gebhart/patrepeval huggingface dataset:
Heparan sulfate: a piece of information (1996)

The sulfated glycosaminoglycans, heparan sulfate and heparin, are increasingly implicated in cell-biological processes such as cytokine action, cell adhesion, and regulation of enzymic catalysis. These activities generally depend on interactions of the polysaccharides with proteins, mediated by distinct saccharide sequences, and expressed at various levels of specificity, selectivity, and molecular organization. The formation of heparin/ heparan sulfate in the cell requires an elaborate biosynthetic machinery, that is conceived in terms of a novel model of glycosaminoglycan assembly and processive modification. Recent advances in the identification and molecular analysis of the enzymes and other proteins involved in the biosynthesis provide novel tools to study the regulation of the process, presently poorly understood, at the subcellular and cellular levels. The potential medical importance of heparin-related compounds is likely to promote the biotechnological exploitation of components of the biosynthetic machinery.
A New Technique for Characterizing the Efficacy of Fugitive Dust Suppressants (2009)

The Portable In-Situ Wind Erosion Laboratory (PI-SWERL) instrument was evaluated for testing the effectiveness of dust suppressants for a range of native and constructed soils. The PM10 (particles with diameter < or = 10 microm) emissions from dust suppressant-treated and untreated soil surfaces were measured periodically over 14 months. No statistically significant differences were found among soil surfaces treated with three dilution mixtures of the dust suppressant. The temporal variation of PM10 emissions from treated and untreated plots for native and constructed soil textures indicated that: (1) reductions of PM10 emissions by the dust suppressant were significant within 2-3 months after the application and diminished substantially thereafter, (2) decomposition of the protective treated layer resulted in high PM10 emissions for longer environmental exposure times, and (3) emissions from untreated soil surfaces declined over time because of the formation of a natural crust. These results demonstrated that the PI-SWERL can provide qualitative and quantitative information on PM10 emissions for a range of soil textures and can be used to estimate the effectiveness of dust suppressants exposed to actual environmental (i.e., weather and solar radiation) conditions over long periods of time.
Enhancement of the biocidal efficacy of a mild disinfectant through enhanced transient cavitation (2002)

Cavitation is known to have biocidal effect upon micro-organisms. The work presented here considered the impact of transient cavitation at elevated hydrostatic pressures as a means to improve the biocidal efficacy of otherwise mild disinfectant solutions. Cultures of Bacillus stearothermophilus and Bacillus subtilis were exposed to a mild isopropyl alcohol-based disinfectant for 15 to 18 minutes, which resulted in negligible cell reduction. Spores from the same cultures were exposed to the disinfectant for 15 to 18 minutes while being cavitated for one minute at a frequency of 24 kHz, and at ambient pressure, with an estimated energy density of 70 watts per liter. This achieved cell reduction of approximately 2%. Spores from the same cultures were exposed to the same cavitation field but at a hydrostatic pressure of approximately 210 kPa. The pressure was selected to exploit ‘‘the anomalous depth effect’’ for enhanced transient cavitation. These conditions achieved cell reduction of approximately 90% after 1 minute of cavitation exposure. The results are suggestive of more efficient means of sterilizing the burgeoning numbers of heat sensitive surgical instruments.
Statistical Analysis of an Automated In-Situ Frequency Response Optimisation Algorithm for Active Loudspeakers (2003)

This paper presents a novel method for automatically selecting the optimal in-situ acoustical frequency response of active loudspeakers within a discrete-valued set of responses offered by room response controls on active loudspeakers. The rationale of the room response controls for the active loudspeakers is explained. The frequency response, calculated from the acquired impulse response, is used as the input for the optimisation algorithm to select the most favourable combination of room response controls. The optimisation algorithm is described. The performance of the algorithm is analysed and discussed. This algorithm has been implemented and is currently in active use by specialist loudspeaker system calibrators who set up and tune studios and listening rooms.
Finger Imprint of Poncirus trifoliata: A Specific Interaction of a Viroid, a Host, and Irrigation (2004)

