gebhart/patrepeval huggingface dataset:
Assessment of Growth Parameters and Life Span of GHR/BP Gene-Disrupted Mice<sup>1</sup> (2000)

GH has many biological roles, including promotion of growth. Most, if not all, of its roles are achieved through interaction with its receptor. We chose to study the effects of loss of GH signaling on growth and aging in a mouse model for Laron Syndrome (LS) in which the GHR/BP gene has been disrupted. We observed that mice homozygous for the disruption (-/-) were significantly smaller than normal wild-type (+/+) mice as well as mice heterozygous for the disruption, even at 1.5 yr of age. IGF-I levels were also significantly lower in the -/- mice and remained low as the mice aged. IGFBP-3 levels were severely reduced in the -/- mice, whereas IGFBP-1, -2, and -4 levels remained unchanged. Finally, the -/- mice lived significantly longer than +/+ and +/- mice. The latter result contradicts the anti-aging GH data and suggests the need for further analysis of GH and aging.
Control of Cell Cycle Progression by Fibronectin Matrix Architecture (1998)

Developmental patterning and differentiation, maintenance of parenchymal cell function, and the size, shape, and invasiveness of tumors are all orchestrated by cell interactions with the extracellular matrix. Here we show that the fibrillar structure of fibronectin (FN) matrix encodes essential regulatory cues and controls cell proliferation and signaling through changes in matrix architecture. A matrix assembled from native FN stimulated cell growth. In contrast, a mutant FN (FNDeltaIII1-7) that contains all known cell binding motifs but forms a structurally distinct matrix inhibited progression from G0/G1 into S phase. Furthermore, FNDeltaIII1-7 suppressed the stimulatory capacity of native FN and induced different levels of tyrosine phosphorylation of pp125(FAK). The differential effects on cell growth were ablated by blocking formation of matrix fibrils. Thus, modification of matrix architecture provides a novel approach to control cell proliferation.
Systemic Delivery of scAAV8-Encoded MiR-29a Ameliorates Hepatic Fibrosis in Carbon Tetrachloride-Treated Mice (2015)

Fibrosis refers to the accumulation of excess extracellular matrix (ECM) components and represents a key feature of many chronic inflammatory diseases. Unfortunately, no currently available treatments specifically target this important pathogenic mechanism. MicroRNAs (miRNAs) are short, non-coding RNAs that post-transcriptionally repress target gene expression and the development of miRNA-based therapeutics is being actively pursued for a diverse array of diseases. Because a single miRNA can target multiple genes, often within the same pathway, variations in the level of individual miRNAs can potently influence disease phenotypes. Members of the miR-29 family, which include miR-29a, miR-29b and miR-29c, are strong inhibitors of ECM synthesis and fibrosis-associated decreases in miR-29 have been reported in multiple organs. We observed downregulation of miR-29a/b/c in fibrotic livers of carbon tetrachloride (CCl4) treated mice as well as in isolated human hepatocytes exposed to the pro-fibrotic cytokine TGF-β. Importantly, we demonstrate that a single systemic injection of a miR-29a expressing adeno-associated virus (AAV) can prevent and even reverse histologic and biochemical evidence of fibrosis despite continued exposure to CCl4. The observed therapeutic benefits were associated with AAV transduction of hepatocytes but not hepatic stellate cells, which are the main ECM producing cells in fibroproliferative liver diseases. Our data therefore demonstrate that delivery of miR-29 to the hepatic parenchyma using a clinically relevant gene delivery platform protects injured livers against fibrosis and, given the consistent fibrosis-associated downregulation of miR-29, suggests AAV-miR-29 based therapies may be effective in treating a variety of fibroproliferative disorders.
Alteration of patch boundaries on the floodplain of the regulated river trent, UK (1994)

Abstract Investigations were carried out into the contemporary distribution and structure of the vegetation communities at Gunthorpe, Nottinghamshire on the floodplain of the River Trent. A 60 km reach of the river was examined to determine the overall distribution and structure of vegetation communities; the Gunthorpe site was chosen as a representative example. Three hundred and thirty‐nine separate plots were examined and the site contained 132 species. It is clear that the extent of zones of discontinuity or transition (ecotones) between different vegetation patches has decreased due to long‐term land‐use management. The overall number of vegetation patches has also been reduced. A hierarchy relating boundaries to external influences is proposed and the relationship of ecotones to more clearly differentiated patch habitats identified. Highest species diversity is seen to be associated with the transition zones or ecotonal habitats, particularly under conditions of moderate disturbance intensity. It is concluded that the ecotones remaining still provide a habitat for a wide range of species with differing autecological requirements, but all typical of less disturbed alluvial meadows and marshes. These zones of transition potentially provide a pool for species expansion given improved ecological conditions following river restoration measures.
NUMA-aware graph-structured analytics (2015)

