gebhart/patrepeval huggingface dataset:
Characterization of SixLeuconostoc fallaxBacteriophages Isolated from an Industrial Sauerkraut Fermentation (2002)

Six bacteriophages active against Leuconostoc fallax strains were isolated from industrial sauerkraut fermentation brines. These phages were characterized as to host range, morphology, structural proteins, and genome fingerprint. They were exclusively lytic against the species L. fallax and had different host ranges among the strains of this species tested. Morphologically, three of the phages were assigned to the family Siphoviridae, and the three others were assigned to the family Myovidae: Major capsid proteins detected by electrophoresis were distinct for each of the two morphotypes. Restriction fragment length polymorphism analysis and randomly amplified polymorphic DNA fingerprinting showed that all six phages were genetically distinct. These results revealed for the first time the existence of bacteriophages that are active against L. fallax and confirmed the presence and diversity of bacteriophages in a sauerkraut fermentation. Since a variety of L. fallax strains have been shown to be present in sauerkraut fermentation, bacteriophages active against L. fallax are likely to contribute to the microbial ecology of sauerkraut fermentation and could be responsible for some of the variability observed in this type of fermentation.
Optimal design of a thermistor probe for surface measurement of cerebral blood flow (1990)

Microthermistors are put on the surface of cerebral cortex to monitor local cerebral blood flow (CBF) continuously with minimal tissue damage and disturbance to the normal physiological state. Using a distributed, dynamic model of the measurement system, we simulated the effects of this flow measurement method under isothermal and adiabatic boundary conditions. Numerical results show that the adiabatic boundary condition can provide maximal sensitivity to perfusion changes at physiological perfusion levels. The constant power and constant temperature operating modes are compared in terms of output relation, sensitivity, and frequency response through analytical and numerical solutions. While the steady-state relations between thermistor measurements and perfusion for the two modes do not differ significantly, the constant temperature mode has better frequency response. Analytical results show that the relative sensitivity is the same for the two modes and is approximately proportional to the radius of thermistor. If there is an unperfused layer surrounding the thermistor, the sensitivity will decrease as the thickness of the layer increases. Simulations predict that the thermal measurement has a low-pass frequency response and the cutoff frequency is inversely proportional to the probe surface area. The results provide a theoretical foundation to the optimal design of thermistor probe for continuous CBF measurement from tissue surface.
Relationships between natural T cells, atopy, IgE levels, and IL‐4 production (2000)

These results show that the number of NT cells, particularly the CD4+ subset, is related to atopy, IL-4 production, and IgE levels. Therefore, this population of T cells is likely to play a role in the Th2 commitment initiating atopic diseases.
Hypocholesterolemic Effect of Bile Acid Sulfonate Analogs in Hamsters. (2001)

We studied the effects of bile acid sulfonate analogs, namely, 3alpha,7alpha,12alpha-trihydroxy-5beta-cholane-24-sulfonate (C-sul), 3alpha,7alpha-dihydroxy-5beta-cholane-24-sulfonate (CDC-sul), and 3alpha,7beta-dihydroxy-5beta-cholane-24-sulfonate (UDC-sul), on serum and liver cholesterol levels, cholesterol 7alpha-hydroxylase activity, and biliary bile acid composition in hamsters fed cholesterol. Of the three analogs studied, UDC-sul slightly but significantly decreased free, esterified, and total cholesterol concentrations in the serum. UDC-sul and CDC-sul reduced liver total cholesterol levels by 25% and 18%, respectively, particularly in the esterified cholesterol fraction. Analysis of biliary bile acids showed the presence of the administered analogs, indicating that sulfonate analogs efficiently participate in enterohepatic cycling. The proportion of cholic acid was increased in all groups fed sulfonate analogs, but the ratio of glycine to taurine conjugated bile acids (G/T) was elevated only in UDC-sul feeding hamsters. There was no significant change in cholesterol 7alpha-hydroxylase activity in hamsters fed C-sul or CDC-sul, while UDC-sul slightly stimulated the enzyme activity compared to the control. The UDC-sul induced decrease in serum and liver cholesterol concentrations may be secondary to enhanced bile acid synthesis. This is supported by the increased cholesterol 7alpha-hydroxylase activity and elevated G/T ratio in biliary bile acids observed following UDC-sul administration.
Isolation of human nm23 genomes and analysis of loss of heterozygosity in primary colorectal carcinomas using a specific genomic probe. (1994)

