gebhart/patrepeval huggingface dataset:
Suppression of macrophage oxidative metabolism by products of malignant and nonmalignant cells. (1982)

Each of 11 tumors tested produced a factor that markedly suppressed the ability of macrophages to release H2O2 or O.2- in response to phorbol myristate acetate or zymosan. Four of seven normal cell types produced a similar activity, which was 3.5-7 times lower in titer than that in tumor cell-conditioned medium (TCM), and which was much more rapidly reversible in its effects. TCM caused 50% inhibition of H2O2 release when it was present in the medium for 48 h at a concentration of 13%, or when 100% TCM was present in the medium for 18 h. The H2O2-releasing capacity of macrophages incubated in TCM only returned to control levels by 6 d after its removal. TCM prevented augmentation of H2O2-releasing capacity by lymphokines. The titer of suppressive activity in TCM depended on both the concentration of tumor cells and the duration of their incubation. TCM did not augment the activity of catalase, myeloperoxidase, glutathione peroxidase, or glutathione reductase or the content of glutathione within macrophages, suggesting that decreased synthesis rather than increased catabolism was responsible for reduced secretion of H2O2. Suppression of the release of H2O2 or O.2- by TCM appeared to be a relatively specific effect, in that TCM increased macrophage spreading and adherence to glass while exerting little influence on rates of phagocytosis, synthesis of protein, or secretion of lysozyme, plasminogen activator, or arachidonic acid and its metabolites. Thus, tumor cells and some normal cells can secrete a factor that selectively deactivates macrophage oxidative metabolism.
Ferrofluids and Magnetorheological Fluids (2008)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Protein kinase C: poised to signal (2009)

Nestled at the tip of a branch of the kinome, protein kinase C (PKC) family members are poised to transduce signals emanating from the cell surface. Cell membranes provide the platform for PKC function, supporting the maturation of PKC through phosphorylation, its allosteric activation by binding specific lipids, and, ultimately, promoting the downregulation of the enzyme. These regulatory mechanisms precisely control the level of signaling-competent PKC in the cell. Disruption of this regulation results in pathophysiological states, most notably cancer, where PKC levels are often grossly altered. This review introduces the PKC family and then focuses on recent advances in understanding the cellular regulation of its diacylglycerol-regulated members.
Selectivity of nonsteroidal antiinflammatory drugs as inhibitors of constitutive and inducible cyclooxygenase. (1993)

Constitutive cyclooxygenase (COX-1; prostaglandin-endoperoxide synthase, EC 1.14.99.1) is present in cells under physiological conditions, whereas COX-2 is induced by some cytokines, mitogens, and endotoxin presumably in pathological conditions, such as inflammation. Therefore, we have assessed the relative inhibitory effects of some nonsteroidal antiinflammatory drugs on the activities of COX-1 (in bovine aortic endothelial cells) and COX-2 (in endotoxin-activated J774.2 macrophages) in intact cells, broken cells, and purified enzyme preparations (COX-1 in sheep seminal vesicles; COX-2 in sheep placenta). Similar potencies of aspirin, indomethacin, and ibuprofen against the broken cell and purified enzyme preparations indicated no influence of species. Aspirin, indomethacin, and ibuprofen were more potent inhibitors of COX-1 than COX-2 in all models used. The relative potencies of aspirin and indomethacin varied only slightly between models, although the IC50 values were different. Ibuprofen was more potent as an inhibitor of COX-2 in intact cells than in either broken cells or purified enzymes. Sodium salicylate was a weak inhibitor of both COX isoforms in intact cells and was inactive against COX in either broken cells or purified enzyme preparations. Diclofenac, BW 755C, acetaminophen, and naproxen were approximately equipotent inhibitors of COX-1 and COX-2 in intact cells. BF 389, an experimental drug currently being tested in humans, was the most potent and most selective inhibitor of COX-2 in intact cells. Thus, there are clear pharmacological differences between the two enzymes. The use of such models of COX-1 and COX-2 activity will lead to the identification of selective inhibitors of COX-2 with presumably less side effects than present therapies. Some inhibitors had higher activity in intact cells than against purified enzymes, suggesting that pure enzyme preparations may not be predictive of therapeutic action.
Experience with hystidine tryptophan ketoglutarate versus University Wisconsin preservation solutions in transplantation. (2004)

