gebhart/patrepeval huggingface dataset:
The Ba813 chromosomal DNA sequence effectively traces the whole Bacillus anthracis community (1999)

Plasmid genes that are responsible for virulence of Bacillus anthracis are important targets for the DNA-based detection of anthrax. We evaluated the distribution of the Ba813 chromosomal DNA sequence (Ba813) within closely related Bacillus species. Ba813 was systematically identified from 47 strains or isolates of B. anthracis tested, thus indicating its reliability as a tracer for that species. From the 60 strains of closely related Bacillus spp. examined, three bona fide B. cereus and one bona fide B. thuringiensis were found to harbour Ba813. This marker was also detected in Bacillus sp. isolates that were present at high levels in soil samples collected in a place where an anthrax outbreak had occurred. The significance and the possible function of the Ba813 locus is discussed.
THE EFFECTS OF BARORECEPTOR STIMULATION ON SHORT-TERM VERBAL MEMORY (2009)

Individuals remember arousing, emotional stimuli better than neutral. Vagus nerve stimulation (VNS) has been associated with changes in such 'affective memory' in clinical samples. The current study utilized carotid baroreceptor stimulation (CBS), an indirect method of vagus nerve stimulation, to investigate this association further in normal, college-aged participants. Results showed that CBS marginally enhanced verbal memory for negative words and slowed heart rate, but these effects were not robust. Our findings indicate that physiological manipulations may contribute to differential rates of memory for arousing, emotional stimuli, suggesting that preferential memory for such stimuli might be attributed, in part, to individual differences in physiology. These findings are discussed within both the context of the Laceys' (1974) hypothesis that baro-afferent signaling may be associated with concomitant changes in heart rate and cognitive function and from the perspective that stimulation may affect brain regions involved in emotion and memory processing.
A survey of mixed transform techniques for speech and image coding (2003)

The goal of transform based coding is to build a representation of a signal using the smallest number of weighted basis functions possible, while maintaining the ability to reconstruct the signal with adequate fidelity. Mixed transform techniques, which employ subsets of non-orthogonal basis functions chosen from two or more transform domains, have been shown to consistently yield more efficient signal representations than those based on one transform. This paper provides a survey of mixed transform techniques, also known as multitransforms or mixed basis representations, which have been developed for speech and image coding.
A Mammalian Telomerase-Associated Protein (1997)

The telomerase ribonucleoprotein catalyzes the addition of new telomeres onto chromosome ends. A gene encoding a mammalian telomerase homolog called TP1 (telomerase-associated protein 1) was identified and cloned. TP1 exhibited extensive amino acid similarity to the Tetrahymena telomerase protein p80 and was shown to interact specifically with mammalian telomerase RNA. Antiserum to TP1 immunoprecipitated telomerase activity from cell extracts, suggesting that TP1 is associated with telomerase in vivo. The identification of TP1 suggests that telomerase-associated proteins are conserved from ciliates to humans.
A Higher Frequency of CD14+CD169+ Monocytes/Macrophages in Patients with Colorectal Cancer (2015)

Our data suggest that an increase in the frequency of CD14+ CD169+ cells may be associated with the development and progression of CRC and is concomitant rise of both, pro-tumor (M2-like, IL-10 producing) and anti-tumor (M1-like, IL-12 producing) monocytes and infiltrating macrophages. The frequency of CD14+ CD169+ circulating monocytes and infiltrating macrophages may serve as a biomarker for evaluating the pathogenic degrees of CRC.
Differential Requirement for TANK-binding Kinase-1 in Type I Interferon Responses to Toll-like Receptor Activation and Viral Infection (2004)

TANK-binding kinase-1 (TBK1) and the inducible IkappaB kinase (IKK-i) have been shown recently to activate interferon (IFN) regulatory factor-3 (IRF3), the primary transcription factor regulating induction of type I IFNs. Here, we have compared the role and specificity of TBK1 in the type I IFN response to lipopolysaccharide (LPS), polyI:C, and viral challenge by examining IRF3 nuclear translocation, signal transducer and activator of transcription 1 phosphorylation, and induction of IFN-regulated genes. The LPS and polyI:C-induced IFN responses were abolished and delayed, respectively, in macrophages from mice with a targeted disruption of the TBK1 gene. When challenged with Sendai virus, the IFN response was normal in TBK1(-/-) macrophages, but defective in TBK1(-/-) embryonic fibroblasts. Although both TBK1 and IKK-i are expressed in macrophages, only TBK1 but not IKK-i was detected in embryonic fibroblasts by Northern blotting analysis. Furthermore, the IFN response in TBK1(-/-) embryonic fibroblasts can be restored by reconstitution with wild-type IKK-i but not a mutant IKK-i lacking kinase activity. Thus, our studies suggest that TBK1 plays an important role in the Toll-like receptor-mediated IFN response and is redundant with IKK-i in the response of certain cell types to viral infection.
Multiple-bandwidth photoacoustic tomography (2004)

