gebhart/patrepeval huggingface dataset:
Combinatorial labeling of single cells for gene expression cytometry (2015)

We present a technically simple approach for gene expression cytometry combining next-generation sequencing with stochastic barcoding of single cells. A combinatorial library of beads bearing cell- and molecular-barcoding capture probes is used to uniquely label transcripts and reconstruct the digital gene expression profile of thousands of individual cells in a single experiment without the need for robotics or automation. We applied the technology to dissect the human hematopoietic system and to characterize heterogeneous response to in vitro stimulation. High sensitivity is demonstrated by detection of low-abundance transcripts and rare cells. Under current implementation, the technique can analyze a few thousand cells simultaneously and can readily scale to 10,000s or 100,000s of cells.
Sialyl Tn antigen expression is associated with the prognosis of patients with advanced colorectal cancer. (1999)

We conclude that not only lymph node metastasis but also STN expression are important prognostic factors in patients with advanced colorectal carcinoma who undergo curative surgical resection.
Investigation of titanium&#8212;nitride layers for solar-cell contacts (1980)

Reactively sputtered titanium-nitride layers have been incorporated as diffusion barriers in a titanium-silver metallization scheme on silicon, Backscattering analysis (2-MeV He <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> , RBS) indicates that the integrity of the system is basically preserved during annealing at 600° for 10 min. Electrical properties were determined for titanium-nitride layers prepared under different deposition conditions. Resistivity and Hall mobility appear to depend on the oxygen contamination of the deposited material. For the lowest oxygen concentration (<5 at %) a resistivity of 170 µΩ . cm has been found.
The structure of dihydrodeoxy-8-epi-austdiol and the absolute configuration of the azaphilones (1976)

The fungal metabolite dihydrodeoxy-8-epi-austdiol, elaborated by Aspergillus ustus, has been identified as (7R,8R)-7,8-dihydro-7,8-dihydroxy-3,5,7-trimethyl-2-benzopyran-6-one. The absolute configuration of the azaphilones has been deduced.
Contact Shape Controls Adhesion of Bioinspired Fibrillar Surfaces (2007)

Following a recent bioinspired paradigm, patterned surfaces can exhibit better adhesion than flat contacts. Previous studies have verified that finer contact structures give rise to higher adhesion forces. In this study, we report on the effect of the tip shape, which was varied systematically in fibrillar PDMS surfaces, produced by lithographic and soft-molding methods. For fiber radii between 2.5 and 25 microm, it is found that shape exerts a stronger effect on adhesion than size. The highest adhesion is measured for mushroom-like and spatular terminals, which attain adhesion values 30 times in excess of the flat controls and similar to a gecko toe. These results explain the shapes commonly found in biological systems, and help in the exploration of the parameter space for artificial attachment systems.
Improved protein kinetics and albumin synthesis by branched chain amino acid-enriched total parenteral nutrition in cancer cachexia: A prospective randomized crossover trial (1986)

A prospective randomized crossover trial was conducted to determine the effect of a branched chain amino acid (BCAA)-enriched solution on whole body leucine kinetics and fractional rates of albumin synthesis in patients with intra-abdominal metastatic adenocarcinoma. Ten malnourished cancer patients were provided isonitrogenous amounts of both a conventional total parenteral nutrition (TPN) formula containing 19% BCAA and a BCAA-enriched TPN formula containing 50% of the amino acids as BCAA in a random order. Whole body protein turnover was determined by a 10 hour continuous infusion of leucine 14C. Increased whole body leucine flux (68 +/- 5 mumols/kg BW/hr versus 145 +/- 11; mean +/- SEM; P less than 0.001) and oxidation (13 +/- 2 mumols/kg BW/hr to 46 +/- 5; P less than 0.001) were determined on the BCAA-enriched TPN. Increased whole body protein synthesis (2.2 +/- 0.2 g protein/kg BW/day versus 3.9 +/- 0.3; P less than 0.005) and leucine balance (2.5 +/- 0.4 g leucine/d versus 6.5 +/- 0.6; P less than 0.001) were also observed in patients receiving the BCAA-enriched TPN solution. Leucine release from protein breakdown was not statistically elevated (1.65 +/- 0.18 g protein/kg BW/d versus 2.48 +/- 0.40; P greater than 0.05) but, incorporation of leucine 14C into plasma albumin was significantly elevated (2.37 +/- 0.23 mumols/g/hr to 4.21 +/- 0.33; P less than 0.001) when the patients received BCAA-enriched TPN. Despite the better leucine balance, the improvement in the 24-hour urinary nitrogen balance was not statistically significant (6.6 +/- 3.9 g protein/d versus 11.4 +/- 2.9; control versus BCAA-enriched; P = 0.15). BCAA-enriched formulas improve whole body leucine kinetics, fractional rates of albumin synthesis, and leucine balance, and thus may favorably influence protein metabolism in cancer cachexia.
Pyrimidine-specific cleavage by an endoribonuclease of Saccharomyces cerevisiae (1985)

