gebhart/patrepeval huggingface dataset:
Cyclic Di-GMP Signaling in Bacteria: Recent Advances and New Puzzles (2006)

Cyclic di-GMP [bis-(3Ј-5Ј)-cyclic di-GMP] (Fig. 1) is a novel second messenger in bacteria that was first described as an allosteric activator of cellulose synthase in Gluconacetobacter xylinus (49).It is now established that this nucleotide is almost ubiquitous in bacteria, where it regulates a range of functions including developmental transitions, aggregative behavior, adhesion, biofilm formation, and the virulence of animal and plant pathogens (for reviews, see references 15, 18, 30, 31, 47, and 48).The level of cyclic di-GMP in bacterial cells is influenced by both synthesis and degradation.The GGDEF protein domain synthesizes cyclic di-GMP, whereas the EAL and HD-GYP domains are involved in cyclic di-GMP hydrolysis (43,50,51,53,54,58).Bacterial genomes encode a number of proteins with GGDEF, EAL, and HD-GYP domains; e.g., in Pseudomonas aeruginosa, there are 40 such proteins.The majority of these proteins contain additional signal input domains.These signaling systems are presumed to use cyclic di-GMP as a second messenger to link the sensing of specific environmental cues to appropriate alterations in bacterial physiology and/or gene expression.Some details about the operation and organization of cyclic di-GMP signaling systems are emerging.Nevertheless, many questions remain to be answered, and new puzzles have arisen as a result of experimental investigations.Here, we review the recent advances and highlight the considerable gaps in our understanding of cyclic di-GMP signaling.In particular, we discuss (i) the protein domains involved in cyclic di-GMP turnover, highlighting HD-GYP, recently described as a novel cyclic di-GMP phosphodiesterase; (ii) signals that are transduced through cyclic di-GMP signaling; (iii) the role of cyclic di-GMP signaling in bacterial virulence; (iv) recent findings addressing the organization of, and interplay between, different cyclic di-GMP signaling systems; (v) the concept of localized pools of cyclic di-GMP within the cell; and (vi) the mechanisms by which cyclic di-GMP exerts its effects on diverse cellular functions.
Mediation of Wound-Related Rous Sarcoma Virus Tumorigenesis by TGF-β (1990)

In Rous sarcoma virus (RSV)-infected chickens, wounding leads to tumor formation with nearly 100% frequency in tissues that would otherwise remain tumor-free. Identifying molecular mediators of this phenomenon should yield important clues to the mechanisms involved in RSV tumorigenesis. Immunohistochemical staining showed that TGF-beta is present locally shortly after wounding, but not unwounded controls. In addition, subcutaneous administration of recombinant transforming growth factor-beta 1 (TGF-beta 1) could substitute completely for wounding in tumor induction. A treatment protocol of four doses of 800 nanograms of TGF-beta resulted in v-src-expressing tumors with 100% frequency; four doses of only 10 nanograms still led to tumor formation in 80% of the animals. This effect was specific, as other growth factors with suggested roles in wound healing did not elicit the same response. Epidermal growth factor (EGF) or TGF-alpha had no effect, and platelet-derived growth factor (PDGF) or insulin-like growth factor-1 (IGF-1) yielded only occasional tumors after longer latency. TGF-beta release during the wound-healing response may thus be a critical event that creates a conducive environment for RSV tumorigenesis and may act as a cofactor for transformation in this system.
Nonalcoholic fatty liver disease: A comprehensive review of a growing epidemic (2014)

Nonalcoholic fatty liver disease (NAFLD) is quickly becoming one of the most prominent causes of liver disease worldwide. The increasing incidence of NAFLD is tied to the obesity epidemic and the subsequent metabolic derangements brought along with it. Current efforts to elucidate the mechanism and causes of the disease have answered some questions, but much remains unknown about NAFLD. The aim of this article is to discuss the current knowledge regarding the pathogenesis of the disease, as well as the current and future diagnostic, preventative, and therapeutic options available to clinicians for the management of NAFLD.
Shared last-level TLBs for chip multiprocessors (2011)

