gebhart/patrepeval huggingface dataset:
Appearance of d-amino acids during aging: d-Amino acids in tumor proteins (1998)

In 1939 Kögl and Erxleben [1-4] reported that tumor proteins contain appreciable amounts of D-amino acids, specifically glutamic acid, valine, leucine and lysine, implying that both the initiation and autonomous character of tumors depends on the formation and maintenance of these D-amino acids in the cell proteins. This postulate remained highly controversial for over 10 years, during which time several papers both supporting and refuting this hypothesis were published. The dispute existed almost entirely between Kögl, a vigorous and able protagonist at the University of Utrecht, Netherlands, and an impressive array of equally vigorous and able dissenters in the United Kingdom and Germany. An excellent review of both sides of this controversy was written by Miller in 1950 [5]. After many years and much effort the controversy then seemed to be put to rest. However, more than 40 years later the development of much more refined analytical techniques for the resolution and detection of amino acid enantiomers provided more definitive evidence that D-amino acids are not common to all tumor tissues and probably are not integral to the cancer process. This is not surprising when one considers that a tumor consists of fast-growing cells. Thus, there would not be sufficient time for any L-amino acid to racemize to the D isomer. Some D-amino acids may originate in foods consumed, but it is uncertain whether enzyme systems are able to incorporate D-amino acids into tumor proteins during growth. Nevertheless, if significant levels of D-amino acids were to be found in tumor proteins, the implications could be far-reaching. Confirmation of the presence of D-amino acids at any concentration in tumors would provide new insights into the mechanism for autogenesis and maintenance of tumors.
Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins (2003)

Cytosine-5 DNA methylation is a critical signal defining heritable epigenetic states of transcription. As aberrant methylation patterns often accompany disease states, the ability to target cytosine methylation to preselected regions could prove valuable in re-establishing proper gene regulation. We employ the strategy of targeted gene methylation in yeast, which has a naturally unmethylated genome, selectively directing de novo DNA methylation via the fusion of C5 DNA methyltransferases to heterologous DNA-binding proteins. The zinc-finger proteins Zif268 and Zip53 can target DNA methylation by M.CviPI or M.SssI 5-52 nt from single zinc-factor binding sites. Modification at specific GC (M.CviPI) or CG (M.SssI) sites is enhanced as much as 20-fold compared with strains expressing either the free enzyme or a fusion protein with the zinc-finger protein moiety unable to bind to DNA. Interestingly, methylation is also selectively targeted as far as 353 nt from the zinc-finger protein binding sites, possibly indicative of looping, nucleosomes or higher-order chromatin structure. These data demonstrate that methylation can be targeted in vivo to a potentially broad range of sequences using specifically engineered zinc-finger proteins. Further more, the selective targeting of methylation by zinc-finger proteins demonstrates that binding of distinct classes of factors can be monitored in living cells.
Dual Cross-Entropy Loss for Small-Sample Fine-Grained Vehicle Classification (2019)

Fine-grained vehicle classification is a challenging topic in computer vision due to the high intraclass variance and low interclass variance. Recently, considerable progress has been made in fine-grained vehicle classification due to the huge success of deep neural networks. Most studies of fine-grained vehicle classification based on neural networks, focus on the neural network structure to improve the classification performance. In contrast to existing works on fine-grained vehicle classification, we focus on the loss function of the neural network. We add a regularization term to the cross-entropy loss and propose a new loss function, Dual Cross-Entropy Loss. The regularization term places a constraint on the probability that a data point is assigned to a class other than its ground-truth class, which can alleviate the vanishing of the gradient when the value of the cross-entropy loss is close to zero. To demonstrate the effectiveness of our loss function, we perform two sets of experiments. The first set is conducted on a small-sample fine-grained vehicle classification dataset, the Stanford Cars-196 dataset. The second set is conducted on two small-sample datasets, the LabelMe dataset and the UIUC-Sports dataset, as well as on one large-sample dataset, the CIFAR-10 dataset. The experimental results show that the proposed loss function improves the fine-grained vehicle classification performance and has good performance on three other general image classification tasks.
Ion separations with membranes (2020)