An endoribonuclease with pyrimidine cleavage site specificity was isolated from Saccharomyces cerevisiae. The enzyme had a pH optimum of 6 to 7 and did not require a divalent cation. It was inhibited by 5 X 10(-5) M ethidium bromide, although it appeared to be single strand specific. The enzyme gave a limited cleavage of yeast mRNA and rRNA, yielding products that were terminated with pyrimidine nucleoside 2',3'-cyclic phosphate. The bonds between pyrimidine and A residues constituted more than 90% of the scission sites when the average product size was 50 nucleotides. Homopolyribonucleotides were cleaved poorly. Poly(A,U) was cleaved rapidly, and analysis of the products of poly(A,U) hydrolysis showed a very stringent cleavage of U-A bonds.
Virus‐like particle production at low multiplicities of infection with the baculovirus insect cell system (2003)

The baculovirus insect cell expression system (BEVS) was used for the production of self-forming Porcine parvovirus-like particles (VLPs) in serum-free medium. A low multiplicity of infection (MOI) strategy was used to overcome an extra virus amplification step, undesirable in industrial production, and to minimize the virus passage effect. It was confirmed that the time of infection (TOI) and MOI are dependent variables. Higher cell densities were obtained at low MOIs, keeping a constant TOI; however, both volumetric and specific productivities were lower. In synchronous infection, at high MOI, the specific productivity decreased when the cells were infected in the late phase of growth. Product degradation due to cell lysis strongly influenced the optimal time of harvest (TOH). Time of harvest was found to be highly dependent on the MOI, and a direct relationship with the cell yield was obtained. Analysis of the culture medium reveals that glutamine depletion occurs in the late phase of the growth. Supplementation of glutamine to uninfected cell cultures resulted in an increased cell yield. Its addition to cultures infected in the middle phase of the growth curve was also able to restore the productivity levels, but addition to cells in their stationary phase caused no observable effect on product expression. The study clearly shows that for a specific TOI it is not obvious what the correct MOI should be to obtain the best volumetric productivity.
Novel thiazolidine-2,4-diones as potent euglycemic agents. (1992)

A new series of thiazolidine-2,4-diones was obtained by replacing the ether function of englitazone with various functional groups, i.e., a ketone, alcohol, or olefin moiety. These compounds lower blood glucose levels in the genetically obese and insulin-resistant ob/ob mouse. Appending an oxazole-based group at the terminus of the chain provided highly potent compounds.
Acute renal failure in the new millennium: time to consider combination therapy. (2000)

Acute renal failure (ARF) occurs frequently and results in an unacceptably high morbidity and mortality. There is no currently accepted specific therapy that alters the course of ischemic ARF. Recent experimental advances and continued funding of ARF studies should allow rapid progress in the new millennium. This will require novel approaches to both basic and clinical evaluations. New experimental models and studies evaluating multiple therapies are needed. In addition, methods to identify ARF early in its course are likely to improve outcomes. Clinical studies should employ very specific definitions of ARF, outcomes evaluated, indications for renal replacement therapy, and severity of illness evaluation methods. Such studies and aggressive preventative measures will significantly improve the incidence and outcome of ARF in the 21st century.
Predicting Relapse with Circulating Tumor DNA Analysis in Lung Cancer (2017)

<b/> Advances in circulating tumor DNA (ctDNA) analysis are revealing new treatment strategies for patients with cancer. Detection of residual disease with ctDNA analysis predicts relapse with high accuracy after treatment for early-stage lung cancer. <i>Cancer Discov; 7(12); 1368-70. ©2017 AACR</i><i>See related article by Chaudhuri et al., p. 1394</i>.
Promotion of adhesion and migration of RPE cells to provisional extracellular matrices by TNF-alpha. (2000)

