gebhart/patrepeval huggingface dataset:
Comparison between Random Forests, Artificial Neural Networks and Gradient Boosted Machines Methods of On-Line Vis-NIR Spectroscopy Measurements of Soil Total Nitrogen and Total Carbon (2017)

Accurate and detailed spatial soil information about within-field variability is essential for variable-rate applications of farm resources. Soil total nitrogen (TN) and total carbon (TC) are important fertility parameters that can be measured with on-line (mobile) visible and near infrared (vis-NIR) spectroscopy. This study compares the performance of local farm scale calibrations with those based on the spiking of selected local samples from both fields into an European dataset for TN and TC estimation using three modelling techniques, namely gradient boosted machines (GBM), artificial neural networks (ANNs) and random forests (RF). The on-line measurements were carried out using a mobile, fiber type, vis-NIR spectrophotometer (305-2200 nm) (AgroSpec from tec5, Germany), during which soil spectra were recorded in diffuse reflectance mode from two fields in the UK. After spectra pre-processing, the entire datasets were then divided into calibration (75%) and prediction (25%) sets, and calibration models for TN and TC were developed using GBM, ANN and RF with leave-one-out cross-validation. Results of cross-validation showed that the effect of spiking of local samples collected from a field into an European dataset when combined with RF has resulted in the highest coefficients of determination (R²) values of 0.97 and 0.98, the lowest root mean square error (RMSE) of 0.01% and 0.10%, and the highest residual prediction deviations (RPD) of 5.58 and 7.54, for TN and TC, respectively. Results for laboratory and on-line predictions generally followed the same trend as for cross-validation in one field, where the spiked European dataset-based RF calibration models outperformed the corresponding GBM and ANN models. In the second field ANN has replaced RF in being the best performing. However, the local field calibrations provided lower R² and RPD in most cases. Therefore, from a cost-effective point of view, it is recommended to adopt the spiked European dataset-based RF/ANN calibration models for successful prediction of TN and TC under on-line measurement conditions.
The piezoelectric valve-less pump - improved dynamic model (2002)

The piezoelectric valve-less pump is an attractive device to be used as a micro pump for low flow rates. The pump converts the reciprocating motion of a diaphragm, activated by a piezoelectric disk, into a pumping action. Instead of conventional valves, which have moving parts, nozzle/diffuser elements that have a preferential flow direction are used to direct the flow from the inlet to the outlet. In this paper, an improved dynamic model for the simulation of valve-less piezoelectric pumps is presented. The model is capable of accurate simulation of the pump performance including the natural frequency, flow rate, and pressure drop. The model is utilized here to study the effect of the driving frequency and the inlet/outlet length and diameter of the leading pipes on the pump performance. Comparison with experiments shows good agreement with a minimal number of adjusting parameters.
Human Hepatocyte Growth Factor Promotes Functional Recovery in Primates after Spinal Cord Injury (2011)

Many therapeutic interventions for spinal cord injury (SCI) using neurotrophic factors have focused on reducing the area damaged by secondary, post-injury degeneration, to promote functional recovery. Hepatocyte growth factor (HGF), which is a potent mitogen for mature hepatocytes and a mediator of the inflammatory responses to tissue injury, was recently highlighted as a potent neurotrophic factor in the central nervous system. We previously reported that introducing exogenous HGF into the injured rodent spinal cord using a herpes simplex virus-1 vector significantly reduces the area of damaged tissue and promotes functional recovery. However, that study did not examine the therapeutic effects of administering HGF after injury, which is the most critical issue for clinical application. To translate this strategy to human treatment, we induced a contusive cervical SCI in the common marmoset, a primate, and then administered recombinant human HGF (rhHGF) intrathecally. Motor function was assessed using an original open field scoring system focusing on manual function, including reach-and-grasp performance and hand placement in walking. The intrathecal rhHGF preserved the corticospinal fibers and myelinated areas, thereby promoting functional recovery. In vivo magnetic resonance imaging showed significant preservation of the intact spinal cord parenchyma. rhHGF-treatment did not give rise to an abnormal outgrowth of calcitonin gene related peptide positive fibers compared to the control group, indicating that this treatment did not induce or exacerbate allodynia. This is the first study to report the efficacy of rhHGF for treating SCI in non-human primates. In addition, this is the first presentation of a novel scale for assessing neurological motor performance in non-human primates after contusive cervical SCI.
Antibodies to synthetic joining segment peptide of the T-cell receptor beta-chain: serological cross-reaction between products of T-cell receptor genes, antigen binding T-cell receptors, and immunoglobulins. (1986)

