Miracle-dz/UniFAR-FTUs huggingface dataset:
Absorption and scattering coefficients in Irondequoit Bay1

Profiles of scalar, downwelling, upwelling, and spectral irradiance were measured on 37 dates in 1982-1983. Values of the attenuation coefficient K were 0.8-1.2 m-l, and the reflectance R was 0.03-0.06. By Kirk’s method, the absorption and scattering coefficients a and b were found to be 0.44-0.83 and 1.8-5.0 m-l. Also measured were turbidity, chlorophyll, and absorption spectra of dissolved yellow substances and of particles. Independent estimates of a, as the sum of absorption components, were in reasonable agreement with values obtained by Kirk’s method. For particles, the average value of the Chl-specific absorption coefficient k, was -0.008-0.010 m* mg-l Chl. Values of the Chl-specific scattering coefficient kb were usually -0.05-0.10 m* mg-l Chl; values were higher (-0.12) when gas-vacuolate cyanobacteria were present. Optical properties most commonly measured in lakes and seas are Secchi transparency, turbidity, and the vertical attenuation coefficient K. Properties measured less frequently include horizontal beam transmission, upwelling and scalar n-radiances, spectral irradiance, and reflectance R (the ratio of upto downwelling irradiance). All of these, except turbidity and horizontal beam transmission, are “apparent optical properties,” so called because they are functions of the radiance distribution as well as of three “inherent properties. ” Inherent properties (defined for collimated light and thus independent of radiance distribution) include the volume absorption and scattering coefficients a and b and the angular scattering function. It is commonly supposed that the scattering function of Petzold (1972) applies to most natural waters. In contrast, values of the absorption and scattering coefficients vary greatly among natural waters, due to differences in kinds and concentrations of dissolved and particulate substances. Differences in a and b underlie the wide variations in apparent properties of natural waters. Significant contributions to the absorption coefficient may be made by water (a,,,), dissolved yellow substances (a,), inorganic particles (ai) if colored, detritus (ad) which The work described here was a part of an investigation of Irondequoit Bay following sewage diversion. Support by Monroe County Pure Waters is acknowledged. may contain pheoor yellow pigments, and phytoplankton (a,). Significant contributions to the scattering coefficient may be made by water and each of the three particle types. If the phytoplankton contributions are expressed in terms of chlorophyll-specific coefficients k, and kb, one can write a = a, + a,, + ai + ad + k,Chl
Activation of ERK1/2 after neonatal rat cerebral hypoxia–ischaemia

Activation of extracellular signal‐related kinases (ERK1/2), also known as p42/44 mitogen‐activated protein kinase (MAPK), is considered important for neuronal survival, cell proliferation and apoptosis. In the present study, activation (phosphorylation) of ERK1/2 (P‐ERK) was investigated in brains of 7‐day‐oldrats after hypoxia‐ischaemia (HI). In damaged areas, P‐ERK‐positive neurons appeared immediately after HI and the staining remained for at least 8 h. At later time points, 24 and 72 h post‐HI, P‐ERK‐positive neurons were found in the core of the infarct and in the border zone to undamaged tissue. These cells also showed signs of DNA damage and calpain‐induced fodrin breakdown, indicative of injury. At 72 h post‐HI, P‐ERK was also observed in microglia in the border zone to the damaged area and in astrocytes and oligodendrocytes in white matter of both hemispheres. P‐ERK was strongly expressed in the subventricular zone in both hemispheres after HI at most time points, although the staining in the ipsilateral (damaged hemisphere) was stronger than in the contralateral (non‐damaged hemisphere). In summary, ERK1/2 activation occurred early in neurons after HI in the neonatal brain, and mainly in cells displaying signs of damage.
Clinicopathological feature and prognosis of primary hepatic gastrointestinal stromal tumor

