gebhart/patrepeval huggingface dataset:
Microbial Genescapes: A Prokaryotic View of the Yeast Genome (1998)

We examine the translated open reading frames (ORFs) of the yeast Saccharomyces cerevisiae, focusing on those that have FASTA matches in phyletically defined sets of completely sequenced genomes. On this basis, we identify archaeal yeast, bacterial yeast, universal yeast, and yeast ORFs that do not have a match in any of nine prokaryote genomes. Similarly, we examine the yeast mitochondrial genome and the subset of the yeast nuclear ORFs identified as being involved in mitochondrial biogenesis. For the yeast ORFs that match one or more ORFs in these prokaryote genomes, we examine the phyletic and functional distributions of these matches as a function of match strength. These results provide genome level insights into the origin of the eukaryotic cell and the origin of mitochondria. More generally, they exemplify how the growing database of prokaryote genome sequences can help us understand eukaryote genomes.
Growth of Helicobacter pylori in media containing cyclodextrins (1993)

We show that solid and liquid media, supplemented only with cyclodextrins and free of blood and its derivatives, support the growth of Helicobacter pylori. These media can be used for primary isolation of the bacteria from biopsy samples, routine laboratory growth, and large-scale industrial fermentation.
Magnetic Devices for Ultra High Throughput Biological Analysis (2006)

We have developed a magnetic biosensor based on a lab-on-a-chip integrated microfluidic cell for detection and sorting of magnetic microbeads in solution comprising magnetoresistive sensors and tapered current carrying striplines integrated with a microfluidic channel. The suspended beads are moved along a microfluidic channel patterned in SU8 over 10 μm diameter ring shaped sensors arranged in Wheatstone bridge. The device reads the realtime voltage signal as a bead perturbs an in-plane applied field in the vicinity of the active bridge elements. Beads of different magnetic moments can be detected and sorted through a magnetostatic sorting gate into different branches of the microchannel. The cell is unique because its design facilitates the integration of magnetic sensors with microfluidics and because it has individually addressable sorting striplines that divert magnetic beads in flow by applying currents locally as opposed to globally applied fields that are used to divert beads in non-flowing mode.
High concentrations of lipopolysaccharide-binding protein in serum of patients with severe sepsis or septic shock inhibit the lipopolysaccharide response in human monocytes (2001)

Lipopolysaccharide-binding protein (LBP), an acute-phase protein recognizing lipopolysaccharide (LPS), catalyzes in low concentrations its transfer to the cellular LPS receptor consisting of CD14 and Toll-like receptor-4. It has recently been shown that high concentrations of recombinant LBP can protect mice in a peritonitis model from the lethal effects of LPS. To determine whether in humans the acute-phase rise of LBP concentrations can inhibit LPS binding to monocytes and induction of proinflammatory cytokines, LBP concentrations were analyzed in 63 patients meeting the American College of Chest Physicians/Society of Critical Care Medicine criteria of severe sepsis or septic shock and the ability of these sera to modulate LPS effects in vitro was assessed employing different assays. Transfer of fluorescein isothiocyanate-labeled LPS to human monocytes was assessed by a fluorescence-activated cell sorter-based method, and activation of monocytes was investigated by measuring LPS-induced tumor necrosis factor-alpha secretion in the presence of the sera. Anti-LBP antibodies and recombinant human LBP were instrumental for depletion and reconstitution of acute-phase sera and subsequent assessment of their modulating effects on LPS activity. Sera of patients with severe sepsis/septic shock exhibited a diminished LPS transfer activity and LPS-induced tumor necrosis factor-alpha secretion as compared with sera from healthy controls. LBP depletion of sepsis sera and addition of rhLBP resulting in concentrations found in severe sepsis confirmed that LBP was the major serum component responsible for the observed effects. In summary, the inhibition of LPS effects by high concentrations of LBP in acute-phase serum, as described here, may represent a novel defense mechanism of the host in severe sepsis and during bacterial infections.
Assessment of bismuth thiols and conventional disinfectants on drinking water biofilms (2003)

