gebhart/patrepeval huggingface dataset:
Identification of a pathogenicity island required for Salmonella survival in host cells. (1996)

We have identified a region unique to the Salmonella typhimurium chromosome that is essential for virulence in mice. This region harbors at least three genes: two (spiA and spiB) encode products that are similar to proteins found in type III secretion systems, and a third (spiR) encodes a putative regulator. A strain with a mutation in spiA was unable to survive within macrophages but displayed wild-type levels of epithelial cell invasion. The culture supernatants of the spi mutants lacked a modified form of flagellin, which was present in the supernatant of the wild-type strain. This suggests that the Spi secretory apparatus exports a protease, or a protein that can alter the activity of a secreted protease. The "pathogenicity island" harboring the spi genes may encode the virulence determinants that set Salmonella apart from other enteric pathogens.
Characterization of the Terminal Iron(IV) Imides {[PhBPtBu2(pz‘)]FeIV⋮NAd}+ (2006)

New hybrid bis(phosphine)(pyrazole)borate tripodal ligands ([PhBPtBu2(pz')]-) are reported that support pseudotetrahedral iron in the oxidation states +1, +2, +3, and +4. The higher oxidation states are stabilized by a terminal FeNR linkage. Of particular interest is the generation and thorough characterization of an S = 1 FeIVNR+ imide cation using this new ligand system. The latter species can be observed electrochemically and spectroscopically, and its solid-state crystal structure is reported.
Femoral and popliteal arteries: reanalysis of results of balloon angioplasty. (1992)

The author presents an alternative statistical analysis of the results of the University of Toronto series of percutaneous transluminal angioplasty (PTA) of the femoral and popliteal arteries (n = 254). After recalculation of the data with the Kaplan-Meier method, the postprocedure success rate ranged from 88.8% +/- 2.0 at 1 month to 35.7% +/- 4.8 at 6 years. With Cox multiple regression analysis, the type of femoropopliteal lesion and the runoff were the variables that were useful to predict late results. For stenoses with good runoff, the success rate was 53% at 5 years; with poor runoff, 31% at 5 years. For occlusions with good runoff, the success rate was 36% at 5 years; with poor runoff, 16% at 5 years. In initially successful cases, ongoing clinical success at 1, 3, and 5 years was better in patients with good runoff at the time of PTA than in those with poor runoff. Now that more recent studies have documented improved technical success in femoropopliteal PTA, a comparative study of the relative safety, long-term clinical efficacy, and cumulative cost of PTA versus surgery seems warranted.
CD8 + T regulatory cells express the Ly49 Class I MHC receptor and are defective in autoimmune prone B6-Yaa mice (2011)

The immune system includes a subpopulation of CD8(+) T cells equipped to inhibit the expansion of follicular T helper (T(FH)) cells, resulting in suppression of autoantibody production and associated lupus-like disease. These CD8(+) T regulatory (Treg) cells recognize Qa-1/peptide complexes on target T(FH) cells and depend on the IL-15 cytokine for development and function. Here we show that these CD8(+) Treg cells express a triad of surface receptors--CD44, CD122, and the class I MHC receptor Ly49--and account for <5% of CD8(+) T cells. Moreover, the development of systemic lupus erythematosus-like disease in B6-Yaa mutant mice is associated with a pronounced defect in CD8(+) Treg cell activity, suggesting that this regulatory subset may represent an effective therapeutic approach to systemic lupus erythematosus-like autoimmune disease.
From trouble to treasure: Integrating stormwater into urban supply (2014)

In Australia, where our challenging climate is as diverse as it can be extreme and some 90% of the population lives in urban areas, significant investment has been made in infrastructure to provide safe and reliable water for our cities, towns and industries and to protect against flood.
Human UDP-Galactose Translocator: Molecular Cloning of a Complementary DNA That Complements the Genetic Defect of a Mutant Cell Line Deficient in UDP-Galactose Translocator (1996)

