gebhart/patrepeval huggingface dataset:
Calibrated Forceps Model of Spinal Cord Compression Injury (2015)

Compression injuries of the murine spinal cord are valuable animal models for the study of spinal cord injury (SCI) and spinal regenerative therapy. The calibrated forceps model of compression injury is a convenient, low cost, and very reproducible animal model for SCI. We used a pair of modified forceps in accordance with the method published by Plemel et al. (2008) to laterally compress the spinal cord to a distance of 0.35 mm. In this video, we will demonstrate a dorsal laminectomy to expose the spinal cord, followed by compression of the spinal cord with the modified forceps. In the video, we will also address issues related to the care of paraplegic laboratory animals. This injury model produces mice that exhibit impairment in sensation, as well as impaired hindlimb locomotor function. Furthermore, this method of injury produces consistent aberrations in the pathology of the SCI, as determined by immunohistochemical methods. After watching this video, viewers should be able to determine the necessary supplies and methods for producing SCI of various severities in the mouse for studies on SCI and/or treatments designed to mitigate impairment after injury.
Solvation and complex formation in strongly solvating solvents (1986)

Abstract
The Basis for Amine Hypotheses in Affective Disorders (1975)

A leading hypothesis concerning a biological basis of the affective disorders is that altered metabolism of brain amines may underlie the cause or pathophysiology of these conditions. Features of affective illnesses supporting biological hypotheses include the somatic symptoms, diurnal rhythm, and apparent "endogenicity" of many severe depressions, and evidence of a genetic basis of manic-depressive illness. Development and preclinical study of medical therapies for the disorders substantially supported a relationship between mood-disturbances and neutrotransmitters and stimulated considerable advances in the physiology and pharmacology of central synaptic neurotransmission. Unfortunately, studies of amine metabolism in patients have not provided consistent support for the amine hypotheses. Moreover, these hypotheses have not led to a coherent biological theory of abnormal behavior, to an objective basis for differential diagnosis, or to the rational development of treatments more effective or safer than those known.
Uszkodzenie płuc związane z wentylacją mechaniczną (2013)

Mechanical ventilation of disease-affected lungs, as well as being an inadequate mode of ventilation for initially healthy lungs, can cause significant changes in their structure and function. In order to differentiate these processes, two terms are used: ventilator-associated lung injury (VALI) and ventilator-induced lung injury (VILI). In both cases, lung injury primarily results from differences in transpulmonary pressure - a consequence of an imbalance between lung stress and strain. This paper focuses on changes in lung structure and function due to this imbalance. Moreover, in this context, barotrauma, volutrauma and atelectrauma are interpreted, and the importance of signal transduction as a process inducing local and systemic inflammatory responses (biotrauma), is determined. None of the assessed methods of reducing VALI and VILI has been found to be entirely satisfactory, yet studies evaluating oscillatory ventilation, liquid ventilation, early ECMO, super-protective ventilation or noisy ventilation and administration of certain drugs are under way. Low tidal volume ventilation and adequately adjusted PEEP appear to be the best preventive measures of mechanical ventilation in any setting, including the operating theatre. Furthermore, this paper highlights the advances in VILI/VALI prevention resulting from better understanding of pathophysiological phenomena.
Narrow band region-based active contours and surfaces for 2D and 3D segmentation (2014)

We describe a narrow band region approach for deformable curves and surfaces in the perspective of 2D and 3D image segmentation. Basically, we develop a region energy involving a fixed-width band around the curve or surface. Classical region-based methods, like the Chan-Vese model, often make strong assumptions on the intensity distributions of the searched object and background. In order to be less restrictive, our energy achieves a trade-off between local features of gradient-like terms and global region features. Relying on the theory of parallel curves and surfaces, we perform a mathematical derivation to express the region energy in a curvature-based form allowing efficient computation on explicit models. We introduce two different region terms, each one being dedicated to a particular configuration of the target object. Evolution of deformable models is performed by means of energy minimization using gradient descent. We provide both explicit and implicit implementations. The explicit models are a parametric snake in 2D and a triangular mesh in 3D, whereas the implicit models are based on the level set framework, regardless of the dimension. Experiments are carried out on MRI and CT medical images, in 2D and 3D, as well as 2D color photographs.
Transforming Growth Factor β Activates Smad2 in the Absence of Receptor Endocytosis (2002)