Graph-structured analytics has been widely adopted in a number of big data applications such as social computation, web-search and recommendation systems. Though much prior research focuses on scaling graph-analytics on distributed environments, the strong desire on performance per core, dollar and joule has generated considerable interests of processing large-scale graphs on a single server-class machine, which may have several terabytes of RAM and 80 or more cores. However, prior graph-analytics systems are largely neutral to NUMA characteristics and thus have suboptimal performance. This paper presents a detailed study of NUMA characteristics and their impact on the efficiency of graph-analytics. Our study uncovers two insights: 1) either random or interleaved allocation of graph data will significantly hamper data locality and parallelism; 2) sequential inter-node (i.e., remote) memory accesses have much higher bandwidth than both intra- and inter-node random ones. Based on them, this paper describes Polymer, a NUMA-aware graph-analytics system on multicore with two key design decisions. First, Polymer differentially allocates and places topology data, application-defined data and mutable runtime states of a graph system according to their access patterns to minimize remote accesses. Second, for some remaining random accesses, Polymer carefully converts random remote accesses into sequential remote accesses, by using lightweight replication of vertices across NUMA nodes. To improve load balance and vertex convergence, Polymer is further built with a hierarchical barrier to boost parallelism and locality, an edge-oriented balanced partitioning for skewed graphs, and adaptive data structures according to the proportion of active vertices. A detailed evaluation on an 80-core machine shows that Polymer often outperforms the state-of-the-art single-machine graph-analytics systems, including Ligra, X-Stream and Galois, for a set of popular real-world and synthetic graphs.
Collagen-Targeting Vascular Endothelial Growth Factor Improves Cardiac Performance After Myocardial Infarction (2009)

The injection of CBD-VEGF improved cardiac function in rats with induced acute myocardial infarction. This could potentially provide a new treatment option for myocardial infarction.
Descriptive analysis of estrogen receptor (ER)‐negative, progesterone receptor (PR)‐negative, and HER2‐negative invasive breast cancer, the so‐called triple‐negative phenotype (2007)

Abstract BACKGROUND. Tumor markers are becoming increasingly important in breast cancer research because of their impact on prognosis, treatment, and survival, and because of their relation to breast cancer subtypes. The triple‐negative phenotype is important because of its relation to the basal‐like subtype of breast cancer. METHODS. Using the population‐based California Cancer Registry data, we identified women diagnosed with triple‐negative breast cancer between 1999 and 2003. We examined differences between triple‐negative breast cancers compared with other breast cancers in relation to age, race/ethnicity, socioeconomic status (SES), stage at diagnosis, tumor grade, and relative survival. RESULTS. A total of 6370 women were identified as having triple‐negative breast cancer and were compared with the 44,704 women with other breast cancers. Women with triple‐negative breast cancers were significantly more likely to be under age 40 (odds ratio [OR], 1.53), and non‐Hispanic black (OR, 1.77) or Hispanic (OR, 1.23). Regardless of stage at diagnosis, women with triple‐negative breast cancers had poorer survival than those with other breast cancers, and non‐Hispanic black women with late‐stage triple‐negative cancer had the poorest survival, with a 5‐year relative survival of only 14%. CONCLUSIONS. Triple‐negative breast cancers affect younger, non‐Hispanic black and Hispanic women in areas of low SES. The tumors were diagnosed at later stage and were more aggressive, and these women had poorer survival regardless of stage. In addition, non‐Hispanic black women with late‐stage triple‐negative breast cancer had the poorest survival of any comparable group. Cancer 2007. © 2007 American Cancer Society.
Speculative synchronization (2002)

Barriers, locks, and flags are synchronizing operations widely used programmers and parallelizing compilers to produce race-free parallel programs. Often times, these operations are placed suboptimally, either because of conservative assumptions about the program, or merely for code simplicity.We propose Speculative Synchronization, which applies the philosophy behind Thread-Level Speculation (TLS) to explicitly parallel applications. Speculative threads execute past active barriers, busy locks, and unset flags instead of waiting. The proposed hardware checks for conflicting accesses and, if a violation is detected, offending speculative thread is rolled back to the synchronization point and restarted on the fly. TLS's principle of always keeping a safe thread is key to our proposal: in any speculative barrier, lock, or flag, the existence of one or more safe threads at all times guarantees forward progress, even in the presence of access conflicts or speculative buffer overflow. Our proposal requires simple hardware and no programming effort. Furthermore, it can coexist with conventional synchronization at run time.We use simulations to evaluate 5 compiler- and hand-parallelized applications. Our results show a reduction in the time lost to synchronization of 34% on average, and a reduction in overall program execution time of 7.4% on average.
Harnessing the antitumor potential of macrophages for cancer immunotherapy (2013)

