gebhart/patrepeval huggingface dataset:
MiRs in RA: possible biomarkers and therapeutic targets (2012)

Rheumatology has pioneered in the study of autoantibodies by showing that they are not only involved in pathogenesis but are also highly useful as diagnostic biomarkers. The diagnostic biomarker aspect of autoimmunity has gained increasing importance in cancer and many of the insights gained in Rheumatology have contributed to understanding the significance of autoantibodies in cancer. Features of autoantibodies in rheumatic disorders: In rheumatic diseases no individual autoantibody-antigen system has sufficient combination of sensitivity and specificity to serve as a useful diagnostic biomarker. Instead, several antigen-antibody systems constructed as profiles of biomarkers are highly effective in distinguishing one disorder from another. In lupus, anti-double strand DNA and anti-Sm distinguishes it from scleroderma, where the profile is anti-DNA topoisomerase 1 and anti-centromere proteins. The autoantigensare cell components involved in universal and basic gene expression pathways, such as Sm in precursor mRNA splicing and DNA topoisomerase 1 in DNA replication and transcription [1]. Features of autoantibodies in cancer: Autoantibodies in cancer target intracellular molecules referred to as TAAs (tumor-associated antigens). As in rheumatic disorders, no individual autoantibody-antigen system has sensitivity and specificity to serve as a stand-alone diagnostic marker [2]. Most tumors show multiple antibody specificities and with panels of TAAanti-TAAs (analogous toprofiles) the cumulative sensitivity and specificity reaches diagnostic significance. Different tumorigenesis pathways are
Hidden Markov Models and Gaussian Mixture Models for Bearing Fault Detection Using Fractals (2006)

Bearing vibration signals features are extracted using time domain fractal based feature extraction technique. This technique uses multi-scale fractal dimension (MFD) estimated using box-counting dimension. The extracted features are then used to classify faults using Gaussian mixture models (GMM) and hidden Markov models (HMM). The results obtained show that the proposed feature extraction technique does extract fault specific information. Furthermore, the experimentation shows that HMM outperforms GMM. However, the disadvantage of HMM is that it is computationally expensive to train compared to GMM. It is therefore concluded that the proposed framework gives enormous improvement to the performance of the bearing fault detection and diagnosis, but it is recommended to use the GMM classifier when time is the major issue.
Isoreticular Homochiral Porous Metal−Organic Structures with Tunable Pore Sizes (2007)

Chiral-layered building motifs of zinc(II) camphorate are linked through linear N-donor ligands, forming series of three-dimensional isoreticular porous homochiral frameworks. The lengths of these linear ligands control the pore sizes and free accessible volumes of the homochiral metal-organic structures.
CK2 Modulation of NF-κB, TP53, and the Malignant Phenotype in Head and Neck Cancer by Anti-CK2 Oligonucleotides In vitro or In vivo via Sub–50-nm Nanocapsules (2010)

Our study reveals a novel role of CK2 in coregulating NF-kappaB activation, TP53/p63 expression, and downstream gene expression. Downregulation of CK2 in HNSCC models in vitro and in vivo shows antitumor effects as well as sensitization to cisplatin.
Determination of Longitudinal Phase Space in SLAC Main Accelerator Beams (2006)

In the E164 Experiment at the Stanford Linear Accelerator Center (SLAC), we drive plasma wakes for electron acceleration using 28.5 GeV bunches from the main accelerator. These bunches can now be made with an RMS length of 12 microns, and accurate direct measurement of their lengths is not feasible shot by shot. Instead, we use an indirect technique, measuring the energy spectrum at the end of the linac and comparing with detailed simulations of the entire machine. We simulate with LiTrack, a 2D particle tracking code developed at SLAC. Understanding the longitudinal profile allows a better understanding of acceleration in the plasma wake, as well as investigation of related effects. We discuss the method and validation of our phase space determinations.
Polymer-Modified Concrete: Review (1997)

Composites of concrete and polymers of various kinds are used in many applications. This paper briefly reviews the history of polymers in combination with cement as a building material, where the polymer is not in the form of fiber or mesh reinforcing, but in the form of a polymerized matrix comingled with the hydrated cement paste. The microstructure and properties of the composite polymer-modified concrete are described, and some current and possible future applications are mentioned. Several recently published articles and technical papers dealing with polymer-modified concrete are critically reviewed.
Preslaughter handling effects on pork quality and glycolytic potential in two muscles differing in fiber type composition (2005)