The unusual symptom, "finger imprint", described exclusively on Poncirus trifoliata, has been reported in only a single field trial investigating the effects of citrus viroids on crop performance. With this, the question has persisted whether the observed growth abnormality was a disease symptom induced by Citrus viroid IIIb (CVd-IIIb) or a consequence of mechanical damage caused by the handling of young trees during propagation or cultural practices in the field. The recurrence of finger imprint symptoms on trees after 5 years in the field in which no abnormal growth features were previously noted now supports the proposition of a viroid-induced disease. The symptom expression results from an unusual etiology of a complex relationship of the specific viroid CVd-IIIb on the specific rootstock P. trifoliata only when supplemental water is applied by sprinkler irrigation.
THE RATIO OF ANABOLIC TO ANDROGENIC ACTIVITY OF 7:17-DIMETHYLTESTOSTERONE, OXYMESTERONE, MESTANOLONE AND FLUOXYMESTERONE (1963)

SUMMARY The ratios of the relative anabolic and androgenic activities, based on assays measuring nitrogen retention and on the increase in weight of the ventral prostate gland of rats, are presented for the following steroids: 7α:17α-dimethyltestosterone (4·2:1·3 = 3·2); oxymesterone (4-hydroxy-17α-methyltestosterone) (1·8:0·36 = 5·0); mestanolone (17α-methylandrostanolone) (0·8:1·0 = 0·8); and fluoxymesterone (9α-fluoro-11β-hydroxy-17α-methyltestosterone) (3·8:1·4 = 2·7). The degree of dissociation of the two activities appears to be considerably less than that reported earlier for certain 19-nor steroids and some heterocyclic steroids of current clinical interest.
ETV6-NCOA2 fusion induces T/myeloid mixed-phenotype leukemia through transformation of nonthymic hematopoietic progenitor cells (2021)

Mixed-phenotype acute leukemia is a rare subtype of leukemia in which both myeloid and lymphoid markers are co-expressed on the same malignant cells. The pathogenesis is largely unknown, and the treatment is challenging. We previously reported the specific association of the recurrent t(8;12)(q13;p13) chromosomal translocation that creates the ETV6-NCOA2 fusion with T/myeloid leukemias. Here we report that ETV6-NCOA2 initiates T/myeloid leukemia in preclinical models; ectopic expression of ETV6-NCOA2 in mouse bone marrow hematopoietic progenitors induced T/myeloid lymphoma accompanied by spontaneous Notch1-activating mutations. Similarly, cotransduction of human cord blood CD34+ progenitors with ETV6-NCOA2 and a nontransforming NOTCH1 mutant induced T/myeloid leukemia in immunodeficient mice; the immunophenotype and gene expression pattern were similar to those of patient-derived ETV6-NCOA2 leukemias. Mechanistically, we show that ETV6-NCOA2 forms a transcriptional complex with ETV6 and the histone acetyltransferase p300, leading to derepression of ETV6 target genes. The expression of ETV6-NCOA2 in human and mouse nonthymic hematopoietic progenitor cells induces transcriptional dysregulation, which activates a lymphoid program while failing to repress the expression of myeloid genes such as CSF1 and MEF2C. The ETV6-NCOA2 induced arrest at an early immature T-cell developmental stage. The additional acquisition of activating NOTCH1 mutations transforms the early immature ETV6-NCOA2 cells into T/myeloid leukemias. Here, we describe the first preclinical model to depict the initiation of T/myeloid leukemia by a specific somatic genetic aberration.
Glucose-6-phosphate dehydrogenase and MEG3 controls hypoxia-induced expression of serum response factor (SRF) and SRF-dependent genes in pulmonary smooth muscle cell (2022)

