gebhart/patrepeval huggingface dataset:
Echocardiographic follow-up of atrial septal defect after catheter closure by double-umbrella device. (1993)

BACKGROUND Transcatheter device occlusion of atrial septal defects is an attractive approach, but its efficacy and place in patient management remain to be determined. METHODS AND RESULTS To evaluate the medium-term results of atrial septal defect device occlusion and factors influencing residual shunting, transesophageal and transthoracic echocardiograms of 49 patients were reviewed. Transesophageal echocardiograms on 48 patients immediately following surgical closure revealed residual shunting in 2% compared with 91% after device occlusion; this proportion decreased to 53% after a mean follow-up of 10 months. The actuarial analysis suggests a progressive resolution of shunting with time. One patient had residual shunting by transesophageal echocardiography immediately after surgical closure compared with 29 after a mean follow-up of 10 months after device occlusion. Residual shunting was not influenced by (1) dimension, location, or position with relation to the device as assessed by transesophageal echocardiography; (2) location of the defect; or (3) device size relative to the stretched dimension of the defect. In 15 patients, a poor correlation existed between transesophageal and transthoracic echocardiographic findings. Variability in serial transthoracic echocardiographic findings was observed in 14. Right ventricular dimension, heart size, and presence of a murmur at follow-up did not correlate with the presence or size of residual shunting after device occlusion. CONCLUSIONS These results suggest that ongoing spontaneous resolution of residual shunting occurs after device insertion. Factors related to the defect or device could not predict eventual resolution of residual shunting. Transthoracic echocardiography in the follow-up of these patients may not be reliable in determining presence of residual shunting.
Human airway secretory cells during development and in mature airway epithelium (1992)

The combined secretions of distinct secretory cells of the airway lining mucosa serve to keep the inspired air moist and free of potentially harmful dust particles, organisms and adsorbed gases. Apart from their role in protecting the respiratory zone of the lung, mucus-secreting cells act as pluripotential stem cells during foetal development and, in the adult, following mucosal injury. The variety of secretory cells include the mucous and serous cells of the surface and glandular epithelium, the non-ciliated bronchiolar (Clara) cell and the less frequent dense-core granulated (neuroendocrine) cell. The last-mentioned is the first type to differentiate at about 10 weeks of gestation; mucus-secreting cells are present from the 13th week of gestation, when mature ciliated cells are already present, and Clara cells begin to mature during the 19th week of human development. The alteration of secretory cell number and chemical composition of their secretions during the second trimester of foetal life is similar to that which occurs in chronic bronchitis in the adult. However, in hypersecretory disease the extent and site of the major change appear to be inappropriate to the defence of the lung.
Electroplated CoFe thin films for electromagnetic microactuators (2006)

To replace NiFe alloys used as flux guides in magnetic microelectromechanical systems, electroplated CoFe thin films were examined. The films were deposited using pulse plating. The results show a strong influence of the reverse current Ireverse on the deposition rate and the saturation flux density Bs. The relative permeability μr is influenced both by the forward current Iforward and by reverse current Ireverse. Based on the examinations an optimized deposition was performed. A film thickness of 15μm was reached during a deposition time of 1h. This film exhibited a saturation flux density Bs of 1.4T, a coercivity Hc of 1130kA∕m, and a relative permeability μr of 290. At this thickness, no delamination occurred and the film showed only minor signs of corrosion, a phenomenon CoFe films are typically prone to.
Production of Clostridium difficile antitoxin (1980)

We have produced antitoxin to the toxin of Clostridium difficile in rabbits and in goats. Antitoxin dilutions of 1/8,000 and 1/5,120 were capable of neutralizing lethal doses of the toxin in mice and in tissue culture, respectively.
IFN induction and associated changes in splenic leukocyte distribution (1993)