Like many other cell surface receptors, transforming growth factor beta (TGF-beta) receptors are internalized upon ligand stimulation. Given that the signaling-facilitating molecules Smad anchor for receptor activation (SARA) and Hrs are mainly localized in early endosomes, it was unclear whether receptor internalization is required for Smad2 activation. Using reversible biotin labeling, we directly monitored internalization of the TGF-beta type I receptor. Our data indicate that TGF-beta type I receptor is endocytosed via a clathrin-dependent mechanism and is effectively blocked by depletion of intracellular potassium or by expression of a mutant dynamin (K44A). However, blockage of receptor endocytosis by these two means has no effect on TGF-beta-mediated Smad2 activation. Furthermore, TGF-beta-induced Smad2 activation was unaffected by inhibition of hVPS34 activity with wortmannin or inhibitory anti-hVPS34 antibodies. Finally, we demonstrated that Smad2 interacted with cell surface receptors and that a SARA binding-deficient Smad2 mutant was phosphorylated by the receptors. Thus, our findings suggest that receptor endocytosis is dispersible for TGF-beta-mediated activation of Smad2 and that this activation can be mediated by both SARA-dependent and -independent mechanisms.
Multiple description video multicast in wireless ad hoc networks (2004)

We consider the problem of multicasting multiple description (MD) video in wireless ad hoc networks. We follow an application-centric, cross-layer approach with the objective of minimizing video distortion. The contribution of this paper is twofold. First, we propose a practical MD video multicast scheme that uses multiple trees to achieve an improved error resilience performance. The proposed scheme also takes into account highly diverse wireless link bandwidths by using scalable coding for each description, thus further improving the overall video quality. Second, we formulate the optimized multicast routing as a combinatorial optimization problem and propose an efficient genetic algorithm (GA)-based metaheuristic solution procedure. Performance comparison with existing approaches show significant gains for a wide range of network operating conditions.
Determination of citric acid in fruit juices using HPLC (2012)

A naturally occurring acid found in many fruit juices, citric acid was quantified using external standards and high-performance liquid chromatography (HPLC). Eight orange juice samples were analyzed ranging in concentrations from 36.0 to 427 mg/oz of citric acid. The California navel orange had the highest citric acid concentration, followed by the 100% orange juices, the orange flavored juices, and with the lowest concentration, Nestle’s Juicy Juice, the 100% mixed fruit juice.
The meiotic competence of in-vitro matured human oocytes is influenced by donor age: evidence that folliculogenesis is compromised in the reproductively aged ovary (1998)

The human oocyte appears to be particularly prone to meiotic errors, and the incidence of these errors is strongly influenced by maternal age. We have initiated studies of human oocytes from unstimulated ovaries and have observed age-related effects on the meiotic process in oocytes from unselected antral follicles. Specifically, in oocytes obtained from donors over the age of 35 years, the majority of oocytes that extruded a first polar body in culture and arrested at second meiotic metaphase had aberrations in spindle formation and chromosome alignment. Similarly, observations of a limited number of oocytes at first meiotic metaphase suggest disturbances at this stage of meiosis as well. Finally, preliminary results of non-disjunction studies suggest that the frequency of errors in chromosome segregation at the first meiotic division is influenced by donor age in in-vitro matured oocytes as it is in oocytes undergoing meiotic maturation in vivo. These data provide direct evidence that the meiotic competence of oocytes from unstimulated ovaries declines with donor age. Similarly, studies of in-vitro fertilization (IVF) pregnancies in older women indicate that the developmental competence of the human oocyte declines with age. Since both meiotic and developmental competence are acquired during the late stages of oocyte growth, we postulate that an age-related decline in the process of folliculogenesis results in reduced oocyte quality and that the well characterized age-related increase in meiotic non-disjunction is one symptom of compromised oocyte growth.
Dityrosine Formation in Calmodulin:  Cross-Linking and Polymerization Catalyzed by <i>Arthromyces</i> Peroxidase (1996)