Genomic clones of nm23-H1 and -H2 were isolated. The nm23-H1 and -H2 genes were located in a tandem array 4 kilobases apart. Each genome contained 5 exons and most of the splicing sites in the exon-intron junctions of two isotypes were essentially identical. A probe derived from intron 4 of nm23-H1 was used to examine the loss of heterozygosity (LOH) in primary colorectal carcinomas. Twenty-nine of 42 samples were informative and LOH was found in 3 of these 29. In all three samples with LOH, cancer tissues expressed lower levels of nm23-H1 mRNA when compared with those without LOH.
T3 releasing activity by Graves' sera from Graves' thyroid in vitro (1986)

The insensitivity of Graves' thyroid to stimulation of cAMP formation by TSH as well as Graves' immunoglobulins in vitro is well known. The present study was performed to find out Graves' sera which may induce a final activation i.e. stimulation of T3 release in Graves' thyroid slices despite this insensitivity of tissue and to characterize determinants responsible for the efficiency of those sera. Out of 20 sera from patients with active untreated Graves' disease 6 were found to stimulate T3 release from Graves' thyroid in vitro. These 6 sera were effective in stimulating different Graves' glands, irrespective of pretreatment with propranolol, thiamazole (methimazole) or thiamazole plus iodine. In contrast, a significant response to bTSH was not observed in any Graves' gland. For comparison, 17/20 of the same sera were able to stimulate T3 release when tested on human goitrous thyroid. Sera which stimulated Graves' slices revealed no higher stimulating activities in goitrous tissue than serum samples which did not. All sera were additionally assessed for TSH binding inhibiting immunoglobulins in a radioreceptor assay. Remarkably, Graves' thyroid stimulating sera had a low or absent TSH binding inhibiting activity. Thus, hormone release from Graves' thyroid in vitro - in contrast to that from goitrous tissue - could only be activated by a minority of Graves' sera. These Graves' thyroid stimulating sera could be characterized to contain a selected spectrum of biologically active antibodies with a high TSH agonistic potency stimulating in the presence of a negligible TSH binding inhibiting activity.
Restricted distribution of integrin beta 6 mRNA in primate epithelial tissues. (1993)

Integrins are cell adhesion receptors that mediate cell-extracellular matrix and cell-cell interactions. Each integrin consists of two glycoprotein subunits (alpha and beta). We have previously described a novel integrin beta-subunit, beta 6, which is expressed in cultured epithelial cells. beta 6 can associate with alpha v to form the fibronectin-binding heterodimer alpha v beta 6. Here we report the tissue distribution of beta 6 integrin mRNA determined by in situ hybridization of a beta 6 cRNA probe with representative frozen tissue sections from a rhesus monkey tissue bank. We detected beta 6 mRNA exclusively in epithelial cells. However, beta 6 mRNA expression varied greatly among different epithelia. High levels of beta 6 mRNA were found only in two very specialized epithelial cell types: a portion of the kidney tubule epithelium, termed macula densa, and the endometrial epithelium of secretory phase uterus. In the endometrium, beta 6 expression was highest in the differentiated epithelium of functional layer glands, suggesting that beta 6 expression can be regulated in a differentiation-dependent manner. beta 6 expression may also depend on the stage in the estrous cycle, since we found much lower beta 6 mRNA levels in a specimen of proliferative phase endometrium. Epithelium in several other tissues, including salivary gland ducts, gall bladder, and epididymis, contained detectable levels of beta 6 mRNA, albeit much lower than in macula densa and endometrium. In other epithelia, including skin and lung, beta 6 mRNA was undetectable. Taken together, these results suggest that in normal adult primates beta 6 expression is regulated in a cell type-specific manner, restricted to a few epithelial tissues.
Two-dimensional current percolation in nanocrystalline vanadiumdioxide films (2006)

Simultaneous measurements of the transmittance and the resistance were carried out on 20-nm-thick VO2 wires during the semiconductor-to-metal transition (SMT). They reveal an offset between the effective electrical and optical switching temperatures. This shift is due to current percolation through a network of nanometer-scale grains of different sizes undergoing a SMT at distinct temperatures. An effective-medium approximation can model this behavior and proves to be an indirect method to calculate the surface coverage of the films.
SISCAPA Peptide Enrichment on Magnetic Beads Using an In-line Bead Trap Device (2009)