Abstract Ion separations are important for resource recovery, water treatment, and energy production and storage. Techniques such as chemical precipitation, selective adsorption, and solvent extraction are effective, but membranes may separate ions continuously with less waste and lower energy costs. Separation of monovalent and multivalent ions with nanofiltration or electrodialysis membranes already enables water softening and edible salt purification. Similar membranes are attractive as separators in vanadium redox flow batteries. Selective partitioning of divalent counter‐ions into ion‐exchange membranes even allows transport of these ions against their concentration gradients in salt mixtures. However, separations of ions with the same charge is more challenging. Recent research demonstrated highly selective ion “sieving” at small scales. Separations using electrical potentials and differences in ion electrophoretic mobilities are promising, but relatively unexplored. Carrier‐mediated transport affords high selectivity in liquid membranes, but these systems are not very stable, and selective transport via hopping between anchored carriers has proven elusive. Finally, this paper discusses how concentration polarization decreases selectivities in many membrane processes. Although development of selective, inexpensive ion‐separation membranes is a work in progress, successes in water softening and edible salt purification suggests that future selective membranes will serve as complementary methods to traditional purification techniques.
Prognostic impact of circulating plasma cells in patients with multiple myeloma: implications for plasma cell leukemia definition (2017)

The presence of circulating plasma cells in patients with multiple myeloma is considered a marker for highly proliferative disease. In the study herein, the impact of circulating plasma cells assessed by cytology on survival of patients with multiple myeloma was analyzed. Wright-Giemsa stained peripheral blood smears of 482 patients with newly diagnosed myeloma or plasma cell leukemia were reviewed and patients were classified into 4 categories according to the percentage of circulating plasma cells: 0%, 1-4%, 5-20%, and plasma cell leukemia with the following frequencies: 382 (79.2%), 83 (17.2%), 12 (2.5%) and 5 (1.0%), respectively. Median overall survival according to the circulating plasma cells group was 47, 50, 6 and 14 months, respectively. At multivariate analysis, the presence of 5 to 20% circulating plasma cells was associated with a worse overall survival (relative risk 4.9, 95% CI 2.6-9.3) independently of age, creatinine, the Durie-Salmon system stage and the International Staging System (ISS) stage. Patients with ≥5% circulating plasma cells had lower platelet counts (median 86×10<sup>9</sup>/L <i>vs</i> 214×10<sup>9</sup>/L, <i>P</i><0.0001) and higher bone marrow plasma cells (median 53% <i>vs</i> 36%, <i>P</i>=0.004). The presence of ≥5% circulating plasma cells in patients with multiple myeloma has a similar adverse prognostic impact as plasma cell leukemia.
Optoelectronic Energy Transfer at Novel Biohybrid Interfaces Using Light Harvesting Complexes from <i>Chloroflexus aurantiacus</i> (2009)

In nature, nanoscale supramolecular light harvesting complexes initiate the photosynthetic energy collection process at high quantum efficiencies. In this study, the distinctive antenna structure from Chloroflexus aurantiacusthe chlorosomeis assessed for potential exploitation in novel biohybrid optoelectronic devices. Electrochemical characterization of bacterial fragments containing intact chlorosomes with the photosynthetic apparatus show an increase in the charge storage density near the working electrode upon light stimulation and suggest that chlorosomes contribute approximately one-third of the overall photocurrent. Further, isolated chlorosomes (without additional photosynthetic components, e.g., reaction centers, biochemical mediators) produce a photocurrent (approximately 8-10 nA) under light saturation conditions. Correlative experiments indicate that the main chlorosome pigment, bacteriochlorophyll-c, contributes to the photocurrent via an oxidative mechanism. The results reported herein are the first to demonstrate that isolated chlorosomes (lipid-enclosed sacs of pigments) directly transduce light energy in an electrochemical manner, laying an alternative, biomimetic approach for designing photosensitized interfaces in biofuel cells and biomedical devices, such as bioenhanced retinal prosthetics.
A Comparison of the Activity of Polymer Immobilised TEMPO (PIPO) with MCM-41 and Silica Supported TEMPO as Heterogeneous Catalysts for the Oxidation of Alcohols (2001)