Macrophages constitute a dominant fraction of the population of immune cells that infiltrate developing tumors. Recruited by tumor-derived signals, tumor-infiltrating macrophages are key orchestrators of a microenvironment that supports tumor progression. However, the phenotype of macrophages is pliable and, if instructed properly, macrophages can mediate robust antitumor functions through their ability to eliminate malignant cells, inhibit angiogenesis, and deplete fibrosis. While much effort has focused on strategies to block the tumor-supporting activity of macrophages, emerging approaches designed to instruct macrophages with antitumor properties are demonstrating promise and may offer a novel strategy for cancer immunotherapy.
Phase Ib Trial of Intravenous Recombinant Humanized Monoclonal Antibody to Vascular Endothelial Growth Factor in Combination With Chemotherapy in Patients With Advanced Cancer: Pharmacologic and Long-Term Safety Data (2001)

rhuMAbVEGF can be safely combined with chemotherapy at doses associated with VEGF blockade and without apparent synergistic toxicity. Its contribution to the treatment of advanced solid tumors should be evaluated in randomized treatment trials.
ChemInform Abstract: Asymmetric Synthesis of Novel Quaternary α‐Hydroxy‐δ‐lactam Dipeptide Surrogates. (1999)

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.
Transthoracic Needle Biopsy of Thoracic Lesions (2004)

In the diagnostic evaluation of thoracic lesions, the image-guided transthoracic needle biopsy was developed, and its role was expanded with the development of cross-sectional detection and characterization of thoracic lesions and advances in biopsy needle design and techniques. Particularly for diagnostic evaluation of solitary pulmonary nodules, transthoracic needle biopsy has emerged as the invasive procedure of choice. This article covers the indication, the pre-procedure preparation, various guidance-modalities and techniques, and complications.
Weakened cadaveric fascial sling: an unexpected cause of failure. (1998)

The use of the pubovaginal sling in all types of stress incontinence is becoming increasingly popular due to reportedly good long-term cure rates.' We report a case in which the anchoring sutures pulled through a pubovaginal sling constructed from human cadaveric fascia lata. CASE REPORT A 48-year-old woman presented with stress urinary incontinence. Neurourological history, physical examination and video urodynamic evaluation confirmed sphincteric incontinence. An uncomplicated pubovaginal sling procedure was performed using donor human allograft (freeze-dried fascia lata). The 14 X 2 cm. sling was anchored using 2-zero polyester sutures on either end with 2 rows of horizontal mattress sutures. The sling was placed as described by McGuire et al.1 On postoperative day 3 a voiding trial immediately demonstrated recurrent stress incontinence. Pelvic examination revealed that 1 end of the sling protruded from the anterior vaginal incision since the nonabsorbable suture was no longer attached to the sling on that side. There was no purulent discharge or any signs of infection. The sling was grasped and easily removed through the vagina. Examination of the fascia showed frayed edges on each side. It was obvious that the sutures had pulled out on both sides of the graft. DISCUSSION
Excitotoxicity and neurodegeneration in amyotrophic lateral sclerosis. (1997)

The pathogenesis of sporadic amyotrophic lateral sclerosis (ALS) is unknown, but several observations suggest that glutamate could participate in selective motor neuron degeneration. Extracellular levels of glutamate are elevated in ALS. Synaptic concentrations of glutamate are regulated by high-affinity glutamate transport, and defects in glutamate transport have also been observed in ALS tissue. Three sodium-dependent glutamate transporters have now been identified: a neuronal transporter EAAC1, and two astroglial transporters GLT-1 and GLAST. The defect in glutamate transport in ALS appears to be relatively specific for the GLT-1 subtype. The role of chronic excess glutamate and glutamate transporter loss has been investigated in experimental paradigms, where it was found that excitotoxicity could account for selective motor neuron degeneration. These culture paradigms have demonstrated that motor neurons are sensitive to glutamate toxicity via non-NMDA receptors and that various agents (e.g., antioxidants, glutamate release inhibitors, non-NMDA receptor antagonists) can be neuroprotective. These experimental studies will provide a basis for understanding the primary and secondary role of glutamate in motor neuron death and will provide important insight into possible therapeutic interventions.
Genes aroA and serC of Salmonella typhimurium constitute an operon (1985)