We present our experience with histidine tryptophan ketoglutarate (HTK) and University Wisconsin (UW) preservation solutions in liver transplantation and a review of the literature in pancreas and kidney transplantation comparing these solutions. A group of 134 liver transplantations in 123 recipients was analyzed retrospectively. Grafts procured in adults were perfused with HTK in 63 cases and with UW in 71 cases. We compared results according to preoperative, intraoperative, and postoperative parameters, as well as complications and survival. No differences regarding donor and recipient data, intraoperative fresh frozen plasma (FFP) substitution, length of intensive care unit (ICU) stay, and ischemic damage of the graft were found. The rate of complications was comparable in both groups. However, the bilirubin was higher in the UW group. The rate of biliary complications was higher in the UW group (n = 8) versus the HTK group (n = 5). HTK ischemic type biliary lesions (ITBL) were only present in the UW group. Patient and graft survival were statistically nonsignificant. The data confirm that HTK and UW, with exception of biliary complications, are considered comparable in clinical liver transplantation. The same conclusion can be taken from the literature analyzed concerning renal transplantation, and in smaller groups of pancreas transplants, similar results were published.
Structural Features and Molecular Evolution of Bowman-Birk Protease Inhibitors and their Potential Application (2005)

The Bowman-Birk inhibitors (BBIs) are well-studied serine protease inhibitors that are abundant in dicotyledonous and monocotyledonous plants. BBIs from dicots usually have a molecular weight of 8k and are double-headed with two reactive sites, whereas those from monocots can be divided into two classes, one approximately 8 kDa in size with one reactive site (another reactive site was lost) and the other approximately 16 kDa in size with two reactive sites. The reactive site is located at unique exposed surfaces formed by a disulfide-linked beta-sheet loop that is highly conserved, rigid and mostly composed of nine residues. The structural features and molecular evolution of inhibitors are described, focusing on the conserved disulfide bridges. The sunflower trypsin inhibitor-1 (SFTI-1), with 14 amino acid residues, is a recently discovered bicyclic inhibitor, and is the most small and potent naturally occurring Bowman-Birk inhibitor. Recently, BBIs have become a hot topic because of their potential applications. BBIs are now used for defense against pathogens and insects in transgenic plants, which has advantages over using toxic and polluting insecticides. BBIs could also be applied in the prevention of cancer, Dengue fever, and inflammatory and allergic disorders, because of their inhibitory activity with respect to the serine proteases that play a pivotal role in the development and pathogenesis of these diseases. The canonical nine-residue loop of BBIs/STFI-1 provides an ideal template for drug design of specific inhibitors to target their respective proteases.
On-the-fly progress detection in iterative stream queries (2009)

Multiple researchers have proposed cyclic query plans for evaluating iterative queries over streams or rapidly changing input. The Declarative Networking community uses cyclic plans to evaluate Datalog programs that track reachability and other graph traversals on networks. Cyclic query plans can also evaluate pattern-matching and other queries based on event sequences. An issue with cyclic queries over dynamic inputs is knowing when the query result has progressed to a certain point in the input, since the number of iterations is data dependent. One option is a "strictly staged" computation, where the query plan quiesces between inputs. This option introduces significant latency, and may also "underload" inter-operator buffers. An alternative is to settle for soft guarantees, such as "eventual consistency". Such imprecision can make it difficult, for example, to know when to purge state from stateful operators. We propose a third option in which cyclic queries run continuously, but detect progress "on the fly" by means of a Flying Fixed-Point (FFP) operator. FFP sits on the cyclic loop and circulates speculative predictions on forward progress, which it then validates. FFP is always able to track progress for a class of queries we term strongly convergent . A key advantage of FFP is that it works with existing algebra operators, thereby inheriting their capabilities, such as windowing and dealing with out-of-order input. Also, for stream systems that explicitly model input-event lifetimes, we know exactly which values are in the query result at each point in time. A key implementation decision is the method for speculating. Using the high-water mark of data events minimizes the number of speculative punctuations. Probing operators on the cyclic loop to determine their external progress circulates many more speculative messages, but tracks actual output progress more closely. We show how a hybrid approach limits predictions while coming close the progress-tracking ability of Probing.
Cytokine inhibitors in the treatment of rheumatoid arthritis (2002)