The objective of the present experiment was to investigate the effects of transportation, lairage, and preslaughter stressor treatment on glycolytic potential and pork quality of the glycolytic longissimus and the oxidative supraspinatus (SSP) or serratus ventralis (SV) muscles. In a 2 x 2 x 2 factorial design, 384 pigs were assigned randomly either to short (50 min) and smooth or long (3 h) and rough transport, long (3 h) or short (< 45 min) lairage, and minimal or high preslaughter stress. Muscle samples were taken from the LM at 135 min and from the SSP at 160 min postmortem for determination of the glycolytic potential and rate of glycolysis. At 23 h postmortem, pork quality was assessed in the LM and the SV. Effects of transport and lairage conditions were similar in both muscle types. Long transport increased (P < 0.01) the glycolytic potential and muscle lactate concentrations compared with short transport. Both long transportation and short lairage decreased (P < 0.01) redness (a* values) and yellowness (b* values) of the LM and SV. In combination with short lairage, long transport decreased (P < 0.05) pork lightness (lower L* values), and electrical conductivity was increased (P < 0.05) after long transport. Several interactions between stress level and muscle type (P < 0.001) were observed. High preslaughter stress decreased (P < 0.001) muscle glycogen in both the LM and SSP, but this decrease was greater in the LM. Lactate concentrations were increased (P < 0.001) only in the LM by high preslaughter stress. Increases in ultimate pH (P < 0.001) and decreases in a* values (P < 0.01) were greatest in the SV, whereas increases in electrical conductivity (P < 0.001) were greatest in the LM. The lack of interactions among transportation, lairage, and muscle type was attributed to the relatively minor differences in stress among treatments. It was concluded that, in glycolytic muscle types such as the LM, the high physical and psychological stress levels associated with stress in the immediate preslaughter period have a greater effect on the water-holding capacity of the meat and may promote PSE development. Conversely, oxidative muscle types tend to have higher ultimate pH values and produce DFD pork in response to intense physical activity and/or high psychological stress levels preslaughter.
Modulation of Gene Expression by Tumor-Derived p53 Mutants (2004)

p53 mutants with a single amino acid substitution are overexpressed in a majority of human cancers containing a p53 mutation. Overexpression of the mutant protein suggests that there is a selection pressure on the cell indicative of an active functional role for mutant p53. Indeed, H1299 cells expressing mutant p53-R175H, p53-R273H or p53-D281G grow at a faster rate compared with a control cell line. Using p53-specific small interfering RNA, we show that the growth rate of mutant p53-expressing cells decreases as mutant p53 level decreases, demonstrating that the increased cellular growth is dependent on p53 expression. Increased growth rate is not observed for H1299 cell clones expressing mutant p53-D281G (L22Q/W23S), which has been shown to be defective in transactivation in transient transcriptional assays. This shows that the increased growth rate imparted by mutant p53 in H1299 cells requires the transactivation function of mutant p53. By performing microarray hybridization analyses, we show that constitutive expression of three common p53 mutants (p53-R175H, p53-R273H, and p53-D281G) in H1299 human lung carcinoma cells evokes regulation of a common set of genes, a significant number of which are involved in cell growth regulation. Predictably, H1299 cells expressing p53-D281G (L22Q/W23S) are defective in up-regulating a number of these genes. The differences in expression profiles induced by individual p53 mutants in the cells may be representative of the p53 mutants and how they can affect gene expression resulting in the observed "gain of function" phenotypes (i.e., increased growth rate, decreased sensitivity to chemotherapeutic agents, and so forth).
Evacuation route planning (2007)

Given a transportation network, a vulnerable population, and a set of destinations, evacuation route planning identifies routes to minimize the time to evacuate the vulnerable population. Evacuation route planning is a vital components of efforts by civil authorities to prepare for both natural and man-made disasters (e.g., hurricanes, terrorist acts, etc). However, evacuation route planning is computationally challenging due to the size of transportation networks, the large number of evacuees, and capacity constraints. For example, the number of evacuees often far exceeds the bottleneck capacity, i.e., the minimum cut of a given network. Current approaches (e.g., linear programming and Capacity Constrained Route Planner (CCRP), a recently proposed evacuation planning algorithm) do not scale well because of intensive computation needs in order to produce the schedules of evacuees as well as routing plans.
DIET AND HUMAN BEHAVIOR: HOW MUCH DO THEY AFFECT EACH OTHER? (1986)