We have cloned a cDNA that codes for a putative human UDP-galactose translocator (UGT) protein. The cDNA contained an open reading frame of 1,179 base pairs encoding a novel protein of 393 amino acids. Introduction of the open reading frame sequence into a UGT-deficient mouse cell line, Had-1, complemented the genetic defect of the mutant, namely the inability to transport UDP-galactose from the cytosol to the Golgi lumen, as judged from the lectin-sensitivity spectrum of the transformant. To our knowledge, this is the first mammalian nucleotide-sugar translocator whose cDNA sequence has been described.
Morphology of programmed cell death in the ventral nerve cord ofCaenorhabditis eleganslarvae (1982)

ABSTRACT In the nematode C. elegans, cells undergoing programmed death in the developing ventral nerve cord were identified by Nomarski optics and prepared for ultrastructural study at various times after their birth in mitosis. The sequence of changes observed suggests that the hypodermis recognizes the dying cell before completion of telophase. The dying cell is engulfed and digestion then occurs until all that remains within the hypodermal cytoplasm is a collection of membranous whorls interspersed with condensed chromatin-like remnants. The process shares several features with apoptosis, the mode of programmed cell death observed in vertebrates and insects. The selection of cells for programmed death appears not to involve competition for peripheral targets.
Enlarged amygdala volume and reduced hippocampal volume in young women with major depression (2004)

Our results are consistent with previous findings of structural abnormalities of amygdala and hippocampus in subjects with recent-onset major depression. It may be suggested that the size of the amygdala is enlarged in the first years of the disorder, and may decrease with prolonged disorder duration.
Community Service (1996)

Review| June 01 1996 Community Service Rewiring Our Networks: Cultural Equity in the 21st Century, 1996 National Conference of the National Alliance for Media Arts and Culture co-sponsored by the National Coalition of Multicultural Media Artists, Berkeley, California, March 29-April 1, 1996 Felicia Sullivan Felicia Sullivan Felicia Sullivan is a writer, media activist and Education Director of the Boston Film/Video Foundation. Search for other works by this author on: This Site PubMed Google Scholar Afterimage (1996) 23 (6): 4. https://doi.org/10.1525/aft.1996.23.6.4 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation Felicia Sullivan; Community Service. Afterimage 1 June 1996; 23 (6): 4. doi: https://doi.org/10.1525/aft.1996.23.6.4 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAfterimage Search This content is only available via PDF. © 1996 by The Regents of the University of California1996 Article PDF first page preview Close Modal You do not currently have access to this content.
XFI: software guards for system address spaces (2006)

XFI is a comprehensive protection system that offers both flexible access control and fundamental integrity guarantees, at any privilege level and even for legacy code in commodity systems. For this purpose, XFI combines static analysis with inline software guards and a two-stack execution model. We have implemented XFI for Windows on the x86 architecture using binary rewriting and a simple, stand-alone verifier; the implementation's correctness depends on the verifier, but not on the rewriter. We have applied XFI to software such as device drivers and multimedia codecs. The resulting modules function safely within both kernel and user-mode address spaces, with only modest enforcement overheads.
Inhibition of the transcriptional kinase CDK7 overcomes therapeutic resistance in HER2-positive breast cancers (2019)

Resistance of breast cancer to human epidermal growth factor receptor 2 (HER2) inhibitors involves reprogramming of the kinome through HER2/HER3 signaling via the activation of multiple tyrosine kinases and transcriptional upregulation. The heterogeneity of induced kinases prevents kinase targeting by a single kinase inhibitor and presents a major challenge to the treatment of therapeutically recalcitrant HER2-positive breast cancers (HER2+ BCs). As a result, there is a critical need for effective treatment that attacks the aberrant kinome activation associated with resistance to HER2-targeted therapy. Here, we describe a novel treatment strategy that targets cyclin-dependent kinase 7 (CDK7) in HER2 inhibitor-resistant (HER2iR) breast cancer. We show that both HER2 inhibitor-sensitive (HER2iS) and HER2iR breast cancer cell lines exhibit high sensitivity to THZ1, a newly identified covalent inhibitor of the transcription regulatory kinase CDK7. CDK7 promotes cell cycle progression through inhibition of transcription, rather than via direct phosphorylation of classical CDK targets. The transcriptional kinase activity of CDK7 is regulated by HER2, and by the receptor tyrosine kinases activated in response to HER2 inhibition, as well as by the downstream SHP2 and PI3K/AKT pathways. A low dose of THZ1 displayed potent synergy with the HER2 inhibitor lapatinib in HER2iR BC cells in vitro. Dual HER2 and CDK7 inhibition induced tumor regression in two HER2iR BC xenograft models in vivo. Our data support the utilization of CDK7 inhibition as an additional therapeutic avenue that blocks the activation of genes engaged by multiple HER2iR kinases.
Total Variation Filtered Demons for Improved Registration of Sliding Organs (2013)

