gebhart/patrepeval huggingface dataset:
Management of Severe Abdominal Infections (2009)

Abdominal infections are associated with significant morbidity and mortality. Nearly all bacteria causing abdominal infections are derived from the endogenous flora of the alimentary tract. The resulting infection is typically polymicrobial and comprised of both aerobic and anaerobic microbes. They can be classified by their severity as uncomplicated and complicated or by their origin as community or hospital acquired. Escherichia coli and Bacteroides fragilis are the most frequently isolated bacteria in community-acquired abdominal infections. Nosocomial infections typically involve a more resistant flora (e.g. Pseudomonas spp., Acinetobacter spp., Gram-negative bacilli producing extended-spectrum β-lactamases [ESBL], vancomycin-resistant enterococci [VRE] and methicillin-resistant Staphylococcus aureus [MRSA]). Antimicrobial therapy should be guided by microbiological testing and frequently requires other interventions as well. In uncomplicated infections antimicrobial prophylaxis for < 24h may be considered. Patients with underlying or acquired immunodeficiency, i.e. organ transplant recipients and other patients on complex immunosuppressant regimens require special attention and antimicrobial coverage. We discuss the relevant microbiota, a rational diagnostic and therapeutic approach including strategies to handle challenging infections. The application of novel compounds and/or drug classes for abdominal infections such as glycylcyclines (i.e. tigecycline), glycopeptides (i.e. dalbavancin, telavancin, oritavancin), carbapenems (i.e. doripenem), and forth generation cephalosporins (i.e. ceftaroline, ceftobiprole) as well as patents on metalloproteinase and caspase inhibitors, interleukin antagonists, fusion proteins and nitric oxide donators is critically reviewed. The information is summarized in flow charts and algorithms for use in daily clinical practice and the review article also shows the useful information of the patents for the treatment of abdominal infections. Keywords: Abdominal infections, anaerobic microbes, Escherichia coli, Bacteroides fragilis, Antimicrobial therapy
GAD Autoantibody Affinity in Adult Patients With Latent Autoimmune Diabetes, the Study Participants of a GAD65 Vaccination Trial (2014)

Intervention with GAD-alum in LADA patients had no effect on GADA affinity. Our data suggest that patients with low GADA affinity have a prolonged preservation of residual β-cell function.
Expression of cutaneous lymphocyte-associated antigen on human CD4+ and CD8+ Th2 cells (2000)

The cutaneous lymphocyte-associated antigen (CLA) represents the homing receptor involved in selective migration of memory/effector T cells to the skin. Numerous reports demonstrated distinct CLA expression on Th1 cells. However, T cells isolated from skin lesions and CLA(+) T cells circulating in peripheral blood of atopic dermatitis patients expressed high IL-5 and IL-13. Accordingly, we investigated the regulation of CLA on human type 1 and type 2 T cells. CLA was induced on freshly generated Th1 and Tc1 cells only, but not on those of type 2. Anti-CD3 stimulation was sufficient to induce CLA on Th2 cells in the absence of serum in the culture medium. In serum containing medium, IL-4 inhibited CLA and related alpha-fucosyltransferase mRNA expression. IL-12 and/or staphylococcal enterotoxin B (SEB) stimulation up-regulated CLA expression on either Th2 and Tc2 cells. On stimulation with IL-12, CLA was expressed on the surface of bee venom phospholipase A(2)-specific Th1, Th2, Th0 and T regulatory 1 clones, representing non-skin-related antigen-specific T cells. In addition, CLA could be re-induced on T cells that had lost CLA expression upon resting. These results suggest that skin-selective homing is not restricted to functional and phenotypic T cell subsets.
Use of chitosan gel for the purification of protein (2007)

The aim of this study was to optimize the preparation of chitosan gel and to use it for protein purification. The optimized preparation parameters were chitosan concentration 2.0%, glutaraldehyde concentration 0.6%, low cross-linking rate, NaOH concentration 1.6%, amount of NaBH4 0.4 g. In order to use the chitosan gel, the elution conditions were optimized as follows. NaCl concentration 0.05 mol/L in the tris-HCl (pH 9.05) at the flow rate of 2.03.0 mL/min. Particle size of chitosan gel was 120-140 µm. Neutral protease could be separated into four ingredients through chitosan gel column. The yield of enzyme was more than 90%. Albumin bovine serum could be separated into two ingredients through gel column and the total yield of albumin bovine serum was more than 70%.
Coengagement of ICAM-3 and Fc Receptors Induces Chemokine Secretion and Spreading by Myeloid Leukocytes (1998)