EVALUATION OF RESEARCH: GENERAL PRINCIPLES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114 Subjects and Sampling . ....... . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .... 114 Nutrient Manipulation or Dosage. .. .. . . . . ....... . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . ... ...... . . 114 GROSS DIETARY DISRUPTION . . . . . . .. . . . . . . . . . . . . ....... . . . . . . . . . . . . ....... . . . . . . . . . . ........ . . 116 ACUTE MALNUTRITION: FASTING VERSUS FED STUDIES . . . . . . . . . . . . . . . . . . .. . . 117 HYPERSENSITIVITY TO DIETARY SUBSTANCES . . . . . . . . . . . . .. . . . . . .. . . . . . . . . . .. .. .. . . . . 119 BEHAVIORAL STUDIES WITH SPECIFIC DIETARY CONSTITUENTS. . . . . . . . . . . . . . . 121 Caffeine . .. . . . . . . . . . . . . . . . . .. ...... . . . . . . . .. ..... . . .. . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . ... 121 Sweeteners........ .. . . . . . . . . . . . . . . . . . . . . . ......... . . . .. . . . . . . . . . .... . . . . . . . . . . . ....... . . . . . . . . . . . . .. 121 Amino Acids. . .. . . . . . . . . .. . . . .. . . . . . . . . . . .. . . . . . . . . . ... .. .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ... . .... . . 125 Vitamins . ... . . . . . . . . . . . . . . . . ..... . . . . . . ......... . . . . . .. . . . . . . . ....... . . . . . . . . . . . . ..... . . . . . . .. . ... . . 126 CONCLUSION . . . . . . . . . . . . . . . . .. . . . . ....... ... . . . . . . . . . . . ..... . . . . . . . . . . . ...... .... . . . . . 126
Impact of fading correlations on MIMO communication systems in geometry-based statistical channel models (2005)

This paper highlights the impact of channel correlations on the capacity and performance of MIMO communications, with a focus on the so-called diagonal correlations. Based on this analysis, the limitations of simplified mathematical representations, such as the Kronecker or the diagonal-decorrelation models, are pointed out. Finally, the correlation properties of popular geometry-based statistical models are studied in order to analyze whether the correlation structure of these models can be adequately represented by simplified mathematical models, as well as to quantify the errors introduced by these simplifications. With respect to channel correlations, neither the Kronecker nor the diagonal-decorrelation assumptions are good representations of the correlation structure of the investigated geometry-based statistical models. When comparing capacity and symbol error probability results, it is found that the diagonal-decorrelation model may yield significant errors on both considered metrics. The Kronecker model generally yields errors less than one order of magnitude on the symbol error rate, but relative errors on ergodic or outage capacity may be more significant.
Palladium-Catalyzed Regioselective Arylalkenylation of Ynamides (2022)

A cationic palladium-catalyzed arylalkenylation of ynamides is presented. The putative keteniminium arylpalladium intermediate likely dictates the regioselective carbopalladation of the ynamide to form a vinylpalladium species. The capture of this complex by the olefin yields linear conjugated β-alkenyl aminodienes (especially with <i>trans</i> selectivity). The transformation features a broad scope with labile functional group tolerance and makes 42 unusual molecular scaffolds with structural diversity. DFT studies provide valuable insights into the reaction mechanism.
Magnetic properties study on Fe-doped calcium phosphate (2009)

Calcium phosphates are very important for applications in medicine due to their properties such as biocompatibility and bioactivity. In order to enhance these properties, substitution of calcium with other ions has been proposed. Partial substitution of calcium by different ions has been made in order to improve the properties of the calcium phosphates and also to allow new applications of apatite in medicine. In this work, hydroxyapatite [Ca 10 (PO 4 ) 6 (OH) 2 —HAP] was prepared by high-energy dry milling (20 h) and mixed with iron oxide (5 wt.%). The mixture was calcinated at 900 °C for 5 h with a heating rate of 3 °C min −1 in an attempt to introduce iron oxide into the HAP structure. The sintered sample was characterized using x-ray diffraction (XRD) and magnetization. The 57 Fe-Mössbauer spectra of the calcium phosphate oxides were also measured, revealing the presence of iron in three different phases: Ca 2 Fe 2 O 5 , Fe 2 O 3 and hydroxyapatite.
The Systematic Closing of the Performance Gap in Hydraulic Fracturing (2014)