PIPO, a readily prepared polymer immobilised TEMPO, is an efficient recyclable heterogeneous catalyst for the chlorinated hydrocarbon solvent- and bromide-free bleach oxidation of a variety of alcohols. Under these environmentally friendly conditions, PIPO is superior to homogeneous TEMPO and the previously described MCM-41 and silica supported TEMPO catalysts. In addition, in combination with CuCl, PIPO is also able to catalyse the aerobic oxidation of benzyl alcohol.
Perceptual system using spiking neural network for an intelligent robot (2010)

This paper discusses a integrated perceptual system for intelligent control of a service robot. The robot should be able to perceive the environment flexibly to realize intelligent behavior. We focus on the perceptual system based on the perceiving-acting cycle discussed in ecological psychology. We propose a perceptual system composed of the retinal model and the spiking-neural network to realize concept of the perceiving-acting cycle. The proposed method is applied to the robot arm equipped with a 3D-range camera. This proposed method features the robot detects the invariant information of a dish, for example the contrast of a distance Information or a luminance information. As experiments, we discuss about the effectiveness of the proposed method by comparing different input.
Lactic Acidosis: From Sour Milk to Septic Shock (2005)

Lactic acidosis is frequently encountered in the intensive care unit. It occurs when there is an imbalance between production and clearance of lactate. Although lactic acidosis is often associated with a high anion gap and is generally defined as a lactate level >5 mmol/L and a serum pH <7.35, the presence of hypoalbuminemia may mask the anion gap and concomitant alkalosis may raise the pH. The causes of lactic acidosis are traditionally divided into impaired tissue oxygenation (Type A) and disorders in which tissue oxygenation is maintained (Type B). Lactate level is often used as a prognostic indicator and may be predictive of a favorable outcome if it normalizes within 48 hours. The routine measurement of serum lactate, however, should not determine therapeutic interventions. Unfortunately, treatment options remain limited and should be aimed at discontinuation of any offending drugs, treatment of the underlying pathology, and maintenance of organ perfusion. The mainstay of therapy of lactic acidosis remains prevention.
High Temperature Metal Deterioration In Atmospheres Containing Carbon-Monoxide and Hydrogen (1959)

Carbon steel and stainless steel equipment exposed to gas mixtures rich in hydrogen and carbon-monoxide at temperatures from 800 to 1200 F have been attacked with resulting loss of metal. Conditions under which this attack has been observed in a coal-to-oil synthesis plant and the nature of metal deterioration are described. Mechanism of this type attack is not fully understood although a possible gas-metal reaction is postulated. 3.2.2
Methods and terminology for diagnostic ultrasound imaging systems (1979)

This paper presents a survey of the basic technical methods and related terminology in common use to describe features of ultrasonic imaging instruments for medical diagnostics. Emphasis is on current commercial practice using the pulse-echo modality. This form of diagnostic technique is in a period of rapid technical change with a consequent proliferation of descriptive terminology. The approach taken is one of defining basic features of instrument operation, then introducing the various descriptive terms in this context and correlating these with each feature. The aim is to provide users of such instrumentation with a more basic understanding of designs to encourage better use of provided features and an appreciation of performance claims. A general introduction to machine configurations used for both static and dynamic imaging is followed by a more detailed examination of individual sections of instruments with emphasis on basic functional needs, user control interaction, and the effects on image appearance produced. It is concluded that the widening clinical use of ultrasound would be assisted by some commonality of terminology among manufacturers but this does not appear imminent. The current situation can be substantially alleviated by recognizing the functional similarities behind the terms used by the manufacturers of different machines.
Gaming Strategy for Electric Power With Random Demand (2005)