Although hypoxia induces aberrant gene expression and dedifferentiation of smooth muscle cells (SMCs), mechanisms that alter dedifferentiation gene expression by hypoxia remain unclear. Therefore, we aimed to gain insight into the hypoxia-controlled gene expression in SMCs. We conducted studies using SMCs cultured in 3% oxygen (hypoxia) and the lungs of mice exposed to 10% oxygen (hypoxia). Our results suggest hypoxia upregulated expression of transcription factor CP2-like protein1, krüppel-like factor 4, and E2f transcription factor 1 enriched genes including basonuclin 2 (Bcn2), serum response factor (Srf), polycomb 3 (Cbx8), homeobox D9 (Hoxd9), lysine demethylase 1A (Kdm1a), etc. Additionally, we found that silencing glucose-6-phosphate dehydrogenase (G6PD) expression and inhibiting G6PD activity downregulated Srf transcript and hypomethylation of SMC genes (Myocd, Myh11, and Cnn1) and concomitantly increased their expression in the lungs of hypoxic mice. Furthermore, G6PD inhibition hypomethylated MEG3, a long non-coding RNA, gene and upregulated MEG3 expression in the lungs of hypoxic mice and in hypoxic SMCs. Silencing MEG3 expression in SMC mitigated the hypoxia-induced transcription of SRF. These findings collectively demonstrate that MEG3 and G6PD codependently regulate Srf expression in hypoxic SMCs. Moreover, G6PD inhibition upregulated SRF-MYOCD-driven gene expression, determinant of a differentiated SMC phenotype.
Beat frequencies in a ring laser gyro with its refractive index over unity (2001)

A frequency shift Δf during rotation in a ring laser gyro with its refractive index of unity was already well known. However, when the refractive index nr is over unity, several expressions for a beat frequency such as 2Δf∝nr, nr0, nr−1, and nr−2 were proposed. In this article, a beat frequency in a uniformly rotating ring laser gyro with nr&amp;gt;1 is calculated using nonrelativistic, special relativistic, and general relativistic theories. To the first order, all the results obtained from these theories show a common beat frequency, which is proportional to the refractive index nr, as far as the dispersion is neglected. When the dispersion is considered, the beat frequency is in proportion to nr0[1−(rΩ/λ0)2(dnr/df)2]−1, where f is a frequency of a laser beam, λ0 is a wavelength of a laser beam when the ring laser stands still, and nr0 is a refractive index at λ0. If nr0=1−(rΩ/λ0)2(dnr/df)2 is satisfied, the beat frequency seems to be independent of the refractive index.
Virtual Machine Warmup Blows Hot and Cold (2016)

Virtual Machines (VMs) with Just-In-Time (JIT) compilers are traditionally thought to execute programs in two phases: the initial warmup phase determines which parts of a program would most benefit from dynamic compilation, before JIT compiling those parts into machine code; subsequently the program is said to be at a steady state of peak performance. Measurement methodologies almost always discard data collected during the warmup phase such that reported measurements focus entirely on peak performance. We introduce a fully automated statistical approach, based on changepoint analysis, which allows us to determine if a program has reached a steady state and, if so, whether that represents peak performance or not. Using this, we show that even when run in the most controlled of circumstances, small, deterministic, widely studied microbenchmarks often fail to reach a steady state of peak performance on a variety of common VMs. Repeating our experiment on 3 different machines, we found that at most 43.5% of pairs consistently reach a steady state of peak performance.
Variants of Shiga-like toxin II constitute a major toxin component in Escherichia coli O157 strains from patients with haemolytic uraemic syndrome (1994)

The prevalence and genotype of Shiga-like toxins (SLTs) in Escherichia coli (O)157 strains from patients in Germany with haemolytic uraemic syndrome (HUS) were investigated. This was done by PCR amplification of the B-subunit genes with two primer pairs--one complementary to slt-IB, and the other homologous to both slt-IIB and slt-IIvB sequences. To distinguish between slt-II and slt-IIv, the amplified DNA was digested with restriction endonucleases HaeIII and FokI. Of the 38 strains examined, 17 harboured sequences for slt-IIv; four contained only slt-IIv, three carried both slt-IIv and slt-I, and 10 strains had slt-IIv and slt-II. A further three genotypes (slt-I, slt-II, slt-I/slt-II) were found in the remaining 21 strains resulting in a total of six slt genotypes. To determine whether the slt genes were expressed, and whether genotypes correlated with phenotypes, all strains were subjected to cytotoxicity assays and colony ELISA. All 38 strains displayed cytotoxic activity to Vero cells in similar quantities. The SLT-I-specific monoclonal antibody (MAb)13C4 reacted with all 10 strains in which slt-I sequences were identified. Colony blot ELISA with the SLT-II specific MAb11E10 detected 27 of 28 strains with slt-II sequences, but did not react with any of the seven strains that carried slt-IIv, or slt-I and slt-IIv. The high SLT variability shown here has diagnostic implications and may well have consequences for the host response in infections associated with these pathogens.
Malate Dehydrogenases in Guard Cells of Pisum sativum (1990)

