gebhart/patrepeval huggingface dataset:
The RFX Family Interacts at the Collagen (COL1A2) Start Site and Represses Transcription (2002)

The transcription start site of the collagen alpha2(1) gene (COL1A2) has a sequence-specific binding site for a DNA methylation-responsive binding protein called regulatory factor for X-box 1 (RFX1) (Sengupta, P. K., Erhlich, M., and Smith, B. D. (1999) J. Biol. Chem. 274, 36649-36655). In this report, we demonstrate that RFX1 forms homodimers as well as heterodimers with RFX2 spanning the collagen transcription start site. Methylation at +7 on the coding strand increases RFX1 complex formation in gel shift assays. Methylation on the template strand, however, does not increase RFX1 complex formation. DNA from human fibroblasts contains minimal methylation on the coding strand (<4%) with variable methylation on the template strand. RFX1 acts as a repressor of collagen transcription as judged by in vitro transcription and co-transfection assays with an unmethylated collagen promoter-reporter construct. In addition, an RFX5 complex present in human fibroblasts interacts with the collagen RFX site, which is not sensitive to methylation. This is the first demonstration of RFX5 complex formation on a gene other than major histocompatibility complex (MHC) promoters. Also, RFX5 represses transcription of a collagen promoter-reporter construct in rat fibroblasts that have no detectable RFX5 complex formation or protein. RFX5 complex activates MHC II transcription by interacting with an interferon-gamma (IFN-gamma)-inducible protein, major histocompatibility class II trans-activator (CIITA). Collagen transcription is repressed by IFN-gamma in a dose-dependent manner in human but not in rat fibroblasts. IFN-gamma enhances RFX5 binding activity, and CIITA is present in the RFX5 complex of IFN-gamma-treated human fibroblasts. CIITA repressed collagen gene transcription more effectively in human fibroblasts than in rat fibroblasts, suggesting that the RFX5 complex may, in part, recruit CIITA protein to the collagen transcription start site. Thus the RFX family may be important repressors of collagen gene transcription through a RFX binding site spanning the transcription start site.
Estradiol-Loaded Poly(ε-caprolactone)/Silk Fibroin Electrospun Microfibers Decrease Osteoclast Activity and Retain Osteoblast Function (2018)

Estrogen, a steroid hormone, plays an important role in modulating osteoclast proliferation and development. Estrogen deficiency boosts osteoclast activity, leading to osteoporosis in elderly women. In this study, 17-ß estradiol (E2)-loaded poly(ε-caprolactone) (PCL)/silk fibroin (SF) electrospun microfibers were developed as a proposed localized E2 delivery system to treat osteoporotic fractures. PCL is a synthetic polymer known for its biocompatibility and excellent mechanical properties. The bioactivity of PCL was enhanced by mixing it with a natural SF polymer that has low immunogenicity and inherent bioactivity. Different ratios of PCL/SF blends were electrospun and characterized by scanning electron microscopy, Fourier transform infrared spectroscopy, and water contact angle measurement. PCL and SF at a ratio of 50:50 (PCL50/SF50) augmented cell proliferation of murine preosteoblast MC3T3-E1 cells and murine preosteoclast RAW 264.7 cells. Hence, PCL50/SF50 was selected and mixed with three concentrations of E2 to produce electrospun fiber mesh (0.1% E2@PCL/SF, 1% E2@PCL/SF, and 5% E2@PCL/SF). Sustained release of E2 was obtained for about 3 weeks at higher E2 concentration 5% E2@PCL/SF. An E2-loaded PCL50/SF50 elecrospun microfiber (1% E2@PCL/SF and 5% E2@PCL/SF) reduced tartrate-resistant acid phosphate activity, total DNA, and multinucleated cell formation of osteoclasts. On the other hand, the alkaline phosphatase activity and collagen I expression of osteoblasts were retained on all E2-loaded electrospun microfibers. The E2@PCL/SF system shows potential to be used for localized E2 delivery for the treatment of osteoporotic fractures.
Lanosterol synthase mutations cause cholesterol deficiency-associated cataracts in the Shumiya cataract rat (2006)

