gebhart/patrepeval huggingface dataset:
CoLIde (2013)

Small RNAs (sRNAs) are 20-25 nt non-coding RNAs that act as guides for the highly sequence-specific regulatory mechanism known as RNA silencing. Due to the recent increase in sequencing depth, a highly complex and diverse population of sRNAs in both plants and animals has been revealed. However, the exponential increase in sequencing data has also made the identification of individual sRNA transcripts corresponding to biological units (sRNA loci) more challenging when based exclusively on the genomic location of the constituent sRNAs, hindering existing approaches to identify sRNA loci. To infer the location of significant biological units, we propose an approach for sRNA loci detection called CoLIde (Co-expression based sRNA Loci Identification) that combines genomic location with the analysis of other information such as variation in expression levels (expression pattern) and size class distribution. For CoLIde, we define a locus as a union of regions sharing the same pattern and located in close proximity on the genome. Biological relevance, detected through the analysis of size class distribution, is also calculated for each locus. CoLIde can be applied on ordered (e.g., time-dependent) or un-ordered (e.g., organ, mutant) series of samples both with or without biological/technical replicates. The method reliably identifies known types of loci and shows improved performance on sequencing data from both plants (e.g., A. thaliana, S. lycopersicum) and animals (e.g., D. melanogaster) when compared with existing locus detection techniques. CoLIde is available for use within the UEA Small RNA Workbench which can be downloaded from: http://srna-workbench.cmp.uea.ac.uk.
Optical Control of the Optical Spin Hall Effect (2016)

The optical spin Hall effect results in a spatial texture in the pseudo-spin of exciton polaritons in semiconductor microcavities. Using circular pump polarization, we demonstrate theoretically and experimentally that this pattern can be optically controlled.
A New Halopropargylation of Alkynes Promoted by Boron Trihalides. Highly Stereo‐ and Regioselective Syntheses of Substituted (Z)‐1‐Halo‐1,4‐enyne Derivatives. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Synchronization in the identically driven systems (1996)

We investigate a transition from chaotic to nonchaotic behavior and synchronization in an ensemble of systems driven by identical random forces. We analyze the synchronization phenomenon in the ensemble of particles moving with friction in the time-dependent potential and driven by the identical noise. We define the threshold values of the parameters for transition from chaotic to nonchaotic behavior and investigate dependencies of the Lyapunov exponents and power spectral density on the nonlinearity of the systems and character of the driven force.
Withdrawal of IL-7 induces Bax translocation from cytosol to mitochondria through a rise in intracellular pH (1999)

IL-7 functions as a trophic factor during T lymphocyte development by a mechanism that is partly based on the induction of Bcl-2, which protects cells from apoptosis. Here we report a mechanism by which cytokine withdrawal activates the prodeath protein Bax. On loss of IL-7 in a dependent cell line, Bax protein translocated from the cytosol to the mitochondria, where it integrated into the mitochondrial membrane. This translocation was attributable to a conformational change in the Bax protein itself. We show that a rise in intracellular pH preceded mitochondrial translocation and triggered the change in Bax conformation. Intracellular pH in the IL-7-dependent cells rose steadily to peak over pH 7.8 by 6 hr after cytokine withdrawal, paralleling the time point of Bax translocation (a similar alkalinization and Bax translocation was also observed after IL-3 withdrawal from a dependent cell line). The conformation of Bax was directly altered by pH of 7.8 or higher and was demonstrated by increased protease sensitivity, exposure of N terminus epitopes, and exposure of a hydrophobic domain in the C terminus. Eliminating charged amino acids at the C or N termini of Bax induced a conformational change similar to that induced by raising pH, implicating these residues in the pH effect. Therefore, we have shown that by either cytokine withdrawal, experimental manipulation of pH, or site-directed mutagenesis, Bax protein changes conformation, exposing membrane-seeking domains, thereby inducing mitochondrial translocation and initiating the cascade of events leading to apoptotic death.
Proteome analysis of aflatoxin B1‐induced hepatocarcinogenesis in tree shrew (Tupaia belangeri chinensis) and functional identification of candidate protein peroxiredoxin II (2008)