Compared to gastric gastrointestinal stromal tumor (GIST), hepatic GIST is very rare in clinic. Reports on clinicopathological feature and prognosis of this rare disease are limited in literature. The purpose of this study was, therefore, to summarize clinical and pathological features as well as prognosis of the primary hepatic GIST. One case of primary hepatic GIST from our center and 22 cases reported in MEDLINE or China National Knowledge Infrastructure (CNKI) were enrolled into this study. Clinicopathological features as well as survival data of hepatic GIST were analyzed and compared with 297 gastric GISTs and 59 small intestinal GISTs from our center. Majority of the 22 cases (95.7%) of hepatic GIST was larger than 5 cm in size, and 75.0% of the tumors were over 5/50 HPF in mitotic index. Most of the hepatic GISTs (85.7%) displayed spindle cell shape in morphology. All of the hepatic GIST (100%) enrolled in this study were classified as high‐risk category by the National Institute of Health (NIH) risk classification. The 5‐year median disease‐free survival (DFS) time was 24.0 months and 5‐year disease‐specific survival (DSS) rate was 33.3%, respectively. Distribution of clinicopathological features was significantly different among hepatic, gastric, and small intestinal GIST. The DFS and DSS of hepatic GIST were significantly lower than those of the other two groups. Majority of the hepatic GIST is large in size and highly malignant. Prognosis of the primary hepatic GIST is worse than that of gastric GIST and small intestinal GIST.
MER3 is required for normal meiotic crossover formation, but not for presynaptic alignment in rice

MER3, a ZMM protein, is required for the formation of crossovers in Saccharomyces cerevisiae and Arabidopsis. Here, MER3, the first identified ZMM gene in a monocot, is characterized by map-based cloning in rice (Oryza sativa). The null mutation of MER3 results in complete sterility without any vegetative defects. Cytological analyses show that chiasma frequency is reduced dramatically in mer3 mutants and the remaining chiasmata distribute randomly among different pollen mother cells, implying possible coexistence of two kinds of crossover in rice. Immunocytological analyses reveal that MER3 only exists as foci in prophase I meiocytes. In addition, MER3 does not colocalize with PAIR2 at the beginning of prophase I, but locates on one end of PAIR2 fragments at later stages, whereas MER3 foci merely locate on one end of REC8 fragments when signals start to be seen in early prophase I. The normal loading of PAIR2 and REC8 in mer3 implies that their loading is independent of MER3. On the contrary, the absence of MER3 signal in pair2 mutants indicates that PAIR2 is essential for the loading and further function of MER3.
Steroids induce a disequilibrium of secreted interleukin-1 receptor antagonist and interleukin-1&bgr; synthesis by human neutrophils

Chronic obstructive pulmonary disease (COPD) is characterised by neutrophilic inflammation in the airways and these neutrophils contribute to the production of inflammatory mediators. Dampening the production of proinflammatory mediators might be an important strategy to treat COPD and glucocorticosteroids are known to do so via inhibition of nuclear factor-&kgr;B. However, this pathway is important for the control of pro- and anti-inflammatory genes. We studied the effects of dexamethasone on production and secretion of pro-inflammatory interleukin (IL)-1&bgr; and anti-inflammatory secreted IL-1 receptor antagonist (sIL-1Ra) by human neutrophils activated with tumor necrosis factor (TNF)-&agr;. In vitro, TNF-&agr;-stimulated neutrophils produced significant amounts of IL-1&bgr; and sIL-1Ra; this production was inhibited by dexamethasone. However, synthesis and secretion of sIL-1Ra was inhibited at lower concentrations dexamethasone compared to IL-1&bgr;, which changed the IL-1&bgr;:sIL-1Ra ratio significantly. This altered ratio resulted in a more pro-inflammatory condition, as visualised by increased intercellular adhesion molecule-1 expression on human endothelial cells. In vivo, moderate-to-severe COPD patients using inhaled glucocorticosteroids have decreased plasma sIL-Ra levels compared with mild-to-moderate patients not on glucocorticosteroid treatment. In conclusion, dexamethasone induces a pro-inflammatory shift in the IL-1&bgr;:sIL-1Ra cytokine balance in neutrophils in vitro, which might contribute to a lack of endogenous anti-inflammatory signals to dampen inflammation in vivo.
Efficient three-node finite shell element for linear and geometrically nonlinear analyses of piezoelectric laminated structures