Immunoglobulin light and heavy chains show sequence homology to one another and to the polypeptide chains of putative T-cell receptors in the J (joining) segment of the variable region. Antibodies produced against synthetic peptides corresponding to the entire JH1 region and part of the diversity segment region cross-react serologically with products of normal T cells and monoclonal T-cell lines. In this study we generate immune affinity-purified rabbit antibodies to a synthetic 16-mer peptide consisting of the entire JT sequence and part of the T-cell diversity sequence corresponding to these segments of the human putative T-cell receptor beta gene YT35. Both free peptide and peptide coupled to bovine serum albumin as carrier were found to stimulate the production of antibody. The immune affinity-purified anti-JT peptide antibodies bound to intact immunoglobulin and to light and heavy chain as detected by enzyme-linked immunosorbent assay and by immunoblot transfer. The antibody reacted by these techniques with membrane components of the human monoclonal amplifier T-cell MOLT-3 and the murine suppressor T-cell WEHI-7. The component detected in the MOLT-3 cell corresponded to the beta-chain of the alpha/beta heterodimer putative T-cell receptor; whereas the molecule detected in the WEHI-7 line had properties corresponding to those of antigen-specific T-cell suppressor receptors. The molecular size of this component under reducing conditions was approximately 68 kDa and the intact form had an apparent mass of 140 kDa. These results provide direct proof of serological cross-reaction among products of putative T-cell receptor genes, antigen-binding T-cell receptors, and immunoglobulins, thereby supporting the concept that antigen receptors of T lymphocytes all represent new immunoglobulin translocons.
Imidazo[1,2-b]pyridazines. XI. Syntheses and Central Nervous System Activities of Some 6-(N-Benzyl-N-methylamino)-3-methoxy-2-phenyl(and substituted phenyl)imidazo[1,2-b]pyridazines (1992)

Syntheses are reported for 196-(N-benzyl- N -methylamino )-3-methoxy-2-phenyl(and substituted phenyl or pyridinyl ) imidazo [1,2- b ] pyridazines from 6-(N-benzyl- N -methylamino)pyridazin-3- amine 2-oxide. The ability of each of these compounds to displace [3H]diazepam from rat brain membrane preparations was measured and the IC50 values (or percentage displacements) are reported and discussed. 6-( N -Benzyl-N-methylamino )-3-methoxy-2-phenylimido[1,2- b ]pyridine was about half as active as its 6-bemylamino analogue, and the most active compound was 6-( N -benzyl- N -methylamino )-2-(2'-fluorophenyl)-3-methoxyimido[1,2-b] pyridazine with IC50 9.8 nM.
MATRIX PROTEOGLYCANS: From Molecular Design to Cellular Function (1998)

The proteoglycan superfamily now contains more than 30 full-time molecules that fulfill a variety of biological functions. Proteoglycans act as tissue organizers, influence cell growth and the maturation of specialized tissues, play a role as biological filters and modulate growth-factor activities, regulate collagen fibrillogenesis and skin tensile strength, affect tumor cell growth and invasion, and influence corneal transparency and neurite outgrowth. Additional roles, derived from studies of mutant animals, indicate that certain proteoglycans are essential to life whereas others might be redundant. The review focuses on the most recent genetic and molecular biological studies of the matrix proteoglycans, broadly defined as proteoglycans secreted into the pericellular matrix. Special emphasis is placed on the molecular organization of the protein core, the utilization of protein modules, the gene structure and transcriptional control, and the functional roles of the various proteoglycans. When possible, proteoglycans have been grouped into distinct gene families and subfamilies offering a simplified nomenclature based on their protein core design. The structure-function relationship of some paradigmatic proteoglycans is discussed in depth and novel aspects of their biology are examined.
A Pilot Study of Human Milk to Reduce Intestinal Inflammation After Bone Marrow Transplant (2019)

