gebhart/patrepeval huggingface dataset:
Fluorescence spectroscopy of tissue: recovery of intrinsic fluorescence from measured fluorescence (1996)

We present a method for recovering the intrinsic fluorescence coefficient, defined as the product of the fluorophore absorption coefficient and the fluorescence energy yield, of an optically thick, homogeneous, turbid medium from a surface measurement of fluorescence and from knowledge of medium optical properties. The measured fluorescence signal is related to the intrinsic fluorescence coefficient by an optical property dependent path-length factor. A simple expression was developed for the path-length factor, which characterizes the penetration of excitation light and the escape of fluorescence from the medium. Experiments with fluorescent tissue phantoms demonstrated that intrinsic fluorescence line shape could be recovered and that fluorophore concentration could be estimated within ±15%, over a wide range of optical properties.
The Incidence and Risk Factors in the Development of Medial Tibial Stress Syndrome among Naval Recruits (2004)

Identifying a pronated foot type prior to training may help reduce the incidence of medial tibial stress syndrome by early intervention to control abnormal pronation. Findings of a higher incidence of medial tibial stress syndrome among female recruits require further investigation.
Peptide and nucleotide sequences of rat CD4 (W3/25) antigen: evidence for derivation from a structure with four immunoglobulin-related domains. (1987)

The rat W3/25 antigen was the first marker antigen of helper T lymphocytes to be identified. Subsequently, the human OKT4 antigen (now called CD4) was described, and cell distribution and functional data suggested that W3/25 and OKT4 antigens were homologous. This is now confirmed by the matching of peptide sequences from W3/25 antigen with sequence predicted from rat cDNA clones detected by cross-hybridization with a cDNA probe for human CD4. Analysis of the two sequences suggests an evolutionary origin from a structure with four immunoglobulin-related domains, although only domain 1 at the NH2 terminus meets the standard criteria for an immunoglobulin-related sequence. CD4 domains 2 and 4 contain disulfide bonds but seem like truncated immunoglobulin domains, whereas domain 3 may have a pattern of beta-strands like an immunoglobulin variable domain, but without the disulfide bond.
Limb remote ischemic post‑conditioning reduces injury and improves long‑term behavioral recovery in rats following subarachnoid hemorrhage: Possible involvement of the autophagic process (2017)

Hemorrhage‑related neurologic injury is a primary cause of disability and mortality following subarachnoid hemorrhage (SAH). The aim of the present study was to investigate the potential neuroprotective effect and the possible role of autophagy in limb remote ischemic post‑conditioning (RIPostC) using an endovascular puncture rat model of SAH. RIPostC was induced by three cycles of occlusion (10 min) and release (10 min) in the bilateral femoral artery using an aneurysm clip. Early RIPostC began immediately following SAH, delayed RIPostC began following a 30 min delay and the repeated RIPostC group underwent the protocol every day for 3 days. Brain water content, SAH grading, terminal deoxynucleotidyl transferase dUTP nick end labeling‑DAPI staining, transmission electron microscopy, and neurological and behavioral tests were conducted three days following surgery. Long term outcomes of behavior and memory were assessed using a rotarod test and Morris water maze test 1 month subsequently. Biomarkers of autophagy, including Beclin‑1 and light chain 3 (LC3), were assessed using western blotting. The results of the present study demonstrated that, compared with other groups, repeated RIPostC was able to alleviate brain edema, prevent neuronal apoptosis, and improve short term and long term neurological function and memory. Beclin‑1 and LC3 in the cortex were upregulated following treatment with repeated RIPostC. Autolysosomes increased 3 days following SAH and were maintained for 1 month in the repeated RIPostC group. Therefore, the present study indicated that the optimized repeated RIPostC may provide a noninvasive strategy to induce neuroprotection, and improve the short and long term outcomes of SAH‑related cerebral injury, possibly involving the autophagy pathway.
Variants in the Human Insulin Gene That Affect Pre-mRNA Splicing (2006)

