gebhart/patrepeval huggingface dataset:
False-Negative Fine-Needle Aspiration Cytology Results Delay Treatment and Adversely Affect Outcome in Patients with Thyroid Carcinoma (2004)

Clinicians have become reliant on fine-needle aspiration (FNA) cytology in the diagnosis of thyroid nodules. We encountered several patients who had thyroid cancer at operation despite having had FNAs that never showed malignant or suspicious cells. Hence, we retrospectively studied 100 consecutive patients with histologically proven thyroid cancer who had undergone preoperative FNA. Fourteen of these patients had cancers that were not detected by FNA, three of whom developed widespread disease. The sensitivity of FNA was 79%, the false-negative rate 21%, and the inadequate rate 12%. FNA was less sensitive in detecting follicular and Hürthle cell carcinomas compared to papillary carcinomas. FNAs interpreted by cytopathologists at a major university center were more sensitive than those performed elsewhere. A single false-negative FNA delayed surgical treatment by 28 months, sometimes despite clinical evidence suggesting malignancy. Subjects whose tumors were not detected by FNA experienced delayed treatment, had higher rates of vascular and capsular invasion, and were more likely to have persistent disease at follow up (hazard ratio 2.28). False-negative results remain a concern in the cytologic diagnosis of thyroid cancer. Although FNA is a useful test, clinical findings should overrule cytologic data in order for timely treatment to occur.
Analysis of Dll4 regulation reveals a combinatorial role for Sox and Notch in arterial development (2013)

The mechanisms by which arterial fate is established and maintained are not clearly understood. Although a number of signaling pathways and transcriptional regulators have been implicated in arterio-venous differentiation, none are essential for arterial formation, and the manner in which widely expressed factors may achieve arterial-specific gene regulation is unclear. Using both mouse and zebrafish models, we demonstrate here that arterial specification is regulated combinatorially by Notch signaling and SoxF transcription factors, via direct transcriptional gene activation. Through the identification and characterization of two arterial endothelial cell-specific gene enhancers for the Notch ligand Delta-like ligand 4 (Dll4), we show that arterial Dll4 expression requires the direct binding of both the RBPJ/Notch intracellular domain and SOXF transcription factors. Specific combinatorial, but not individual, loss of SOXF and RBPJ DNA binding ablates all Dll4 enhancer-transgene expression despite the presence of multiple functional ETS binding sites, as does knockdown of sox7;sox18 in combination with loss of Notch signaling. Furthermore, triple knockdown of sox7, sox18 and rbpj also results in ablation of endogenous dll4 expression. Fascinatingly, this combinatorial ablation leads to a loss of arterial markers and the absence of a detectable dorsal aorta, demonstrating the essential roles of SoxF and Notch, together, in the acquisition of arterial identity.
RHABDOMYOLYSIS, ACUTE RENAL FAILURE, AND COMPARTMENT SYNDROME IN A CHILD WITH PARAINFLUENZA TYPE 1 INFECTION (2009)

We present a case of para-influenza type 1 induced rhabdomyolysis, acute renal failure, and extensive compartment syndrome in a 6-year-old previously well child. Fasciotomies and subsequent skin grafting of both lower extremities and a prolonged course of hemodialysis led to a complete clinical and biochemical recovery.
Cell Surface Tumor Endothelium Marker 8 Cytoplasmic Tail-independent Anthrax Toxin Binding, Proteolytic Processing, Oligomer Formation, and Internalization (2003)

