gebhart/patrepeval huggingface dataset:
A conserved 90 nucleotide element mediates translational repression of nanos RNA (1996)

Correct formation of the Drosophila body plan requires restriction of nanos activity to the posterior of the embryo. Spatial regulation of nanos is achieved by a combination of RNA localization and localization-dependent translation such that only posteriorly localized nanos RNA is translated. Cis-acting sequences that mediate both RNA localization and translational regulation lie within the nanos 3' untranslated region. We have identified a discrete translational control element within the nanos 3' untranslated region that acts independently of the localization signal to mediate translational repression of unlocalized nanos RNA. Both the translational regulatory function of the nanos 3'UTR and the sequence of the translational control element are conserved between D. melanogaster and D. virilis. Furthermore, we show that the RNA helicase Vasa, which is required for nanos RNA localization, also plays a critical role in promoting nanos translation. Our results specifically exclude models for translational regulation of nanos that rely on changes in polyadenylation.
The effect of osteogenin (a bone morphogenetic protein) on the formation of bone in orthotopic segmental defects in rats. (1994)

We studied the effects of partially purified, natural osteogenin, a bone morphogenetic protein, on the formation of bone in rats. An osteoperiosteal segmental defect, eight millimeters wide, in the middle of the femoral diaphysis was created bilaterally in thirty-six adult male Fischer rats and stabilized with a polyacetyl plate and threaded Kirschner wires. One defect was filled with a cylinder of 60 per cent hydroxyapatite and 40 per cent tricalcium phosphate ceramic (pore diameter, 250 to 400 micrometers) containing 100 micrograms of partially purified bovine osteogenin, and the contralateral defect was filled with a hydroxyapatite-tricalcium ceramic cylinder without osteogenin. Eighteen animals (six animals each at one, two, and four months after the operation) were studied histologically and histomorphometrically. The implants from eighteen additional animals (six animals each at one, two, and four months after the operation) were subjected to biomechanical testing. Histomorphometry revealed that the total area of bone, the area of bone outside of the implant, and the amount of bone within the pores of the implant were all significantly (p < or = 0.05) greater in the femora that had an implant with osteogenin than in those that had an implant without osteogenin at most time-periods. The presence of osteogenin had no significant effect on the biomechanical parameters measured in this study.
Intestinal floras of populations that have a high risk of colon cancer (1995)

The fecal floras of polyp patients, Japanese-Hawaiians, North American Caucasians, rural native Japanese, and rural native Africans were compared. The polyp patients and Japanese-Hawaiians were considered to be groups at high risk of colon cancer, and the rural native Japanese and rural native Africans were considered to be groups at low risk. The North American Caucasians were found to have a flora composition intermediate between these two groups. Fifteen bacterial taxa from the human fecal flora were significantly associated with high risk of colon cancer, and five were significantly associated with low risk of colon cancer. Total concentrations of Bacteroides species and, surprisingly, Bifidobacterium species were generally positively associated with increased risk of colon cancer. Some Lactobacillus species and Eubacterium aerofaciens, which also produces major amounts of lactic acid, showed closest associations with low risk of colon cancer.
p27: a pleiotropic regulator of cellular phenotype and a target for cell cycle dysregulation in cancer. (2000)

The eukaryotic cell cycle is regulated by the sequential activation of cyclin-dependent kinases (CDKs). CDK activation is regulated by phosphorylation of the catalytic subunit, by binding to activating (cyclins) and inactivating subunits (cyclin-dependent kinase inhibitor). In this review, we will focus on the role of the cyclin-dependent kinase inhibitor p27 which has been recently the subject of extensive work. This negative regulator of cell growth indeed illustrates the pleiotropic biological effects of such molecules in both normal and cancer cells and the complexity of the regulatory mechanisms involved.
Effectiveness of the Maze Procedure Using Cooled-Tip Radiofrequency Ablation in Patients With Permanent Atrial Fibrillation and Rheumatic Mitral Valve Disease (2005)

The SICTRA is effective for treating permanent AF associated with rheumatic MV disease.
Rce1 deficiency accelerates the development of K-RAS–induced myeloproliferative disease (2006)

