gebhart/patrepeval huggingface dataset:
Protein glycosylation in development and disease (1999)

N- and O-linked glycan structures of cell surface and secreted glycoproteins serve a variety of functions related to cell-cell communication in systems affecting development and disease. The more sophisticated N-glycan biosynthesis pathway of metazoans diverges from that of yeast with the appearance of the medial-Golgi beta-N-acetylglucosaminyltransferases (GlcNAc-Ts). Tissue-specific regulation of medial- and trans-Golgi glycosyltransferases contribute structural diversity to glycoproteins in metazoans, and this can affect their molecular properties including localization, half-life, and biological activity. Null mutations in glycosyltransferase genes positioned later in the biosynthetic pathway disrupt expression of smaller subsets of glycan structures and are progressively milder in phenotype. In this review, we examine data on targeted mutations affecting glycosylation in mice and congenital mutations in man, with a view to understanding the molecular functions of glycan structures as modulators of glycoprotein activity. Finally, pathology associated with the expression of GlcNAc-Ts in cancer and diabetes-induced cardiac hypertrophy suggest that inhibitors of these enzymes may have therapeutic value.
Renal arginine synthesis: studies in vitro and in vivo. (1990)

Renal arginine synthesis is a major endogenous source of arginine. Argininosuccinate lyase occurs almost exclusively in kidney cortex. In studies with isolated renal cortical tubules, we observed rapid rates of arginine synthesis from citrulline, provided a source of the N atom of the guanidino group of arginine was supplied. Aspartate, glutamate, or glutamine were effective, whereas glycine, alanine, serine, or NH4Cl were ineffective as this second substrate. Arginine synthesis as a function of citrulline concentration was determined and was found to be highly sensitive to citrulline concentrations in the physiological range (60 microM), suggesting that renal arginine synthesis in vivo could be regulated by circulating citrulline levels. Therefore, arginine synthesis by the kidney was investigated in vivo by measuring the net flux of citrulline and arginine in saline-infused (control group) and citrulline-infused rats. In normal animals, uptake of citrulline was 60.5 +/- 20.7 nmol.min-1.100 g body wt-1, and a similar arginine release was observed. Citrulline infusion that increased circulating citrulline levels fourfold resulted in a similar increase in renal citrulline uptake (224 +/- 33 nmol.min-1.100 g-1) and a similar increase in renal production of arginine. The results suggest that the availability of citrulline is a limiting factor for renal arginine synthesis in rats.
An ultrastructural study of epididymal mouse spermatozoa binding to zonae pellucidae in vitro: Sequential relationship to the acrosome reaction (1979)

Mouse sperm bind to the zona pellucida of the egg prior to penetration of the zona and entry into the perivitelline space. The question then arises: when does the acrosome reaction occur relative to these processes? An ultrastructural study of mouse epididymal sperm bound to the surface of the zona and in the privitelline space was undertaken to clarify this point. Cumulus-free mouse eggs were inseminated in either a complete defined culture medium capable of supporting in vitro fertilization or in Tris/NaCl buffer containing Ca+2. Both media support sperm binding to the zona to the same extent; binding is complete in 15 minutes. Unbound sperm were removed by a step gradient density centrifugation to yield a preparation of eggs with sperm firmly bound. All sperm in the perivitelline space had undergone the acrosome reaction. Sperm bound at the surface of the zonae pellucidae of eggs recovered at ten minutes after insemination all had intact acrosomes. At 40 minutes after insemination, half of the sperm were intact; the other half were in the initial stages of the acrosome reaction. At 90 minutes after insemination, 12% of the sperm had undergone the full acrosome reaction and were starting to penetrate the zona; of the balance, half were in various stages of the acrosome reaction, while half were still intact. These findings support the hypothesis that the sequence of the early reactions leading to fertilization in the mouse is: intact sperm binding to zona; acrosome reaction at the zona surface; penetration of the zona.
Microfluidics: A high-throughput system for the assessment of the endotheliopathy of trauma and the effect of timing of plasma administration on ameliorating shock-associated endothelial dysfunction (2017)