Abstract Hydraulic fracturing is the overwhelming completion method in the international petroleum industry. It is estimated, that today it has become a $20 billion industry. It is also one of the most challenging enterprises, incorporating scientific information from geology, reservoir and production engineering, rock mechanics, complex fluid rheology and field economics. More than a decade ago we introduced the concept of Unified Fracture Design (UFD) as a means towards physical optimization. Since then UFD has been adopted by a great number of practitioners and hundreds of papers have been published. Not all approaches have been successful, nor have they been done appropriately. In this work we relook at the whole issue in a systematic way. We have identified and describe here a 9-step sequence to mitigate the gaps and help in the optimized field application of modern hydraulic fracturing. These include:Required minimum reservoir characterization: Typical log description.Estimate of k, h, interlayer stress contrast, distance from water.Optimization of fracture size using UFD. Maximum dimensionless PI at optimum conductivity. Optimization of drainage shape and stimulated reservoir volume (SRV).Unique monitoring execution, other than the traditional net pressure or injection variables. New benchmark indicators are used, cross-plotting descriptive variables such as: level of pressure vs. volume of fluid injected vs. operational characteristics, such as tip screen-out.4. Fracture injection tests, designed for fluid efficiency, closure pressure, leak-off coefficient and the newly developed capability for after-closure analysis for well and reservoir variables.For multifrac applications such as shale gas, horizontal wells in very low-permeability formations, zonal isolation and perforation strategies are essential issues.Design of injection schedule to accomplish the desired fracture geometry is the next concern. What happens if things go wrong? The strategy of contingencies must be in place before the execution starts.On-the-fly redesign responding to contingencies, such as net pressure constraints and formation barriers. Ability for alternative plans quickly.Once the job is completed the next step is whatever is necessary to close the fracture and flow the well back. What needs to be done in different geologic settings?Finally, to close the circle, performance evaluation is indicated, which involves comparison between actual performance and expectations and the definitive reconciliation of any discrepancies.
CO2-Responsive CCT Protein interacts with 14-3-3 proteins and controls the expression of starch synthesis-related genes (2021)

CO2 responsive CCT protein (CRCT) is a positive regulator of starch synthesis related genes such as ADP-glucose pyrophosphorylase large subunit 1 and starch branching enzyme I particularly in the leaf sheath of rice (Oryza sativa L.). The promoter GUS analysis revealed that CRCT expressed exclusively in the vascular bundle, whereas starch synthesis related genes were expressed in different sites such as mesophyll cell and starch storage parenchyma cell. However, the chromatin immunoprecipitation (ChIP) using a FLAG-CRCT overexpression line and subsequent qPCR analyses showed that the 5’-flanking regions of these starch synthesis-related genes tended to be enriched by ChIP, suggesting that CRCT can bind to the promoter regions of these genes. The monomer of CRCT is 34.2 kDa, however CRCT was detected at 270 kDa via gel filtration chromatography, suggesting that CRCT forms a complex in vivo. Immunoprecipitation and subsequent MS analysis pulled down several 14-3-3-like proteins. A yeast two-hybrid analysis and bimolecular fluorescence complementation assays confirmed the interaction between CRCT and 14-3-3-like proteins. Although there is an inconsistency in the place of expression, this study provide important findings regarding the molecular function of CRCT to control the expression of key starch synthesis-related genes.
Bacteroides acidifaciens in the gut plays a protective role against CD95-mediated liver injury (2022)