Photoacoustic tomography, also referred to as optoacoustic tomography, employs short laser pulses to generate ultrasonic waves in biological tissues. The reconstructed images can be characterized by the convolution of the structure of samples, the laser pulse and the impulse response of the ultrasonic transducer used for detection. Although the laser-induced ultrasonic waves cover a wide spectral range, a single transducer can receive only part of the spectrum because of its limited bandwidth. To systematically analyse this problem, we constructed a photoacoustic tomographic system that uses multiple ultrasonic transducers simultaneously, each at a different central frequency. The photoacoustic images associated with the different transducers were compared and analysed. The system was tested by imaging both mouse brains and phantom samples. The vascular vessels in the brain were revealed by all of the transducers, but the image resolutions differed. The higher frequency detectors provided better image resolution while the lower frequency detectors delineated the major structural traits with a higher signal-noise ratio.
Properties of Cyclodextrins. Part VI. Water‐Soluble Cyclodextrin‐Derivatives. Preparation and Analysis (1971)

Abstract Inclusion compounds with cyclodextrins in aqueous solution are only known in case the included compound is a polar substance; with apolar substances only very slightly soluble inclusion compounds are formed. In order to be able to make inclusion compounds with apolar substances in solution, hydrophylic cyclodextrin derivatives have been prepared, viz. the carboxymethylether Na‐salt, the sulfopropylether Na‐salt and a soluble epichlorohydrin resin of both a and ß cyclodextrin. The molecular weight (apparent void concentration, respectively) of the derivatives is determined in a number of different ways.
Endothelial barrier protection by activated protein C through PAR1-dependent sphingosine 1–phosphate receptor-1 crossactivation (2004)

Endothelial cells normally form a dynamically regulated barrier at the blood-tissue interface, and breakdown of this barrier is a key pathogenic factor in inflammatory disorders such as sepsis. Pro-inflammatory signaling by the blood coagulation protease thrombin through protease activated receptor-1 (PAR1) can disrupt endothelial barrier integrity, whereas the bioactive lipid sphingosine 1-phosphate (S1P) recently has been demonstrated to have potent barrier protective effects. Activated protein C (APC) inhibits thrombin generation and has potent anti-inflammatory effects. Here, we show that APC enhanced endothelial barrier integrity in a dual-chamber system dependent on binding to endothelial protein C receptor, activation of PAR1, and activity of cellular sphingosine kinase. Small interfering RNA that targets sphingosine kinase-1 or S1P receptor-1 blocked this protective signaling by APC. Incubation of cells with PAR1 agonist peptide or low concentrations of thrombin (approximately 40 pM) had a similar barrier-enhancing effect. These results demonstrate that PAR1 activation on endothelial cells can have opposite biologic effects, reveal a role for cross-communication between the prototypical barrier-protective S1P and barrier-disruptive PAR1 pathway, and suggest that S1P receptor-1 mediates protective effects of APC in systemic inflammation.
THE ASTROSPHERE OF THE ASYMPTOTIC GIANT BRANCH STAR IRC+10216 (2010)

We have discovered a very extended shock structure (i.e., with a diameter of about 24 arcmin) surrounding the well-known carbon star IRC+10216 in ultraviolet images taken with the GALEX satellite. We conclude that this structure results from the interaction of IRC+10216's molecular wind with the interstellar medium (ISM), as it moves through the latter. All important structural features expected from theoretical models of such interactions are identified: the termination shock, the astrosheath, the astropause, the bowshock, and an astrotail (with vortices). The extent of the astropause provides new lower limits to the envelope age (69,000 years) and mass (1.4 solar masses, for a mass-loss rate of 2 x 10^(-5) solar masses/year). From the termination-shock standoff distance, we find that IRC+10216 is moving at a speed of about > 91 km/s [1 cm^(-3)/n_(ISM)]^1/2 through the local ISM.
Diagnostic and therapeutic approach of systemic amyloidosis. (2004)