A temporal effect to plasma administration was noted in our biomimetic model of the endothelial vascular barrier following shock. This suggests a protective role to "early" plasma administration in the severely injured patient.
Seven Hundred Fifty-Three Consecutive Deaths in a Level I Trauma Center: The Argument for Injury Prevention (2003)

Dramatically improving therapy (no errors, cure for multiple organ failure, sepsis, and pulmonary embolus) in a modern trauma system would decrease trauma mortality by 13%. In contrast, more than half of all deaths are potentially preventable with preinjury behavioral changes. Injury prevention is critical to reducing deaths in the modern trauma system.
Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis (2000)

The 4 202 353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125 contains 4066 predicted protein coding sequences (CDSs), 2141 (52.7%) of which have functional assignments, 1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no match to any protein database. Among the total CDSs, 8.8% match sequences of proteins found only in Bacillus subtilis and 66.7% are widely conserved in comparison with the proteins of various organisms, including B.subtilis. The B. halodurans genome contains 112 transposase genes, indicating that transposases have played an important evolutionary role in horizontal gene transfer and also in internal genetic rearrangement in the genome. Strain C-125 lacks some of the necessary genes for competence, such as comS, srfA and rapC, supporting the fact that competence has not been demonstrated experimentally in C-125. There is no paralog of tupA, encoding teichuronopeptide, which contributes to alkaliphily, in the C-125 genome and an ortholog of tupA cannot be found in the B.subtilis genome. Out of 11 sigma factors which belong to the extracytoplasmic function family, 10 are unique to B. halodurans, suggesting that they may have a role in the special mechanism of adaptation to an alkaline environment.
Model Bicontinuous Microemulsions in Ternary Homopolymer/Block Copolymer Blends (1999)

We have identified a channel of bicontinuous microemulsion in three chemically distinct hompolymer/hompolymer/block copolymer (A/B/A−B) ternary bends. Experiments were conducted along the isopleth, defined by equal volumes of homopolymer and varying amounts of block copolymer, as a function of temperature. A symmetric condition was achieved through the use of homopolymers with matched degrees of polymerization (NA ≈ NB = NH) and compositionally symmetric diblock copolymers (f ≈ 0.5) where α ≡ NAB/NH ≈ 0.2. We explored PE−PEP/PE/PEP (EP), PEE−PDMS/PEE/PDMS (EED), and PE−PEO/PE/PEO (EO) ternary systems differing in molecular weight by nearly 2 orders of magnitude. Using a combination of small-angle neutron scattering (SANS), rheology, and cloud point measurements, we mapped the phase diagram along the isopleth for each of these systems. On the block-copolymer-rich side of the phase diagrams, a line of lamellar-disorder transitions was observed. On the homopolymer-rich side of the phase diagrams a line of transitions separating one-phase and phase-separated regions was found. A narrow channel of bicontinuous microemulsion separates these two regimes in all three systems. This bicontinuous microemulsion phase is similar to the analogous bicontinuous phases found in oil/water/surfactant mixtures. We have demonstrated that there is a common region in phase space over which the bicontinuous microemulsion is stable in these polymeric systems and that the general phase behavior is independent of polymer molecular weight. The low molecular weight of the EO system is ideal for fundamental phase behavior studies in polymeric blends, since the kinetic limitations that plague high-molecular-weight mixtures are avoided. Furthermore, the EO system utilizes polyethylene−poly(ethylene oxide) block copolymers that are chemically very similar to well-known nonionic surfactants, and thus, connections to surfactancy can readily be made.
High-quality ultra-thin HfO/sub 2/ gate dielectric MOSFETs with TaN electrode and nitridation surface preparation (2002)

A surface preparation technique using an NH/sub 3/ anneal has been investigated to reduce interface reaction and consequently the equivalent oxide thickness (EOT) of hafnium oxide for alternative gate dielectric applications. MOSCAPs and MOSFETs were fabricated on the NH/sub 3/ nitrided substrates with HfO/sub 2/ dielectric and TaN gate electrode. Using this nitridation technique, EOT of as thin as 7.1 /spl Aring/ with 10/sup -2/ A/cm/sup 2/ at -1.5 V was obtained. Furthermore, excellent device characteristics and reasonable reliability have been achieved.
A cloud computing approach to complex robot vision tasks using smart camera systems (2010)

