gebhart/patrepeval huggingface dataset:
A 65nm logic technology featuring 35nm gate lengths, enhanced channel strain, 8 Cu interconnect layers, low-k ILD and 0.57 μm/sub 2/ SRAM cell (2005)

A 65nm generation logic technology with 1.2nm physical gate oxide, 35nm gate length, enhanced channel strain, NiSi, 8 layers of Cu interconnect, and low-k ILD for dense high performance logic is presented. Transistor gate length is scaled down to 35nm while not scaling the gate oxide as a means to improve performance and reduce power. Increased NMOS and PMOS drive currents are achieved by enhanced channel strain and junction engineering. 193nm lithography along with APSM mask technology is used on critical layers to provide aggressive design rules and a 6-T SRAM cell size of 0.57/spl mu/m/sup 2/. Process yield, performance and reliability are demonstrated on a 70 Mbit SRAM test vehicle with >0.5 billion transistors.
Bacteriophage protein Gp46 is a cross-species inhibitor of nucleoid-associated HU proteins (2022)

The architectural protein histone-like protein from <i>Escherichia coli</i> strain U93 (HU) is the most abundant bacterial DNA binding protein and highly conserved among bacteria and Apicomplexan parasites. It not only binds to double-stranded DNA (dsDNA) to maintain DNA stability but also, interacts with RNAs to regulate transcription and translation. Importantly, HU is essential to cell viability for many bacteria; hence, it is an important antibiotic target. Here, we report that Gp46 from bacteriophage SPO1 of <i>Bacillus subtilis</i> is an HU inhibitor whose expression prevents nucleoid segregation and causes filamentous morphology and growth defects in bacteria. We determined the solution structure of Gp46 and revealed a striking negatively charged surface. An NMR-derived structural model for the Gp46-HU complex shows that Gp46 occupies the DNA binding motif of the HU and therefore, occludes DNA binding, revealing a distinct strategy for HU inhibition. We identified the key residues responsible for the interaction that are conserved among HUs of bacteria and Apicomplexans, including clinically significant <i>Mycobacterium tuberculosis</i>, <i>Acinetobacter baumannii</i>, <i>and Plasmodium falciparum</i>, and confirm that Gp46 can also interact with these HUs. Our findings provide detailed insight into a mode of HU inhibition that provides a useful foundation for the development of antibacteria and antimalaria drugs.
Compartmental Hollow Fiber Capillary Membrane–Based Bioreactor Technology for <i>In Vitro</i> Studies on Red Blood Cell Lineage Direction of Hematopoietic Stem Cells (2011)

Continuous production of red blood cells (RBCs) in an automated closed culture system using hematopoietic stem cell (HSC) progenitor cell populations is of interest for clinical application because of the high demand for blood transfusions. Previously, we introduced a four-compartment bioreactor that consisted of two bundles of hollow fiber microfiltration membranes for transport of culture medium (forming two medium compartments), interwoven with one bundle of hollow fiber membranes for transport of oxygen (O(2)), carbon dioxide (CO(2)), and other gases (forming one gas compartment). Small-scale prototypes were developed of the three-dimensional (3D) perfusion cell culture systems, which enable convection-based mass transfer and integral oxygenation in the cell compartment. CD34(+) HSC were isolated from human cord blood units using a magnetic separation procedure. Cells were inoculated into 2- or 8-mL scaled-down versions of the previously designed 800-mL cell compartment devices and perfused with erythrocyte proliferation and differentiation medium. First, using the small-scale 2-mL analytical scale bioreactor, with an initial seeding density of 800,000 cells/mL, we demonstrated approximately 100-fold cell expansion and differentiation after 7 days of culture. An 8-mL laboratory-scale bioreactor was then used to show pseudocontinuous production by intermediately harvesting cells. Subsequently, we were able to use a model to demonstrate semicontinuous production with up to 14,288-fold expansion using seeding densities of 800,000 cells/mL. The down-scaled culture technology allows for expansion of CD34(+) cells and stimulating these progenitors towards RBC lineage, expressing approximately 40% CD235(+) and enucleation. The 3D perfusion technology provides an innovative tool for studies on RBC production, which is scalable.
HDL Phospholipid Content and Composition as a Major Factor Determining Cholesterol Efflux Capacity From Fu5AH Cells to Human Serum (1997)