After treatment with TNF-alpha, there is increased expression of specific integrins associated with increased adhesion and migration on provisional ECM (fibronectin and collagen type I). This effect is mediated, at least in part, by activation of MAPK signaling pathway.
Microfluidic fabrication of microparticles for biomedical applications (2018)

Droplet microfluidics offers exquisite control over the flows of multiple fluids in microscale, enabling fabrication of advanced microparticles with precisely tunable structures and compositions in a high throughput manner. The combination of these remarkable features with proper materials and fabrication methods has enabled high efficiency, direct encapsulation of actives in microparticles whose features and functionalities can be well controlled. These microparticles have great potential in a wide range of bio-related applications including drug delivery, cell-laden matrices, biosensors and even as artificial cells. In this review, we briefly summarize the materials, fabrication methods, and microparticle structures produced with droplet microfluidics. We also provide a comprehensive overview of their recent uses in biomedical applications. Finally, we discuss the existing challenges and perspectives to promote the future development of these engineered microparticles.
Molecular Cobalt Pentapyridine Catalysts for Generating Hydrogen from Water (2011)

A set of robust molecular cobalt catalysts for the generation of hydrogen from water is reported. The cobalt complex supported by the parent pentadentate polypyridyl ligand PY5Me(2) features high stability and activity and 100% Faradaic efficiency for the electrocatalytic production of hydrogen from neutral water, with a turnover number reaching 5.5 × 10(4) mol of H(2) per mole of catalyst with no loss in activity over 60 h. Control experiments establish that simple Co(II) salts, the free PY5Me(2) ligand, and an isostructural PY5Me(2) complex containing redox-inactive Zn(II) are all ineffective for this reaction. Further experiments demonstrate that the overpotential for H(2) evolution can be tuned by systematic substitutions on the ancillary PY5Me(2) scaffold, presaging opportunities to further optimize this first-generation platform by molecular design.
TGF-beta down-regulates stromal IL-7 secretion and inhibits proliferation of human B cell precursors (1997)

Development of lymphoid progenitors in vivo requires interaction with a bone marrow stromal microenvironment containing multiple cytokines involved in the development of nonlymphoid hemopoietic lineages. We tested the effect of one such cytokine, TGF-beta, on the proliferation of early human clonogenic lymphoid progenitors using a stroma-dependent in vitro culture system. TGF-beta caused a dose-dependent inhibition of lymphoid progenitor colonies that was reversible at low TGF-beta doses by addition of exogenous IL-7 to the cultures. IL-7 was unable to reverse the inhibitory effect of higher TGF-beta concentrations or inhibition caused by IL-1alpha, IL-4, or TNF-alpha. Stromal IL-7 mRNA expression and protein secretion were markedly down-regulated by TGF-beta, suggesting that inhibition of stromal IL-7 secretion partially accounts for the inhibitory effect of TGF-beta on lymphopoiesis in this culture system. It is likely that higher TGF-beta concentrations do not inhibit lymphopoiesis by down-regulating IL-7 receptor expression, since this cytokine did not reduce IL-7R alpha or gamma c mRNA levels in normal B cell precursors. Since direct stromal contact is required for in vitro lymphopoiesis, the potential regulation of the IL-7 pathway by cell adhesion was examined. Adhesion of human B cell precursors to stroma did not alter stromal IL-7 expression or expression of IL-7R alpha or gamma c-chains by B cell precursors. These results indicate that TGF-beta is a significant negative regulator of stroma-dependent proliferation of early human lymphoid progenitors and acts in part by down-regulating stromal IL-7 secretion.
Cloning, Expression, and Modification of Antibody V Regions (2002)

Cloned variable (V) regions of antibodies can be expressed joined to any constant (C) region, from either the same or a different species. The resulting antibodies will have the desired associated effector functions. Chimeric antibodies obtained by joining murine V regions to human C regions should have decreased immunogenicity in humans. The process of complementarity determining region (CDR) grafting, in which the CDRs from an antibody of one species are transferred to the framework regions of another species, constitutes a further modification of this approach. The protocols presented in this unit are designed to permit PCR-based cloning of heavy and light chain V regions. This is an advanced molecular biology protocol and should be employed only by investigators who are sufficiently skilled and experienced.
Digital microfluidics for bioassays and drug delivery (2005)