In this paper we show our work on enabling service robot systems to distribute parts of the image processing functions to different off-board computer systems in the working environment of the robot. Thus complex algorithms can be carried out on high performance systems circumventing the restrictions considering space and power consumption that a mobile platform imposes. As high resolution cameras provide a huge amount of image data and the bandwidth of a wireless network connection is strongly limited, we are using intelligent camera systems on the mobile robot platform to execute parts of the image processing functions directly on the robot. This way only preprocessed image information will be transmitted instead of raw image data. We are using a flexible modular software framework that allows us to split image processing tasks into a pipeline of modular functions that can run on different systems. We show how our approach can be used to enable a service robot system to speed up high resolution SIFT-based object detection.
Robust Loop Detection for Interactively Placing Evenly Placed Streamlines (2007)

The authors present a robust and fast loop-detection strategy to interactively place dense, uncluttered, evenly spaced streamlines, which help visualize complex flows. Although loop detection is critical to streamline placement, few researchers have addressed this issue. In this paper an effective, robust, and fast loop-detection strategy for creating evenly spaced streamlines is described. At a negligible additional cost, it allows interactive streamline placement for complex flows on an ordinary PC.
Low-Variance and Zero-Variance Baselines for Extensive-Form Games (2019)

Extensive-form games (EFGs) are a common model of multi-agent interactions with imperfect information. State-of-the-art algorithms for solving these games typically perform full walks of the game tree that can prove prohibitively slow in large games. Alternatively, sampling-based methods such as Monte Carlo Counterfactual Regret Minimization walk one or more trajectories through the tree, touching only a fraction of the nodes on each iteration, at the expense of requiring more iterations to converge due to the variance of sampled values. In this paper, we extend recent work that uses baseline estimates to reduce this variance. We introduce a framework of baseline-corrected values in EFGs that generalizes the previous work. Within our framework, we propose new baseline functions that result in significantly reduced variance compared to existing techniques. We show that one particular choice of such a function --- predictive baseline --- is provably optimal under certain sampling schemes. This allows for efficient computation of zero-variance value estimates even along sampled trajectories.
Acute Lymphoblastic Leukemia (2002)

This is a comprehensive overview on the most recent developments in diagnosis and treatment of acute lymphoblastic leukemia (ALL). Dr. Dieter Hoelzer and colleagues give an overview of current chemotherapy approaches, prognostic factors, risk stratification, and new treatment options such as tyrosine kinase inhibitors and monoclonal antibodies. Furthermore the role of minimal residual disease (MRD) for individual treatment decisions in prospective clinical studies in adult ALL is reviewed. Drs. Ching-Hon Pui and Mary Relling discuss late treatment sequelae in childhood ALL. The relation between the risk of second cancer and treatment schedule, pharmacogenetics, and gene expression profile studies is described. Also pathogenesis, risk factors, and management of other complications such as endocrinopathy, bone demineralization, obesity, and avascular necrosis of bone is reviewed. Dr. Fred Appelbaum addresses long-term results, late sequelae and quality of life in ALL patients after stem cell transplantation. New options for reduction of relapse risk, e.g., by intensified conditioning regimens or donor lymphocyte infusions, for reduction of mortality and new approaches such as nonmyeloablative transplantation in ALL are discussed. Drs. Jacques van Dongen and Tomasz Szczepanski demonstrate the prognostic value of MRD detection via flow cytometry or PCR analysis in childhood ALL. They discuss the relation between MRD results and type of treatment protocol, timing of the follow-up samples, and the applied technique and underline the importance of standardization and quality control. They also review MRD-based risk group definition and clinical consequences.
Integrated multilayer microfluidic device with a nanoporous membrane interconnect for online coupling of solid-phase extraction to microchip electrophoresis (2007)