In order to explore the proteins responsible for hepatocellular carcinoma (HCC), aflatoxin B(1)-induced hepatocarcinogenesis in tree shrew (Tupaia belangeri chinensis) was analyzed with 2-DE and MS. By comparing HCC samples with their own precancerous biopsies and HCC-surrounding tissues, a group of candidate proteins that differentially expressed in HCC were obtained. Peroxiredoxin (Prx) II, one of the candidates with distinct alteration, was further investigated and validated. Western blot and RT-PCR assays confirmed the overexpression of Prx II in both tree shrew and human HCC tissues. RNA interference for silencing Prx II was employed subsequently to explore the function and underlying mechanism of Prx II on liver cancer cell line Hep3B. Results showed the cell proliferation and clone formation decreased obviously when Prx II expression was inhibited, while the flow cytometer analysis showed the percentage of cell apoptosis enhanced. Inhibition of Prx II expression also obviously increased the generation of ROS and malondialdehyde, both are the products from peroxidation. These results imply the important role of Prx II in hepatocarcinogenesis, possibly through its function in regulating peroxidation and hereby to provide a favorable microenvironment for cancer cell surviving and progressing.
Enhancement of light-extraction efficiency of organic light-emitting diodes using silica nanoparticles embedded in TiO_2 matrices (2014)

We investigate two types of internal light-extraction layer structures for organic light-emitting diodes (OLEDs) that consist of silica nanoparticles (NPs) embedded in high-refractive-index TiO₂ matrices. The composite of silica NPs and TiO₂ matrices was coated on the glass substrate and fabricated with and without a SiO₂ planarization layer. An increase in the optical out-coupling efficiency by a factor of 2.0 was obtained at a high luminance of 3,000 cd/m² from OLEDs containing the silica NPs embedded in TiO₂ matrices between glass substrates and Zn-doped In₂O₃ (IZO) electrodes after additional planarization processes. This is consistent with the analytical result using the finite-difference time-domain (FDTD) method. Randomly distributed silica NPs acting as scattering centers could reduce the optical loss when extracting light. By using additional planarization processes with a PECVD-derived SiO₂ layer, one can assure that smoother surfaces provide higher out-coupling efficiency, which attain 100% and 97% enhancements in power (lm/W) and current (cd/A) efficiencies, respectively.
The slime of coagulase-negative staphylococci: Biochemistry and relation to adherence (1993)

In recent years, infections of implanted plastic devices by coagulase-negative staphylococci have become a major cause of septicaemia in human patients. The causal bacterial species is usually Staphylococcus epidermidis and these organisms grow as a biofilm adherent to a solid surface. Several methods have been introduced to assess the mass of adherent bacteria and the slimy matrix in which they are embedded. Some methods measure total biofilm, others measure the organisms or the slime alone. In vitro, the type of medium, the atmosphere during incubation, and the nature of the solid surface, affect the quantity of biofilm that is formed. In most studies on the chemistry of the slime, the material used was formed on complex media solidified with agar. Contamination by ingredients of the media or by agar may not always have been recognised. Recent work with chemically defined medium (liquid or solidified with silica gel) shows that the slime is a mixture of about 80% (w/w) teichoic acid and 20% protein. Growth as a biofilm may protect the staphylococci from antibiotics. At present, the greatest success in preventing infection has come from improved surgical techniques during the insertion of implants.
Tumor Necrosis Factor Alpha Exerts Powerful Anti-Influenza Virus Effects in Lung Epithelial Cells (2002)

Previous studies have associated influenza virus-induced expression of inflammatory cytokines, including tumor necrosis factor alpha (TNF-alpha), with influenza pathogenesis in the human respiratory tract and have suggested that alpha and beta interferons are the first cytokines recruited to counteract such infection. However, we report here that TNF-alpha has powerful anti-influenza virus activity. When infected with influenza virus, cultured porcine lung epithelial cells expressed TNF-alpha in a dose-dependent manner. Expression of TNF-alpha was induced only by replicating virus. TNF-alpha showed strong antiviral activity against avian, swine, and human influenza viruses, and the antiviral effect of TNF-alpha was greater than that of gamma or alpha interferon. These findings suggest that TNF-alpha serves as the first line of defense against influenza virus infection in the natural host.
Gut Microbiota, Host Gene Expression, and Aging (2014)