Administration of human milk resulted in decreased markers of intestinal inflammation and could be a valuable adjunct for patients after BMT.
Expression of the p185 encoded by her2 oncogene in normal and transformed human tissues (1990)

The human homolog of the rat neu oncogene, HER2 (also termed c-erbB2) has been demonstrated in amplified form in human breast tumors with poor prognosis. Although amplification of the gene correlates with expression of a 185-kDa transmembrane glycoprotein, no extensive information is available regarding the extent of tissue and tumor specificity of this gene product. We have addressed this issue by immunohistochemically evaluating the expression of p185 HER2 in normal tissue and various tumors using monoclonal antibodies (MAbs) to distinct epitopes of its extracellular domain. No detectable levels of p185 HER2 were found in fetal tissues analyzed, with the exception of renal tubules in 2 out of 3 specimens tested and in intestinal epithelium. In adult tissues, detectable levels of this glycoprotein were found in a restricted number of cell types, the expression being heterogeneous among individuals and cell histotypes. Among the neoplasms assayed p185 HER2 was expressed in 46% of primary breast cancers, in 28% of ovarian tumors and in 30% of colon rectum malignancies. No male breast adenocarcinomas were p185-positive. A large number of other tumors tested revealed only a low incidence of expression of the p185. In metastatic breast tumors p185 HER2 was demonstrated homogeneously among multiple autologous lesions and almost invariably (80%) the expression of p185 in the primary lesion correlated with that of the deriving metastases. Our findings indicate that the expression of the p185 HER2 represents a tumor marker of clinical relevance in breast cancer. Whether this holds true for other malignancies remains to be explored.
Straightforward Synthesis of the Near-Infrared Fluorescent Voltage-Sensitive Dye RH1691 and Analogues Thereof (2009)

A highly straightforward synthesis of the near-infrared voltage-sensitive dye RH1691 is reported featuring two sequential anionic additions of C-nucleophilic heterocycles on a cyanine. This convergent approach led to the synthesis of four new probes, which also exhibit fluorescence in the near-infrared region.
Lymphokine-activated killer (LAK) cells. V. 8-Mercaptoguanosine as an IL-2-sparing agent in LAK generation. (1990)

Guanine ribonucleosides, substituted at the C8 position with either a bromine or a thiol group, have recently been shown to regulate several immunologic responses. We have previously shown that 8-mercaptoguanosine (8MG) can replace the requirement for cytokines in the generation of MHC-restricted CTL. In this paper, we examined the ability of 8MG to induce MHC-nonrestricted killer cells. We found that 8MG did not induce significant lytic activity from normal resting lymphocytes. However, 8MG was able to synergize with minimal amounts of IL-2 in inducing lytic activity similar to lymphokine-activated killers (LAK) in that both NK-sensitive and NK-resistant tumor cells were killed. Both the precursors and effectors of 8MG-LAK activity were similar to NK cells and were CD4- CD8- asialo-GM1+ NK1.1+. Similar to IL-2-induced LAK, 8MG-LAK were B220+. 8MG appeared to "stage" these precursor lymphocytes to become more responsive to IL-2 because optimal induction of 8MG-LAK required preincubation with 8MG before the addition of IL-2. This "staging" appeared to be due to the release of a "second signal" since it was readily inhibited by cyclosporine A. Anti-IFN-alpha beta was as efficient as cyclosporine A in inhibiting 8MG-LAK generation, whereas anti-IFN-gamma and anti-IL-1 did not exhibit significant inhibition. These findings suggest that 8MG can be of possible utility as an IL-2-sparing agent in LAK generation from NK cells.
Design and Synthesis of Water-Soluble Glucuronide Derivatives of Camptothecin for Cancer Prodrug Monotherapy and Antibody-Directed Enzyme Prodrug Therapy (ADEPT) (1999)