ICAM-3 is expressed at high levels on myeloid leukocytes, but its function on these cells is unknown. We tested the hypothesis that it transduces outside-in proinflammatory signals using immobilized mAbs to engage ICAM-3 on freshly isolated human monocytes and neutrophils. Two immobilized Abs that recognize epitopes in the extracellular domain 1 of ICAM-3, which is critical for recognition by the alphaL/beta2 integrin, potently induced secretion of MIP-1alpha, IL-8, and MCP-1 by monocytes and triggered IL-8 secretion by neutrophils. These chemokines are products of immediate-early genes that are induced when myeloid cells are activated. Chemokine secretion induced by "triggering" Abs was greater than that induced by isotype-matched immobilized Abs against ICAM-1, ICAM-2, PECAM-1, control Igs, or immobilized control proteins. Coengagement of ICAM-3 and Fc receptors (FcgammaRI or FcgammaRII) was required for maximal chemokine secretion by monocytes. Microscopy documented that there is also dramatic spreading of monocytes when surface ICAM-3 is engaged by immobilized Abs. Spreading was induced by Fab and F(ab')2 fragments of triggering anti-ICAM-3 mAb, demonstrating direct outside-in signaling, but was not required for chemokine secretion. These experiments indicate that ICAM-3 may transmit outside-in signals when it is engaged by beta2 integrins during myeloid cell-cell interactions in inflammatory lesions. Binding of Fc receptors by Ig in the local environment can amplify the responses.
Laser based fast prototyping methodology of producing stretchable and conformable electronic systems (2008)

For user comfort and reliability reasons, electronic circuits for human body related applications should ideally be soft, elastic and stretchable, for smart textile application, but also for applications which need a high level of biocompatibility. We are developing several roll-to roll technologies using MID (Molded Interconnect Device) and low cost standard PCB technology (Printed Circuit Board) to produce soft, stretchable, human-compatible packaging. All those technologies are based on a sacrificial layer on where meander shaped interconnections are patterned. Those stretchable interconnections are connecting together non-stretchable functional islands on where SMD components are soldered. All the system is then embedded in stretchable polymer matrix, silicone rubber or polyurethane. All these technologies are using standards methodologies for PCB productions (lamination, photolithography, copper etching, reflow oven lead free soldering). A fast prototyping technology has been developed to ease the development of stretchable electronic circuits. Less than 1 day is necessary from CAD design to finalization: Rigid or flexible standard components or electronic sub-systems are interconnected with YAG laser shaped meander interconnections and molded in silicone rubber afterwards. From any kind of flexible circuit, stretchable circuit can be produced using this methodology. The stretchable meander interconnection can be stretched more than 100% and can sustain at least 3000 cycles at 20% of deformation. This paper presents a general overview of stretchable electronic process, a detailed view of the fast prototyping technology using YAG laser cutting, and the demonstrators developed in the frame of the European project STELLA (Stretchable Electronic for large area) [7] and in the Belgian project SWEET (Stretchable and washable electronic in textile) [8] and BIOFLEX (Biocompatible stretchable electronic system) [9].
Signals from Embryonic Fibroblasts Induce Adult Intestinal Epithelial Cells to Form Nestin‐Positive Cells with Proliferation and Multilineage Differentiation Capacity In Vitro (2006)