Recent work has shown that the profit maximizing problem for a generator in a competitive electricity market can be written as a mathematical program with equilibrium constraints (MPECs). In this paper, the problem of optimal generator bidding when there is a single demand is considered. The simplifications to the MPEC afforded by the assumption on the demand are shown. When the demand is stochastic and assumed to be normally distributed, the optimization that each player undertakes is written as a chance constrained program. It is shown that the solution to this stochastic problem can be found by solving a deterministic MPEC. The problem is considered with and without supply capacity constraints. By considering each of these cases as a game theory problem, the existence and uniqueness of Nash points are analyzed. These properties of the Nash point are then inferred onto the stochastic problem.
Down-regulation of human alloimmune responses by genetically engineered expression of CD95 ligand on stimulatory and target cells (2001)

Transgenic expression of apoptosis-inducing molecules could be a strategy to protect cells and tissues from destruction by apoptosis-susceptible effector T cells. Some evidence for the potency of this approach has been obtained in mouse and rat transplantation models. However, limited data are available on the capacity of apoptosis-inducing molecules to modulate human alloimmune responses. In this study we analyzed the in vitro consequences of an interaction of human T cells with allogeneic 293 cells and 293 transfectants stably expressing high levels of the apoptosis-inducing CD95 ligand (CD95L). Both, CD95L(-) and CD95L(+) 293 cells were able to activate allogeneic T cells as demonstrated by comparable CD25 expression at day 2 of culture. The analysis of viable T cells at day 7, however, revealed anti-293 cytotoxic activity only in cultures that had been stimulated with CD95L(-) 293 cells. Alloactivated effector T cells lysed CD95L(-) and CD95L(+) 293 targets with similar efficiency when tested in a 4-h 51Cr-release assay. Prolongation of the effector phase to 20 h resulted in a further increase in the destruction of CD95L(-) target cells, whereas lysis of CD95L(+) targets remained low. These data suggest that genetically engineered expression of CD95L on cells or tissues could be an approach to control human T cell reactivity towards allografts. During the induction of an alloimmune response depletion of cytotoxic precursor cells may be obtained by overexpressing CD95L on stimulatory cells; CD95L expression on graft tissue might limit T cell-mediated destruction of the transplant during the effector phase of the response.
Immunity to Trichinella spiralis infection in vitamin A-deficient mice. (1992)

Vitamin A-deficient (A-) mice make strikingly poor IgG responses when they are immunized with purified protein antigens. Previously, we showed that A- T cells overproduce interferon gamma (IFN-gamma), which then could inhibit interleukin 4 (IL-4)-stimulated B cell IgG responses. To determine if the altered IFN-gamma regulation pattern and its immunological consequences would extend to a natural infection, we studied mice infected with the parasitic helminth Trichinella spiralis. The course of the infection was similar in A- and A-sufficient (A+) mice. These mice did not differ with respect to newborn larvae/female/hour produced in the intestine, or muscle larvae burden 5 wk postinfection. They also did not differ in the intestinal worm expulsion rate until day 15, when A- mice still harbored parasites, whereas A+ mice had cleared intestinal worms. Vitamin A deficiency reduced both the frequency of B lymphocytes secreting IgG1 antibodies to parasite antigens, and the bone marrow eosinophilia associated with helminth infection. The cytokine secretion patterns in infected mice were consistent with these observations and with previous studies. Mesenteric lymph node cells from infected A- mice secreted significantly more IFN-gamma, and significantly less IL-2, IL-4, and IL-5 than infected A+ controls. A- splenocytes secreted significantly more IFN-gamma, and equivalent amounts of IL-2, IL-4, and IL-5 compared with A+ controls. Interestingly, CD4-CD8- cells secreted the majority of the IL-4 produced in the spleen. The IL-2, IL-4, and IL-5 steady-state transcript levels correlated with secreted protein levels, but IFN-gamma transcripts did not. Although they secreted more protein, A- cells contained fewer IFN-gamma transcripts than A+ cells. These results suggest two vitamin A-mediated regulation steps in IFN-gamma gene expression: positive regulation of IFN-gamma transcript levels, and negative regulation posttranscriptionally. The essentially unaltered outcome of T. spiralis infection in vitamin A-deficient mice probably reflects a balance between cellular and humoral responses. The IFN-gamma overproduction might have a positive effect on the gut inflammatory response, but the decrease eosinophilia, cytokine production in mesenteric lymph node, and IgG1-secreting cell frequency might have a negative effect on T. spiralis immunity.
The Processing of Holliday Junctions by BLM and WRN Helicases Is Regulated by p53 (2002)