Amyloidosis is a group of diseases, all characterised by deposition of protein fibrils with a beta-sheet structure. This structure generates affinity of amyloid for Congo red dye and is resistant to proteolysis. Three types of systemic amyloidosis are important for the clinician: AA (related to underlying chronic inflammation), AL (related to underlying monoclonal light chain production) and ATTR amyloidosis (related to old age or underlying hereditary mutations of transthyretin). Signs and symptoms vary considerably among the three types and the choice of treatment differs completely. A stepwise approach in diagnosis and therapy is presented. When amyloidosis is suspected the first step is histological proof of amyloid and the second is proof of systemic involvement. The next two steps are determination of the type of amyloid followed by detection of the precursor protein. The fifth step is a thoughtful clinical evaluation, necessary for assessment of prognosis and therapy. Subsequently, the choice of therapy is based on the 'precursor-product' concept. In the final step, the effects of therapy on the underlying disease as well as on the amyloidosis are assessed during follow-up. In this evaluation serum amyloid P component (SAP) scintigraphy helps to show organ involvement and therapy response.
Changes in inferred spawning areas of Todarodes pacificus(Cephalopoda: Ommastrephidae) due to changing environmental conditions (2000)

Changes in inferred spawning areas of Todarodes pacificus (Cephalopoda: Ommastrephidae
Congestion driven quadratic placement (1998)

This paper introduces and demonstrates an extension to quadratic placement that accounts for wiring congestion. The algorithm uses an A* router and line-probe heuristics on region-based routing graphs to compute routing cost. The interplay between routing analysis and quadratic placement using a growth matrix permits global treatment of congestion. Further reduction in congestion is obtained by the relaxation of pin constraints. Experiments show improvements in wireability.
Major clinical research advances in gynecologic cancer in 2011 (2012)

The annual review of 2011 comprised 11 themes of major research achievements in gynecologic oncology including breast cancer. A potential paradigm shift in the management of ovarian cancer was reviewed through comprehensive genomic analyses and a tumor-specific new intraoperative fluorescence imaging technique using folate receptor-α targeted agent, which is expected to improve intraoperative staging and more radical cytoreduction. In addition, updates of bevacizumab and poly (ADP-ribose) polymerase inhibitors, risk-reducing salpingo-oophorectomy, and risk evaluation of pelvic mass were discussed. Regarding cervical cancer, this review covered new findings on human papillomavirus vaccines and human papillomavirus tests as well as the current status of clinical trials on locally advanced cervical cancer. The promising role of sentinel lymph node biopsy in the management of early stage endometrial cancer was followed by two notable clinical researches on: exemestane, an aromatase inhibitor, for the prevention of breast cancer and eribulin, a non-taxane microtubule dynamics inhibitor for the treatment of metastatic breast cancer. Lastly, in premenopausal women with breast cancer, the effect of gonadotropin-releasing hormone analogue on the occurrence of chemotherapy-induced early menopause was discussed.
Nearfield of a large acoustic transducer. Part IV: Second harmonic and sum frequency radiation (1984)

The theory presented in two previous papers [J. Acoust. Soc. Am. 74, 1013–1020 (1983) and J. Acoust. Soc. Am. 75, 769–779 (1984)] is generalized to the second harmonic and sum frequency components in the acoustic beam from a moderate amplitude parametric radiator. The theory also applies to the second harmonic component in the acoustic field from a moderate amplitude monochromatic transducer. Asymptotic formulas are presented, showing the development of the second harmonic and sum frequency sound from the source (transducer) into the farfield. Numerical results for the axisymmetric case are given. The results are compared with earlier theories and observations.
A hypermorphic IκBα mutation is associated with autosomal dominant anhidrotic ectodermal dysplasia and T cell immunodeficiency (2003)

