gebhart/patrepeval huggingface dataset:
Trps1 transcription factor represses phosphate-induced expression of SerpinB2 in osteogenic cells (2020)

Serine protease inhibitor SerpinB2 is one of the most upregulated proteins following cellular stress. This multifunctional serpin has been attributed a number of pleiotropic activities, including roles in cell survival, proliferation, differentiation, immunity and extracellular matrix (ECM) remodeling. Studies of cancer cells demonstrated that expression of SerpinB2 is directly repressed by the Trps1 transcription factor, which is a regulator of skeletal and dental tissues mineralization. In our previous studies, we identified SerpinB2 as one of the novel genes highly upregulated by phosphate (P<sub>i</sub>) at the initiation of the mineralization process, however SerpinB2 has never been implicated in formation nor homeostasis of mineralized tissues. The aim of this study was to establish, if SerpinB2 is involved in function of cells producing mineralized ECM and to determine the interplay between P<sub>i</sub> signaling and Trps1 in the regulation of SerpinB2 expression specifically in cells producing mineralized ECM. Analyses of the SerpinB2 expression pattern in mouse skeletal and dental tissues detected high SerpinB2 protein levels specifically in cells producing mineralized ECM. qRT-PCR and Western blot analyses demonstrated that SerpinB2 expression is activated by elevated P<sub>i</sub> specifically in osteogenic cells. However, the P<sub>i</sub>-induced SerpinB2 expression was diminished by overexpression of Trps1. Decreased SerpinB2 levels were also detected in osteoblasts and odontoblasts of 2.3Col1a1-Trps1 transgenic mice. Chromatin immunoprecipitation assay (ChIP) revealed that the occupancy of Trps1 on regulatory elements in the SerpinB2 gene changes in response to P<sub>i</sub>. In vitro functional assessment of the consequences of SerpinB2 deficiency in cells producing mineralized ECM detected impaired mineralization in SerpinB2-deficient cells in comparison with controls. In conclusion, high and specific expression of SerpinB2 in cells producing mineralized ECM, the impaired mineralization of SerpinB2-deficient cells and regulation of SerpinB2 expression by two molecules regulating formation of mineralized tissues suggest involvement of SerpinB2 in physiological mineralization.
Figure S2 from Cathepsin B Is Dispensable for Cellular Processing of Cathepsin B-Cleavable Antibody–Drug Conjugates (2023)

&lt;p&gt;Supplementary Figure 2: Dose titration curves for BT-474M1 parental and CTSB deleted cells (A) and BJAB parental and cathepsin B knockdown cells exposed to mAb-VC(S)-MMAE.&lt;/p&gt;
Robust Type-specific Hemisynapses Induced by Artificial Dendrites (2016)

Type-specificity of synapses, excitatory and inhibitory, regulates information process in neural networks via chemical neurotransmitters. To lay a foundation of synapse-based neural interfaces, artificial dendrites are generated by covering abiotic substrata with ectodomains of type-specific synaptogenic proteins that are C-terminally tagged with biotinylated fluorescent proteins. The excitatory artificial synapses displaying engineered ectodomains of postsynaptic neuroligin-1 (NL1) induce the formation of excitatory presynapses with mixed culture of neurons in various developmental stages, while the inhibitory artificial dendrites displaying engineered NL2 and Slitrk3 induce inhibitory presynapses only with mature neurons. By contrast, if the artificial dendrites are applied to the axonal components of micropatterned neurons, correctly-matched synaptic specificity emerges regardless of the neuronal developmental stages. The hemisynapses retain their initially established type-specificity during neuronal development and maintain their synaptic strength provided live neurons, implying the possibility of durable synapse-based biointerfaces.
Three hours of intermittent hypoxia increases circulating glucose levels in healthy adults (2017)