The Shumiya cataract rat (SCR) is a hereditary cataractous strain. It is thought that the continuous occurrence of poorly differentiated epithelial cells at the bow area of the lens forms the pathophysiological basis for cataract formation in SCRs. In this study, we attempted to identify the genes associated with cataract formation in SCRs by positional cloning. Genetic linkage analysis revealed the presence of a major cataract locus on chromosome 20 as well as a locus on chromosome 15 that partially suppressed cataract onset. Hypomorphic mutations were identified in genes for lanosterol synthase (Lss) on chromosome 20 and farnesyl diphosphate farnesyl transferase 1 (Fdft1) on chromosome 15, both of which function in the cholesterol biosynthesis pathway. A null mutation for Lss was also identified. Cataract onset was associated with the specific combination of Lss and Fdft1 mutant alleles that decreased cholesterol levels in cataractous lenses to about 57% of normal. Thus, cholesterol insufficiency may underlie the deficient proliferation of lens epithelial cells in SCRs, which results in the loss of homeostatic epithelial cell control of the underlying fiber cells and eventually leads to cataractogenesis. These findings may have some relevance to other types of cataracts, inborn defects of cholesterol synthesis, and the effects of cholesterol-lowering medication.
The role of excision and surveillance alone in subclinical DCIS of the breast. (1994)

Mammography has led to the earlier detection of nonpalpable, subclinical DCIS, either as nonpalpable calcifications or as an incidental finding in a biopsy. Concurrently, the inevitable progression of DCIS to invasive carcinoma has been questioned, so that traditional treatment of this disease has been challenged. Local excision alone for carefully selected patients with DCIS can result in a recurrence rate as low as 15%. Candidates for treatment by surveillance alone after local excision are those patients with a limited area of DCIS on mammography, detected as an area of calcifications 6 cm2 (2.0 to 2.5 cm diameter) or less. Subgroups of DCIS, such as the comedo form, may be more likely to recur. The ultimate objective is to identify the population of patients with subclinical DCIS who are unlikely to suffer recurrence of disease after local excision alone, sparing them from either mastectomy or irradiation.
Lightweight Approach to Detect Drive-by Download Attacks Based on File Type Transition (2014)

A web-based attack, drive-by download attack, has been posing serious threats to Internet users. There are code analysis based methods and rule-based methods as countermeasures against drive-by download attacks. However, code analysis based methods require high analytical costs. Also, rule-based methods have difficulty in forming comprehensive detection rules to keep up with a change in the attack pattern. For network administrators to inspect a huge amount of communication data, a detection method must be developed that requires less costs to describe the attack's distinctive features and less effort to form detection rules. In this paper, we propose a lightweight and machine learning-based approach and evaluate the effectiveness.
Performance evaluation of memory consistency models for shared-memory multiprocessors (1991)

The memory consistency model supported by a multiprocessor architecture determines the amount of buffering and pipelining
Book Reports (2015)

This is a book on how people working on software code in an attempt to produce Artificial Intelligence (AI) (whatever that is) have consistently failed, despite the inaccurate hype in the media.
Microtenotomy Using a Radiofrequency Probe to Treat Lateral Epicondylitis (2005)

Level IV.
Diagnosis and validation of damaged piezoelectric sensor in electromechanical impedance technique (2016)

Piezoelectric sensor diagnosis and validity assessment as a prior component of structural health monitoring system are necessary in the practical application of electromechanical impedance technique. This article proposed an innovative sensor self-diagnosis process based on extracting the characterization of the real admittance (inverse of impedance) signature within a high-frequency range, which covered both diagnosis on damaged sensor after its installation and discrimination of sensor and structural damages during structural health monitoring process. Theoretical analysis was derived from the impedance model of piezoelectric-bonding layer-structure dynamic interaction system. Experimental investigations on piezoelectric sensor-bonded steel beam involved with structural damages of mass addition and notch damage were conducted to verify the process. It was found that the real admittance was reliable and critical in sensor diagnosis, and sensor faults of debonding, scratch, and breakage can be identified and differentiated from structural damage. Validity assessment of the diagnosed damaged sensor was addressed through resonant frequency shift method. The results showed that the validity of damaged sensor for structural health monitoring was inordinately depreciated by sensor damage. This article is expected to be useful for structural health monitoring application especially when damaged piezoelectric sensors existed.
MLL, a mammalian <i>trithorax-</i> group gene, functions as a transcriptional maintenance factor in morphogenesis (1998)