The interaction of anthrax toxin protective antigen (PA) and target cells was assessed, and the importance of the cytosolic domain of tumor endothelium marker 8 (TEM8) in its function as a cellular receptor for PA was evaluated. PA binding and proteolytic processing on the Chinese hamster ovary cell surface occurred rapidly, with both processes nearly reaching steady state in 5 min. Remarkably, the resulting PA63 fragment was present on the cell surface only as an oligomer, and furthermore, the oligomer was the only PA species internalized, suggesting that oligomerization of PA63 triggers receptor-mediated endocytosis. Following internalization, the PA63 oligomer was rapidly and irreversibly transformed to an SDS/heat-resistant form, in a process requiring an acidic compartment. This conformational change was functionally correlated with membrane insertion, channel formation, and translocation of lethal factor into the cytosol. To explore the role of the TEM8 cytosolic tail, a series of truncated TEM8 mutants was transfected into a PA receptor-deficient Chinese hamster ovary cell line. Interestingly, all of the cytosolic tail truncated TEM8 mutants functioned as PA receptors, as determined by PA binding, processing, oligomer formation, and translocation of an lethal factor fusion toxin into the cytosol. Moreover, cells transfected with a TEM8 construct truncated before the predicted transmembrane domain failed to bind PA, demonstrating that residues 321-343 are needed for cell surface anchoring. Further evidence that the cytosolic domain plays no essential role in anthrax toxin action was obtained by showing that TEM8 anchored by a glycosylphosphatidylinositol tail also functioned as a PA receptor.
Recombinant Fragment of Protein Kinase Inhibitor Blocks Cyclic AMP-Dependent Gene Transcription (1987)

Transcriptional regulation by cyclic adenosine monophosphate (cAMP) in mammalian cells could be mediated by a phosphoprotein substrate of the cAMP-dependent protein kinase or, as in prokaryotes, by a cAMP-binding protein. Two synthetic genes that code for an active fragment of the protein inhibitor of this kinase and a mutant inactive fragment were constructed and used to distinguish these alternatives. Transient expression of the active peptide product specifically inhibited the cAMP-stimulated expression of a cotransfected reporter gene by more than 90 percent, whereas the expression of the inactive peptide did not alter cAMP-stimulated gene expression. The results indicate that an active kinase catalytic subunit is a necessary intermediate in the cAMP stimulation of gene transcription.
Local Administration of PF-3512676 CpG-B Instigates Tumor-Specific CD8+ T-Cell Reactivity in Melanoma Patients (2008)

These data show an increase in melanoma-specific CD8(+) T-cell frequencies as well as an increased effector NK cell rate after a single dose of PF-3512676 and thus support the utility of local PF-3512676 administration as adjuvant treatment in early-stage melanoma to try and halt metastatic spread.
The Aqua approximate query answering system (1999)

Aqua is a system for providing fast, approximate answers to aggregate queries, which are very common in OLAP applications. It has been designed to run on top of any commercial relational DBMS. Aqua precomputes synopses (special statistical summaries) of the original data and stores them in the DBMS. It provides approximate answers along with quality guarantees by rewriting the queries to run on these synopses. Finally, Aqua keeps the synopses up-to-date as the database changes, using fast incremental maintenance techniques.
Highly Coherent, Microcavity Brillouin Laser on Silicon (2011)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text J. Li, H. Lee, T. Chen, O. Painter, and K. Vahala, "Highly Coherent, Microcavity Brillouin Laser on Silicon," in Frontiers in Optics 2011/Laser Science XXVII, OSA Technical Digest (Optica Publishing Group, 2011), paper FTuD4. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
The nicer side of E. coli: Escherichia coli as a model organism (2005)

The enteric bacterium Escherichia coli is a ubiquitous component of every human being, forming a part of the normal gut flora, and is arguably the most well understood free-living organism on the planet. It is a model organism that is also well known by the general public -- usually by the abbreviated name E. coli. Most people associate E. coli with illness and have some recollection of cows, undercooked burgers and strains like O157:H7, after the outbreaks that killed elderly people in Lanarkshire, Scotland, in the 1990s. This article introduces the side of E. coli that the public know less about -- its role in the past, present and future as a model organism in the study of biology and the numerous applications that have been spawned from E. coli research.
Th1 cytokine pattern in sarcoidosis is expressed by bronchoalveolar CD4+ and CD8+ T cells (2000)