BT presents a new approach to containing water biofilms. BT action is not as rapid, but is more thorough than chlorine, and less caustic. BTs may also be more efficacious in hot water systems. At sub-minimum inhibition concentration levels, BTs uniquely inhibit bacterial exopolysaccharide, thereby retarding biofilm formation. Thus, the combination of bactericidal and residual effects may prevent slime build-up in hot water systems.
A murine homologue of the human DAZ gene is autosomal and expressed only in male and female gonads (1996)

We have isolated a homologue of the human Y linked DAZ (deleted in azoospermia) gene from mouse. This gene, Dazla (Daz like, autosomal), is autosomal, located on chromosome 17 and apparently single copy. The predicted protein is highly homologous to that encoded by the DAZ gene in the N-terminal regions of the two proteins and this homology is not confined to the RNA binding domain. Analysis of its expression pattern by reverse transcription PCR shows that the transcript is only detectable in male and female gonads and that testes lacking germ cells do not contain detectable amounts of transcript. We have been unable to detect a Y-linked DAZ homologue in mouse and our results point to the possibility of a role for autosomal RNA binding proteins in mammalian gametogenesis.
Affinity maturation of the BR96 anti-carcinoma antibody by codon-based mutagenesis (1995)

Abstract We have increased up to 65-fold the avidity of BR96, a mAb recognizing Lewis Y (Le(y))-related Ags expressed on the surface of many human carcinomas. Libraries of mutations in the complementarity-determining regions (CDRs) of BR96 were constructed in an M13 phage Fab expression vector by codon-based mutagenesis, a method that efficiently introduces large numbers and potentially all combinations of amino acid substitutions. Two mutants that improved the affinity of BR96 to tumor Ag were identified by screening the libraries on carcinoma cell lines. One mutant, M1, at position 97 (Asp to Ala) in CDR3 of the heavy chain, resulted in an 8- to 10-fold improvement in Ag binding, as assessed by ELISA. A second mutant, M2, at position 53 (Gly to Asp) in CDR2 of VH increased binding three- to fivefold. When these mutations were combined, the resulting Fab M3 was improved approximately 30-fold. An additional library was constructed in CDR1 of M1. M4, a mutation with three amino acid substitutions in CDR1, was isolated by screening the library with an enzyme conjugate of synthetic Le(y) tetrasaccharide (sLe(y)). This mutant improved BR96 Fab affinity to sLe(y) an estimated 15- to 20-fold by ELISA, and 14-fold as measured by surface plasmon resonance. The M4 IgG had 65-fold improved avidity to sLe(y) relative to the BR96 IgG. The mutants will be useful for comparison of the efficacy of Abs with different affinities for delivery of cytotoxic agents to tumor cells.
The PD‐1/PD‐L1 (B7‐H1) Pathway in Chronic Infection‐Induced Cytotoxic T Lymphocyte Exhaustion (2011)

Cytotoxic CD8 T lymphocytes (CTLs) play a pivotal role in the control of infection. Activated CTLs, however, often lose effector function during chronic infection. PD-1 receptor and its ligand PD-L1 of the B7/CD28 family function as a T cell coinhibitory pathway and are emerging as major regulators converting effector CTLs into exhausted CTLs during chronic infection with human immunodeficiency virus, hepatitis B virus, hepatitis C virus, and other pathogens capable of establishing chronic infections. Importantly, blockade of the PD-1/PD-L1 pathway is able to restore functional capabilities to exhausted CTLs and early clinical trials have shown promise. Further research will reveal how chronic infection induces upregulation of PD-1 on CTLs and PD-L1 on antigen-presenting cells and other tissue cells and how the PD-1/PD-L1 interaction promotes CTLs exhaustion, which is crucial for developing effective prophylactic and therapeutic vaccination against chronic infections.
Plasmonic nanostructures in aperture‐less scanning near‐field optical microscopy (aSNOM) (2008)