Our studies were undertaken to evaluate early events associated with IFN expression and IFN-induced cellular changes in the spleen. Polyinosinic-polycytidylic acid (poly(I:C)) was used to induce IFN in C57BL/6 mice. Biologically active IFN was present in spleens and sera of poly(I:C)-treated mice as early as 3 h and peaked at 6 to 12 h posttreatment. Neutralization assays and Northern blot analyses demonstrated that IFN-beta was the form of IFN preferentially induced in the spleens. Immunohistochemical staining and in situ hybridization studies of splenic tissue sections demonstrated that, although many cells were induced to express low levels of IFN-beta, low frequency cells were particularly potent expressers of IFN-beta. Perivascular cells expressed high levels of IFN-beta. Other positive cells were localized in red pulp at early times and in white pulp at later times posttreatment. Histologic examination of splenic sections showed that the IFN production was accompanied by dramatic architectural changes. There were significant 1.4-fold increases in the proportion of white pulp area and > 50% decreases in red pulp leukocyte number. These architectural changes appeared at 6 h and lasted through 36 h after poly(I:C) treatment. They were not due to increased cell proliferation as splenic weights and cell yields were not elevated. The changes in splenic leukocyte distribution were shown to be a result of IFN induction as: 1) treatment with anti-IFN antibodies inhibited poly(I:C)-induced depletion of red pulp leukocytes, and 2) administration of purified IFN-beta induced both an increase in white pulp area and a decrease in red pulp leukocytes. Splenic leukocytes were labeled with the lipophilic fluorescent dye, 1,1'-dioctadecyl-3,3,3',3'-tetramethyl indocarbocyanine perchlorate, to evaluate cell traffic after IFN induction. Poly(I:C) enhanced accumulation of cells in white pulp regions. In contrast to the 76 +/- 2 labeled cells that accumulated in 0.5 mm2 of white pulp area in control PBS-treated mice, 131 +/- 4 labeled cells accumulated in 0.5 mm2 of white pulp area in poly(I:C)-treated mice. The poly(I:C)-enhanced leukocyte accumulation in short term cell migration to white pulp regions was dependent on preexposure of both splenic leukocytes and recipient environments to the IFN inducer. These data demonstrate that poly(I:C) is a potent and rapid inducer of IFN-beta production by splenic cells and that IFN induces cellular redistribution in the spleen. The results suggest that margination of leukocytes into splenic white pulp may be another important immunoregulatory function of IFN.
An Improved Method for Conjugating Monoclonal Antibodies with N-Hydroxysulfosuccinimidyl DOTA (2001)

A simple, water-soluble procedure for conjugation of monoclonal antibodies to 1,4,7,10-tetraazacyclododecane-N,N',N",N"'-tetraacetic acid (DOTA) has been improved by optimizing pH, buffer, and temperature conditions for the preparation of N-hydroxysulfosuccinimidyl DOTA and its conjugation to the human/murine chimeric anti-carcinoembryonic antigen antibody cT84.66. This improved method results in a 6-fold increase in conjugation efficiency, a 3-7-fold decrease in antibody cross-linking, a more homogeneous population of conjugate species, and a 5-fold decrease in the quantities of reagents needed for conjugation. The cT84.66-DOTA conjugate was labeled to high specific activity with 111In, 90Y, 88Y, 64Cu, and 67Cu, affording near-quantitative incorporation of the majority of these radiometals. This improved conjugation procedure facilitates large-scale production and radiometal labeling of cT84.66-DOTA for clinical radioimmunotherapy trials.
Hydrogen Peroxide--Producing Lactobacilli and Acquisition of Vaginal Infections (1996)

This cohort study of 182 women attending a sexually transmitted disease clinic evaluated the hypothesis that women colonized by lactobacilli have decreased acquisition of vaginal infections. During a 2-year follow-up, 50 women acquired bacterial vaginosis (BV), 25 acquired symptomatic vulvovaginal candidiasis (YYC), and 7 acquired vaginal trichomoniasis. By multivariate analysis, utilizing Cox proportional hazards modeling with time-dependent covariates, acquisition of BV was independently associated with lack of vaginal H202-producing lactobacilli (hazard ratio [HR] = 4.0, P < .001) or presence of only non–H202-producing lactobacilli (HR = 2.2, P = .02). Acquisition of BV was associated with having a new sex partner (HR = 2.5, P = .004) and with douching for hygiene (HR = 2.1, P = .05). Absence of lactobacilli did not increase acquisition of VVC. Trichomoniasis was associated only with having a new sex partner (HR = 4.7, P = .05). These results support the hypothesis that H202-producing vaginal lactobacilli protect against acquisition of BV but do not protect against VVC or vaginal trichomoniasis.
A cost-effective RNA sequencing protocol for large-scale gene expression studies (2015)