Rheumatoid arthritis (RA) is an immune-mediated disease characterised by articular inflammation and subsequent tissue damage leading to severe disability and increased mortality. A variety of cytokines are produced locally in the rheumatoid joints. Numerous studies have demonstrated that IL-1 and TNF-alpha, two prototypic pro-inflammatory cytokines, play an important role in the mechanisms involved in synovial inflammation and in progressive joint destruction. Indeed, the administration of TNF-alpha and IL-1 inhibitors in patients with RA led to a dramatic improvement of clinical and biological signs of inflammation and a reduction of radiological signs of bone erosion and cartilage destruction. However, despite these encouraging results, a significant percentage of patients do not respond to these agents, suggesting that other mediators are also involved in the pathophysiology of arthritis. This review describes the results of clinical trials with TNF-alpha inhibitors and a specific IL-1 inhibitor (IL-1 receptor antagonist [IL-1Ra]). In addition, other therapeutic strategies are also discussed.
A unified framework for analysis of individual-based models in ecology and beyond (2019)

Individual-based models, 'IBMs', describe naturally the dynamics of interacting organisms or social or financial agents. They are considered too complex for mathematical analysis, but computer simulations of them cannot give the general insights required. Here, we resolve this problem with a general mathematical framework for IBMs containing interactions of an unlimited level of complexity, and derive equations that reliably approximate the effects of space and stochasticity. We provide software, specified in an accessible and intuitive graphical way, so any researcher can obtain analytical and simulation results for any particular IBM without algebraic manipulation. We illustrate the framework with examples from movement ecology, conservation biology, and evolutionary ecology. This framework will provide unprecedented insights into a hitherto intractable panoply of complex models across many scientific fields.
Structure of the SOCS4-ElonginB/C Complex Reveals a Distinct SOCS Box Interface and the Molecular Basis for SOCS-Dependent EGFR Degradation (2007)

Tyrosine kinase signaling is tightly controlled by negative feedback inhibitors including suppressors of cytokine signaling (SOCS). SOCS assemble as SH2 domain substrate recognition modules in ElonginB/C-cullin ubiquitin ligases. In accordance, SOCS4 reduces STAT3 signaling from EGFR through increased receptor degradation. Variable C-termini in SOCS4-SOCS7 exclude these family members from a SOCS2-type domain arrangement in which a strictly conserved C terminus determines domain packing. The structure of the SOCS4-ElonginC-ElonginB complex reveals a distinct SOCS structural class. The N-terminal ESS helix functionally replaces the CIS/SOCS1-SOCS3 family C terminus in a distinct SH2-SOCS box interface that facilitates further interdomain packing between the extended N- and C-terminal regions characteristic for this subfamily. Using peptide arrays and calorimetry the STAT3 site in EGFR (pY(1092)) was identified as a high affinity SOCS4 substrate (K(D) = 0.5 microM) revealing a mechanism for EGFR degradation. SOCS4 also bound JAK2 and KIT with low micromolar affinity, whereas SOCS2 was specific for GH-receptor.
Neuron‐oligodendrocyte myelination co‐culture derived from embryonic rat spinal cord and cerebral cortex (2012)

