a cycloheptapeptide isolated from the Indonesian red alga Ceratodictyon spongiosum and the symbiotic sponge Sigmadocia symbiotica, was accomplished. The heptapeptide chain 8 was produced by a stepwise connection of the following segments: (L-Phe-L-Pro)-thiazole residue, L-Phe-L-Pro-OMe, and L-Ile-L-aThr-OMe. Macrolactamization of 8, followed by cyclization to an oxazoline ring, provided cis,cis-ceratospongamide 1a along with its diastereomer 1c, which was different from the reported trans,trans-ceratospongamide 1b. The structural determination of 1c and its conversion to 1a were successfully achieved.
Function of Perlecan Domain I in Prostate Cancer (2005)

Abstract : Perlecan (Pln), the major heparan sulfate proteoglycan (HSPG) in the bone marrow stromal ECM functions as a permissive ECM molecule, or co-receptor, that delivers HBGF's to high affinity receptors. Heparan sulfate chains on Pln are located in a unique N-terminal domain I (PlnDI) which functions as the co-receptor for HBGFs. Our purpose is to study the functions of Pln in prostate cancer cell survival, proliferation and apoptosis. We hypothesize that Pln, acting through PlnDI, delivers HBGFs to the cancer cell surface, promotes proliferation, cell survival and protects them from apoptosis. The Pln knockdown studies showed that Pln knockdown clones grow poorly compared to the parental or control transfected C4-2B cells. PlnDI failed to rescue the poorly proliferation. Western blot of Akt/MAPK pathway of these knockdown clones showed that Pln is not a major regulator in these pathways. We used three different prostate cancer cell lines: LnCaP, its derivative, C4-2B, and PC3 as model systems to study the protection function of PlnDI. We harvested conditioned medium from bone stromal cell lines, HS27a and HS5, which produce abundant Pln. The proteoglycan rich fraction containing Pln was obtained using anion exchange bead chromatography, then tested as a survival factor for the three different prostate cancer cell lines. DNA fragmentation experiments showed that bone stromal derived Pln from conditioned medium protected all three lines of prostate cancer cells from camptothecin induced apoptosis. We also supplied purified, fully glycosylated recombinant PlnDI protein to prostate cancer cells, which also protected cells from apoptosis. The Pln knockdown cell are also more susceptible in response to the apoptosis inducers anti-Fas and camptothecin, and that exogenous PlnDI can rescue survival. Taken together, these studies demonstrate that Pln present in the bone marrow compartment can promote cell proliferation.
The Recession of 2008 and Its Impact on Light-Duty Vehicle Emissions in Three Western United States Cities (2014)

The global economic recession of 2008-2010 severely depressed light-duty vehicle sales in the United States. On-road fleets observed with a remote vehicle exhaust sensor in 2013 at three historical sampling locations in Denver, Los Angeles, and Tulsa showed large reductions in the fleet fractions of 2009 model year vehicles of 40%, 38%, and 35%, respectively, when compared to prerecession 2007 levels with the light-duty truck category suffering the largest percentage declines. The fleet fraction for these ∼ 5 year old vehicles is normally reserved for vehicles more than twice their age. This resulted in a significant increase in the on-road freeway fleet age, which had been relatively stable. The fleet average age increased by two years in Denver and Los Angeles but only by one year in Tulsa, likely due to its faster economic recovery. Using fleet fractions from previous data sets, we estimated age-adjusted mean emissions increases for the 2013 fleet to be 17-29% higher for carbon monoxide, 9-14% higher for hydrocarbons, 27-30% higher for nitric oxide, and 7-16% higher for ammonia emissions than if historical fleet turnover rates had prevailed.
T+31C Polymorphism of Angiotensinogen Gene and Essential Hypertension (2001)

A common variant at codon 235 of the angiotensinogen gene with methionine to threonine amino acid substitution (AGT M235T) has been reported as a genetic risk for essential hypertension. However, the frequency of AGT T235 was heterogeneous among races, and a positive association between AGT M235T and hypertension was not settled. To examine the association in a general population of Japanese (n=4013), we introduced the TaqMan polymerase chain reaction method and examined the relation between hypertension and T+31C polymorphism, which was in absolute linkage disequilibrium with AGT M235T. The C+31 allele of AGT was significantly associated with the positive family history of hypertension (FH) but not with the presence of hypertension or blood pressure. The subjects with CC tended to have hypertensive relatives, especially a hypertensive father or siblings, and its statistical significance was stronger in men. Adjustment of confounding factor did not alter the results of simple association study, suggesting that this positive association with FH is independent and significant. Our findings revealed that the TaqMan polymerase chain reaction method is a powerful tool for genetic association study with a large number of subjects and that AGT T+31C is significantly associated with paternal FH.
A Microservice Migration Approach to Controlling Latency in 5G/6G Networks (2023)