RNA sequencing has increasingly become an indispensable tool for biological research. While sequencing costs have fallen dramatically in recent years, the current cost of RNA sequencing, nonetheless, remains a barrier to even more widespread adoption. Here, we present a simple RNA sequencing protocol with substantially reduced costs. This protocol uses as little as 10 ng of total RNA, allows multiplex sequencing of up to 96 samples per lane, and is strand specific. Extensive validation using human embryonic stem cells showed high consistency between technical replicates at various multiplexing levels.
Proof-carrying code (1997)

This paper describes proof-carrying code (PCC), a mechanism by which a host system can determine with certainty that it is safe to execute a program supplied (possibly in binary form) by an untrusted source. For this to be possible, the untrusted code producer must supply with the code a safety proof that attests to the code's adherence to a previously defined safety policy. The host can then easily and quickly validate the proof without using cryptography and without consulting any external agents.In order to gain preliminary experience with PCC, we have performed several case studies. We show in this paper how proof-carrying code might be used to develop safe assembly-language extensions of ML programs. In the context of this case study, we present and prove the adequacy of concrete representations for the safety policy, the safety proofs, and the proof validation. Finally, we briefly discuss how we use proof-carrying code to develop network packet filters that are faster than similar filters developed using other techniques and are formally guaranteed to be safe with respect to a given operating system safety policy.
RNA Silencing: The Genome's Immune System (2002)

Genomes are databases sensitive to invasion by viruses. In recent years, a defense mechanism has been discovered, which turns out to be conserved among eukaryotes. The system can be compared to the immune system in several ways: It has specificity against foreign elements and the ability to amplify and raise a massive response against an invading nucleic acid. The latter property is beginning to be understood at the molecular level.
Flt-1 Intraceptors Inhibit Hypoxia-Induced VEGF Expression In Vitro and Corneal Neovascularization In Vivo (2005)

Flt-1 intraceptors, which are endoplasmic reticulum retention signal-coupled VEGF receptors, significantly suppress hypoxia-induced VEGF secretion by corneal epithelial cells in vitro. In vivo, delivery of naked plasmids expressing these intraceptors inhibits injury-induced upregulation of VEGF, leukocyte infiltration, and corneal neovascularization.
Derivation of Dendritic Cells from Myeloid and Lymphoid Precursors (2001)

The antigen presenting dendritic cells (DC) found in mouse and human lymphoid tissues are heterogeneous. Several subsets of mature DC have been described and these may correspond to distinct lineages. In this review, we present evidence obtained from a series of studies on the lineage origin of DC. This evidence points to the existence of at least three pathways for DC development, namely one from myeloid progenitors, a second from lymphoid progenitors and the third for Langerhans cells from precursors whose relationship to myeloid or lymphoid cell types is not yet clearly defined.
Topic sentiment mixture (2007)

In this paper, we define the problem of topic-sentiment analysis on Weblogs and propose a novel probabilistic model to capture the mixture of topics and sentiments simultaneously. The proposed Topic-Sentiment Mixture (TSM) model can reveal the latent topical facets in a Weblog collection, the subtopics in the results of an ad hoc query, and their associated sentiments. It could also provide general sentiment models that are applicable to any ad hoc topics. With a specifically designed HMM structure, the sentiment models and topic models estimated with TSM can be utilized to extract topic life cycles and sentiment dynamics. Empirical experiments on different Weblog datasets show that this approach is effective for modeling the topic facets and sentiments and extracting their dynamics from Weblog collections. The TSM model is quite general; it can be applied to any text collections with a mixture of topics and sentiments, thus has many potential applications, such as search result summarization, opinion tracking, and user behavior prediction.
Secretogranin III: a Bridge between Core Hormone Aggregates and the Secretory Granule Membrane (2010)