The intestinal epithelium has one of the greatest regenerative capacities in the body; however, neither stem nor progenitor cells have been successfully cultivated from the intestine. In this study, we applied an "artificial niche" of mouse embryonic fibroblasts to derive multipotent cells from the intestinal epithelium. Cocultivation of adult mouse and human intestinal epithelium with fibroblast feeder cells led to the generation of a novel type of nestin-positive cells (intestinal epithelium-derived nestin-positive cells [INPs]). Transcriptome analyses demonstrated that mouse embryonic fibroblasts expressed relatively high levels of Wnt/bone morphogenetic protein (BMP) transcripts, and the formation of INPs was specifically associated with an increase in Lef1, Wnt4, Wnt5a, and Wnt/BMP-responsive factors, but a decrease of BMP4 transcript abundance. In vitro, INPs showed a high but finite proliferative capacity and readily differentiated into cells expressing neural, pancreatic, and hepatic transcripts and proteins; however, these derivatives did not show functional properties. In vivo, INPs failed to form chimeras following injection into mouse blastocysts but integrated into hippocampal brain slice cultures in situ. We conclude that the use of embryonic fibroblasts seems to reprogram adult intestinal epithelial cells by modulation of Wnt/BMP signaling to a cell type with a more primitive embryonic-like stage of development that has a high degree of flexibility and plasticity.
Direct monitoring of toxic compounds in air using a portable mass spectrometer (2006)

A portable tandem mass spectrometer, capable of performing atmospheric pressure chemical ionization (APCI) using a direct atmospheric inlet, is applied to the real-time monitoring of toxic compounds in air. Analytes of interest include dimethyl methylphosphonate, arsine, benzene, toluene, pyridine and vinyl acetate. The detection, identification and quantification of organic and inorganic compounds in air is demonstrated using short analysis times (<5 seconds) with detection limits in the low ppb (v/v) levels and linear dynamic ranges of several orders of magnitude. Highly specific detection and identification is achieved, even when the analyte is a trace component in a complex mixture including such interferents as fuels, lubricants, and cleaners. The effects of environmental conditions, including temperature and humidity, are delineated. Receiver operating characteristic (ROC) curves are presented to show the trade-off between false positive and false negative detection rates. Tandem mass spectrometry based both on collision-induced dissociation and on selective atmospheric pressure ion/molecule reactions is also used to increase selectivity and sensitivity.
Structural implications of spectroscopic characterization of a putative zinc finger peptide from HIV-1 integrase. (1992)

The N-terminal domain of human immunodeficiency virus (HIV-1) integrase (IN) contains the sequence motif His-Xaa3-His-Xaa23-Cys-Xaa2-Cys, which is strongly conserved in all retroviral and retrotransposon IN proteins. This structural motif constitutes a putative zinc finger in which a metal ion may be coordinately bound by the His and Cys residues. A recombinant peptide, IN(1-55), composed of the N-terminal 55 amino acids of HIV-1 IN was expressed in Escherichia coli and purified. Utilizing a combination of techniques including UV-visible absorption, circular dichroism, Fourier transform infrared, and fluorescence spectroscopies, we have demonstrated that metal ions (Zn2+, Co2+, and Cd2+) are bound with equimolar stoichiometry by IN(1-55). The liganded peptide assumes a highly ordered structure with increased alpha-helical content and exhibits remarkable thermal stability. UV-visible difference spectra of the peptide-Co2+ complexes directly implicate thiols in metal coordination, and Co2+ d-d transitions in the visible range indicate that Co2+ is tetrahedrally coordinated. Mutant peptides containing conservative substitutions of one of the conserved His or either of the Cys residues displayed no significant Zn(2+)-induced conformational changes as monitored by CD and fluorescence spectra. We conclude that the N terminus of HIV-1 IN contains a metal-binding domain whose structure is stabilized by tetrahedral coordination of metal by histidines 12 and 16 and cysteines 40 and 43. A preliminary structural model for this zinc finger is presented.
Transmission of human immunodeficiency virus through bone transplantation: a case report. (2001)

Human immunodeficiency virus (HIV) can be transmitted through tissue or organ transplantation. Since 1988, eight cases of bone transplantation-associated HIV infection have been reported. We describe a 34-year-old woman with osteoarthritis, who was hospitalized in 1996 because of painful locomotion and deformity in the right knee. An old fracture of the femur and genu varum in the right knee was repaired by open reduction and internal fixation, with allogeneic bone transplantation for defect reconstruction. Five months later, she presented at another hospital with pain and swelling of the right thigh, where screening for HIV was positive. The transmission was tracked to a 50-year-old man with no history of HIV screening, from whom the femoral head was procured when he underwent a hip replacement for left femoral neck fracture. This is the first reported case of HIV infection through bone transplantation in Taiwan, and the preventable nature of this transmission should be underscored.
Inhibition of HIV‐1 Fusion by Hydrogen‐Bond‐Surrogate‐Based α Helices (2008)