BLM, WRN, and p53 are involved in the homologous DNA recombination pathway. The DNA structure-specific helicases, BLM and WRN, unwind Holliday junctions (HJ), an activity that could suppress inappropriate homologous recombination during DNA replication. Here, we show that purified, recombinant p53 binds to BLM and WRN helicases and attenuates their ability to unwind synthetic HJ in vitro. The p53 248W mutant reduces abilities of both to bind HJ and inhibit helicase activities, whereas the p53 273H mutant loses these abilities. Moreover, full-length p53 and a C-terminal polypeptide (residues 373-383) inhibit the BLM and WRN helicase activities, but phosphorylation at Ser(376) or Ser(378) completely abolishes this inhibition. Following blockage of DNA replication, Ser(15) phospho-p53, BLM, and RAD51 colocalize in nuclear foci at sites likely to contain DNA replication intermediates in cells. Our results are consistent with a novel mechanism for p53-mediated regulation of DNA recombinational repair that involves p53 post-translational modifications and functional protein-protein interactions with BLM and WRN DNA helicases.
Linguistic Reflections of Student Engagement in Massive Open Online Courses (2014)

While data from Massive Open Online Courses (MOOCs) offers the potential to gain new insights into the ways in which online communities can contribute to student learning, much of the richness of the data trace is still yet to be mined. In particular, very little work has attempted fine-grained content analyses of the student interactions in MOOCs. Survey research indicates the importance of student goals and intentions in keeping them involved in a MOOC over time. Automated fine-grained content analyses offer the potential to detect and monitor evidence of student engagement and how it relates to other aspects of their behavior. Ultimately these indicators reflect their commitment to remaining in the course. As a methodological contribution, in this paper we investigate using computational linguistic models to measure learner motivation and cognitive engagement from the text of forum posts. We validate our techniques using survival models that evaluate the predictive validity of these variables in connection with attrition over time. We conduct this evaluation in three MOOCs focusing on very different types of learning materials. Prior work demonstrates that participation in the discussion forums at all is a strong indicator of student commitment. Our methodology allows us to differentiate better among these students, and to identify danger signs that a struggling student is in need of support within a population whose interaction with the course offers the opportunity for effective support to be administered. Theoretical and practical implications will be discussed.
Chemically stable ionic viologen-organic network: an efficient scavenger of toxic oxo-anions from water (2018)

Detoxification of water has been demonstrated with a viologen-based cationic organic network (compound-<b>1</b>), which was stable not only in water, but also in acidic and basic media. The presence of free exchangeable Cl<sup>-</sup> ions inside the network of compound-<b>1</b> and a high physiochemical stability of the materials offered a suitable scope for the capture of hazardous anionic pollutants from water. Rapid removal of the toxic water pollutant and carcinogenic chromate (CrO<sub>4</sub> <sup>2-</sup>) from water was shown with compound-<b>1</b>. Furthermore, the oxo-anion of the radioactive isotope of technetium (<sup>99</sup>Tc), <i>i.e.</i> the TcO<sub>4</sub> <sup>-</sup> ion, also counts as a toxic water pollutant and by using surrogate anions (MnO<sub>4</sub> <sup>-</sup> and ReO<sub>4</sub> <sup>-</sup>), a model capture study was performed. Notably, compound-<b>1</b> showed high capacity values for each of the oxo-anions and these were comparable to some of the well-performing compounds reported in the literature. Furthermore, to check the real time aspect, removal of all of the aforementioned anions from water was demonstrated, even in the presence of other concurrent anions.