We present a new approach to regularize the displacement field of the accelerated Demons registration algorithm. The accelerated Demons algorithm uses Gaussian smoothing to penalize oscillatory motion in the displacement fields during registration. This regularization approach is often applied and ensures a smooth deformation field. However, when registering images with discontinuities in their motion field such as from organs sliding along the chest wall, the assumption of a smooth deformation field is invalid. In this work, we propose using total variation based smoothing that is known to better retain the discontinuities in the deformation field. The proposed approach is a first step towards automatically recovering breathing induced organ motion with good accuracy.
Significant improvement of islet yield from obese donor pancreata for human islet isolation and transplantation (2003)

Matsumoto, Ippei1; Sawada, Toshiya1; Nakano, Masahiko1; Liu, Baolin1; Ansite, Jeffrey D.1; Zhang, Hui J.1; Kandaswamy, Raja1; Sutherland, David E.R.1; Hering, Bernhard J.1 Author Information
The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak – an update on the status (2020)

An acute respiratory disease, caused by a novel coronavirus (SARS-CoV-2, previously known as 2019-nCoV), the coronavirus disease 2019 (COVID-19) has spread throughout China and received worldwide attention. On 30 January 2020, World Health Organization (WHO) officially declared the COVID-19 epidemic as a public health emergency of international concern. The emergence of SARS-CoV-2, since the severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, marked the third introduction of a highly pathogenic and large-scale epidemic coronavirus into the human population in the twenty-first century. As of 1 March 2020, a total of 87,137 confirmed cases globally, 79,968 confirmed in China and 7169 outside of China, with 2977 deaths (3.4%) had been reported by WHO. Meanwhile, several independent research groups have identified that SARS-CoV-2 belongs to β-coronavirus, with highly identical genome to bat coronavirus, pointing to bat as the natural host. The novel coronavirus uses the same receptor, angiotensin-converting enzyme 2 (ACE2) as that for SARS-CoV, and mainly spreads through the respiratory tract. Importantly, increasingly evidence showed sustained human-to-human transmission, along with many exported cases across the globe. The clinical symptoms of COVID-19 patients include fever, cough, fatigue and a small population of patients appeared gastrointestinal infection symptoms. The elderly and people with underlying diseases are susceptible to infection and prone to serious outcomes, which may be associated with acute respiratory distress syndrome (ARDS) and cytokine storm. Currently, there are few specific antiviral strategies, but several potent candidates of antivirals and repurposed drugs are under urgent investigation. In this review, we summarized the latest research progress of the epidemiology, pathogenesis, and clinical characteristics of COVID-19, and discussed the current treatment and scientific advancements to combat the epidemic novel coronavirus.
Enhanced Thermoelectric Figure of Merit of p-Type Half-Heuslers (2011)

Half-Heuslers would be important thermoelectric materials due to their high temperature stability and abundance if their dimensionless thermoelectric figure of merit (ZT) could be made high enough. The highest peak ZT of a p-type half-Heusler has been so far reported about 0.5 due to the high thermal conductivity. Through a nanocomposite approach using ball milling and hot pressing, we have achieved a peak ZT of 0.8 at 700 °C, which is about 60% higher than the best reported 0.5 and might be good enough for consideration for waste heat recovery in car exhaust systems. The improvement comes from a simultaneous increase in Seebeck coefficient and a significant decrease in thermal conductivity due to nanostructures. The samples were made by first forming alloyed ingots using arc melting and then creating nanopowders by ball milling the ingots and finally obtaining dense bulk by hot pressing. Further improvement in ZT is expected when average grain sizes are made smaller than 100 nm.
Recent insights into the immunopathogenesis of psoriasis provide new therapeutic opportunities (2004)