Glucuronide prodrugs of 9-aminocamptothecin were synthesized. Prodrug 4, in which 9-aminocamptothecin was connected to glucuronic acid by an aromatic spacer via a carbamate linkage, was stable in both aqueous solution and human plasma. Prodrug 4 and its potassium salt 12 were 20-80-fold less toxic than 9-aminocamptothecin to human tumor cell lines. The simultaneous addition of beta-glucuronidase and 4 or 12 to tumor cells resulted in a cytotoxic effect equal to that of 9-aminocamptothecin alone. Prodrugs 4 and 12 were over 80 and 4000 times more soluble than 9-aminocamptothecin in aqueous solutions at pH 4.0, respectively. Compounds 4 and 12 may be useful for prodrug monotherapy of tumors that accumulate extracellular lysosomal beta-glucuronidase as well as for antibody-directed enzyme prodrug therapy (ADEPT) of cancer.
Quenching and Blinking of Fluorescence of a Single Dye Molecule Bound to Gold Nanoparticles (2006)

A fluorescein derivative (SAMSA) bound to gold nanoparticles of different diameters is investigated by time-resolved fluorescence at the single molecule level in a wide dynamic range, from nanosecond to second time scale. The significant decrease of both SAMSA excited state lifetime and fluorescence quantum yield observed upon binding to gold nanoparticles can be essentially traced back to an increase of the nonradiative deactivation rate, probably due to energy transfer, that depends on the nanoparticle size. A slow single molecule fluorescence blinking, in the ms time scale, has a marked dependence on the excitation intensity both under single and under two photon excitation. The blinking dynamics is limited by a low probability nonlinear excitation to a high energy state from which a transition to a dark state occurs. The results point out a strong coupling between the vibro-electronic configuration of the dye and the plasmonic features of the metal nanoparticles that provide dye radiationless deactivation channels on a wide dynamic range.
Checkpoint processing and recovery: towards scalable large instruction window processors (2003)

Large instruction window processors achieve high performance by exposing large amounts of instruction level parallelism. However, accessing large hardware structures typically required to buffer and process such instruction window sizes significantly degrade the cycle time. This paper proposes a checkpoint processing and recovery (CPR) microarchitecture, and shows how to implement a large instruction window processor without requiring large structures thus permitting a high clock frequency. We focus of four critical aspects of a microarchitecture: 1) scheduling instructions; 2) recovering from branch mispredicts; 3) buffering a large number of stores and forwarding data from stores to any dependent load; and 4) reclaiming physical registers. While scheduling window size is important, we show the performance of large instruction windows to be more sensitive to the other three design issues. Our CPR proposal incorporates novel microarchitecture scheme for addressing these design issues-a selective checkpoint mechanism for recovering from mispredicts, a hierarchical store queue organization for fast store-load forwarding, and an effective algorithm for aggressive physical register reclamation. Our proposals allow a processor to realize performance gains due to instruction windows of thousands of instructions without requiring large cycle-critical hardware structures.
High density lipoprotein complexes as delivery vehicles for anticancer drugs. (2002)

Our studies indicated that rHDL complexes can be used as efficient drug delivery vehicles due to the ability of cancer cells to acquire HDL core components. Targeting of anticancer drugs as components of the rHDL complex could result in reduction of toxic side-effects during chemotherapy.
Regulation of Cytokine Signaling by B Cell Antigen Receptor and Cd40-Controlled Expression of Heparan Sulfate Proteoglycans (2000)

Recently, biochemical, cell biological, and genetic studies have converged to reveal that integral membrane heparan sulfate proteoglycans (HSPGs) are critical regulators of growth and differentiation of epithelial and connective tissues. As a large number of cytokines involved in lymphoid tissue homeostasis or inflammation contain potential HS-binding domains, HSPGs presumably also play important roles in the regulation of the immune response. In this report, we explored the expression, regulation, and function of HSPGs on B lymphocytes. We demonstrate that activation of the B cell antigen receptor (BCR) and/or CD40 induces a strong transient expression of HSPGs on human tonsillar B cells. By means of these HSPGs, the activated B cells can bind hepatocyte growth factor (HGF), a cytokine that regulates integrin-mediated B cell adhesion and migration. This interaction with HGF is highly selective since the HSPGs did not bind the chemokine stromal cell-derived factor (SDF)-1 alpha, even though the affinities of HGF and SDF-1alpha for heparin are similar. On the activated B cells, we observed induction of a specific HSPG isoform of CD44 (CD44-HS), but not of other HSPGs such as syndecans or glypican-1. Interestingly, the expression of CD44-HS on B cells strongly promotes HGF-induced signaling, resulting in an HS-dependent enhanced phosphorylation of Met, the receptor tyrosine kinase for HGF, as well as downstream signaling molecules including Grb2-associated binder 1 (Gab1) and Akt/protein kinase B (PKB). Our results demonstrate that the BCR and CD40 control the expression of HSPGs, specifically CD44-HS. These HSPGs act as functional coreceptors that selectively promote cytokine signaling in B cells, suggesting a dynamic role for HSPGs in antigen-specific B cell differentiation.
Requirements for the nuclear export of the small ribosomal subunit (2002)

