gebhart/patrepeval huggingface dataset:
A genome-wide RNA interference screen identifies putative chromatin regulators essential for E2F repression (2007)

Regulation of chromatin structure is critical in many fundamental cellular processes. Previous studies have suggested that the Rb tumor suppressor may recruit multiple chromatin regulatory proteins to repress E2F, a key regulator of cell proliferation and differentiation. Taking advantage of the evolutionary conservation of the E2F pathway, we have conducted a genome-wide RNAi screen in cultured Drosophila cells for genes required for repression of E2F activity. Among the genes identified are components of the putative Domino chromatin remodeling complex, as well as the Polycomb Group (PcG) protein-like fly tumor suppressor, L3mbt, and the related CG16975/dSfmbt. These factors are recruited to E2F-responsive promoters through physical association with E2F and are required for repression of endogenous E2F target genes. Surprisingly, their inhibitory activities on E2F appear to be independent of Rb. In Drosophila, domino mutation enhances cell proliferation induced by E2F overexpression and suppresses a loss-of-function cyclin E mutation. These findings suggest that potential chromatin regulation mediated by Domino and PcG-like factors plays an important role in controlling E2F activity and cell growth.
Reciprocal generation of Th1/Th17 and Treg cells by B1 and B2 B cells (2007)

Regulatory T (T(reg)) cells are indispensable for maintaining peripheral tolerance, whereas T helper (Th)1 and Th17 cells induce inflammation and tissue destruction. Using Foxp3-GFP knock-in mice, we report a novel regulatory role for B cell subsets in influencing the differentiation of T(reg) versus Th1/Th17 cells. Peritoneal B1 cells strongly promoted T cell proliferation and cytokine secretion when presenting nominal or allogeneic antigens, as compared to conventional follicular B (B2) cells. However, peritoneal B1 cells largely failed to convert naive Foxp3(-)CD4(+) T cells into Foxp3(+) T(reg) cells in the presence of TGF-beta and IL-2, in marked contrast to conventional B2 cells, which excelled in T(reg) conversion. Interestingly, under the same T(reg) conversion conditions, peritoneal B1 cells preferentially promoted Th1 and Th17 cell differentiation. Blockade of CD86 but not CD80 costimulation markedly enhanced T(reg) cell induction by B1 cells. Thus, B cell antigen presentation function is inversely correlated with de novo T(reg) cell induction for these B cell subsets. Our findings suggest that B1 and B2 cell subsets play distinct roles in immune regulation by promoting reciprocal differentiation of T cell lineages.
Telmisartan: An angiotensin receptor blocker regulates osteoclastogenesis via inhibition of the ERK triggering in osteoporotic male rats (2022)

Great attention was recently given to the importance of RAS in controlling inflammatory bone diseases, following the discovery of its local existence in skeletal tissues. Local RAS was found to be expressed on osteoblastic and osteoclastic cells and to exert its action via angiotensin II (AngII) receptors, including angiotensin II type 1 receptor (AT<sub>1</sub> R) and angiotensin II type 2 receptors. Telmisartan (TLM), an AT<sub>1</sub> R blocker (ARBs), was investigated in the present study for its therapeutic effect on bone health in osteoporotic rats. d-Galactose, a reducing sugar at a dose of 200 mg/kg/day/i.p., was used to induce osteoporosis in male rats. TLM, at a dose of 5 mg/kg/day, was orally introduced in the osteoporotic rats for four consecutive weeks. Tibia and femur bone densitometry was estimated, bone formation and bone resorption biomarkers serum levels were measured, mineral content in blood was also valued, and finally the extracellular regulated kinase (ERK) expression in bone was determined. TLM considerably improved the deleterious effect of d-galactose on bone mineral density. It blunted serum bone-specific alkaline phosphatase and osteocalcin while elevating serum osteoprotegrin (OPG). On the other hand, TLM turned off the pronounced elevation in serum receptor activator of nuclear factor-κβ ligand (RANKL), tartrate-resistant acid phosphatase, and cathepsin K. Furthermore, it significantly hindered the bone expression of ERK which hampered osteoclastogenesis. AT<sub>1</sub> R inhibition abolished the rise in serum calcium and phosphorus and normalized serum superoxide dismutase and catalase. These TLM protective effects in d-galactose-treated rats were confirmed by the histopathological examination. The results all together denote the potential therapeutic value of ARBs therapy in osteoporosis.
N-Hydroxypyrazolyl Glycine Derivatives as SelectiveN-Methyl-d-aspartic Acid Receptor Ligands (2008)