Determinative events in vertebrate embryogenesis appear to require the continuous expression of spatial regulators such as the clustered homeobox genes. The mechanisms that govern long-term patterns of gene expression are not well understood. In Drosophila, active and silent states of developmentally regulated loci are maintained by trithorax and Polycomb group. We have examined the developmental role of a mammalian homolog of trx and putative oncogene, Mll. Knockout mice reveal that Mll is required for maintenance of gene expression early in embryogenesis. Downstream targets of Mll including Hoxa7 are activated appropriately in the absence of Mll but require Mll for sustaining their expression. The Mll-/- phenotype manifests later in development and is characterized by branchial arch dysplasia and aberrant segmental boundaries of spinal ganglia and somites. Thus, Mll represents an essential mechanism of transcriptional maintenance in mammalian development, which functions in multiple morphogenetic processes.
Exhaled Breath Condensate in Asthma: From Bench to Bedside (2011)

The need for non-invasive assessment of airway inflammation is imperative, since inflammatory airway diseases, such as asthma and COPD, are characterized by variation in their clinical presentation throughout their course. Exhaled breath condensate (EBC) collection represents a rather appealing method that can be used to conveniently and noninvasively collect a wide range of volatile and non-volatile molecules from the respiratory tract, without affecting airway function or inflammation. Although promising, EBC is currently used only as a research tool, due to the lack of appropriate standardization and the absence of reference values. A large number of mediators of inflammation, oxidative and nitrosative stress, including adenosine, ammonia, hydrogen peroxide, isoprostanes, leukotrienes, prostanoids, nitrogen oxides, peptides and cytokines, have been studied in EBC. This review focuses mainly on the presentation of the above biomarkers in asthma as well as on the effect of various factors on their concentrations. Concentrations of such mediators have been shown to be related to the underlying asthma and its severity and to be modulated by therapeutic interventions. Despite the encouraging positive results up-to-date, the introduction of EBC in everyday clinical practice requires the work-out of some methodological pitfalls, the standardization of EBC collection, and finally the identification of a reliable biomarker which is reproducible, has normal values and provides information for the underlying inflammatory process and the response to treatment. So far none of the parameters studied in EBC fulfils the aforementioned requirements.
Robust Stability Investigation of the Interactions Among Grid-Forming and Grid-Following Converters (2019)

State-of-the-art grid-connected converters can be classified as “grid-following,” meaning that they require a dedicated synchronization unit in order to inject active and reactive currents into the grid. Recently, other converter control concepts have been proposed in the literature, such as the synchronverter, which can instead achieve synchronization without a dedicated unit and, within its physical limitations, make the converter behave as an ideal voltage source. Since it should be expected that the grid-connected converters having different control philosophies will coexist for many years, in this article, the interaction among the converters operating nearby are addressed. First, the component connection method (CCM) technique is introduced, as a means for obtaining the state-space representation of a complex system with several units operating nearby. Due to the complexity of the grid and the difficulty in obtaining its exact representation, μ-analysis is adopted in this article for assessing the robust stability of the converter under different operating conditions, according to a defined set of plant uncertainties. Simulation results and experimental tests in a laboratory environment by means of a power hardware-in-the-loop (PHIL) test bench are performed to demonstrate the validity of the presented analysis.
AC electrohydrodynamic instabilities in thin liquid films (2009)