Predisposition to type 1 diabetes and juvenile obesity is influenced by the susceptibility locus IDDM2 that includes the insulin gene (INS). Although the risk conferred by IDDM2 has been attributed to a minisatellite upstream of INS, intragenic variants have not been ruled out. We examined whether INS polymorphisms affect pre-mRNA splicing and proinsulin secretion using minigene reporter assays. We show that IVS1-6A/T (-23HphI+/-) is a key INS variant that influences alternative splicing of intron 1 through differential recognition of its 3' splice site. The A allele resulted in an increased production of mature transcripts with a long 5' leader in several cell lines, and the extended mRNAs generated more proinsulin in culture supernatants than natural transcripts. The longer mRNAs were significantly overrepresented among beta-cell-expressed sequenced tags containing the A allele as compared with those with T alleles. In addition, we show that a rare insertion/deletion polymorphism IVS1+5insTTGC (IVS-69), which is exclusively present in Africans, activated a downstream cryptic 5' splice site, extending the 5' leader by 30 bp. These results indicate that -23HphI and IVS-69 are the most important INS variants affecting pre-mRNA splicing and suggest that -23HphI+/- is a common functional single nucleotide polymorphism at IDDM2.
Clearing a path through the jungle: progress in Arabidopsis genomics (1999)

Progress in sequencing the genome of the model plant Arabidopsis is reviewed. The resulting analysis of the sequence indicates an information-rich genome that is being tackled by a variety of high-throughput approaches aimed at understanding the functions of plant genes. The information derived from these systematic studies is providing important new knowledge of biological processes found uniquely in plants for comparison with that obtained in other multicellular organisms.
Plexiform neurofibroma with and without associated malignant peripheral nerve sheath tumor: a clinicopathologic and immunohistochemical analysis of 54 cases. (1998)

Plexiform neurofibroma (PNF) is an important part of the diagnostic criteria for neurofibromatosis type 1 (NF1) and is a known precursor lesion of malignant peripheral nerve sheath tumor (MPNST). We studied the clinicopathologic features of 54 cases of PNF for which the hematoxylin- and eosin-stained slides and paraffin blocks were available and adequate clinical follow-up could be obtained. In addition, in all cases, a representative section of the PNF and, when present, MPNST, was evaluated immunohistochemically with an antibody for p53 (DO7). The cohort included 28 male patients and 26 female patients, with an age range from 4 to 79 years (mean, 27 yr). Of these 54 patients, 46 (85%) met the strict diagnostic criteria for NF1. Thirty-nine patients had PNF alone; 15 patients had an MPNST arising from the PNF (PNF/MPNST). Those patients with PNF/MPNST tended to be older (38 yr vs. 22 yr) and to have larger tumors (10.5 cm mean vs. 7.4 cm mean) than those with PNF alone. In 9 patients (23%) of 39 with PNF alone, local recurrence developed, whereas in 7 patients (47%) of 15 with PNF/MPNST, recurrent MPNST developed, and metastases developed in 3 (20%) of the 15. Immunohistochemically, only 1 case (2.5%) of 39 cases of PNF alone stained for p53. On the other hand, 12 (80%) of 15 cases of PNF/MPNST showed p53 immunoreactivity in the MPNST component, 2 of which also showed staining in the PNF areas. In conclusion, we found that the vast majority of patients with PNF met the strict diagnostic criteria for NF1. The immunohistochemical detection of intranuclear p53 protein is common in the malignant areas of PNF/MPNST but is rare in the PNF regions. The rarity of p53 staining in the PNF regions precludes its use in predicting those tumors that are likely to progress to MPNST.
Snail blocks the cell cycle and confers resistance to cell death (2004)

The Snail zinc-finger transcription factors trigger epithelial-mesenchymal transitions (EMTs), endowing epithelial cells with migratory and invasive properties during both embryonic development and tumor progression. During EMT, Snail provokes the loss of epithelial markers, as well as changes in cell shape and the expression of mesenchymal markers. Here, we show that in addition to inducing dramatic phenotypic alterations, Snail attenuates the cell cycle and confers resistance to cell death induced by the withdrawal of survival factors and by pro-apoptotic signals. Hence, Snail favors changes in cell shape versus cell division, indicating that with respect to oncogenesis, although a deregulation/increase in proliferation is crucial for tumor formation and growth, this may not be so for tumor malignization. Finally, the resistance to cell death conferred by Snail provides a selective advantage to embryonic cells to migrate and colonize distant territories, and to malignant cells to separate from the primary tumor, invade, and form metastasis.
Formation and properties of rate earth aluminosilicate glasses (1991)

On etudie les zones de formation vitreuse et differentes proprietes de verres du systeme: Al 2 O 3 −SiO 2 −R 2 O x (ou R 2 O x =Nd 2 O 3 , Sm 2 O 3 , Tb 4 O 7 , Er 2 O 3 , Y 2 O 3 )
Real-time depth enhanced monocular odometry (2014)

