gebhart/patrepeval huggingface dataset:
Properties of Switch-like Bioregulatory Networks Studied by Simulation of the Hypoxia Response Control System (2004)

A complex bioregulatory network could be more easily comprehended if its essential function could be described by a small "core" subsystem, and if its response characteristics were switch-like. We tested this proposition by simulation studies of the hypoxia response control network. We hypothesized that a small subsystem governs the basics of the cellular response to hypoxia and that this response has a sharp oxygen-dependent transition. A molecular interaction map of the network was prepared, and an evolutionarily conserved core subsystem was extracted that could control the activity of hypoxia response promoter elements on the basis of oxygen concentration. The core subsystem included the hypoxia-inducible transcription factor (HIFalpha:ARNT heterodimer), proline hydroxylase, and the von Hippel-Lindau protein. Simulation studies showed that the same core subsystem can exhibit switch-like responses both to oxygen level and to HIFalpha synthesis rate, thus suggesting a mechanism for hypoxia response promoter element-dependent responses common to both hypoxia and growth factor signaling. The studies disclosed the mechanism responsible for the sharp transitions. We show how parameter sets giving switch-like behavior can be found and how this type of behavior provides a foundation for quantitative studies in cells.
Impact of 24 h continuous hypothermic perfusion on heart preservation by assessment of oxidative stress (2004)

CHP reduces OS associated with prolonged hypothermic preservation and may allow longer preservation periods without compromising function. CHP offers several potential advantages: (1) resuscitation of non-beating heart donor organs, (2) time for HLA tissue typing, (3) facilitate interventions improving graft function, and (4) increased organ sharing.
Pre-mRNA splicing: the discovery of a new spliceosome doubles the challenge (1997)

A rare class of pre-mRNA introns with non-canonical consensus sequences has been identified in metazoan genes. The novel, low-abundance spliceosome that excises these introns contains one small nuclear ribonucleoprotein (snRNP) in common with the major spliceosome (U5) and four snRNPs that are distinct from, but structurally and functionally analogous to U1, U2 and U4-U6. The architecture of RNA components at the presumptive core of the AT-AC splicesome supports current models of the spliceosomal active center and raises tantalizing questions about spliceosome evolution.
Interspecific interference betweenApoanagyrus lopeziandA. diversicornis, parasitoids of the cassava mealybugPhenacoccus manihoti (1996)

Abstract The parasitoids Apoanagyrus lopezi De Santis and A. diversicornis (Howard) (Hymenoptera: Encyrtidae) have been introduced into Africa for the biological control of the cassava mealybug Phenacoccus manihoti Matile‐Ferrero (Homoptera: Pseudococcidae). We have studied competition between these species to investigate if they can coexist. Here we report on the influence of the simultaneous presence of non‐conspecific adult females on searching efficiency on patches. Wasps of either species foraged on discs of cassava leaf with mealybugs, while at the same time different numbers of non‐conspecifics were also depleting the patch. Patch area per parasitoid and number of hosts available to each parasitoid were equal in all treatments. In both species, the presence of other foragers clearly affected several aspects of the parasitoids' behaviour. Patch residence time increased with the number of non‐conspecifics in A. diversicornis. In both parasitoid species, the proportion of hosts left unparasitized after the patch visit decreased with increasing numbers of females on the patch. The proportions of super‐ and multiparasitism did not change with the number of females. Both species produced more offspring during a patch visit in the presence of more non‐conspecifics. These behavioural changes did not, however, lead to a change in the offspring production rate on patches. A. diversicornis produced offspring at a rate three times that of A. lopezi when one A. lopezi and one A. diversicornis foraged simultaneously. This is the first report of an aspect of interspecific competition where A. diversicornis has an advantage over A. lopezi. Interference between adult females thus promotes coexistence of the two species on P. manihoti.
Androgens and masculinization of genitalia in the spotted hyaena ( Crocuta crocuta ). 1. Urogenital morphology and placental androgen production during fetal life (1998)