When DC electric fields are applied to a thin liquid film, the interface may become unstable and form a series of pillars. In this paper, we apply lubrication theory to examine the possibility of using AC electric fields to exert further control over the size and shape of the pillars. For perfect dielectric films, linear stability analysis shows that the influence of an AC field can be understood by considering an effective DC field. For leaky dielectric films, Floquet theory is applied to carry out the linear stability analysis, and it reveals that high frequencies may be used to inhibit the accumulation of interfacial free charge, leading to a lowering of growth rates and wavenumbers. Nonlinear simulations confirm the results of the linear stability analysis while also uncovering additional mechanisms for tuning overall pillar height and width. The results presented here may be of interest for the controlled creation of surface topographical features in applications such as patterned coatings and microelectronics.
Effect of Surface-Active Agents on Fluoride-Enamel Interactions. I (1983)

The effect of surface-active agents (SAA) on fluoride deposition in enamel from topical application was studied in vitro. Preliminary imbibition experiments with blocks of human enamel showed that some SAA increased the fluoride penetration in depth during a 5-min fluoride application. Inclusion of several SAA in the fluoride solutions caused increased deposition of apatitically bound fluoride during a postapplication incubation period. Detailed observations on cetylpyridinium chloride or Lodyne S-110 fluorosurfactant showed that addition of these SAA to solutions of KF at pH 8.5, 7.0, and 5.0 tended to decrease the immediate penetration of fluoride at the acidic pH without compromising fluorapatite formation during the postapplication incubation. The fluorapatite formation was greatly enhanced when Lodyne S-110 was added to a treatment solution of KF with orthophosphate at pH 5. Addition of cetylpyridinium chloride to the currently frequently used acid phosphate fluoride solution increased the ability of this formulation to cause fluorapatite formation in enamel. Both SAA reduced the immediate fluoride penetration from acidic solutions of ammonium fluoride with orthophosphate without compromising postapplication fluorapatite formation and increased fluorapatite formation from application of neutral solutions.
The modified nucleosides of tRNAs. II. Synthesis of 2<sup>′</sup>-O-methylcytidylyl (3<sup>′</sup>-5<sup>′</sup>) cytidine (1975)

The synthesis of 2'-O-methylcytidylyl (3'-5')cytidine by the triester method using as protecting groups, 2,2,2-trichloroethyl for phosphate hydroxyl group, p-chlorophenyoxyacetyl for 5-hydroxyl group, methoxymethylidene for 2',3'-cis-diol system, and benzoyl for the exo-amino group of cytidine is presented. The obtained product was characterised by UV, electrophoresis, chromatography and an enzymatic digestion.
The Value and Application of the 6-Minute-Walk Test in Idiopathic Pulmonary Fibrosis (2017)

The 6-minute-walk test is a commonly used assessment of performance ability in a variety of cardiopulmonary diseases. It provides important functional information that is not captured in standardized pulmonary function testing. The test may be influenced by factors other than the severity of lung disease, including frailty, deconditioning, and musculoskeletal issues. The primary output measure from the 6-minute-walk test is the distance walked, which appears to confer prognostic information in many diverse disease states. The 6-minute-walk test distance has served as a primary endpoint in many drug trials, most notably in the field of pulmonary arterial hypertension, and to a lesser extent in idiopathic pulmonary fibrosis (IPF). Although the 6-minute-walk test has been used in clinical practice and research trials of IPF, there are no specific guidelines regarding its implementation in this growing patient population. Given that there is increasing evidence and experience with its use in clinical trials, development of nuanced standards designed specifically for IPF are much needed. This review touches on a number of complex and crucial issues in the application of this test and provides a framework for future development of 6-minute-walk test guidelines customized for IPF.
Body Awareness and Dance-Based Training for Persons with Acquired Blindness—Effects on Balance and Gait Speed (2006)