X-linked anhidrotic ectodermal dysplasia with immunodeficiency (XL-EDA-ID) is caused by hypomorphic mutations in the gene encoding NEMO/IKKgamma, the regulatory subunit of the IkappaB kinase (IKK) complex. IKK normally phosphorylates the IkappaB-inhibitors of NF-kappaB at specific serine residues, thereby promoting their ubiquitination and degradation by the proteasome. This allows NF-kappaB complexes to translocate into the nucleus where they activate their target genes. Here, we describe an autosomal-dominant (AD) form of EDA-ID associated with a heterozygous missense mutation at serine 32 of IkappaBalpha. This mutation is gain-of-function, as it enhances the inhibitory capacity of IkappaBalpha by preventing its phosphorylation and degradation, and results in impaired NF-kappaB activation. The developmental, immunologic, and infectious phenotypes associated with hypomorphic NEMO and hypermorphic IKBA mutations largely overlap and include EDA, impaired cellular responses to ligands of TIR (TLR-ligands, IL-1beta, and IL-18), and TNFR (TNF-alpha, LTalpha1/beta2, and CD154) superfamily members and severe bacterial diseases. However, AD-EDA-ID but not XL-EDA-ID is associated with a severe and unique T cell immunodeficiency. Despite a marked blood lymphocytosis, there are no detectable memory T cells in vivo, and naive T cells do not respond to CD3-TCR activation in vitro. Our report highlights both the diversity of genotypes associated with EDA-ID and the diversity of immunologic phenotypes associated with mutations in different components of the NF-kappaB signaling pathway.
Regular review: Ulcerative colitis (2000)

Ulcerative colitis is a relapsing and remitting disease characterised by acute non-infectious inflammation of the colorectal mucosa. In the United Kingdom the annual incidence is around 7 cases per 100 000 population.1 The rectal mucosa is invariably affected. Confluent inflammation and shallow ulceration extend proximally from the anal margin. A patient may have proctitis, left sided colitis (the proximal limit being below the splenic flexure), extensive colitis (involving the transverse colon), or pan colitis. At any point in time, 50% of patients are asymptomatic, 30% have mild symptoms, and 20% have moderate to severe symptoms.2 Many patients have long periods of complete remission, but the cumulative probability of remaining free from relapse at two years is only 20%, decreasing to less than 5% at 10 years.3 Later relapses generally affect the same region of the colon as previous episodes.


Several of the current clinical and therapeutic issues in ulcerative colitis include: (a) medical treatment options for relapse and for maintenance of remission; (b) management of the minority of patients who develop a severe life threatening relapse or chronic unremitting disease; (c) surgical treatment of ulcerative colitis; and (d) long term complications in patients with extensive disease—namely, colonic and biliary cancers and sclerosing cholangitis. 


Summary points


Ulcerative colitis may present at any age, but the anatomical distribution of involvement at presentation is different between children and adults


All patients with bloody diarrhoea need to have infection excluded


Outpatient rigid sigmoidoscopy is the best method of diagnosing the nature of inflammation


The extent of inflammation may be established by total colonoscopy (or a double contrast barium enema)


The mainstays of treatment are rectal and systemic 5-aminosalicylic acid derivatives and corticosteroids, with azathioprine in steroid dependent or resistant cases


Restorative proctocolectomy with ileal pouch-anal anastomosis should be considered in every patient in whom colectomy is contemplated
Highly‐efficient gene transfer with retroviral vectors into human T lymphocytes on fibronectin (1998)

Genetically modified lymphocytes have been successfully used for correction of ADA deficiency in children and in controlling graft-versus-host disease (GvHD) after allogeneic bone marrow transplantation. Low transduction efficiencies are, however, limiting for gene therapeutic strategies based on lymphocytes. In this study we compared protocols for highly efficient gene transfer into human T cells using retroviral vector-containing supernatant. We showed that infection of both human primary T cells and CD4+ Jurkat cells is most efficient on the matrix component fibronectin. Transduction was carried out with a retroviral vector encoding both the human intracytoplasmatically truncated low-affinity nerve growth factor receptor (deltaLNGFR) as a gene transfer marker and the Herpes simplex virus thymidine kinase for negative selection. Based on LNGFR expression genetically modified cells were enriched to near purity by magnetic cell sorting (MACS). Enriched cells could be shown to be highly sensitive to ganciclovir.
t(3;22)(q27;q11): a novel translocation associated with diffuse non- Hodgkin's lymphoma [see comments] (1989)