According to common understanding of sexual differentiation, the formation and development of a penile clitoris in female spotted hyaenas requires the presence of naturally circulating androgens during fetal life. The purpose of the present study was to determine potential source(s) of such fetal androgens by investigating the timing of urogenital development and placental production of androgen during early and mid-gestation. Fetuses determined to be female by molecular techniques (lack of SRY gene) at days 33 and 48 of gestation had undifferentiated gonads, but the clitoris was already 'masculinized' and was generally similar to the phallus of a 50-day-old male fetus. Wolffian and Müllerian ducts terminated at the urogenital sinus in both sexes and a urethra was present along the entire length of the clitoris and penis. The adrenal gland was large and histologically differentiated at 33 days. Steroid gradients across the uterus (a drop in delta 4-androstenedione, with increases in oestrogen and androgen), and high androstenedione in ovarian veins indicated that ovarian androstenedione was metabolized and secreted as testosterone by the placenta throughout gestation. In vitro, whole or homogenized placentae at days 48 and 58 of gestation (110 days total) metabolized radiolabelled androstenedione into testosterone and oestradiol; the specific enzymatic activity of early placental tissues was higher than at later stages. A human placental homogenate had higher aromatase activity but did not produce testosterone unless aromatase was inhibited. Infusion of labelled androstenedione into the uterine arteries of hyaenas demonstrated the conversion of this substrate into testosterone and oestradiol and their secretion into the fetal circulation. Evidently, androgen is produced by the placenta and secreted into the fetal circulation from early in pregnancy when masculinization is first evident, before differentiation of the fetal ovary.
[The recovery of cognitive functions in the patients with organic brain disorders as a component of combined rehabilitation with the use of the method of bioacoustic correction]. (2012)

This study was designed to follow up dynamics of the recovery of cognitive functions after comprehensive medical rehabilitation of the patients with organic brain disorders using a bioacoutsic correction technique. A peculiar feature of this method is it allows for involuntary self-regulation of the functional state of the central nervous system and therefore can be used to treat patients experiencing cognitive problems. It was shown that the application of the method of bioacoustic correction promotes restoration of cognitive functions, reduces anxiety, and normalizes parameters of electroencephalograms.
Comparing measurements of breast density (2007)

Breast density measurements can be made from mammograms using either area-based methods, such as the six category classification (SCC), or volumetric based methods, such as the standard mammogram form (SMF). Previously, we have shown how both types of methods generate breast density estimates which are generally close. In this paper, we switch our attention to the question of why, for certain cases, they provide widely differing estimates. First, we show how the underlying physical models of the breast employed in the methods need to be consistent, and how area-based methods are susceptible to projection effects. We then analyse a set of patients whose mammograms show large differences between their SCC and SMF assessments. More precisely, 12% of 657 patients were found to fall into this category. Of these, 2.7% were attributable to errors either in the SMF segmentation algorithms, human error in SCC categorization or poor image exposure. More importantly, 9.3% of the cases appear to be due to fundamental differences between the area- and volume-based techniques. We conclude by suggesting how we might remove half of those discrepancies by introducing a new categorization of the SMF estimates based on the breast thickness. We note however, that this still leaves 6% of patients with large differences between SMF and SCC estimates. We discuss why it might not be appropriate to assume SMF (or any volume measure) has a similar breast cancer risk prediction capability to SCC.
Changes in Glomerular Filtration Rate After Renal Revascularization Correlate With Microvascular Hemodynamics and Inflammation in Swine Renal Artery Stenosis (2012)

Low basal STK-GFR with preserved response to acetylcholine may predict benefit from revascularization in RAS, whereas renal inflammation and robust STK-R2* responses to furosemide (possibly reflecting avid tubular oxygen consumption) are associated with less favorable outcomes. These tools may be useful for identification of patients likely to improve renal function after revascularization.
Fabrication and Piezoelectric Properties of Grain-Oriented (Bi1/2K1/2)TiO3–BaTiO3 Ceramics (2008)