An independent association exists between sleep apnea and diabetes. Animal models suggest exposure to intermittent hypoxia, a consequence of sleep apnea, results in altered glucose metabolism and fasting hyperglycemia. However, it is unknown if acute exposure to intermittent hypoxia increases glucose concentrations in nondiabetic humans. We hypothesized plasma glucose would be increased from baseline following 3 h of intermittent hypoxia in healthy humans independent of any effect on insulin sensitivity. Eight (7M/1F, 21-34 years) healthy subjects completed two study visits randomized to 3 h of intermittent hypoxia or continuous normoxia, followed by an oral glucose tolerance test. Intermittent hypoxia consisted of 25 hypoxic events per hour where oxygen saturation (SpO<sub>2</sub>) was significantly reduced (Normoxia: 97 ± 1%, Hypoxia: 90 ± 2%, P < 0.01). Venous plasma glucose concentrations were measured on both visits before and after the 3 h protocol. No changes in plasma glucose were observed from baseline after 3 h of continuous normoxia (5.1 ± 0.2 vs. 5.1 ± 0.1 mmol/L, P > 0.05). In contrast, circulating glucose concentrations were increased after 3 h of intermittent hypoxia when compared to baseline (5.0 ± 0.2 vs. 5.3 ± 0.2 mmol/L, P = 0.01). There were no detectable changes in insulin sensitivity following intermittent hypoxia when compared to continuous normoxia, as assessed by the oral glucose tolerance test (P > 0.05). Circulating glucose is increased after 3 h of intermittent hypoxia in healthy humans, independent of any lasting changes in insulin sensitivity. These novel findings could explain, in part, the high prevalence of diabetes in patients with sleep apnea and warrant future studies to identify underlying mechanisms.
Subtherapeutic Photodynamic Treatment Facilitates Tumor Nanomedicine Delivery and Overcomes Desmoplasia (2020)

Limited tumor nanoparticle accumulation remains one of the main challenges in cancer nanomedicine. Here, we demonstrate that subtherapeutic photodynamic priming (PDP) enhances the accumulation of nanoparticles in subcutaneous murine prostate tumors ∼3-5-times without inducing cell death, vascular destruction, or tumor growth delay. We also found that PDP resulted in an ∼2-times decrease in tumor collagen content as well as a significant reduction of extracellular matrix density in the subendothelial zone. Enhanced nanoparticle accumulation combined with the reduced extravascular barriers improved therapeutic efficacy in the absence of off-target toxicity, wherein 5 mg/kg of Doxil with PDP was equally effective in delaying tumor growth as 15 mg/kg of Doxil. Overall, this study demonstrates the potential of PDP to enhance tumor nanomedicine accumulation and alleviate tumor desmoplasia without causing cell death or vascular destruction, highlighting the utility of PDP as a minimally invasive priming strategy that can improve therapeutic outcomes in desmoplastic tumors.
Multidimensional signal analysis and measurements for cognitive radio systems (2008)

This paper suggests a roadmap for signal intelligence and multidimensional signal analysis in Cognitive Radio and Software-Defined radio (CR/SDR). The paper reviews some methods of linear and quadratic time frequency representation (TFR) as an initiative for multidimensional signal analysis. The paper also addresses recent developments in the use of TFR for CR/SDR applications.
Quantitative In Situ Mass Spectrometry Analysis of Mannitol Decomposition Products under Hydrothermal Conditions (2017)

In situ mass spectrometry analysis was conducted for the hydrothermal decomposition of mannitol at different temperatures and residence times in a batch reactor. The temperature was varied in the range of 140–220 °C, and the residence time was varied between 5 and 20 min. The products of mannitol decomposition included furfural, 5-hydroxymethylfurfural, phenol, formic acid, and levulinic acid. At high temperatures, the mass spectrum showed peaks at m/z 46 and 116 that corresponded to formic acid and levulinic acid, respectively. Conventional high-performance liquid chromatography could not detect these acids. Quantification of these products and the rate constants for the mannitol decomposition network were also obtained. The reaction rate coefficients were determined by fitting the experimental results.
Characteristics of InGaN light‐emitting diodes on GaN substrates with low threading dislocation densities (2007)