Visual odometry can be augmented by depth information such as provided by RGB-D cameras, or from lidars associated with cameras. However, such depth information can be limited by the sensors, leaving large areas in the visual images where depth is unavailable. Here, we propose a method to utilize the depth, even if sparsely available, in recovery of camera motion. In addition, the method utilizes depth by triangulation from the previously estimated motion, and salient visual features for which depth is unavailable. The core of our method is a bundle adjustment that refines the motion estimates in parallel by processing a sequence of images, in a batch optimization. We have evaluated our method in three sensor setups, one using an RGB-D camera, and two using combinations of a camera and a 3D lidar. Our method is rated #2 on the KITTI odometry benchmark irrespective of sensing modality, and is rated #1 among visual odometry methods.
Soluble epoxide hydrolase deficiency inhibits dextran sulfate sodium-induced colitis and carcinogenesis in mice. (2013)

Soluble epoxide hydrolase (sEH) hydrolyses/inactivates anti-inflammatory epoxyeicosatrienoic acids (EETs) to their corresponding diols, and targeting sEH leads to strong anti-inflammatory effects. In the present study, using a tissue microarray and immunohistochemical approach, a significant increase of sEH expression was identified in ulcerative colitis (UC)-associated dysplasia and adenocarcinoma. The effects of deficiency in the sEH gene were determined on dextran sulfate sodium (DSS) colitis-induced carcinogenesis. The effects of EETs on lipopolysaccharide (LPS)-activated macrophages were analyzed in vitro. With extensive histopathological and immunohistochemical analyses, compared to wild-type mice, sEH(-/-) mice exhibited a significant decrease in tumor incidence (13/20 vs. 6/19, p<0.05) and a markedly reduced average tumor size (59.62±20.91 mm(3) vs. 22.42±11.22 mm(3)), and a significant number of pre-cancerous dysplasia (3±1.18 vs. 2±0.83, p<0.01). The inflammatory activity, as measured by the extent/proportion of erosion/ulceration/dense lymphoplasmacytosis (called active colitis index) in the colon, was significantly lower in sEH(-/-) mice (44.7%±24.9% vs. 20.2%±16.2%, p<0.01). The quantitative polymerase chain reaction (qPCR) assays demonstrated significantly low levels of cytokines/chemokines including monocyte chemoattractant protein (MCP-1), inducible nitric oxide synthase (iNOS), vasopressin-activated calcium-mobilizing (VCAM-1), interleukin-1 beta (IL-1β) and tumor necrosis factor-alpha (TNF-α). In vitro, LPS-activated macrophages treated with 14,15-EET showed a significant reduction of LPS-triggered IL-1β and TNF-α expression. Eicosanoic acid metabolic profiling revealed a significant increase of the ratios of EETs/ dihydroeicosatrienoic acids (DHETs) and epoxyoctadecennoic acid/dihydroxyoctadecenoic acid (EpOMEs/DiHOMEs). These results indicate that sEH plays an important role in the development of colitis and in inducing carcinogenesis.
Evaluation of the Potential Impact of Ebola Virus Genomic Drift on the Efficacy of Sequence-Based Candidate Therapeutics (2015)

Until recently, Ebola virus (EBOV) was a rarely encountered human pathogen that caused disease among small populations with extraordinarily high lethality. At the end of 2013, EBOV initiated an unprecedented disease outbreak in West Africa that is still ongoing and has already caused thousands of deaths. Recent studies revealed the genomic changes this particular EBOV variant undergoes over time during human-to-human transmission. Here we highlight the genomic changes that might negatively impact the efficacy of currently available EBOV sequence-based candidate therapeutics, such as small interfering RNAs (siRNAs), phosphorodiamidate morpholino oligomers (PMOs), and antibodies. Ten of the observed mutations modify the sequence of the binding sites of monoclonal antibody (MAb) 13F6, MAb 1H3, MAb 6D8, MAb 13C6, and siRNA EK-1, VP24, and VP35 targets and might influence the binding efficacy of the sequence-based therapeutics, suggesting that their efficacy should be reevaluated against the currently circulating strain.
A new era for giant cell arteritis (2019)