The piezoelectric properties of (1 - x)(Bi1/2K1/2)TiO3–xBaTiO3 (x = 0.1) [abbreviated as BKT–BT10] ceramics prepared by ordinary solid-state reaction and reactive templated grain growth (RTGG) using platelike Bi4Ti3O12 particles as a template were investigated. All samples showed a single-phase perovskite structure, and relative densities compared with theoretical densities were all higher than 95%. The degree of orientation F was determined by the Lotgering method using an X-ray diffraction (XRD) pattern. The F values of textured BKT–BT10 ceramics were relatively low at ∼35%. However, field-induced strains and piezoelectric properties of BKT–BT10 ceramics were improved by grain orientation. In particular, the piezoelectric strain constant d33 and the strain of textured BKT–BT10 ceramics in a direction parallel (∥) to the tape stacking direction were 84.5 pC/N and 168 pm/V (at 80 kV/cm), respectively.
Improving the Spacer-Concrete Interface for Bond Strength and Durability (2019)

Spacers are important devices in reinforced concrete that are used to support reinforcing steel during concreting in order to achieve the required concrete cover. They are placed at every meter length or less of steel reinforcement and left permanently in the structure. However, it has been shown that the weak interface between spacer and concrete is highly porous and microcracked. This lowers the resistance of the concrete cover to ingress of aggressive agents causing degradation. This study aims to address this problem by improving spacer design to enhance bond strength and durability of the spacer-concrete interface. Cementitious spacers with a range of surface textures were produced prior to casting into concrete. Samples were prepared with CEM I Portland cement at a water/cement (w/c) ratio of 0.4 and cured for 3, 7, and 28 days in a fog room and then conditioned at 50°C to equilibrium moisture content. The spacer-concrete interface was then tested for tensile bond strength and mass transport properties including oxygen diffusivity, oxygen permeability, water absorption and electrical conductivity. The results were compared against control samples made of either the entire cementitious spacer or concrete. The measured surface properties were then correlated to the measured bond strength and transport properties to establish the effects of surface texture on the spacer-concrete interface.
A 2GHz line scan time-stretch imaging system based on multi-wavelength source (2014)

A fast line scan time-stretch imaging system based on multi-wavelength source and wavelength division technique is proposed and demonstrated. This scheme has a record 2GHz scan rate for scanning surface imaging applications.
Physicochemical studies of binary eutectic of ibuprofen and ketoprofen for enhanced transdermal drug delivery (2010)

The proposed flux ratio equations correctly predicted flux increase.
Improved Ammonia Finishing of Corduroys1 (1980)

Commercial use of the liquid ammonia process has expanded from its initial application as a pure finish technique on denims and bottomweight fabrics. In recent developments it is being used in con junction with crosslinking resin treatments, resulting in a rebirth of 100% cotton shirtings. It now promises a similar result for 100% cotton sheetings, which will soon be introduced to the market. Utilization of the process in specific areas has often required extensive product development in order to achieve the proper balance of physical and aesthetic properties required by today's consumer. One of the areas that has remained illusive has been in the application of ammonia finishing to corduroys. Previous attempts have resulted in significant improvements in performance after laundering, but the appearance of the fabric at the point of sale was not totally satisfactory. The major difficulty has been associated with excessive shrinkage and disorientation of the pile structure during ammonia treatment. New developments in ammonia finishing of corduroys have now been achieved by stabilizing the pile structure through a controlled resin treatment prior to ammonia treatment. This has proven to be effective in limiting excessive shrinkage and distortion of the pile as well as minimizing the flattening of the pile during ammonia removal. These results have been achieved in addition to re taining most of the benefits normally associated with liquid ammonia treatment.
The maximum-entropy method in superspace (2003)