Abstract Apertureless scanning near‐field optical microscopy offers superb spatial resolution, but interpreting the recorded signal can still be a challenge. Especially images of eigenmodes in plasmonic nanostructures are very often obscured by concurrent scattering from the tip and/or coupling effects in the tip‐sample system. We show here how the use of orthogonal polarizations in excitation and detection affords us with an elegant method to map near‐fields of plasmonic eigenmodes and other optical phenomena. We demonstrate with a variety of samples possible applications of this cross‐polarization scheme, such as verification of functional nanooptical structures, systematic studies of localized and propagating plasmonic eigenmodes, and their susceptibility to disturbance from structural defects. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Stromal cells from subcutaneous adipose tissue seeded in a native collagen/elastin dermal substitute reduce wound contraction in full thickness skin defects. (1995)

Adipose tissue cell isolates included vascular fragments containing endothelial cells. Seeded in dermal substitutes, these vascular fragments induced hypergranulation tissue formation and caused wound contraction. SF substitutes contained few endothelial cells. As a result, the contraction arresting effect of the seeded stromal cell fraction was effective. Our concept of a cellular dermal substitute seeded with stromal cells from adipose tissue is feasible and allows immediate treatment of full thickness skin defects.
The lac operon of Lactobacillus casei contains lacT, a gene coding for a protein of the Bg1G family of transcriptional antiterminators (1997)

The 5' region of the lac operon of Lactobacillus casei has been investigated. An open reading frame of 293 codons, designated lacT, was identified upstream of lacE. The gene product encoded by lacT is related to the family of transcriptional antiterminator proteins, which includes BglG from Escherichia coli, ArbG from Erwinia chrysanthemi, SacT, SacY, and LicT from Bacillus subtilis, and BglR from Lactococcus lactis. Amino acid sequence identities range from 35 to 24%, while similarities range from 56 to 47%. The transcriptional start site of the lac operon was identified upstream of lacT. The corresponding mRNA would contain in the 5' region a sequence with high similarity to the consensus RNA binding site of transcriptional antiterminators overlapping a sequence capable of folding into a structure that resembles a rho-independent terminator. LacT was shown to be active as an antiterminator in a B. subtilis test system using the sacB target sequence. lacT directly precedes lacEGF, the genes coding for enzyme IICB, phospho-beta-galactosidase, and enzyme IIA, and these genes are followed by a sequence that appears to encode a second rho-independent transcription terminator-like structure. Northern hybridizations with probes against lacT, lacE, and lacF revealed transcripts of similar sizes for the lac mRNAs of several L. casei strains. Since the length of the lac mRNA is just sufficient to contain lacTEGF, we conclude that the lac operon of L. casei does not contain the genes of the accessory tagatose-6-phosphate pathway as occurs in the lac operons of Lactococcus lactis, Streptococcus mutans, or Staphylococcus aureus.
Synthesis and Fibroblast Growth Factor Binding of Oligosaccharides Related to Heparin and Heparan Sulphate (1995)