The microservice paradigm is widely adopted in the design of Virtualized Network Functions (VNFs). Still, 5G/6G networks require to carefully orchestrate the allocation and re-arrangement of (micro)services to avoid a largely segmented solution space while services arrive and leave the network. To support latency-effective service provisioning, we introduce a novel placement and migration strategy that chooses the microservice(s) to migrate and selects the optimal destination (data center) while considering the impact of the migration on other microservices. For this purpose, we devise fast and effective heuristics and we implement a prototype that maps the service in the deployment field. Extensive simulations show our proposed approach significantly reduces the service latency.
Modified CD4+ T-cell response in recipients of old cardiac allografts (2011)

With an increasing demand, organs from elderly donors are more frequently utilized for transplantation. Herein, we analyzed the impact of donor age on CD4+ T-cell responses with regard to regulatory and effector mechanisms. Young (3 months) BM12 recipients were engrafted with young or old (18 months) B6 cardiac allografts. Systemic CD4+ T-cell responses and intragraft changes were monitored and compared to age-matched syngenic transplant controls. While elderly, nonmanipulated hearts contained significantly elevated frequencies of donor-derived leukocytes prior to transplantation, allograft survival was age-independent. T-cell activation, however, was delayed and associated with a compromised immune response in mixed lymphocyte cultures (MLR; P = 0.0002) early after transplantation (day 14). During the time course after transplantation, recipients of old grafts demonstrated an augmented immune response as shown by significantly higher frequencies of activated CD4+ T-cells and a stronger in vitro alloreactivity (MLR; ELISPOT; P < 0.01). In parallel, frequencies of regulatory T-cells had increased systemically and overall fewer CD4+ T-cells were detected intragraft. Interestingly, changes in the CD4+ T-cell response were not reflected by graft morphology. Of note, transplantation of young and old syngenic hearts did not show age-related differences of the CD4+ T-cells response suggesting that old grafts can recover from a period of short cold ischemia time. Our data suggest that donor age is associated with an augmented CD4+ T-cells response which did not affect graft survival in our model. These findings contribute to a better understanding of the immune response following the engraftment of older donor organs.
The structural polypeptides of aphthovirus are phosphoproteins. (1980)

Analysis of aphthovirus A12, strain 119ab, grown in the presence of inorganic 32P revealed that two of the major viral polypeptides, VP4 and trypsin-sensitive protein VP3, were highly phosphorylated. The other major polypeptides, VP1 and VP2, were also phosphorylated but to a much lesser extent. Polypeptides VP0 and P56, of which there are approximately one of two copies per aphthovirion, were also labeled with 32P. Phosphoserine and phosphothreonine appeared to be the amino acids labeled with 32P.
Immunothérapie fondée sur les cellules natural killer : implication des cellules dendritiques (2003)

Les cellules dendritiques (CD), decrites initialement comme des cellules presentatrices d‘antigenes pour les lymphocytes T, sont egalement capables d‘interagir et d‘activer les cellules lymphocytaires a cytotoxicite naturelle (NK). Ce dialogue entre CD et NK est maintenant considere comme une etape essentielle de l‘induction des reponses immunitaires innees et adaptatives. De plus, l‘activation des cellules NK par les CD matures est optimale car elle se caracterise non seulement par l‘augmentation de leurs proprietes cytotoxiques et de la secretion d‘interferon γ, mais aussi par l‘amelioration de leur survie et leur proliferation. Par ailleurs, les recents progres realises dans la comprehension de leur biologie, incitent a reconsiderer la place des lymphocytes NK dans l‘immunotherapie antitumorale. Nous exposerons dans un premier temps comment les premieres experiences d‘immunotherapie fondee sur la cytotoxicite naturelle et les donnees biologiques recentes permettent d‘impliquer les cellules NK dans des effets antitumoraux. Puis, nous rappellerons les principes du dialogue entre les CD et les NK et les utilisations possibles de ce concept dans des protocoles d‘immunotherapie.
Agents and Complex Systems. (2002)

Traditional objects can be thought of as passive, because they wait for a message before performing an operation. Then, once invoked, they execute their method and go back to "sleep" until the next message. A trend in many systems now is to design objects that react to events in their environment, as well as be proactive. In UML 2.0, these are known as active objects; in the agent community, they are known as agents. Whether they are called active objects or agents, this new direction is going to radically change how we design systems. The biggest challenge, however, that we face is the degree of complexity that we are about to unleash. Imagine setting free a million proactive entities to run a supply chain. We are no longer choreographing their every movement as we would with traditional agents; instead, they decide when and how to execute their methods. This is both liberating -and scary. We can create complex systems, but we will not always know how to control them. In complex systems: designing the parts is not the same as designing the whole.