A series of analogues based on N-hydroxypyrazole as a bioisostere for the distal carboxylate group of aspartate have been designed, synthesized, and pharmacologically characterized. Affinity studies on the major glutamate receptor subgroups show that these 4-substituted N-hydroxypyrazol-5-yl glycine (NHP5G) derivatives are selectively recognized by N-methyl- d-aspartic acid (NMDA) receptors and that the ( R)-enantiomers are preferred. Moreover, several of the compounds are able to discriminate between individual subtypes among the NMDA receptors, providing new pharmacological tools. For example, 4-propyl NHP5G is an antagonist at the NR1/NR2A subtype but an agonist at the NR1/NR2D subtype. Molecular docking studies indicate that the substituent protrudes into a region that may be further exploited to improve subtype selectivity, thereby opening up a design strategy for ligands which can differentiate individual NMDA receptor subtypes.
Ocular Penetration of Cyclosporine A in the Rat Eye (1990)

The treatment of rats with cyclosporine A by the oral, intraperitoneal, or intravenous routes results in a high level of the drug within the liver and spleen in all cases. The blood level varies and is highest after intravenous injection. The eyes of these animals do not show any significant accumulation of the drug, either extraocularly or intraocularly except for the rats treated by intravenous injection, where radioactive cyclosporine A is detected within the chorioretinal complex. Even in these cases, however, no radioactivity is observed within the vitreous. After local application of 2% cyclosporine A eye drops in olive oil, a high concentration of the drug is found in the cornea and conjunctiva only. No intraocular penetration is observed in these cases. However, when cyclosporine A eye drops in absolute alcohol are used, high levels of the drug are also found in intraocular tissues. Thus, in the intact eye, the cornea and conjunctiva on the one hand and the blood retinal barrier on the other hand prevent the intraocular penetration of cyclosporine A.
Mononuclear Cells from Dedifferentiation of Mouse Myotubes Display Remarkable Regenerative Capability (2014)

Certain lower organisms achieve organ regeneration by reverting differentiated cells into tissue-specific progenitors that re-enter embryonic programs. During muscle regeneration in the urodele amphibian, postmitotic multinucleated skeletal myofibers transform into mononucleated proliferating cells upon injury, and a transcription factor-msx1 plays a role in their reprograming. Whether this powerful regeneration strategy can be leveraged in mammals remains unknown, as it has not been demonstrated that the dedifferentiated progenitor cells arising from muscle cells overexpressing Msx1 are lineage-specific and possess the same potent regenerative capability as their amphibian counterparts. Here, we show that ectopic expression of Msx1 reprograms postmitotic, multinucleated, primary mouse myotubes to become proliferating mononuclear cells. These dedifferentiated cells reactivate genes expressed by embryonic muscle progenitor cells and generate only muscle tissue in vivo both in an ectopic location and inside existing muscle. More importantly, distinct from adult muscle satellite cells, these cells appear both to fuse with existing fibers and to regenerate myofibers in a robust and time-dependent manner. Upon transplantation into a degenerating muscle, these dedifferentiated cells generated a large number of myofibers that increased over time and replenished almost half of the cross-sectional area of the muscle in only 12 weeks. Our study demonstrates that mammals can harness a muscle regeneration strategy used by lower organisms when the same molecular pathway is activated.
Kinetics of pressure induced structural changes in super- or near-critical CO2-microemulsions (2014)