Inhibition with a twist: An artificial α helix obtained by replacing an N-terminal main-chain i and i+4 hydrogen bond with a carbon–carbon bond (see structure) inhibits gp41-mediated cell fusion. This work suggests that hydrogen-bond-surrogate-derived helices may provide a general class of scaffolds for the generation of leads against viral entry. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z704227_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Differential Maturation and Structure–Function Relationships in Mesenchymal Stem Cell- and Chondrocyte-Seeded Hydrogels (2009)

Degenerative disease and damage to articular cartilage represents a growing concern in the aging population. New strategies for engineering cartilage have employed mesenchymal stem cells (MSCs) as a cell source. However, recent work has suggested that chondrocytes (CHs) produce extracellular matrix (ECM) with superior mechanical properties than MSCs do. Because MSC-biomaterial interactions are important for both initial cell viability and subsequent chondrogenesis, we compared the growth of MSC- and CH-based constructs in three distinct hydrogels-agarose (AG), photocrosslinkable hyaluronic acid (HA), and self-assembling peptide (Puramatrix, Pu). Bovine CHs and MSCs were isolated from the same group of donors and seeded in AG, Pu, and HA at 20 million cells/mL. Constructs were cultured for 8 weeks with biweekly analysis of construct physical properties, viability, ECM content, and mechanical properties. Correlation analysis was performed to determine quantitative relationships between formed matrix and mechanical properties for each cell type in each hydrogel. Results demonstrate that functional chondrogenesis, as evidenced by increasing mechanical properties, occurred in each MSC-seeded hydrogel. Interestingly, while CH-seeded constructs were strongly dependent on the 3D environment in which they were encapsulated, similar growth profiles were observed in each MSC-laden hydrogel. In every case, MSC-laden constructs possessed mechanical properties significantly lower than those of CH-seeded AG constructs. This finding suggests that methods for inducing MSC chondrogenesis have yet to be optimized to produce cells whose functional matrix-forming potential matches that of native CHs.
Interactions between fibronectin and chondroitin sulfate are modulated by molecular context. (1994)

Interactions between fibronectin (FN) and glycosaminoglycans are essential for extracellular matrix morphology and cell adhesion. One of the most abundant glycosaminoglycans is chondroitin sulfate, and here we show that recombinant FNs (deminectins (DN)) containing the carboxyl-terminal cell, heparin, and fibrin domains bind specifically to chondroitin sulfate in affinity chromatography assays. Using a panel of mutant DNs, important determinants for chondroitin sulfate binding have been localized to repeats III13 and III14 within the heparin domain. In particular, mutation of an arginine pair in repeat III13 to neutral residues ablated binding to chondroitin sulfate as we previously reported for heparin (Barkalow, F.J.B., and Schwarzbauer, J.E. (1991) J. Biol. Chem. 266, 7812-7818). These results, in combination with the ability of heparin and chondroitin sulfate to compete for binding to DNs, demonstrate that these two glycosaminoglycans interact with similar or overlapping sites in FN. One important difference between FN interactions with heparin and chondroitin sulfate is that, while FN and DNs bound equally to heparin, FN bound less efficiently than DNs to chondroitin sulfate. Reduced binding to chondroitin sulfate was also observed with a larger recombinant FN lacking internal repeats III1-7 indicating that the amino-terminal region acts to limit binding to the carboxyl-terminal domain. Our results demonstrate that interactions between FN and chondroitin sulfate are modulated by molecular context.
Light field superresolution (2009)

Light field cameras have been recently shown to be very effective in applications such as digital refocusing and 3D reconstruction. In a single snapshot these cameras provide a sample of the light field of a scene by trading off spatial resolution with angular resolution. Current methods produce images at a resolution that is much lower than that of traditional imaging devices. However, by explicitly modeling the image formation process and incorporating priors such as Lambertianity and texture statistics, these types of images can be reconstructed at a higher resolution. We formulate this method in a variational Bayesian framework and perform the reconstruction of both the surface of the scene and the (superresolved) light field. The method is demonstrated on both synthetic and real images captured with our light-field camera prototype.
Model-Driven Redox Pathway Manipulation for Improved Isobutanol Production in Bacillus subtilis Complemented with Experimental Validation and Metabolic Profiling Analysis (2014)