The pathogenesis of pulmonary sarcoidosis has been related to an increased production of Th1-like cytokines. However, cytokine expression in sarcoidosis has not been systematically studied at a single-cell level. We therefore investigated the expression of IL-2, IL-4, IL-13, tumour necrosis factor-alpha (TNF-alpha) and interferon-gamma (IFN-gamma) intracellularly in bronchoalveolar lavage (BAL) and peripheral blood CD3+ T lymphocytes from patients with pulmonary sarcoidosis (radiologic stage II-III, n = 8) and normal controls (n = 9) by flow cytometry. In contrast to IL-4 and IL-13, the percentage of T lymphocytes expressing intracellular IL-2 (49.3 +/- 21.3% versus 14.5 +/- 15.6%), IFN-gamma (75.5 +/- 14.9% versus 32.6 +/- 18.7%) and TNF-alpha (68.3 +/- 18.7% versus 36.8 +/- 20.8%) was significantly higher in patients with sarcoidosis than in normal controls (each P < 0.005). In contrast to BAL lymphocytes, expression of these cytokines in peripheral blood lymphocytes did not differ between patients with sarcoidosis and normal controls. Close correlations were observed between the percentages of BAL lymphocytes expressing intracellular IL-2, IFN-gamma and TNF-alpha, but not for IL-4 or IL-13. Analysis of the expression of these cytokines in T lymphocyte subsets revealed IL-2, IFN-gamma, and TNF-alpha in CD4+ as well as CD8+ T lymphocytes, suggesting a contribution of TC1 cells to the production of proinflammatory cytokines in sarcoidosis. We conclude that a Th1-like cytokine pattern can be observed in CD4+ as well as in CD8+ BAL T lymphocytes in patients with pulmonary sarcoidosis.
Genipin-crosslinked fibrin hydrogels as a potential adhesive to augment intervertebral disc annulus repair (2011)

Treatment of damaged intervertebral discs is a significant clinical problem and, despite advances in the repair and replacement of the nucleus pulposus, there are few effective strategies to restore defects in the annulus fibrosus. An annular repair material should meet three specifications: have a modulus similar to the native annulus tissue, support the growth of disc cells, and maintain adhesion to tissue under physiological strain levels. We hypothesized that a genipin crosslinked fibrin gel could meet these requirements. Our mechanical results showed that genipin crosslinked fibrin gels could be created with a modulus in the range of native annular tissue. We also demonstrated that this material is compatible with the in vitro growth of human disc cells, when genipin:fibrin ratios were 0.25:1 or less, although cell proliferation was slower and cell morphology more rounded than for fibrin alone. Finally, lap tests were performed to evaluate adhesion between fibrin gels and pieces of annular tissue. Specimens created without genipin had poor handling properties and readily delaminated, while genipin crosslinked fibrin gels remained adhered to the tissue pieces at strains exceeding physiological levels and failed at 15-30%. This study demonstrated that genipin crosslinked fibrin gels show promise as a gap-filling adhesive biomaterial with tunable material properties, yet the slow cell proliferation suggests this biomaterial may be best suited as a sealant for small annulus fibrosus defects or as an adhesive to augment large annulus repairs. Future studies will evaluate degradation rate, fatigue behaviors, and long-term biocompatibility.
Stereoisomers of Deoxynucleoside 5′-Triphosphates as Substrates for Template-dependent and -independent DNA Polymerases (1997)

All four possible stereoisomers of dNTP with regard to deoxyribofuranose C-1' and C-4' carbon atoms were studied as substrates for several template-dependent DNA polymerases and template-independent terminal deoxynucleotidyl transferase. It was shown that DNA polymerases alpha, beta, and epsilon from human placenta and reverse transcriptases of human immunodeficiency virus and avian myeloblastosis virus incorporate into the DNA chain only natural beta-D-dNTPs, whereas calf thymus terminal deoxynucleotidyl transferase incorporates two nucleotide residues of alpha-D-dNTP and extends the resulting oligonucleotide in the presence of beta-D-dNTPs. The latter enzyme also extended alpha-anomeric D-oligodeoxynucleotide primers in the presence of beta-D-dNTPs. None of the studied enzymes utilized L-dNTPs. These data indicate that template-dependent DNA polymerases are highly stereospecific with regard to dNTPs, whereas template-independent terminal deoxynucleotidyl transferase shows less stereodifferentiation. It is likely that the active center of the latter enzyme forms no specific contacts with the nucleic bases of both nucleotide substrate and oligonucleotide primer.
Influence of sire line and halothane genotype on growth performance, carcass characteristics, and meat quality in pigs (2000)