CO2-microemulsions show strong pressure dependent properties. Using time-resolved SANS to investigate the kinetics of structural changes upon periodic pressure jumps of adjustable amplitude, we found that the compression-induced formation of cylinders occurs on a timescale of one second, whereas the expansion-induced disintegration into CO2 swollen spherical micelles is much faster.
Supplementary Data from Stress-Mediated Attenuation of Translation Undermines T-cell Activity in Cancer (2023)

&lt;p&gt;Supplemental Figures S1-S11&lt;/p&gt;
Online Load Balancing Under Graph Constraints (2015)

In several data center settings, each arriving job may only be served by one of a subset of servers. Such a graph constraint can arise due to several reasons. One is locality of the data needed by a job; for example, in content farms (e.g., in Netflix or YouTube) a video request can only be served by a machine that possesses a copy. Motivated by this, we consider a setting where each job, on arrival, reveals a deadline and a subset of servers that can serve it. The job needs to be immediately allocated to one of these servers, and cannot be moved thereafter. Our objective is to maximize the fraction of jobs that are served before their deadlines. For this online load balancing problem, we prove an upper bound of 1-1/e on the competitive ratio of nonpreemptive online algorithms for systems with a large number of servers. We propose an algorithm - INSERT RANKING - which achieves this upper bound. The algorithm makes decisions in a correlated random way and it is inspired by the work of Karp, Vazirani, and Vazirani on online matching for bipartite graphs. We also show that two more natural algorithms, based on independent randomness, are strictly suboptimal, with a competitive ratio of 1/2.
The influence of morphology on the dielectric and dynamic mechanical behavior of a linear low‐density polyethylene (1985)

Abstract The dielectric and viscoelastic relaxation behavior of linear low‐density polyethylene has been investigated. All three usual relaxation regions occur; however, the α process is more dominant than in conventional low‐density polyethylene made dielectrically active through the introduction of carbonyl groups. The observed behavior is very sensitive to orientation and morphology. There are significant differences between oriented samples (stretching or extrusion) and a single‐crystal texture specimen. Effects are caused by dipolar orientation and dipolar immobilization, the relative importance of each effect varying with specimen preparation. Active dipolar groups are not carbonyls, or any common organic species, but appear to be due to chain ends having residual dipoles caused by the catalyst used in synthesis.
Catalytic hydroprocessing of biomass fast pyrolysis bio‐oil to produce hydrocarbon products (2009)

Abstract Catalytic hydroprocessing has been applied to biomass fast pyrolysis liquid product (bio‐oil) in a bench‐scale continuous‐flow fixed‐bed reactor system. The intent of the research was to develop process technology to convert the bio‐oil into a petroleum refinery feedstock to supplement fossil energy resources and to displace imported feedstock. The project was a cooperative research and development agreement among UOP LLC, the National Renewable Energy Laboratory and the Pacific Northwest National Laboratory (PNNL). This article is focused on the process experimentation and product analysis undertaken at PNNL. This article describes the experimental methods used and relates the results of the product analyses. A range of catalyst formulations were tested over a range of operating parameters including temperature, pressure, and flow rate with bio‐oil derived from several different biomass feedstocks. Effects of liquid hourly space velocity and catalyst bed temperature were assessed. Details of the process results were presented included product yields and hydrogen consumption. Detailed analysis of the products were provided including elemental composition, chemical functional type determined by mass spectrometry, and product descriptors such as density, viscosity, and total acid number. In conclusion, this article provides an understanding of the efficacy of hydroprocessing as applied to bio‐oil. © 2009 American Institute of Chemical Engineers Environ Prog, 2009
Leveraging mm-Wave Communication for Security. (2018)

The fact that Millimeter Wave (mmWave) communication needs to be directional is usually perceived as a challenge; in this paper we argue that it enables efficient secret key sharing that are unconditionally secure from passive eavesdroppers, by building on packet erasures. We showcase the potential of our approach in two setups: beam sweeping to align receiver/transmitter pairs, and vehicle platooning. We show that in the first case, we can establish a few hundred secret bits at virtually no additional transmission cost; and in the second case, we can potentially establish keys in the order of tenths of Mbps. These first results are based on some simplifying assumptions, yet we believe they give incentives to further explore such techniques.
A Novel Isolated Current Sensor for High-Performance Power Electronics Applications (2006)