The relationships of cell cholesterol efflux to HDL phospholipid (PL) content and composition in human serum were analyzed in two groups of subjects selected on the basis of their HDL cholesterol (HDL-C) levels: a norm-HDL group (1.10 mmol/L < HDL-C < 1.50 mmol/L) and a high-HDL group (HDL-C > 1.75 mmol/L). In the high-HDL group, the relative fractional efflux was significantly higher than in the norm-HDL group, and in both groups, fractional efflux was correlated with a number of lipoprotein parameters, the best correlation and the only one that remained significant after multivariate analysis being with HDL phospholipid (HDL-PL). Analysis of the HDL-PL subclasses revealed that HDL in the high-HDL sera was enriched with phosphatidylethanolamine (HDL-PE) and relatively deficient in sphingomyelin (HDL-SM) compared with norm-HDL sera. Moreover, the fractional efflux values in the high-HDL group were negatively correlated with the proportion of HDL-PE (r = -.64, P < .0001) and positively correlated with the proportion of HDL-SM (r = .43, P < .01). Thus, this study provides evidence that HDL-PL concentration can be used to predict the capacity of serum to accept cellular cholesterol. Among the differences described between norm-HDL and high-HDL sera, the variability in PE to SM ratio might reflect changes in serum cholesterol acceptors that modulate the first step of reverse cholesterol transport.
Healing of back pain and some other neurological problems using preparations from the skin of the Arabian Gulf catfish (Arius Bilineatus Val.) (2006)

The Arabian Gulf catfish elaborates gel‐like proteinacious secretions when threatened or injured. It was established that preparations from the skin of the catfish can lead to accelerated wound healing and healing of diabetic foot ulcers. The preparations contain highly active proteins and lipids, including a group of enzymes, growth factors, high levels of arachidonic acid and it,s metabolites, cholesterol and chlesterol esters, components that act on blood vessels, components that act on blood cells and factors that cause vascular permeabilty. The preparations which were found to cure 80% of treated back pain patients, sciatica, some forms of paralysis, facial palsy and demyelination, were found to have noticeable effecs on a spastic case resulting from spinal chord injury. Both lipids and proteins seem to play important roles in the healing proceses. Such results provide new venues in understanding and curing a number of neurological problems. (Partly funded by His Highness Shaikh Jaber Al‐Ahmad Al‐Sabah, The Amir of Kuwait; Shaikh Nasser. Mohd. Al‐Ahmad Al‐Sabah, Minister of the Amiri Diwan; Kuwait foundation for the Advancement of Sciences grant No.; Kuwait University grant No. SBO‐19; and Jassim M. Al‐Hassan).
Characterization of rat 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4 isomerase cDNAs and differential tissue-specific expression of the corresponding mRNAs in steroidogenic and peripheral tissues. (1991)

The conversion of 3 beta-hydroxy-5-ene steroids by the enzyme complex 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4 isomerase (3 beta-HSD) is an essential step in the biosynthesis of all classes of hormonal steroids. We report the characterization of two types of cDNA clones encoding rat 3 beta-HSD isolated from a rat ovary lambda gt11 cDNA library with a human 3 beta-HSD cDNA probe. Both type I and type II cDNAs encode proteins of 372 amino acids having 94% homology. Transient expression of the type I and the type II 3 beta-HSD cDNAs in HeLa human cervical carcinoma cells reveals that both proteins possess 3 beta-hydroxysteroid dehydrogenase as well as delta 5-delta 4 isomerase activities for both delta 5-pregnene and delta 5-androstene precursors, although the type I 3 beta-HSD protein is more active than the type II. RNA blot analysis using type I 3 beta-HSD cDNA identifies major mRNA transcripts of 1.7 kilobase in rat ovary, testis, and adrenal poly(A)+ RNA. RNase protection assay using type I- and type II-specific cRNA probes revealed the existence of the two corresponding mRNAs in male and female rat adrenals and gonads as well as in female adipose tissue while only type I mRNA is present in male and female kidney. Moreover, in situ hybridization performed using type-specific labeled 24-mer oligonucleotides confirms that type I is the major mRNA species in the ovary and further indicates that both mRNA species have a similar cellular distribution in the ovarian tissue with the highest level of expression found in corpora lutea. Immunoblot analysis using polyclonal antibodies raised against purified human placental 3 beta-HSD identified a single 42-kDa band in rat ovary, testis, and adrenal, which agrees with the calculated molecular masses of 41,911 and 42,150 daltons for the type I and II proteins, respectively. Determination of 3 beta-HSD enzymatic activity using [14C]pregnenolone and [14C]dehydroepiandrosterone as substrates shows that 3 beta-HSD activity is present not only in the gonads and adrenals of animals of both sexes, but also in many peripheral tissues including adipose tissue, mammary gland, kidney, liver, prostate, seminal vesicle, uterus, skin, brain, heart, thymus, pancreas, lung, and spleen. The present data indicate the existence of two mRNAs encoding rat 3 beta-HSD and their differential tissular distribution in both steroidogenic and peripheral tissues.(ABSTRACT TRUNCATED AT 400 WORDS)
Detecting Concept Drift in Processes using Graph Metrics on Process Graphs (2017)