Fiber-reinforced composite laminates involving piezoelectric layers represent a very attractive material system. It combines the advantages of using rather lightweight and stiff material with the possibility of sensing structural changes and actively influencing its state by means of sensors and actuators. A three-node shell element is proposed as an efficient tool for modeling structures made of such a material system. Thoroughly tested solutions are implemented to resolve locking problems intrinsic for shell elements. The embedded piezoelectric layers are considered to be polarized in the thickness direction. Furthermore, the extension of the formulation to geometrically nonlinear finite element analysis is based on a co-rotational formulation. Numerical examples are given to demonstrate the applicability of developed element in linear and geometrically nonlinear finite element analyses covering both actuator and sensor cases.
Two-Year Prospective Study of the Humoral Immune Response of Patients with Severe Acute Respiratory Syndrome

Abstract In a cohort study of 56 convalescent patients with severe acute respiratory syndrome (SARS), titers of immunoglobulin G (IgG) antibodies and neutralizing antibodies (NAbs) against SARS-associated coronavirus were assessed at regular intervals (at 1, 4, 7, 10, 16, and 24 months after the onset of disease) by use of enzyme-linked immunosorbent assay and neutralization assay. IgG antibody and NAb titers were highly correlated, peaking at month 4 after the onset of disease and decreasing thereafter. IgG antibodies remained detectable in all patients until month 16, and they became undetectable in 11.8% of patients at month 24. The finding that NAbs remained detectable throughout follow-up is reassuring in terms of protection provided against reinfection; however, NAb titers decreased markedly after month 16
Distinct frequencies and mutation spectrums of genetic thrombophilia in Korea in comparison with other Asian countries both in patients with thromboembolism and in the general population

Hereditary natural anticoagulant deficiencies are the major cause of genetic thrombophilia in Asia. Given the growing acknowledgment of the risk of venous thromboembolism in Asian populations, we investigated the frequency and mutation spectrums of natural anticoagulant deficiency in Korea. The group of patients consisted of consecutive patients with venous thromboembolism screened for thrombophilia. Genetic tests were performed on suspicion of natural anticoagulant deficiency. For the population group, >3,000 individuals were screened from routine check-ups, and those with a low level (<1st percentile) of natural anticoagulant underwent genetic tests. Mutations were detected by direct sequencing of PROC, PROS1, and SERPINC1, followed by additional multiplex ligation-dependent probe amplification for PROS1 and SERPINC1 for dosage mutations. Among 500 patients screened, 127 were suspected of having a natural anticoagulant deficiency, and this was genetically confirmed in 71: protein C deficiency in 36 (50.7%), antithrombin deficiency in 21 (29.6%), and protein S deficiency in 14 (19.7%). Among 3,129 individuals from the population who were screened, the frequency of natural anticoagulant deficiency was ~1.0%: antithrombin deficiency 0.49%, protein C deficiency 0.35%, and protein S deficiency 0.16%. Two PROC mutations causing type I protein C deficiency were prevalent (Arg211Trp and Met406Ile in patients and Arg211Trp in the population). Two SERPINC1 mutations causing type II antithrombin deficiency, Arg79Cys and Ser158Pro, were prevalent in the population group. This is the first study on the genetic epidemiology of natural anticoagulant deficiencies in Korea. The results demonstrated that the frequencies and spectrum of mutations underlying genetic thrombophilia in Korea are different not only from those in Caucasians but also those in other Asian populations.
Femorofemoral bypass grafts: Factors influencing long-term patency rate and outcome.