Eukaryotic ribosome biogenesis requires multiple steps of nuclear transport because ribosomes are assembled in the nucleus while protein synthesis occurs in the cytoplasm. Using an in situ RNA localization assay in the yeast Saccharomyces cerevisiae, we determined that efficient nuclear export of the small ribosomal subunit requires Yrb2, a factor involved in Crm1-mediated export. Furthermore, in cells lacking YRB2, the stability and abundance of the small ribosomal subunit is decreased in comparison with the large ribosomal subunit. To identify additional factors affecting small subunit export, we performed a large-scale screen of temperature-sensitive mutants. We isolated new alleles of several nucleoporins and Ran-GTPase regulators. Together with further analysis of existing mutants, we show that nucleoporins previously shown to be defective in ribosomal assembly are also defective in export of the small ribosomal subunit.
High‐yields and extended serum half‐life of human interferon α2b expressed in tobacco cells as arabinogalactan‐protein fusions (2007)

Therapeutic proteins like human interferon alpha2 generally possess short serum half-lives due to their small size, hence rapid renal clearance, and susceptibility to serum proteases. Chemical derivatization, such as addition of polyethylene glycol (PEG) groups overcomes both problems, but at the expense of greatly decreased bioactivity. We describe a new method that yields biologically potent interferon alpha2b (IFNalpha2) in high yields and with increased serum half-life when expressed as arabinogalactan-protein (AGP) chimeras in cultured tobacco cells. Thus IFNalpha2-AGPs targeted for secretion typically gave 350-1400-fold greater secreted yields than the non-glycosylated IFNalpha2 control. The purified AGP domain itself was not immunogenic when injected into mice and only mildly so when injected as a fusion glycoprotein. Importantly, the AGP-IFNalpha2 chimeras showed up to a 13-fold increased in vivo serum half-life while the biological activity remained similar to native IFNalpha2. The use of arabinogalactan glycomodules may provide a general approach to the enhanced production of therapeutic proteins by plants.
Probing DNA Surface Attachment and Local Environment Using Single Molecule Spectroscopy (2001)

We have employed single molecule fluorescence spectroscopy, using a total internal reflection geometry and wide-angle detection, to study the attachment of singly fluorescently labeled DNA to a silica surface by either a streptavidin−biotin or a covalent linkage. In both cases the DNA is highly monodispersed with no evidence for aggregation. The covalent coupling gave higher signal-to-noise than the streptavidin−biotin linkage and was therefore studied in more detail. Two components in the photobleaching times, corresponding to different states of the tetramethyl rhodamine probe, were observed: a short and long component with populations in the ratio 6.7:1. Only rarely was interconversion between these two states detected during the 30-s observation time of the experiment. Hybridization experiments using a complementary strand of DNA labeled with a different fluorophore gave a low level of colocalized fluorescence, indicating a significant fraction of the surface attached DNA was not available for hybridization. These results are consistent with the surface attached DNA spending significant time collapsed on the surface.
Archaea : a laboratory manual (1995)

The protocols in these three books are selected to provide a detailed guide to experiments with the methanogenic, extremely halophilic, and thermophilic sulfur-utilizing Archaea, with overviews to highlight areas of future development. The individual protocols consist of an introduction describing the specific applications of the techniques, step-by-step procedures for applying the protocols, followed by any additional comments that will facilitate successful application of the protocol. A feature of research in this area is the interplay between microbiology, bioengineering, biochemistry, and molecular biology, and authors from all of these fields have been selected to provide these three concise and comprehensive resources for scientists interested in conducting research on the Archaea.