The RAS proteins undergo farnesylation of a carboxyl-terminal cysteine (the "C" of the carboxyl-terminal CaaX motif). After farnesylation, the 3 amino acids downstream from the farnesyl cysteine (the -aaX of the CaaX motif) are released by RAS-converting enzyme 1 (RCE1). We previously showed that inactivation of Rce1 in mouse fibroblasts mislocalizes RAS proteins away from the plasma membrane and inhibits RAS transformation. Therefore, we hypothesized that the inactivation of Rce1 might inhibit RAS transformation in vivo. To test this hypothesis, we used Cre/loxP recombination techniques to simultaneously inactivate Rce1 and activate a latent oncogenic K-RAS allele in hematopoietic cells in mice. Normally, activation of the oncogenic K-RAS allele in hematopoietic cells leads to rapidly progressing and lethal myeloproliferative disease. Contrary to our hypothesis, the inactivation of Rce1 actually increased peripheral leukocytosis, increased the release of immature hematopoietic cells into the circulation and the infiltration of cells into liver and spleen, and caused mice to die more rapidly. Moreover, in the absence of Rce1, splenocytes and bone marrow cells expressing oncogenic K-RAS yielded more and larger colonies when grown in methylcellulose. We conclude that the inactivation of Rce1 worsens the myeloproliferative disease caused by oncogenic K-RAS.
[Perioperative tobacco cessation: potential benefits and principles of management]. (2010)

Thirty percent of surgical patients undergoing routine surgery are smokers, and smoking is an additional risk for these patients. During the perioperative period, smokers are more prone than non smokers to present either systemic complications interesting the cardiovascular and pulmonary functions or specific complications related to the surgical procedure, such as infections, wound problems and delayed osteosynthesis. Therefore, coming-off from smoking addiction is an obvious prerequisite in these patients. Diagnosing smoking habit, evaluating its severity and its systemic repercussions on vital functions, as well as proposing an efficacious and appropriate help to smokers before surgery become one essential objective of pre-anesthetic assessment.
Comprehensive single-cell transcriptional profiling of a multicellular organism (2017)

To resolve cellular heterogeneity, we developed a combinatorial indexing strategy to profile the transcriptomes of single cells or nuclei, termed sci-RNA-seq (single-cell combinatorial indexing RNA sequencing). We applied sci-RNA-seq to profile nearly 50,000 cells from the nematode <i>Caenorhabditis elegans</i> at the L2 larval stage, which provided >50-fold "shotgun" cellular coverage of its somatic cell composition. From these data, we defined consensus expression profiles for 27 cell types and recovered rare neuronal cell types corresponding to as few as one or two cells in the L2 worm. We integrated these profiles with whole-animal chromatin immunoprecipitation sequencing data to deconvolve the cell type-specific effects of transcription factors. The data generated by sci-RNA-seq constitute a powerful resource for nematode biology and foreshadow similar atlases for other organisms.
Role of Complement Receptor Type Three and Serum Opsonins in the Neutrophil Response to Yeast (1987)

Previous studies have suggested that neutrophil complement receptor type three (CR3) has two binding sites: (1) a site for fixed iC3b that does not trigger ingestion or a superoxide (O2-) burst, and (2) a function-triggering site for the beta-glucan component of yeast (Saccharomyces cerevisiae) cell walls. In the present study it was found that yeast (Y) coated with C3b (YC3b) or iC3b (YC3bi), prepared with purified complement in an IgG-free system, were avidly ingested ans stimulated a vigorous O2- burst, whereas sheep erythrocytes (E) bearing C3b or iC3b, were not ingested and did not give an O2- burst. YC3b and YC3bi contained an amount of fixed C3 that was approximately equal to serum-opsonized Y (OY), and produced O2- bursts comparable to OY. Experiments utilizing rabbit F(ab')2 anticomplement receptor type one (anti-CR1) to block fixed C3b binding to CR1, and monoclonal anti-CR3 (MN-41 or OKM1) to block fixed iC3b and Y cell wall binding to CR3, indicated that the O2- burst response to OY was primarily due to fixed iC3b and Y cell wall binding to CR3. Fixed C3b (that represented 33% of the fixed C3 on OY) and IgG anti-Y antibodies that bound to CR1 and Fc receptors, respectively, were found to contribute little to the response. Although YC3b did bind avidly to neutrophil CR1, the results suggested that the O2- burst response to YC3b was triggered after the initial YC3b binding by the secondary attachment of Y cell wall components to CR3. When neutrophils were treated with anti-CR3, 90% of neutrophils bound YC3b (via CR1), but phagocytosis and an O2- burst were completely absent. Similar findings were made with OKM1-treated neutrophils and YC3bi. Responses of OKM1-treated neutrophils were inhibited because only the iC3b-binding site of CR3 was ligated by the YC3bi. Thus, fixed C3b or iC3b on Y mediate avid binding of Y to neutrophils via CR1 or the iC3b-binding site of CR3, respectively, but ingestion and an O2- burst response are only triggered when glucans in the Y cell wall secondarily bind to neutrophils via the beta-glucan binding site of CR3.
Pulmonary hypertension in the obstructive sleep apnoea syndrome: prevalence, causes and therapeutic consequences (1996)