This presentation will focus on the development of microscale and nanoscale platform technologies for the interrogation and manipulation of biological and physiological activities. One platform we are developing can generate micro and nanoscale droplets/particles/vesicles by controlling amphiphilic interfaces in microfluidic devices. I utilize self-assembly forces in nature to design nanoscale structures that interface biological components with physical transducers that interrogate their activities or allow external manipulation. Through the design of microfluidic channel networks, droplet arrays present a novel method for controlling biochemistry and self-assembly at picoliter to femtoliter volumes, approaching the level of cellular activities. Nanoscale features can be designed into these vesicles that mimic biological functions such as molecular recognition, protein synthesis, and molecular transport. Based on the materials delivered, droplets can then form polymer nanoparticles (e.g. photopolymerization), lipid bilayer vesicles, and multilayer drug particles. Applications that we are pursuing include smart vesicles for targeted imaging and therapeutics for cardiovascular diseases, synthetic antibodies by molecular imprint polymer nanoparticles, protein crystallization, quantum dot synthesis in droplet microreactors, combinatorial cell-based assays, and cell-encapsulation for combinatorial assays and tissue engineering.
Parenteral immunization with a glycoconjugate vaccine containing the O157 antigen ofEscherichia coliO157:H7 elicits a systemic humoral immune response in mice, but fails to prevent colonization by the pathogen (1999)

The results of the present study show that whereas both BALB/c and C57BL/6 mice parenterally inoculated with a horse serum albumin-Escherichia coli O157 antigen conjugate vaccine develop systemic, specific antibodies to the carrier protein, only the former mice routinely develop antibodies to the carbohydrate O157 moiety. However, little convincing evidence was found to show that these antibodies transuded into the intestinal tract either naturally or in response to an oral inoculum of the pathogen. Moreover, this vaccination procedure failed to protect mice against intestinal colonization following oral challenge with the pathogen. Thus, the results of this study suggest that parenteral vaccination might be an unsuitable strategy for combatting E. coli O157:H7 organisms located in the gut.
High Frequency of Loss of Heterozygosity in Imprinted, Compared with Nonimprinted, Genomic Regions in Follicular Thyroid Carcinomas and Atypical Adenomas (2006)

Our observations suggest that IRs are more prone to genomic instability in FTCs. The fact that the ATY trended toward differential IR/NIR LOH, similar to FTC, may suggest that loss of IR might be instrumental in the adenoma-carcinoma sequence in thyroid carcinogenesis and that ATY could be an important intermediate in this pathway.
Embryo development and establishment of pregnancy after embryo transfer in pigs: coping with limitations in the availability of viable embryos (2002)

Embryo transfer and pregnancy maintenance strategies in pigs were evaluated with reference to situations in which limited numbers of viable embryos or micromanipulated embryos are available, such as pig cloning. Development of embryos with compromised zona pellucida was compared with development of embryos with intact zona pellucida. Micromanipulation had no effect on blastocyst production rates after development in vivo or in vitro, but development in vivo improved the number of embryos reaching the blastocyst stage. Transfer of embryos with compromised zona pellucida resulted in live piglets. Several hormone treatments to maintain pregnancy were tested in a model in which three embryos were transferred into unmated recipient gilts, compared with transfer of three embryos into mated recipients. None of the hormonal treatments resulted in pregnancy rates of more than 25% at term and no more than 9% of transferred embryos survived, in comparison with 50% of the mated recipients successfully carrying 25% of transferred embryos. Lastly, the developmental potential of parthenogenetic embryos was assessed and 62% of transferred embryos resulted in pregnancies, none of which continued beyond day 55 of gestation. After co-transfer of three fertilized embryos with 55-60 parthenogenetic embryos into each of six recipients, two live piglets were delivered. The results from the present study indicate that transfer of zona pellucida compromised embryos can yield litters of normal piglets. In addition, it was demonstrated in a model system involving the transfer of three fertilized embryos into mature gilts that hormonal pregnancy maintenance strategies support a low proportion of embryos to term. Lastly, the present study shows for the first time a comparably effective but novel alternative for pregnancy maintenance in the pig involving the co-transfer of parthenote embryos.
Thrombin-Elicited Contractile Responses of Aortic Smooth Muscle (1985)