We employ bovine brain calmodulin, a protein that is subject to photoactivated dityrosine formation [Malencik, D. A., & Anderson, S. R. (1987) Biochemistry 26, 695; (1994) Biochemistry 33, 13363], as a model for the development of an efficient enzyme-catalyzed protein cross-linking technique. Key steps in the elaboration of the procedure are (1) identification of a peroxidase, from Arthromyces ramosus, that catalyzes dityrosine production in proteins that are not acted on by other common peroxidases, (2) monitoring of the intrinsic fluorescence of dityrosine to determine optimum reaction conditions, achieved with calmodulin in solutions containing boric acid-sodium borate (concentration > or = 0.2 M), approximately pH 8.3, approximately 40 degrees C, and (3) quenching of the reaction with reduced glutathione. Arthromyces peroxidase is the only common peroxidase able to catalyze significant dityrosine production in calmodulin, through a reaction that is largely intermolecular. Gel filtration yields fractions (accounting for approximately 40% of the initial calmodulin) that represent differing mobility ranges in NaDodSO4 polyacrylamide gel electrophoresis and contain close to the maximum possible amounts of dityrosine. The various fractions undergo Ca2+-dependent conformational changes detected in sedimentation velocity and/or fluorescence anisotropy measurements. Most of the samples stimulate the Ca2+-dependent activity of smooth muscle myosin light chain kinase. In catalytic assays utilizing the synthetic phosphatic acceptor peptide, the average activities range from 50 to 100% of that determined for native calmodulin. However, only the least polymerized fraction and the photogenerated calmodulin dimers significantly enhance the p-nitrophenylphosphatase activity of calcineurin. The ability to prepare soluble calmodulin polymers that retain a substantial degree of biological activity and exhibit the intense visible fluorescence of dityrosine illustrates the potential usefulness of Arthromyces peroxidase in the zero-length cross-linking of proteins.
Metabolite Profiling of <i>Cheonggukjang</i>, a Fermented Soybean Paste, Inoculated with Various <i>Bacillus</i> Strains during Fermentation (2010)

Metabolite profiling of Cheonggukjang inoculated with different Bacillus strains including Bacillus amyloliqueciens CH86-1, Bacillus licheniformis 58, and Bacillus licheniformis 67 during fermentation, was performed using gas chromatography-time of flight-mass spectrometry after derivatization, combined with multivariate statistical analysis. A total of 20 amino acids, 10 sugars, five sugar alcohols, and seven organic acids were identified in three Cheonggukjang samples. With fermentation time, most of the amino acids showed increasing amounts. On the other hand, most of the sugars including sucrose, fructose, and glucose decreasing patterns, and the amounts of organic acids varied. In order to observe differences in metabolites with fermentation time and inoculated Bacillus strains, principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were carried out, respectively. On PCA plots, some sugars and organic acids including sucrose, fructose, glucose, mannose, succinic acid, and malonic acid, as well as most of the amino acids, contributed mainly to differentiation of the Cheonggukjang samples fermentation time. On the other hand, on PLS-DA, mannose, xylose, glutamic acid, and proline were mainly responsible for differentiating the Cheonggukjang among into various inoculated strains.
KAP1 regulates gene networks controlling mouse B-lymphoid cell differentiation and function (2012)

Chromatin remodeling is fundamental for B-cell differentiation. In the present study, we explored the role of KAP1, the cofactor of KRAB-ZFP transcriptional repressors, in this process. B-lymphoid-specific Kap1-KO mice displayed reduced numbers of mature B cells, lower steady-state levels of Abs, and accelerated rates of decay of neutralizing Abs after viral immunization. Transcriptome analyses of Kap1-deleted B splenocytes revealed an up-regulation of PTEN, the enzymatic counteractor of PIK3 signaling, and of genes encoding DNA-damage response factors, cell-cycle regulators, and chemokine receptors. ChIP/seq studies established that KAP1 bound at or close to several of these genes and controlled chromatin status at their promoters. Genome wide, KAP1 binding sites lacked active B cell-specific enhancers and were enriched in repressive histone marks, further supporting a role for this molecule in gene silencing in vivo. Likely responsible for tethering KAP1 to at least some of these targets, a discrete subset of KRAB-ZFPs is enriched in B lymphocytes. Our results therefore reveal the role of KRAB/KAP1-mediated epigenetic regulation in B-cell development and homeostasis.
A Novel Class of Somatic Small RNAs Similar to Germ Cell Pachytene PIWI-interacting Small RNAs (2014)

PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that bind PIWI family proteins exclusively expressed in the germ cells of mammalian gonads. MIWI2-associated piRNAs are essential for silencing transposons during primordial germ cell development, and MIWI-bound piRNAs are required for normal spermatogenesis during adulthood in mice. Although piRNAs have long been regarded as germ cell-specific, increasing lines of evidence suggest that somatic cells also express piRNA-like RNAs (pilRNAs). Here, we report the detection of abundant pilRNAs in somatic cells, which are similar to MIWI-associated piRNAs mainly expressed in pachytene spermatocytes and round spermatids in the testis. Based on small RNA deep sequencing and quantitative PCR analyses, pilRNA expression is dynamic and displays tissue specificity. Although pilRNAs are similar to pachytene piRNAs in both size and genomic origins, they have a distinct ping-pong signature. Furthermore, pilRNA biogenesis appears to utilize a yet to be identified pathway, which is different from all currently known small RNA biogenetic pathways. In addition, pilRNAs appear to preferentially target the 3'-UTRs of mRNAs in a partially complementary manner. Our data suggest that pilRNAs, as an integral component of the small RNA transcriptome in somatic cell lineages, represent a distinct population of small RNAs that may have functions similar to germ cell piRNAs.
The Tumor Microenvironment: A Pitch for Multiple Players (2013)

The cancer microenvironment may be conceptually regarded as a pitch where the main players are resident and non-resident cellular components, each covering a defined role and interconnected by a complex network of soluble mediators. The crosstalk between these cells and the tumor cells within this environment crucially determines the fate of tumor progression. Immune cells that infiltrate the tumor bed are transported there by blood circulation and exert a variety of effects, either counteracting or favoring tumor outgrowth. Here, we review and discuss the multiple populations composing the tumor bed, with special focus on immune cells subsets that positively or negatively dictate neoplastic progression. In this scenario, the contribution of cancer stem cells within the tumor microenvironment will also be discussed. Finally, we illustrate recent advances on new integrated approaches to investigate the tumor microenvironment in vitro.
Stimulation of angiotensinogen production in primary cultures of rat hepatocytes by glucocorticoid, cyclic adenosine 3',5'-monophosphate, and interleukin-6. (1992)

The effects of hormones and cytokines on angiotensinogen production were studied in primary cultured rat hepatocytes. The basal secretion of angiotensinogen decreased during culture. The addition of dexamethasone and (Bu)2cAMP completely prevented this decrease. Angiotensinogen secretion by freshly plated hepatocytes was slightly increased in response to dexamethasone, but after 24 h in culture, hepatocytes no longer responded to dexamethasone alone. When hepatocytes were treated with (Bu)2cAMP, glucagon, or forskolin, angiotensinogen secretion increased in response to dexamethasone in a concentration-dependent manner. 17 beta-Estradiol and T3 failed to stimulate angiotensinogen secretion in either the presence or absence of (Bu)2cAMP. Interleukin-6 (IL-6) exhibited a stimulatory activity on angiotensinogen secretion, which was dependent on the presence of dexamethasone, whereas IL-1 and tumor necrosis factor had no effect in either the presence or absence of dexamethasone and/or (Bu)2cAMP. Unlike primary cultured hepatocytes, angiotensinogen secretion by rat hepatoma H4IIEC3 cells increased in response to dexamethasone alone. This increase was not enhanced by (Bu)2cAMP, but was enhanced by IL-6. Thus, in primary cultures of rat hepatocytes, neither glucocorticoid, cAMP, nor IL-6 alone stimulated angiotensinogen production, but a combination of glucocorticoid and cAMP or of glucocorticoid and IL-6 exhibited a stimulatory activity on angiotensinogen production. These results suggest that angiotensinogen production in the liver is synergistically regulated by these factors, whereas the hepatoma cell line H4IIEC3 lacks the regulatory mechanism of cAMP on glucocorticoid-induced angiotensinogen production.
Resting Microglia Directly Monitor the Functional State of Synapses<i>In Vivo</i>and Determine the Fate of Ischemic Terminals (2009)