"Cor pulmonale" is a classic feature of the "Pickwickian syndrome". Earlier studies have reported a high prevalence of pulmonary hypertension (PH) in obstructive sleep apnoea (OSA) patients, but this has not been confirmed by recent studies with a more adequate methodology, including larger groups of patients. The first part of this review is devoted to the prevalence of PH in OSA; most recent studies agree on prevalence of 15-20%. The second (and major) part of the study deals with the causes and mechanisms of PH in OSA. Pulmonary hypertension is rarely observed in the absence of day-time hypoxaemia, and the severity of nocturnal events (apnoea index (AI), apnoea+ hypopnoea index (AHI) does not appear to be the determining factor of PH. Diurnal arterial blood gas disturbances and PH are most often explained by the presence of severe obesity (obesity-hypoventilation syndrome) and, principally, by association of OSA with chronic obstructive pulmonary disease (the so called "overlap syndrome"). Bronchial obstruction is generally of mild-to-moderate degree and may be asymptomatic. The final part of the review analyses the therapeutic consequences of the presence of PH in OSA patients. Pulmonary hypertension, which is generally mild-to-moderate, does not need a specific treatment. When nasal continuous positive airway pressure (CPAP) fails to correct sleep-related hypoxaemia, supplementary oxygen must be administered. In patients with marked daytime hypoxaemia (arterial oxygen tension (Pa,O2), < or = 7.3 kPa (55 mmHg) conventional O2 therapy (nocturnal + diurnal) is required.
Differential tumor necrosis factor receptor 2-mediated editing of virus-specific CD8+effector T cells (2004)

Much of the CD8(+) T cell response in H2(b) mice with influenza pneumonia is directed at the nucleoprotein(366-374) (NP(366)) and acid polymerase(224-233) (PA(224)) peptides presented by the H2D(b) MHC class I glycoprotein. These D(b)NP(366)- and D(b)PA(224)-specific T cell populations are readily analyzed by staining with tetrameric complexes of MHC(+) peptide (tetramers) or by cytokine production subsequent to in vitro stimulation with the cognate peptides. The D(b)PA(224)-specific CD8(+) effector T cells make more tumor necrosis factor (TNF) alpha than the comparable CD8(+)D(b)NP(366)(+) set, a difference reflected in the greater sensitivity of the CD8(+)D(b)PA(224)(+) population to TNF receptor (TNFR) 2-mediated apoptosis under conditions of in vitro culture. Freshly isolated CD8(+)D(b)NP(366)(+) and CD8(+)D(b)PA(224)(+) T cells from influenza-infected TNFR2(-/-) mice produce higher levels of IFN-gamma and TNF-alpha after in vitro stimulation with peptide, although the avidity of the T cell receptor-epitope interaction does not change. Increased numbers of both CD8(+)D(b)PA(224)(+) and CD8(+)D(b)NP(366)(+) T cells were recovered from the lungs (but not the spleens) of secondarily challenged TNFR2(-/-) mice, a pattern that correlates with the profiles of TNFR expression in the TNFR2(+/+) controls. Thus, it seems that TNFR2-mediated editing of influenza-specific CD8(+) T cells functions to limit the numbers of effectors that have localized to the site of pathology in the lung but does not modify the size of the less activated responder T cell populations in the spleen. Therefore, the massive difference in magnitude for the secondary, although not the primary, response to these D(b)NP(366) and D(b)PA(224) epitopes cannot be considered to reflect differential TNFR2-mediated T cell editing.
BRAF V600E Mutation Analysis of Thyroid Nodules Needle Aspirates in Relation to Their Ultrasongraphic Classification: A Potential Guide for Selection of Samples for Molecular Analysis (2010)