Progeny of three commercial sire lines mated to the same halothane negative crossbreed dam line were compared for growth, carcass and meat quality characteristics. Sire line A (halothane reactor) produced halothane carrier progeny; line C was halothane negative and produced negative progeny; line B (a cross between lines A and C) was a halothane carrier line that produced both carrier (BNn) and negative (BNN) progeny within the same litter. Line A pigs grew more slowly (P ≤ 0.05) and consumed less feed (P ≤ 0.05) than the progeny of the other lines (885, 1049, 1057 and 1082 g d −1 and 2.37, 2.82, 2.72 and 2.79 kg d −1 for lines a, BNN, BNn and C respectively). However, gain:feed was similar for all lines. Dressing percentage was similar for lines A, BNn and BNN (77.42, 77.62 and 77.00% respectively) but lower for line C (75.31%: P ≤ 0.05). Line differences for linear carcass measurements, lean cut yield and fat-free lean content were relatively small. Line A had higher shear force than the others (4.32, 3.21, 3.57, and 3.30 kg for A, BNN, BNn and C, respectively; P ≤ 0.05) and lines A and BNn had reduced taste panel tenderness and juiciness (P ≤ 0.05) compared with lines BNN and C. This study highlights commercially important differences between sire lines for pork quality traits. the variation in pork quality within this study resulted from the halothane gene and, potentially, other single genes that affect meat quality parameters. Key words: halothane gene, meat quality, sire line, pigs, carcass quality
Long‐Term Effects of Triptolide on Spermatogenesis, Epididymal Sperm Function, and Fertility in Male Rats (2000)

Prior studies had suggested that triptolide, a diterpene triepoxide isolated from a Chinese medicinal plant, might be an attractive candidate as a post-testicular male contraceptive agent. Despite the promise that triptolide would not affect testis function, nagging concerns remained that a delayed onset of testicular effect might exist. The objectives of this study were to assess the effects of relatively longer treatment duration of triptolide on fertility, spermatogenesis, and epididymal sperm pathophysiology; and to evaluate the reversibility of these effects after the cessation of treatment. Adult male Sprague-Dawley rats were fed daily with either 30% gum acacia as a vehicle control (n = 12) or 100 microg/kg body weight (BW) of triptolide for 82 days (n = 12) followed by a recovery period of up to 14 weeks (n = 6). At the end of the treatment period, all rats treated with triptolide were sterile. Cauda epididymal sperm content decreased by 84.8% and sperm motility was reduced to zero. In addition, virtually all cauda epididymal sperm in the triptolide-treated group exhibited severe structural abnormalities. The most striking changes observed were head-tail separation, premature chromatin decondensation of sperm nuclei, a complete absence of the plasma membrane of the entire middle and principle pieces, disorganization of the mitochondrial sheath, and aggregation of many sperm tails. Longer treatment duration of triptolide also affected spermatogenesis, with marked variability in the response of individual animals. The degree of damage ranged from apparently normal-looking seminiferous tubules to flattened seminiferous epithelium lined by a single layer of cells consisting of Sertoli cells and a few spermatogonia. Affected tubules exhibited intraepithelial vacuoles of varying sizes, multinucleated giant cells, germ cell exfoliation, and tubular atrophy. Recovery occurred as early as 6 weeks after cessation of treatment. By 14 weeks, 4 out of 6 triptolide-treated males were fertile and the females that were impregnated by 3 out of 4 triptolide-treated male rats produced apparently normal litters. These results suggest that triptolide has 2 phenotypic effects on mature and maturing germ cells. The first action appears earlier and manifests mainly in epididymal sperm. The second action presumably is directly on germ cells in testis and causes a variable impairment of spermatogenesis that may not be completely reversible. It is unclear if the earlier effect is a delayed manifestation of subtle testicular injury or post-testicular action.
A conserved cleavage‐site motif in chloroplast transit peptides (1990)

A collection of 32 stroma-targeting chloroplast transit peptides with known cleavage sites have been analysed in terms of amino acid preferences in the vicinity of the processing site. A loosely conserved consensus motif (Val/Ile)-X-(Ala/Cys) decreases Ala is found in the majority of the transit peptides. About 30% of the sequences have a perfect match to the consensus. When such a match is found, there is a 90% probability that it specifies the correct cleavage site.
The Cadaver experience of the nursing students (2017)