Secretory granules in endocrine cells selectively store bioactive peptide hormones and amines, which are secreted in a regulated manner upon appropriate stimulation. In addition to bioactive substances, various proteins and lipids characteristic of secretory granules are likely recruited to a restricted space at the trans-Golgi Network (TGN), and the space then matures to the secretory granule. Although experimental findings so far have strongly suggested that aggregation- and receptor-mediated processes are essential for the formation of secretory granules, the putative link between these two processes remains to be clarified. Recently, secretogranin III (SgIII) has been identified as a specific binding protein for chromogranin A (CgA), a representative constituent of the core aggregate within secretory granules, and it was later revealed that SgIII can also bind to the cholesterol-rich membrane domain at the TGN. Based on its multifaceted binding properties, SgIII may act as a central player in the formation of cholesterol-rich membrane platforms. Upon these platforms, essential processes for secretory granule biogenesis coordinately occur; that is, selective recruitment of prohormones, processing and modifying of prohormones, and condensation of mature hormones as an aggregate. This review summarizes the findings and theoretical concepts on the issue to date and then focuses on the putative role of SgIII in secretory granule biogenesis in endocrine cells.
Stress-Dependent Regulation of FOXO Transcription Factors by the SIRT1 Deacetylase (2004)

The Sir2 deacetylase modulates organismal life-span in various species. However, the molecular mechanisms by which Sir2 increases longevity are largely unknown. We show that in mammalian cells, the Sir2 homolog SIRT1 appears to control the cellular response to stress by regulating the FOXO family of Forkhead transcription factors, a family of proteins that function as sensors of the insulin signaling pathway and as regulators of organismal longevity. SIRT1 and the FOXO transcription factor FOXO3 formed a complex in cells in response to oxidative stress, and SIRT1 deacetylated FOXO3 in vitro and within cells. SIRT1 had a dual effect on FOXO3 function: SIRT1 increased FOXO3's ability to induce cell cycle arrest and resistance to oxidative stress but inhibited FOXO3's ability to induce cell death. Thus, one way in which members of the Sir2 family of proteins may increase organismal longevity is by tipping FOXO-dependent responses away from apoptosis and toward stress resistance.
Acute Vocal Fold Wound Healing in a Rabbit Model (2005)

Several authors have eloquently described the characteristics of vocal fold scar, a long-term consequence of vocal fold injury. However, events in the acute stage of mucosal injury, which lead up to fibrosis, have been largely overlooked. The current study describes acute events with regard to mucosal re-formation in a rabbit model. Vocal fold injury was induced surgically. A fibrinous clot was present 1 day after injury. Massive cellular infiltration was noted on day 3, and complete epithelial coverage was achieved by day 5. Also, neo-matrix deposition was noted as early as 5 days after injury, and more mature collagen was seen by day 7. The general timetable described in the current study can contribute to the experimental foundation for the development of regenerative models of healing in the vocal folds. Most notably, the proliferation phase of wound healing appears to occur approximately 3 days after injury, indicating a critical time for intervention. Manipulation and/or alteration of naturally occurring neo-matrix deposition and organization may yield improved biophysical function of the injured vocal fold.
Organization and Sequences ofp-Hydroxybenzaldehyde Dehydrogenase and Other Plasmid-Encoded Genes for Early Enzymes of thep-Cresol Degradative Pathway inPseudomonas PutidaNCIMB 9866 and 9869 (1999)

The gene (designated pchA) encoding the aldehyde dehydrogenase that is required to metabolise the p-hydroxybenzaldehyde produced by the degradation of p-cresol in Pseudomonas putida NCIMB 9866 and 9869 has been identified on plasmids pRA4000 and pRA500, respectively. The gene lies immediately upstream of the pchC and pchF genes encoding the subunits of p-cresol methylhydroxylase (PCMH), the preceeding enzyme in the p-cresol degradative pathway. In pRA500 the latter genes are followed by the genes encoding the alpha (pcaG) and beta (pcaH) subunits of protocatechuate-3,4-dioxygenase, whereas in pRA4000 the genes encoding PCMH are followed by an open reading frame encoding a protein that is similar to the maturase-related protein of P. alcaligenes. A gene, designated pchX, that encodes a protein of unknown function was identified between the pchC and pchF genes in both plasmids.
Requirements at the 3′ End of the Sindbis Virus Genome for Efficient Synthesis of Minus-Strand RNA (2005)