An integrated microfluidic device was developed for online coupling of solid-phase extraction to microchip electrophoresis (chip SPE-CE). With a nanoporous membrane sandwiched between two PDMS substrates, SPE preconcentration and electrophoretic separation can be carried out in upper and lower fluidic layers, separately and sequentially. During the SPE process, the thin membrane can act as a fluid isolator to prevent intermixing between two fluidic channels. However, when a pulse voltage is applied, the membrane becomes a gateable interconnect so that a small plug of concentrated analytes can be online injected into the lower channel for subsequent separations. This multilayer design provides a universal solution to online SPE-CE hyphenation. Both electroosmotic flow and hydrodynamic pumps have been adopted for SPE operation. SPE was performed on a 2.5 mm long microcolumn, with two weirs on both sides to retain the C(18)-coated silica beads. Rhodamine 123 and FITC-labelled ephedrine were used to test the operational performance of the hyphenation system. High separation efficiency and thousand-fold signal enhancement were achieved.
Trim coil system for the RIKEN superconducting ring cyclotron (2002)

A superconducting ring cyclotron proposed as a booster of the existing RIKEN Ring Cyclotron (RRC), is composed of six superconducting sector magnets. In each sector magnet, the pole pieces are placed at 4 K to be used as a support structure of the coil vessel against large electromagnetic forces and also to enhance magnetic flux efficiently. The field trimming system suitable for such a cyclotron is thought to be a combination of superconducting and normal trim coils. Considering their differing properties, optimization of a trimming system has been carried out using numerical methods. The trimming system is required to isochronize the magnetic fields for various ions in a wide range of beam energy. Features of the trim coils and the results of optimization are described.
A nonnucleoside reverse transcriptase inhibitor active on human immunodeficiency virus type 1 isolates resistant to related inhibitors (1993)

Pyridinone derivatives are potent and specific inhibitors of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) and HIV-1 replication in cell culture. However, the potential clinical usefulness of these compounds as monotherapeutic agents may be limited by the selection of inhibitor-resistant viral variants. Resistance in cell culture is due primarily to mutational alterations at RT amino acid residues 103 and 181. A recombinant HIV-1 RT containing both of these mutations was used to screen a panel of pyridinone analogs for inhibitory activity. L-696,229 and L-697,661, pyridinones currently undergoing clinical evaluation, were more than 4,000-fold weaker against the mutant enzyme than against the wild-type enzyme. In contrast, one derivative of L-696,229, L-702,019 (3-[2-(4,7-dichlorobenzoxazol-2-yl)ethyl]-5-ethyl-6-methylpyrid in-2(1H)-thione), showed only three-fold different potencies against the two enzymes. L-702,019 was also a potent inhibitor of the replication of mutant HIV-1 containing the individual mutations at amino acid 103 or 181 as well as of clinical isolates resistant to L-697,661 and L-696,229. Isolation and analysis of resistant viral variants in cell culture showed that significant resistance to L-702,019 could be engendered only by multiple amino acid substitutions in RT. Accordingly, these studies demonstrated the potential of identifying second-generation specific HIV-1 RT inhibitors that can overcome the viral resistance selected by the first generation of inhibitors.
Effects of prophylactic antibiotics on endometrial flora in women with postcesarean endometritis (1998)

Ampicillin and cefazolin prophylaxis alters endometrial and endocervical microflora of women who develop endometritis. Whereas these changes had no effect on endometritis cure rate (power > 80%), the association between cefazolin prophylaxis followed by an extended-spectrum cephalosporin and wound infection may warrant caution against the use of the combination.
The MHC class Ib protein ULBP1 is a nonredundant determinant of leukemia/lymphoma susceptibility to γδ T-cell cytotoxicity (2010)