A planar current sensor, comprised of a magnetic current transformer and a Hall-effect element, is presented. The sensor has a broad frequency bandwidth from DC up to 30 MHz, a high current rating (40 A DC), superior linearity, high EMI immunity, small size, robustness and low realization cost. The main design formulations are given analytically; simulations and finite element results are presented for verification. Experimental results of current step response and dv/dt immunity are included.
Are large side holes associated with reduced rates of pancreatic stent occlusion? Results of a prospective study. (2009)

Pancreatic stents are mostly occluded as early as 1 month after insertion. Larger side holes may prevent stents within the pancreas from becoming clogged.
A Novel Pathway Responsible for Lipopolysaccharide-Induced Translational Regulation of TNF-α and IL-6 Expression Involves Protein Kinase C and Fascin (2011)

Fascin, as a substrate of protein kinase C (PKC), is a well-known cytoskeletal regulatory protein required for cell migration, invasion, and adhesion in normal and cancer cells. In an effort to identify the role of fascin in PKC-mediated cellular signaling, its expression was suppressed by stable transfection of specific short hairpin RNAs (shRNAs) in mouse monocytic leukemia RAW264.7 cells. Suppression of fascin expression resulted in impaired cellular migration and invasion through extracellular matrix proteins. Unexpectedly, the specific shRNA transfectants exhibited a marked reduction in LPS-induced expression of TNF-α and IL-6 by blocking the translation of their mRNAs. Transient transfection assay using a luciferase expression construct containing the 3' untranslated region of TNF-α or IL-6 mRNA revealed a significant reduction in both LPS- and PMA- (the direct activator of PKC) induced reporter activity in cells transfected with fascin-specific shRNA, indicating that fascin-mediated translational regulation targeted 3' untranslated region. Furthermore, LPS-induced translational activation of reporter expression was blocked by a pharmacological inhibitor of PKC, and the dominant-negative form of PKCα attenuated LPS-induced translational activation. The same type of regulation was also observed in the human monocytic leukemia cell line THP-1 and in mouse peritoneal macrophages. These data demonstrate the involvement of fascin in the PKC-mediated translational regulation of TNF-α and IL-6 expression during the LPS response.
Impairment of Sodium Balance in Mice Deficient in Renal Principal Cell Mineralocorticoid Receptor (2007)

Germline inactivation of the mineralocorticoid receptor (MR) gene in mice results in postnatal lethality as a result of massive loss of sodium and water. The knockout mice show impaired epithelial sodium channel (ENaC) activity in kidney and colon. For determination of the role of renal MR in aldosterone-driven ENaC-mediated sodium reabsorption, mice with principal cell MR deficiency were generated using the Cre-loxP system. For driving Cre recombinase expression in principal cells, the regulatory elements of the mouse aquaporin 2 (AQP2) gene were used. Mutant mice (MR(AQP2Cre)) were obtained by crossing AQP2Cre mice with mice that carried a conditional MR allele. Under standard diet, MR(AQP2Cre) mice develop normally and exhibit unaltered renal sodium excretion but show strongly elevated aldosterone levels. Increased renal sodium and water excretion, resulting in continuous loss of body weight, occur under low-sodium diet. Immunofluorescence revealed that the loss of MR and apical ENaC staining is restricted to principal cells of the collecting duct (CD) and late connecting tubule (CNT) and that MR is crucial for ENaC trafficking to the apical membrane. These results demonstrate that inactivation of MR in CD and late CNT can be compensated under standard diet but no longer when sodium supply is limited. Because the mutant mice show preserved renal ENaC activity, this study provides evidence that the late distal convoluted tubule and early CNT can compensate to a large extent deficient ENaC-mediated sodium reabsorption in late CNT and CD.
Metasurface‐Enhanced Infrared Spectroscopy: An Abundance of Materials and Functionalities (2022)