Of 187 specimens of non-Hodgkin's lymphoma and four hyperplastic lymphoid proliferations with clonal chromosome abnormalities ascertained serially over a 4 1/2-year period, nine cases with t(3;22)(q27;q11) were identified. Seven of the lymphomas were diffuse tumors, predominantly large cell type. The eighth tumor, a follicular small cleaved cell lymphoma, exhibited a t(3;22) and a t(14;18)(q32;q21). The ninth case was a lymph node from a human immunodeficiency virus-positive patient which showed atypical hyperplasia. Overall survival of t(3;22) diffuse lymphoma patients was not different from that of patients with abnormal karyotypes without t(3;22). The t(3;22) diffuse tumors studied showed a disproportionate frequency of lambda light chain on their cell surfaces, a finding similar to that observed in t(8;22)(q24;q11) Burkitt's lymphomas. Our results indicate that the t(3;22)(q27;q11) is the third most common recurring translocation in diffuse non-Hodgkin's lymphoma.
Routing Requirements for Low Power And Lossy Networks (2007)

The need for high quality routing for Low power and Lossy Network
(L2N) such as sensor networks comprised of highly constrained devices
(CPU, memory, ...) in sometimes unstable wireless environments is
critical now and will continue to increase. Interest in this class of
applications has grown dramatically in recent years and a routing
solution addressing the specific environments of such networks is
highly required considering the numerous, incompatible open-source and
proprietary routing protocols as well as several industrial forums.
The aim of this document is to define the routing requirements for
Sensor Networks at the IP layer. Such routing protocol(s) would need
to address several unique aspects of this class of embedded devices
and would operate in networks comprising links of various nature.
Reconstitution of Drug Transport by Purified P-glycoprotein (1995)

P-glycoprotein confers multidrug resistance upon cells in which it is highly expressed, reducing the effectiveness of numerous cytotoxic drugs, including many of those used for chemotherapy of cancer. Although P-glycoprotein is widely believed to function as an ATP-dependent drug efflux pump, the unusually broad substrate specificity of P-glycoprotein has engendered the proposal of other, less direct mechanisms. None of the hypothetical mechanisms has been definitively tested, however, in a purified system where other cellular components and processes are absent. We have used a fluorescent substrate of P-glycoprotein, Hoechst 33342, to measure transport activity in real-time of highly purified P-glycoprotein in a reconstituted liposome system in which the P-glycoprotein has a uniformly inside-out orientation. Using this system, we demonstrated MgATP-dependent, chemosensitizer-inhibitable transport of Hoechst 33342. Transport was prevented by omission of Mg2+, by substitution of nonhydrolyzable adenylyl-beta,gamma-imidodiphosphate for ATP, by inhibition of the ATPase activity of P-glycoprotein with vanadate and N-ethylmaleimide, and by the chemosensitizers verapamil and amiodarone. Measurements of intraliposomal pH during Hoechst 33342 transport detected no large pH changes in P-glycoprotein-containing liposomes. These results are inconsistent with a mechanism in which P-glycoprotein affects drug accumulation by directly altering intracellular pH. The Hoechst 33342 transport assay results are consistent with mechanisms in which P-glycoprotein alone is sufficient to transport drugs out of the membrane bilayer.
Distinct in vitro Complement Activation by Various Intravenous Iron Preparations (2016)

This study provides evidence that iron dextran and ferric carboxymaltose have complement-activating capacities in-vitro, and hypersensitivity reactions to these drugs could be CARPA-mediated.
Real-time motion tracking on a cellphone using inertial sensing and a rolling-shutter camera (2013)

All existing methods for vision-aided inertial navigation assume a camera with a global shutter, in which all the pixels in an image are captured simultaneously. However, the vast majority of consumer-grade cameras use rolling-shutter sensors, which capture each row of pixels at a slightly different time instant. The effects of the rolling shutter distortion when a camera is in motion can be very significant, and are not modelled by existing visual-inertial motion-tracking methods. In this paper we describe the first, to the best of our knowledge, method for vision-aided inertial navigation using rolling-shutter cameras. Specifically, we present an extended Kalman filter (EKF)-based method for visual-inertial odometry, which fuses the IMU measurements with observations of visual feature tracks provided by the camera. The key contribution of this work is a computationally tractable approach for taking into account the rolling-shutter effect, incurring only minimal approximations. The experimental results from the application of the method show that it is able to track, in real time, the position of a mobile phone moving in an unknown environment with an error accumulation of approximately 0.8% of the distance travelled, over hundreds of meters.