An in vitro myelination model derived from rat central nervous system (CNS) remains to be established. Here, we describe a simple and reproducible myelination culture method using dissociated neuron-oligodendrocyte (OL) co-cultures from either the embryonic day 16 (E16) rat spinal cord or cerebral cortex. The dissociated cells are plated directly on poly-L-lysine-coated cover slips and maintained in a modified myelination medium that supports both OL and neuron differentiation. The spinal cord derived OL progenitor cells develop quickly into myelin basic protein (MBP)+ mature OLs and start to myelinate axons around 17 days in vitro (DIV17). Myelination reaches its peak around six weeks (DIV40) and the typical nodes of Ranvier are revealed by paranodal proteins Caspr and juxaparanodal protein Kv1.2 immunoreactivity. Electron microscopy (EM) shows typical myelination cytoarchitecture and synaptic organization. In contrast, the cortical-derived co-culture requires triiodothyronine (T3) in the culture medium for myelination. Finally, either hypomyelination and/or demyelination can be induced by exposing proinflammatory cytokines or demyelinating agents to the co-culture, suggesting the feasibility of this modified in vitro myelination model for myelin-deficit investigation.
Early left ventricular gene expression profile in response to increase in blood pressure (2006)

The heart adapts to increased pressure overload by hypertrophic growth of terminally differentiated cardiomyocytes. At the genetic level, the hypertrophic response is characterized by the reprogramming of gene expression, i.e. upregulation of immediate early genes, natriuretic peptide genes and genes encoding structural proteins. In the present study, we characterized the early changes in gene expression with cDNA expression arrays in response to increase in blood pressure produced by arginine8-vasopressin infusion (0.05 microg/kg/min, i.v.) for 30 min and 4 h in conscious normotensive rats. Expression profiling revealed differential expression of 14 genes in the left ventricle, and several novel factors of immediate early genetic response to pressure overload were identified, such as growth arrest and DNA damage inducible protein 45 (GADD45alpha), epidermal fatty acid-binding protein (E-FABP) and Bcl-X. Administration of angiotensin II (Ang II) for 6 h by osmotic minipumps also increased left ventricular GADD45alpha, E-FABP and Bcl-X gene expression. Furthermore, the induction of GADD45alpha and Bcl-X gene expression by Ang II was blocked by angiotensin II type 1 receptor antagonist losartan. In summary, our analysis provided new insights into the pathogenesis of pressure overload-induced hypertrophy by suggesting the existence of novel regulators of the immediate early gene expression program.
High-flow, small-hole arteriovenous fistulas: treatment with electrodetachable coils. (1995)

We present one case of carotid-cavernous fistula caused by percutaneous treatment of trigeminal neuralgia and one case of vertebrovertebral fistula caused by percutaneous internal jugular vein cannulation. Each fistula had a small arteriovenous communication that prevented the use of detachable balloons. Endovascular transarterial treatment of these two iatrogenic fistulas with electrically detachable platinum coils was performed. Both fistulas were occluded with preservation of the parent artery, and the patients have fully recovered.
The Effects of Therapeutic Ultrasound on Tendon Healing (1989)

The effect of 1 MHz therapeutic ultrasound on the healing strength of tendons was studied in the tenotomized, repaired and immobilized right Achilles tendons of 26 rabbits. Twelve tendons were sonicated daily in continuous waves at a spatial averaged intensity of 1 W cm(2) [corrected] for 5 min. After nine consecutive treatments, the tendons were excised under anesthesia and compared biomechanically. Exposure to ultrasound induced a significant increase in both the tensile strength and the energy absorption capacity of the tendons. Although healing in rabbits may not translate directly to healing in humans, these findings suggest that surgically repaired human Achilles tendons may heal faster if ultrasound is applied during the early stages of healing.
Ligand Depot: a data warehouse for ligands bound to macromolecules (2004)

Ligand Depot is available at http://ligand-depot.rutgers.edu/. Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux.
FimH Antagonists for the Oral Treatment of Urinary Tract Infections: From Design and Synthesis to in Vitro and in Vivo Evaluation (2010)