Genetic analysis of aroA554::Tn10 derivatives of two mouse-virulent Salmonella typhimurium strains, "FIRN" and "WRAY," and of a nonreverting derivative of each constructed for use as a live vaccine, showed the site of the insertion among mapped aroA point mutants. The WRAY live-vaccine strain gave no aro+ recombinants in crosses with aroA point mutations to one side of the insertion, indicating a deletion from Tn10 through the sites of these point mutations. The FIRN live-vaccine strain gave wild-type recombinants with all tested point mutants; it probably has a deletion or inversion extending from Tn10 into aroA but not as far as the nearest point mutation. Some tetracycline-sensitive mutants of aroA554::Tn10 strains required serine and pyridoxine, indicating loss of serC function, and some that were found to be SerC- did not produce gas from glucose, indicating a loss of pfl function. These results show the gene order pfl-serC-aroA, as in Escherichia coli. Ampicillin enrichment applied to pools of tetracycline-sensitive mutants of strains with Tn10 insertions near aroA (i.e., zbj::Tn10 strains) yielded Aro- SerC- Pfl-, Aro- SerC+ Pfl+, and Aro- SerC- Pfl+ mutants but none which were Aro+ SerC-. All of the mutants are explicable by deletions or inversions extending clockwise from zbj::Tn10 into or through an operon comprising serC (promoter-proximal) and aroA. Such an operon was also shown by the identification of two Tn10 insertions causing phenotype Aro- SerC-, each able to revert to Aro+ SerC+ by precise excision. serC corresponds to the open reading frame promoter-proximal to aroA that was identified elsewhere by base sequencing of a cloned aroA segment of S. typhimurium (Comai et al., Science 221:370-371, 1983). Both serine and chorismate are precursors of enterochelin; this may be why serC and aroA are in a single operon.
Magnetless Microwave Circulators Based on Spatiotemporally Modulated Rings of Coupled Resonators (2016)

Nonreciprocal components are ubiquitous in electronic and optical systems. To date, the use of magneto-optical materials has been the prevailing method to achieve nonreciprocity. However, magnetic-based devices are accompanied by several drawbacks, such as the requirement of bulky biasing devices and their incompatibility with semiconductor technology, which make their integration challenging. Recently, strong magnetless nonreciprocity was demonstrated in spatiotemporally modulated coupled-resonator networks as a result of an effective spin imparted to the structure by an RF signal. These structures can be easily integrated, and they potentially exhibit good power and noise performance, as any parametric device. Here, we develop an analytical theory for such devices, which allows determining the conditions for designing them with optimum characteristics, and present two designs based on lumped- and distributed-element circuits for applications at the very high-frequency and wireless-communications bands, respectively. The circulators exhibit large isolation and low insertion loss within reasonable modulation requirements. Furthermore, they can be realized with a modulation frequency substantially lower than the input frequency, significantly simplifying the design. Measurements for the lumped-element design are provided and show good agreement with theory and full-wave simulations. The nonlinear characteristics of the presented designs are also studied, and possible ways to reduce nonlinear distortion by increasing the static bias of the varactors or using advanced varactor topologies are explored.
Synchronization of fault-tolerant clocks in the presence of malicious failures (1988)

The problem of achieving global clock synchronization in fault-tolerant clocks by preventing so-called multiple cliques in the presence of malicious clock failures (i.e. clock failures that are perceived differently by different nonfaulty clocks) is addressed. A solution to the problem, referred to as the averaging rule, is developed, and its use is analytically justified using the notions of clock partitions and generalized clock partitions. Experimental characterization of the multiple cliques problem has been undertaken, and certain conditions that induce their occurrence in practical hardware implementation are identified. The effects of clock-receiver triggering variations and phase-detector operating range on the instantaneous frequencies of the clock modules are investigated. The efficacy of the averaging rule is established not only by analysis but also by means of simulations and experimentation with hardware clock implementations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Limit-cycle prediction of a fuzzy control system based on describing function method (2000)

A limit-cycle is the phenomenon that can be observed in systems composed of nonlinear elements. The phenomenon is of fundamental importance in nonlinear systems and, as far as the design of a nonlinear system is concerned, it should be considered along with the stability analysis. In the paper, the limit-cycle of a system controlled by a fuzzy logic controller (FLC) is addressed via some of the classical control techniques used to analyze nonlinear systems in the frequency domain. First, reasonable assumptions are made on the structure of the FLC by using fuzzy basis functions (FBFs) and the describing function of the FLC is derived to analyze and predict the existence of the limit-cycle of the closed-loop system including the FLC. Finally computer simulation is performed to show how the analysis given in the paper is used to predict the existence of the limit-cycle of the fuzzy control system.
Accurate activity recognition in a home setting (2008)

A sensor system capable of automatically recognizing activities would allow many potential ubiquitous applications. In this paper, we present an easy to install sensor network and an accurate but inexpensive annotation method. A recorded dataset consisting of 28 days of sensor data and its annotation is described and made available to the community. Through a number of experiments we show how the hidden Markov model and conditional random fields perform in recognizing activities. We achieve a timeslice accuracy of 95.6% and a class accuracy of 79.4%.