Novel concepts of disease susceptibility and development suggest an important role of gastrointestinal microbiota and microbial pathogens. They can contribute to physiological systems and disease processes, even outside of the gastrointestinal tract. There is increasing evidence that genetics of the host influence and interact with gut microbiota. Moreover, aging-associated oxidative stress may cause morphologic alterations of bacterial cells, thus influencing the aggressive potential and virulence markers of an anaerobic bacterium and finally the type of interaction with the host. At the same time, microbiota may influence host gene expression and it is becoming apparent that it may occur through the regulation of microRNAs. They are short single-stranded noncoding RNAs that regulate posttranscriptional gene expression by affecting mRNA stability and/or translational repression of their target mRNAs. The introduction of -omics approaches (such as metagenomics, metaproteomics, and metatranscriptomics) in microbiota research will certainly advance our knowledge of this area. This will lead to greatly deepen our understanding of the molecular targets in the homeostatic interaction between the gut microbiota and the host and, thereby, promises to reveal new ways to treat diseases and maintain health.
SCAFFOLD GUIDED BONE TISSUE ENGINEERING IN A RABBIT ANIMAL MODEL (2010)

Aim: The aim of the current study is to investigate if viscosupplemetation therapy will increase the effect of microfracture technique by acting the quality and quantity of the new cartilage after microfracture. Material and Method: Full thickness chondral defects were created to intercondylar notch as a nonweightbearing area by using a handle drill bit. Microfracture holes between bridges were performed with a 1mm K wire. The present study was performed on 30 mature white rabbits (male range, 2800–3500 gr). The right knees were accepted as study and left knees as control group. Group 1 was received intraarticular 0.1ml sodium hyaluronate treatment, rabbits in group 2 were received 0.1 ml Serum Physiologique once a week for three weeks. Biopsy was taken from both knees at the 3rd and 6th week. Histopathological evaluation was performed by a pathologist who is blind to study according to modified Mankin score. Results: Although the difference of the scores between study and control group was not statistically different at the third week, it was seen different at the sixth week histologically. Conclusion: Hyaluronic acid may be benefecial in the treatment of chondral lesion addition to arthroscopic microfracture technique.
Drug-Induced Sleep Endoscopy: A Guide for Treatment Selection (2020)

Identifying the sites, severity, and pattern of upper airway obstruction in obstructive sleep apnea is crucial for determining the treatment options, particularly the surgical plan. Although early methods of assessment, such as Muller's maneuver, computed tomography, and magnetic resonance imaging in awake patients have been utilized to assess obstructive sites, the physiologic and anatomical differences between awake and sleeping patients showed a limited ability of those methods as diagnostic tools. Recently, drug-induced sleep endoscopy (DISE) was introduced as a useful diagnostic and evaluation tool to identify dynamic upper airway collapse during sedation that simulates natural sleep. In this article, we review all aspects of DISE, including the technique, evaluation methods, and clinical application.
Predictive Maintenance of Boiler Feed Water Pumps Using SCADA Data (2020)

IoT enabled predictive maintenance allows companies in the energy sector to identify potential problems in the production devices far before the failure occurs. In this paper, we propose a method for early detection of faults in boiler feed pumps using existing measurements currently captured by control devices. In the experimental part, we work on real measurement data and events from a coal fired power plant. The main research objective is to implement a model that detects deviations from the normal operation state based on regression and to check which events or failures can be detected by it. The presented technique allows the creation of a predictive system working on the basis of the available data with a minimal requirement of expert knowledge, in particular the knowledge related to the categorization of failures and the exact time of their occurrence, which is sometimes difficult to identify. The paper shows that with modern technologies, such as the Internet of Things, big data, and cloud computing, it is possible to integrate automation systems, designed in the past only to control the production process, with IT systems that make all processes more efficient through the use of advanced analytic tools.
D221 in Thymidylate Synthase Controls Conformation Change, and Thereby Opening of the Imidazolidine, (1998)