Translation Lookaside Buffers (TLBs) are critical to processor performance. Much past research has addressed uniprocessor TLBs, lowering access times and miss rates. However, as chip multiprocessors (CMPs) become ubiquitous, TLB design must be re-evaluated. This paper is the first to propose and evaluate shared last-level (SLL) TLBs as an alternative to the commercial norm of private, per-core L2 TLBs. SLL TLBs eliminate 7-79% of system-wide misses for parallel workloads. This is an average of 27% better than conventional private, per-core L2 TLBs, translating to notable runtime gains. SLL TLBs also provide benefits comparable to recently-proposed Inter-Core Cooperative (ICC) TLB prefetchers, but with considerably simpler hardware. Furthermore, unlike these prefetchers, SLL TLBs can aid sequential applications, eliminating 35-95% of the TLB misses for various multiprogrammed combinations of sequential applications. This corresponds to a 21% average increase in TLB miss eliminations compared to private, per-core L2 TLBs. Because of their benefits for parallel and sequential applications, and their readily-implementable hardware, SLL TLBs hold great promise for CMPs.
What Do Single-View 3D Reconstruction Networks Learn? (2019)

Convolutional networks for single-view object reconstruction have shown impressive performance and have become a popular subject of research. All existing techniques are united by the idea of having an encoder-decoder network that performs non-trivial reasoning about the 3D structure of the output space. In this work, we set up two alternative approaches that perform image classification and retrieval respectively. These simple baselines yield better results than state-of-the-art methods, both qualitatively and quantitatively. We show that encoder-decoder methods are statistically indistinguishable from these baselines, thus indicating that the current state of the art in single-view object reconstruction does not actually perform reconstruction but image classification. We identify aspects of popular experimental procedures that elicit this behavior and discuss ways to improve the current state of research.
An Aged Rat Model of Partial Androgen Deficiency: Prevention of Both Loss of Bone and Lean Body Mass by Low-Dose Androgen Replacement1 (2000)

The aim of this study was to evaluate the effects of different doses of androgen replacement, both on body composition and bone, in an aged male orchidectomized rat model. Testosterone was administered by 0.5, 1, and 2.5-cm sc SILASTIC implants (release of, respectively, 11.5, 23, and 55 microg/day) to aged (12 months old, +/- 550 g) male orchidectomized Wistar rats during a 15-week experimental period. T 0.5 only partially prevented decrease of ventral prostate and seminal vesicle weight, compared with an intact group that received an empty implant (Intact). The 1-cm implant (T 1) completely prevented decrease of both seminal vesicles and ventral prostate weight. The 2.5-cm implant (T 2.5) was clearly supraphysiological, as demonstrated by significant hypertrophy of both androgen-sensitive organs. Serum testosterone was lower in T 0.5 and T 1 (0.38 +/- 0.06 ng/ml and 0.92 +/- 0.06 ng/ml, respectively) and higher in T 2.5 (2.4 +/- 0.28. ng/ml), compared with both Intact (1.6 +/- 0.23 ng/ml) and the baseline group(1.6 +/- 0.11 ng/ml). As expected, orchidectomized rats that received an empty SILASTIC implant had significantly lower bone mineral content (-7.9%), apparent density (-5.7%), and lean body mass (-10.8%), as measured by dual-energy x-ray absorptiometry, without significant changes in body weight and fat mass, compared with Intact. Also, cancellous (-50.3%) and cortical (-1.8%) volumetric density, as measured by peripheral quantitative computed tomography, were decreased in the tibia. Bone turnover, as measured by serum osteocalcin and urinary deoxypyridinoline excretion, was increased in orchidectomized rats that received an empty SILASTIC implant. T 0.5 prevented all changes, not only in bone mineral content, density, and turnover but also in lean body mass. Moreover, there were no significant differences, for all these parameters, between the different doses of testosterone replacement. In conclusion, low-dose androgen replacement does not lead to lower bone mineral density, higher bone turnover, and lower lean body mass in aged male rats, whereas complete androgen deficiency does. Therefore, the threshold concentration of testosterone necessary for prevention of both bone and lean body mass loss in aged male rats is clearly lower than for prostate and seminal vesicles.
Preparation and Characterization of Monoclonal Antibodies Directed Against Antigenic Determinants of Recombinant Human Tumour Necrosis Factor (rTNF) (1987)