The 3'-untranslated region of the Sindbis virus genome is 0.3 kb in length with a 19-nucleotide conserved sequence element (3' CSE) immediately preceding the 3'-poly(A) tail. The 3' CSE and poly(A) tail have been assumed to constitute the core promoter for minus-strand RNA synthesis during genome replication; however, their involvement in this process has not been formally demonstrated. Utilizing both in vitro and in vivo analyses, we have examined the role of these elements in the initiation of minus-strand RNA synthesis. The major findings of this study with regard to efficient minus-strand RNA synthesis are the following: (i) the wild-type 3' CSE and the poly(A) tail are required, (ii) the poly(A) tail must be a minimum of 11 to 12 residues in length and immediately follow the 3' CSE, (iii) deletion or substitution of the 3' 13 nucleotides of the 3' CSE severely inhibits minus-strand RNA synthesis, (iv) templates possessing non-wild-type 3' sequences previously demonstrated to support virus replication do not program efficient RNA synthesis, and (v) insertion of uridylate residues between the poly(A) tail and a non-wild-type 3' sequence can restore promoter function to a limited extent. This study shows that the optimal structure of the 3' component of the minus-strand promoter is the wild-type 3' CSE followed a poly(A) tail of at least 11 residues. Our findings also show that insertion of nontemplated bases can restore function to an inactive promoter.
Quasi-phase-matched 1064-μm-pumped optical parametric oscillator in bulk periodically poled LiNbO_3 (1995)

We report a quasi-phase-matched optical parametric oscillator, using bulk periodically poled LiNbO(3). The optical parametric oscillator, pumped by a 1.064-microm Q-switched Nd:YAG laser, was temperature tuned over the wavelength range 1.66-2.95 microm. The oscillation threshold of approximately 0.1 mJ was more than a factor of 10 below the damage limit. The LiNbO(3) crystal, fabricated by application of an electric field to a sample with liquid and metal surface electrodes, was 0.5 mm thick with a 5.2-mm interaction length and a quasi-phase-matched period of 31 microm.
Carbohydrate Protection of Enzyme Structure and Function against Guanidinium Chloride Treatment Depends on the Nature of Carbohydrate and Enzyme (1997)

Baker's yeast cells accumulate osmolytes as a response to several stress conditions such as high-temperature and low-temperature shifts, dehydration, or osmotic stress. One of the major osmolytes that accumulates is trehalose, which plays an essential role affecting the survival of yeast at the time of stress. In this report, we show that trehalose efficiently protects the function and the structure of two yeast cytosolic enzymes against chemical denaturation by guanidinium chloride. Other sugars tested also protected yeast pyrophosphatase and glucose-6-phosphate dehydrogenase structure against guanidinium chloride effects, but were not as efficient at protecting enzyme activity. The thermostable pyrophosphatase from Bacillus stearothermophilus was also protected by several sugars against the chaotropic properties of guanidinium chloride, but was only protected by trehalose against functional inactivation. The function of the membrane-embedded H+-ATPase from yeast could not be protected by any of the tested sugars, although all of the sugars protected its structure from guanidinium-chloride-induced unfolding. The results presented in this study suggest that several sugars are able to prevent protein unfolding induced by a chaotropic compound. However, prevention of functional inactivation depends on the nature of the sugar. Trehalose was the most efficient, being able to protect many cytosolic enzymes against guanidinium chloride. The efficiency of protection also depended on the nature of the protein tested. This might explain why trehalose is one of the osmolytes accumulated in yeast and also why it is not the only osmolyte to accumulate.
Optical redshift in the Raman scattering spectra of Fe-doped multiwalled carbon nanotubes: Experiment and theory (2012)

Electron doping of arc-grown multiwalled carbon nanotubes coated with iron nanoparticles is established by the redshift of the graphite peak and a larger redshift of the defect peak in the Raman spectra of doped samples compared to the corresponding peak positions in undoped samples. This is unlike the blue Raman shift usually observed in defect-induced double-Raman-resonance studies. On doping, the defect peak splits into two peaks. One has approximately the same dispersion (50 cm${}^{\ensuremath{-}1}$ eV${}^{\ensuremath{-}1}$) as the defect peak of undoped samples. The other peak has a very large dispersion (110 cm${}^{\ensuremath{-}1}$ eV${}^{\ensuremath{-}1}$). We show that the above observations are consequences of drastic changes in the electronic band structure of the graphitic systems under doping. Experimental observations of the splitting of the defect peak into two and larger dispersions of one of the peaks are explained via double-Raman-resonance processes studied through detailed theoretical calculations of electronic and phonon band structures based on a first principles ab initio method.