Abstract A series of six disaccharides, α-l-IdoA-(l →4)-α-d-GlcNAc-l→OMe, α-l-IdoA-(l →4)-α-d-GlcNSO3-l →OMe, β-d-GlcA-(l →4)-α-d-GlcNAc-l →OMe, β-d-GlcA-(l→4)-α-d-GlcNSO3-l→OMe, α-d-GlcNAc-(l →4)-β-d-GlcA-l →OMe, β-d-GlcNAc-(l→4)-β-d-GlcA-l→OMe, and two trisaccharide, β-d-GlcA-(1 y4)-α-d-GlcNAc-(1 →4)-β-d-GlcA-l →OMe, α-l-IdoA-(l →4)-α-d-GIcNSO3-(1 →4)-β-d-GlcA-l →OMe was prepared and screened for biological activity in vitro. The oligosaccharides were tested, together with a previously synthesized trisaccharide, α-l-IdoA-(l →4)-α-d-GlcNAc-(l →4)-β-d-GlcA-l →OMe, and three tetrasaccharides, α-l-IdoA-(l →4)-α-d-GlcNAc-(l →4)-β-d-GlcA-(l →3)-β-d-Gal-l →OMe, β-d-GlcA-(l →3)-β-d-Gal-(l →3)-α-d-Gal-(1→3)-2-PO3-β-d-Xyl-l →OMe, β-d-GlcA-(1 →3)-β-d-Gal-(1 →3)-β-d-Gal-(1→3)-β-d-Xyl-l →OMe, for competitive binding to acidic and basic fibroblast growth factor in an assay using 125I labelled heparin. It was found that the non-sulphated trisaccharides, α-l-IdoA-(l →4)-α-d-GlcNAc-(l →4)-β-d-GlcA-l →OMe and β-d-GlcA-(l →4)-α-d-GlcNAc-(l →4)-β-d-GlcA-l- →OMe, and two of the disaccharides can bind to acidic as well as basic FGF.
Targeting of glycoprotein I (gE) of varicella-zoster virus to the trans-Golgi network by an AYRV sequence and an acidic amino acid-rich patch in the cytosolic domain of the molecule (1996)

Previous studies suggested that varicella-zoster virus (VZV) envelope glycoproteins (gps) are selectively transported to the trans-Golgi network (TGN) and that the cytosolic domain of gpI (gE) targets it to the TGN. To identify targeting signals in the gpI cytosolic domain, intracellular protein trafficking was studied in transfected cells expressing chimeric proteins in which a full-length or mutated gpI cytosolic domain was fused to the gpI transmembrane domain and interleukin-2 receptor (tac) ectodomain. Expressed protein was visualized with antibodies to tac. A targeting sequence (AYRV) and a second, acidic amino acid-rich region of the gpI cytosolic domain (putative signal patch) were each sufficient to cause expressed protein to colocalize with TGN markers. This targeting was lost when the tyrosine of the AYRV sequence was replaced with glycine or lysine, when arginine was replaced with glutamic acid, or when valine was substituted with lysine. In contrast, tyrosine could be replaced by phenylalanine and valine could be substituted with leucine. Mutation of alanine to aspartic acid or deletion of alanine abolished TGN targeting. Exposure of transfected cells to antibodies to the tac ectodomain revealed that the TCN targeting of expressed tac-gpI chimeric proteins occurred as a result of selective retrieval from the plasmalemma. These data suggest that the AYRV sequence and a second signaling patch in the cytosolic domain of gpI are responsible for its targeting to the TGN. The observations also support the hypothesis that the TGN plays a critical role in the envelopment of VZV.
Prevention ofHemophilus influenzaeType B Bacteremic Infections with the Capsular Polysaccharide Vaccine (1984)

A long-term follow-up of approximately 50,000 children who received the Hemophilus influenzae type b capsular polysaccharide vaccine in 1974 at three months to five years of age has shown good protective efficacy in those who received the vaccine at 18 months or older. No adverse effects were observed. Analysis of paired serum samples from 514 vaccinated children showed that effective immunization with this vaccine could be performed after but not before the age of 16 to 20 months. An analysis of 956 bacteremic H. influenzae infections occurring in Finland over a period of five years showed that 94 per cent of all cases were in children under 10 years of age. Of these, 40 per cent occurred in children under 18 months, and 60 per cent in children between the ages of 1 1/2 and 9 years. These 60 per cent are potentially preventable with the capsular polysaccharide vaccine.
Ig VH1 genes expressed in B cell chronic lymphocytic leukemia exhibit distinctive molecular features (1997)