Work in organisations is often structured into business processes, implemented using process-aware information systems (PAISs). These systems aim to enforce employees to perform work in a certain way, executing tasks in a specified order. However, the execution strategy may change over time, leading to expected and unexpected changes in the overall process. Especially the unexpected changes may manifest without notice, which can have a big impact on the performance, costs, and compliance. Thus it is important to detect these hidden changes early in order to prevent monetary consequences. Traditional process mining techniques are unable to identify these execution changes because they usually generalise without considering time as an extra dimension, and assume stable processes. Most algorithms only produce a single process model, reflecting the behaviour of the complete analysis scope. Small changes cannot be identified as they only occur in a small part of the event log. This paper proposes a method to detect process drifts by performing statistical tests on graph metrics calculated from discovered process models. Using process models allows to additionally gather details about the structure of the drift to answer the question which changes were made to the process.
A Comparison Of Various Probit Methods For Analyzing Yes/No Data On A Log Scale. (1996)

Abstract : A study of the various probit methods to analyze biological data was undertaken to understand the various methods and to determine the requirements for the input data as to distribution, number, and tightness of data for the desired results. Calculations were run for many data sets, and results were compared. Graphical analysis and the Karber method were used along with the SAS Probit Procedure and EZ-Probit. All four methods provided very close agreement on most data sets, and the EZ-Probit program provided almost identical information to the SAS Probit Procedure. Real biological data sets were used for comparison purposes, and three other data sets were made up to simulate real data (with variations in the number and distribution of data points). Fiducial limits at the 95% confidence level were also calculated and compared. For those data sets which had no fiducial limits with SAS Probit at the 95% confidence interval, 85% confidence levels were calculated with the EZ-Probit method because it is not possible to adjust the confidence levels with SAS Probit. Different data sets were run in an attempt to minimize the amount of additional data points needed for an existing data set to tighten the fiducial limits and to show the correlation with a chi square distribution. Finally, it will be shown that the probability distributions from 0.01 to 0.99 are identical out to four decimal places for the SAS Probit and EZ-Probit and that there are only minor differences in the fiducial limits between the two methods for some data sets. Appendix A contains the program required to run the SAS Probit on a PC computer. The EZ-Probit method is included in Appendix B.
Directed shift of vaginal flora after topical application of sucrose gel in a phase III clinical trial: a novel treatment for bacterial vaginosis. (2010)

These findings suggest that sucrose gel restores normal vaginal flora more rapidly than metronidazole gel and can be used as a novel treatment for BV.
Epitaxial SiGeC/Si photodetector with response in the 1.3-1.55 μm wavelength range (2002)

We demonstrate a Si-based photodetector with a response in the 1.3-1.55 /spl mu/m wavelength range. The active absorption layer of the pin photodiode consists of a pseudomorphic SiGeC alloy grown on a Si substrate with a Ge content of 55% and a thickness of 800 /spl Aring/. By using a single-mode fiber butt coupled to the waveguide facet, the external quantum efficiency for a 400-/spl mu/m long waveguide is 0.2% at 1.55 /spl mu/m, and 8% at 1.3 /spl mu/m. The external efficiency can be further improved by using a multiple layer absorber structure. The high efficiency and high speed characteristics together with the low leakage current density imply potential application of the SiGeC/Si photodetector for optical fiber communications and optical interconnects in the 1.3-1.55 /spl mu/m wavelength range.
Anticariogenic Effects of Tea in Rats (1984)