Guard cell protoplasts of Pisum sativum show considerable NADP-dependent malate dehydrogenase (MDH) activity in darkness which can be enhanced severalfold by illumination or treatment with dithiothreitol (DTT). The question arose whether guard cells possess an NADP-MDH different from that present in the chloroplasts of the mesophyll (which is inactive in darkness or in the absence of DTT). MDH activities were determined in extracts of isolated protoplasts from mesophyll and epidermis, and in mechanically prepared epidermal pieces (with guard cells as the only living cells and no interference from proteases originating from the cell wall digesting enzymes). Guard cells possessed NAD-dependent MDHs of high activity and incomplete exclusion of NADP as a coenzyme. This NADP-dependent activity of the NAD-MDH(s) could not be stimulated by DTT or, inferentially, by light. The DTT- (and light-) dependent NADP-MDH represented 0.05% of the total protein of the guard cells and had a specific activity of 0.1 unit per milligram protein; both values are in the same range as the corresponding ones of the mesophyll cells. Agreement was also found in the extent of light activation, in subunit molecular weight, immunological cross-reactions, and in the behavior on an ion exchange column. The activity of the chloroplastic NADP-MDH in guard cells barely suffices to meet the malate requirement for stomatal opening in the light. It is therefore likely that NAD-MDHs residing in other compartments of the guard cells supplement the activity of the chloroplastic NADP-MDH particularly during stomatal opening in darkness.
Single-center retrospective study of the technique, safety, and 12-month efficacy of the MiniArc™ single-incision sling: a new minimally invasive procedure for treatment of female SUI. (2009)

This study was conducted to report on the technique, safety, and early efficacy of a single-incision mini-sling to treat female stress urinary incontinence (SUI). Women suffering from SUI were offered a single-incision approach to place a suburethral polypropylene mesh tape in a position similar to that of a transobturator sling without passage of needles through the groin. Retrospective data was collected on 61 patients that received the new MiniArc™ single-incision sling at a single center in the United States. Patient selection and concomitant procedures were determined by the senior authors at the center, and the senior authors were the primary surgeons in all cases. Procedures were completed under general, regional, or MAC anesthesia as determined by the surgeon. Average operative time for the sling procedure alone was short and the average blood loss was 29 cc. There were no intraoperative complications. There was one postoperative adverse event secondary to urinary retention that was resolved by loosening of the sling under local anesthesia in an office setting. The overall cure rate at 12 months determined by physician and patient assessment in 58/61 patients was 91.4%. No patients suffered pain or dyspareunia secondary to the sling, and no erosions or extrusions were reported. In this initial study, the MiniArc™ single-incision sling appears to be a safe approach to treat female SUI, and the early clinical results are encouraging.
Toward a pathway-centered approach for the treatment of adrenocortical carcinoma (2010)

Short-term, therapeutic development should target the Gap 2/mitosis transition and the downstream signaling of the insulin-like growth factor 1 receptor receptor. Long-term, additional characterization of patient samples, particularly at the sequence level, is required to fully understand adrenocortical carcinoma biology and apply that knowledge to clinical practice.
CIT-7, a crystalline, molecular sieve with pores bounded by 8 and 10-membered rings (2015)

CIT-7, a new microporous material that contains 8 and 10-membered rings prepared as a silicate, an aluminosilicate or titanosilicate.
Synthesis of a Monolithic Carbon-Based Acid Catalyst with a Honeycomb Structure for Flow Reaction Systems (2013)