The intestinal flora plays an important role in the development of many human and animal diseases. Microbiome association studies revealed the potential regulatory function of intestinal bacteria in many liver diseases, such as autoimmune hepatitis, viral hepatitis and alcoholic hepatitis. However, the key intestinal bacterial strains that affect pathological liver injury and the underlying functional mechanisms remain unclear. We found that the gut microbiota from gentamycin (Gen)-treated mice significantly alleviated concanavalin A (ConA)-induced liver injury compared to vancomycin (Van)-treated mice by inhibiting CD95 expression on the surface of hepatocytes and reducing CD95/CD95L-mediated hepatocyte apoptosis. Through the combination of microbiota sequencing and correlation analysis, we isolated 5 strains with the highest relative abundance, <i>Bacteroides acidifaciens</i> (BA), <i>Parabacteroides distasonis</i> (PD), <i>Bacteroides thetaiotaomicron</i> (BT), <i>Bacteroides dorei</i> (BD) and <i>Bacteroides uniformis</i> (BU), from the feces of Gen-treated mice. Only BA played a protective role against ConA-induced liver injury. Further studies demonstrated that BA-reconstituted mice had reduced CD95/CD95L signaling, which was required for the decrease in the L-glutathione/glutathione (GSSG/GSH) ratio observed in the liver. BA-reconstituted mice were also more resistant to alcoholic liver injury. Our work showed that a specific murine intestinal bacterial strain, BA, ameliorated liver injury by reducing hepatocyte apoptosis in a CD95-dependent manner. Determination of the function of BA may provide an opportunity for its future use as a treatment for liver disease.
Resource constrained efficient acoustic source localization and tracking using a distributed network of microphones (2008)

In this paper we present an efficient method to perform acoustic source localization and tracking using a distributed network of microphones. In this scenario, there is a trade-off between the localization performance and the expense of resources: in fact, a minimization of the localization error would require to use as many sensors as possible; at the same time, as the number of microphones increases, the cost of the network inevitably tends to grow, while in practical applications only a limited amount of resources is available. Therefore, at each time instant only a subset of the sensors should be enabled in order to meet the cost constraints. We propose a heuristic method for the optimal selection of this subset of microphones, using as distortion metrics the Cramer-Rao lower bound (CRLB) and as cost function the total distance between the selected sensors. The heuristic approach has been compared to an optimal algorithm, which searches the best sensor configuration among the full set of microphones, while satisfying the cost constraint. The proposed heuristic algorithm yields similar performance w.r.t. the full-search procedure, but at a much less computational cost. We show that this method can be used effectively in an acoustic source tracking application.
Auf den Spuren der richtigen Hegelschen Ästhetik (2008)

Heinrich Gustav Hotho (1802–1873) published the three-volume Ästhetik (1835) four years after the death of Hegel. From archive research it has become clear that in the ‘compilation’ of his Hegelian Ästhetik Hotho employed mainly his own lectures of 1823. This has led to the view that Hothos’s 1823 lectures taken all together actually constitute Hegelian aesthetics. The present article seeks to challenge this notion. Hegel gave four series of lectures on aesthetics in Berlin in 1820/21, 1823, 1826, and 1828/29. Since he never wrote his own work on aesthetics, one might consider the edition of four series of lectures to be the ‘real’ Hegelian Ästhetik. This amalgam conceals difficulties linked with the analysis of particular works of art. These difficulties are not resolved in the Hegelian Ästhetik, nor can they be with the edition of the lecture notes. Towards the end of the article, the author therefore comments on two other attempts at interpretation. AbstraktVier Jahre nach dem Tode Hegels im Jahre 1835 hat Heinrich Gustav Hotho (1802–1873) die dreibändige Ästhetik herausgegeben. Aufgrund von Archivforschungen ist inzwischen klar, dass Hotho sich bei der „Zusammenstellung” der Hegelschen Ästhetik textlich vor allem auf seine eigene, im Jahre 1823 verfertigte Mitschrift gestützt hat. So ist die Meinung entstanden, dass die Mitschriften Hothos aus dem Jahre 1823 die eigentliche Hegelsche Ästhetik beinhalten. In meinem Aufsatz möchte ich diese These anfechten. Hegel hat in Berlin viermal über Ästhetik Vorlesungen gehalten: in den Jahren 1820/21, 1823, 1826 und 1828/29. Da Hegel aber nie eine eigene Ästhetik geschrieben und veröffentlicht hat, könnte man eigentlich nur eine komparative Ausgabe der vier Vorlesungen als die „eigentliche“ Hegelsche Ästhetik betrachten. Hinter der Verschmelzung stecken Schwierigkeiten, die mit den Analysen der konkreten Kunstwerke verbunden sind. Diese Schwierigkeiten wurden in der Hegelschen Ästhetik nicht gelöst und konnten auch durch die Edition der Mitschriften nicht gelöst werden. Am Ende des Aufsatzes werden deswegen noch zwei Interpretationsversuche kommentiert.