Abstract InGaN light‐emitting diodes (LEDs) on GaN substrates with low threading dislocation densities (TDDs) were fabricated, and the characteristics of the LEDs were compared with those on sapphire substrates. LEDs with 3 nm‐thick‐quantum‐wells (QWs) grown on GaN as well as on sapphire substrates showed a decrease of the external quantum efficiency (EQE) with increasing forward current, indicating that carrier localization is in play in both cases. The decrease in the EQE was, however, suppressed in LEDs grown on GaN substrates by adopting thicker QWs. The LED with 5 nm‐thick‐QWs on GaN substrate mounted p‐side down and molded with epoxy showed EQE as high as 26% at 125 A/cm 2 . Cathodo luminescence (CL) observations revealed the formation of dark areas related to TDDs, and the dark areas deteriorated the EQE of the LED on the sapphire substrate. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Transparente Filme aus CO2‐basierten polyungesättigten Polyethercarbonaten: eine neue Synthesestrategie und schnelle Vernetzung (2016)

Abstract Transparente Filme wurden durch Vernetzung polyungesättigter Polyethercarbonate hergestellt, die durch Mehrkomponentenpolymerisation von CO 2 , Propylenoxid, Maleinsäureanhydrid und Allylglycidylether erhalten wurden. Polyethercarbonate mit ABXBA‐Multiblockstruktur wurden über sequenzielle Zugabe von Mischungen aus Propylenoxid/Maleinsäureanhydrid und Propylenoxid/Allylglycidylether während der Polymerisation erzielt. Die simultane Zugabe beider Monomermischungen ergab Polyethercarbonate mit ABA‐Triblockstruktur. Beide Typen polyungesättigter Polyethercarbonate sind durch unterschiedliche funktionelle Gruppen gekennzeichnet. Terminale Hydroxygruppen, Maleinatestereinheiten entlang des Polymerrückgrats und laterale Allylgruppen ermöglichen eine vielfältige polymeranaloge Chemie. Die Kombination aus Doppelbindungen, die mit Elektronenakzeptoren und ‐donoren substituiert sind, fördert die wirkungsvolle UV‐ oder redoxinitiierte radikalische Vernetzung. Die resultierenden Materialien sind transparent und interessant für Lackanwendungen.
Solar Review: Characterizing Thin Film Photovoltaics (2010)

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Dynamically Optimized Production Planning Using Cross-Layer SOA (2008)

Responding to the dynamic requirements of the changing market and optimising costs are two challenges faced by corporate manufacturing plants globally. In order to be agile, modern manufacturing plants employ optimized supply chain mechanisms to reduce the response time of the market needs. However bringing changes to the shop floor after a production is planned is costly. In this paper we demonstrate how Service Oriented Architecture (SOA) driven approaches offer the flexibility to adapt manufacturing plants based on a dynamic production plan in close cooperation with a backend system. The methods discussed were deployed on a prototype test rig and integrated with SAP ERP. The results introduce dynamic behaviour of the production plan by adapting to the changing nature of the shop floor, and at the same time, providing the real time status of the machines to the enterprise services which optimize further the production plan dynamically.
Characterization of the Osteoclast Ruffled Border Chloride Channel and Its Role in Bone Resorption (1997)

Bone resorption by osteoclasts requires massive transcellular acid transport, which is accomplished by the parallel action of a V-type proton pump and a chloride channel in the osteoclast ruffled border. We have studied the molecular basis for the appearance of acid transport as avian bone marrow mononuclear cells acquire a bone resorptive phenotype in vitro. We demonstrate a critical role for regulated expression of a ruffled border chloride channel as the cells become competent to resorb bone. Molecular characterization of the chloride channel shows that it is related to the renal microsomal chloride channel, p64. In planar bilayers, the ruffled border channel is a stilbene sulfonate-inhibitable, outwardly rectifying chloride channel. A mechanism by which outward rectification of the single channel chloride current could allow efficient regulation of acidification by the channel is discussed.
Purely endoscopic appendectomy (2022)

Video 1Submucosal nodule in the cecum. After submucosal injection, a circumferential incision of the mucosa surrounding the lesion is performed with DualKnife (Olympus America, Center Valley, Pa, USA). The fore-balloon of the double-balloon endoluminal interventional platform (DBEIP) is deployed and the edges of the circumferential incision are attached with 2 endoscopic clips to the long suture-loop mounted on the fore-balloon of the DBEIP. The fore-balloon is retracted in anal direction, pulling the lesion into the cecum. Careful endoscopic submucosal dissection is performed with DualKnife and HookKnife (Olympus America). Dissection is markedly facilitated by traction and continued until the entire appendix is pulled into the cecum. The tip of the appendix is separated from surrounding tissues, resulting in a full-thickness cecal wall defect. The suture-loop holding the resected appendix is cut with LoopCutter (Olympus America). The resected appendix is removed through DBEIP and the Overstitch endoscopic suturing device (Apollo Endosurgery, Austin, Tex, USA) is advanced into the cecum. The full-thickness defect in the cecal wall is completely closed with 2 continuous sutures. The final view demonstrates the entire resected appendix.
The Digital Battlefield: A Behind-the-Scenes Look from a Systems Perspective (2014)