Anatomy is one of the basic subjects of the nursing course, which is included in the curriculum of the nursing. Anatomy is a basic course for understanding major in nursing and it is the first gateway to acquire expertise. It is mainly opened in nursing and first to second grades. Therefore, students who have advanced to the nursing department have great interest and expectation on the anatomy subjects. In general, nursing students are studying anatomy with theories and models, and some universities practice on tour after dissection of medical consortium for short time. This is called the Cadaver practice. This study was carried out to investigate the thoughts and experiences of bioethics through nursing students' Cadaver practice. The interview data were processed through the analysis and interpretation process using the phenomenological research method, Giorgi method. As a result, 48 semantic units were derived, and then they were divided into 10 subcomponents and divided into 6 categories. As a result of the analysis, the experience of nursing students' bioethics was tied to the topic of six questions. For example, ‘what about the respect and responsibility of nursing students in Cadaver?’, ‘What about your experience with the Cadaver experiment and bioethics?’, ‘What was the academic achievement of the actual human body structure viewing experience with cadaver?’, ‘What was the connection with theory?’, ‘What was your intention to recommend to others?’, ‘What was your perception and interest in the Cadaver experiment?’. Analyzes were integrated into 10 structures;「Thank you for your donation」,「want others to refuse donation」,「Burden of practice」, 「Good opportunities for learning」,「Understand better」,「Should study harder」 ,「Memory is better」, 「Compared to theory」,「Good experience」,「Want to rejoin」. The general structural description of the participants' meanings is summarized as follows. Nursing college students who participated in the Cadaver had a gratitude for the donor, but they said they would like to talk to others about donating organs. Before they went to practice, they felt a lot of pressure on the dissection of the cadaver, but they went to the practice and thought that it was a good opportunity to learn by doing well. Specifically, they understood that they had better understanding than the theoretical lesson, and that they were more eager to study their major through practice. In other words, most of them were more memorable and they would like to participate again if the opportunity comes next time. The results of this study show that the practice of Cadaver in nursing college students is very positive in terms of educational effectiveness. However, in terms of bioethics, it can be seen that the education process is somewhat unsatisfactory. Therefore, the systematic bioethics education should be prepared before the practice in the nursing college students' Cadaver practice.
Diagnosis and treatment of demodectic blepharitis. (2009)

The aim of this study was to investigate the prevalence of Demodex spp. in the eyelash follicles obtained from patients seen in our ophthalmology clinic, to define the symptoms of this infestation, and to examine the effectivity of the therapy. This study was conducted in Department of Ophthalmology and Parasitology, Dokuz Eylül University, School of Medicine. Our study included 82 cases that were seen in the Ophthalmology Department and Parasitology Department for various reasons. We have also observed that the presence of Demodex spp. provokes itching and redness in the eyes and that using baby shampoo for cleansing the face reduces the risk of infestation. After the treatment of 32 cases with 4% pilocarpin HCl gel, we achieved a total cure in 12 eyes (37.5%), partial improvement in 13 eyes (40.6%), (making a total of 25 eyes, 78.1%). The treatment was unsuccessful in 7 eyes (21.9%). In patients with Demodex spp. cleansing with baby shampoo and treating by pilocarpin gel may be used in treatment.
Function of RasGRP3 in the formation and progression of human breast cancer (2014)

Taken together, our results suggest that the Ras activator RasGRP3 may have a role in the pathological behavior of breast cancer cells and may constitute a therapeutic target for human breast cancer.
IRRITABLE BOWEL SYNDROME (2000)

Patients with IBS need an integrated, individualized approach to treatment, with a foundation based on a successful patient-physician relationship. The emotional and psychologic needs of the patients need to be considered in a successful management plan. Further advances in the pathophysiology of disease are essential to develop suitable and more comprehensive treatment options.
Dispersion phase vector quantization for enhancement of waveform interpolative coder (1999)

This paper presents an efficient analysis-by-synthesis vector quantizer for the dispersion phase of the excitation signal which was used to enhance a waveform-interpolative coder. The scheme can be used to enhance other harmonic coders, such as the sinusoidal-transform coder and the multiband-excitation coder. The scheme incorporates perceptual weighting, and does not require any phase unwarping. The proposed quantizer achieves a segmental signal-to-noise ratio of up to 14 dB for as low as 6-bit quantization. Subjective testing shows improvement in synthesized speech quality using the quantized phase over a male speaker extracted phase. The improvement was larger for female speakers.