In thymidylate synthase (TS), the invariant residue Asp-221 provides the only side chain that hydrogen bonds to the pterin ring of the cofactor, 5,10-methylene-5,6,7,8-tetrahydrofolate. All mutants of D221 except cysteine abolish activity. We have determined the crystal structures of two ternary complexes of the Escherichia coli mutant D221N. In a complex with dUMP and the antifolate 10-propargyl-5,8-dideazafolate (CB3717), dUMP is covalently bound to the active site cysteine, as usual. CB3717, which has no imidazolidine ring, is also bound in the usual productive orientation, but is less ordered than in wild-type complexes. The side chain of Asn-221 still hydrogen bonds to N3 of the quinazoline ring of CB3717, which must be in the enol form. In contrast, the structure of D221N with 5-fluoro-dUMP and 5,10-methylene-5,6,7, 8-tetrahydrofolate shows the cofactor bound in two partially occupied, nonproductive binding sites. In both binding modes, the cofactor has a closed imidazolidine ring and adopts the solution conformation of the unbound cofactor. In one of the binding sites, the pterin ring is turned around such that Asn-221 hydrogen bonds to the unprotonated N1 instead of the protonated N3 of the cofactor. This orientation blocks the conformational change required for forming covalent ternary complexes. Taken together, the two crystal structures suggest that the hydrogen bond between the side chain of Asp-221 and N3 of the cofactor is most critical during the early steps of cofactor binding, where it enforces the correct orientation of the pterin ring. Proper orientation of the cofactor appears to be a prerequisite for opening the imidazolidine ring prior to formation of the covalent steady-state intermediate in catalysis.
Knowledge Map Automatic Update System Using Graph Convolutional Network (2023)

Instead of face-to-face learning, online learning plays a significant role now. Some teachers, schools, and colleges have started using online learning systems, such as Massive Open Online Courses (MOOCs). The online learning system contains the learning part and the exercising part. Our laboratory has released a brand new way of exercising part. Students could do some exercises through our system, and each exercise would map to a knowledge concept in the knowledge map. In this paper, we propose a knowledge map update system. It comprises two main parts: a Graph Convolutional Network (GCN) and a knowledge map renewing algorithm. This system would give the students a better and more reasonable knowledge map. The proposed system could predict students’ learning condition indicators in GCN, use GCN as a evaluation metric and update a new knowledge map. We collected data for five classes and 486 students. As the results show, our GCN model has an average of 76% accuracy in predicting.
Cholesterol Chip for the Study of Cholesterol–Protein Interactions Using SPR (2022)

Cholesterol, an important lipid in animal membranes, binds to hydrophobic pockets within many soluble proteins, transport proteins and membrane bound proteins. The study of cholesterol-protein interactions in aqueous solutions is complicated by cholesterol's low solubility and often requires organic co-solvents or surfactant additives. We report the synthesis of a biotinylated cholesterol and immobilization of this derivative on a streptavidin chip. Surface plasmon resonance (SPR) was then used to measure the kinetics of cholesterol interaction with cholesterol-binding proteins, hedgehog protein and tyrosine phosphatase 1B.
Gly-Gly-X, a Novel Consensus Sequence for the Proteolytic Processing of Viral and Cellular Proteins (1989)

Three African swine fever virus structural proteins of relative molecular weights 150,000, 37,000, and 34,000 (p150, p37, and p34) are derived from precursors with relative molecular weights 220,000, 60,000, and 39,000 (pp220, pp60, and pp39) by proteolytic cleavage after the second Gly residue in the sequence Gly-Gly-Ala/Gly. A search of the National Biomedical Research Foundation Data Bank revealed that several adenovirus proteins, ubiquitin, and an interferon-induced 15-kDa protein are also derived from precursors that are cleaved at the sequence Gly-Gly-X, where X is often an amino acid residue with a hydrophobic side chain. The sequence Gly-Gly-X together with other physical properties of the protein seems to be a recognition sequence for the processing of a variety of viral and cellular proteins.
ChemInform Abstract: A Facile, Convenient, and Green Route to (E)‐Propenylbenzene Flavors and Fragrances by Alkene Isomerization. (2016)