Infrared spectroscopy provides unique information on the composition and dynamics of biochemical systems by resolving the characteristic absorption fingerprints of their constituent molecules. Based on this inherent chemical specificity and the capability for label-free, noninvasive, and real-time detection, infrared spectroscopy approaches have unlocked a plethora of breakthrough applications for fields ranging from environmental monitoring and defense to chemical analysis and medical diagnostics. Nanophotonics has played a crucial role for pushing the sensitivity limits of traditional far-field spectroscopy by using resonant nanostructures to focus the incident light into nanoscale hot-spots of the electromagnetic field, greatly enhancing light-matter interaction. Metasurfaces composed of regular arrangements of such resonators further increase the design space for tailoring this nanoscale light control both spectrally and spatially, which has established them as an invaluable toolkit for surface-enhanced spectroscopy. Starting from the fundamental concepts of metasurface-enhanced infrared spectroscopy, a broad palette of resonator geometries, materials, and arrangements for realizing highly sensitive metadevices is showcased, with a special focus on emerging systems such as phononic and 2D van der Waals materials, and integration with waveguides for lab-on-a-chip devices. Furthermore, advanced sensor functionalities of metasurface-based infrared spectroscopy, including multiresonance, tunability, dielectrophoresis, live cell sensing, and machine-learning-aided analysis are highlighted.
A Sheep Model for the Study of Hemorheology With Assisted Circulation (1994)

Hemorheologic investigations were performed on nine sheep during the in vivo evaluation of a new axial flow ventricular assist device, the Nimbus AxiPump (Nimbus, Inc., Rancho Cordova, CA). Blood hematocrit, plasma and whole blood viscosity, red blood cell (RBC) deformability and aggregation, plasma fibrinogen, and free hemoglobin (hemolysis) levels were measured. Changes in the main rheologic parameters of sheep blood relative to the pre-implant values were minor and transient. The exception was RBC aggregation, which appeared on the third day of implantation. (Sheep blood does not normally demonstrate RBC aggregation.) Sheep RBCs started to form classic rouleaux typically on the third post-operative day simultaneously with increasing fibrinogen level. To investigate the relative effects of mechanical stress and elevated fibrinogen levels on RBC aggregability, in vitro studies were conducted with blood from control sheep. These studies indicated that neither mechanical trauma nor elevated fibrinogen alone caused RBC aggregation as seen in vivo. However, combined mechanical stress and elevated fibrinogen did cause this unusual effect for sheep blood.
China's New Sorrow: Water-Management Policies, Environmental Degradation, and Salar-Tibetan Minority Relations in Qinghai Province, 1862–1978 (2013)

This article analyzes the effect of post-1949 policies on minority peoples in China's watershed—Qinghai province. Salar and Tibetan peoples had lived in relative harmony for centuries in Xunhua County. Access to the Tibetan highlands and a monopoly on wool production had provided Tibetan herders with an upper hand. New policies that encouraged agricultural production over the course of the twentieth century not only brought radical changes to these long-standing relationships but also initiated new strains on the local environment. The Mao era saw a particularly rapid expansion of new water projects designed to tame the Yellow River. The resulting environmental catastrophe is a major contributing factor to the river's current inability to flow to the Yellow Sea.
What do ultrasound velocity and attenuation tell us about crystal nucleation? (2017)

Akulichev and Bulanov showed that a coupling between ultrasound and crystals in equilibrium with their melt would occur leading to high attenuation. This phenomenon is well established. However, what happens in circumstances such as in the induction period where critical fluctuations occur and crystal embryos appear and disappear, i.e. under non-equilibrium circumstances? Evidence is presented that the mean solution adiabatic compressibility is altered by these transient phenomena, providing a unique insight into a poorly understood and industrially crucial process step. Fluctuations in adiabatic compressibility observed as a result of the high measurement rates available with high frequency pulsed ultrasound provide further insight into the early stages of crystal growth phenomena. Later on, when individual crystals begin to interact and sinter a frame modulus emerges which necessitates a semi-phenomenological interpretation.