A large number of monoclonal antibodies (McAb) binding to antigenic determinants of human tumour necrosis factor (TNF) were prepared from two fusions of mouse myeloma NSO cells with spleen cells from Balb/c mice immunized with highly purified recombinant (r)TNF. Several of these McAbs were highly neutralizing with respect to the biological activity (cytotoxicity) of TNF manifested in L-929 C1.10 cells. Antibody competition experiments suggested the presence of at least two antigenic determinants on the rTNF molecule through which binding of McAb effects neutralization of biological activity. Some of these McAbs were shown to be suitable for the development of immunoassays to quantify rTNF.
Beat-to-Beat QT Interval Variability (1997)

DCM is associated with beat-to-beat fluctuations in QT interval that are larger than normal and uncoupled from variations in heart rate. QT interval variability increases with worsening functional class but is independent of ejection fraction. These data indicate that DCM leads to temporal lability in ventricular repolarization.
Gold Nanocages for Cancer Detection and Treatment (2007)

Gold nanocages represent a novel class of biocompatible vectors with potential applications in drug delivery, tumor/tissue imaging and photothermal therapy. They are prepared through the galvanic-replacement reaction between Ag nanostructures and HAuCl(4). By controlling the amount of HAuCl(4) added, we can tune the surface-plasmon resonance peaks of the Au nanocages into the near-infrared, where the attenuation of light by blood and soft tissue is relatively low. Here, we highlight recent advances in the synthesis and utilization of Au nanocages for cancer detection and treatment. We have tailored the optical properties of Au nanocages for use as contrast agents in optical coherence tomography and as transducers for the selective photothermal ablation of cancer cells. Our results show improved optical coherence tomography image contrast when Au nanocages are added to tissue phantoms as well as the selective photothermal destruction of breast cancer cells in vitro when immunotargeted Au nanocages are used.
Intein-Mediated Synthesis of Proteins Containing Carbohydrates and Other Molecular Probes (2000)

We report here the use of an intein-mediated protein ligation strategy for the synthesis of glycoproteins and proteins containing various molecular probes. Several simple cysteine derivatives are synthesized and used as nucleophiles for specific incorporation onto the C-terminus of proteins expressed as N-terminal intein fusions. Examples of C-terminal carbohydrate labeling, fluorescence labeling, incorporation of a metal chelator, and incorporation of a nucleotide are presented.
Atopic and non-atopic eczema (2006)

Delays in intensive care unit (ICU) admission are associated with higher mortality in community acquired pneumonia (CAP). (<i>Phua J, Eur Resp J 2010;36:826</i>). In 2008 we employed minor severity criteria from the 2007 IDSA/ATS guidelines<i> plus</i> point of care lactate to identify high risk patients in the emergency department (ED) for rapid resuscitation and direct admission to the ICU. (<i>Phua J, Thorax 2009;64:598</i>) This was associated with reduced mortality in severe CAP, without increasing ICU admission rates. (<i>Lim TK, Int. Forum on Quality &amp; Safety in Healthcare 2012</i>). <b>Intervention:</b> In July 2010 we implemented peer-to-peer feedback(p2p) on severe CAP management between ED &amp; ICU teams to improve teamwork and safety. (<i>Hudson DW, et al Am J Med Qual. 2011 Dec 27</i>) <b>Results:</b> From Jul 2010-Dec 2011 we admitted 243 patients with severe CAP in our ICU. ICU admission were delayed in 36% and hospital deaths 22.2%. Delays in ICU admission increased from 31% in 2010 to 40% in 2011. Nevertheless, there was a small drop in overall mortality (25.5% to 20%) mostly in patients directly admitted to ICU which fell from 26.5% to 17.2%. Mortality in delayed ICU admissions was stable (23.9% to 23.3%). Adherence to the resuscitation bundle was high in 2010: point of care lactate test 91%, antibiotics 97%, intravenous fluids 95% &amp; vaso-pressors 100%. But it fell in 2011 to 84%, 80%, 98% &amp; 86% respectively. <b>Conclusions:</b> In the management of severe CAP p2p was associated with reduction in mortality without increasing early/direct ICU admissions rates. Timely and sustained p2p feedback may be required to maintain a high degree of adherence to resuscitation bundles and to further improve patient outcomes in severe CAP.
High average power 2-D laser diode arrays on silicon Microchannel coolers (1989)

Due to significant improvements in efficiency and reliability, diode laser arrays are becoming very attractive both as pump sources for practical solid state lasers and direct sources of coherent radiation. These uses, however, are frequently limited by current packaging technologies which are adequate only for low power or low duty factor applications.
Racial and Ethnic Differences in Girls' Sexual, Marital, and Birth Expectations (1998)