Human alpha-thrombin at physiologically relevant concentrations of 0.75 to 225 nM (0.01 to 22 clotting units/ml) caused rabbit thoracic aorta to slowly contract in isolated organ baths. Near maximum contractile tension (10% below the irreversible contraction caused by 22 units/ml) was slowly generated by 75 nM alpha-thrombin (8 units/ml) over 18 min and was 50% that of the norepinephrine (NE) control. The initial tonus could only be regained by repeated washing and 60 min equilibration. Tissues were refractory to a second 75 nM alpha-thrombin challenge but responded fully to 1.0 microM NE. Conversion of human alpha-thrombin to nonclotting but estero/amidolytically active gamma-thrombin (less than 0.1% clotting activity) or nitration of the enzyme (1% clotting activity) did not interfere with the contractile activity, whereas chemical conjugates of the parent enzyme at the catalytic site were inactive. Neither atropine, phentolamine, nor indomethacin blocked the thrombin-induced contractions, whereas D-600 was markedly inhibitory. Preincubation of the tissue with inactive forms of thrombin did not prevent the alpha-thrombin-induced response. Removal of the vascular endothelium did not prevent contraction. Aorta preparations with intact endothelium relaxed in the presence of very low concentrations (0.75 to 750 pM) of alpha-thrombin prior to contracting in response to higher concentrations during cumulative dose-response experiments. Our data suggest that catalytically active thrombin forms (alpha- or nonclotting beta- and gamma-thrombins) may have hemostatic functions at the vascular levels in hemostasis.
Antibody to Interleukin-5 Inhibits Helminth-Induced Eosinophilia in Mice (1989)

When rodents are infected with the nematode Nippostrongylus brasiliensis, large numbers of eosinophils appear in their blood and lungs and their serum immunoglobulin E (IgE) is increased. Injection of a monoclonal antibody to interleukin-5 completely suppressed the blood eosinophilia and the infiltration of eosinophils in the lungs of parasitized mice but had no effect on serum IgE. In contrast, an antibody to interleukin-4 inhibited parasite-induced IgE but not the eosinophilia. These results show that interleukin-5 is important in eosinophil production in vivo and that IgE and eosinophil production are regulated by different cytokines produced by the TH2 subset of CD4-expressing T cells.
Bioresorbable nanofiber‐based systems for wound healing and drug delivery: Optimization of fabrication parameters (2004)

Wound healing is a complex process that often requires treatment with antibiotics. This article reports the initial development of a biodegradable polymeric nanofiber-based antibiotic delivery system. The functions of such a system would be (a) to serve as a biodegradable gauze, and (b) to serve as an antibiotic delivery system. The polymer used in this study was poly(lactide-co-glycolide) (PLAGA), and nanofibers of PLAGA were fabricated with the use of the electrospinning process. The objective of this study was to determine the effect of fabrication parameters: orifice diameter (needle gauge), polymer solution concentration, and voltage per unit length, on the morphology and diameter of electrospun nanofibers. The needle gauges studied were 16 (1.19 mm), 18 (0.84 mm), and 20 (0.58 mm), and the range of polymer solution concentration studied was from 0.10 g/mL to 0.30 g/mL. The effect of voltage was determined by varying the voltage per unit electrospinning distance, and the range studied was from 0.375 kV/cm to 1.5 kV/cm. In addition, the mass per unit area of the electrospun nanofibers as a function of time was determined and the feasibility of antibiotic (cefazolin) loading into the nanofibers was also studied. The results indicate that the diameter of nanofibers decreased with an increase in needle gauge (decrease in orifice diameter), and increased with an increase in the concentration of the polymer solution. The voltage study demonstrated that the average diameter of the nanofibers decreased with an increase in voltage. However, the effect of voltage on fiber diameter was less pronounced as compared to polymer solution concentration. The results of the areal density study indicated that the mass per unit area of the electrospun nanofibers increased linearly with time. Feasibility of drug incorporation into the nanofibers was demonstrated with the use of cefazolin, a broad-spectrum antibiotic. Overall, these studies demonstrated that PLAGA nanofibers can be tailored to desired diameters through modifications in processing parameters, and that antibiotics such as cefazolin can be incorporated into these nanofibers. Therefore, PLAGA nanofibers show potential as antibiotic delivery systems for the treatment of wounds.