The last decade and a half has seen major advances in computing, communication, and display technologies. The U.S. Army has been proactive in harnessing and combining these technologies under a common rubric called the “digital battlefield.” The digital battlefield, which has become the primary mechanism for real-time situation awareness, has become a force multiplier that has transformed the Army to meet and overcome the challenges of the 21st century. Today, all elements of a U.S. Army combat team – tanks, fighting vehicles, helicopters, artillery, and convoy/support vehicles – are interconnected within the digital battlefield. The result has been a dramatic improvement in combat power, accompanied by a marked decrease in U.S. force casualties. This paper takes a behind the scenes look at the science and technology that led to this signature transformation of the U.S. Army combat forces. The paper discusses critical success factors and lessons learned. The paper concludes with a brief discussion of civilian sector benefits of FBCB2 technology and subsequent variants created by DoD.
Corpus of Early English Correspondence Extension Sampler part 1 (CEECES 1) (2021)

The Corpus of Early English Correspondence Extension Sampler part 1 (CEECES 1) is the first public release of the 18th-century part of the Corpora of Early English Correspondence (CEEC-400). The full CEECES will be released in 3 parts over the course of 2021. See the accompanying manual for more. See https://varieng.helsinki.fi/CoRD/corpora/CEEC/ for more on the CEEC-400. Citation: CEECES 1 = <em>Corpus of Early English Correspondence Extension Sampler</em> part 1. Compiled by Terttu Nevalainen, Helena Raumolin-Brunberg, Samuli Kaislaniemi, Mikko Laitinen, Minna Nevala, Arja Nurmi, Minna Palander-Collin, Tanja Säily and Anni Sairio at the Department of Languages, University of Helsinki. XML conversion and encoding by Lassi Saario. <strong>ETA</strong> Some of the hyperlinks in the manual don't work: use the link above instead.
Link adaptation in massive MIMO: Throughput-fairness trade-off (2017)

The fifth-generation cellular networks aim to provide uniform and very high throughput. Massive MIMO is widely seen as the most promising 5G radio technology as it promises very high throughput to many users while also guaranteeing fairness, thanks to the channel hardening effect limiting the small-scale fading. A key question though is to what extent this achieved throughput is homogeneous among users, and what degrees of freedom exist to improve fairness. A promising option to provide uniform throughput using Massive MIMO would be a proper power control, based on long-term channel statistics. This paper studies the trade-off between throughput and fairness and it compares different power-allocation schemes. Assuming users affected by log-normal large-scale fading, simulations show that the trade-off is critical. as user-dependent differences caused by large-scale fading are causing unfairness in the system and fairness is achieved at the price of throughput reduction. In a limited large-scale fading scenario, throughput or fairness optimization is possible without incurring huge losses on the other dimension. For heavy large-scale fading scenarios the cost of enforcing fairness is very large: more than 50% of throughput reduction is observed. Despite the critical trade-off, Massive MIMO is shown to be less sensitive to throughput losses when enforcing fairness, compared with traditional communication systems.
Machine Learning Model for Monitoring Rheological Properties of Synthetic Oil-Based Mud (2022)