This study examines potential racial and ethnic differences in early adolescent girls' desired and perceived normative role timing and the extent to which various socioeconomic and family factors and school and job aspirations might be linked with girls' role-timing expectations. Using a racially and ethnically diverse sample, (<i>n</i> = 574; 183 Hispanics, 177 Blacks, 93 Whites, and 70 Southeast Asians; <i>M</i> age = 12.9), results indicated that young women of different races and ethnicities saw their life course unfold in different sequences based on different timetables and independent of their socioeconomic circumstances. Hispanics desired rapid transitions at a young age, and Southeast Asians desired more gradual transitions at an older age. Blacks perceived the greatest likelihood of nonmarital childbearing for themselves, the longest normative interval between first sex and first birth, but they desired the shortest interval between first marriage and first birth. Within-race regressions revealed that girls' future aspirations were important for their expected role timing, even within the context of socioeconomic disadvantage (welfare receipt, low family income). Findings suggest the importance of culture-specific age norms for motivating role timing and role sequencing in young women's lives.
Conditional entropy-constrained vector quantization of displaced frame difference subband signals (2002)

We study the performance of conditional entropy-constrained vector quantizers when used to quantize subbands of the displaced frame differences derived from video sequences. Chou and Lookabaugh (1990) originally suggested a locally optimal design of this new kind of vector quantizer which can be accomplished through a generalization of the well known entropy-constrained vector quantizer (ECVQ) algorithm. This generalization of the ECVQ algorithm to a conditional entropy-constrained is called CECVQ, i.e., conditional ECVQ. The non-memoryless quantization performed by the conditional entropy-constrained VQ is based on the current vector to be encoded and the previous encoded vector. A new algorithm for conditional entropy-constrained vector quantizer design is derived and it is based on the pairwise nearest neighbour technique presented by Equitz (1989).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nanoparticle Architectures Templated by SiO2/Fe2O3 Nanocomposites (2006)

Reverse microemulsion techniques combined with templating strategies have led to the synthesis of four types of nanoparticles. First, homogeneous SiO2-coated Fe2O3 (SiO2/Fe2O3) nanoparticles with controlled SiO2 shell thickness (1.8−30 nm) were synthesized by reverse microemulsion. These nanocomposite particles were used as templates for the deposition of a mesoporous silica shell. The iron oxide core in SiO2/Fe2O3 could be partially and completely etched to produce rattle-type SiO2/Fe2O3 nanoballs and hollow SiO2 nanoballs, respectively. These facile synthetic methods led to the formation of different nanoparticle architectures with tailored silica shell thickness and porosity.
Development of an Advanced Primary Human In Vitro Model of the Small Intestine (2016)

Intestinal in vitro models are valuable tools in drug discovery and infection research. Despite several advantages, the standard cell line-based Transwell(®) models based for example on colonic epithelial Caco-2 cells, lack the cellular complexity and transport activity associated with native small intestinal tissue. An additional experimental set-back arises from the most commonly used synthetic membranes, on which the cells are routinely cultured. These can lead to an additional barrier activity during in vitro testing. To overcome these limitations, we developed an alternative primary human small intestinal tissue model. This novel approach combines previously established gut organoid technology with a natural extracellular matrix (ECM) based on porcine small intestinal scaffold (SIS). Intestinal crypts from healthy human small intestine were expanded as gut organoids and seeded as single cells on SIS in a standardized Transwell-like setting. After only 7 days on the ECM scaffold, the primary cells formed an epithelial barrier while a subpopulation differentiated into intestinal specific cell types such as mucus-producing goblet cells or hormone-secreting enteroendocrine cells. Furthermore, we tested the influence of subepithelial fibroblasts and dynamic culture conditions on epithelial barrier function. The barrier integrity was stabilized by coculture in the presence of gut-derived fibroblasts. Compared to static or dynamic culture on an orbital shaker, dynamic culture in a defined perfusion bioreactor had an additional significant impact on epithelial cell differentiation, indicated by high prismatic cell morphology and upregulation of CYP3A4 enzyme and Mdr1 transporter activity. In summary, more physiological tissue models as presented in our study might be useful tools in preclinical research and development.
Transcription Factor-Specific Requirements for Coactivators and Their Acetyltransferase Functions (1998)