A carbon-based monolithic acid catalyst with a honeycomb structure (CMHC) was synthesized via carbonization of a resorcinol-formaldehyde resin and subsequent sulfonation using sulfuric acid. The CMHC has nearly straight flow-through macropores (e.g., 47–78 μm) formed by the directional freezing of the resin precursor. These macropores are surrounded by thin carbon walls of approximately 6-μm thickness that are micro- and mesoporous as characterized by nitrogen adsorption experiments. The straight macropores enable a low hydraulic resistance to a liquid flow as demonstrated by >1000-fold less pressure drops of water flowing through the CMHC than those calculated for a packed bed of spherical particles with the same diameter as the approximate wall thickness of the CMHC. The CMHC shows a stable catalytic activity in the liquid-phase esterification of acetic acid with ethanol at 333 K in a flow reaction system for 50 h of operation. These results show prospective features of the CMHC for applications in flow reaction systems.
Interplay between Ovine Bone Marrow Stromal Cell Antigen 2/Tetherin and Endogenous Retroviruses (2010)

Endogenous betaretroviruses (enJSRVs) of sheep are expressed abundantly in the female reproductive tract and play a crucial role in conceptus development and placental morphogenesis. Interestingly, the colonization of the sheep genome by enJSRVs is likely still ongoing. During early pregnancy, enJSRV expression correlates with the production of tau interferon (IFNT), a type I IFN, by the developing conceptus. IFNT is the pregnancy recognition signal in ruminants and possesses potent antiviral activity. In this study, we show that IFNT induces the expression of bone marrow stromal cell antigen 2 (BST2) (also termed CD317/tetherin) both in vitro and in vivo. The BST2 gene is duplicated in ruminants. Transfection assays found that ovine BST2 proteins (oBST2A and oBST2B) block release of viral particles produced by intact enJSRV loci and of related exogenous and pathogenic jaagsiekte sheep retrovirus (JSRV). Ovine BST2A appears to restrict enJSRVs more efficiently than oBST2B. In vivo, the expression of BST2A/B and enJSRVs in the endometrium increases after day 12 and remains high between days 14 and 20 of pregnancy. In situ hybridization analyses found that oBST2A is expressed mainly in the endometrial stromal cells but not in the luminal and glandular epithelial cells, in which enJSRVs are highly expressed. In conclusion, enJSRVs may have coevolved in the presence of oBST2A/B by being expressed in different cellular compartments of the same organ. Viral expression in cells unable to express BST2 may be one of the mechanisms used by retroviruses to escape restriction.
EONS an Online Synaptic Modeling Platform (2011)

The objective of the work presented here is to develop a computational tool designed specifically for the study of the complex mechanisms that occur at chemical synapses. This tool should enable students and researchers (biologists with very little training in computational biology, as well as experienced modelers) worldwide to study the roles of diverse parameters that impact synaptic transmission from presynaptic to postsynaptic depolarization in an integrated modeling platform, using an easy, user-friendly and modular graphical interface.
Memory Patterns and Executive Functioning in Mild Cognitive Impairment and Alzheimer's Disease (2002)

Abstract The present study examined the similarities in the pattern of cognitive loss in Alzheimer's Disease (AD) and Mild Cognitive Impairment (MCI). We administered a battery of neuropsychological tests to individuals with these disorders as well as to a group of cognitively intact controls. The battery included measures of memory acquisition, consolidation, and retrieval, as well as tests of language, visuospatial ability, psychomotor speed, and executive functioning. All subjects (N =62) were evaluated in a memory disorder clinic and were diagnosed by a consensus procedure. Multivariate and univariate statistical methods were used to examine differences in level of performance on all neuropsychological tests and in the pattern of performance for memory measures. We found a significant difference between controls and the MCI and AD groups in terms of consolidation, but not in acquisition or retrieval. The MCI and AD groups did not differ in the pattern of memory processing. Also, the only non-memory neurocognitive domain in which MCI group differed significantly from the control group was executive functioning. Our findings suggest that the pattern of loss of memory function of MCI patients parallels that of AD patients. Also, our finding that executive functioning was the only other neurocognitive domain in which the control and MCI groups differed significantly is in contrast to traditional clinical lore that implicates language dysfunction and/or visuospatial deficits early in AD. These findings provide preliminary evidence that consolidation deficits and subtle declines in executive functioning may be the most useful cognitive markers for the early direction of AD.