BACKGROUND Crossover femorofemoral bypass graft (CFFBG) was proposed in the early days of modern vascular surgery to treat patients affected with unilateral iliac artery disease who were a high surgical risk. We investigated factors influencing short- and long-term outcomes of CFFBG: METHODS The study was designed as a retrospective clinical study in a university hospital setting with a base of 228 patients. Of these patients, 154 (67.5%) presented a high surgical risk. The indication for operation was limb-threatening ischemia in 188 (82.5%) patients. All patients underwent CFFBG: The procedure was performed in 150 patients as the primary operation and in 78 patients after previous vascular graft failure or infection, or both. A preoperative percutaneous transluminal angioplasty was performed in 57 patients (25%) to correct donor iliac artery disease. In 127 patients (55.7%), an associated vascular procedure was performed to improve the outflow. Postoperative complications; 5- and 10-year primary, secondary, and limb salvage rates; and factors influencing short- and long-term results were assessed. RESULTS Thirteen (5.7%) postoperative deaths occurred. Postoperative mortality and morbidity rates were significantly higher in patients aged more than 65 years (7.9% versus 3.5% and 18.6% versus 6.1%, respectively, P <.03). Primary and secondary patency rates at 5 and 10 years were 70.2% and 48.1%, 82.8% and 63.2%, respectively; 5- and 10-year limb salvage and survival rates were 85.5% and 80.1%, 63.3% and 31.0%, respectively. Ten-year primary and secondary patency and limb salvage rates were significantly lower when the procedure was performed after previous vascular graft failures (50.2% versus 26.5%, P <.007; 74.1% versus 44.1%, P <.01; and 84.3% versus 72.5%, P <.03, respectively). Five- and 8-year patency rates of autogenous vein CFFBG (34.3% and 22.8%, respectively, P <.03) were significantly lower than those of expanded polytetrafluoroethylene (71.1% and 59.8%, respectively) and polyester (77.3% and 50.3%, respectively) CFFBG: Moreover, 5- and 10-year primary and secondary patency rates were significantly better when externally supported grafts were used as compared with those without external support (80.1% and 69.9% versus 61.1% and 21.1%, P <.01; 88.8% and 75.9% versus 78.9% and 45.4%, P <.05, respectively). Multivariate analysis showed that the only variable associated with poor primary and secondary patency and limb salvage rates was the operation performed after previous vascular graft failures (P <.04, P <.03 and P<.05, respectively). CONCLUSIONS CFFBG allows early and long-term results similar to those obtained with reconstructions originating from the aorta when it is performed as a primary operation when an adequate outflow is provided and externally supported prosthetic material is used.
CSF protein dynamic driver network: At the crossroads of brain tumorigenesis

To get a better understanding of the ongoing in situ environmental changes preceding the brain tumorigenesis, we assessed cerebrospinal fluid (CSF) proteome profile changes in a glioma rat model in which brain tumor invariably develop after a single in utero exposure to the neurocarcinogen ethylnitrosourea (ENU). Computationally, the CSF proteome profile dynamics during the tumorigenesis can be modeled as non-smooth or even abrupt state changes. Such brain tumor environment transition analysis, correlating the CSF composition changes with the development of early cellular hyperplasia, can reveal the pathogenesis process at network level during a time before the image detection of the tumors. In this controlled rat model study, matched ENU and salineexposed rats' CSF proteomics changes were quantified at approximately 30, 60, 90, 120, 150 days of age (P30, P60, P90, P120, P150). We applied our transition-based network entropy (TNE) method to compute the CSF proteome changes in the ENU rat model and test the hypothesis of the critical transition state prior to impending hyperplasia. Our analysis identified a dynamic driver network (DDN) of CSF proteins related with the emerging tumorigenesis progressing from the non-hyperplasia state. The DDN associated leading network CSF proteins can allow the early detection of such dynamics before the catastrophic shift to the clear clinical landmarks in gliomas. An improved understanding of the critical transition state (P60) during the brain tumor progression can provide the scientific groundwork to device novel therapeutics preventing tumor formation.
Sebaceous Carcinoma, Basal Cell Carcinoma, Trichoadenoma, Trichoblastoma, and Syringocystadenoma Papilliferum Arising within a Nevus Sebaceus

BACKGROUND Nevus sebaceus has a well-documented potential to develop a wide variety of neoplasms of both epidermal and adnexal origins. It is highly unusual for more than three tumors to arise simultaneously within a single nevus sebaceus. Sebaceous carcinoma arising within a nevus sebaceus is a rare occurrence. OBJECTIVE The objective was to report the case of a patient with a nevus sebaceus that simultaneously developed five distinct neoplasms of epidermal and various adnexal origins and to report the fourth case of sebaceous carcinoma arising within a nevus sebaceus. METHODS A 45-year-old woman presented with a nevus sebaceusthat contained five separate neoplasms, including sebaceous carcinoma, basal cell carcinoma, trichoadenoma, trichoblastoma, and syringocystadenoma papilliferum. RESULTS Complete excision of the nevus sebaceus and the five tumors was performed. Systemic work-up showed no evidence of metastatic disease or association with Muir-Torre syndrome. CONCLUSION This case report highlights the diverse neoplastic potential of nevus sebaceus and demonstrates the capacity of this hamartoma to develop aggressive tumors, such as sebaceous carcinoma. Prophylactic excision or at least close clinical surveillance for sudden development of new growths is warranted in all cases of nevus sebaceus.
Adenovirus-Mediated Prothymosin α Gene Transfer Inhibits the Development of Atherosclerosis in Apoe-Deficient Mice