Background: Visual impairment may cause difficulties with motor skills involving postural control. As a part of rehabilitation, it is important to assess whether training can affect postural control in individuals with visual impairment. Aim: The purpose was to assess the effect of body awareness exercises and dance-based training on balance and gait speed in individuals of working age with acquired blindness. Method: Eight subjects with acquired blindness, aged 30–62 years, were recruited from the Low Vision Clinic of Stockholm. An ABA Single Subject Research Design was used. Results of one-leg stance, functional reach, maximum step length, timed up and go, and self-selected and maximum gait speeds were inspected visually and analyzed according to the 2-SD band method. The intervention included body awareness exercises and dance-based training twice a week for eight weeks. Results: Seven subjects completed the study. According to the 2-SD band technique, functional reach increased significantly in six of the subjects and was the variable that changed the most. Timed Up and Go decreased significantly in one subject and was the variable that changed the least. In one subject there was no change in any of the variables. Conclusion: According to the results, the main improvement was in the ability to reach forward. In some subjects, however, there was also improvement in other balance functions and in gait speed. Further studies are needed to assess the effect of body awareness and dance-based training in blind individuals.
Multicomponent Petasis‐borono Mannich Preparation of Alkylaminophenols and Antimicrobial Activity Studies (2016)

In this work we report the antibacterial activity of alkylaminophenols. A series of such compounds was prepared by a multicomponent Petasis-borono Mannich reaction starting from salicylaldehyde and its derivatives. The obtained compounds were tested against a large panel of microorganisms, Gram-positive and Gram-negative bacteria, and a yeast. Among the several tertiary amine derivatives tested, indoline-derived aminophenols containing a nitro group at the para-phenol position showed considerable activity against bacteria tested with minimal inhibitory concentrations as low as 1.36 μm against Staphyloccocus aureus and Mycobacterium smegmatis. Cytotoxicity of the new para-nitrophenol derivatives was observed only at concentrations much higher than those required for antibacterial activity.
Serum Anion Gap (2006)

The serum anion gap, calculated from the electrolytes measured in the chemical laboratory, is defined as the sum of serum chloride and bicarbonate concentrations subtracted from the serum sodium concentration. This entity is used in the detection and analysis of acid-base disorders, assessment of quality control in the chemical laboratory, and detection of such disorders as multiple myeloma, bromide intoxication, and lithium intoxication. The normal value can vary widely, reflecting both differences in the methods that are used to measure its constituents and substantial interindividual variability. Low values most commonly indicate laboratory error or hypoalbuminemia but can denote the presence of a paraproteinemia or intoxication with lithium, bromide, or iodide. Elevated values most commonly indicate metabolic acidosis but can reflect laboratory error, metabolic alkalosis, hyperphosphatemia, or paraproteinemia. Metabolic acidosis can be divided into high anion and normal anion gap varieties, which can be present alone or concurrently. A presumed 1:1 stoichiometry between change in the serum anion gap (DeltaAG) and change in the serum bicarbonate concentration (DeltaHCO(3)(-)) has been used to uncover the concurrence of mixed metabolic acid-base disorders in patients with high anion gap acidosis. However, recent studies indicate variability in the DeltaAG/DeltaHCO(3)(-) in this disorder. This observation undercuts the ability to use this ratio alone to detect complex acid-base disorders, thus emphasizing the need to consider additional information to obtain the appropriate diagnosis. Despite these caveats, calculation of the serum anion gap remains an inexpensive and effective tool that aids detection of various acid-base disorders, hematologic malignancies, and intoxications.
Effect of Hydrogen Bonding on the Vibrations of <i>p</i>-Benzosemiquinone Radical Anion (1998)

The vibrational bands experimentally observed for aqueous p-benzosemiquinone radical anion are analyzed by use of electronic structure calculations. To clarify the effects of solvation, calculations on the isolated semiquinone anion are compared to those on supermolecule clusters having two to four water molecules strongly hydrogen-bonded at the semiquinone oxygen atoms. The results allow satisfactory assignment of all experimentally known aqueous vibrational bands, some being assigned here for the first time. The clusters considered give reasonable accounts both of the observed frequencies in water and of the frequency shifts between acetonitrile and water that arise from hydrogen bonding.