Prior studies revealed that the leukemic B cells of patients with chronic lymphocytic leukemia (CLL) express a restricted Ig heavy chain variable region gene (VH gene) repertoire. However, this restriction needs to be re-evaluated in light of findings that the repertoire of Ig VH genes used by primary B cells of normal adults is actually more restricted than originally assumed. Because of this, we critically examined the Ig VH1 and VH7 genes expressed by leukemia cells of a random panel of patients with B cell CLL (n = 117). Forty-one (35%) had leukemia cells with functional VH1 gene rearrangements. Of these, the large majority expressed Ig VH1-69 (n = 26; 63%). The remaining leukemia cell samples expressed VH1-2 (n = 4; 10%), VH1-3 (n = 2; 5%), VH1-8 (n = 2; 5%), VH1-18 (n = 1; 2%), VH1-45 (n = 1; 2%), and VH1-46 (n = 5; 12%). Only 1 of the 117 examined (<1%) used Ig VH genes of the VH7 subgroup. We found that certain alleles of the IgVH1-69 locus are favored in CLL. Also, leukemia B cells that express VH1-69 have a distinctive use distribution of D and JH gene segments compared with that of VH1-expressing CLL B cells that do not use VH1-69 or non-neoplastic B cells that express VH1-69. Finally, the average length of the heavy chain third complementarity-determining regions (CDR3) of VH1-69-expressing leukemia cells is significantly longer than that of normal adult B cells that also express Ig encoded by VH1-69 genes. Collectively, this study indicates that the Ig expressed in CLL have distinctive molecular features that are not representative of the Ig expressed by primary B cells of normal adults.
A clinically relevant mouse model of human multiple myeloma? (2005)

Comment on Tassone et al, page [713][1]

In this issue of Blood, Tassone and colleagues describe a novel in vivo model of human multiple myeloma (MM) that relies on the engraftment of the IL-6–dependent human myeloma cell line INA-6 in a human bone marrow milieu implanted in SCID-hu mice. Because
Oral administration of doxycycline reduces collagenase and gelatinase activities in extracts of human osteoarthritic cartilage. (1998)

Oral administration of doxycycline significantly inhibited collagenase and gelatinase activity in human OA cartilage. The effective dose is likely to be well tolerated during chronic administration, e.g., in a clinical trial to assess the potential of the drug to modify cartilage breakdown in OA.
Fully Integrated Startup at 70 mV of Boost Converters for Thermoelectric Energy Harvesting (2016)

This paper presents an inductive DC-DC boost converter for energy harvesting using a thermoelectric generator with a minimum startup voltage of 70 mV and a regulated output voltage of 1.25 V. With a typical generator resistance of 40 Ω, an output power of 17 μW can be provided, which translates to an end-to-end efficiency of 58%. The converter employs Schmitt-trigger logic startup control circuitry and an ultra-low voltage charge pump using modified Schmitt-trigger driving circuits optimized for driving capacitive loads. Together with a novel ultra-low leakage power switch and the required control scheme, to the best of the authors' knowledge, this enables the lowest minimum voltage with fully integrated startup.
COMPORTEMENT MECANIQUE ET RUPTURE DANS LES ROCHES ARGILEUSES ETUDIES PAR MICRO TOMOGRAPHIE A RAYONS X (2006)