Chronic and excessive inflammation in skin and joints causes significant morbidity in psoriasis patients. As a prevalent T lymphocyte-mediated disorder, psoriasis, as well as the side effects associated with its treatment, affects patients globally. In this review, recent progress is discussed in the areas of genetics, the immunological synapse, the untangling of the cytokine web and signaling pathways, xenotransplantation models, and the growing use of selectively targeted therapies. Since psoriasis is currently incurable, new management strategies are proposed to replace previous serendipitous approaches. Such strategic transition from serendipity to the use of novel selective agents aimed at defined targets in psoriatic lesions is moving rapidly from research benches to the bedsides of patients with this chronic and debilitating disease
Use of abciximab-Modified Thrombelastography in Patients Undergoing Cardiac Surgery (1999)

Thrombelastography (TEG) is a reliable coagulation monitoring system that can guide blood product transfusion in cardiac surgery. The maximum amplitude (MA) of TEG measures clot strength, which is dependent on both fibrinogen level and platelet function. Inhibition of platelet function with abciximab-fab is suggested to permit quantitative assessment of the contribution of fibrinogen to clot strength. We hypothesized that abciximab-modified TEG permits prediction of plasma fibrinogen levels and that the difference of standard MA and abciximab-modified MA (ΔMA) is a correlate for platelet function. We correlated abciximab-modified MA with plasma fibrinogen levels and ΔMA with platelet count in patients undergoing coronary revascularization. Correlation between plasma fibrinogen levels and abciximab-modified MA was significant (adjusted r2: 0.8; P < 0.0001). Correlation of ΔMA with platelet count was not significant when calculated in millimeters (adjusted r2: 0.04; P = 0.73). However, when ΔMA was calculated in dynes per square centimeter (ΔGMA), it correlated significantly with platelet count (adjusted r2: 0.51; P < 0.0001). We conclude that abciximab-modified TEG may therefore help to discriminate between hypofibrinogenemia and platelet dysfunction as a cause of decreased MA. Implications We examined the use of abciximab-modified thrombelastography in patients undergoing cardiac surgery. Modification of thrombelastography with abciximab-fab allows prediction of fibrinogen levels, despite coagulation altered by cardiac surgery. The difference of standard maximum amplitude and abciximab-modified maximum amplitude correlates with platelet function when expressed in dynes per square centimeter.
Safety of the concurrent treatment of dogs with Bravecto™ (fluralaner) and Scalibor™ protectorband (deltamethrin) (2014)

Concurrent treatment with Bravecto in dogs fitted with Scalibor Protectorband is well tolerated.
Molecular iodine mediated one step synthesis and antibacterial properties of some 3-aryl-6-(6-substituted-4-methylcinnolin-3-yl)- 7H -1,2,4-triazolo[3,4- b ][1,3,4]thiadiazines (2012)

Novel cinnoline derivatives (III) are synthesized in a facile one-step procedure mediated by molecular iodine.
In situ interferometric alignment systems for the assembly of microchannel relay systems (1997)

An interferometric alignment technique developed for the assembly of microchannel relay systems is described. The method uses pairs of diffractive lenslets that are arranged to form compact in situ interferometers. The relative transverse, longitudinal, and rotational alignment of the two lenslet arrays can be quantitatively determined from the resulting interference patterns. The theoretical analysis is compared with the experimental performance.
Identification of Peptide Ligands Facilitating Nanoparticle Attachment to Erythrocytes (2007)

Peptide ligands capable of mediating nanoparticle adhesion to human red blood cells (RBCs) were identified from a large bacterial display peptide library. Peptides were displayed on the surface of fluorescent Escherichia coli, enabling quantitative measurement of RBC binding and high-throughput screening using fluorescence-activated cell sorting. One of the isolated clones remained attached to RBCs under high-shear stresses equivalent to those encountered in vivo. Furthermore, nanoparticles functionalized with the identified RBC-binding peptides exhibited nearly 100-fold increased RBC binding relative to nonfunctionalized particles in the presence of physiologically relevant concentrations of human serum albumin, indicating that peptides remained functional in the absence of the protein scaffold used for display. The RBC-binding peptides identified here provide new opportunities for sustained therapeutic delivery applications whereby nanoparticulate drug carriers can be attached to RBCs to achieve long-circulating carrier systems.
A design for high-performance flash disks (2007)