One of the applications of the maximum-entropy method (MEM) in crystallography is the reconstruction of the electron density from phased structure factors. Here the application of the MEM to incommensurately modulated crystals and incommensurate composite crystals is considered. The MEM is computed directly in superspace, where the electron density in the (3+d)-dimensional unit cell (d > 0) is determined from the scattering data of aperiodic crystals. Periodic crystals (d = 0) are treated as a special case of the general formalism. The use of symmetry in the MEM is discussed and an efficient algorithm is proposed for handling crystal symmetry. The method has been implemented into a computer program BayMEM and applications are presented to the electron density of the periodic crystal NaV(2)O(5) and the electron density of the incommensurate composite crystal (LaS)(1.14)NbS(2). The MEM in superspace is shown to provide a model-independent estimate of the shapes of the modulation functions of incommensurate crystals. The discrete character of the electron density is found to be the major source of error, limiting the accuracy of the reconstructed modulation functions to approximately 10% of the sizes of the pixels. MaxEnt optimization using the Cambridge and Sakata-Sato algorithms are compared. The Cambridge algorithm is found to perform better than the Sakata-Sato algorithm, being faster, always reaching convergence, and leading to more reliable density maps. Nevertheless, the Sakata-Sato algorithm leads to similar density maps, even in cases where it does not reach complete convergence.
MOLECULAR APPROACHES TO DISEASE RESISTANCE (2015)

Genetic resistance to infectious diseases has been a subject of many controversies. The finding in the last 30 years of a number of polymorphisms in genes strongly influencing the outcome of the infectious process in
Transfection Microarray of Nonadherent Cells on an Oleyl Poly(Ethylene Glycol) Ether-Modified Glass Slide (2004)

Cell-based microarrays are emerging as a tool for analyzing the functions of genes in cells. However, partly due to the difficulty of cell immobilization, the application of this method has been limited to adherent cells. We previously reported a method that rapidly and strongly attached living nonadherent cells to glass slides modified with a cell membrane anchoring reagent, designated a biocompatible anchor for membrane (BAM). Here we demonstrate that plasmid DNA deposited in a defined area on BAM-modified glass slides was transfected into nonadherent K562 cells immobilized on the DNA-deposited and BAM-modified slides. This method allowed the transfection of K562 cells not only with plasmid cDNA expression vectors but also with small interfering RNA (siRNA) at a defined location on the BAM-modified slides. We expect this methodology to greatly expand the scope of current cell microarray technology.
Kinetics of Reaction of Sulfide with Thiosulfate in Aqueous Solution (1999)

The kinetics of the reaction 2H2S(aq) + S2O32- + 2H+ → 1/2S8(s) + 3H2O has been investigated at 0−40 °C in the pH interval from 5 to 7. The rate law was found to be r = −d[S2O32-]/dt = k[H2S][S2O32-], where k = 8 × 1011 exp(−74 300/RT) M-1 s-1. Thermodynamic calculation shows that the reaction is unfavorable at pH ≥ 8, which is confirmed by the experimental observation. The ionic strength effect on the reaction also has been studied. The mechanism postulated to account for the observed rate law involves the formation and subsequent reactions of an intermediate H2S3O32-.
Integrating approximate depth data into dense image correspondence estimation (2012)

High-quality dense image correspondence estimation between two images is an essential prerequisite for many tasks in visual media production, one prominent example being view interpolation. Due to the ill-posed nature of the correspondence estimation problem, errors occur frequently for a number of problematic conditions, among them occlusions, large displacements and low-textured regions. In this paper, we propose to use approximate depth data from low-resolution depth sensors or coarse geometric proxies to guide the high-resolution image correspondence estimation. We counteract the effect of uncertainty in the prior by exploiting the coarse-to-fine image pyramid used in our estimation algorithm. Our results show that even with only approximate priors, visual quality improves considerably compared to an unguided algorithm or a pure depth-based interpolation.
ChemInform Abstract: Zero Thermal Expansion in a Flexible, Stable Framework: Tetramethylammonium Copper(I) Zinc(II) Cyanide. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Receptive-field properties of Q retinal ganglion cells of the cat (1995)