The application of BRAF(V600E) mutation analysis in FNA specimens is more effective for thyroid nodules with malignant US features as compared with nodules without malignant US features. The use of the AS-PCR is more valuable as compared with the direct DNA sequencing to refine the diagnosis in a clinical setting.
Comparison of genome-wide gene expression in suture- and alkali burn-induced murine corneal neovascularization. (2011)

Sutures and alkali burn to the corneas produced types of damage that affected transparency differentially, but gene profiling revealed similar patterns of changes in gene expression in these two CorNV models. Further studies of the primary genes found to be involved in CorNV will supplement current understanding about the pathogenesis of neovascularization diseases.
Achieving Long-Term Isolation for Thin Gas Zones in the Adriatic Sea Region (2005)

Abstract This paper describes the application of a flexible cement system to isolate pay zones, spaced 1 m apart, in the Barbara gas field in the Adriatic Sea, off the coast of Italy. This field presents several challenges to achieving long-term zonal isolation—crossflow between pressured zones, changing mud weights, and a high-pressure cold-fluid injection fracture treatment. One or more of these conditions may contribute to a loss of isolation; hence, there is a need for an effective sealant material that can handle these challenges. Conventional cement systems have been unable to address zonal isolation at such a scale. In view of these various challenges, the team in charge of cementing these wells redesigned the cement program to mitigate the risks in the field. The main objective was to minimize the Young's modulus (maximize flexibility) and maximize the compressive strength of the set cement. Thus, an extensive program was carried out to measure the mechanical properties of the set cement. The new cement program used a flexible, expandable slurry system that isolated five zones behind 7-in. casing in the Barbara gas field. A cement-bond log evaluation confirmed isolation of the pay zone. No losses were observed during cement placement across the low-fracture-gradient formations. The new slurry system brought substantial value to the operation by enabling use of 7-in. casing as the production casing. It also eliminated any interzonal pressure communication between formations and the need for an additional 5-in. liner, which saved rig time and rig costs.
Selection of Virulence-Associated Determinants of Streptococcus suis Serotype 2 by In Vivo Complementation (2001)

Within Streptococcus suis serotype 2, pathogenic, weakly pathogenic, and nonpathogenic strains can be found. We introduced a genomic library of a pathogenic strain into a weakly pathogenic strain. After infection of the library into young piglets pathogenic transformants were selected. One specific transformant containing a 3-kb fragment of the pathogenic strain appeared to be dominantly enriched in diseased pigs. The observed enrichment was not tissue specific. The selected fragment, when introduced into two different weakly pathogenic strains, increased the virulence of these strains considerably. In contrast, introduction of the corresponding fragment of a weakly pathogenic strain had only minor effects on virulence. Nucleotide sequence analysis of the selected fragment of the pathogenic strain revealed the presence of two potential open reading frames, both of which were found to be mutated in the corresponding fragment of the weakly pathogenic strain. These data strongly suggest that the selected fragment contains determinants important for virulence.
Helical Rosette Nanotubes:  Design, Self-Assembly, and Characterization (2001)

Peer reviewed: Yes
Induction of Tumor-Specific Cytotoxic T Lymphocytes in Cancer Patients by Autologous Tumor RNA-Transfected Dendritic Cells (2002)

DCs transfected with total tumor RNA may represent a method for inducing immune responses against the entire repertoire of tumor antigens of surgically resected malignancies.
l‐type amino acid transporter 1 and CD98 expression in primary and metastatic sites of human neoplasms (2008)