Most commodity flash disks exhibit very poor performance when presented with writes that are not sequentially ordered. We argue that performance can be significantly improved through the addition of sufficient RAM to hold data structures describing a fine-grain mapping between disk logical blocks and physical flash addresses. We present a design that accomplishes this.
Immunization with the Chlamydia trachomatis Mouse Pneumonitis Major Outer Membrane Protein by Use of CpG Oligodeoxynucleotides as an Adjuvant Induces a Protective Immune Response against an Intranasal Chlamydial Challenge (2002)

Recently, we have shown that a vaccine consisting of a purified preparation of the Chlamydia trachomatis mouse pneumonitis (MoPn) major outer membrane protein (MOMP) and Freund's adjuvant can protect mice against a genital challenge. Here, we wanted to determine if CpG motifs could be used as an immune modulator to the MOMP to induce protection in mice against an intranasal (i.n.) challenge. One-week-old BALB/c mice were immunized intramuscularly and subcutaneously either once or three times at 2-week intervals with MOMP and CpG suspended in aluminum hydroxide (alum). Negative controls received ovalbumin, CpG, and alum. Positive controls were immunized i.n. with C. trachomatis MoPn elementary bodies (EB). Six weeks after the last immunization, mice were challenged i.n. with 10(4) inclusion-forming units (IFU) of the C. trachomatis MoPn serovar. Mice that received MOMP, CpG, and alum had a strong immune response, as shown by a high titer of serum antibodies to Chlamydia and significant lymphoproliferation of T-cells following stimulation with C. trachomatis EB. After the i.n. challenge mice immunized with MOMP, CpG, and alum showed significantly less body weight loss than the corresponding control mice immunized with ovalbumin, CpG, and alum. Ten days after the challenge the animals were euthanized, their lungs were weighed, and the numbers of IFU in the lungs were determined. The average weight of the lungs of the mice immunized with MOMP, CpG, and alum was significantly less than average weight of the lungs of the mice immunized with ovalbumin, CpG, and alum. Also, the average number of IFU recovered per mouse immunized with MOMP, CpG, and alum was significantly less than the average number of IFU per mouse detected in the mice inoculated with ovalbumin, CpG, and alum. In conclusion, our data show that CpG sequences can be used as an effective adjuvant with the C. trachomatis MoPn MOMP to elicit a protective immune response in mice against a chlamydial respiratory challenge.
Binding of Pyridine Nucleotide Coenzymes to the β-Subunit of the Voltage-sensitive K+ Channel (2001)

The beta-subunit of the voltage-sensitive K(+) (K(v)) channels belongs to the aldo-keto reductase superfamily, and the crystal structure of K(v)beta2 shows NADP bound in its active site. Here we report that K(v)beta2 displays a high affinity for NADPH (K(d) = 0.1 micrometer) and NADP(+) (K(d) = 0.3 micrometer), as determined by fluorometric titrations of the recombinant protein. The K(v)beta2 also bound NAD(H) but with 10-fold lower affinity. The site-directed mutants R264E and N333W did not bind NADPH, whereas, the K(d)(NADPH) of Q214R was 10-fold greater than the wild-type protein. The K(d)(NADPH) was unaffected by the R189M, W243Y, W243A, or Y255F mutation. The tetrameric structure of the wild-type protein was retained by the R264E mutant, indicating that NADPH binding is not a prerequisite for multimer formation. A C248S mutation caused a 5-fold decrease in K(d)(NADPH), shifted the pK(a) of K(d)(NADPH) from 6.9 to 7.4, and decreased the ionic strength dependence of NADPH binding. These results indicate that Arg-264 and Asn-333 are critical for coenzyme binding, which is regulated in part by Cys-248. The binding of both NADP(H) and NAD(H) to the protein suggests that several types of K(v)beta2-nucleotide complexes may be formed in vivo.
Viral Vectors for Gene Therapy (2002)

Viral Vectors for Gene Therapy: Methods and Protocols consists of 30 ch- ters detailing the use of herpes viruses, adenoviruses, adeno-associated viruses, simple and complex retroviruses, including le