The drilling fluid rheology is a critical parameter during the oil and gas drilling operation to achieve optimum drilling performance without nonproductive time or extra remedial operation cost. The close monitoring for rheological properties will help the drilling fluid crew to take quick actions to maintain the designed profiles for the drilling fluid rheology, especially when it comes to the flat rheology drilling fluid system, which is a new generation for harsh and specific drilling conditions that require flat profiles for the mud rheology regarding the temperature condition changes. The current study introduces a machine learning application toward predicting the rheology of synthetic oil-based mud (flat rheology type) for the full automation system of monitoring the mud rheological properties. Four models are developed, for the first time, to determine the rheological characteristics of flat rheology synthetic oil-based system using artificial neural networks. The developed models are capable of predicting the plastic and apparent viscosities, yield point, and flow behavior index from only the mud density and Marsh funnel as model inputs. The proposed models were trained and optimized from a real field dataset (369 measurements) with further testing the models using an unseen dataset of 153 data points. The predicted rheological properties achieved a high degree of accuracy versus the actual measurements and showed a coefficient of correlation range from 0.91 to 0.97 with an average absolute percentage error of less than 9.66% during the training and testing phases. Besides, machine learning-based correlations are proposed for estimating the rheological properties on the rig site without running the machine learning system for easy field applications.
Study of density in pulsed-laser deposited amorphous carbon films using x-ray reflectivity (1994)

We report the accurate determination of the absolute density of the pulsed-laser deposited amorphous carbon ultrathin films as well as the film density evolution with the substrate temperatures Ts (22–300 °C) using high-resolution x-ray reflectivity. The density values ρ for the films deposited with laser power density of 8×108 W/cm2 varied from 3.10 to 2.40 g/cm3 as the substrate temperature increased from 22 to 300 °C. This result, together with the optical band-gap values obtained by transmittance measurements, clearly indicates a diamond-like to graphite-like microstructure change near Ts=200 °C.
Controlled Neurotrophic Factor Delivery To Promote Functional Peripheral Nerve Regeneration (2010)

Wood, Matthew D. PhD; MacEwan, Matthew R. MSc; French, Alexander R. BS; Moore, Amy M. MD; Hunter, Daniel A. RA; Mackinnon, Susan E. MD; Moran, Daniel W. PhD; Sakiyama-Elbert, Shelly E. PhD; Borschel, Gregory H. MD
Isolation and Physiology of Bacteria from Contaminated Subsurface Sediments (2010)

The majority of environmental microorganisms cannot be grown by traditional techniques. Here we employed, and contrasted with conventional plating, an alternative approach based on cultivation of microorganisms inside diffusion chambers incubated within natural samples, followed by subculturing in petri dishes. Using this approach, we isolated microorganisms from subsurface sediments from the Field Research Center (FRC) in Oak Ridge, TN. The sediments were acidic and highly contaminated with uranium, heavy metals, nitrate, and organic pollutants. Phylogenetic analysis of 16S rRNA gene sequences revealed clear differences between diversity of isolates obtained by the diffusion chamber approach and those obtained by conventional plating. The latter approach led to isolation of members of the Alpha- and Gammaproteobacteria, Actinobacteria, and Verrucomicrobia. Isolates obtained via the diffusion chamber approach represented the Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Notably, one-third of the isolates obtained by the new method were closely related to species known from previous molecular surveys conducted in the FRC area. Since the initial growth of microorganisms inside diffusion chambers occurred in the presence of the environmental stress factors, we expected the isolates we obtained to be tolerant of these factors. We investigated the physiologies of selected isolates and discovered that the majority were indeed capable of growth under low pH and/or high concentrations of heavy metals and nitrate. This indicated that in contrast to conventional isolation, the diffusion chamber-based approach leads to isolation of species that are novel, exhibit tolerance to extant environmental conditions, and match some of the species previously discovered by molecular methods.
On optimizing CSMA for wide area ad-hoc networks (2011)

Recent deployments of data-rich smart phones has provided a fresh impetus for designing, deploying and understanding the performance of wide area ad-hoc networks. The most popular medium access mechanism for such ad hoc networks is CSMA/CA with RTS/CTS. In this paper, using tools from stochastic geometry, we study and optimize the throughput performance of such networks. We show that in ad-hoc networks enabled with SIR based scheduling, a simple modification to the transmit power level - setting it to be inversely proportional to the square root of the link gain - leads to large improvements in network throughput. This simple power-level selection is optimal over the class of all ”local” transmit power selection strategies when channels are stationary, and further is at most a factor of two away from optimality in the fading case. Using stochastic geometric techniques, we also provide analytical expressions for the medium access probability in different scenarios.