Different classes of mammalian transcription factors-nuclear receptors, cyclic adenosine 3',5'-monophosphate-regulated enhancer binding protein (CREB), and signal transducer and activator of transcription-1 (STAT-1)-functionally require distinct components of the coactivator complex, including CREB-binding protein (CBP/p300), nuclear receptor coactivators (NCoAs), and p300/CBP-associated factor (p/CAF), based on their platform or assembly properties. Retinoic acid receptor, CREB, and STAT-1 also require different histone acetyltransferase (HAT) activities to activate transcription. Thus, transcription factor-specific differences in configuration and content of the coactivator complex dictate requirements for specific acetyltransferase activities, providing an explanation, at least in part, for the presence of multiple HAT components of the complex.
Experience with Silastic Slings for Female Urinary Incontinence (1989)

Between September 1, 1985 and December 31, 1987, 54 patients with stress urinary incontinence were treated with a reinforced silastic sling using an abdominovaginal approach; 42 patients were cured, two improved and nine were the same or worse. Five patients who are continent required periodic intermittent self-catheterization. Eight patients developed detrusor instability postoperatively. One patient had to have the sling removed due to a persistent sinus. Fifteen patients had to have the sling adjusted.
Position vs. Velocity Control for Tilt-Based Interaction (2020)

Research investigating factors in the design of tilt-based interfaces is presented. An experiment with 16 participants used a tablet and a 2D pointing task to compare position-control and velocity-control using device tilt to manipulate an on-screen cursor. Four selection modes were also evaluated, ranging from instantaneous selection upon hitting a target to a 500-ms time delay prior to selection. Results indicate that position-control was approximately 2× faster than velocity-control, regardless of selection delay. Position-control had higher pointing throughput (3.3 bps vs. 1.2 bps for velocity-control), more precise cursor motion, and was universally preferred by participants.
Gestures of healing : themed issue in honour of Laura Mulvey : editorial (2015)

This de arte accommodates a broader audience and gathers scholars from a wider variety of heritages and allegiances than usual. An array of voices is assembled here, springing from diverse South African, continental European and British institutions, and articulating a multiplicity of disciplinary approaches: continentally oriented image studies; Anglo-American-inspired visual culture studies; art history; film studies; and philosophical aesthetics. However diverse, the articles all point at the complexities, fragility, fluidity and ambivalences of imaging processes, often related to inter-racial understandings and crossovers between race and gender. In doing so, they resonate with Laura Mulvey's work and confirm its pertinence in an era of plurality and digital imaging.
Gelling, and melting, large graphs by edge manipulation (2012)

Controlling the dissemination of an entity (e.g., meme, virus, etc) on a large graph is an interesting problem in many disciplines. Examples include epidemiology, computer security, marketing, etc. So far, previous studies have mostly focused on removing or inoculating nodes to achieve the desired outcome.
Chemical speciation of ethylenediamine-N,N′- disuccinic acid (EDDS) and its metal complexes in solution (1999)

AbstractComputer simulation of chemical speciation has been used to assess the ability of the readily-biodegradable ligand SS-EDDS4− to replace the non readily-biodegradable ligand EDTA4−. Potential replacement ligands for EDTA4−, from the EDDS4− homologous series, which are readily biodegradable were assessed for their technical compatibility with EDTA4− using chemical speciation analysis based upon computer modelling. Chelating agents considered were EDTA(ethylenediaminetetraacetic acid), EDDS (ethylenediamine-N,N’-disuccinic acid), EDDM (ethylenediamaine-N,N’-dimalonic acid), and EDDG (ethylenediamine-N,N’-diglutaric acid) all producing 4-anionic ligands upon deprotonation. Formation constants with Ba2+, Sr2+, Mg2+, Ca2+, Mn2+, Cd2+, Co2+, Zn2+, Pb2+, Ni2+ , Cu2+, Hg2+ and Fe3+ions are listed (Table 2), some being determined as part of this study. The speciation modelling suggests that varying the total concentration conditions and using a limited supply of the EDDS ligand can, relative to EDTA, increase the complexing of Cu2+ in the presence of other ions, by a factor of 13, giving rise to the ‘more for less’ concept.Keywords: Ethylenediamine-N,N’-disuccinic acidmetal complexes