The landscape of the investigation and management of giant cell arteritis (GCA) is advancing. In this review we will outline the recent advances by searching the current English literature for relevant articles using key words of giant cell arteritis, temporal arteritis, Horton's disease, investigation, and treatment. Delay in diagnosis, diagnostic uncertainty and glucocorticoid (GC) morbidity are among the highest concerns of clinicians and patients in this disease area. The positive news is that fast track pathways, imaging techniques and new therapies are emerging for routine management of GCA. Future directions for intervention in the treatment paradigm will be discussed.
Up‐Regulation of Epidermal Growth Factor‐Receptors (EGF‐R) by Nicotine in Cervical Cancer Cell Lines: This Effect May Be Mediated by EGF (2000)

Our data show that nicotine-induced proliferation of cervical cancer cells is mediated through EGF-R over-expression and that this action of nicotine utilizes EGF.
Active immunization against renin in normotensive marmoset. (1987)

Primate renins (human and monkey) are very similar. We used pure human renin to immunize marmosets (Callithrix jacchus) and thereby produce a chronic blockade of the renin-angiotensinogen reaction. After a control period of 2 months, five male marmosets, on their usual sodium-poor diet, were immunized against pure human renin by three subcutaneous injections of 30 micrograms each, with complete and then incomplete Freund's adjuvant. Three marmosets were injected with adjuvant only and served as controls. Blood sampling and blood pressure measurements were performed weekly. After the third injection, the five marmosets immunized against renin developed a high titer of renin antibodies (50% binding of 125I-labeled human renin at a dilution of greater than or equal to 1:10,000). The antibodies inhibited the enzymatic activity of both marmoset and human renins. At the same time, systolic blood pressure decreased significantly from 125 +/- 13 mm Hg to 87 +/- 8 mm Hg (mean +/- SD; 1 mm Hg = 133 Pa). Plasma renin enzyme activity was undetectable in three animals. Plasma aldosterone decreased significantly. After 1-4 months with low blood pressure, a normal urinary output, and a normal plasma creatinine, the five marmosets became sick and died within one month. At autopsy an immunological renal disease, characterized by the presence of immunoglobulin and macrophage infiltration colocalized with renin, was found. Granulomatous formations, probably due to Freund's adjuvant, could be seen in the lungs and in the kidney. No immunoglobulin was detectable in extrarenal vessels or in other organs. These experiments demonstrate that, in this primate, a chronic blockade of the renin-angiotensin system can be achieved by active immunization against homologous renin, but this blockade is associated with the development of an autoimmune disease localized in the kidney.
[Clinical study on norfloxacin in children]. (1990)

Norfloxacin (NFLX, AM-715), a new synthetic antibacterial agent, was administered to 18 child patients with infectious diseases. The patients included 5 boys and 13 girls from 3 to 14 years of ages. They were given orally dosage ranging 5.2-17.9 mg/kg/day for 4 to 14 days. Clinical efficacies were excellent in 1 case, good in 16 cases, unknown in 1 case, hence the total efficacy rate was determined to be 100%. There were no cases which showed side effects of the drug and no abnormal laboratory test values were observed during the treatment.
Phospholipase D Activity Is Required for Actin Stress Fiber Formation in Fibroblasts (2001)

Phospholipase D (PLD) is a ubiquitously expressed enzyme of ill-defined function. In order to explore its cellular actions, we inactivated the rat PLD1 (rPLD1) isozyme by tagging its C terminus with a V5 epitope (rPLD1-V5). This was stably expressed in Rat-2 fibroblasts to see if it acted as a dominant-negative mutant for PLD activity. Three clones that expressed rPLD1-V5 were selected (Rat2V16, Rat2V25, and Rat2V29). Another clone (Rat2V20) that lost expression of rPLD1-V5 was also obtained. In the three clones expressing rPLD1-V5, PLD activity stimulated by phorbol myristate acetate (PMA) or lysophosphatidic acid (LPA) was reduced by ~50%, while the PLD activity of Rat2V20 cells was normal. Changes in the actin cytoskeleton in response to LPA or PMA were examined in these clones. All three clones expressing rPLD1-V5 failed to form actin stress fibers after treatment with LPA. However, Rat2V20 cells formed stress fibers in response to LPA to the same extent as wild-type Rat-2 cells. In contrast, there was no significant change in membrane ruffling induced by PMA in the cells expressing rPLD1-V5. Since Rho is an activator both of rPLD1 and stress fiber formation, the activation of Rho was monitored in wild-type Rat-2 cells and Rat2V25 cells, but no significant difference was detected. The phosphorylation of vimentin mediated by Rho-kinase was also intact in Rat2V25 cells. Rat2V25 cells also showed normal vinculin-containing focal adhesions. However, the translocation of alpha-actinin to the cytoplasm and to the detergent-insoluble fraction in Rat2V25 cells was reduced. These results indicate that PLD activity is required for LPA-induced rearrangement of the actin cytoskeleton to form stress fibers and that PLD might be involved in the cross-linking of actin filaments mediated by alpha-actinin.
Adverse functions of IL‐17A in experimental sepsis (2008)