A SISCAPA (stable isotope standards and capture by anti-peptide antibodies) method for specific antibody-based capture of individual tryptic peptides from a digest of whole human plasma was developed using a simplified magnetic bead protocol and a novel rotary magnetic bead trap device. Following off-line equilibrium binding of peptides by antibodies and subsequent capture of the antibodies on magnetic beads, the bead trap permitted washing of the beads and elution of bound peptides inside a 150-microm-inner diameter capillary that forms part of a nanoflow LC-MS/MS system. The bead trap sweeps beads against the direction of liquid flow using a continuous succession of moving high magnetic field-gradient trap regions while mixing the beads with the flowing liquid. This approach prevents loss of low abundance captured peptides and allows automated processing of a series of SISCAPA reactions. Selected tryptic peptides of alpha(1)-antichymotrypsin and lipopolysaccharide-binding protein were enriched relative to a high abundance serum albumin peptide by 1,800 and 18,000-fold, respectively, as measured by multiple reaction monitoring. A large majority of the peptides that are bound nonspecifically in SISCAPA reactions were shown to bind to components other than the antibody (e.g. the magnetic beads), suggesting that substantial improvement in enrichment could be achieved by development of improved inert bead surfaces.
cGAS/STING Pathway in Cancer: Jekyll and Hyde Story of Cancer Immune Response (2017)

The last two decades have witnessed enormous growth in the field of cancer immunity. Mechanistic insights of cancer immunoediting have not only enhanced our understanding but also paved the way to target and/or harness the innate immune system to combat cancer, called cancer immunotherapy. Cyclic GMP-AMP synthase (cGAS)/Stimulator of interferon genes(STING) pathway has recently emerged as nodal player in cancer immunity and is currently being explored as potential therapeutic target. Although therapeutic activation of this pathway has shown promising anti-tumor effects in vivo, evidence also indicates the role of this pathway in inflammation mediated carcinogenesis. This review highlights our current understanding of cGAS/STING pathway in cancer, its therapeutic targeting and potential alternate approaches to target this pathway. Optimal therapeutic targeting and artificial tunability of this pathway still demand in depth understanding of cGAS/STING pathway regulation and homeostasis.
Communication channel equalisation using minimal radial basis function neural networks (2002)

Results of nonlinear channel equalisation problems in data communications using a recently developed minimal radial basis function neural network structure, minimal resource allocation network (MRAN), are presented. A parsimonious network structure is ensured by the MRAN algorithm which uses online learning and has the capability to grow and prune the RBF network's hidden neurons. Compared to earlier methods, the proposed scheme does not have to estimate the channel order first, and fix the model parameters. Results showing the superior performance of the MRAN algorithm for a linear channel equalisation problem, along with a nonlinear channel problem, are presented.
SURF: rubber-band routing system for multichip modules (1993)

Current PCB (printed circuit board)-based routing tools cannot meet the performance and cost constraints presented by today's packaging technologies, including thin-film multichip modules. The authors describe SURF, a routing system designed specifically to meet these challenges. The strength of the SURF system comes from its extremely flexible rubber-band data representation. The rubber-band model is an ideal framework for performance-driven and cost-driven routing and naturally supports rectilinear, octilinear, and all-angle wiring patterns: one-and-a-half-layer routing; even wiring distribution; and powerful manual editing. The integrated spoke-based design-rule-checking/enforcement mechanism supports an incremental design style. As objects are moved or wires are resized, the wires are adjusted incrementally so that they maintain the same wiring topology. By working in the topological domain instead of the geometrical one, the designer can focus on higher-level design issues while the tool handles the precise geometrical details.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Molecular Studies Reveal Frequent Misidentification of Aspergillus fumigatus by Morphotyping (2006)