WITHIN THE FRAMEWORK OF FEASABILITY STUDIES OF UNDERGROUND REPOSITORIES FOR RADIOACTIVE WASTE, THE STUDY OF PERMEABILITY EVOLUTION WITH DAMAGE OF THE HOST LAYER IS CRUCIAL. THE GOALS OF THIS WORK WERE : (i) TO CHARACTERIZE EXPERIMENTALLY THE DAMAGE OF TWO CLAYEY ROCKS (BEAUCAIRE MARL AND EAST SHALE) WITH X-RAY MICRO TOMOGRAPHY, (ii) TO DEVELOPP A HIGH PRESSURE TRIAXIAL SET-UP ADAPTED TO PERMEABILITY MEASUREMENT ON VERY LOW PERMEABILITY ROCKS.A NUMBER OF ORIGINAL TRIAXIAL DEVICES HAVE BEEN REALISED TO CHARACTERIZE DAMAGE OF CLAYEY ROCKS, UNDER DEVIATORIC LOADING, WITH X-RAY MICRO TOMOGRAPHY ON A SYNCHROTRON BEAMLINE AT THE ESRF (GRENOBLE). LOCALIZED DAMAGE AND ITS EVOLUTION HAVE BEEN CHARACTERIZED AT A FINE SCALE (OF ORDER OF TEN MICRONS). DIGITAL IMAGE CORRELATION TECHNIQUES, EXTENDED TO 3D IMAGES, HAVE BEEN USED TO MEASURE INCREMENTAL STRAIN FIELDS FROM TOMOGRAPHIC IMAGES. WE DEMONSTRATED THAT THESE TECHNIQUES ARE VERY USEFUL IN THE STUDY OF THE LOCALIZED DAMAGE OF GEOMATERIALS AND ESPECIALLY FOR THE INITIATION.A HIGH PRESSURE TRIAXIAL DEVICE HAS BEEN REALISED TO MEASURE PERMEABILITY EVOLUTION OF THE EAST SHALE AS A FUNCTION OF APLLIED STRESS (ISOTROPIC AND DEVIATORIC). THE PARTICULARITY OF THIS SET-UP IS THE SMALL SIZE OF THE TEST SPECIMEN (CYLINDER OF 10MM IN DIAMETER AND 20MM IN HEIGHT) WHICH ALLOWS SIGNIFICANT REDUCTION OF TEST DURATION.
Prolonged fecal excretion of hepatitis A virus in adult patients with hepatitis A as determined by polymerase chain reaction (1996)

In hepatitis A virus (HAV) infection, fecal excretion of the virus has been reported to cease shortly after symptoms occur. Although there have been several reports on detection of HAV in feces using polymerase chain reaction (PCR), the duration of fecal HAV shedding in human adult hepatitis A has not been well described. In the present study, we applied the reverse-transcription (RT)-PCR system to the detection of fecal HAV RNA in 10 patients with sporadic hepatitis A. The viral genomic RNA was detected in the stools from five patients after the onset of clinical symptoms. All stool samples collected within 10 days of onset of illness were HAV-RNA-positive, and the duration of positivity lasted from a few days to as long as 3 months. In four patients, HAV RNA was detected in the stool even after the serum alanine transaminase (ALT) levels had peaked, and in one patient well after ALT levels fell to normal. These results show that fecal shedding of HAV can last for months after resolution of symptoms and such patients could be a source of further spreading of the virus in the community.
Silicon surface passivation by atomic layer deposited Al2O3 (2008)

Thin Al2O3 films with a thickness of 7–30 nm synthesized by plasma-assisted atomic layer deposition (ALD) were used for surface passivation of crystalline silicon (c-Si) of different doping concentrations. The level of surface passivation in this study was determined by techniques based on photoconductance, photoluminescence, and infrared emission. Effective surface recombination velocities of 2 and 6 cm/s were obtained on 1.9 Ω cm n-type and 2.0 Ω cm p-type c-Si, respectively. An effective surface recombination velocity below 1 cm/s was unambiguously obtained for nearly intrinsic c-Si passivated by Al2O3. A high density of negative fixed charges was detected in the Al2O3 films and its impact on the level of surface passivation was demonstrated experimentally. The negative fixed charge density results in a flat injection level dependence of the effective lifetime on p-type c-Si and explains the excellent passivation of highly B-doped c-Si by Al2O3. Furthermore, a brief comparison is presented between the surface passivations achieved for thermal and plasma-assisted ALD Al2O3 films prepared in the same ALD reactor.