To rationally guide the improvement of isobutanol production, metabolic network and metabolic profiling analysis were performed to provide global and profound insights into cell metabolism of isobutanol-producing Bacillus subtilis. The metabolic flux distribution of strains with different isobutanol production capacity (BSUL03, BSUL04 and BSUL05) drops a hint of the importance of NADPH on isobutanol biosynthesis. Therefore, the redox pathways were redesigned in this study. To increase NADPH concentration, glucose-6-phosphate isomerase was inactivated (BSUL06) and glucose-6-phosphate dehydrogenase was overexpressed (BSUL07) successively. As expected, NADPH pool size in BSUL07 was 4.4-fold higher than that in parental strain BSUL05. However, cell growth, isobutanol yield and production were decreased by 46%, 22%, and 80%, respectively. Metabolic profiling analysis suggested that the severely imbalanced redox status might be the primary reason. To solve this problem, gene udhA of Escherichia coli encoding transhydrogenase was further overexpressed (BSUL08), which not only well balanced the cellular ratio of NAD(P)H/NAD(P)+, but also increased NADH and ATP concentration. In addition, a straightforward engineering approach for improving NADPH concentrations was employed in BSUL05 by overexpressing exogenous gene pntAB and obtained BSUL09. The performance for isobutanol production by BSUL09 was poorer than BSUL08 but better than other engineered strains. Furthermore, in fed-batch fermentation the isobutanol production and yield of BSUL08 increased by 11% and 19%, up to the value of 6.12 g/L and 0.37 C-mol isobutanol/C-mol glucose (63% of the theoretical value), respectively, compared with parental strain BSUL05. These results demonstrated that model-driven complemented with metabolic profiling analysis could serve as a useful approach in the strain improvement for higher bio-productivity in further application.
Fibromyalgia syndrome: review of clinical presentation, pathogenesis, outcome measures, and treatment. (2005)

Fibromyalgia syndrome (FM) is a common chronic pain condition that affects at least 2% of the adult population in the USA and other regions in the world where FM is studied. Prevalence rates in some regions have not been ascertained and may be influenced by differences in cultural norms regarding the definition and attribution of chronic pain states. Chronic, widespread pain is the defining feature of FM, but patients may also exhibit a range of other symptoms, including sleep disturbance, fatigue, irritable bowel syndrome, headache, and mood disorders. Although the etiology of FM is not completely understood, the syndrome is thought to arise from influencing factors such as stress, medical illness, and a variety of pain conditions in some, but not all patients, in conjunction with a variety of neurotransmitter and neuroendocrine disturbances. These include reduced levels of biogenic amines, increased concentrations of excitatory neurotransmitters, including substance P, and dysregulation of the hypothalamic-pituitary-adrenal axis. A unifying hypothesis is that FM results from sensitization of the central nervous system. Establishing diagnosis and evaluating effects of therapy in patients with FM may be difficult because of the multifaceted nature of the syndrome and overlap with other chronically painful conditions. Diagnostic criteria, originally developed for research purposes, have aided our understanding of this patient population in both research and clinical settings, but need further refinement as our knowledge about chronic widespread pain evolves. Outcome measures, borrowed from clinical research in pain, rheumatology, neurology, and psychiatry, are able to distinguish treatment response in specific symptom domains. Further work is necessary to validate these measures in FM. In addition, work is under way to develop composite response criteria, intended to address the multidimensional nature of this syndrome. A range of medical treatments, including antidepressants, opioids, nonsteroidal antiinflammatory drugs, sedatives, muscle relaxants, and antiepileptics, have been used to treat FM. Nonpharmaceutical treatment modalities, including exercise, physical therapy, massage, acupuncture, and cognitive behavioral therapy, can be helpful. Few of these approaches have been demonstrated to have clear-cut benefits in randomized controlled trials. However, there is now increased interest as more effective treatments are developed and our ability to accurately measure effect of treatment has improved. The multifaceted nature of FM suggests that multimodal individualized treatment programs may be necessary to achieve optimal outcomes in patients with this syndrome.