Abstract The goal of this work was to provide a detailed quantitative description of the recepii ve-field properties of one of the types of rarely encountered retinal ganglion cells of cat; the cell named the Q-cell by Enroth-Cugell et al. (1983). Quantitative comparisons are made between the discharge statistics and between the spatial receptive properties of Q-cells and the most common of cat retinal ganglion cells, the X-cells. The center-surround receptive field of the Q-cell is modeled here quantitatively and the typical Q-cell is described. The temporal properties of the Q-cell receptive field were also investigated and the dynamics of the center mechanism of the Q-cell modeled quantitatively. In addition, the response vs . contrast relationship for a Q-cell at optimal spatial and temporal frequencies is shown, and Q-cells are also demonstrated to have nonlinear spatial summation somewhat like that exhibited by Y-cells, although much higher contrasts are required to reveal this nonlinear behavior. Finally, the relationship between Q-cells and Barlow and Levick's (1969) luminance units was investigated and it was found that most Q-cells could not be luminance units.
Abstract 88: Changes in Mouse Skeletal Progenitor Cells in a Model of Osteoporosis (2018)

PURPOSE: Osteoporosis is a disease characterized by low bone mass and structural deterioration of bone tissue. People with osteoporosis are more prone to fracture due to the decrease in bone mass with 40% of post-menopausal women developing an osteoporotic fracture. Of those suffering a fracture, 20% will die and only 30% will fully recover indicating that there is also a deficit in fracture healing. Our group recently described mouse skeletal progenitor cells. One sub-population, the mouse skeletal stem cell (mSSC) has been shown to be capable of forming all components of the skeleton. Another sub-population, the bone cartilage skeletal progenitor (BCSP) has been found to be important in fracture healing. We hypothesized that the changes in skeletal anatomy following estrogen depletion will be reflected by alterations in skeletal progenitor cell populations. METHODS: C57/BL6 mice underwent either sham operation or oophorectomy. Bone mineral density (BMD) was assessed by microCT. For fracture healing, mice underwent femur fracture 10 weeks after oophorectomy. Skeletal progenitor cells were harvested from uninjured bone or fracture callus as previously described and sorted by FACS. For colony forming units (CFUs), sorted cells were placed in growth medium for two weeks prior to colony counting. RESULTS: We first examined the impact of oophorectomy on BMD. 10 weeks after oophorectomy, mice were examined by microCT and BMD calculated from the femur. As expected, there was a significant decrease in BMD following oophorectomy compared to sham. Analysis of skeletal progenitors from uninjured bone showed significantly fewer mSSCs with decreased CFUs in oophorectomized versus sham. Following fracture, there was visibly less callus formed at the fracture site. Following fracture in oophorectomized mice, there was some increase in BCSPs in response, but it was nearly an order of magnitude less than seen in sham. CONCLUSIONS: Osteoporosis is a disease that can have devastating consequences for the health of older women. Our aging population will only increase the demand for viable therapies for the consequences of osteoporosis. While the impact of estrogen depletion on bone are well-characterized, it has not been very well understood at the cellular level. Here, we show the impact of oophorectomy on an important cellular component of the skeleton, and propose that therapies targeted at this cell population may be effective in combatting the disease. <!--EndFragment--> T. Andrew: None. D. Struck: None. M. Lopez: None. T. Boyko: None. M. Longaker: None. C. Chan: None. G. Yang: None.
Bounding the quantum capacity with flagged extensions (2022)

In this article we consider agged extensions of convex combination of quantum channels, and find general sufficient conditions for the degradability of the agged extension. An immediate application is a bound on the quantum Q and private P capacities of any channel being a mixture of a unitary map and another channel, with the probability associated to the unitary component being larger than 1/2. We then specialize our sufficient conditions to agged Pauli channels, obtaining a family of upper bounds on quantum and private capacities of Pauli channels. In particular, we establish new state-of-the-art upper bounds on the quantum and private capacities of the depolarizing channel, BB84 channel and generalized amplitude damping channel. Moreover, the agged construction can be naturally applied to tensor powers of channels with less restricting degradability conditions, suggesting that better upper bounds could be found by considering a larger number of channel uses.