Aspergillus fumigatus has been understood to be the most common cause of invasive aspergillosis (IA) in all epidemiological surveys. However, recent studies have uncovered a large degree of genetic heterogeneity between isolates morphologically identified as A. fumigatus, leading to the description of a new species, Aspergillus lentulus. Here, we examined the genetic diversity of clinical isolates identified as A. fumigatus using restriction enzyme polymorphism analysis and sequence-based identification. Analysis of 50 clinical isolates from geographically diverse locations recorded the presence of at least three distinct species: A. lentulus, Aspergillus udagawae, and A. fumigatus. In vitro, A. lentulus isolates demonstrated decreased susceptibility to antifungal drugs currently used for IA, including amphotericin B, voriconazole, and caspofungin; A. udagawae isolates demonstrated decreased in vitro susceptibility to amphotericin B. Results of the present study demonstrate that current phenotypic methods to identify fungi do not differentiate between genetically distinct species in the A. fumigatus group. Differential antifungal susceptibilities of these species may account for some of the reported poor outcomes of therapy in clinical studies.
Highly stable meso-diaminopimelate dehydrogenase from an Ureibacillus thermosphaericus strain A1 isolated from a Japanese compost: purification, characterization and sequencing (2011)

We screened various thermophiles for meso-diaminopimelate dehydrogenase (meso-DAPDH, EC 1.4.1.16), which catalyzes the NAD(P)-dependent oxidative deamination of meso-diaminopimelate, and found the enzyme in a thermophilic bacterium isolated from compost in Japan. The bacterium grew well aerobically at around 55°C and was identified as Ureibacillus thermosphaericus strain A1. We purified the enzyme about 47-fold to homogeneity from crude cell extract using five successive purification steps. The molecular mass of the purified protein was about 80 kDa, and the molecule consists of a homodimer with the subunit molecular mass of about 40 kDa. The optimum pH and temperature for the catalytic activity of the enzyme are about 10.5 and 65°C, respectively. The enzyme is highly selective for meso-diaminopimelate as the electron donor, and NADP but not NAD can serve as the electron acceptor. The Km values for meso-diaminopimelate and NADP at 50°C and pH 10.5 are 1.6 mM and 0.13 mM, respectively. The nucleotide sequence of this meso-DAPDH gene encodes a 326-amino acid peptide. When the gene was cloned and overexpressed in Escherichia coli Rosetta (DE3), the specific activity in the crude extract of the recombinant cells was about 18.0-fold higher than in the extract from U. thermosphaericus strain A1. This made more rapid and simpler purification of the enzyme possible.
High immunohistochemical expression of p‐AKT predicts inferior survival in patients with diffuse large B‐cell lymphoma treated with immunochemotherapy (2010)

Summary Chemotherapy and rituximab (R) is current standard therapy in diffuse large B‐cell lymphoma (DLBCL), but a substantial proportion of patients still fail to reach sustained remission. In vitro studies have indicated that rituximab resistance could be accompanied by dysregulated apoptotic pathways, such as the phosphatidylinositol 3‐kinase (PI3K)/AKT signaling pathway, which can be constitutively activated in DLBCL. In this retrospective, immunohistochemical study on 106 patients treated with R‐CHO(E)P (cyclophosphamide, doxorubicin, vincristine, prednisone, rituximab [+etoposide]), we investigated the prognostic role of proteins involved in different apoptotic pathways; phosphorylated AKT (p‐AKT), bcl‐2, MCL1, bcl‐xL, Bax and Bak. High p‐AKT expression (&gt;108 cells/mm 2 , highest quartile, n = 27) predicted worse progression‐free (PFS) ( P = 0·02) and overall (OS) ( P = 0·01) survival, independent of International Prognostic Index and sex. Also bcl‐2+ (cut‐off 50%) predicted worse PFS ( P = 0·005) and OS ( P = 0·05) but after adjustment for clinical factors only the influence on PFS ( P = 0·03) remained significant. The prognostic impact of p‐AKT overexpression was independent of bcl‐2 status. MCL1, bcl‐xL, Bax and Bak expression did not add any prognostic information. Our results suggest that high p‐AKT expression predicts worse outcome , possibly indicating that inhibition of the activated PI3K/AKT pathway could be of clinical interest in DLBCL patients. In addition, bcl‐2 status could have prognostic importance also in the era of immunochemotherapy.
RING Finger Z Protein of Lymphocytic Choriomeningitis Virus (LCMV) Inhibits Transcription and RNA Replication of an LCMV S-Segment Minigenome (2001)