Urinary tract infection (UTI) by uropathogenic Escherichia coli (UPEC) is one of the most common infections, particularly affecting women. The interaction of FimH, a lectin located at the tip of bacterial pili, with high mannose structures is critical for the ability of UPEC to colonize and invade the bladder epithelium. We describe the synthesis and the in vitro/in vivo evaluation of α-D-mannosides with the ability to block the bacteria/host cell interaction. According to the pharmacokinetic properties, a prodrug approach for their evaluation in the UTI mouse model was explored. As a result, an orally available, low molecular weight FimH antagonist was identified with the potential to reduce the colony forming units (CFU) in the urine by 2 orders of magnitude and in the bladder by 4 orders of magnitude. With FimH antagonist, the great potential for the effective treatment of urinary tract infections with a new class of orally available antiinfectives could be demonstrated.
Sampling density compensation in MRI: Rationale and an iterative numerical solution (1999)

Data collection of MRI which is sampled nonuniformly in k-space is often interpolated onto a Cartesian grid for fast reconstruction. The collected data must be properly weighted before interpolation, for accurate reconstruction. We propose a criterion for choosing the weighting function necessary to compensate for nonuniform sampling density. A numerical iterative method to find a weighting function that meets that criterion is also given. This method uses only the coordinates of the sampled data; unlike previous methods, it does not require knowledge of the trajectories and can easily handle trajectories that "cross" in k-space. Moreover, the method can handle sampling patterns that are undersampled in some regions of k-space and does not require a post-gridding density correction. Weighting functions for various data collection strategies are shown. Synthesized and collected in vivo data also illustrate aspects of this method.
Spliceosome integrity is defective in the motor neuron diseases ALS and SMA (2012)

Two motor neuron diseases, amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA), are caused by distinct genes involved in RNA metabolism, TDP-43 and FUS/TLS, and SMN, respectively. However, whether there is a shared defective mechanism in RNA metabolism common to these two diseases remains unclear. Here, we show that TDP-43 and FUS/TLS localize in nuclear Gems through an association with SMN, and that all three proteins function in spliceosome maintenance. We also show that in ALS, Gems are lost, U snRNA levels are up-regulated and spliceosomal U snRNPs abnormally and extensively accumulate in motor neuron nuclei, but not in the temporal lobe of FTLD with TDP-43 pathology. This aberrant accumulation of U snRNAs in ALS motor neurons is in direct contrast to SMA motor neurons, which show reduced amounts of U snRNAs, while both have defects in the spliceosome. These findings indicate that a profound loss of spliceosome integrity is a critical mechanism common to neurodegeneration in ALS and SMA, and may explain cell-type specific vulnerability of motor neurons.
Adaptive quantization of image subbands with efficient overhead rate selection (2002)

Subband image coding techniques owe much of their success to an effective use of adaptive quantization and adaptive entropy coding. It is often the case that adaptive quantization is achieved by defining a discrete set of quantizers from which one is chosen for a given set of coefficients. This type of forward adaptation thus requires that overhead information (the choice of quantizer) be sent to the decoder. Then, the quantized coefficients are transmitted using adaptive entropy coding, typically through backward adaptive arithmetic coding. We show that a combination of forward and backward adaptation methods can be used to update the quantizers thus reducing the overhead requirements while still providing good performance. Specifically, we present an algorithm where each coefficient is classified into several classes based on the past quantized data and where the quantizer to be used for each class can itself be adapted on the fly.
Gametes from Embryonic Stem Cells: A Cup Half Empty or Half Full? (2007)

When first reported 4 years ago, gametogenesis from embryonic stem (ES) cells promised an accessible in vitro model to facilitate molecular analysis of the germ lineage. Formation of primordial germ cells is robust, but terminal gametogenesis remains inefficient and doubts about gamete function persist. Although useful for research, clinical use of ES cell-derived gametes appears a distant prospect.