On the path to successful immunotherapy of hematopoietic tumors, gammadelta T cells offer great promise because of their human leukocyte antigen (HLA)-unrestricted targeting of a wide variety of leukemias/lymphomas. However, the molecular mechanisms underlying lymphoma recognition by gammadelta T cells remain unclear. Here we show that the expression levels of UL16-binding protein 1 (ULBP1) determine lymphoma susceptibility to gammadelta T cell-mediated cytolysis. Consistent with this, blockade of NKG2D, the receptor for ULBP1 expressed on all Vgamma9(+) T cells, significantly inhibits lymphoma cell killing. Specific loss-of-function studies demonstrate that the role of ULBP1 is nonredundant, highlighting a thus far unique physiologic relevance for tumor recognition by gammadelta T cells. Importantly, we observed a very wide spectrum of ULBP1 expression levels in primary biopsies obtained from lymphoma and leukemia patients. We suggest this will impact on the responsiveness to gammadelta T cell-based immunotherapy, and therefore propose ULBP1 to be used as a leukemia/lymphoma biomarker in upcoming clinical trials.
Antibody‐Drug Conjugates for the Treatment of Cancer (2012)

With over 20 antibody-drug conjugates in clinical trials as well as a recently FDA-approved drug, it is clear that this is becoming an important and viable approach for selectively delivering highly cytotoxic agents to tumor cells while sparing normal tissue. This review discusses the critical aspects for this approach with an emphasis on the properties of the linker between the antibody and the cytotoxic payload that are required for an effective antibody-drug conjugate. Different linkers are illustrated with attention focused on (i) the specifics of attachment to the antibody, (ii) the polarity of the linker, (iii) the trigger on the linker that initiates cleavage from the drug, and (iv) the self-immolative spacer that liberates the active payload. Future directions in the field are proposed.
Front Matter and Table of Contents (1984)

This entry contains the front cover, front matter and back cover.
Prior Bordetella pertussis infection modulates allergen priming and the severity of airway pathology in a murine model of allergic asthma (2004)

Contrary to the above premise, a Th1 response induced by a common childhood infection does not protect against bronchial hyper-reactivity, but rather exacerbates the allergic asthmatic response, despite modulation of immune mediators.
The ghost of past species occurrence: improving species distribution models for presence‐only data (2006)

Summary Model‐based approaches have been used increasingly in conservation biology over recent years. Species presence data used for predictive species distribution modelling are abundant in natural history collections, whereas reliable absence data are sparse, most notably for vagrant species such as butterflies and snakes. As predictive methods such as generalized linear models (GLM) require absence data, various strategies have been proposed to select pseudo‐absence data. However, only a few studies exist that compare different approaches to generating these pseudo‐absence data. Natural history collection data are usually available for long periods of time (decades or even centuries), thus allowing historical considerations. However, this historical dimension has rarely been assessed in studies of species distribution, although there is great potential for understanding current patterns, i.e. the past is the key to the present. We used GLM to model the distributions of three ‘target’ butterfly species, Melitaea didyma , Coenonympha tullia and Maculinea teleius , in Switzerland. We developed and compared four strategies for defining pools of pseudo‐absence data and applied them to natural history collection data from the last 10, 30 and 100 years. Pools included: (i) sites without target species records; (ii) sites where butterfly species other than the target species were present; (iii) sites without butterfly species but with habitat characteristics similar to those required by the target species; and (iv) a combination of the second and third strategies. Models were evaluated and compared by the total deviance explained, the maximized Kappa and the area under the curve (AUC). Among the four strategies, model performance was best for strategy 3. Contrary to expectations, strategy 2 resulted in even lower model performance compared with models with pseudo‐absence data simulated totally at random (strategy 1). Independent of the strategy model, performance was enhanced when sites with historical species presence data were not considered as pseudo‐absence data. Therefore, the combination of strategy 3 with species records from the last 100 years achieved the highest model performance. Synthesis and applications. The protection of suitable habitat for species survival or reintroduction in rapidly changing landscapes is a high priority among conservationists. Model‐based approaches offer planning authorities the possibility of delimiting priority areas for species detection or habitat protection. The performance of these models can be enhanced by fitting them with pseudo‐absence data relying on large archives of natural history collection species presence data rather than using randomly sampled pseudo‐absence data.
One for All—A Highly Efficient and Versatile Method for Fluorescent Immunostaining in Fish Embryos (2011)

Our method overcomes the loss of sections and damage of tissue and cell morphology, and allows parallel immunostaining in multiple colors, co-immunostaining with fluorescent proteins in transgenic fish lines and in combination with whole mount in situ hybridization.