Recent studies have identified the important contribution of glial cells to the plasticity of neuronal circuits. Resting microglia, the primary immune effector cells in the brain, dynamically extend and retract their processes as if actively surveying the microenvironment. However, just what is being sampled by these resting microglial processes has not been demonstrated in vivo, and the nature and function of any interactions between microglia and neuronal circuits is incompletely understood. Using in vivo two-photon imaging of fluorescent-labeled neurons and microglia, we demonstrate that the resting microglial processes make brief (approximately 5 min) and direct contacts with neuronal synapses at a frequency of about once per hour. These contacts are activity-dependent, being reduced in frequency by reductions in neuronal activity. After transient cerebral ischemia, the duration of these microglia-synapse contacts are markedly prolonged (approximately 1 h) and are frequently followed by the disappearance of the presynaptic bouton. Our results demonstrate that at least part of the dynamic motility of resting microglial processes in vivo is directed toward synapses and propose that microglia vigilantly monitor and respond to the functional status of synapses. Furthermore, the striking finding that some synapses in the ischemic areas disappear after prolonged microglial contact suggests microglia contribute to the subsequent increased turnover of synaptic connections. Further understanding of the mechanisms involved in the microglial detection of the functional state of synapses, and of their role in remodeling neuronal circuits disrupted by ischemia, may lead to novel therapies for treating brain injury that target microglia.
Subassembly identification and motion generation for assembly: a geometric approach (2002)

A method for automated generation of an assembly procedure for a given assembly is presented. The procedure is generated from the parts geometry and topology model, and thus explicit specification of mating relations between parts is not required. The approach also prevents wrong mating relations from being presented and makes checking for validity unnecessary. The geometric considerations in the generation of the assembly sequence make it possible to evaluate assembly performance directly and to easily generate detailed assembly plans, such as grasping, transferring, and manipulation, based on the given geometry of the assembly. Algorithms are presented for finding a collision-free path for disassembly motions. The efficiency and feasibility of the algorithms is demonstrated through a case study
TraffickStop: Detecting and Measuring Illicit Traffic Monetization Through Large-Scale DNS Analysis (2019)

Illicit traffic monetization is a type of Internet fraud that hijacks users' web requests and reroutes them to a traffic network (e.g., advertising network), in order to unethically gain monetary rewards. Despite its popularity among Internet fraudsters, our understanding of the problem is still limited. Since the behavior is highly dynamic (can happen at any place including client-side, transport-layer and server-side) and selective (could target a regional network), prior approaches like active probing can only reveal a small piece of the entire ecosystem. So far, questions including how this fraud works at a global scale and what fraudsters' preferred methods are, still remain unanswered. To fill the missing pieces, we developed TraffickStop the first system that can detect this fraud passively. Our key contribution is a novel algorithm that works on large-scale DNS logs and efficiently discovers abnormal domain correlations. TraffickStop enables the first landscape study of this fraud, and we have some interesting findings. By analyzing over 231 billion DNS logs of two weeks, we discovered 1,457 fraud sites. Regarding its scale, the fraud sites receive more than 53 billion DNS requests within one year, and a company could lose up to 53K dollars per day due to fraud traffic. We also discovered two new strategies that are leveraged by fraudsters to evade inspection. Our work provides new insights into illicit traffic monetization, raises its public awareness, and contributes to a better understanding and ultimate elimination of this threat.
High Voltage Low On-Resistance VDMOS FET (1982)

Recent theoretical analyses on MOS FETs revealed that most of the on-resistance came from the epi-layer so that thin and low resistivity epi-layer was desirable for low on-resistance. This paper presents a new junction termination technology suitable for achieving near ideal breakdown voltage for such low resistance epi-layer. This paper also describes design optimization of source pattern and impurity diffusion profile with aid of a two dimensional numerical model. On the basis of these techniques, a power MOS FET with 450 V sustaining voltage and 0.35 Ω on-resistance was realized at a high manufacturing yield.