The significance of L-type amino acid transporter (LAT) 1 expression remains unclear in the metastatic process of human neoplasms, whereas experimental studies have demonstrated that LAT1 is associated with the metastatic process of cancer cells. We compared the immunohistochemical expression of LAT1 and CD98 between the primary site and a concordant pulmonary metastatic site in 93 cancer patients, all of whom had undergone thoracotomy. LAT1, CD98, Ki-67 labeling index, vascular endothelial growth factor (VEGF), CD31, and CD34 were analyzed by immunohistochemical staining in the resected tumors of 93 cancer patients: 45 colon cancers; nine breast cancers; eight head and neck cancers; 11 genital cancers; 14 soft-tissue sarcomas; and six other cancers. The expression of these markers was significantly higher in the metastatic sites than in the primary sites. In total, the positive rates of LAT1, CD98, Ki-67, VEGF, CD31, and CD34 were 40, 24, 56, 41, 45, and 39%, respectively, in the primary sites and 65, 45, 84, 67, 73, and 61%, respectively, in the metastatic sites. LAT1 expression was closely correlated with CD98 expression, angiogenesis, and cell proliferation. The association between LAT1 and CD98 expression was strongest in the primary and metastatic sites. The present study suggests that overexpression of LAT1 and CD98 has an important role to play in the metastatic process of variable human neoplasms. Moreover, LAT1 expression was significantly correlated with cell proliferation and angiogenesis.
Prostanoids in therapy of peripheral arterial occlusive disease. (1992)

Therapy of chronical arterial occlusive disease primarily includes evaluation and treatment of risk factors as prophylaxis for preventing progression of arteriosclerosis. When patients suffer from claudication walking exercise is the therapy of choice. Only in cases with severe claudication (walking distance under 100 m) and rest pain or ischemic ulcers reopening procedures are necessary. Bypass surgery is supported by the different transluminal angioplasty techniques, which are suited even for the older and multimorbide patients. A pharmacological treatment of peripheral arterial occlusive disease should be introduced only for preventing progression of the disease or reocclusions following surgery or angioplasty or in those cases in whom reopening techniques are not possible or not successful. Here prostaglandin E1 has been proven to be effective in many clinical trials. The combination of surgery, angioplasty and pharmacological treatment allows to avoid major amputations in most patients with critical limb ischemia.
Isolation and characterization of a cDNA encoding a human liver/bone/kidney-type alkaline phosphatase. (1986)

Alkaline phosphatases (ALPs) [orthophosphoric-monoester phosphohydrolase (alkaline optimum), EC 3.1.3.1] isolated from human liver, bone, and kidney (L/B/K) exhibit very similar biochemical and immunologic properties that differentiate them from other human ALPs, such as those characteristically found in placenta and intestine. Despite their similarities, the L/B/K ALPs produced in different tissues show slight physical differences. To examine structural and evolutionary relationships between the various ALPs, a cDNA corresponding to L/B/K ALP mRNA has been isolated. A lambda 11 cDNA expression library was constructed using poly(A) RNA from the osteosarcoma cell line Saos-2 and screened with anti-liver ALP antiserum. The 2553-base-pair cDNA contains an open reading frame that encodes a 524 amino acid polypeptide with a predicted molecular mass of 57.2 kDa. This ALP precursor protein contains a presumed signal peptide of 17 amino acids followed by 37 amino acids that are identical to the amino-terminal sequence determined from purified liver ALP. In addition, amino acid sequences of several CNBr peptides obtained from liver ALP are found within the cDNA-encoded protein. The deduced L/B/K ALP precursor polypeptide shows 52% homology to human placental ALP and 25% homology to Escherichia coli ALP precursor polypeptides. Sixty percent nucleotide homology exists between the human L/B/K and placental cDNAs over the protein coding regions. The 5' and 3' untranslated regions of the L/B/K ALP cDNA, 176 and 805 base pairs, respectively, show no homology to the corresponding regions of placental ALP cDNA.
Effects of Low-Dose and Very Low-Dose Ketamine among Patients with Major Depression: a Systematic Review and Meta-Analysis (2015)

Low-dose ketamine appears more effective than very low dose. There is substantial heterogeneity in clinical response, with remission among one-fifth of patients at 1 week but most others having benefits that are less durable. Larger, longer term parallel group trials are needed to determine if efficacy can be extended and to further assess safety.