Teas varying in fluoride and tannin concentration were evaluated in rats for anticariogenic activity. There was a direct correlation between fluoride in tea and the inhibition of sulcal caries in rats, whereas no relationship was observed between tannin and this type of lesion. Teas also had a significant effect on caries progression and imparted a black stain to the teeth.
Authentication of Metropolitan Quantum Key Distribution Network with Post-quantum Cryptography (2021)

Quantum key distribution (QKD) provides information theoretically secures key exchange requiring authentication of the classic data processing channel via pre-sharing of symmetric private keys. In previous studies, the lattice-based post-quantum digital signature algorithm Aigis-Sig, combined with public-key infrastructure (PKI) was used to achieve high-efficiency quantum security authentication of QKD, and its advantages in simplifying the MAN network structure and new user entry were demonstrated. This experiment further integrates the PQC algorithm into the commercial QKD system, the Jinan field metropolitan QKD network comprised of 14 user nodes and 5 optical switching nodes. The feasibility, effectiveness and stability of the post-quantum cryptography (PQC) algorithm and advantages of replacing trusted relays with optical switching brought by PQC authentication large-scale metropolitan area QKD network were verified. QKD with PQC authentication has potential in quantum-secure communications, specifically in metropolitan QKD networks.
Zebrafish as a model to assess cancer heterogeneity, progression and relapse (2014)

Clonal evolution is the process by which genetic and epigenetic diversity is created within malignant tumor cells. This process culminates in a heterogeneous tumor, consisting of multiple subpopulations of cancer cells that often do not contain the same underlying mutations. Continuous selective pressure permits outgrowth of clones that harbor lesions that are capable of enhancing disease progression, including those that contribute to therapy resistance, metastasis and relapse. Clonal evolution and the resulting intratumoral heterogeneity pose a substantial challenge to biomarker identification, personalized cancer therapies and the discovery of underlying driver mutations in cancer. The purpose of this Review is to highlight the unique strengths of zebrafish cancer models in assessing the roles that intratumoral heterogeneity and clonal evolution play in cancer, including transgenesis, imaging technologies, high-throughput cell transplantation approaches and in vivo single-cell functional assays.
The Id-protein family in developmental and cancer-associated pathways (2017)

Inhibitors of DNA binding and cell differentiation (Id) proteins are members of the large family of the helix-loop-helix (HLH) transcription factors, but they lack any DNA-binding motif. During development, the Id proteins play a key role in the regulation of cell-cycle progression and cell differentiation by modulating different cell-cycle regulators both by direct and indirect mechanisms. Several Id-protein interacting partners have been identified thus far, which belong to structurally and functionally unrelated families, including, among others, the class I and II bHLH transcription factors, the retinoblastoma protein and related pocket proteins, the paired-box transcription factors, and the S5a subunit of the 26 S proteasome. Although the HLH domain of the Id proteins is involved in most of their protein-protein interaction events, additional motifs located in their N-terminal and C-terminal regions are required for the recognition of diverse protein partners. The ability of the Id proteins to interact with structurally different proteins is likely to arise from their conformational flexibility: indeed, these proteins contain intrinsically disordered regions that, in the case of the HLH region, undergo folding upon self- or heteroassociation. Besides their crucial role for cell-fate determination and cell-cycle progression during development, other important cellular events have been related to the Id-protein expression in a number of pathologies. Dysregulated Id-protein expression has been associated with tumor growth, vascularization, invasiveness, metastasis, chemoresistance and stemness, as well as with various developmental defects and diseases. Herein we provide an overview on the structural properties, mode of action, biological function and therapeutic potential of these regulatory proteins.
Purification and some properties of a lectin from the fruit juice of the tomato (<i>Lycopersicon esculentum</i>) (1980)

In the tomato (Lycopersicon esculentum) plant, the fruit juice was found to be the richest source of agglutinating activity. The lectin responsible could be inhibited by oligomers of N-acetylglucosamine, and this property was exploited to purify the lectin by affinity adsorption on trypsin-treated erythrocytes. The lectin is a glycoprotein that cross-reacts immunologically with the lectin from Datura stramonium (thorn-apple).
The common ancestral core of vertebrate and fungal telomerase RNAs (2012)