Arenaviruses have a bisegmented negative-strand RNA genome whose proteomic capability is limited to only four polypeptides, namely, nucleoprotein (NP), surface glycoprotein (GP) that is proteolytically processed into GP1+GP2, polymerase (L), and a small (11-kDa) RING finger protein (Z). The role of Z during the Lymphocytic choriomeningitis virus (LCMV) life cycle is poorly understood. We investigated the function of Z in virus transcription and replication by using a reverse genetic system for the prototypic arenavirus LCMV. This system involves an LCMV minigenome and the minimal viral trans-acting factors (NP and L), expressed from separated cotransfected plasmids. Cotransfection of the Z cDNA strongly inhibited LCMV minigenome expression. The effect required synthesis of Z protein; its magnitude was dose dependent and occurred with levels of Z protein substantially lower than those observed in LCMV-infected cells. Coexpression of Z did not prevent the encapsidation of plasmid supplied minigenome, but it affected both transcription and RNA replication similarly. Mutations in Z that unfolded its RING finger domain eliminated its inhibitory activity, but RING proteins not related to Z did not affect LCMV minigenome expression. Consistent with the minigenome results, cells transiently expressing Z exhibited decreased susceptibility to infection with LCMV.
Memory-Mapped Transactions (2005)

Memory-mapped transactions combine the advantages of both memory mapping and transactions to provide a programming interface for concurrently accessing data on disk without explicit I/O or locking operations. This interface enables a programmer to design a complex serial program that accesses only main memory, and with little to no modification, convert the program into correct code with multiple processes that can simultaneously access disk. I implemented Libxac, a prototype for an efficient and portable system supporting memory-mapped transactions. Libxac is a C library that supports atomic transactions on memory-mapped files. Libxac guarantees that transactions are serializable, and it uses a multiversion concurrency control algorithm to ensure that all transactions, even aborted transactions, always see a consistent view of a memorymapped file. Libxac was tested on Linux, and it is portable because it is written as a user-space library, and because it does not rely on special operating system support for transactions. With
The Mechanisms of Lithium and Sodium Insertion in Carbon Materials (2001)

In this paper, we compare the interactions of lithium and sodium with a range of carbon materials in electrochemical cells. Through wide angle in situ X-ray scattering studies, we demonstrate that both lithium and sodium can be inserted into the interlayer space in disordered carbon materials. This insertion process is accompanied by an increase in the interlayer spacing in these materials. Small-angle in situ scattering studies are presented to clearly show the insertion of lithium and sodium into nanopores within disordered hard carbons. We also show that very little, if any, sodium can be inserted into graphitic materials in contrast to the large capacity seen for lithium insertion. © 2001 The Electrochemical Society. All rights reserved.
Inhibition of Epithelial Ductal Branching in the Prostate by Sonic Hedgehog Is Indirectly Mediated by Stromal Cells (2003)

Sonic hedgehog (Shh), a vertebrate homologue of the Drosophila segment-polarity gene hedgehog, has been reported to play an important role during normal development of various tissues. Abnormal activities of Shh signaling pathway have been implicated in tumorigenesis such as basal cell carcinomas and medulloblastomas. Here we show that Shh signaling negatively regulates prostatic epithelial ductal morphogenesis. In organotypic cultures of developing rat prostates, Shh inhibited cell proliferation and promoted differentiation of luminal epithelial cells. The expression pattern of Shh and its receptors suggests a paracrine mechanism of action. The Shh receptors Ptc1 (Patched1) and Ptc2 were found to be expressed in prostatic stromal cells adjacent to the epithelium, where Shh itself was produced. This paracrine model was confirmed by co-culturing the developing prostate in the presence of stromal cells transfected with a vector expressing a constitutively active form of Smoothened, the real effector of the Shh signaling pathway. Furthermore, expression of activin A and TGF-beta1 that were shown previously to inhibit prostatic epithelial branching was up-regulated following Shh treatment in the organotypic cultures. Taken together, these results suggest that Shh negatively regulates prostatic ductal branching indirectly by acting on the surrounding stromal cells, at least partly via up-regulating expression of activin A and TGF-beta1.
Clinical Experience of Sutureless Closed Hemorrhoidectomy with LigaSure™ (2003)

This study confirms that LigaSure system can achieve a radical ablation of hemorrhoids, reduce operative time, and result in less postoperative pain on postoperative Days 1 and 2.