IL-17A is a proinflammatory cytokine produced by a variety of cells. In the current study, we examined the role of IL-17A in sepsis induced in mice by cecal ligation and puncture (CLP). IL-17A levels, which rose time-dependently in plasma after CLP, were not affected in the absence of alphabeta T cells or neutrophils. In sharp contrast, gammadelta T cell-knockout or gammadelta T cell-depleted mice displayed baseline IL-17A plasma levels after CLP. Neutralization of IL-17A by two different antibodies improved sepsis (survival from approximately 10% to nearly 60%). Unexpectedly, antibody treatment was protective, even when administration of anti-IL-17A was delayed for up to 12 h after CLP. These protective effects of IL-17A blockade were associated with substantially reduced levels of bacteremia together with significant reductions of systemic proinflammatory cytokines and chemokines in plasma. In vitro incubation of mouse peritoneal macrophages with lipopolysaccharide (LPS) in the copresence of IL-17A substantially increased the production of TNF-alpha, IL-1beta, and IL-6 by these cells. These data suggest that, during experimental sepsis, gammadelta T cell-derived IL-17A promotes high levels of proinflammatory mediators and bacteremia, resulting in enhanced lethality. IL-17A may be a potential therapeutic target in sepsis.
Viroreplicative Gene Therapy Targeted to Prostate Cancer (2010)

Abstract : Replication-competent retrovirus (RCR) vectors can propagate specifically within actively dividing cancer cells and achieve highly efficient and tumor-selective gene delivery. To improve their tumor-specificity and safety profile, we have developed RCR vectors regulated by two different tissue-specific promoters. The first is regulated by a synthetic variant of the probasin promoter (ARR2PB), exhibits high specificity for androgen receptor (AR)-positive prostate cancer cells. The second incorporates a newly developed androgen-independent synthetic regulatory element (PSES) which is highly active in PSA-/PSMA-positive prostate cancer cells, both in the presence and absence of androgen. The wild type promoter in the retrovirus long-terminal repeat (LTR) sequence was replaced with ARR2PB and PSES promoter sequences, and the efficiency and specificity of transduction and replication by the resultant RCR vectors was examined in vitro and in vivo. We have also developed prostate-targeted RCR vectors carrying the yeast cytosine deaminase (yCD) gene, which converts the nontoxic prodrug 5-fluorocytosine (5FC) into the chemotoxin 5-fluorouracil, and the potency and selectivity of the cytotoxic effect mediated by these vectors was examined.
BEOL compatible (300&#x00B0;C) TiN/TiO<inf>x</inf>/Ta/TiN 3D nanoscale (&#x223C;10nm) IMT selector (2013)

TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> based Insulator-Metal-Transition (IMT) devices with TiN electrode were investigated for selector application. To maximize heat confinement, we adopted localized filament by breaking stoichiometric ALD TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> layer. Using Ti <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sub> target and reduction annealing with Ta electrode, IMT layer was formed. By optimizing device structure to maximize heat confinement and oxygen stoichiometry to obtain IMT Ti <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> layer, we could maximize IMT characteristics at low threshold power. Scaling device area significantly improves the IMT characteristics. Moreover, reliable 1S1R characteristics were also confirmed.
Robocup field distortion calibration with variational image registration (2005)

The Global Vision System is widely used among teams of Robocup F180 (Small Size League). This architecture as well as the 1-hour preparation time limit before each match poses strict requirements to the accuracy and efficiency of the calibration method against pitch field distortions. Because of the curvature-preserving feature of these distortions, we propose a brand-new image registration approach, which does not require calibrating the camera, but directly maps the distorted image to the real pitch. While this method substantially simplifies the pre-match manipulation, it also maintains high accuracy - our experimental result shows that, with double camera, the mean error ratio is limited within 0.22%, accurate enough for Robocup matches.