Prothymosin α (ProT) is involved in regulating expression of the oxidative stress-protective genes and it also exerts immunomodulatory activities. In this study, we investigated the therapeutic effects of ProT gene transfer on atherosclerosis in endothelial cells and in ApoE-deficient mice. Adenoviruses encoding mouse ProT (AdProT) were used for the management of atherosclerosis. In vitro, the effects of ProT on antioxidant gene expressions and the protection effect against oxidant-mediated injury in endothelial cells were examined. In vivo, AdProT were administered intraventricularly into the heart of ApoE-/- mice. Histopathological and immunohistochemical assessments of the aortic tissues were performed. Expressions of HO-1 and antioxidant genes in the aortic tissues were also determined. Our results demonstrated that ProT gene transfer increased antioxidant gene expressions, eNOS expression and NO release, as well as reduced the reactive oxygen species production in endothelial cells. Intraventricular administration of AdProT reduced the lesion formation, increased expressions of HO-1 and SOD genes, and reduced infiltrating macrophages in the aorta of ApoE-/- mice. This study suggests that ProT gene transfer may have the therapeutic potential for the management of atherosclerosis via inducing antioxidant gene expressions, eNOS expression and NO release, reducing ROS production and macrophage infiltration in endothelium.
An Assessment of Pulse Transit Time For Detecting Heavy Blood Loss During Surgical Operation

The main contribution of this paper is the use of non-invasive measurements such as electrocardiogram (ECG) and photoplethysmographic (PPG) pulse oximetry waveforms to develop a new physiological signal analysis technique for detecting blood loss during surgical operation. Urological surgery cases were considered as the control group due to its generality, and cardiac surgery as experimental group since it involves blood loss and water supply. Results show that the control group has the tendency of a reduction of the pulse transient time (PTT), and this indicates an increment in the blood flow velocity changes from slow to fast. While for the experimental group, the PTT indicates high values during blood loss, and low values during water supply. Statistical analysis shows considerable differences (i.e., P <0.05) between both groups leading to the conclusion that PTT could be a good indicator for monitoring patients' blood loss during a surgical operation.
English stress acquisition by native speakers of Tibetan

Previous studies show that language differences cause corresponding influences on Second Language Acquisition. Based on the Corpus of Chinese, English, and Tibetan spoken by Tibetan Speakers (CETTS), this study conducted English stress production and perception experiments and analyze the English stress acquisition by native speakers of Tibetan, to find out whether stress position and syllable structures will affect their stress acquisition. By analyzing 2,176 productions and 4,352 perception response by 17 subjects, as well as adopting ANOVA analysis and Mann-Whitney U test, this study finds out that: (1) The Tibetan group has a lower accuracy rate in English stress production and perception experiments; besides, unlike Americans, native Tibetan speakers do not employ the range of F0 to realize English stress. (2) Stress position affects stress production by the Tibetan group, but exerts no effect to stress production by the American group, and stress perception by both groups. (3) The tonal distribution rule of Tibetan does not affect the acquisition of English stress. (4) Schwa makes no statistical difference in accuracy rate, but can shorten the subjects' response time. Such findings will provide empirical data for more effective teaching of English to minority groups.
M ay 2 01 0 A self-normalized approach to confidence interval construction in time series 1 May 12 , 2010

University of Illinois at Urbana-Champaign Abstract: We propose a new method to construct confidence intervals for quantities that are associated with a stationary time series, which avoids direct estimation of the asymptotic variances. Unlike the existing tuning-parameter-dependent approaches, our method has the attractive convenience of being free of choosing any user-chosen number or smoothing parameter. The interval is constructed on the basis of an asymptotically distribution-free self-normalized statistic, in which the normalizing matrix is computed using recursive estimates. Under mild conditions, we establish the theoretical validity of our method for a broad class of statistics that are functionals of the empirical distribution of fixed or growing dimension. From a practical point of view, our method is conceptually simple, easy to implement and can be readily used by the practitioner. Monte-Carlo simulations are conducted to compare the finite sample performance of the new method with those delivered by the normal approximation and the block bootstrap approach.