Abstract The very effective scalable isomerization reactions are performed in the presence of either a homogeneous Ru‐catalyst or polymer‐supported analogues thereof.
Membrane Bioreactors for Green Processing in a Sustainable Production System (2013)

This chapter contains sections titled: Introduction Membrane Bioreactors Biocatalytic Membrane Reactors Case Studies: Membrane Bioreactors Green Processing Impact of Membrane Bioreactors Conclusion References
Automated Mechanical Exfoliation of MoS2 and MoTe2 Layers for Two-Dimensional Materials Applications (2018)

An automated technique is presented for mechanically exfoliating single-layer and few-layer transition metal dichalcogenides using controlled shear and normal forces imposed by a parallel plate rheometer. A thin sample that is removed from bulk MoS <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> or MoTe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> is initially attached to the movable upper fixture of the rheometer using blue dicing tape while the lower base plate also has the same tape to capture and exfoliate samples when the two plates are brought into contact then separated. A step-and-repeat exfoliation process is initiated using a preprogrammed contact force and liftoff speed. It was determined that atomically thin films of these materials could be obtained reproducibly using this technique, achieving single-layer and few-layer thicknesses for engineering novel two-dimensional transistor devices for future electronic technologies. We show that varying the parameters of the rheometer program can improve the mechanical exfoliation process.
Insulin resistance in transgender individuals correlates with android fat mass (2021)

Android fat more strongly correlates with insulin resistance than gynoid fat in transgender individuals. Higher fat mass and insulin resistance in trans women may predispose to increased cardiovascular risk. Despite adverse fat distribution, insulin resistance was not higher in trans men.
Using Compression to Identify Classes of Inauthentic Texts (2006)

Recent events have made it clear that some kinds of technical texts, generated by machine and essentially meaningless, can be confused with authentic, technical texts written by humans. We identify this as a potential problem, since no existing systems for, say the web, can or do discriminate on this basis. We believe that there are subtle, short- and long-range word or even string repetitions extant in human texts, but not in many classes of computer generated texts, that can be used to discriminate based on meaning. In this paper we employ universal lossless source coding to generate features in a high-dimensional space and then apply support vector machines to discriminate between the classes of authentic and inauthentic expository texts. Compression profiles for the two kinds of text are distinct—the authentic texts being bounded by various classes of more compressible or less compressible texts that are computer generated. This in turn led to the high prediction accuracy of our models which support a conjecture that there exists a relationship between meaning and compressibility. Our results show that the learning algorithm based upon the compression profile outperformed standard term-frequency text categorization on several non-trivial classes of inauthentic texts. Availability: http://www.informatics.indiana.edu/predrag/fsi.htm.
Fracture‐Toughness Test of Silicon Nitrides with Different Microstructures Using Vickers Indentation (2007)

This chapter contains sections titled: Introduction Experimental Procedure Results Discussion Conclusion Acknowledgment
Association Between Very Young Age and Adverse Characteristics of Breast Cancer at Presentation Amongst Israeli Women (2010)

Very young age among Israeli women with breast cancer is associated with higher stage at diagnosis, adverse pathologic characteristics and adverse outcome but is not an independent prognostic factor for survival.
Clotting in dialyzers due to low pH of dialysis fluid. (1977)

During November and December 1975 frequent clotting occurred in the extracorporeal circuits of different dialyzers used in our unit. After installation of new automatically regenerating ion exchange resin columns,, the pH of deionized water ranged from 4.2 to 8.4 during 24 hr periods. Dialysate pH ranged between 5.3 and 8.2, and the patient's whole blood pHs ranged from 7.15 to 7.4 at the dialyzer inlet and from 6.2 (!) to 7.4 at the outlet. A strong correlation was seen between the acidity of the water and the frequency of clotting, and it was considered possible that the clotting was due to structural changes within the heparin molecules induced by the low pH. Following the introduction of an automatic titration device into our dialyzate preparation system, clotting with consecutive blood loss and subjective clinical symptoms have disappeared.