Telomerase is a ribonucleoprotein with an intrinsic telomerase RNA (TER) component. Within yeasts, TER is remarkably large and presents little similarity in secondary structure to vertebrate or ciliate TERs. To better understand the evolution of fungal telomerase, we identified 74 TERs from Pezizomycotina and Taphrinomycotina subphyla, sister clades to budding yeasts. We initially identified TER from Neurospora crassa using a novel deep-sequencing-based approach, and homologous TER sequences from available fungal genome databases by computational searches. Remarkably, TERs from these non-yeast fungi have many attributes in common with vertebrate TERs. Comparative phylogenetic analysis of highly conserved regions within Pezizomycotina TERs revealed two core domains nearly identical in secondary structure to the pseudoknot and CR4/5 within vertebrate TERs. We then analyzed N. crassa and Schizosaccharomyces pombe telomerase reconstituted in vitro, and showed that the two RNA core domains in both systems can reconstitute activity in trans as two separate RNA fragments. Furthermore, the primer-extension pulse-chase analysis affirmed that the reconstituted N. crassa telomerase synthesizes TTAGGG repeats with high processivity, a common attribute of vertebrate telomerase. Overall, this study reveals the common ancestral cores of vertebrate and fungal TERs, and provides insights into the molecular evolution of fungal TER structure and function.
HIV-Protease Inhibitors Contribute to P-Glycoprotein Efflux Function Defect in Peripheral Blood Lymphocytes From HIV-Positive Patients Receiving HAART (2001)

Summary: P-glycoprotein (P-gp) has been found expressed in normal human cells, such as bone marrow and peripheral blood cells. The aim of this study was to investigate whether HIV-protease inhibitors (HIV-PIs) interact with P-gp efflux function in normal human peripheral blood lymphocytes (PBLs) and CD34+ progenitor cells. Moreover, we analyzed the in vivo effect of HIV-PIs on P-gp function in PBLs from HIV-infected patients receiving highly active antiretroviral therapy (HAART). We found that HIV-PIs (i.e., ritonavir, saquinavir, nelfinavir and indinavir) interfere with P-gp function in normal PBLs as demonstrated by the reduced efflux of rhodamine 123 (Rh123). This effect was dose-dependent and suggested the following hierarchy: ritonavir > saquinavir > nelfinavir > indinavir. We further analyzed the effect of HIV-PIs on the P-gp function in specific PBLs subsets. Our results show an HIV-PI-induced inhibition of P-gp function in CD4+ and CD8+ T cell subsets, mostly caused by the effect on the naive compartment of both CD4+ and CD8+ T cells. The same inhibitory effect was found in CD34+ hematopoietic progenitor cells. With respect to the in vivo evaluation of P-gp function in PBLs from HIV-infected patients, we found reduced levels of Rh123 efflux that reached the lowest value in AIDS patients receiving HAART. We concluded that HIV-PIs interfere with P-gp function in major cellular targets for HIV infection, such as CD4+ T cells and CD34+ progenitor cells. This ability may contribute to P-gp efflux function defect found in HIV-infected patients and suggests that drug interaction studies are crucial to an overall understanding of the effects of this important group of drugs.
An Integration SPWM Strategy for High-Frequency Link Matrix Converter With Adaptive Commutation in One Step Based on De-Re-Coupling Idea (2011)

When matrix converter (MC) and high-frequency link (HFL) are combined together, they become more complex and gain a safe commutation for the use of high-frequency transformer. To realize energy conversion and transmission, and to achieve reliable and safe commutation at the same time are particularly important and desirable. HFL matrix converter (HFLMC) can be divided into two types: high-frequency link matrix inverter (HFLMI) and high-frequency link matrix rectifier (HFLMR). A three-phase output HFLMI is selected as the object of this study, and a novel integration sinusoidal pulse width modulation (SPWM) control strategy with one-step adaptive commutation based on De-Re-coupling idea is proposed for it. After expounding on the De-Re-coupling idea, a kind of HFLMC equivalent circuit model based on the high-frequency transformer equivalent circuit is built up. Then, a detailed analysis of the voltage stress on power devices of the HFLMC by using this model is performed. A safe operation evaluation criterion of HFLMC is also gained. A suggestion of how to select carrier wave for integration SPWM is ascertained through detail discussion, and two kinds of specific Re-coupling logic circuits are presented, and at last some experimental results are shown to make a certification for feasibility and effectiveness of the new proposed SPWM strategy.